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Davis, CA, United States

The University of California, Davis , is a public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced. UC Davis also has the third-largest enrollment in the UC System after UCLA and UC Berkeley.The 2015 U.S. News & World Report college rankings named UC Davis as the 9th best public university, 38th nationally, and 4th of the UC schools, following UC Berkeley, UCLA, and UC San Diego. UC Davis is one of 62 members in the Association of American Universities.The Carnegie Foundation classifies UC Davis as a comprehensive doctoral research university with a medical program, and very high research activity. UC Davis faculty includes 23 members of the National Academy of science, 25 members of the American Academy of Arts and science, 17 members of the American Law Institute, 14 members of the Institute of Medicine, and 14 members of the National Academy of Engineering. Among other honors, university faculty, alumni, and researchers have won the Nobel Peace Prize, Presidential Medal of Freedom, Pulitzer Prize, MacArthur Fellowship, National Medal of Science, and Presidential Early Career Award in Science and Engineering.The university has expanded over the past century to include graduate and professional programs in medicine , law, veterinary medicine, education, nursing, and business management, in addition to 90 research programs offered by UC Davis Graduate Studies. UC Davis' School of Veterinary Medicine is the largest in the United States and is ranked second in the nation.The UC Davis Aggies athletic teams compete in the NCAA Division I level, primarily in the Big West Conference as well as the Big Sky Conference and the Mountain Pacific Sports Federation. In its first year of full Division I status, 11 UC Davis teams qualified for NCAA post-season competition. Wikipedia.


Ng C.-Y.,University of California at Davis
Annual Review of Physical Chemistry | Year: 2014

Recent advances in high-resolution photoionization, photoelectron, and photodissociation studies based on single-photon vacuum ultraviolet (VUV) and two-color infrared (IR)-VUV, visible (Vis)-ultraviolet (UV), and VUV-VUV laser excitations are illustrated with selected examples. VUV laser photoionization coupled with velocity-map-imaging threshold photoelectron (VMI-TPE) detection can achieve comparable energy resolution but has higher-detection sensitivities than those observed in VUV laser pulsed field ionization photoelectron (PFI-PE) measurements. For molecules with known intermediate states, IR-VUV and Vis-UV excitation schemes are highly sensitive for rovibronically selected and resolved PFI-PE studies. The successful applications of the VUV-PFI-PE, VUV-VMI-TPE, and Vis-UV-PFI-PE methods to state-resolved and state-to-state photoelectron studies of transient radicals and transitional metal-containing molecules are highlighted. The most recently established VUV-VUV pump-probe time-slice VMI photoion method is shown to be promising for state-to-state photodissociation studies of small molecules relevant to planetary atmospheres and for the fundamental understanding of photodissociation dynamics. Copyright © 2014 by Annual Reviews. Source


Yang L.H.,University of California at Davis | Rudolf V.H.W.,Rice University
Ecology Letters | Year: 2010

Climate change is altering the phenology of many species and the timing of their interactions with other species, but the impacts of these phenological shifts on species interactions remain unclear. Classical approaches to the study of phenology have typically documented changes in the timing of single life-history events, while phenological shifts affect many interactions over entire life histories. In this study, we suggest an approach that integrates the phenology and ontogeny of species interactions with a fitness landscape to provide a common mechanistic framework for investigating phenological shifts. We suggest that this ontogeny-phenology landscape provides a flexible method to document changes in the relative phenologies of interacting species, examine the causes of these phenological shifts, and estimate their consequences for interacting species. © 2009 Blackwell Publishing Ltd/CNRS. Source


Marcu L.,University of California at Davis
Annals of Biomedical Engineering | Year: 2012

This article presents an overview of time-resolved (lifetime) fluorescence techniques used in biomedical diagnostics. In particular, we review the development of time-resolved fluorescence spectroscopy (TRFS) and fluorescence lifetime imaging (FLIM) instrumentation and associated methodologies which allow in vivo characterization and diagnosis of biological tissues. Emphasis is placed on the translational research potential of these techniques and on evaluating whether intrinsic fluorescence signals provide useful contrast for the diagnosis of human diseases including cancer (gastrointestinal tract, lung, head and neck, and brain), skin and eye diseases, and atherosclerotic cardiovascular disease. © 2012 Biomedical Engineering Society. Source


Kortet R.,University of Eastern Finland | Hedrick A.V.,University of California at Davis | Vainikka A.,University of Oulu
Ecology Letters | Year: 2010

Trade-offs between behavioural traits promoting high life-history productivity and mortality may fuel the evolution of animal personalities. We propose that parasites, including pathogens, impose fitness costs comparable to those from predators, and influence the adaptiveness of personality traits associated with productivity (PAPs). Whether personality traits are adaptive or not may also depend on individual immunological capacity. We illustrate this using a conceptual example in which the optimal level of PAPs depends on predation, parasitism and host compensation (resistance and tolerance) of parasitism's negative effects. We assert that inherent differences in host immune function can produce positive feedback loops between resource intake and compensation of parasitism's costs, thereby providing variation underlying the evolution of stable personalities. Our approach acknowledges the condition dependence of immune function and co-evolutionary dynamics between hosts and parasites. © 2010 Blackwell Publishing Ltd/CNRS. Source


Chang C.,University of California at Davis
Journal of Autoimmunity | Year: 2010

Ultrafine particles and engineered nanoparticles have unique aerodynamic and biochemical properties that affect the immune system and human health in ways that are different from or exceed those seen with gases or larger particulates. These effects result from a unique set of physical characteristics and surface moieties, which generate an ability of UFPs to enter tissues and cells, interact with proteins and DNA at a molecular level and directly and indirectly modulate the immune system by novel mechanisms. In recent years, a new field known as nanotechnology has impacted multiple industries by taking advantage of the special qualities of these small "atomic-sized" particles. Nanomedicine has already opened up a new avenue of research in cancer therapy, drug delivery and immune regulation. While the benefits of this new science to human civilization are seemingly immeasurable, it is also important to appreciate that these particles can also lead to harmful effects on human health. In vitro and animal studies are showing that nanoparticles and UFPs are capable of activating proinflammatory cytokines, chemokines and adhesion molecules, with recruitment of inflammatory cells including basophils, macrophages, dendritic cells, T cells, neutrophils and eosinophils. These changes may have an impact on immune defense, but also on the Th1/Th2 balance, and even on non-immunologic function. Resulting immune system derangement can lead to increases in incidence of autoimmune, allergic and even neoplastic diseases. Cardiorespiratory effects have been observed to occur in humans. Much further research is needed to establish safe exposure levels for this important new class of particulates. © 2009 Elsevier Ltd. All rights reserved. Source


Carter C.S.,University of California at Davis | Barch D.M.,Washington University in St. Louis
Schizophrenia Bulletin | Year: 2012

The Cognitive Neuroscience Treatment Research to Improve Cognition in Schizophrenia initiative, funded by an R13 conference grant from the National Institute of Mental Health, has sought to facilitate the translation of measures from the basic science of cognition into practical brain-based tools to measure treatment effects on cognition in schizophrenia. In this overview article, we summarize the process and products of the sixth meeting in this series, which focused on the identification of promising imaging paradigms, based on the measurement of cognitive evoked potentials (event-related potential) of cognition-related time-frequency analyses of the electroencephalography as well as functional magnetic resonance imaging. A total of 23 well-specified paradigms from cognitive neuroscience that measure cognitive functions previously identified as targets for treatment development were identified at the meeting as being recommended for the further developmental work needed in order to validate and optimize them as biomarker measures. Individual paradigms are discussed in detail in 6 domain-based articles in this volume. Ongoing issues related to the development of these and other measures as valid, sensitive and reliable measurement, and assessment tools, as well as the steps necessary for the development of specific measures for use as biomarkers for treatment development and personalized medicine, are discussed. © 2011 The Author. Source


Comai L.,University of California at Davis
PLoS Biology | Year: 2014

During the course of our history, humankind has been through different periods of agricultural improvement aimed at enhancing our food supply and the performance of food crops. In recent years, it has become apparent that future crop improvement efforts will require new approaches to address the local challenges of farmers while empowering discovery across industry and academia. New plant breeding approaches are needed to meet this challenge to help feed a growing world population. Here I discuss how a basic research discovery is being translated into a potential future tool for plant breeding, and share the story of researcher Simon Chan, who recognized the potential application of this new approach-genome elimination-for the breeding of staple food crops in Africa and South America. © 2014 Luca Comai. Source


Ronald P.C.,University of California at Davis | Ronald P.C.,Joint BioEnergy Institute
PLoS Biology | Year: 2014

Over the last 300 years, plant science research has provided important knowledge and technologies for advancing the sustainability of agriculture. In this Essay, I describe how basic research advances have been translated into crop improvement, explore some lessons learned, and discuss the potential for current and future contribution of plant genetic improvement technologies to continue to enhance food security and agricultural sustainability. © 2014 Pamela C. Source


Morgan D.J.,University of Maryland, Baltimore | Wright S.M.,Johns Hopkins University | Dhruva S.,University of California at Davis
JAMA Internal Medicine | Year: 2015

CONCLUSIONS AND RELEVANCE The literature on overuse of medical care is rapidly expanding. In 2013, both clinical trials and observational studies highlighted frequently overused or unnecessary care. Overuse of testing causes false-positive results and overdiagnosis. Negative test results do not appear to genuinely reassure patients. Overtreatment, with both medical therapies and procedural interventions, places patients at risk of unnecessary adverse events.OBJECTIVE To identify and highlight the most significant clinical articles published in 2013 related to medical overuse. EVIDENCE REVIEW A systematic review of English-language articles published in 2013 that related to medical overuse in adults.IMPORTANCE Overuse of medical care, consisting primarily of overdiagnosis and overtreatment, is a common clinical problem.FINDINGS We reviewed 478 published articles that met our inclusion criteria. Of these, 126 were ranked most relevant based on quality of methodology, strength of results, potential effects on patient care, and the number of patients potentially affected. The 10 most relevant articles were selected using the same criteria. These 10 articles (organized into the categories overdiagnosis, overtreatment, and methods to avoid overuse) were reviewed and interpreted for their effect on clinical medicine. Source


Heil M.,CINVESTAV | Karban R.,University of California at Davis
Trends in Ecology and Evolution | Year: 2010

In spite of initial doubts about the reality of 'talking trees', plant resistance expression mediated by volatile compounds that come from neighboring plants is now well described. Airborne signals usually improve the resistance of the receiver, but without obvious benefits for the emitter, thus making the evolutionary explanation of this phenomenon problematic. Here, we discuss four possible non-exclusive explanations involving the role of volatiles: in direct defense, as within-plant signals, as traits that synergistically interact with other defenses, and as cues among kin. Unfortunately, there is a lack of knowledge on the fitness consequences of plant communication for both emitter and receiver. This information is crucial to understanding the ecology and evolution of plant communication via airborne cues. © 2009 Elsevier Ltd. All rights reserved. Source


Wang I.J.,University of California at Davis | Summers K.,East Carolina University
Molecular Ecology | Year: 2010

Phenotypic and genetic divergence can be influenced by a variety of factors, including sexual and natural selection, genetic drift and geographic isolation. Investigating the roles of these factors in natural systems can provide insight into the relative influences of allopatric and ecological modes of biological diversification in nature. The strawberry poison frog, Dendrobates pumilio, presents an excellent opportunity for this kind of research, displaying a diverse array of colour morphs and inhabiting a heterogeneous landscape that includes oceanic islands, fragmented rainforest patches and wide expanses of suitable habitat. In this study, we use 15 highly polymorphic microsatellite loci to estimate population structure and gene flow among populations from across the range of D. pumilio and a causal modelling framework to statistically test 12 hypotheses regarding the geographic and phenotypic variables that explain genetic differentiation within this system. Our results demonstrate that the genetic distance between populations is most strongly associated with differences in dorsal coloration. Previous experimental studies have shown that phenotypic differences can result in sexual and natural selection against non-native phenotypes, and our results now show that these forces lead to genetic isolation between different colour morphs in the wild, presenting a potential case of incipient speciation through selection. © 2009 Blackwell Publishing Ltd. Source


Changes in phenology are correlated with climate change. However, we still struggle to understand the traits making species susceptible to climate change, and the implications of species' reactions for communities and food webs. Butterflies and moths are an ecologically important group that have shown pronounced phenological changes over the last decades. Tests using a > 150-year dataset from 566 European butterfly and moth species demonstrated that variation in phenological change was strongly related to traits describing plant-herbivore interactions (larval diet breadth, diet composition), and the life cycle. The results indicate that climate change related shifts in phenology are correlated with the seasonal availability and palatability of food plants. Lepidopterans feeding on herbaceous plants showed smaller shifts in flight periods but larger increases in voltinism than lepidopterans feeding on woody plants. Consequently, the effect of herbivorous lepidopterans may increase in herb-rich grassland ecosystems under warmer conditions, and not in forest ecosystems. © 2010 Blackwell Publishing Ltd/CNRS. Source


Mcbride C.S.,University of California at Davis | Singer M.C.,University of Texas at Austin
PLoS Biology | Year: 2010

Gene flow between populations that are adapting to distinct environments may be restricted if hybrids inherit maladaptive, intermediate phenotypes. This phenomenon, called extrinsic postzygotic isolation (EPI), is thought to play a critical role in the early stages of speciation. However, despite its intuitive appeal, we know surprisingly little about the strength and prevalence of EPI in nature, and even less about the specific phenotypes that tend to cause problems for hybrids. In this study, we searched for EPI among allopatric populations of the butterfly Euphydryas editha that have specialized on alternative host plants. These populations recall a situation thought typical of the very early stages of speciation. They lack consistent host-associated genetic differentiation at random nuclear loci and show no signs of reproductive incompatibility in the laboratory. However, they do differ consistently in diverse host-related traits. For each of these traits, we first asked whether hybrids between populations that use different hosts (different-host hybrids) were intermediate to parental populations and to hybrids between populations that use the same host (same-host hybrids). We then conducted field experiments to estimate the effects of intermediacy on fitness in nature. Our results revealed strong EPI under field conditions. Different-host hybrids exhibited an array of intermediate traits that were significantly maladaptive, including four behaviors. Intermediate foraging height slowed the growth of larvae, while intermediate oviposition preference, oviposition site height, and clutch size severely reduced the growth and survival of the offspring of adult females. We used our empirical data to construct a fitness surface on which different-host hybrids can be seen to fall in an adaptive valley between two peaks occupied by same-host hybrids. These findings demonstrate how ecological selection against hybrids can create a strong barrier to gene flow at the early stages of adaptive divergence. © 2010 McBride, Singer. Source


Dall'Era M.A.,University of California at Davis
Current Opinion in Urology | Year: 2013

PURPOSE OF REVIEW: To review the economics of managing low-risk prostate cancer with active surveillance compared with other standard therapies. RECENT FINDINGS: The expenses of caring for men with prostate cancer vary depending on treatment modality chosen and appear to be escalating. Costs are generally lowest with traditional watchful waiting and highest with radiation therapy. Compared with immediate treatment, active surveillance can result in a net per-patient savings of $12 194 at 5 years and $4329 at 10 years. Active surveillance demonstrates lower 5-year costs over other initial treatments as long as fewer than 70% exit active surveillance in any given year and at least 12% of men remain on active surveillance at year 5. Yearly surveillance biopsy reduces the average simulated cost savings at 10 years by $4951 per patient. SUMMARY: Active surveillance represents a cost-effective strategy for managing low-risk prostate cancer, as the majority of men remain without additional treatment over time. Prostate biopsy is the highest expenditure associated with active surveillance, and increasing the frequency of prostate biopsy will reduce the cost-effectiveness of this approach. © 2013 Wolters Kluwer Health | Lippincott Williams & Wilkins. Source


Mittler R.,University of Nevada, Reno | Mittler R.,Hebrew University of Jerusalem | Blumwald E.,University of California at Davis
Annual Review of Plant Biology | Year: 2010

Abiotic stress conditions such as drought, heat, or salinity cause extensive losses to agricultural production worldwide. Progress in generating transgenic crops with enhanced tolerance to abiotic stresses has nevertheless been slow. The complex field environment with its heterogenic conditions, abiotic stress combinations, and global climatic changes are but a few of the challenges facing modern agriculture. A combination of approaches will likely be needed to significantly improve the abiotic stress tolerance of crops in the field. These will include mechanistic understanding and subsequent utilization of stress response and stress acclimation networks, with careful attention to field growth conditions, extensive testing in the laboratory, greenhouse, and the field; the use of innovative approaches that take into consideration the genetic background and physiology of different crops; the use of enzymes and proteins from other organisms; and the integration of QTL mapping and other genetic and breeding tools. Copyright © 2010 by Annual Reviews. All rights reserved. Source


Middle and Late Pleistocene fossil hominin specimens with severe antemortem tooth loss are often regarded as evidence for the precocious evolution of human-like behaviors, such as conspecific care or cooking, in ancient hominin species. The goal of this project was to ask whether the theoretical association between antemortem tooth loss and uniquely human behaviors is supported empirically in a large skeletal sample of human hunter-gatherers, chimpanzees, orangutans, and baboons. Binomial regression modeling in a Bayesian framework allows for the investigation of the effects of tooth class, genus, age, and sex on the likelihood of tooth loss. The results strongly suggest that modern humans experience more antemortem tooth loss than non-human primates and identify age in years as an important predictor. Once age is accounted for, the difference between the humans and the closest non-human genus (chimpanzees) is less pronounced; humans are still more likely on average to experience antemortem tooth loss though 95% uncertainty envelopes around the average prediction for each genus show some overlap. These analyses support theoretical links between antemortem tooth loss and modern human characteristics; humans' significantly longer life history and a positive correlation between age and antemortem tooth loss explain, in part, the reason why humans are more likely to experience tooth loss than non-human primates, but the results do not exclude behavioral differences as a contributing factor. © 2013 Wiley Periodicals, Inc. Copyright © 2013 Wiley Periodicals, Inc. Source


Hastings A.,University of California at Davis
Ecology | Year: 2010

Explicit consideration of timescales and dynamics is required for an understanding of fundamental issues in ecology. Endogenous dynamics can lead to transient states where asymptotic behavior is very different from dynamics on short timescales. The causes of these kinds of transients can be placed in one of three classes: linear systems with different timescales embedded or exhibiting reactive behavior, the potentially long times to reach synchrony across space for oscillating systems, and the complex dynamics of systems with strong density-dependent (nonlinear) interactions. It is also important to include the potentially disparate timescales inherent in ecological systems when determining the endogenous dynamics. I argue that the dynamics of ecological systems can best be understood as the response, which may include transient dynamics, to exogenous influences leading to the observed dynamics on ecologically relevant timescales. This view of ecosystem behavior as responses of ecological systems governed by endogenous dynamics to exogenous influences provides a synthetic way to unify different approaches to population dynamics, to understand mechanisms that determine the distribution and abundance of species, and to manage ecosystems on appropriate timescales. There are implications for theoretical approaches, empirical approaches, and the statistical approaches that bridge theory and observation. © 2010 by the Ecological Society of America. Source


D'Souza R.M.,University of California at Davis | Nagler J.,ETH Zurich
Nature Physics | Year: 2015

The emergence of large-scale connectivity on an underlying network or lattice, the so-called percolation transition, has a profound impact on the system's macroscopic behaviours. There is thus great interest in controlling the location of the percolation transition to either enhance or delay its onset and, more generally, in understanding the consequences of such control interventions. Here we review explosive percolation, the sudden emergence of large-scale connectivity that results from repeated, small interventions designed to delay the percolation transition. These transitions exhibit drastic, unanticipated and exciting consequences that make explosive percolation an emerging paradigm for modelling real-world systems ranging from social networks to nanotubes. © 2015 Macmillan Publishers Limited. All rights reserved. Source


Sanford E.,University of California at Davis
Proceedings. Biological sciences / The Royal Society | Year: 2014

There is growing concern that global environmental change might exacerbate the ecological impacts of invasive species by increasing their per capita effects on native species. However, the mechanisms underlying such shifts in interaction strength are poorly understood. Here, we test whether ocean acidification, driven by elevated seawater pCO2, increases the susceptibility of native Olympia oysters to predation by invasive snails. Oysters raised under elevated pCO2 experienced a 20% increase in drilling predation. When presented alongside control oysters in a choice experiment, 48% more high-CO2 oysters were consumed. The invasive snails were tolerant of elevated CO2 with no change in feeding behaviour. Oysters raised under acidified conditions did not have thinner shells, but were 29-40% smaller than control oysters, and these smaller individuals were consumed at disproportionately greater rates. Reduction in prey size is a common response to environmental stress that may drive increasing per capita effects of stress-tolerant invasive predators. Source


Bosch J.,University of California at Davis
Astronomical Journal | Year: 2010

Gauss-Hermite and Gauss-Laguerre ("shapelet") decompositions of images have become important tools in galaxy modeling, particularly for the purpose of extracting ellipticity and morphological information from astronomical data. However, the standard shapelet basis functions cannot compactly represent galaxies with high ellipticity or large Sérsic index, and the resulting underfitting bias has been shown to present a serious challenge for weak-lensing methods based on shapelets. We present here a new convolution relation and a compound "multiscale" shapelet basis to address these problems and provide a proof-of-concept demonstration using a small sample of nearby galaxies. © 2010. The American Astronomical Society. All rights reserved. Source


Baar K.,University of California at Davis
Sports Medicine | Year: 2014

Very few sports use only endurance or strength. Outside of running long distances on a flat surface and power-lifting, practically all sports require some combination of endurance and strength. Endurance and strength can be developed simultaneously to some degree. However, the development of a high level of endurance seems to prohibit the development or maintenance of muscle mass and strength. This interaction between endurance and strength is called the concurrent training effect. This review specifically defines the concurrent training effect, discusses the potential molecular mechanisms underlying this effect, and proposes strategies to maximize strength and endurance in the high-level athlete. © 2014, The Author(s). Source


Viers J.H.,University of California at Davis
Journal of the American Water Resources Association | Year: 2011

Hydropower represents approximately 20% of the world's energy supply, is viewed as both vulnerable to global climate warming and an asset to reduce climate-altering emissions, and is increasingly the target of improved regulation to meet multiple ecosystem service benefits. It is within this context that the recent decision by the United States Federal Energy Regulatory Commission to reject studies of climate change in its consideration of reoperation of the Yuba-Bear Drum-Spaulding hydroelectric facilities in northern California is shown to be poorly reasoned and risky. Given the rapidity of climate warming, and its anticipated impacts to natural and human communities, future long-term fixed licenses of hydropower operation will be ill prepared to adapt if science-based approaches to incorporating reasonable and foreseeable hydrologic changes into study plans are not included. The licensing of hydroelectricity generation can no longer be issued in isolation due to downstream contingencies such as domestic water use, irrigated agricultural production, ecosystem maintenance, and general socioeconomic well-being. At minimum, if the Federal Energy Regulatory Commission is to establish conditions of operation for 30-50years, licensees should be required to anticipate changing climatic and hydrologic conditions for a similar period of time. © 2011 American Water Resources Association. Source


McCarthy B.,University of California at Davis
Archives of sexual behavior | Year: 2014

Explanations of adult involvement in sex work typically adopt one of two approaches. One perspective highlights a variety of negative experiences in childhood and adolescence, including physical and sexual abuse, family instability, poverty, associations with "pimps" and other exploiters, homelessness, and drug use. An alternative account recognizes that some of these factors may be involved, but underscores the contribution of more immediate circumstances, such as current economic needs, human capital, and employment opportunities. Prior research offers a limited assessment of these contrasting claims: most studies have focused exclusively on people working in the sex industry and they have not assessed the independent effects of life course variables central to these two perspectives. We add to this literature with an analysis that drew on insights from life course and life-span development theories and considered the contributions of factors from childhood, adolescence, and adulthood. Our comparative approach examined predictors of employment in sex work relative to two other low-income service or care work occupations: food and beverage serving and barbering and hairstyling. Using data from a study of almost 600 workers from two cities, one in Canada and the other in the United States, we found that both immediate circumstances and negative experiences from early life are related to current sex work involvement: childhood poverty, abuse, and family instability were independently associated with adult sex work, as were limited education and employment experience, adult drug use, and marital status. Source


Omalu B.,University of California at Davis
Progress in Neurological Surgery | Year: 2014

Chronic traumatic encephalopathy (CTE) is a progressive neurodegenerative syndrome, which is caused by single, episodic, or repetitive blunt force impacts to the head and transfer of accelerationdeceleration forces to the brain. CTE presents clinically as a composite syndrome of mood disorders and behavioral and cognitive impairment, with or without sensorimotor impairment. Symptoms of CTE may begin with persistent symptoms of acute traumatic brain injury (TBI) following a documented episode of brain trauma or after a latent period that may range from days to weeks to months and years, up to 40 years following a documented episode of brain trauma or cessation of repetitive TBI. Posttraumatic encephalopathy is distinct from CTE, can be comorbid with CTE, and is a clinicopathologic syndrome induced by focal and/or diffuse, gross and/or microscopic destruction of brain tissue following brain trauma. The brain of a CTE sufferer may appear grossly unremarkable, but shows microscopic evidence of primary and secondary proteinopathies. The primary proteinopathy of CTE is tauopathy, while secondary proteinopathies may include, but are not limited to, amyloidopathy and TDP proteinopathy. Reported prevalence rates of CTE in cohorts exposed to TBI ranges from 3 to 80% across age groups. © 2014 S. Karger AG, Basel. Source


Cappa C.D.,University of California at Davis | Wilson K.R.,Lawrence Berkeley National Laboratory
Atmospheric Chemistry and Physics | Year: 2011

Vacuum Ultraviolet (VUV) photoionization mass spectrometry has been used to measure the evolution of chemical composition for two distinct organic aerosol types as they are passed through a thermodenuder at different temperatures. The two organic aerosol types considered are primary lubricating oil (LO) aerosol and secondary aerosol from the α-pinene + O3 reaction (αP). The evolution of the VUV mass spectra for the two aerosol types with temperature are observed to differ dramatically. For LO particles, the spectra exhibit distinct changes with temperature in which the lower peaks, corresponding to compounds with higher vapor pressures, disappear more rapidly than the high peaks. In contrast, the αP aerosol spectrum is essentially unchanged by temperature even though the particles experience significant mass loss due to evaporation. The variations in the LO spectra are found to be quantitatively in agreement with expectations from absorptive partitioning theory whereas the αP spectra suggest that the evaporation of αP derived aerosol appears to not be governed by partitioning theory. We postulate that this difference arises from diffusivity within the ±P particles being sufficiently slow that they do not exhibit the expected liquid-like behavior and perhaps exist in a glassy state. To reconcile these observations with decades of aerosol growth measurements, which indicate that OA formation is described by equilibrium partitioning, we present a conceptual model wherein the secondary OA is formed and then rapidly converted from an absorbing form to a non-absorbing form. The results suggest that, although OA growth may be describable by equilibrium partitioning theory, the properties of organic aerosol once formed may differ significantly from the properties determined in the equilibrium framework. © 2011 Author(s). Source


Raybould H.E.,University of California at Davis
Autonomic Neuroscience: Basic and Clinical | Year: 2010

Chemosensing in the gastrointestinal tract is less well understood than many aspects of gut mechanosensitivity; however, it is important in the overall function of the GI tract and indeed the organism as a whole. Chemosensing in the gut represents a complex interplay between the function of enteroendocrine (EEC) cells and visceral (primarily vagal) afferent neurons. In this brief review, I will concentrate on a new data on endocrine cells in chemosensing in the GI tract, in particular on new findings on glucose-sensing by gut EEC cells and the importance of incretin peptides and vagal afferents in glucose homeostasis, on the role of G protein coupled receptors in gut chemosensing, and on the possibility that gut endocrine cells may be involved in the detection of a luminal constituent other than nutrients, the microbiota. The role of vagal afferent pathways as a downstream target of EEC cell products will be considered and, in particular, exciting new data on the plasticity of the vagal afferent pathway with respect to expression of receptors for GI hormones and how this may play a role in energy homeostasis will also be discussed. © 2009 Elsevier B.V. All rights reserved. Source


Ekstrom A.,University of California at Davis
Brain Research Reviews | Year: 2010

Functional magnetic resonance imaging (fMRI) has become the dominant means of measuring behavior-related neural activity in the human brain. Yet the relation between the blood oxygen-level dependent (BOLD) signal and underlying neural activity remains an open and actively researched question. A widely accepted model, established for sensory neo-cortex, suggests that the BOLD signal reflects peri-synaptic activity in the form of the local field potential rather than the spiking rate of individual neurons. Several recent experimental results, however, suggest situations in which BOLD, spiking, and the local field potential dissociate. Two different models are discussed, based on the literature reviewed to account for this dissociation, a circuitry-based and vascular-based explanation. Both models are found to account for existing data under some testing situations and in certain brain regions. Because both the vascular and local circuitry-based explanations challenge the BOLD-LFP coupling model, these models provide guidance in predicting when BOLD can be expected to reflect neural processing and when the underlying relation with BOLD may be more complex than a direct correspondence. © 2009 Elsevier B.V. Source


Blaimer B.B.,University of California at Davis
Molecular Phylogenetics and Evolution | Year: 2012

This study unravels the evolution and biogeographic history of the globally distributed ant genus Crematogaster on the basis of a molecular phylogeny, reconstructed from five nuclear protein-coding genes and a total of 3384. bp of sequence data. A particular emphasis is placed on the evolutionary history of these ants in the Malagasy region. Bayesian and likelihood analyses performed on a dataset of 124 Crematogaster ingroup taxa lend strong support for three deeply diverging phylogenetic lineages within the genus: the Orthocrema clade, the Global Crematogaster clade and the Australo-Asian Crematogaster clade. The 15 previous subgenera within Crematogaster are mostly not monophyletic. Divergence dating analyses and ancestral range reconstructions suggest that Crematogaster evolved in South-East Asia in the mid-Eocene (40-45. ma). The three major lineages also originated in this region in the late Oligocene/early Miocene (∼24-30. ma). A first dispersal out of S-E Asia by an Orthocrema lineage is supported for 22-30. ma to the Afrotropical region. Successive dispersal events out of S-E Asia began in the early, and continued throughout the late Miocene. The global distribution of Crematogaster was achieved by subsequent colonizations of all major biogeographic regions by the Orthocrema and the Global Crematogaster clade. Molecular dating estimates and ancestral range evolution are discussed in the light of palaeogeographic changes in the S-E Asian region and an evolving ocean circulation system throughout the Eocene, Oligocene and Miocene. Eight dispersal events to/from Madagascar by Crematogaster are supported, with most events occurring in the late Miocene to Pliocene (5.0-9.5. ma). These results suggest that Crematogaster ants possess exceptional dispersal and colonization abilities, and emphasize the need for detailed investigations of traits that have contributed to the global evolutionary success of these ants. © 2012 Elsevier Inc. Source


Wun T.,University of California at Davis
Thrombosis research | Year: 2010

The association of malignancies and venous thromboembolism (VTE) is a long held axiom in medicine. A growing number of studies have demonstrated that the risk of VTE associated with the hematological malignancies acute leukemia, lymphoma, and multiple myeloma is considerable. In fact, the incidence associated with these malignancies exceeds that for many solid tumors. Contributing factors include malignancy associated hypercoagulable factors; antineoplastic therapies such as high dose corticosteroids, L-asparaginase, and new immunomodulatory agents; central venous catheters; and hematopoietic growth factors. Primary and secondary pharmacological prophylaxis can be problematic in these patients who are often thrombocytopenic. Strategies to prevent VTE, especially upper extremity catheter-associated thrombosis need to be developed. Source


Carlip S.,University of California at Davis
International Journal of Modern Physics D | Year: 2014

The discovery in the early 1970s that black holes radiate as black bodies has radically affected our understanding of general relativity, and offered us some early hints about the nature of quantum gravity. In this paper, will review the discovery of black hole thermodynamics and summarize the many independent ways of obtaining the thermodynamic and (perhaps) statistical mechanical properties of black holes. I will then describe some of the remaining puzzles, including the nature of the quantum microstates, the problem of universality, and the information loss paradox. © 2014 World Scientific Publishing Company. Source


Mcsorley S.J.,University of California at Davis
Immunological Reviews | Year: 2014

Salmonella are a common source of food- or water-borne infection and cause a wide range of clinical disease in human and animal hosts. Salmonella are relatively easy to culture and manipulate in a laboratory setting, and the infection of laboratory animals induces robust innate and adaptive immune responses. Thus, immunologists have frequently turned to Salmonella infection models to expand understanding of host immunity to intestinal pathogens. In this review, I summarize current knowledge of innate and adaptive immunity to Salmonella and highlight features of this response that have emerged from recent studies. These include the heterogeneity of the antigen-specific T-cell response to intestinal infection, the prominence of microbial mechanisms to impede T- and B-cell responses, and the contribution of non-cognate pathways for elicitation of T-cell effector functions. Together, these different issues challenge an overly simplistic view of host-pathogen interaction during mucosal infection, but also allow deeper insight into the real-world dynamic of protective immunity to intestinal pathogens. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd. Source


Experiments were conducted in 2006 to 2008 to study growth, phenology, and competitive ability of glyphosate-resistant (GR) and -susceptible (GS) biotypes of horseweeds from San Joaquin Valley (SJV), CA. When grown alone, in pots, the GR horseweeds consistently developed more rapidly than the GS weeds, as evidenced by their earlier bolting, flowering, and seed set; the GR horseweeds set seeds nearly 25 d (approximately 190 fewer growing degree days) sooner than the GS horseweed. At seed set, the relatively slow-developing GS horseweeds had amassed 40% more shoot dry matter than the GR weeds at the same phenological stage, but neither biotype was consistently more fecund than the other. Although the GR biotype had lower shoot dry mass than the GS biotype when grown alone, in mixed populations under increasing levels of competition (in a replacement series design) and limited resources (mainly moisture), the GR weeds were not only taller, but also accumulated more dry matter than the GS weeds. Thus, the GR biotype was more competitive than the GS biotype, particularly when grown at high densities and under moisture-deficit stress. Therefore, under California conditions there is no apparent fitness penalty for this particular GR horseweed biotype, and it is likely to persist in the environment and outcompete the GS biotypes regardless of further glyphosate selection pressure. If so, this biotype of GR horseweed is likely to become increasingly common in the SJV until effective management strategies are developed and adopted. © 2010 Weed Science Society of America. Source


Rogawski M.A.,University of California at Davis
Epilepsia | Year: 2013

Pharmacoresistance to antiepileptic drugs (AEDs) is a barrier to seizure freedom for many persons with epilepsy. For nearly two decades, pharmacoresistance has been framed in terms of factors affecting the access of AEDs to their molecular targets in the brain or the actions of the drugs on these targets. Shortcomings in this prevailing view led to the formulation of the intrinsic severity hypothesis of pharmacoresistance to AEDs, which is based on the recognition that there are neurobiologic factors that confer phenotypic variation among individuals with etiologically similar forms of epilepsy and postulates that more severe epilepsy is more difficult to treat with AEDs. In recent years, progress has been made identifying potential genetic mechanisms of variation in epilepsy severity, including subclinical mutations in ion channels that increase or reduce epilepsy severity in mice. Efforts are underway to identify clinically important genetic modifiers. If it can be demonstrated that such severity factors play a role in pharmacoresistance, treatments could be devised to reverse severity mechanisms. By overcoming pharmacoresistance, this new approach to epilepsy therapy may allow drug refractory patients to achieve seizure freedom without side effects. Wiley Periodicals, Inc. © 2013 International League Against Epilepsy. Source


Delucchi M.,University of California at Davis
Biomass and Bioenergy | Year: 2011

In this paper I discuss general conceptual issues in the estimation of the impacts of CO2 emissions from soils and biomass, over time, as a result of land-use change (LUC) due to increased demand for energy crops. The effect of LUC on climate depends generally on the magnitude and timing of changes in soil and plant carbon, and in particular on the timing and extent of the reversion of land to original ecosystems at the end of the bioenergy program. Depending on whether one counts the climate impacts of any reversion of land uses, and how one values future climate-change impacts relative to present impacts, one can estimate anywhere from zero to very large climate impacts due to land-use change (LUC). I argue that the best method is to estimate the net present value (NPV) of the impacts of climate change due to LUC. With this approach, one counts the reversion impacts at the end of the program and applies a continuous discounting function to future impacts to express them in present terms. In this case, the impacts of CO2 emissions from the initial LUC then are at least partially offset by the impacts of CO2 sequestration from reversion. © 2010 Elsevier Ltd. Source


Hamilton A.M.,University of California at Davis
Neural plasticity | Year: 2013

The ubiquitin-proteasome system (UPS) is most widely known for its role in intracellular protein degradation; however, in the decades since its discovery, ubiquitination has been associated with the regulation of a wide variety of cellular processes. The addition of ubiquitin tags, either as single moieties or as polyubiquitin chains, has been shown not only to mediate degradation by the proteasome and the lysosome, but also to modulate protein function, localization, and endocytosis. The UPS plays a particularly important role in neurons, where local synthesis and degradation work to balance synaptic protein levels at synapses distant from the cell body. In recent years, the UPS has come under increasing scrutiny in neurons, as elements of the UPS have been found to regulate such diverse neuronal functions as synaptic strength, homeostatic plasticity, axon guidance, and neurite outgrowth. Here we focus on recent advances detailing the roles of the UPS in regulating the morphogenesis of axons, dendrites, and dendritic spines, with an emphasis on E3 ubiquitin ligases and their identified regulatory targets. Source


Rogawski M.A.,University of California at Davis
Acta neurologica Scandinavica. Supplementum | Year: 2013

Epileptic seizures occur as a result of episodic abnormal synchronous discharges in cerebral neuronal networks. Although a variety of non-conventional mechanisms may play a role in epileptic synchronization, cascading excitation within networks of synaptically connected excitatory glutamatergic neurons is a classical mechanism. As is the case throughout the central nervous system, fast synaptic excitation within and between brain regions relevant to epilepsy is mediated predominantly by AMPA receptors. By inhibiting glutamate-mediated excitation, AMPA receptor antagonists markedly reduce or abolish epileptiform activity in in vitro preparations and confer seizure protection in a broad range of animal seizure models. NMDA receptors may also contribute to epileptiform activity, but NMDA receptor blockade is not sufficient to eliminate epileptiform discharges. AMPA receptors move into and out of the synapse in a dynamic fashion in forms of synaptic plasticity, underlying learning and memory. Often, the trigger for these dynamic movements is the activation of NMDA receptors. While NMDA receptor antagonists inhibit these forms of synaptic plasticity, AMPA receptor antagonists do not impair synaptic plasticity and do not inhibit memory formation or retrieval. The demonstrated clinical efficacy of perampanel, a high-potency, orally active non-competitive AMPA receptor antagonist, supports the concept that AMPA receptors are critical to epileptic synchronization and the generation and spread of epileptic discharges in human epilepsy. © 2013 John Wiley & Sons A/S. Source


Gusfield D.,University of California at Davis
Journal of Computational Biology | Year: 2010

The Multi-State Perfect Phylogeny Problem is an extension of the Binary Perfect Phylogeny Problem, allowing characters to take on more than two states. In this article, we consider three problems that extend the utility of the multi-state perfect phylogeny model: (1) the Missing Data (MD) Problem, where some entries in the input are missing and the question is whether (bounded) values for the missing data can be imputed so that the resulting data has a multi-state perfect phylogeny; (2) the Character-Removal (CR) Problem, where we want to minimize the number of characters to remove from the data so that the resulting data has a multi-state perfect phylogeny; and (3) the Missing-Data Character-Removal (MDCR) Problem, where the input has missing data and we want to impute values for the missing data to minimize the solution to the resulting Character-Removal Problem. We discuss Integer Linear Programming (ILP) solutions to these problems for the special case of three, four, and five permitted states per character, and we report on extensive empirical testing of these solutions. Then we develop a general theory to solve the MD problem for an arbitrary number of permitted states, using chordal graph theory and results on minimal triangulation of non-chordal graphs. This establishes new necessary and sufficient conditions for the existence of a perfect phylogeny with (or without) missing data. We implement the general theory using integer linear programming, although other optimization methods are possible. We extensively explore the empirical behavior of the general solution, showing that the methods are very practical for data of size and complexity that is characteristic of many current applications in phylogenetics. Some of the empirical results for the MD problem with an arbitrary number of permitted states are very surprising, suggesting the existence of additional combinatorial structure in multi-state perfect phylogenies. Finally, we note some relationships between our chordal-graph approach to the multi-state perfect phylogeny, without missing data, and prior methods. © Copyright 2010, Mary Ann Liebert, Inc. Source


Allen L.H.,University of California at Davis
Annals of Nutrition and Metabolism | Year: 2012

This article provides an overview of child feeding recommendations and how these relate to actual practice and dietary adequacy, primarily in developing countries. From birth to 6 months, recommendations focus on optimal breastfeeding practices, although these are still suboptimal in about one third of infants in developing countries. From 6 months of age, breast milk can no longer meet all the nutrient requirements of the child, so from 6 months through at least 24 months, the recommendation is to continue breastfeeding but gradually introduce complementary foods. In poorer populations, the available foods for complementary feeding are primarily cereals and legumes, to which small amounts of fruits and vegetables are added, and even less animal source foods. Based on intake data from infants and preschoolers, it is evident that usual diets typically fall far short of supplying micronutrient needs. By adding more fruits, vegetables, and animal source foods the diet can be improved. Intervention studies show that increasing animal source food intake improves growth, muscle mass, and cognitive function of school children. Milk and dairy product intakes are correlated with greater child growth in many studies, even in industrialized countries. However, for many families, substantially improving children's diets by providing higher quality foods is often financially unrealistic. Newer approaches to home fortification of children's foods using micronutrient powders or lipid-based nutrient supplements hold great potential to prevent micronutrient deficiencies at reasonable cost, thus preventing the adverse consequences of these deficiencies for child development. Copyright © 2013 S. Karger AG, Basel. Source


Meeting the high nutrient needs of pregnant and lactating women and their young children in regions such as South Asia is challenging because diets are dominated by staple foods with low nutrient density and poor mineral bioavailability. Gaps in nutritional adequacy in such populations probably date back to the agricultural revolution ~10000years ago. Options for improving diets during the first 1000days include dietary diversification and increased intake of nutrient-rich foods, improved complementary feeding practices, micronutrient supplements and fortified foods or products specifically designed for these target groups. Evidence from intervention trials indicates that several of these strategies, both prenatal and post-natal, can have a positive impact on child growth, but results are mixed and a growth response is not always observed. Nutrition interventions, by themselves, may not result in the desired impact if the target population suffers from frequent infection, both clinical and subclinical. Further research is needed to understand the mechanisms underlying both prenatal and post-natal growth restriction. In the meantime, implementation and rigorous evaluation of integrated interventions that address the multiple causes of stunting is a high priority. These intervention packages should ideally include improved nutrition during both pregnancy and the post-natal period, prevention and control of prenatal and post-natal infection and subclinical conditions that restrict growth, care for women and children and stimulation of early child development. In regions such as South Asia, such strategies hold great promise for reducing stunting and enhancing human capital formation. © 2016 John Wiley & Sons Ltd. Source


Selmi C.,University of California at Davis
Clinical Reviews in Allergy and Immunology | Year: 2012

The mechanisms leading to the onset and perpetuation of systemic and tissue-specific autoimmune diseases are complex, and numerous hypotheses have been proposed or confirmed over the past 12 months. It is particularly of note that the number of articles published during 2011 in the major immunology and autoimmunity journals increased by 3 % compared to the previous year. The present article is dedicated to a brief review of the reported data and, albeit not comprehensive of all articles, is aimed at identifying common and future themes. First, clinical researchers were particularly dedicated to defining refractory forms of diseases and to discuss the use and switch of therapeutic monoclonal antibodies in everyday practice. Second, following the plethora of genome-wide association studies reported in most multifactorial diseases, it became clear that genomics cannot fully explain the individual susceptibility and additional environmental or epigenetic factors are necessary. Both these components were widely investigated, both in organ-specific (i.e., type 1 diabetes) and systemic (i.e., systemic lupus erythematosus) diseases. Third, a large number of 2011 works published in the autoimmunity area are dedicated to dissect pathogenetic mechanisms of tolerance breakdown in general or in specific conditions. While our understanding of T regulatory and Th17 cells has significantly increased in 2011, it is of note that most of the proposed lines of evidence identify potential targets for future treatments and should not be overlooked. © Springer Science+Business Media, LLC 2012. Source


D'Souza R.M.,University of California at Davis | D'Souza R.M.,Santa Fe Institute | Mitzenmacher M.,Harvard University
Physical Review Letters | Year: 2010

We introduce perhaps the simplest models of graph evolution with choice that demonstrate discontinuous percolation transitions and can be analyzed via mathematical evolution equations. These models are local, in the sense that at each step of the process one edge is selected from a small set of potential edges sharing common vertices and added to the graph. We show that the evolution can be accurately described by a system of differential equations and that such models exhibit the discontinuous emergence of the giant component. Yet they also obey scaling behaviors characteristic of continuous transitions, with scaling exponents that differ from the classic Erdos-Rényi model. © 2010 The American Physical Society. Source


Biro P.A.,University of New South Wales | Stamps J.A.,University of California at Davis
Trends in Ecology and Evolution | Year: 2010

Consistent individual differences (CIDs) in behavior are a widespread phenomenon in animals, but the proximate reasons for them are unresolved. We discuss evidence for the hypothesis that CIDs in energy metabolism, as reflected by resting metabolic rate (RMR), promote CIDs in behavior patterns that either provide net energy (e.g. foraging activity), and/or consume energy (e.g. courtship activity). In doing so, we provide a framework for linking together RMR, behavior, and life-history productivity. Empirical studies suggest that RMR is (a) related to the capacity to generate energy, (b) repeatable, and (c) correlated with behavioral output (e.g. aggressiveness) and productivity (e.g. growth). We conclude by discussing future research directions to clarify linkages between behavior and energy metabolism in this emerging research area. © 2010 Elsevier Ltd. Source


Singh R.R.P.,University of California at Davis
Physical Review Letters | Year: 2010

We present a theory for site dilution in the kagome lattice Heisenberg model. The presence of an empty site leads to strong singlet bonds opposite to the impurity. It also creates a free spin which delocalizes near the impurity. Finite impurity concentration leads to a valence bond glass phase with no spin gap, large spin susceptibilities, linear specific heat due to two-level systems, as well as singlet and triplet excitations that decompose into kink-antikink pairs. It provides a framework for a comprehensive understanding of thermodynamic, neutron, and Raman measurements in the herbertsmithite material ZnCu3(OH)6Cl2, including recently reported H/T and ω/T scaling. © 2010 The American Physical Society. Source


Human milk lactoferrin (hmLF) is the most abundant glycoprotein present in human milk and displays a broad range of protective functions in the gut of newborn infants. hmLF is N-glycosylated, but little is known about the lactation stage-related development of the glycosylation phenotype. hmLF glycosylation from milk samples from five donors during the first 10 weeks of lactation was assessed and observed to be more diverse than previously reported. During this period dynamic changes in glycosylation were observed corresponding to a decrease in glycosylation in the second week followed by an increase in total glycosylation as well as higher order fucosylation thereafter. Gene expression analysis was performed in milk somatic cells from a sixth subject. It was found that fucosyltransferase expression increased during entire period, whereas expression of genes for the oligosaccharyl transferase complex decreased in the second week. The effect of hmLF glycosylation was examined for the protein's ability to affect bacterial binding to epithelial cells. hmLF significantly inhibited pathogen adhesion and purified hmLF glycans significantly reduced Salmonella invasion of colonic epithelial cells to levels associated with non-invasive deletion mutants. This study indicates that hmLF glycosylation is tightly regulated by gene expression and that glyco-variation is involved in modulating pathogen association. Source


Espiritu E.B.,University of California at Davis
Developmental biology | Year: 2012

Microtubule dynamics are thought to play an important role in regulating microtubule interactions with cortical force generating motor proteins that position the spindle during asymmetric cell division. CLASPs are microtubule-associated proteins that have a conserved role in regulating microtubule dynamics in diverse cell types. Caenorhabditis elegans has three CLASP homologs in its genome. CLS-2 is known to localize to kinetochores and is needed for chromosome segregation at meiosis and mitosis; however CLS-1 and CLS-3 have not been reported to have any role in embryonic development. Here, we show that depletion of CLS-2 in combination with either CLS-1 or CLS-3 results in defects in nuclear rotation, maintenance of spindle length, and spindle displacement in the one-cell embryo. Polarity is normal in these embryos, but reduced numbers of astral microtubules reach all regions of the cortex at the time of spindle positioning. Analysis of the microtubule plus-end tracker EB1 also revealed a reduced number of growing microtubules reaching the cortex in CLASP depleted embryos, but the polymerization rate of astral microtubules was not slower than in wild type. These results indicate that C. elegans CLASPs act partially redundantly to regulate astral microtubules and position the spindle during asymmetric cell division. Further, we show that these spindle pole-positioning roles are independent of the CLS-2 binding proteins HCP-1 and HCP-2. Copyright © 2012 Elsevier Inc. All rights reserved. Source


Coping with perturbations of the environment such as severe storms and other climatic extremes, habitat degradation, changes in predator numbers, invasive species and social disruption is one of the most essential physiological and behavioural processes. The palaeontological record shows that organisms have had to cope with environmental perturbations throughout the history of life on Earth. These ancient processes show highly conserved mechanisms, but also great flexibility in responses to social and physical environment challenges. Adrenocortical responses to perturbations can trigger a coping response called the emergency life history stage (EHLS). However, if the adaptive value of the ELHS declines because of trade-offs with other life history stages such as breeding, then the adrenocortical response to acute perturbations (stress) can be modulated. Mechanisms involve allostasis and reactive scope with three foci of regulation: hormone secretion, transport and response. It is now well known that modulation of the adrenocortical responses to perturbations occur through gene-environment interactions during development and throughout the life cycle. These modulations involve individual differences in gender, age, experience and condition as well as latitudinal, altitudinal and hemispheric variations. Dramatic consequences of human-induced rapid environmental change such as increasing frequency and intensity of environmental perturbations will likely have implications for continued adaptation to extreme events. Note that modulation of the stress response also involves three major processes: modulation of robustness (i.e. become more resistant to acute stress); modulation of responsiveness (i.e. modulate the actual response to stress for more flexibility); and modulation of resilience (i.e. how quickly and completely the recovery is after the perturbation has passed). Mechanisms underlying these modulations remain largely unexplored. © 2013 The Association for the Study of Animal Behaviour. Source


Lonnerdal B.,University of California at Davis
Journal of Paediatrics and Child Health | Year: 2013

Human milk contains many proteins that have been shown to be bioactive, but it is still not known whether these activities are exerted in breast-fed infants. These bioactivities include enzyme activities, enhancement of nutrient absorption, growth stimulation, modulation of the immune system and defence against pathogens. The antimicrobial activities are very diverse, ranging from stimulation of beneficial microorganisms (i.e. prebiotic effects), killing or inhibition of growth of pathogens, to mechanisms preventing attachment or invasion of harmful microorganisms. Among the bioactive proteins are lactoferrin, lysozyme, secretory immunoglobulin A, haptocorrin, lactoperoxidase, α-lactalbumin, bile salt stimulated lipase, β- and κ-casein, and tumour growth factor β. Human milk proteins may be largely resistant against digestion in the gastrointestinal tract, be partially digested into bioactive peptides, or be more or less completely digested and utilised as a source of amino acids. These events can be studied using an in vitro digestion model, which is useful for predicting results in human infants. Some bovine milk proteins, for example, lactoferrin and tumour growth factor β, may also resist proteolysis and be capable of exerting bioactivities similar to those of human milk proteins. © 2013 The Author. Paediatrics and Child Health Division (Royal Australasian College of Physicians). Source


Berben L.A.,University of California at Davis
Chemistry - A European Journal | Year: 2015

Non-Innocent ligand complexes of aluminum are described in this Concept article, beginning with a discussion of their synthesis, and then structural and electronic characterization. The main focus concerns the ability of the ligands in these complexes to mediate proton transfer reactions. As examples, aluminum-ligand cooperation in the activation of polar bonds is described, as is the importance of hydrogen bonding to stabilization of a transition state for b-hydride abstraction. Taken together these reactions enable catalytic processes such as the dehydrogenation of formic acid. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA. Source


Inderjit,University of Delhi | Wardle D.A.,Swedish University of Agricultural Sciences | Karban R.,University of California at Davis | Callaway R.M.,University of Montana
Trends in Ecology and Evolution | Year: 2011

Plants can release chemicals into the environment that suppress the growth and establishment of other plants in their vicinity: a process known as 'allelopathy'. However, chemicals with allelopathic functions have other ecological roles, such as plant defense, nutrient chelation, and regulation of soil biota in ways that affect decomposition and soil fertility. These ecosystem-scale roles of allelopathic chemicals can augment, attenuate or modify their community-scale functions. In this review we explore allelopathy in the context of ecosystem properties, and through its role in exotic invasions consider how evolution might affect the intensity and importance of allelopathic interactions. © 2011 Elsevier Ltd. Source


Eisen D.B.,University of California at Davis
Journal of the American Academy of Dermatology | Year: 2011

Surgical site infections are an important complication resulting from surgery. Before the 20th century a significant number of surgeries resulted in death from sepsis. One of the rituals resulting from efforts to reduce infection is the donning of surgical garb. A large body of literature has developed on the efficacy of these specialized garments. The available evidence for the efficacy of each individual garb at reducing surgical site infections will be explored. The relevance of this evidence to the outpatient dermatologic surgery setting will also be discussed. © 2010 by the American Academy of Dermatology, Inc. Source


Green T.J.,University of California at Davis
Theory of Computing Systems | Year: 2011

We study containment and equivalence of (unions of) conjunctive queries on relations annotated with elements of a commutative semiring. Such relations and the semantics of positive relational queries on them were introduced in a recent paper as a generalization of set semantics, bag semantics, incomplete databases, and databases annotated with various kinds of provenance information. We obtain positive decidability results and complexity characterizations for databases with lineage, why-provenance, and provenance polynomial annotations, for both conjunctive queries and unions of conjunctive queries. At least one of these results is surprising given that provenance polynomial annotations seem "more expressive" than bag semantics and under the latter, containment of unions of conjunctive queries is known to be undecidable. The decision procedures rely on interesting variations on the notion of containment mappings. We also show that for any positive semiring (a very large class) and conjunctive queries without self-joins, equivalence is the same as isomorphism. © 2011 Springer Science+Business Media, LLC. Source


Hull M.L.,University of California at Davis
Journal of Bone and Joint Surgery - Series A | Year: 2010

Background: Understanding the relationship between the radii of the medial and lateral femoral condyles in varus and valgus knees is important for aligning the femoral component and for restoring kinematics in total knee arthroplasty. The purpose of this study was to test the hypothesis that the asymmetry between the radii of the medial and lateral femoral condyles in varus and valgus knees with osteoarthritis is small enough to be clinically unimportant. Methods: A magnetic resonance imaging scan was obtained with use of a biplanar, rotational alignment protocol in a consecutive series of subjects with end-stage osteoarthritis prior to total knee arthroplasty. The alignment protocol oriented the scanning plane so that both condyles were imaged in a plane perpendicular to the primary femoral axis of the knee about which the tibia flexes and extends. The study included 155 varus knees and forty-four valgus knees. Radii were calculated from the area of the best-fit circle overlaid from 10° to 160° on the subchondral corticocancellous bone interface of the medial and lateral femoral condyles. The radius of a condyle was the average of the radii on four adjacent images that showed the femoral condyle with the largest curvature. Results: In the 155 varus knees, the radius of the lateral condyle was an average of 0.1 mm larger than that of the medial condyle (p = 0.003). In the forty-four valgus knees, the radius of the lateral condyle was an average of 0.2 mm larger than that of the medial condyle (p < 0.006). There was a strong association between the radii of the medial and lateral femoral condyles in both the varus (r2 = 0.9210) and the valgus (r2 = 0.9129) knees. Conclusions: As determined by imaging of the femoral condyles perpendicular to the primary femoral axis of the knee, the asymmetry between the radii of the medial and lateral femoral condyles in varus and valgus knees with end-stage osteoarthritis was ≤0.2 mm, which is small enough to be considered clinically unimportant when aligning a total knee prosthesis. Copyright © 2010 by the Journal of Bone and Joint Surgery, Incorporated. Source


Rodriguez-Fortea A.,Rovira i Virgili University | Balch A.L.,University of California at Davis | Poblet J.M.,Rovira i Virgili University
Chemical Society Reviews | Year: 2011

In this tutorial review taking X-ray crystallographically characterized compounds as a starting point a walk is taken through the electronic and structural properties of endohedral metallofullerenes. After classification of the fullerenes according to the encapsulated guest, particular attention is given to identifying factors that determine the selection of a particular carbon cage network by the internal metal cluster. Some of the physical rules that determine which particular fullerene cage is formed will be discussed. Concepts such as charge transfer between the cage and the guest metal ions, the topology of the cage, the separations between the 12 pentagons on the fullerene surface, and the effect of entropic factors are used to rationalize the selection of a particular cage. The roles of electrochemistry and vibrational spectroscopy in combination with theoretical calculations are considered in understanding the structures of the endohedral fullerenes. © 2011 The Royal Society of Chemistry. Source


Anacker B.L.,University of California at Davis
American Journal of Botany | Year: 2014

Serpentine soils are a model system for the study of plant adaptation, speciation, and species interactions. Serpentine soil is an edaphically stressful, low productivity soil type that hosts stunted vegetation and a spectacular level of plant endemism. One of the first papers on serpentine plant endemism was by Arthur Kruckeberg, titled "Intraspecific variability in the response of certain native plant species to serpentine soil. " Published in the American Journal of Botany in 1951, it has been cited over 100 times. Here, I review the context and content of the paper, as well as its impact. On the basis of the results of reciprocal transplant experiments in the greenhouse, Kruckeberg made three important conclusions on the nature of serpentine plant endemism: (1) Plants are locally adapted to serpentine soils, forming distinct soil ecotypes; (2) soil ecotypes are the first stage in the evolutionary progression toward serpentine endemism; and (3) serpentine endemics are restricted from more fertile nonserpentine soils by competition. Kruckeberg's paper inspired a substantial amount of research, especially in the three areas reviewed here: local adaptation and plant traits, speciation, and the interaction of climate and soil in plant endemism. In documenting soil ecotypes, Kruckeberg identi-fied serpentine soils as a potent selective factor in plant evolution and helped establish serpentine soils as a model system in evolution and ecology. © 2014 Botanical Society of America. Source


Townsend M.S.,University of California at Davis
American Journal of Clinical Nutrition | Year: 2010

Nutrient profiling is defined as the science of ranking or categorizing foods on the basis of their nutritional composition. Validity is a general term meaning accuracy. Nutrient profiling systems in the United States have not undergone any systematic validation effort to assess their accuracy against a comparison measure or group of measures. Different types of validation studies should be conducted: content, face, convergent, criterion, and predictive. This article provides a conceptual framework for establishing the validity of nutrient profiling systems with the desired objective of assisting US consumers with food selection to improve diet quality. For a profiling system to work successfully in the American marketplace, it must function well with consumers from most or all cultural groups, from all racial groups, and with low-literate as well as highly literate people. Emphasis should be placed on conducting different types of validation studies and multiple studies with different subpopulation groups. The use of consistent standards to assess the accuracy and usefulness of multiple profiling systems is imperative to successfully identify a nutrient profiling intervention that will have the potential to lead to improved diet quality and eventually to an improved health status in US consumers. © 2010 American Society for Nutrition. Source


Ustin S.L.,University of California at Davis | Gamon J.A.,University of Alberta
New Phytologist | Year: 2010

Contents: Summary795I.Introduction796II.History of functional-type classifications of vegetation796III.History of remote sensing of vegetation 799IV.New sensors and perspectives802V.Measuring detailed canopy structure806VI.The emerging hypothesis of 'optical types'810VII.Conclusions811Acknowledgements811References811 Summary: Conceptually, plant functional types represent a classification scheme between species and broad vegetation types. Historically, these were based on physiological, structural and/or phenological properties, whereas recently, they have reflected plant responses to resources or environmental conditions. Often, an underlying assumption, based on an economic analogy, is that the functional role of vegetation can be identified by linked sets of morphological and physiological traits constrained by resources, based on the hypothesis of functional convergence. Using these concepts, ecologists have defined a variety of functional traits that are often context dependent, and the diversity of proposed traits demonstrates the lack of agreement on universal categories. Historically, remotely sensed data have been interpreted in ways that parallel these observations, often focused on the categorization of vegetation into discrete types, often dependent on the sampling scale. At the same time, current thinking in both ecology and remote sensing has moved towards viewing vegetation as a continuum rather than as discrete classes. The capabilities of new remote sensing instruments have led us to propose a new concept of optically distinguishable functional types ('optical types') as a unique way to address the scale dependence of this problem. This would ensure more direct relationships between ecological information and remote sensing observations. © The Authors (2010). Journal compilation © New Phytologist Trust (2010). Source


Ronald P.C.,University of California at Davis
PLoS biology | Year: 2014

Over the last 300 years, plant science research has provided important knowledge and technologies for advancing the sustainability of agriculture. In this Essay, I describe how basic research advances have been translated into crop improvement, explore some lessons learned, and discuss the potential for current and future contribution of plant genetic improvement technologies to continue to enhance food security and agricultural sustainability. Source


Fiscella K.,University of Rochester | Franks P.,University of California at Davis
Annals of Family Medicine | Year: 2010

PURPOSE: Findings are conflicting about the relationship between vitamin D levels and cardiovascular mortality. We wanted to determine the contribution of vitamin D levels to black-white disparities in cardiovascular mortality. METHODS: We examined the association of serum 25(OH)D levels with cardiovascular mortality and its contribution to elevated risk among blacks through a retrospective cohort using baseline data from the third National Health and Nutrition Examination Survey 1988-1994 and cause-specific mortality through 2001 using the National Death Index. Using piecewise Poisson regression models, we examined the risk of cardiovascular death (coronary heart disease, heart failure, and stroke) by sample 25(OH)D quartile, adjusting for cardiovascular risk factors, and compared models of adjusted race-related cardiovascular mortality with and without further adjustment for 25(OH)D levels. RESULTS: Participants with 25(OH)D levels in the lowest quartile (mean = 13.9 ng/mL) compared with those in the 3 higher quartiles (mean = 21.6, 28.4, and 41.6 ng/mL) had higher adjusted risk of cardiovascular death (incident rate ratio [IRR] = 1.40; 95% confidence interval [CI], 1.16 -1.70). The higher age- and sex-adjusted cardiovascular mortality observed in blacks vs whites (IRR = 1.38; 95% CI, 1.13-1.70) was attenuated (IRR = 1.14; 95% CI, 0.91-1.44) by adjustment for 25(OH)D levels and fully eliminated with further adjustment for income (IRR = 1.01; 95% CI, 0.82-1.24). CONCLUSIONS: Low serum levels of 25(OH)D are associated with increased cardiovascular mortality in a nationally representative US sample. Black-white differences in 25(OH)D levels may contribute to excess cardiovascular mortality in blacks. Interventional trials among persons with low vitamin D levels are needed to determine whether oral supplementation improves cardiovascular outcomes. Source


Hastings A.,University of California at Davis
Population Ecology | Year: 2014

The management of populations that are distributed in space is an important problem, both for ensuring the persistence of threatened populations and for the eradication or prevention of spread of invasive species. I provide an overview of conditions for persistence which underlie management in both scenarios. The idea that persistence essentially depends on two aspects, local dynamics and connectivity, provides a way to organize management approaches and leads to rules of thumb for management. This can guide management or suggest what additional information would be needed. Examples from a variety of systems and taxa illustrate the results. © 2013 The Society of Population Ecology and Springer Japan. Source


Doyle J.A.,University of California at Davis
Annual Review of Earth and Planetary Sciences | Year: 2012

Molecular data on relationships within angiosperms confirm the view that their increasing morphological diversity through the Cretaceous reflected their evolutionary radiation. Despite the early appearance of aquatics and groups with simple flowers, the record is consistent with inferences from molecular trees that the first angiosperms were woody plants with pinnately veined leaves, multiparted flowers, uniovulate ascidiate carpels, and columellar monosulcate pollen. Molecular data appear to refute the hypothesis based on morphology that angiosperms and Gnetales are closest living relatives. Morphological analyses of living and fossil seed plants that assume molecular relationships identify glossopterids, Bennettitales, and Caytonia as angiosperm relatives; these results are consistent with proposed homologies between the cupule of glossopterids and Caytonia and the angiosperm bitegmic ovule. Jurassic molecular dates for the angiosperms may be reconciled with the fossil record if the first angiosperms were restricted to wet forest understory habitats and did not radiate until the Cretaceous. © 2012 by Annual Reviews. All rights reserved. Source


Saxton M.J.,University of California at Davis
Journal of Physical Chemistry B | Year: 2014

Scalable tracers are potentially a useful tool to examine diffusion mechanisms and to predict diffusion coefficients, particularly for hindered diffusion in complex, heterogeneous, or crowded systems. Scalable tracers are defined as a series of tracers varying in size but with the same shape, structure, surface chemistry, deformability, and diffusion mechanism. Both chemical homology and constant dynamics are required. In particular, branching must not vary with size, and there must be no transition between ordinary diffusion and reptation. Measurements using scalable tracers yield the mean diffusion coefficient as a function of size alone; measurements using nonscalable tracers yield the variation due to differences in the other properties. Candidate scalable tracers are discussed for two-dimensional (2D) diffusion in membranes and three-dimensional diffusion in aqueous solutions. Correlations to predict the mean diffusion coefficient of globular biomolecules from molecular mass are reviewed briefly. Specific suggestions for the 3D case include the use of synthetic dendrimers or random hyperbranched polymers instead of dextran and the use of core-shell quantum dots. Another useful tool would be a series of scalable tracers varying in deformability alone, prepared by varying the density of crosslinking in a polymer to make say "reinforced Ficoll" or "reinforced hyperbranched polyglycerol." (Figured Presented). © 2014 American Chemical Society. Source


The colonization of new adaptive zones is widely recognized as one of the hallmarks of adaptive radiation. However, the adoption of novel resources during this process is rarely distinguished from phenotypic change because morphology is a common proxy for ecology. How can we quantify ecological novelty independent of phenotype? Our study is split into two parts: we first document a remarkable example of ecological novelty, scale-eating (lepidophagy), within a rapidly-evolving adaptive radiation of Cyprinodon pupfishes on San Salvador Island, Bahamas. This specialized predatory niche is known in several other fish groups, but is not found elsewhere among the 1,500 species of atherinomorphs. Second, we quantify this ecological novelty by measuring the time-calibrated phylogenetic distance in years to the most closely-related species with convergent ecology. We find that scale-eating pupfish are separated by 168 million years of evolution from the nearest scale-eating fish. We apply this approach to a variety of examples and highlight the frequent decoupling of ecological novelty from phenotypic divergence. We observe that novel ecology is not always tightly correlated with rates of phenotypic or species diversification, particularly within recent adaptive radiations, necessitating the use of additional measures of ecological novelty independent of phenotype. Source


Janata P.,University of California at Davis
Annals of the New York Academy of Sciences | Year: 2012

Singing in one's mind or forming expectations about upcoming notes both require that mental images of one or more pitches will be generated. As with other musical abilities, the acuity with which such images are formed might be expected to vary across individuals and may depend on musical training. Results from several behavioral tasks involving intonation judgments indicate that multiple memory systems contribute to the formation of accurate mental images for pitch, and that the functionality of each is affected by musical training. Electrophysiological measures indicate that the ability to form accurate mental images is associated with greater engagement of auditory areas and associated error-detection circuitry when listeners imagine ascending scales and make intonation judgments about target notes. A view of auditory mental images is espoused in which unified mental image representations are distributed across multiple brain areas. Each brain area helps shape the acuity of the unified representation based on current behavioral demands and past experience. © 2012 New York Academy of Sciences. Source


Ronald P.C.,University of California at Davis | Ronald P.C.,Joint BioEnergy Institute | Ronald P.C.,Kyung Hee University | Beutler B.,Scripps Research Institute
Science | Year: 2010

The last common ancestor of plants and animals may have lived 1 billion years ago. Plants and animals have occasionally exchanged genes but, for the most part, have countered selective pressures independently. Microbes (bacteria, eukaryotes, and viruses) were omnipresent threats, influencing the direction of multicellular evolution. Receptors that detect molecular signatures of infectious organisms mediate awareness of nonself and are integral to host defense in plants and animals alike. The discoveries leading to elucidation of these receptors and their ligands followed a similar logical and methodological pathway in both plant and animal research. Source


Chen L.,University of California at Davis
Journal of the American Heart Association | Year: 2012

Mitochondrial fusion protein mutations are a cause of inherited neuropathies such as Charcot-Marie-Tooth disease and dominant optic atrophy. Previously we reported that the fusion protein optic atrophy 1 (OPA1) is decreased in heart failure. We investigated cardiac function, mitochondrial function, and mtDNA stability in a mouse model of the disease with OPA1 mutation. The homozygous mutation is embryonic lethal. Heterozygous OPA(+/-) mice exhibit reduced mtDNA copy number and decreased expression of nuclear antioxidant genes at 3 to 4 months. Although initial cardiac function was normal, at 12 months the OPA1(+/-) mouse hearts had decreased fractional shortening, cardiac output, and myocyte contraction. This coincided with the onset of blindness. In addition to small fragmented mitochondria, aged OPA1(+/-) mice had impaired cardiac mitochondrial function compared with wild-type littermates. OPA1 mutation leads to deficiency in antioxidant transcripts, increased reactive oxygen species, mitochondrial dysfunction, and late-onset cardiomyopathy. Source


Rannala B.,University of California at Davis
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2016

Bayesian inference of species divergence times is an unusual statistical problem, because the divergence time parameters are not identifiable unless both fossil calibrations and sequence data are available. Commonly used marginal priors on divergence times derived from fossil calibrations may conflict with node order on the phylogenetic tree causing a change in the prior on divergence times for a particular topology. Care should be taken to avoid confusing this effect with changes due to informative sequence data. This effect is illustrated with examples. A topology-consistent prior that preserves the marginal priors is defined and examples are constructed. Conflicts between fossil calibrations and relative branch lengths (based on sequence data) can cause estimates of divergence times that are grossly incorrect, yet have a narrow posterior distribution. An example of this effect is given; it is recommended that overly narrow posterior distributions of divergence times should be carefully scrutinized. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. © 2016 The Author(s) Published by the Royal Society. All rights reserved. Source


Sanchez-Adams J.,Rice University | Athanasiou K.A.,University of California at Davis
Biomaterials | Year: 2012

Adult stem cells from the dermal layer of skin are an attractive alternative to primary cells for meniscus engineering, as they may be easily obtained and used autologously. Recently, chondroinducible dermis cells from caprine skin have shown promising characteristics for cartilage tissue engineering. In this study, their multilineage differentiation capacity is determined, and methods of expanding and tissue engineering these cells are investigated. It was found that these cells could differentiate along adipogenic, osteogenic, and chondrogenic lineages, allowing them to be termed dermis isolated adult stem cells (DIAS cells). Focusing on cartilage tissue engineering, it was found that passaging these cells in chondrogenic medium and forming them into self-assembled tissue engineered constructs caused upregulation of collagen type II and COMP gene expression. Further investigation showed that applying transforming growth factor β1 (TGF-β1) or bone morphogenetic protein 2 (BMP-2) to DIAS constructs caused increased sulfated glycosaminoglycan content. Additionally, TGF-β1 treatment caused significant increases in compressive properties and construct contraction. In contrast, BMP-2 treatment resulted in the largest constructs, but did not increase compressive properties. These results show that DIAS cells can be easily manipulated for cartilage tissue engineering strategies, and may also be a useful cell source for other mesenchymal tissues. © 2011 Elsevier Ltd. Source


Halloran S.K.,University of California at Davis
PloS one | Year: 2012

The peak in influenza incidence during wintertime in temperate regions represents a longstanding, unresolved scientific question. One hypothesis is that the efficacy of airborne transmission via aerosols is increased at lower humidities and temperatures, conditions that prevail in wintertime. Recent work with a guinea pig model by Lowen et al. indicated that humidity and temperature do modulate airborne influenza virus transmission, and several investigators have interpreted the observed humidity dependence in terms of airborne virus survivability. This interpretation, however, neglects two key observations: the effect of ambient temperature on the viral growth kinetics within the animals, and the strong influence of the background airflow on transmission. Here we provide a comprehensive theoretical framework for assessing the probability of disease transmission via expiratory aerosols between test animals in laboratory conditions. The spread of aerosols emitted from an infected animal is modeled using dispersion theory for a homogeneous turbulent airflow. The concentration and size distribution of the evaporating droplets in the resulting "Gaussian breath plume" are calculated as functions of position, humidity, and temperature. The overall transmission probability is modeled with a combination of the time-dependent viral concentration in the infected animal and the probability of droplet inhalation by the exposed animal downstream. We demonstrate that the breath plume model is broadly consistent with the results of Lowen et al., without invoking airborne virus survivability. The results also suggest that, at least for guinea pigs, variation in viral kinetics within the infected animals is the dominant factor explaining the increased transmission probability observed at lower temperatures. Source


Boettiger C.,Center for Population Biology | Hastings A.,University of California at Davis
Journal of the Royal Society Interface | Year: 2012

Catastrophic regime shifts in complex natural systems may be averted through advanced detection. Recent work has provided a proof-of-principle that many systems approaching a catastrophic transition may be identified through the lens of early warning indicators such as rising variance or increased return times. Despite widespread appreciation of the difficulties and uncertainty involved in such forecasts, proposed methods hardly ever characterize their expected error rates. Without the benefits of replicates, controls or hindsight, applications of these approaches must quantify how reliable different indicators are in avoiding false alarms, and how sensitive they are to missing subtle warning signs. We propose a model-based approach to quantify this trade-off between reliability and sensitivity and allow comparisons between different indicators. We show these error rates can be quite severe for common indicators even under favourable assumptions, and also illustrate how a model-based indicator can improve this performance. We demonstrate how the performance of an early warning indicator varies in different datasets, and suggest that uncertainty quantification become a more central part of early warning predictions. © 2012 The Royal Society. Source


MacLean K.A.,University of California at Davis
Psychological science : a journal of the American Psychological Society / APS | Year: 2010

The ability to focus one's attention underlies success in many everyday tasks, but voluntary attention cannot be sustained for extended periods of time. In the laboratory, sustained-attention failure is manifest as a decline in perceptual sensitivity with increasing time on task, known as the vigilance decrement. We investigated improvements in sustained attention with training (approximately 5 hr/day for 3 months), which consisted of meditation practice that involved sustained selective attention on a chosen stimulus (e.g., the participant's breath). Participants were randomly assigned either to receive training first (n = 30) or to serve as waiting-list controls and receive training second (n = 30). Training produced improvements in visual discrimination that were linked to increases in perceptual sensitivity and improved vigilance during sustained visual attention. Consistent with the resource model of vigilance, these results suggest that perceptual improvements can reduce the resource demand imposed by target discrimination and thus make it easier to sustain voluntary attention. Source


Invernizzi P.,Center for Autoimmune Liver Diseases | Invernizzi P.,University of California at Davis
Hepatology | Year: 2011

Primary biliary cirrhosis (PBC) is an autoimmune biliary disease characterized by injury of small and medium size bile ducts, eventually leading to liver cirrhosis and death. Although the causes remain enigmatic, recent evidence has strengthened the importance of genetic factors in determining the susceptibility to the disease. Besides the strong heritability suggested by familial occurrence and monozygotic twins concordance, for decades there has not been a clear association with specific genes, with the only exception of a low risk conferred by a class II human leukocyte antigen (HLA) variant, the DRB1*08 allele, at least in some populations. The picture has become more complete when strong protective associations between PBC and the HLA DRB1*11 and DRB1*13 alleles were found in Italian and UK series. However, HLA genes have begun again to attract interest thanks to recent genome-wide association studies (GWAS), which clearly demonstrated that the major components of the genetic architecture of PBC are within the HLA region. As expected in a genetically complex disease, GWAS also identified several novel non-HLA variants, but it is worth noting that all of them are in immuno-related genes. In this review, the paradigmatic tale of what, and how, we learned about HLA genes in PBC will be retraced with particular focus on how GWAS are enabling a rewriting the story of PBC pathogenesis. These recent discoveries will not only drive functional studies but will also hold the promise of developing novel disease-specific treatments. © 2011 American Association for the Study of Liver Diseases. Source


Deng W.,University of California at Davis
BioEssays | Year: 2010

Current methods of reprogramming differentiated cells into induced pluripotent stem cells remain slow and inefficient. In a recent report published online in Nature, Bhutani et al. [1] developed a cell fusion strategy, achieving quick and efficient reprogramming toward pluripotency. Using this assay, they identified an immune system protein called activation-induced cytidine deaminase, or AID, which unexpectedly is actually able to "aid" in reprogramming due to its involvement in DNA demethylation that is required for induction of the two key pluripotency genes, Oct4 and Nanog. More recently, Popp et al. [2] also reported online in Nature that AID is important for complete cell reprogramming in mammals. Together, these findings provide new insights into how cells are reprogrammed, identify the specific role of AID in cell fate reversal, and advance the field of regenerative medicine. © 2010 WILEY Periodicals, Inc. Source


Hell J.W.,University of California at Davis
Science Signaling | Year: 2010

When we are frightened, our hearts beat more rapidly and forcefully so we can fight more intensely or run away faster. This fight-or-flight response is triggered by the release of norepinephrine from neurons of the sympathetic nervous system. Norepinephrine activates the classic β-adrenergic receptor-heterotrimeric Gs protein-adenylyl cyclase-adenosine 3′,5′-monophosphate-protein kinase A (PKA) signaling cascade. One of the main PKA targets implicated in this response is the L-type Ca2+ channel CaV1.2, which mediates Ca2+ influx into cardiomyocytes. Because of its central function in regulating heartbeat, and because the underlying molecular mechanism has remained elusive, understanding the regulation of CaV1.2 has been considered the holy grail for the field of channel regulation. New evidence from the quest to solve the mystery of CaV1.2 regulation has revealed that reproducible reconstitution of this regulation in heterologous cells requires a perfect balance of the ratio of CaV1.2 to A-kinase anchor proteins (AKAPs). Proteolytic processing of the cytosolic C terminus of the central, pore-forming α11.2 subunit of CaV1.2 contributed to its regulation by PKA, and Ser 1700 in the C terminus of the α11.2 subunit emerged as the relevant PKA phosphorylation site. Source


Webster D.W.,Johns Hopkins University | Wintemute G.J.,University of California at Davis
Annual Review of Public Health | Year: 2015

This article summarizes and critiques available evidence from studies published between 1999 and August 2014 on the effects of policies designed to keep firearms from high-risk individuals in the United States. Some prohibitions for high-risk individuals (e.g., those under domestic violence restraining orders, violent misdemeanants) and procedures for checking for more types of prohibiting conditions are associated with lower rates of violence. Certain laws intended to prevent prohibited persons from accessing firearms - rigorous permit-to-purchase, comprehensive background checks, strong regulation and oversight of gun dealers, and requiring gun owners to promptly report lost or stolen firearms - are negatively associated with the diversion of guns to criminals. Future research is needed to examine whether these laws curtail nonlethal gun violence and whether the effects of expanding prohibiting conditions for firearm possession are modified by the presence of policies to prevent diversion. Copyright © 2015 by Annual Reviews. All rights reserved. Source


Dhir A.,University of California at Davis
Expert Opinion on Therapeutic Targets | Year: 2010

The 39th Annual meeting of the Society for Neuroscience was held in Chicago, Illinois, USA from 17 to 21 October, 2009. The conference was attended by more than 33,000 delegates from across the globe including scientists from both basic and clinical settings. Co-incidentally, this year, the scientific community is commemorating the 200th anniversary of the birth of the famous English naturalist and biologist, Charles Darwin, who described the theory of natural selection. Keeping its traditions, the congress discussed various new advances in the area of neuroscience. The topics were divided into symposia, mini-symposia, nano-symposia, special lectures and poster sessions. The main areas of discussion were novel discoveries in Alzheimer's, Parkinson's, drug addiction, autism, epilepsy and major depression. According to the WHO, neurological disorders are one of the greatest threats to public health. There are many unknown and challenging facts in the field of neuroscience that needs exploration. It is unfortunate that despite the availability of various drugs for treating these disorders, a sizeable population still do not achieve complete remission. Therefore, organizing such events and addressing the latest developments may open new treatment vistas for patients suffering from these disorders. The present review discusses some of the outcomes of the deliberations in the field of epilepsy and major depression. © 2010 Informa UK Ltd. Source


Cardiff R.D.,University of California at Davis
Journal of Mammary Gland Biology and Neoplasia | Year: 2010

Epithelial-mesenchymal-transition (EMT) tumorigenesis in the mouse was first described over 100 years ago using various terms such as carcinosarcoma and without any comprehension of the underlying mechanisms. Such tumors have been considered artifacts of transplantation and of tissue culture. Recently, EMT tumors have been recognized in mammary glands of genetically engineered mice. This review provides a historical perspective leading to the current status in the context of some of the key molecular biology. The biology of mouse mammary EMT tumorigenesis is discussed with comparisons to human breast cancer. © 2010 The Author(S). Source


Pakyurek M.,University of California at Davis
Telemedicine journal and e-health : the official journal of the American Telemedicine Association | Year: 2010

The literature on the efficacy of telepsychiatry for assessing and treating children and adolescents with mental health problems is still developing, but there is evidence that telepsychiatry is diagnostically valid, and that there is high patient and provider satisfaction. Outcome studies are awaited, with the assumption that telepsychiatry has to demonstrate at least as good outcomes and reliability as face-to-face psychiatric care. In this article we suggest, by reviewing the process of telepsychiatry with children, and illustrating relevant issues with five case studies of patients we have seen, that there is a valid case for arguing that in certain children and adolescents, telepsychiatry, as a consultation process, might actually be a superior method of psychiatric assessment to face-to-face consultation. Four factors stand out supporting this view. These are the novelty of the consultation, the capacity to provide direction, the extra distance involved (both psychological and physical), and the authenticity of the interaction. More research in child and adolescent telepsychiatry is indicated. Source


Epanchin-Niell R.S.,Resources for the Future | Wilen J.E.,University of California at Davis
Journal of Environmental Economics and Management | Year: 2012

This study examines the spatial nature of optimal bioinvasion control. We develop a spatially explicit two-dimensional model of species spread that allows for differential control across space and time, and we solve for optimal spatial-dynamic control strategies. The qualitative nature of optimal strategies depends in interesting ways on aspects of landscape and invasion geometry. For example, reducing the extent of exposed invasion edge, through spread, removal, or strategically employing landscape features, can be optimal because it reduces long-term containment costs. Optimal invasion control is spatially and temporally "forward-looking" in the sense that strategies should be targeted to slow or prevent the spread of an invasion in the direction of greatest potential long-term damages. These spatially explicit characterizations of optimal policies contribute insights and intuition to the largely nonspatial literature on controlling invasions and to understanding control of spatial-dynamic processes in general. © 2011 Elsevier Inc. Source


Marshall D.J.,University of Queensland | Morgan S.G.,University of California at Davis
Current Biology | Year: 2011

Naturalists and scientists have been captivated by the diversity of marine larval forms since they were discovered following the advent of the microscope. Because they often bear little resemblance to adults, larvae were identified initially as new life forms, classified into different groups based on the similarity of their body plans and given new names that are still with us today. The radically different body plans and lifestyles of marine larvae and adults have led most investigators historically to study the two phases of complex life cycles in isolation. More recently, important ecological insights have sprung from taking a holistic view of marine life cycles. Meanwhile, the evolutionary (phenotypic and genetic) links among life-history phases remain less appreciated. In this review, our objective is to evaluate the evolutionary links within marine life cycles, and explore their ecological and evolutionary consequences. We provide a brief overview of marine life histories, discuss the phenotypic and genetic links between the two phases of the life cycle and pose challenges to advance our understanding of the evolutionary constraints acting on marine life histories. © 2011 Elsevier Ltd. All rights reserved. Source


Tucker R.P.,University of California at Davis
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution | Year: 2013

Horizontal gene transfer (HGT), also known as lateral gene transfer, results in the rapid acquisition of genes from another organism. HGT has long been known to be a driving force in speciation in prokaryotes, and there is evidence for HGT from symbiotic and infectious bacteria to metazoans, as well as from protists to bacteria. Recently, it has become clear that as many as a 1,000 genes in the genome of the choanoflagellate Monosiga brevicollis may have been acquired by HGT. Interestingly, these genes reportedly come from algae, bacteria, and other choanoflagellate prey. Some of these genes appear to have allowed an ancestral choanoflagellate to exploit nutrient-poor environments and were not passed on to metazoan descendents. However, some of these genes are also found in animal genomes, suggesting that HGT into a common ancestor of choanozoans and animals may have contributed to metazoan evolution. © 2012 Wiley Periodicals, Inc. Source


Mease P.J.,Swedish Medical Center | Armstrong A.W.,University of California at Davis
Drugs | Year: 2014

Psoriatic arthritis (PsA) is a chronic, systemic inflammatory disease. Up to 40 % of patients with psoriasis will go on to develop PsA, usually within 5-10 years of cutaneous disease onset. Both conditions share common pathogenic mechanisms involving genetic and environmental factors. Because psoriasis is typically present for years before PsA-related joint symptoms emerge, dermatologists are in a unique position to detect PsA earlier in the disease process through regular, routine screening of psoriasis patients. Distinguishing clinical features of PsA include co-occurrence of psoriatic skin lesions and nail dystrophy, as well as dactylitis and enthesitis. Patients with PsA are usually seronegative for rheumatoid factor, and radiographs may reveal unique features such as juxta-articular new bone formation and pencil-in-cup deformity. Early treatment of PsA with disease-modifying anti-rheumatic drugs has the potential to slow disease progression and maintain patient quality of life. Optimally, a single therapeutic agent will control both the skin and joint psoriatic symptoms. A number of traditional treatments used to manage psoriasis, such as methotrexate and cyclosporine, are also effective for PsA, but these agents are often inadequately effective, temporary in benefit and associated with significant safety concerns. Biologic anti-tumour necrosis factor agents, such as etanercept, infliximab and adalimumab, are effective for treating patients who have both psoriasis and PsA. However, a substantial number of patients may lose efficacy, have adverse effects or find intravenous or subcutaneous administration inconvenient. Emerging oral treatments, including phosphodiesterase 4 inhibitors, such as apremilast, and new biologics targeting interleukin-17, such as secukinumab, brodalumab and ixekizumab, have shown encouraging clinical results in the treatment of psoriasis and/or PsA. Active and regular collaboration of dermatologists with rheumatologists in managing patients who have psoriasis and PsA is likely to yield more optimal control of psoriatic dermal and joint symptoms, and improve long-term patient outcomes. © 2014 The Author(s). Source


Yang Z.,CAS Institute of Zoology | Yang Z.,University College London | Rannala B.,CAS Institute of Zoology | Rannala B.,University of California at Davis
Nature Reviews Genetics | Year: 2012

Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken phylogenetic analysis to a new height. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use. © 2012 Macmillan Publishers Limited. All rights reserved. Source


Keesing F.,Bard College | Young T.P.,University of California at Davis
BioScience | Year: 2014

African savannas are home to an abundant and diverse assemblage of wild herbivores, but the very grasses that sustain these wild herds also make savannas attractive to humans and their livestock. We used the Kenya Long-term Exclosure Experiment to investigate the ecological effects of different combinations of native and domestic grazers. The experimental removal of large grazing mammals set into motion a cascade of consequences, beginning with the doubling in abundance of a small grazing mammal, the pouched mouse (Saccostomus mearnsi). The presence of abundant mice attracted venomous snakes such as the olive hissing snake (Psammophis mossambicus); devastated seedlings of the dominant tree (Acacia drepanolobium); and doubled the abundance of fleas, which potentially increased the risk of transmission of flea-borne pathogens. Together, these results show the potential for the loss of large mammals to have cryptic consequences for African savannas, with important and often undesirable repercussions for humans. © The Author(s) 2014. Source


Goymann W.,Max Planck Institute For Ornithologie | Wingfield J.C.,University of California at Davis
Behavioral Ecology | Year: 2014

Testosterone is a key hormone for the development of secondary sexual characters and dimorphisms in behavior and morphology of male vertebrates. Because females often express detectable levels of testosterone, testosterone has been suggested to also play a role in the modulation of secondary sexual traits in females. Previous comparative analyses in birds and fish demonstrated a relationship between male-to-female testosterone ratios and the degree of sexual dimorphism. Furthermore, female maximum testosterone was related to mating system and coloniality. Here, we reevaluate these previous ideas using phylogenetic analyses and effect size measures for the relationship between birds' male-to-female maximum testosterone levels. Further, we investigate the seasonal androgen response of female birds (the difference from baseline to maximum testosterone), which in males is strongly related to mating system. We could not confirm a relationship between male-to-female testosterone, maximum female testosterone, or the seasonal androgen response of females with any life-history parameter. We conclude that the expectation that testosterone regulates traits in females in a similar manner as in males should be reconsidered. This expectation may be partially due to hormone manipulation studies using pharmacological doses of testosterone that had similar effects in females than in males but may be of limited importance for the physiological range of testosterone concentrations occurring within ecological and evolutionary contexts. Thus, the assumption that circulating testosterone should covary with ecologically relevant secondary sexual traits in females may be misleading: selection pressures on females differ from those on males and females may regulate behavior differently. © 2014 The Author. Source


Aim: In this study, I examined the relative contributions of geography and ecology to species diversification within the genus Nerita, a prominent clade of marine snails that is widely distributed across the tropics and intertidal habitats. Specifically, I tested whether geographical patterns of speciation correspond primarily to allopatric or sympatric models, and whether habitat transitions have played a major role in species diversification. Location: Indo-West Pacific, eastern Pacific, Atlantic, tropical marine intertidal. Methods: I used a previously reconstructed molecular phylogeny of Nerita as a framework to assess the relative importance of geographical and ecological factors in species diversification. To evaluate whether recently diverged clades exhibit patterns consistent with allopatric or sympatric speciation, I mapped the geo-graphical distribution of each species onto the species-level phylogeny, and examined the relationship between range overlap and time since divergence using age-range correlation analyses. To determine the relative contribution of habitat transitions to divergence, I traced shifts in intertidal substrate affinity and vertical zonation across the phylogeny using parsimony, and implemented randomization tests to evaluate the resulting patterns of ecological change. Results: Within the majority of Nerita clades examined, age-range correlation analysis yielded a low intercept and a positive slope, similar to that expected under allopatric speciation. Approximately 75% of sister species pairs have maintained allopatric distributions; whereas more distantly related sister taxa often exhibited complete or nearly complete geographical overlap. In contrast, only 19% of sister species occupy distinct habitats. For both substrate and zonation, habitat transitions failed to concentrate towards either the tips or the root of the phylogeny. Instead, habitat shifts have occurred throughout the history of Nerita, with a general transition from the lower and mid-littoral towards the upper and supra-littoral zones, and multiple independent shifts from hard (rock) to softer substrates (mangrove, mud and sand). Main conclusions: Both geography and ecology appear to have influenced diversification in Nerita, but to different extents. Geography seems to play a principal role, with allopatric speciation driving the majority of Nerita divergences. Habitat transitions appear insignificant in shaping the early and recent history of speciation, and promoting successive diversification in Nerita; however, shifts may have been important for respective divergences (i.e. those that correspond to the transitions) and enhancing diversity throughout the clade. © 2010 Blackwell Publishing Ltd. Source


Perkins T.A.,University of California at Davis
The American naturalist | Year: 2012

Both exotic and native species have been shown to evolve in response to invasions, yet the impacts of rapidly evolving interactions between novel species pairs have been largely ignored in studies of invasive species spread. Here, I use a mathematical model of an interacting invasive predator and its native prey to determine when and how evolutionary lability in one or both species might impact the dynamics of the invader's spatial advance. The model shows that evolutionarily labile invaders continually evolve better adapted phenotypes along the moving invasion front, offering an explanation for accelerating spread and spatial phenotype clines following invasion. I then analytically derive a formula to estimate the relative change in spread rate due to evolution. Using parameter estimates from the literature, this formula shows that moderate heritabilities and selection strengths are sufficient to account for changes in spread rates observed in historical and ongoing invasions. Evolutionarily labile native species can slow invader spread when genes flow from native populations with exposure to the invader into native populations ahead of the invasion front. This outcome is more likely in systems with highly diffuse native dispersal, net directional movement of natives toward the invasion front, or human inoculation of uninvaded native populations. Source


Lagattuta K.H.,University of California at Davis
Child Development Perspectives | Year: 2014

Remembering the past can shape current emotions and behaviors as well as bias anticipations of the future. This awareness that mental states and emotions cohere across time-sometimes called mental time travel-is a fundamental component of social cognition critical for assessing risk, making decisions, and understanding others. In this article, I highlight early competencies and development in young children's reasoning about connections among life history, mind, and emotion. I focus primarily on children's knowledge about emotions and decisions caused by being reminded about the past and thinking about the future. Findings reveal surprising insights in children as young as 3-4 years of age, age-related changes through middle childhood into adulthood, and individual differences that have implications for mental health. © 2014 The Society for Research in Child Development. Source


Kopp A.,University of California at Davis
Trends in Genetics | Year: 2012

Most animals are sexually dimorphic, but different taxa have different sex-specific traits. Despite major differences in the genetic control of sexual development among animal lineages, the doublesex/mab-3 related (Dmrt) family of transcription factors has been shown to be involved in sex-specific differentiation in all animals that have been studied. In recent years the functions of Dmrt genes have been characterized in many animal groups, opening the way to a broad comparative perspective. This review focuses on the similarities and differences in the functions of Dmrt genes across the animal kingdom. I highlight a number of common themes in the sexual development of different taxa, discuss how Dmrt genes have acquired new roles during animal evolution, and show how they have contributed to the origin of novel sex-specific traits. © 2012 Elsevier Ltd. Source


Fannjiang A.C.,University of California at Davis
Inverse Problems | Year: 2010

Inverse scattering methods capable of compressive imaging are proposed and analyzed. The methods employ randomly and repeatedly (multiple-shot) the single-input-single-output (SISO) measurements in which the probe frequencies, the incident, and the sampling directions are related in a precise way and are capable of recovering exactly scatterers of sufficiently low sparsity. For point targets, various sampling techniques are proposed to transform the scattering matrix into the random Fourier matrix. Two schemes are particularly interesting: the first one employs multiple frequencies with the sampling angle always in the back-scattering direction resembling the synthetic aperture (SA) imaging; the second employs only single frequency with the sampling angle in the (nearly) forward-scattering direction in the high-frequency limit, resembling the setting of x-ray tomography. The results for point targets are then extended to the case of localized extended targets by interpolating from grid points. In particular, an explicit error bound is derived for the piece-wise constant interpolation which is shown to be a practical way of discretizing localized extended targets and enabling the compressed sensing techniques. For distributed extended targets, the Littlewood-Paley basis is used in analysis. A specially designed sampling scheme then transforms the scattering matrix into a block-diagonal matrix with each block being the random Fourier matrix corresponding to one of the multiple dyadic scales of the extended target. In other words, by the Littlewood-Paley basis and the proposed sampling scheme the different dyadic scales of the target are decoupled and therefore can be reconstructed scale-by-scale by the proposed method. Moreover, with probes of any single frequency ω the coefficients in the Littlewood-Paley expansion for scales up to ω/(2π) can be exactly recovered. © 2010 IOP Publishing Ltd. Source


Kliebenstein D.J.,University of California at Davis | Kliebenstein D.J.,Copenhagen University
Trends in Plant Science | Year: 2014

Research over the past decades has made immense progress in identifying some genes and mechanisms underlying plant defense against biotic organisms. The recent movement towards systems biology approaches has increased mechanistic knowledge, revealing a need for understanding how all the genes and mechanisms integrate to create a response to any given biotic interaction. This begins with evidence that diverse molecular patterns converge, suggesting that the plant perceives signals not the interacting species. These signals then coordinate across regulatory networks via molecular interactions and cause non-cell autonomous responses in neighboring and systemic cells. Finally, the identification of transporters is showing that plant defenses are harmonized across tissues and even show the potential for coordination across individuals within a population. © 2014 Elsevier Ltd. Source


Urayama S.,University of California at Davis
World Journal of Gastroenterology | Year: 2015

Pancreatic ductal adenocarcinoma (PDAC) is the fourth and fifth leading cause of cancer death for each gender in developed countries. With lack of effective treatment and screening scheme available for the general population, the mortality rate is expected to increase over the next several decades in contrast to the other major malignancies such as lung, breast, prostate and colorectal cancers. Endoscopic ultrasound, with its highest level of detection capacity of smaller pancreatic lesions, is the commonly employed and preferred clinical imaging-based PDAC detection method. Various molecular biomarkers have been investigated for characterization of the disease, but none are shown to be useful or validated for clinical utilization for early detection. As seen from studies of a small subset of familial or genetically high-risk PDAC groups, the higher yield and utility of imaging-based screening methods are demonstrated for these groups. Multiple recent studies on the unique cancer metabolism including PDAC, demonstrate the potential for utility of the metabolites as the discriminant markers for this disease. In order to generate an early PDAC detection screening strategy available for a wider population, we propose to expand the population of higher risk PDAC group with combination clinical and metabolomics parameters. © The Author(s) 2015. Source


Leal W.S.,University of California at Davis
Annual Review of Entomology | Year: 2013

Our knowledge of the molecular basis of odorant reception in insects has grown exponentially over the past decade. Odorant receptors (ORs) from moths, fruit flies, mosquitoes, and the honey bees have been deorphanized, odorant-degrading enzymes (ODEs) have been isolated, and the functions of odorant-binding proteins (OBPs) have been unveiled. OBPs contribute to the sensitivity of the olfactory system by transporting odorants through the sensillar lymph, but there are competing hypotheses on how they act at the end of the journey. A few ODEs that have been demonstrated to degrade odorants rapidly may act in signal inactivation alone or in combination with other molecular traps. Although ORs in Drosophila melanogaster respond to multiple odorants and seem to work in combinatorial code involving both periphery and antennal lobes, reception of sex pheromones by moth ORs suggests that their labeled lines rely heavily on selectivity at the periphery. © 2013 by Annual Reviews. All rights reserved. Source


Aviran S.,University of California at Davis | Pachter L.,University of California at Berkeley
RNA | Year: 2014

Structure mapping is a classic experimental approach for determining nucleic acid structure that has gained renewed interest in recent years following advances in chemistry, genomics, and informatics. The approach encompasses numerous techniques that use different means to introduce nucleotide-level modifications in a structure-dependent manner. Modifications are assayed via cDNA fragment analysis, using electrophoresis or next-generation sequencing (NGS). The recent advent of NGS has dramatically increased the throughput, multiplexing capacity, and scope of RNA structure mapping assays, thereby opening new possibilities for genome-scale, de novo, and in vivo studies. From an informatics standpoint, NGS is more informative than prior technologies by virtue of delivering direct molecular measurements in the form of digital sequence counts. Motivated by these new capabilities, we introduce a novel model-based in silico approach for quantitative design of large-scale multiplexed NGS structure mapping assays, which takes advantage of the direct and digital nature of NGS readouts. We use it to characterize the relationship between controllable experimental parameters and the precision of mapping measurements. Our results highlight the complexity of these dependencies and shed light on relevant tradeoffs and pitfalls, which can be difficult to discern by intuition alone. We demonstrate our approach by quantitatively assessing the robustness of SHAPE-Seq measurements, obtained by multiplexing SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemistry in conjunction with NGS. We then utilize it to elucidate design considerations in advanced genome-wide approaches for probing the transcriptome, which recently obtained in vivo information using dimethyl sulfate (DMS) chemistry. © 2014 Aviran and Pachter. Source


Despa F.,University of California at Davis
Biophysical Journal | Year: 2010

This study suggests a molecular mechanism that explains the accumulation of denaturated proinsulin in the endoplasmic reticulum (ER) of βcells. Such states were frequently observed in β-cells experiencing increased demand for insulin production and were shown to lead to secretory dysfunction and diabetes. Here, a self-consistent kinetic model is used to investigate changes in protein translation due to ER overloading. The model is based on a molecular theory that relates the molecular composition and level of molecular crowding in the ER to the kinetic rates of protein folding/misfolding and transit to the Golgi apparatus (GA). This study suggests that molecular crowding forces can Increase protein misfoldlng and impair the transport to the GA, thus overwhelming the quality control mechanism in the ER. A continual accumulation of toxic residues in the ER enhances even further the molecular crowding, accelerating protein denaturation. This article shows that molecular crowding affects differently the transit of various proteins through the ER. Apparently, the molecular crowding level that can inhibit the transport of native proinsulin to the GA influences to a lesser extent the transit of proamylin, a much smaller peptide cosynthesized with proinsulin in the ER. Smaller-volume misfolded proinsulin species may also win the passage competition through the ER and move on the secretory track. However, misfolded proinsulin fails the conversion to active insulin. This study can help us to decipher circumstances leading to the alteration of the secretory function in susceptible β-cells and the onset of diabetes. © 2010 by the Biophysical Society. Source


Fannjiang A.,University of California at Davis
Inverse Problems | Year: 2012

Random illumination is proposed to enforce absolute uniqueness and resolve all types of ambiguity, trivial or nontrivial, in phase retrieval. Almost sure irreducibility is proved for any complex-valued object whose support set has rank 2. While the new irreducibility result can be viewed as a probabilistic version of the classical result by Bruck, Sodin and Hayes, it provides a novel perspective and an effective method for phase retrieval. In particular, almost sure uniqueness, up to a global phase, is proved for complex-valued objects under general two-point conditions. Under a tight sector constraint absolute uniqueness is proved to hold with probability exponentially close to unity as the object sparsity increases. Under a magnitude constraint with random amplitude illumination, uniqueness modulo global phase is proved to hold with probability exponentially close to unity as object sparsity increases. For general complex-valued objects without any constraint, almost sure uniqueness up to global phase is established with two sets of Fourier magnitude data under two independent illuminations. Numerical experiments suggest that random illumination essentially alleviates most, if not all, numerical problems commonly associated with the standard phasing algorithms. © 2012 IOP Publishing Ltd. Source


Saxton M.J.,University of California at Davis
Biophysical Journal | Year: 2010

Lateral diffusion in the plasma membrane is obstructed by proteins bound to the cytoskeleton. The most important parameter describing obstructed diffusion is the percolation threshold. The thresholds are well known for point tracers, but for tracers of nonzero radius, the threshold depends on the excluded area, not just the obstacle concentration. Here thresholds are obtained for circular obstacles on the continuum. Random obstacle configurations are generated by Brownian dynamics or Monte Carlo methods, the obstacles are immobilized, and the percolation threshold is obtained by solving a bond percolation problem on the Voronoi diagram of the obstacles. The percolation threshold is expressed as the diameter of the largest tracer that can cross a set of immobile obstacles at a prescribed number density. For random overlapping obstacles, the results agree with the known analytical solution quantitatively. When the obstacles are soft disks with a 1/r 12 repulsion, the percolating diameter is ∼20% lower than for overlapping obstacles. A percolation model predicts that the threshold is highly sensitive to the tracer radius. To our knowledge, such a strong dependence has so far not been reported for the plasma membrane, suggesting that percolation is not the factor controlling lateral diffusion. A definitive experiment is proposed. © 2010 by the Biophysical Society. Source


Whitehead A.,University of California at Davis
Journal of Experimental Biology | Year: 2012

Organisms that live in variable environments must adjust their physiology to compensate for environmental change. Modern functional genomics technologies offer global top-down discovery-based tools for identifying and exploring the mechanistic basis by which organisms respond physiologically to a detected change in the environment. Given that populations and species from different niches may exhibit different acclimation abilities, comparative genomic approaches may offer more nuanced understanding of acclimation responses, and provide insight into the mechanistic and genomic basis of variable acclimation. The physiological genomics literature is large and growing, as is the comparative evolutionary genomics literature. Yet, expansion of physiological genomics experiments to exploit taxonomic variation remains relatively undeveloped. Here, recent advances in the emerging field of comparative physiological genomics are considered, including examples of plants, bees and fish, and opportunities for further development are outlined particularly in the context of climate change research. Elements of robust experimental design are discussed with emphasis on the phylogenetic comparative approach. Understanding how acclimation ability is partitioned among populations and species in nature, and knowledge of the relevant genes and mechanisms, will be important for characterizing and predicting the ecological and evolutionary consequences of human-accelerated environmental change. © 2012. Published by The Company of Biologists Ltd. Source


Cappa C.D.,University of California at Davis
Atmospheric Measurement Techniques | Year: 2010

Aerosol thermodenuders provide a measure of particle volatility. The information provided by a thermodenuder is fundamentally related to the kinetics of evaporation and condensation within the device. Here, a time-dependent, multi-component model of particle and gas-phase mass transfer in a thermodenuder is described. This model empirically accounts for the temperature profile along the length of a typical thermodenuder and distinguishes between the influence of the heating section and of the adsorbent denuder section. It is shown that "semi-volatile" aerosol is particularly sensitive to the inclusion of an adsorbent denuder in the model. As expected, the mass loss from evaporation of particles as they pass through the thermodenuder is directly related to the compound vapor pressure, although the assumptions regarding the enthalpy of vaporization are shown to also have a large influence on the overall calculated mass thermograms. The model has been validated by comparison with previously measured mass thermograms for single-component aerosols and is shown to provide reasonable semi-quantitative agreement. The model that has been developed here can be used to provide quantitative understanding of aerosol volatility measurements of single and multi-component aerosol made using thermodenuders that include adsorbent denuder sections. © Author(s) 2010. Source


Coats R.,University of California at Davis
Climatic Change | Year: 2010

The purpose of this study was to quantify the decadal-scale time trends in air temperature, precipitation phase and intensity, spring snowmelt timing, and lake temperature in the Tahoe basin, and to relate the trends to large-scale regional climatic trends in the western USA. Temperature data for six long-term weather stations in the Tahoe region were analyzed for trends in annual and monthly means of maximum and minimum daily temperature. Precipitation data at Tahoe City were analyzed for trends in phase (rain versus snow), decadal standard deviation, and intensity of rainfall. Daily streamflow data for nine gaging stations in and around the Tahoe basin were examined for trends in snowmelt timing, by two methods, and an existing record for the temperature of Lake Tahoe was updated. The results for the Tahoe basin, which contrast somewhat with the surrounding region, indicate strong upward trends in air temperature, a shift from snow to rain, a shift in snowmelt timing to earlier dates, increased rainfall intensity, increased interannual variability, and continued increase in the temperature of Lake Tahoe. Two hypotheses are suggested that may explain why the basin could be warming faster than surrounding regions. Continued warming in the Tahoe basin has important implications for efforts to manage biodiversity and maintain clarity of the lake. © 2010 The Author(s). Source


A pro-thrombotic, pro-inflammatory diet can play a causative role in atherosclerotic-cardiovascular diseases. Dietary intervention studies provide insight into their pathophysiological manifestations and opportunities for prevention and management. We previously showed in an acute-meal setting that a beverage containing polyphenolic- and antioxidant-rich strawberry (Fragaria) vs placebo attenuated postprandial (fed-state) increases in biomarkers of oxidative and inflammatory stress, and insulin concentrations, induced by a high carbohydrate/fat (HCF) meal. In the present study, we aimed to extend our findings and investigate hypotheses related to the effects of chronic/6-week (wk) strawberry consumption on HCF meal-induced increases in glucose, insulin, and indicators of inflammation and hemostasis.Methods: In a crossover design, 14 women and 10 men (mean age, BMI: 50.9±15 years, 29.2±2.3 kg/m(2), respectively), were randomized to a 6-wk strawberry or placebo beverage followed by an HCF meal with assessments for 6-hours (h) postprandially. HCF meal responses after 6-wk strawberry beverage showed significantly attenuated postprandial PAI-1 concentrations compared to the placebo (p =0.002); the difference was most notable at 6 h. The IL-1 β response was attenuated with strawberry compared to the placebo (p =0.05). IL-6 attenuation was apparent but non-significant; IL-6 rose significantly from baseline to 6 h after the HCF meal following a placebo (p ≤0.01), although it remained relatively flat following the strawberry beverage from fasting to 6 h. No significant treatment-related differences were apparent for platelet aggregation, hsCRP, TNF-α, insulin, or glucose. These data are the first to suggest that regular consumption of strawberry, a polyphenolic- and antioxidant-rich fruit, may provide protection from HCF meal-induced increases in fibrinolytic and inflammatory factors in at-risk men and women. Source


Cowgill E.,University of California at Davis
Bulletin of the Geological Society of America | Year: 2010

The Pamir salient defi nes the western end of the Himalayan-Tibetan orogen and has overthrust the Tarim-Tajik basin to the north by ~300 km along a late Cenozoic, south-dipping intracontinental subduction zone. Field mapping, structural measurements, and analysis of mesoscale structures along a 32-km-long reach of the Yarkand River document the tectonic evolution of the east fl ank of this salient, between the North Pamir to the west and the Western Kunlun Shan to the east. The study area is cut by a set of four, north-northwest-striking, steeply dipping brittle faults. Microstructures and asymmetric outcrop-to map-scale folds indicate right slip along these faults. Between these structures, fault-bounded panels of Phanerozoic strata are deformed by en echelon folds with axes that trend more westerly than the adjacent faults, consistent with dextral transpression. The fault system described here extends for ~350 km along the eastern fl ank of the Pamir salient. Transpressional right slip along this set of faults, here called the Kashgar-Yecheng transfer system, appears to have accommodated late Cenozoic separation of the North Pamir from the Western Kunlun Shan during south-directed intracontinental subduction beneath the leading edge of the Pamir salient. Correlation of major faults suggests total slip along the Kashgar-Yecheng transfer system is likely on the order of ~280 km. This offset estimate implies long-term slip rates of 7-15 mm/a along the Kashgar-Yecheng transfer system when combined with previous sedimentologic, stratigraphic, and thermochronologic data that indicate deformation along the east fl ank of the Pamir started between the late Eocene and early Miocene. These results imply that the fi rst-order structures on the western and eastern fl anks of the Pamir are asymmetric: previous work has shown that deformation in the west was accommodated by anticlockwise vertical axis rotation of the Pamir over the eastern margin of the Tajik basin. This rotation is generally interpreted to refl ect n orthwest-directed radial thrusting, in contrast to the transpressional right-slip transfer faulting on the east side reported here. © 2009 Geological Society of America. Source


Hoffman M.D.,University of California at Davis
International journal of sports physiology and performance | Year: 2014

PURPOSE: To examine pacing among the most successful runners in the 161-km Western States Endurance Run (WSER) to determine if variations in segmental speed relate to performance, ambient temperature, and calendar year.METHODS: Segmental speed and coefficient of variation (CV) in speed were analyzed for 10 race segments of 24 races from 1985 through 2013.RESULTS: Segmental speeds did not differ between the eventual winners and lead runners and only differed between the 1st and 2nd finishers in the 2nd half of the race. Mean CV in speed was lower (P < .01) for the winners (12%) than for the other top-5 finishers (14-15%). CV in speed was related (r = .80, P = .006) to finish time for the fastest 10 finish times at the WSER. Multiple linear-regression analysis revealed mean CV in speed for the top-5 runners to be related to maximum ambient temperature (coefficient =.14, P < .05) and calendar year (coefficient = -.086, P = .034).CONCLUSIONS: Mountain trail running is characterized by wide variations in speed, but the fastest times are achieved when speed fluctuations are limited. This is generally accomplished by the winners remaining relatively close behind the lead runners before taking the lead in the middle half of the race, and then avoiding slowing as much as the other top runners in the latter race stages. Variations in speed increase with high ambient temperatures, and the small decrease in segmental speed variability among top runners across the nearly 30 y of this study suggests that the best runners have improved at pacing this race. Source


Adcock D.M.,Laboratory Corporation of America Holdings | Gosselin R.,University of California at Davis
Thrombosis Research | Year: 2015

Direct oral anticoagulant therapies, including direct anti-Xa and thrombin inhibitors have recently been introduced and may have advantages over vitamin K antagonists such as warfarin. This review describes briefly the clinical utility and mechanism of action of these agents. Detailed information is provided on effect of these agents on routine assays including the APTT and PT as well as their impact on specialty laboratory assays. Also included are the use of drug specific assays and a discussion of alternative methods to determine relative drug concentration, such as evaluating drug calibrators in APTT and PT assays and using heparin calibrated anti-Xa assays to measure direct Xa inhibitors. © 2015 The Authors. Source


Carroll S.P.,Institute for Contemporary Evolution | Carroll S.P.,University of California at Davis
Evolutionary Applications | Year: 2011

Biotic invaders and similar anthropogenic novelties such as domesticates, transgenics, and cancers can alter ecology and evolution in environmental, agricultural, natural resource, public health, and medical systems. The resulting biological changes may either hinder or serve management objectives. For example, biological control and eradication programs are often defeated by unanticipated resistance evolution and by irreversibility of invader impacts. Moreover, eradication may be ill-advised when nonnatives introduce beneficial functions. Thus, contexts that appear to call for eradication may instead demand managed coexistence of natives with nonnatives, and yet applied biologists have not generally considered the need to manage the eco-evolutionary dynamics that commonly result from interactions of natives with nonnatives. Here, I advocate a conciliatory approach to managing systems where novel organisms cannot or should not be eradicated. Conciliatory strategies incorporate benefits of nonnatives to address many practical needs including slowing rates of resistance evolution, promoting evolution of indigenous biological control, cultivating replacement services and novel functions, and managing native-nonnative coevolution. Evolutionary links across disciplines foster cohesion essential for managing the broad impacts of novel biotic systems. Rather than signaling defeat, conciliation biology thus utilizes the predictive power of evolutionary theory to offer diverse and flexible pathways to more sustainable outcomes. © 2011 Blackwell Publishing Ltd. Source


Rogawski M.A.,University of California at Davis
Epilepsy Currents | Year: 2011

In the 1990s there was intense interest in ionotropic glutamate receptors as therapeutic targets for diverse neurological disorders, including epilepsy. NMDA receptors were thought to play a key role in the generation of seizures, leading to clinical studies of NMDA receptor blocking drugs in epilepsy. Disappointing results dampened enthusiasm for ionotropic glutamate receptors as a therapeutic target. Eventually it became appreciated that another type of ionotropic glutamate receptor, the AMPA receptor, is actually the predominant mediator of excitatory neurotransmission in the central nervous system and moreover that AMPA receptors are critical to the generation and spread of epileptic activity. As drugs became available that selectively target AMPA receptors, it was possible to demonstrate that AMPA receptor antagonists have powerful antiseizure activity in in vitro and in vivo models. A decade later, promising clinical studies with AMPA receptor antagonists, including the potent noncompetitive antagonist perampanel, are once again focusing attention on AMPA receptors as a drug target for epilepsy therapy. © American Epilepsy Society. Source


Goshima G.,Nagoya University | Scholey J.M.,University of California at Davis
Annual Review of Cell and Developmental Biology | Year: 2010

The mitotic spindle accurately segregates genetic instructions by moving chromosomes to spindle poles (anaphase A) and separating the poles (anaphase B) so that, in general, the chromosomes and poles are positioned near the centers of the nascent daughter cell products of each cell division. Because the size of different types of dividing cells, and thus the spacing of their daughter cell centers, can vary significantly, the length of the metaphase or postanaphase B spindle often scales with cell size. However, significant exceptions to this scaling rule occur, revealing the existence of cell size-independent, spindle-associated mechanisms of spindle length control. The control of spindle length reflects the action of mitotic force-generating mechanisms, and its study may illuminate general principles by which cells regulate the size of internal structures. Here we review molecules and mechanisms that control spindle length, how these mechanisms are deployed in different systems, and some quantitative models that describe the control of spindle length. Copyright © 2010 by Annual Reviews. All rights reserved. Source


Baar K.,University of California at Davis
Sports Medicine | Year: 2014

Maximizing metabolic stress at a given level of mechanical stress can improve the adaptive response to endurance training, decrease injury, and potentially improve performance. Calcium and metabolic stress, in the form of heat, decreases in the adenosine triphosphate/ adenosine diphosphate ratio, glycogen depletion, caloric restriction, and oxidative stress, are the primary determinants of the adaptation to training. These stressors increase the activity and amount of peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1a), a protein that can directly induce the primary adaptive responses to endurance exercise: mitochondrial biogenesis, angiogenesis, and increases in fat oxidation. The activity of PGC-1a is regulated by its charge (phosphorylation and acetylation), whereas its transcription is regulated by proteins that bind to myocyte enhancing factor 2, enhancer box, and cyclic adenosine monophosphate response element sites within the PGC-1a promoter. This brief review will describe what is known about the control of PGC-1a by these metabolic stressors. As the duration of calcium release and the amount of metabolic stress, and therefore the activation of PGC-1a, can be directly modulated by training and nutrition, a simple strategy can be generated to maximize the adaptive response to endurance training. © The Author(s) 2014. Source


Kroeker K.J.,University of California at Davis | Gambi M.C.,Stazione Zoologica Anton Dohrn | Micheli F.,Stanford University
Proceedings of the National Academy of Sciences of the United States of America | Year: 2013

Disturbances are natural features of ecosystems that promote variability in the community and ultimately maintain diversity. Although it is recognized that global change will affect environmental disturbance regimes, our understanding of the community dynamics governing ecosystem recovery and the maintenance of functional diversity in future scenarios is very limited. Here, we use one of the few ecosystems naturally exposed to future scenarios of environmental change to examine disturbance and recovery dynamics. We examine the recovery patterns of marine species from a physical disturbance across different acidification regimes caused by volcanic CO2 vents. Plots of shallow rocky reef were cleared of all species in areas of ambient, low, and extreme low pH that correspond to near-future and extreme scenarios for ocean acidification. Our results illustrate how acidification decreases the variability of communities, resulting in homogenization and reduced functional diversity at a landscape scale. Whereas the recovery trajectories in ambient pH were highly variable and resulted in a diverse range of assemblages, recovery was more predictable with acidification and consistently resulted in very similar algaldominated assemblages. Furthermore, low pH zones had fewer signs of biological disturbance (primarily sea urchin grazing) and increased recovery rates of the dominant taxa (primarily fleshy algae). Together, our results highlight how environmental change can cause ecosystem simplification via environmentally mediated changes in community dynamics in the near future, with cascading impacts on functional diversity and ecosystem function. © PNAS 2013. Source


Carlson S.J.,University of California at Davis
Annual Review of Earth and Planetary Sciences | Year: 2016

Brachiopods are (perhaps all too) familiar to any geology student who has taken an invertebrate paleontology course; they may well be less familiar to biology students. Even though brachiopods are among the most significant components of the marine fossil record by virtue of their considerable diversity, abundance, and long evolutionary history, fewer than 500 species are extant. Reconciling the geological and biological perspectives is necessary in order to test hypotheses, not only about phylogenetic relationships among brachiopods but also about their spectacular decline in diversity in the end-Permian mass extinction, which permanently reset their evolutionary trajectory. Studying brachiopod ontogeny and development, population genetics, ecology, physiology, and biogeography, as well as molecular systematics and phylogenomics, enables us to better understand the context of evolutionary processes over the short term. Investigating brachiopod morphological, taxonomic, and stratigraphic records over the Phanerozoic Eon reveals historical patterns of long-term macroevolutionary change, patterns that are simply unknowable from a biological perspective alone. Copyright ©2016 Carlson. Source


Bruot C.,Arizona State University | Hihath J.,Arizona State University | Hihath J.,University of California at Davis | Tao N.,Arizona State University
Nature Nanotechnology | Year: 2012

Research in molecular electronics often in olves the demonstration of devices that are analogous to conventional semiconductor devices, such as transistors and diodes, but it is also possible to perform experiments that have no parallels in conventional electronics. For example, by applying a mechanical force to a molecule bridged between two electrodes, a device known as a molecular junction, it is possible to exploit the interplay between the electrical and mechanical properties of the molecule to control charge transport through the junction. 1,4′2-Benzenedithiol is the most widely studied molecule in molecular electronics 9-18, and it was shown recently that the molecular orbitals can be gated by an applied electric field. Here, we report how the electromechanical properties of a 1,4ĝ€2- benzenedithiol molecular junction change as the junction is stretched and compressed. Counterintuitively, the conductance increases by more than an order of magnitude during stretching, and then decreases again as the junction is compressed. Based on simultaneously recorded current-voltage and conductance-voltage characteristics, and inelastic electron tunnelling spectroscopy, we attribute this finding to a strain-induced shift of the highest occupied molecular orbital towards the Fermi level of the electrodes, leading to a resonant enhancement of the conductance. These results, which are in agreement with the predictions of theoretical models 14-17,19,20, also clarify the origins of the long-standing discrepancy between the calculated and measured conductance values of 1,4′2-benzenedithiol, which often differ by orders of magnitude 21. © 2012 Macmillan Publishers Limited. All rights reserved. Source


Volk H.E.,University of Southern California | Lurmann F.,Sonoma Technology Inc. | Penfold B.,Sonoma Technology Inc. | Hertz-Picciotto I.,University of California at Davis | McConnell R.,University of Southern California
Archives of General Psychiatry | Year: 2013

Context: Autism is a heterogeneous disorder with genetic and environmental factors likely contributing to its origins. Examination of hazardous pollutants has suggested the importance of air toxics in the etiology of autism, yet little research has examined its association with local levels of air pollution using residence-specific exposure assignments. Objective: To examine the relationship between trafficrelated air pollution, air quality, and autism. Design : This population-based case-control study includes data obtained from children with autism and control children with typical development who were enrolled in the Childhood Autism Risks from Genetics and the Environment study in California. The mother's address from the birth certificate and addresses reported from a residential history questionnaire were used to estimate exposure for each trimester of pregnancy and first year of life. Traffic-related air pollution was assigned to each location using a line-source air-quality dispersion model. Regional air pollutant measures were based on the Environmental Protection Agency's Air Quality System data. Logistic regression models compared estimated and measured pollutant levels for children with autism and for control children with typical development. Setting: Case-control study from California. Participants: A total of 279 children with autism and a total of 245 control children with typical development. Main Outcome Measures: Crude and multivariable adjusted odds ratios (AORs) for autism. Results: Children with autism were more likely to live at residences that had the highest quartile of exposure to traffic-related air pollution, during gestation (AOR, 1.98 [95% CI, 1.20-3.31]) and during the first year of life (AOR, 3.10 [95% CI, 1.76-5.57]), compared with control children. Regional exposure measures of nitrogen dioxide and particulate matter less than 2.5 and 10 μm in diameter (PM2.5 and PM10) were also associated with autism during gestation (exposure to nitrogen dioxide: AOR, 1.81 [95% CI, 1.37-3.09]; exposure to PM 2.5: AOR, 2.08 [95% CI, 1.93-2.25]; exposure to PM10: AOR, 2.17 [95% CI, 1.49-3.16) and during the first year of life (exposure to nitrogen dioxide: AOR, 2.06 [95% CI, 1.37-3.09]; exposure to PM2.5: AOR, 2.12 [95% CI, 1.45-3.10]; exposure to PM10: AOR, 2.14 [95% CI, 1.46-3.12]). All regional pollutant estimates were scaled to twice the standard deviation of the distribution for all pregnancy estimates. Conclusions: Exposure to traffic-related air pollution, nitrogen dioxide, PM2.5, and PM10 during pregnancy and during the first year of life was associated with autism. Further epidemiological and toxicological examinations of likely biological pathways will help determine whether these associations are causal. ©2013 American Medical Association. All rights reserved. Source


Denny M.W.,Stanford University | Gaylord B.,University of California at Davis
Annual Review of Marine Science | Year: 2010

The emerging field of marine ecomechanics provides an explicit physical framework for exploring interactions among marine organisms and between these organisms and their environments. It exhibits particular utility through its construction of predictive, mechanistic models, a number of which address responses to changing climatic conditions. Examples include predictions of (a) the change in relative abundance of corals as a function of colony morphology, ocean acidity, and storm intensity; (b) the rate of disturbance and patch formation in beds of mussels, a competitive dominant on many intertidal shores; (c) the dispersal and recruitment patterns of giant kelps, an important nearshore foundation species; (d) the effects of turbulence on external fertilization, a widespread method of reproduction in the sea; and (e) the long-term incidence of extreme ecological events. These diverse examples emphasize the breadth of marine ecomechanics. Indeed, its principles can be applied to any ecological system. © 2010 by Annual Reviews. Source


Cappa C.D.,University of California at Davis | Jimenez J.L.,University of Colorado at Boulder
Atmospheric Chemistry and Physics | Year: 2010

Measurements of the sensitivity of organic aerosol (OA, and its components) mass to changes in temperature were recently reported by Huffman et al.∼(2009) using a tandem thermodenuder-aerosol mass spectrometer (TD-AMS) system in Mexico City and the Los Angeles area. Here, we use these measurements to derive quantitative estimates of aerosol volatility within the framework of absorptive partitioning theory using a kinetic model of aerosol evaporation in the TD. OA volatility distributions (or "basis-sets") are determined using several assumptions as to the enthalpy of vaporization (ΔH vap). We present two definitions of "non-volatile OA," one being a global and one a local definition. Based on these definitions, our analysis indicates that a substantial fraction of the organic aerosol is comprised of non-volatile components that will not evaporate under any atmospheric conditions; on the order of 50-80% when the most realistic ΔHvap assumptions are considered. The sensitivity of the total OA mass to dilution and ambient changes in temperature has been assessed for the various ΔHvap assumptions. The temperature sensitivity is relatively independent of the particular ΔHvap assumptions whereas dilution sensitivity is found to be greatest for the low (ΔH vap Combining double low line 50 kJ/mol) and lowest for the high (ΔHvap Combining double low line 150 kJ/mol) assumptions. This difference arises from the high ΔHvap assumptions yielding volatility distributions with a greater fraction of non-volatile material than the low ΔHvap assumptions. If the observations are fit using a 1 or 2-component model the sensitivity of the OA to dilution is unrealistically high. An empirical method introduced by Faulhaber et al. (2009) has also been used to independently estimate a volatility distribution for the ambient OA and is found to give results consistent with the high and variable ΔH vap assumptions. Our results also show that the amount of semivolatile gas-phase organics in equilibrium with the OA could range from ∼20% to 400% of the OA mass, with smaller values generally corresponding to the higher ΔHvap assumptions. The volatility of various OA components determined from factor analysis of AMS spectra has also been assessed. In general, it is found that the fraction of non-volatile material follows the pattern: biomass burning OA < hydrocarbon-like OA < semivolatile oxygenated OA < low-volatility oxygenated OA. Correspondingly, the sensitivity to dilution and the estimated amount of semivolatile gas-phase material for the OA factors follows the reverse order. Primary OA has a substantial semivolatile fraction, in agreement with previous results, while the non-volatile fraction appears to be dominated by oxygenated OA produced by atmospheric aging. The overall OA volatility is thus controlled by the relative contribution of each aerosol type to the total OA burden. Finally, the model/measurement comparison appears to require OA having an evaporation coefficient (γe) substantially greater than 10-2 at this point it is not possible to place firmer constraints on γe based on the observations. © 2010 Author(s). Source


Cocanour C.S.,University of California at Davis
Surgical Infections | Year: 2011

Background: Clostridium difficile infection (CDI) is the primary cause of antibiotic-associated colitis and 15-25% of nosocomial antibiotic-associated diarrhea. Its clinical manifestations can range from mild diarrhea to toxic megacolon, bowel perforation, septic shock, and death. Over the past decade, more virulent strains have become increasingly common causes, and the incidence of CDI has risen, especially in elderly patients. These developments have led to an increase in recurrent CDI, which is more difficult to treat. This review focuses on recurrent CDI and its treatment. Methods: MEDLINE review using search terms Clostridium difficile, Clostridium difficile infection, recurrent Clostridium difficile infection. Results: A first recurrence may be treated with the same regimen as the first episode. Metronidazole 500 mg q 8 h for 10-14 days is the drug of choice for moderate infection, and vancomycin 125 mg q 6 h for 10-14 days is the drug of choice for severe CDI. Metronidazole should not be used for treatment of subsequent recurrences because of potential neurotoxicity and hepatic toxicity. Second recurrences should be treated with an oral vancomycin course and taper: 125 mg q 6 h × 10-14 days, 125 mg q 12 h × 7 days, 125 mg q 24 h × 7 days, 125 mg q 48-72 h × 2-8 weeks. Alternative agents are fecal bacteriotherapy, a "rifaximin chaser," nitazoxanide, probiotics, and intravenous immunoglobulin. Fidaxomicin has been approved recently. Monoclonal antibodies against C. difficile toxin remain investigational. Conclusion: Treatment of recurrent CDI remains challenging. Because of the lack of high-quality studies, recommendations for treatment are based on expert opinion. Metronidazole and vancomycin are the mainstays of treatment for both the initial infection and the first recurrence. For second recurrences, a vancomycin course plus taper is recommended. For subsequent recurrences, treatment options are many, with no one approach being entirely satisfactory. New drugs (fidaximicin) and treatments (monoclonal antibodies against the causative toxin) appear promising. © Copyright 2011, Mary Ann Liebert, Inc. Source


Rapson D.,University of California at Davis
Journal of Environmental Economics and Management | Year: 2014

I estimate a dynamic structural model of demand for air conditioners, the most energy-intensive home appliance in the US. The model explores the links between demand for durable goods and expected changes in key attributes: energy efficiency and price. I incorporate expectations explicitly as a feature of the choice setting, and use parameter estimates from the model to calculate durable good demand elasticities with respect to energy efficiency, electricity price, and price of the durable itself. These estimates fill a large gap in the literature, and also shed light on consumer behavior in this setting. Results indicate that consumers are forward-looking and value the stream of future savings derived from energy efficiency. © 2014 Elsevier Inc. Source


Pfeiffer L.,National Oceanic and Atmospheric Administration | Lin C.-Y.C.,University of California at Davis
Journal of Environmental Economics and Management | Year: 2014

Encouraging the use of more efficient irrigation technology is often viewed as an effective, politically feasible method to reduce the consumptive use of water for agricultural production. Despite its pervasive recommendation, it is not clear that increasing irrigation efficiency will lead to water conservation in practice. In this paper, we evaluate the effect of a widespread conversion from traditional center pivot irrigation systems to higher efficiency dropped-nozzle center pivot systems that has occurred in western Kansas. State and national cost-share programs subsidized the conversion. On an average, the intended reduction in groundwater use did not occur; the shift to more efficient irrigation technology has increased groundwater extraction, in part due to shifting crop patterns. © 2013 Elsevier Inc. Source


Farouki R.T.,University of California at Davis
Computer Aided Geometric Design | Year: 2012

One hundred years after the introduction of the Bernstein polynomial basis, we survey the historical development and current state of theory, algorithms, and applications associated with this remarkable method of representing polynomials over finite domains. Originally introduced by Sergei Natanovich Bernstein to facilitate a constructive proof of the Weierstrass approximation theorem, the leisurely convergence rate of Bernstein polynomial approximations to continuous functions caused them to languish in obscurity, pending the advent of digital computers. With the desire to exploit the power of computers for geometric design applications, however, the Bernstein form began to enjoy widespread use as a versatile means of intuitively constructing and manipulating geometric shapes, spurring further development of basic theory, simple and efficient recursive algorithms, recognition of its excellent numerical stability properties, and an increasing diversification of its repertoire of applications. This survey provides a brief historical perspective on the evolution of the Bernstein polynomial basis, and a synopsis of the current state of associated algorithms and applications. © 2012 Elsevier B.V. All rights reserved. Source


Ferris H.,University of California at Davis
European Journal of Soil Biology | Year: 2010

Metabolic footprints provide metrics for the magnitudes of ecosystem functions and services provided by component organisms of the soil food web. Nematodes occupy various trophic roles and perform important functions within the web. They are convenient indicators of similar functions performed by other organisms in the web and are well-documented indicators of ecosystem condition. The generally vermiform shapes of nematodes, and the standardized morphometric characteristics used in their description, facilitate assessment of body volume and weight. Prescribed coefficients allow calculation of their carbon metabolism. Their production of body structure and eggs can be standardized for life course duration. Consequently, standardized metabolic activity levels, attributable to the abundance of nematodes performing various functional roles, can be calculated from existing and accessible morphometric data. Metabolic footprints of nematode assemblages provide measures of ecosystem services performed by each functional guild. © 2010 Elsevier Masson SAS. All rights reserved. Source


Frankel E.N.,University of California at Davis
Journal of Agricultural and Food Chemistry | Year: 2010

Much analytical work has been published on the chemistry of extra virgin olive oil (EVOO) as a basis for the detection and quantitative analyses of the type and amount of adulteration with cheaper vegetable oils and deodorized olive oils. The analysis and authentication of EVOO represent very challenging analytical chemical problems. A significant amount of literature on EVOO adulteration has depended on sophisticated statistical approaches that require analyses of large numbers of samples. More effort is needed to exploit reliable chemical and instrumental methods that may not require so much statistical interpretation. Large assortments of methods have been used to determine lipid oxidation and oxidative stability and to evaluate the activity of the complex mixtures of phenolic antioxidants found in EVOO. More reliable chemical methods are required in this field to obviate excessive dependence on rapid antiradical methods that provide no information on the protective properties of antioxidants. The extensive literature on olive oil sensory tests, using many descriptors varying in different countries, should be supplemented by more precise gas chromatographic analyses of volatile compounds influencing the odor and flavors of EVOO. © 2010 American Chemical Society. Source


Oakes L.M.,University of California at Davis
Journal of Cognition and Development | Year: 2010

Habituation of looking time has become the standard method for studying cognitive processes in infancy. This method has a long history and derives from the study of memory and habituation itself. Often, however, it is not clear how researchers make decisions about how to implement habituation as a tool to study processes such as categorization, object representation, and memory. This article describes the challenges for implementing this tool and describes a set of best practices for its use to study perception and cognition in infancy. © 2010 Taylor & Francis Group, LLC. Source


Baskett M.L.,University of California at Davis
Journal of Experimental Biology | Year: 2012

This paper presents an overview of how mechanistic knowledge of organism-environment interactions, including biomechanical interactions of heat, mass and momentum transfer, can be integrated into basic theoretical population biology through mechanistic functional responses that quantitatively describe how organisms respond to their physical environment. Integrating such functional responses into simple community and microevolutionary models allows scaling up of the organism-level understanding from biomechanics both ecologically and temporally. For community models, Holling-type functional responses for predator-prey interactions provide a classic example of the functional response affecting qualitative model dynamics, and recent efforts are expanding analogous models to incorporate environmental influences such as temperature. For evolutionary models, mechanistic functional responses dependent on the environment can serve as fitness functions in both quantitative genetic and game theoretic frameworks, especially those concerning function-valued traits. I present a novel comparison of a mechanistic fitness function based on thermal performance curves to a commonly used generic fitness function, which quantitatively differ in their predictions for response to environmental change. A variety of examples illustrate how mechanistic functional responses enhance model connections to biologically relevant traits and processes as well as environmental conditions and therefore have the potential to link theoretical and empirical studies. Sensitivity analysis of such models can provide biologically relevant insight into which parameters and processes are important to community and evolutionary responses to environmental change such as climate change, which can inform conservation management aimed at protecting response capacity. Overall, the distillation of detailed knowledge or organism-environment interactions into mechanistic functional responses in simple population biology models provides a framework for integrating biomechanics and ecology that allows both tractability and generality. © 2012. Published by The Company of Biologists Ltd. Source


Weare B.C.,University of California at Davis
Journal of Geophysical Research: Atmospheres | Year: 2010

Links are sought between Madden-Julian Oscillation (MJO)-related variations in the troposphere and stratospheric winds, temperature, and ozone. Tropospheric variations of equatorial MJO-filtered 200 hPa zonal winds define indices of MJO activity for two equatorial regions in the Indian and Western Pacific oceans. These indices are used to calculate composite means of MJO filtered winds, temperature, and ozone mixing ratio for eight height levels from the upper troposphere well into the stratosphere. Strong evidence is presented for significant and coherent MJO departures throughout the lower stratosphere. At 100 hPa, these departures show easterlies in the equatorial regions of the compositing centers and nearly symmetric anticyclonic centers at 25 poleward of those centers, which are associated with significant negative departures in both temperature and ozone mixing ratio. Near 40N MJO departures of meridional velocity, temperature, and ozone mixing ratio generally tilt westward with height. The most important aspects of these features propagate eastward at a rate of about 5 m/s in the Eastern Hemisphere and several times faster in the Western Hemisphere. Copyright © 2010 by the American Geophysical Union. Source


Leigh E.G.,Smithsonian Tropical Research Institute | O'Dea A.,Smithsonian Tropical Research Institute | Vermeij G.J.,University of California at Davis
Biological Reviews | Year: 2014

About 3million years ago (Ma), the Isthmus of Panama joined the Americas, forming a land bridge over which inhabitants of each America invaded the other-the Great American Biotic Interchange. These invasions transformed land ecosystems in South and Middle America. Humans invading from Asia over 12000years ago killed most mammals over 44kg, again transforming tropical American ecosystems. As a sea barrier, the isthmus induced divergent environmental change off its two coasts-creating contrasting ecosystems through differential extinction and diversification. Approximately 65Ma invading marsupials and ungulates of North American ancestry, and xenarthrans of uncertain provenance replaced nearly all South America's non-volant mammals. There is no geological evidence for a land bridge at that time. Together with rodents and primates crossing from Africa 42 to 30Ma, South America's mammals evolved in isolation until the interchange's first heralds less than 10Ma. Its carnivores were ineffective marsupials. Meanwhile, North America was invaded by more competitive Eurasian mammals. The Americas had comparable expanses of tropical forest 55Ma; later, climate change confined North American tropical forest to a far smaller area. When the isthmus formed, North American carnivores replaced their marsupial counterparts. Although invaders crossed in both directions, North American mammals spread widely, diversified greatly, and steadily replaced South American open-country counterparts, unused to effective predators. Invading South American mammals were less successful. South America's birds, bats, and smaller rainforest mammals, equally isolated, mostly survived invasion. Its vegetation, enriched by many overseas invaders, remained intact. This vegetation resists herbivory effectively. When climate permitted, South America's rainforest, with its bats, birds and mammals, spread to Mexico. Present-day tropical American vegetation is largely zoned by trade-offs between exploiting well-watered settings versus surviving droughts, exploiting fertile versus coping with poor soil, and exploiting lowland warmth versus coping with cooler altitudes. At the start of the Miocene, a common marine biota extended from Trinidad to Ecuador and western Mexico, which evolved in isolation from the Indo-Pacific until the Pleistocene. The seaway between the Americas began shoaling over 12Ma. About 10Ma the land bridge was briefly near-complete, allowing some interchange of land mammals between the continents. By 7Ma, the rising sill had split deeper-water populations. Sea temperature, salinity and sedimentary carbon content had begun to increase in the Southern Caribbean, but not the Pacific. By 4Ma, the seaway's narrowing began to extinguish Caribbean upwellings. By 2Ma, upwellings remained only along Venezuela; Caribbean plankton, suspension-feeding molluscs and their predators had declined sharply, largely replaced by bottom-dwelling corals and calcareous algae and magnificent coral reefs. Closing the seaway extinguished the Eastern Pacific's reef corals (successors recolonized from the Indo-Pacific 6000years ago), whereas many molluscs of productive waters that once thrived in the Caribbean now survive only in the Eastern Pacific. The present-day productive Eastern Pacific, with few, small coral reefs and a plankton-based ecosystem contrasts with the Caribbean, whose clear water favours expansive coral reefs and bottom-dwelling primary producers. These ecosystems reflect the trade-off between fast growth and effective defence with attendant longevity. Overfishing with new technologies during the last few centuries, however, has caused population crashes of ever-smaller marine animals, devastating Caribbean ecosystems. © 2013 Cambridge Philosophical Society. Source


Power P.P.,University of California at Davis
Accounts of Chemical Research | Year: 2011

We showed in 2005 that a digermyne, a main group compound with a digermanium core and aromatic substituents, reacted directly with hydrogen at 25 °C and 1 atm to give well-defined hydrogen addition products. This was the first report of a reaction of main group molecules with hydrogen under ambient conditions. Our group and a number of others have since shown that several classes of main group molecules, either alone or in combination, react directly (in some cases reversibly) with hydrogen under mild conditions. Moreover, this reactivity was not limited to hydrogen but also included direct reactions with other important small molecules, including ammonia, boranes, and unactivated olefins such as ethylene. These reactions were largely unanticipated because main group species were generally considered to be too unreactive to effect such transformations.In this Account, we summarize recent developments in the reactions of the multiple bonded and other open shell derivatives of the heavier main group elements with hydrogen, ammonia, olefins, or related molecules. We focus on results generated primarily in our laboratory, which are placed in the context of parallel findings by other researchers. The close relationship between HOMO-LUMO separations, symmetry considerations, and reactivity of the open shell in main group compounds is emphasized, as is their similarity in reactivity to transition metal organometallic compounds.The unexpectedly potent reactivity of the heavier main group species arises from the large differences in bonding between the light and heavy elements. Specifically, the energy levels within the heavier element molecules are separated by much smaller gaps as a result of generally lower bond strengths. In addition, the ordering and symmetries of the energy levels are generally different for their light counterparts. Such differences lie at the heart of the new reactions. Moreover, the reactivity of the molecules can often be interpreted qualitatively in terms of simple molecular orbital considerations. More quantitative explanations are accessible from increasingly sophisticated density functional theory (DFT) calculations.We open with a short description of the background developments that led to this work. These advances involved the synthesis and characterization of numerous new main group molecules involving multiple bonds or unsaturated configurations; they were pursued over the latter part of the last century and the beginning of the new one. The results firmly established that the structures and bonding in the new compounds differed markedly from those of their lighter element congeners. The knowledge gained from this fundamental work provided the framework for an understanding of their structures and bonding, and hence an understanding of the reactivity of the compounds discussed here. © 2011 American Chemical Society. Source


The sensory outer segments (OS) of vertebrate retinal photoreceptors, which detect photons of light, resemble the distal segments of Caenorhabditis elegans sensory cilia, which detect chemical ligands that influence the chemotactic movements of the animal. Based on fluorescence microscopy assays performed in sensory cilia of living, transgenic " wild type" and mutant C. elegans, combined with in vitro motility assays using purified motors, we have proposed that two types of kinesin-2 motor, heterotrimeric kinesin-II and homodimeric OSM-3, cooperate to build amphid and phasmid sensory cilia on chemosensory neurons. Specifically, we propose that these motors function together in a redundant manner to build the axoneme core (aka middle segments (MS)), whereas OSM-3 alone serves to build the distal segments (DS). Furthermore, our data suggest that these motors accomplish this by driving two sequential steps of anterograde transport of cargoes consisting of IFT-particles, retrograde dynein motors, and ciliary tubulin subunits, from the transition zone to the tips of the axonemal microtubules (MTs). Homologs of kinesin-II (KIF3) and OSM-3 (KIF17) are also proposed to contribute to the assembly of vertebrate photoreceptors, although how they do so is currently unclear. Here I review our work on kinesin-2 motors, intraflagellar transport (IFT) and cilium biogenesis in C. elegans sensory cilia, and comment on its possible relevance to current research on vertebrate photoreceptor cilia assembly and function. © 2012 Elsevier Ltd. Source


Cytidine 5'-monophosphate (CMP)-sialic acid synthetases (CSSs) catalyze the formation of CMP-sialic acid from CTP and sialic acid, a key step for sialyltransferase-catalyzed biosynthesis of sialic acid-containing oligosaccharides and glycoconjugates. More than 50 different sialic acid forms have been identified in nature. To facilitate the enzymatic synthesis of sialosides with diverse naturally occurring sialic acid forms and their non-natural derivatives, CMP-sialic acid synthetases with promiscuous substrate specificity are needed. Herein we report the cloning, characterization, and substrate specificity studies of a new CSS from Pasteurella multocida strain P-1059 (PmCSS) and a CSS from Haemophillus ducreyi (HdCSS). Based on protein sequence alignment and substrate specificity studies of these two CSSs and a Neisseria meningitidis CSS (NmCSS), as well as crystal structure modeling and analysis of NmCSS, NmCSS mutants (NmCSS_S81R and NmCSS_Q163A) with improved substrate promiscuity were generated. The strategy of combining substrate specificity studies of enzymes from different sources and protein crystal structure studies can be a general approach for designing enzyme mutants with improved activity and substrate promiscuity. Source


Canter R.J.,University of California at Davis
Current opinion in oncology | Year: 2015

PURPOSE OF REVIEW: This review highlights the ongoing importance of surgical resection as the primary treatment modality for localized soft tissue sarcomas (STSs) in all locations and for the majority of histologic types. Accomplishing this goal in an oncologic fashion is of paramount importance for all patients eligible for treatment with curative intent and for selected patients with metastatic disease.RECENT FINDINGS: Ongoing advances in combined modality therapy and improved knowledge regarding the natural history and disease biology of individual sarcoma subtypes have allowed for better surgical planning and tailoring of the extent of resection depending on individual clinical, radiographic, and pathologic factors.SUMMARY: Successful therapy for localized STS remains contingent on surgical resection with tumor-free margins. It is hoped that ongoing advances in the molecular and genetic understanding of the pathogenesis and biology of STS will lead to sustained improvements in the care of these patients, and success will come from the ongoing development of targeted therapies and immunotherapies specific to histologic type. Source


Isman M.B.,University of British Columbia | Grieneisen M.L.,University of California at Davis | Grieneisen M.L.,Wenzhou University
Trends in Plant Science | Year: 2014

Our analysis of >20. 000 papers on botanical insecticides from 1980 to 2012, indicates major growth in the number of papers published annually (61 in 1980 to 1207 in 2012), and their proportion among all papers on insecticides (1.43% in 1980 to 21.38% in 2012). However, only one-third of 197 random articles among the 1086 papers on botanical insecticides published in 2011 included any chemical data or characterization; and only a quarter of them included positive controls. Therefore, a substantial portion of recently published studies has design flaws that limit reproducibility and comparisons with other and/or future studies. In our opinion, much of the scientific literature on this subject is of limited use in the progress toward commercialization or advancement of knowledge, given the resources expended. © 2013 Elsevier Ltd. Source


Vermeij G.J.,University of California at Davis
Trends in Ecology and Evolution | Year: 2015

Future environments may resemble conditions that have not existed for millions of years. To assess the adaptive options available to organisms evolving under such circumstances, it is instructive to probe paleophysiology, the ways in which ancient life coped with its physical and chemical surroundings. To do this, we need reliable proxies that are based on fundamental principles, quantitatively verified in living species, and observable in fossil remains. Insights have already come from vertebrates and plants, and others will likely emerge for marine animals if promising proxies are validated. Many questions remain about the circumstances for the evolution of environmental tolerances, metabolic rates, biomineralization, and physiological responses to interacting species, and about how living organisms will perform under exceptional conditions. Conditions of the past can provide a key to those of the future.The physiology of fossil life shows how organisms can adapt to future change.Reliable proxies are needed to infer paleophysiology. © 2015 Elsevier Ltd. Source


Winter C.K.,University of California at Davis
Journal of Agricultural and Food Chemistry | Year: 2012

Consumers are frequently urged to avoid imported foods as well as specific fruits and vegetables due to health concerns from pesticide residues and are often encouraged to choose organic fruits and vegetables rather than conventional forms. Studies have demonstrated that while organic fruits and vegetables have lower levels of pesticide residues than do conventional fruits and vegetables, pesticide residues are still frequently detected on organic fruits and vegetables; typical dietary consumer exposure to pesticide residues from conventional fruits and vegetables does not appear to be of health significance. Similarly, research does not demonstrate that imported fruits and vegetables pose greater risks from pesticide residues than do domestic fruits and vegetables or that specific fruits and vegetables singled out as being the most highly contaminated by pesticides should be avoided in their conventional forms. © 2012 American Chemical Society. Source


Richerson P.J.,University of California at Davis | Boydb R.,University of California at Los Angeles | Henrichc J.,University of British Columbia
Proceedings of the National Academy of Sciences of the United States of America | Year: 2010

The use of socially learned information (culture) is central to human adaptations. We investigate the hypothesis that the process of cultural evolution has played an active, leading role in the evolution of genes. Culture normally evolves more rapidly than genes, creating novel environments that expose genes to new selective pressures. Many human genes that have been shown to be under recent or current selection are changing as a result of new environments created by cultural innovations. Some changed in response to the development of agricultural subsistence systems in the Early and Middle Holocene. Alleles coding for adaptations to diets rich in plant starch (e.g., amylase copy number) and to epidemic diseases evolved as human populations expanded (e.g., sickle cell and G6PD deficiency alleles that provide protection against malaria). Large-scale scans using patterns of linkage disequilibrium to detect recent selection suggest that many more genes evolved in response to agriculture. Genetic change in response to the novel social environment of contemporary modern societies is also likely to be occurring. The functional effects of most of the alleles under selection during the last 10,000 years are currently unknown. Also unknown is the role of paleoenvironmental change in regulating the tempo of hominin evolution. Although the full extent of culture-driven gene-culture coevolution is thus far unknown for the deeper history of the human lineage, theory and some evidence suggest that such effects were profound. Genomic methods promise to have a major impact on our understanding of gene-culture coevolution over the span of hominin evolutionary history. Source


Clevers H.C.,University Utrecht | Bevins C.L.,University of California at Davis
Annual Review of Physiology | Year: 2013

Paneth cells are highly specialized epithelial cells of the small intestine, where they coordinate many physiological functions. First identified more than a century ago on the basis of their readily discernible secretory granules by routine histology, these cells are located at the base of the crypts of Lieberkühn, tiny invaginations that line the mucosal surface all along the small intestine. Investigations over the past several decades determined that these cells synthesize and secrete substantial quantities of antimicrobial peptides and proteins. More recent studies have determined that these antimicrobial molecules are key mediators of host-microbe interactions, including homeostatic balance with colonizing microbiota and innate immune protection from enteric pathogens. Perhaps more intriguing, Paneth cells secrete factors that help sustain and modulate the epithelial stem and progenitor cells that cohabitate in the crypts and rejuvenate the small intestinal epithelium. Dysfunction of Paneth cell biology contributes to the pathogenesis of chronic inflammatory bowel disease. Copyright © 2013 by Annual Reviews. All rights reserved. Source


Gepts P.,University of California at Davis
Current Opinion in Plant Biology | Year: 2014

The application of genomic approaches to the phenomenon of plant domestication promises a better understanding of the origins of agriculture, but also of the way plant genomes in general are organized and expressed. Building on earlier genetic research, more detailed information has become available on the organization of genetic diversity at the genome level and the effects of gene flow on diversity in different regions of the genome. In addition, putative domestication genes have been identified through population genomics approaches (selective sweeps or divergence scanning). Further information has been obtained on the origin of domestication syndrome mutations and the dispersal and adaptation of crops after domestication. For the future, increasingly multidisciplinary approaches using combinations of genomics and other approaches will prevail. © 2014 Elsevier Ltd. Source


Schreiber S.J.,University of California at Davis
Proceedings of the Royal Society B: Biological Sciences | Year: 2010

It is an ecological truism that population persistence depends on a population's growth rate when rare. To understand the interplay between temporal correlations, spatial heterogeneity and dispersal on persistence, an analytic approximation for this growth rate is derived for partially mixing populations. Partial mixing has two effects on population growth. In the absence of temporal correlations in relative fitness, greater movement to patches with, on average, higher relative fitness increases population growth rates. In the absence of spatial heterogeneity in the average relative fitnesses, lower dispersal rates enhance population growth when temporal autocorrelations of relative fitness within a patch exceed temporal cross-correlations in relative fitness between patches. This approximation implies that metapopulations whose expected fitness in every patch is less than 1 can persist if there are positive temporal autocorrelations in relative fitness, sufficiently weak spatial correlations and the population disperses at intermediate rates. It also implies that movement into lower quality habitats increases the population growth rate whenever the net temporal variation in per capita growth rates is sufficiently larger than the difference in the means of these per capita growth rates. Moreover, temporal autocorrelations, whether they be negative or positive, can enhance population growth for optimal dispersal strategies © 2010 The Royal Society. Source


Axsen J.,Simon Fraser University | Kurani K.S.,University of California at Davis
Global Environmental Change | Year: 2013

This paper explores the possibilities of consumer transitions to sustainability-oriented values. We draw from sociological and psychological literature to develop a conceptual framework that reflexively links an individual's values and self-concept to their behaviors. We inductively explore the consideration, and in some cases development, of sustainability-oriented values in a small number of narrative accounts of peoples' encounter with a plug-in hybrid electric vehicle during a multi-week trial. Because a plug-in hybrid vehicle substitutes electricity for gasoline, it is a technology that potentially symbolizes sustainability-oriented values. We classify participating households according to Schwartz's 10 motivation types, where households associate sustainability with different motivations, namely benevolence, universalism or self-direction. We categorize households into three groups: those that demonstrate no interests in sustainability-oriented values, those that demonstrate interest in developing such values during their plug-in hybrid vehicle demonstration experience, and those that were already committed to sustainability-oriented values and behaviors. We observe that households open to change are more likely to develop sustainability-oriented values if: (i) their self-concept is open to change (liminal), either as a temporary transitional state or sustained as a value, (ii) they associate sustainability with broader motivational values that are already central to their self-concept, in this case benevolence, universalism or self-direction, and (iii) they experience positive social support for new, sustainability-oriented values within their social networks. Our exploratory findings imply that sustainability-oriented values can be developed in households who did not previously express them. Value change opens new possibilities for sustainable consumer behavior, practices, and policy. © 2012 Elsevier Ltd. Source


Whether a sea turtle embryo develops into a male or a female depends, as with many other reptiles, on the temperature during incubation of the eggs. With sea turtles, warm temperatures produce 100% females and, thus, increasing global temperatures have the potential to significantly alter offspring sex ratios. Nest-site selection provides a potential mechanism by which females might adjust the sex of their offspring, but necessitates a reliable cue which provides information about the thermal properties of a nest. Overstory vegetation cover was found to significantly predict temperatures in nests of the hawksbill sea turtle Eretmochelys imbricata. Nests placed under high vegetation cover are significantly cooler and remain within the male-producing range of temperatures throughout incubation. Interestingly, metabolic heating of the developing clutch is less pronounced under vegetation, further reinforcing the importance of this nesting habitat with respect to the production of males. This underscores the importance of preserving natural vegetation cover at hawksbill nesting beaches in order to maintain the thermal diversity of nesting sites and, potentially, mitigate the impacts of increasing global temperatures. © Inter-Research 2013. Source


Insulin resistance progressing to type 2 diabetes mellitus (T2DM) is marked by a broad perturbation of macronutrient intermediary metabolism. Understanding the biochemical networks that underlie metabolic homeostasis and how they associate with insulin action will help unravel diabetes etiology and should foster discovery of new biomarkers of disease risk and severity. We examined differences in plasma concentrations of >350 metabolites in fasted obese T2DM vs. obese non-diabetic African-American women, and utilized principal components analysis to identify 158 metabolite components that strongly correlated with fasting HbA1c over a broad range of the latter (r = -0.631; p<0.0001). In addition to many unidentified small molecules, specific metabolites that were increased significantly in T2DM subjects included certain amino acids and their derivatives (i.e., leucine, 2-ketoisocaproate, valine, cystine, histidine), 2-hydroxybutanoate, long-chain fatty acids, and carbohydrate derivatives. Leucine and valine concentrations rose with increasing HbA1c, and significantly correlated with plasma acetylcarnitine concentrations. It is hypothesized that this reflects a close link between abnormalities in glucose homeostasis, amino acid catabolism, and efficiency of fuel combustion in the tricarboxylic acid (TCA) cycle. It is speculated that a mechanism for potential TCA cycle inefficiency concurrent with insulin resistance is "anaplerotic stress" emanating from reduced amino acid-derived carbon flux to TCA cycle intermediates, which if coupled to perturbation in cataplerosis would lead to net reduction in TCA cycle capacity relative to fuel delivery. Source


Caro T.,University of California at Davis
Seminars in Cell and Developmental Biology | Year: 2013

In this review I survey pelage and skin colouration patterns of the 29 orders of extant mammals and assess their functional significance. The vast majority of mammals are shades of grey or brown. Concealment is probably the principal evolutionary driver of pelage colouration in this Class likely through background matching and self-shadow concealment. A small minority of species are aposematic while many others have distinctive markings used in intraspecific and interspecific communication although the meaning of these markings is unclear. Colouration in mammals also has physiological consequences but these are barely understood as yet. © 2013 Elsevier Ltd. Source


Bers D.M.,University of California at Davis | Shannon T.R.,Rush University
Journal of Molecular and Cellular Cardiology | Year: 2013

Sarcoplasmic reticulum (SR) Ca content ([Ca]SRT) is critical to both normal cardiac function and electrophysiology, and changes associated with pathology contribute to systolic and diastolic dysfunction and arrhythmias. The intra-SR free [Ca] ([Ca]SR) dictates the [Ca]SRT, the driving force for Ca release and regulates release channel gating. We discuss measurement of [Ca]SR and [Ca]SRT, how [Ca]SR regulates activation and termination of release, and how Ca diffuses within the SR and influences SR Ca release during excitation-contraction coupling, Ca sparks and Cac waves. The entire SR network is connected and its lumen is also continuous with the nuclear envelope. Rapid Ca diffusion within the SR could stabilize and balance local [Ca]SR within the myocyte, but restrictions to diffusion can create spatial inhomogeneities. Experimental measurements and mathematical models of [Ca]SR to date have greatly enriched our understanding of these [Ca]SR dynamics, but controversies exist and may stimulate new measurements and analysis. This article is part of a Special Issue entitled "Calcium Signaling in Heart". © 2013 Elsevier Ltd. Source


Schreiber S.J.,University of California at Davis
American Naturalist | Year: 2015

In the 1970s,John Gillespie introduced two principles in which evolution selects for genotypes with lower variation in offspring numbers. First, if the variation in offspring number primarily occurs within generations, the strength of this selective force is inversely proportional to population size. Second, if this variation primarily occurs between generations, the strength of this selective force is proportional to the variance and independent of population size. These principles lie at the core of bet-hedging theory. Using the common currency of fixation probabilities, I derive a general principle for which within-generation correlation of individual fitness acts as a dial between Gillespie’s limiting cases. At low correlations, within generation variation is the primary selective force. At high correlations, between-generation variation is the dominant selective force. As corollary of this general principle, selection for diversified bet-hedging strategies is shown to require higher within-generation environmental correlations in smaller populations. © 2015 by The University of Chicago. Source


Lawson D.W.,London School of Hygiene and Tropical Medicine | Mulder M.B.,University of California at Davis
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2016

The idea that trade-offs between offspring quantity and quality shape reproductive behaviour has long been central to economic perspectives on fertility. It also has a parallel and richer theoretical foundation in evolutionary ecology. We review the application of the quantity-quality trade-off concept to human reproduction, emphasizing distinctions between clutch size and lifetime fertility, and the wider set of forces contributing to fertility variation in iteroparous and sexually reproducing species like our own. We then argue that in settings approximating human evolutionary history, several factors limit costly sibling competition. Consequently, while the optimization of quantity-quality trade-offs undoubtedly shaped the evolution of human physiology setting the upper limits of reproduction, we argue it plays a modest role in accounting for socio-ecological and individual variation in fertility. Only upon entering the demographic transition can fertility limitation be clearly interpreted as strategically orientated to advancing offspring quality via increased parental investment per child, with low fertility increasing descendant socio-economic success, although not reproductive success. We conclude that existing economic and evolutionary literature has often overemphasized the centrality of quantity-quality trade-offs to human fertility variation and advocate for the development of more holistic frameworks encompassing alternative life-history trade-offs and the evolved mechanisms guiding their resolution. © 2016 The Author(s) Published by the Royal Society. All rights reserved. Source


Barton N.H.,AM Technology | Turelli M.,University of California at Davis
American Naturalist | Year: 2011

Unlike unconditionally advantageous "Fisherian" variants that tend to spread throughout a species range once introduced anywhere, "bistable" variants, such as chromosome translocations, have two alternative stable frequencies, absence and (near) fixation. Analogous to populations with Allee effects, bistable variants tend to increase locally only once they become sufficiently common, and their spread depends on their rate of increase averaged over all frequencies. Several proposed manipulations of insect populations, such as using Wolbachia or "engineered underdominance" to suppress vector-borne diseases, produce bistable rather than Fisherian dynamics. We synthesize and extend theoretical analyses concerning three features of their spatial behavior: rate of spread, conditions to initiate spread from a localized introduction, and wave stopping caused by variation in population densities or dispersal rates. Unlike Fisherian variants, bistable variants tend to spread spatially only for particular parameter combinations and initial conditions. Wave initiation requires introduction over an extended region, while subsequent spatial spread is slower than for Fisherian waves and can easily be halted by local spatial inhomogeneities. We present several new results, including robust sufficient conditions to initiate (and stop) spread, using a one-parameter cubic approximation applicable to several models. The results have both basic and applied implications. © 2011 by The University of Chicago. Source


Kaloper N.,University of California at Davis | Padilla A.,University of Nottingham
Physical Review Letters | Year: 2014

We propose a very simple reformulation of general relativity, which completely sequesters from gravity all of the vacuum energy from a matter sector, including all loop corrections and renders all contributions from phase transitions automatically small. The idea is to make the dimensional parameters in the matter sector functionals of the 4-volume element of the Universe. For them to be nonzero, the Universe should be finite in spacetime. If this matter is the standard model of particle physics, our mechanism prevents any of its vacuum energy, classical or quantum, from sourcing the curvature of the Universe. The mechanism is consistent with the large hierarchy between the Planck scale, electroweak scale, and curvature scale, and early Universe cosmology, including inflation. Consequences of our proposal are that the vacuum curvature of an old and large universe is not zero, but very small, that wDE-1 is a transient, and that the Universe will collapse in the future. © 2014 American Physical Society. Source


Anderes E.,University of California at Davis
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

The reconstruction of the cosmic microwave background lensing potential is based on a Taylor expansion of lensing effects which is known to have poor convergence properties. For lensing of temperature fluctuations, an understanding of the higher order terms in this expansion which is accurate enough for current experimental sensitivity levels has been developed in Hanson et al. (2010), as well as a slightly modified Hu and Okamoto quadratic estimator which incorporates lensed rather than unlensed spectra into the estimator weights to mitigate the effect of higher order terms. We extend these results in several ways: (1) we generalize this analysis to the full set of quadratic temperature/polarization lensing estimators, (2) we study the effect of higher order terms for more futuristic experimental noise levels, (3) we show that the ability of the modified quadratic estimator to mitigate the effect of higher order terms relies on a delicate cancellation which occurs only when the true lensed spectra are known. We investigate the sensitivity of this cancellation to uncertainties in or knowledge of these spectra. We find that higher order terms in the Taylor expansion can impact projected error bars at experimental sensitivities similar to those found in future ACTpol/SPTpol experiments. © 2013 American Physical Society. Source


Firearms have widely supported legitimate purposes but are also frequently used in violent crimes. Owners and senior executives of federally licensed firearms dealers and pawnbrokers are a potentially valuable source of information on retail commerce in firearms, links between legal and illegal commerce, and policies designed to prevent the firearms they sell from being used in crimes. To our knowledge, there has been no prior effort to gather such information. In 2011, we conducted the Firearms Licensee Survey on a probability sample of 1,601 licensed dealers and pawnbrokers in the United States believed to sell 50 or more firearms per year. This article presents details of the design and execution of the survey and describes the characteristics of the respondents and their business establishments. The survey was conducted by mail, using methods developed by Dillman and others. Our response rate was 36.9 % (591 respondents), similar to that for other establishment surveys using similar methods. Respondents had a median age of 54; 89 % were male, 97.6 % were White, and 98.1 % were non-Hispanic. Those who held licenses under their own names had been licensed for a median of 18 years. A large majority of 96.3 % agreed that "private ownership of guns is essential for a free society"; just over half (54.9 %) believed that "it is too easy for criminals to get guns in this country." A match between the job and a personal interest in the shooting sports was the highest-ranking reason for working as a firearms retailer; the highest-ranking concerns were that "there are too many 'gun control' regulations" and that "the government might confiscate my guns." Most respondents (64.3 %) were gun dealers, with significant variation by region. Residential dealers accounted for 25.6 % of all dealers in the Midwest. Median annual sales volume was 200 firearms for both dealers and pawnbrokers. Dealers appeared more likely than pawnbrokers to specialize; they were more likely to rank in the highest or lowest quartile on sales of handguns, inexpensive handguns, and tactical rifles. Sales of inexpensive handguns and sales to women were more common among pawnbrokers. Internet sales were reported by 28.3 % of respondents and sales at gun shows by 14.3 %. A median of 1 % of sales were denied after purchasers failed background checks; firearm trace requests equaled <1 % of annual sales. Trace frequency was directly associated with the percentage of firearm sales involving handguns, inexpensive handguns, and sales to women. Frequency of denied sales was strongly and directly associated with frequency of trace requests (p < 0.0001). These results are based on self-report but are consistent with those from studies using objective data. © 2012 The New York Academy of Medicine. Source


Nevitt G.A.,University of California at Davis
Integrative and Comparative Biology | Year: 2011

Information transfer influences food-web dynamics in the marine environment, but infochemicals involved in these processes are only beginning to be understood. Dimethylsulfoniopropionate (DMSP) is produced by phytoplankton and other marine algae, and has been studied primarily in the context of sulfur cycling and regulation of global climate. My laboratory has been investigating DMSP and its breakdown product, dimethyl sulfide as infochemicals associated with trophic interactions in marine habitats, including sub-Antarctic and coral reef ecosystems. Using a neuroecological approach, our work has established that these biogenic sulfur compounds serve as critical signal molecules in marine systems and provides us with a more mechanistic understanding of how climate change may impact information transfer within marine food webs. © The Author 2011. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. Source


Yan W.,University of California at Davis
Oncogene | Year: 2013

Mutation of the p53 gene is the most common genetic alteration in human cancer and contributes to malignant process by enhancing transformed properties of cells and resistance to anticancer therapy. Mutant p53 is often highly expressed in tumor cells at least, in part, due to its increased half-life. However, whether mutant p53 expression is regulated by other mechanisms in tumors is unclear. Here we found that histone deacetylase (HDAC) inhibitors suppress both wild-type and mutant p53 transcription in time- and dose-dependent manners. Consistent with this, the levels of wild-type and mutant p53 proteins are decreased upon treatment with HDAC inhibitors. Importantly, we found that upon knockdown of each class I HDAC, only HDAC8 knockdown leads to decreased expression of wild-type and mutant p53 proteins and transcripts. Conversely, we found that ectopic expression of wild-type, but not mutant HDAC8, leads to increased transcription of p53. Furthermore, we found that knockdown of HDAC8 results in reduced expression of HoxA5 and consequently, attenuated ability of HoxA5 to activate p53 transcription, which can be rescued by ectopic expression of HoxA5. Because of the fact that HDAC8 is required for expression of both wild-type and mutant p53, we found that targeted disruption of HDAC8 expression remarkably triggers proliferative defect in cells with a mutant, but not wild-type, p53. Together, our data uncover a regulatory mechanism of mutant p53 transcription via HDAC8 and suggest that HDAC inhibitors and especially HDAC8-targeting agents might be explored as an adjuvant for tumors carrying a mutant p53. Source


Chichlowski M.,University of California at Davis
Annual review of food science and technology | Year: 2011

In addition to a nutritive role, human milk also guides the development of a protective intestinal microbiota in the infant. Human milk possesses an overabundance of complex oligosaccharides that are indigestible by the infant yet are consumed by microbial populations in the developing intestine. These oligosaccharides are believed to facilitate enrichment of a healthy infant gastrointestinal microbiota, often associated with bifidobacteria. Advances in glycomics have enabled precise determination of milk glycan structures as well as identification of the specific glycans consumed by various gut microbes. Furthermore, genomic analysis of bifidobacteria from infants has revealed specific genetic loci related to milk oligosaccharide import and processing, suggesting coevolution between the human host, milk glycans, and the microbes they enrich. This review discusses the current understanding of how human milk oligosaccharides interact with the infant microbiota and examines the opportunities for translating this knowledge to improve the functionality of infant formulas. Source


Adams S.H.,University of California at Davis
Advances in Nutrition | Year: 2011

Dysregulation of insulin action is most often considered in the context of impaired glucose homeostasis, with the defining feature of diabetes mellitus being elevated blood glucose concentration. Complications arising from the hyperglycemia accompanying frank diabetes are well known and epidemiological studies point to higher risk toward development of metabolic disease in persons with impaired glucose tolerance. Although the central role of proper blood sugar control in maintaining metabolic health is well established, recent developments have begun to shed light on associations between compromised insulin action [obesity, prediabetes, and type 2 diabetes mellitus (T2DM)] and altered intermediary metabolism of fats and amino acids. For amino acids, changes in blood concentrations of select essential amino acids and their derivatives, in particular BCAA, sulfur amino acids, tyrosine, and phenylalanine, are apparent with obesity and insulin resistance, often before the onset of clinically diagnosed T2DM. This review provides an overview of these changes and places recent observations from metabolomics research into the context of historical reports in the areas of biochemistry and nutritional biology. Based on this synthesis, a model is proposed that links the FFA-rich environment of obesity/insulin resistance and T2DM with diminution of BCAA catabolic enzyme activity, changes in methionine oxidation and cysteine/cystine generation, and tissue redox balance (NADH/NAD+). Adv. Nutr. 2: 445-456, 2011. © 2011 American Society for Nutrition. Source


Mozhayskiy V.,University of California at Davis
BMC bioinformatics | Year: 2012

BACKGROUND: Horizontal gene transfer (HGT) is a process that facilitates the transfer of genetic material between organisms that are not directly related, and thus can affect both the rate of evolution and emergence of traits. Recent phylogenetic studies reveal HGT events are likely ubiquitous in the Tree of Life. However, our knowledge of HGT's role in evolution and biological organization is very limited, mainly due to the lack of ancestral evolutionary signatures and the difficulty to observe complex evolutionary dynamics in a laboratory setting. Here, we utilize a multi-scale microbial evolution model to comprehensively study the effect of HGT on the evolution of complex traits and organization of gene regulatory networks. RESULTS: Large-scale simulations reveal a distinct signature of the Distribution of Fitness Effect (DFE) for HGT events: during evolution, while mutation fitness effects become more negative and neutral, HGT events result in a balanced effect distribution. In either case, lethal events are significantly decreased during evolution (33.0% to 3.2%), a clear indication of mutational robustness. Interestingly, evolution was accelerated when populations were exposed to correlated environments of increasing complexity, especially in the presence of HGT, a phenomenon that warrants further investigation. High HGT rates were found to be disruptive, while the average transferred fragment size was linked to functional module size in the underlying biological network. Network analysis reveals that HGT results in larger regulatory networks, but with the same sparsity level as those evolved in its absence. Observed phenotypic variability and co-existing solutions were traced to individual gain/loss of function events, while subsequent re-wiring after fragment integration was necessary for complex traits to emerge. Source


BACKGROUND: During their lifetime, microbes are exposed to environmental variations, each with its distinct spatio-temporal dynamics. Microbial communities display a remarkable degree of phenotypic plasticity, and highly-fit individuals emerge quite rapidly during microbial adaptation to novel environments. However, there exists a high variability when it comes to adaptation potential, and while adaptation occurs rapidly in certain environmental transitions, in others organisms struggle to adapt. Here, we investigate the hypothesis that the rate of evolution can both increase or decrease, depending on the similarity and complexity of the intermediate and final environments. Elucidating such dependencies paves the way towards controlling the rate and direction of evolution, which is of interest to industrial and medical applications. RESULTS: Our results show that the rate of evolution can be accelerated by evolving cell populations in sequential combinations of environments that are increasingly more complex. To quantify environmental complexity, we evaluate various information-theoretic metrics, and we provide evidence that multivariate mutual information between environmental signals in a given environment correlates well with the rate of evolution in that environment, as measured in our simulations. We find that strong positive and negative correlations between the intermediate and final environments lead to the increase of evolutionary rates, when the environmental complexity increases. Horizontal Gene Transfer is shown to further augment this acceleration, under certain conditions. Interestingly, our simulations show that weak environmental correlations lead to deceleration of evolution, regardless of environmental complexity. Further analysis of network evolution provides a mechanistic explanation of this phenomenon, as exposing cells to intermediate environments can trap the population to local neighborhoods of sub-optimal fitness. Source


Markowska A.I.,Tufts University | Liu F.-T.,University of California at Davis | Panjwani N.,Tufts University
Journal of Experimental Medicine | Year: 2010

Recent studies have shown that a carbohydrate-binding protein, galectin-3, is a novel pro-angiogenic molecule. The mechanism by which galectin-3 promotes angiogenesis remains unknown. We demonstrate here that galectin-3 is a mediator of vascular endothelial growth factor (VEGF)- and basic fibroblast growth factor (bFGF)-mediated angiogenic response. Angiogenesis assays revealed that galectin-3 inhibitors, β-lactose and dominant-negative galectin-3, reduce VEGF- and bFGF-mediated angiogenesis in vitro and that VEGF- and bFGF-mediated angiogenic response is reduced in galectin-3 knockdown cells and Gal3 -/- animals. Integrin αvβ3 was identified as the major galectin-3-binding protein and anti-αv, -β3, and -αvβ3 integrin function-blocking antibodies significantly inhibited the galectin-3-induced angiogenesis. Furthermore, galectin-3 promoted the clustering of integrin αvβ3 and activated focal adhesion kinase. Knockdown of GnTV, an enzyme that synthesizes high-affinity glycan ligands for galectin-3, substantially reduced: (a) complex N-glycans on αvβ3 integrins and (b) VEGF- and bFGF-mediated angiogenesis. Collectively, these data suggest that galectin-3 modulates VEGF- and bFGF-mediated angiogenesis by binding via its carbohydrate recognition domain, to the GnTV synthesized N-glycans of integrin αvβ3, and subsequently activating the signaling pathways that promote the growth of new blood vessels. These findings have broad implications for developing novel, carbohydrate-based therapeutic agents for inhibition of angiogenesis. © 2010 Markowska et al. Source


Guerry J.D.,University of North Carolina at Chapel Hill | Hastings P.D.,University of California at Davis
Clinical Child and Family Psychology Review | Year: 2011

Dysregulation of the Hypothalamic-pituitary-adrenal (HPA) axis in adults with major depressive disorder is among the most consistent and robust biological findings in psychiatry. Given the importance of the adolescent transition to the development and recurrence of depressive phenomena over the lifespan, it is important to have an integrative perspective on research investigating the various components of HPA axis functioning among depressed young people. The present narrative review synthesizes evidence from the following five categories of studies conducted with children and adolescents: (1) those examining the HPA system's response to the dexamethasone suppression test (DST); (2) those assessing basal HPA axis functioning; (3) those administering corticotropin-releasing hormone (CRH) challenge; (4) those incorporating psychological probes of the HPA axis; and (5) those examining HPA axis functioning in children of depressed mothers. Evidence is generally consistent with models of developmental psychopathology that hypothesize that atypical HPA axis functioning precedes the emergence of clinical levels of depression and that the HPA axis becomes increasingly dysregulated from child to adult manifestations of depression. Multidisciplinary approaches and longitudinal research designs that extend across development are needed to more clearly and usefully elucidate the role of the HPA axis in depression. © 2011 The Author(s). Source


Kliebenstein D.J.,University of California at Davis | Osbourn A.,John Innes Center
Current Opinion in Plant Biology | Year: 2012

Plants have adapted to their environments by diversifying in various ways. This diversification is reflected at the phytochemical level in their production of numerous specialized secondary metabolites that provide protection against biotic and abiotic stresses. Plant speciation is therefore intimately linked to metabolic diversification, yet we do not currently have a deep understanding of how new metabolic pathways evolve. Recent evidence indicates that genes for individual secondary metabolic pathways can be either distributed throughout the genome or clustered, but the relative frequencies of these two pathway organizations remain to be established. While it is possible that clustering is a feature of pathways that have evolved in recent evolutionary time, the answer to this and how dispersed and clustered pathways may be related remain to be addressed. Recent advances enabled by genomics and systems biology are beginning to yield the first insights into network evolution in plant metabolism. This review focuses on recent progress in understanding the evolution of clustered and dispersed pathways for new secondary metabolites in plants. © 2012 Elsevier Ltd. Source


Leal W.S.,University of California at Davis
Current Opinion in Insect Science | Year: 2015

Repellents are important prophylactic tools for travelers and populations living in endemic areas of malaria, dengue, encephalitis, and other vector-borne diseases. DEET is a safe, broad spectrum repellent, which provides complete protection over a long period of time. Despite its low cost, more affordable alternatives are highly desirable, particularly for those in endemic areas where cost is an impediment. Alternative compounds like IR 3535 and picaridin have been developed using molecular modeling, but the lack of knowledge of the molecular target(s) for DEET has retarded progress toward low cost alternatives. It is known that DEET acts at a distance as an odorant as well as by direct contact, that is, as a tastant, although DEET reception is primarily mediated by the olfactory system. There is unambiguous evidence that olfactory receptor neurons are involved, and that an odorant receptor co-receptor Orco is essential for DEET reception. In the southern house mosquito, Culex quinquefasciatus, DEET triggers repellence by direct activation of an odorant receptor, CquiOR136, which is also sensitive to a plant defense compound, methyl jasmonate. © 2014 Elsevier Inc. Source


Pham A.-V.,University of California at Davis
IEEE Microwave Magazine | Year: 2011

Electronics packages provide housing, protection, electrical interconnections, thermal dissipation, and assembly for integrated circuits and devices. At high frequency, cavity packages are used more often than over-molded plastic packages to achieve lower electrical losses. The major drawback of cavity packages is the open area that water and other contamination can be accumulated on the surface of a packaged device to cause degradation such as corrosion. © 2011 IEEE. Source


Saiz L.,University of California at Davis
Journal of Physics Condensed Matter | Year: 2012

Protein-DNA interaction networks play a central role in many fundamental cellular processes. In gene regulation, physical interactions and reactions among the molecular components together with the physical properties of DNA control how genes are turned on and off. A key player in all these processes is the inherent flexibility of DNA, which provides an avenue for long-range interactions between distal DNA elements through DNA looping. Such versatility enables multiple interactions and results in additional complexity that is remarkably difficult to address with traditional approaches. This topical review considers recent advances in statistical physics methods to study the assembly of protein-DNA complexes with loops, their effects in the control of gene expression, and their explicit application to the prototypical lac operon genetic system of the E.coli bacterium. In the last decade, it has been shown that the underlying physical properties of DNA looping can actively control transcriptional noise, cell-to-cell variability, and other properties of gene regulation, including the balance between robustness and sensitivity of the induction process. These physical properties are largely dependent on the free energy of DNA looping, which accounts for DNA bending and twisting effects. These new physical methods have also been used in reverse to uncover the actual invivo free energy of looping double-stranded DNA in living cells, which was not possible with existing experimental techniques. The results obtained for DNA looping by the lac repressor inside the E.coli bacterium showed a more malleable DNA than expected as a result of the interplay of the simultaneous presence of two distinct conformations of looped DNA. © 2012 IOP Publishing Ltd. Source


Bevins C.L.,University of California at Davis | Salzman N.H.,Childrens Research Institute
Cellular and Molecular Life Sciences | Year: 2011

Animals, ranging from basal metazoans to primates, are host to complex microbial ecosystems; engaged in a symbiotic relationship that is essential for host physiology and homeostasis. Epithelial surfaces vary in the composition of colonizing microbiota as one compares anatomic sites, developmental stages and species origin. Alterations of microbial composition likely contribute to susceptibility to several distinct diseases. The forces that shape the colonizing microbial composition are the focus of much current investigation, and it is evident that there are pressures exerted both by the host and the external environment to mold these ecosystems. The focus of this review is to discuss recent studies that demonstrate the critical importance of host factors in selecting for its microbiome. Greater insight into host-microbiome interactions will be essential for understanding homeostasis at mucosal surfaces, and developing useful interventions when homeostasis is disrupted. © Springer Basel AG 2011. Source


Kliebenstein D.J.,University of California at Davis
Annual Review of Phytopathology | Year: 2012

Systems biology attempts to answer biological questions by integrating across diverse genomic data sets. With the increasing ability to conduct genomics experiments, this integrative approach is being rapidly applied across numerous biological research communities. One of these research communities investigates how plants utilize secondary metabolites or defense metabolites to defend against attack by pathogens and other biotic organisms. This use of systems biology to integrate across transcriptomics, metabolomics, and genomics is significantly enhancing the rate of discovery of genes, metabolites, and bioactivities for plant defense compounds as well as extending our knowledge of how these compounds are regulated. Plant defense compounds are also providing a unique proving platform to develop new approaches that enhance the ability to conduct systems biology with existing and previously unforseen genomics data sets. This review attempts to illustrate both how systems biology is helping the study of plant defense compounds and vice versa. © 2012 by Annual Reviews. All rights reserved. Source


Despite the described central role of jasmonate signaling in plant defense against necrotrophic pathogens, the existence of intraspecific variation in pathogen capacity to activate or evade plant jasmonate-mediated defenses is rarely considered. Experimental infection of jasmonate-deficient and jasmonate-insensitive Arabidopsis thaliana with diverse isolates of the necrotrophic fungal pathogen Botrytis cinerea revealed pathogen variation for virulence inhibition by jasmonate-mediated plant defenses and induction of plant defense metabolites. Comparison of the transcriptional effects of infection by two distinct B. cinerea isolates showed only minor differences in transcriptional responses of wild-type plants, but notable isolate-specific transcript differences in jasmonate-insensitive plants. These transcriptional differences suggest B. cinerea activation of plant defenses that require plant jasmonate signaling for activity in response to only one of the two B. cinerea isolates tested. Thus, similar infection phenotypes observed in wild-type plants result from different signaling interactions with the plant that are likely integrated by jasmonate signaling. Source


Garen J.W.,University of California at Davis
Annual Review of Public Health | Year: 2015

This brief review summarizes the basic epidemiology of firearm violence, a large and costly public health problem in the United States for which the mortality rate has remained unchanged for more than a decade. It presents findings for the present in light of recent trends. Risk for firearm violence varies substantially across demographic subsets of the population and between states in patterns that are quite different for suicide and homicide. Suicide is far more common than homicide and its rate is increasing; the homicide rate is decreasing. As with other important health problems, most cases of fatal firearm violence arise from large but low-risk subsets of the population; risk and burden of illness are not distributed symmetrically. Compared with other industrialized nations, the United States has uniquely high mortality rates from firearm violence. Copyright © 2015 by Annual Reviews. All rights reserved. Source


The androgen receptor (AR) is overexpressed and hyperactivated in human castration-resistant prostate cancer (CRPC). However, the determinants of AR overexpression in CRPC are poorly defined. Here we show that retinoic acid receptor–related orphan receptor γ (ROR-γ) is overexpressed and amplified in metastatic CRPC tumors, and that ROR-γ drives AR expression in the tumors. ROR-γ recruits nuclear receptor coactivator 1 and 3 (NCOA1 and NCOA3, also known as SRC-1 and SRC-3) to an AR–ROR response element (RORE) to stimulate AR gene transcription. ROR-γ antagonists suppress the expression of both AR and its variant AR-V7 in prostate cancer (PCa) cell lines and tumors. ROR-γ antagonists also markedly diminish genome-wide AR binding, H3K27ac abundance and expression of the AR target gene network. Finally, ROR-γ antagonists suppressed tumor growth in multiple AR-expressing, but not AR-negative, xenograft PCa models, and they effectively sensitized CRPC tumors to enzalutamide, without overt toxicity, in mice. Taken together, these results establish ROR-γ as a key player in CRPC by acting upstream of AR and as a potential therapeutic target for advanced PCa. © 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. Source


Roth J.R.,University of California at Davis | Andersson D.I.,Uppsala University
Cell | Year: 2012

A multistep process of gene amplification, mutation, and reduction allows poxvirus to overcome host antiviral defenses. The mechanism speeds genetic adaptation and promises to be broadly applicable in many biological settings. © 2012 Elsevier Inc. Source


Agrawal A.A.,Cornell University | Weber M.G.,University of California at Davis
Ecology Letters | Year: 2015

Species comparisons are a cornerstone of biology and there is a long tradition of using the comparative framework to study the ecology and evolution of plant defensive traits. Early comparative studies led to the hypothesis that plant chemistry plays a central role in plant defence, and the evolution of plant secondary chemistry in response to insect herbivory remains a classic example of coevolution. However, recent comparative work has disagreed with this paradigm, reporting little connection between plant secondary chemicals and herbivory across distantly related plant taxa. One conclusion of this new work is that the importance of secondary chemistry in plant defence may have been generally overstated in earlier research. Here, we attempt to reconcile these contradicting viewpoints on the role of plant chemistry in defence by critically evaluating the use and interpretation of species correlations as a means to study defence-herbivory relationships. We conclude that the notion that plant primary metabolites (e.g. leaf nitrogen content) are the principal determinants of herbivory (or the target of natural selection by herbivores) is not likely to be correct. Despite the inference of recent community-wide studies of herbivory, strong evidence remains for a prime role of secondary compounds in plant defence against herbivores. © 2015 John Wiley & Sons Ltd/CNRS. Source


Navrotsky A.,University of California at Davis
Journal of Materials Chemistry | Year: 2010

Oxides based on the fluorite structure are important as electrolytes in solid oxide fuel cells, thermal barrier coatings, gate dielectrics, catalysts, and nuclear materials. Though the parent fluorite structure is simple, the substitution of trivalent for tetravalent cations, coupled with the presence of charge-balancing oxygen vacancies, leads to a wealth of short-range and long-range ordered structures and complex thermodynamic properties. The location of vacancies and the nature of clusters affect the energetics of mixing in rare earth doped zirconia, hafnia, ceria, urania, and thoria, with systematic trends in energetics as a function of cation radius. High temperature oxide melt solution calorimetry has provided direct measurement of formation enthalpies of these refractory materials. Surface and interfacial energies have also been measured in yttria stabilized zirconia (YSZ) nanomaterials. Other ionic conductors having perovskite, apatite, and mellilite structures are discussed briefly. © 2010 The Royal Society of Chemistry. Source


Lasalle J.M.,University of California at Davis
Journal of Human Genetics | Year: 2013

Autism spectrum disorders (ASD) have been increasing in prevalence over the last two decades, primarily because of increased awareness and diagnosis. However, autism is clearly a complex human genetic disorder that involves interactions between genes and environment. Epigenetic mechanisms, such as DNA methylation, act at the interface of genetic and environmental risk and protective factors. Advancements in genome-wide sequencing has broadened the view of the human methylome and revealed the organization of the human genome into large-scale methylation domains that footprint over neurologically important genes involved in embryonic development. Future integrative epigenomic analyses of genetic risk factors with environmental exposures and methylome analyses are expected to be important for understanding the complex etiology of ASD. © 2013 The Japan Society of Human Genetics All rights reserved. Source


Kung H.-J.,University of California at Davis
Hormones and Cancer | Year: 2011

Tyrosine kinases play significant roles in tumor progression and therapy resistance. Inhibitors of tyrosine kinases are on the forefront of targeted therapy. For prostate cancer, tyrosine kinases play an additional role in the development of castration-resistant disease state, the most troubling aspect of prostate cancinogenesis which presently defies any effective treatment. Among the 30 or so tyrosine kinases expressed in a typical prostate cancer cell, nearly one third of them have been implicated in prostate carcinogenesis. Interestingly, most of them channel signals through a trio of non-receptor tyrosine kinases, Src/Etk/FAK, referred here as Src tyrosine kinase complex. This complex has been shown to play a significant role in the aberrant activation of androgen receptor (AR) mediated by growth factors (e.g., epidermal growth factor (EGF)), cytokines (interleukin (IL)-6), chemokines (IL-8), and neurokines (gastrin-releasing peptide). These factors are induced and released from the prostate cancer to the stromal cells upon androgen withdrawal. The Src kinase complex has the ability to phosphorylate androgen receptor, resulting in the nuclear translocation and stabilization of un-liganded androgen receptor. Indeed, tyrosine kinase inhibitors targeting Src can inhibit androgen-independent growth of prostate cancer cells in vitro and in preclinical xenograft model. While effective in inducing growth arrest and inhibiting metastasis of castration-resistant tumors, Src inhibitors rarely induce a significant level of apoptosis. This is also reflected by the general ineffectiveness of tyrosine kinase inhibitors as monotherapy in clinical trials. One of the underlying causes of apoptosis resistance is "autophagy," which is induced by tyrosine kinase inhibitors and by androgen withdrawal. Autophagy is a self-digesting process to regenerate energy by removal of long-lived proteins and retired organelles to provide a survival mechanism to cells encountering stresses. Excessive autophagy, sometimes, could lead to type II programmed cell death. We demonstrated that autophagy blockade sensitizes prostate cancer cells toward Src tyrosine kinase inhibitor. Thus, a combination therapy based on Src tyrosine kinase inhibitor and autophagy modulator deserves further attention as a potential treatment for relapsed prostate cancer. © 2010 The Author(s). Source


Necrotizing enterocolitis (NEC) is the most common intestinal emergency among premature infants. Risk factors in premature infants include immature intestinal immunity and an intestinal microbiota dominated by hospital-acquired bacteria. Some probiotics have been shown to decrease the incidence of NEC in premature infants. Among term infants, NEC is rare. However, among term infants with cyanotic congenital heart disease (CCHD), the incidence of NEC is similar to that of premature infants but with even greater mortality rates. Mechanisms by which NEC occurs in term infants with CCHD are unknown. Of central interest is the potential role of changes in the intestinal microbiota and whether these can be modified with probiotic bacteria; accordingly, we review the literature, propose hypotheses and present the rationale for future studies involving preliminary probiotic clinical trials. © 2010 Landes Bioscience Source


Katzberg R.W.,University of California at Davis | Newhouse J.H.,Columbia University
Radiology | Year: 2010

From the multiple perspectives described, it is our belief that the risk of CIN with CE CT has been exaggerated. Clinical rates and adverse outcomes from cardiac catheterization and intervention cannot be extrapolated to the clinical experience with CE CT. It appears that all currently used nonionic CM have similar safety profiles. We believe that modern CM pose only a small risk to renal function and that thresholds of creatinine above which CM are withheld for CT should be increased to improve the accuracy of CT examinations. The population of patients with mild to moderate renal dysfunction who would then receive CM should be analyzed carefully to determine whether the thresholds subsequently can be increased further. International radiologic professional organizations, such as the American College of Radiology, should revisit the basis of their practice guidelines to reduce their implications about the danger of CIN with CE CT. © RSNA, 2010. Source


Rogawski M.A.,University of California at Davis
Acta Neurologica Scandinavica | Year: 2013

Epileptic seizures occur as a result of episodic abnormal synchronous discharges in cerebral neuronal networks. Although a variety of non-conventional mechanisms may play a role in epileptic synchronization, cascading excitation within networks of synaptically connected excitatory glutamatergic neurons is a classical mechanism. As is the case throughout the central nervous system, fast synaptic excitation within and between brain regions relevant to epilepsy is mediated predominantly by AMPA receptors. By inhibiting glutamate-mediated excitation, AMPA receptor antagonists markedly reduce or abolish epileptiform activity in in vitro preparations and confer seizure protection in a broad range of animal seizure models. NMDA receptors may also contribute to epileptiform activity, but NMDA receptor blockade is not sufficient to eliminate epileptiform discharges. AMPA receptors move into and out of the synapse in a dynamic fashion in forms of synaptic plasticity, underlying learning and memory. Often, the trigger for these dynamic movements is the activation of NMDA receptors. While NMDA receptor antagonists inhibit these forms of synaptic plasticity, AMPA receptor antagonists do not impair synaptic plasticity and do not inhibit memory formation or retrieval. The demonstrated clinical efficacy of perampanel, a high-potency, orally active non-competitive AMPA receptor antagonist, supports the concept that AMPA receptors are critical to epileptic synchronization and the generation and spread of epileptic discharges in human epilepsy. © 2013 John Wiley & Sons A/S. Source


Vermeij G.J.,University of California at Davis
Annual Review of Earth and Planetary Sciences | Year: 2013

Organisms have been important agents of selection throughout the history of life. The processes and outcomes of this selection are the subject of this review. Among these, escalation is the most widespread. The primary selective agents are powerful competitors and consumers, which together push many populations toward higher performance in acquiring and defending resources while relegating less competitive species to physiologically marginal settings, where escalation also ensues. The extent to which performance standards rise depends on enabling factors, which control availability of and access to resources. By establishing positive feedbacks between species and enabling factors, effective competitors regulate and enhance resource supply. The pace of escalation toward greater power and reach is dictated by geological factors as well as by growing interdependencies between species and their resources. Evolutionary events on land related to the production of oxygen may have been instrumental in triggering the major episodes of escalation. © Copyright ©2013 by Annual Reviews. All rights reserved. Source


Currently there are three major hypotheses that have been proposed for estrogen induced carcinogenicity, however exact etiology remains unknown. Based on the chemical logic, studies were undertaken to investigate if estrogens could generate quinone methides in an oxidative environment which then could cause DNA damage in humans. In presence of MnO2 estrogens were oxidized to quinone methides. Surprisingly quinone methides were found to be stable with t1/2 of 20.8 and 4.5 min respectively. Incubation of estrogens with lactoperoxidase (LPO) and H2O2 resulted in formation of respective quinone methides (E1(E2)-QM). Subsequent addition of adenine to the assay mixture lead to trapping of E1(E2)-QM, resulting in formation of adenine adducts of estrogens, E1(E2)-9-N-Ade. Targeted ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) based metabolomic analysis of the breast tissue extracts showed the presence of adenine adducts of estrogens, E1(E2)-9-N-Ade, along with other estrogen related metabolites. Identity of E1(E2)-N-Ade in LPO assay extracts and breast tissue extracts were confirmed by comparing them to pure synthesized E1(E2)-9-N-Ade standards. From these results, it is evident that peroxidase enzymes or peroxidase-like activity in human breast tissue could oxidize estrogens to electrophilic and stable quinone methides in a single step that covalently bind to DNA to form adducts. The error prone repair of the damaged DNA can result in mutation of critical genes and subsequently cancer. This article reports evidence for hitherto unknown estrogen metabolic pathway in human breast, catalyzed by peroxidase, which could initiate cancer. © 2013 Nilesh W. Source


Louie A.,University of California at Davis
Journal of Magnetic Resonance Imaging | Year: 2013

Interest in MRI contrast agents for molecular imaging of biological function experienced a surge of excitement approximately 20 years ago with the development of the first activatable contrast agents that could act as biosensors and turn "on" in response to a specific biological activity. This brief tutorial, based on a short course lecture from the 2011 ISMRM meeting, provides an overview of underlying principles governing the design of biosensing contrast agents. We describe mechanisms by which an MRI contrast agent can be made into a sensor for both T1 and T2 types contrast agents. Examples of biological activities that can interact with a contrast agent are discussed using specific examples from the recent literature to illustrate the primary mechanisms of action that have been used to achieve activation. MRI sensors for pH, ion binding, enzyme cleavage, and oxidation-reduction are presented. This article is not meant to be an exhaustive review, but an illustrative primer to explain how activation can be achieved for an MRI contrast agent. Chemical exchange saturation transfer (CEST) is not covered as these agents were covered in a separate lecture. © 2013 Wiley Periodicals, Inc. Source


Wang I.J.,University of California at Berkeley | Bradburd G.S.,University of California at Davis
Molecular Ecology | Year: 2014

The interactions between organisms and their environments can shape distributions of spatial genetic variation, resulting in patterns of isolation by environment (IBE) in which genetic and environmental distances are positively correlated, independent of geographic distance. IBE represents one of the most important patterns that results from the ways in which landscape heterogeneity influences gene flow and population connectivity, but it has only recently been examined in studies of ecological and landscape genetics. Nevertheless, the study of IBE presents valuable opportunities to investigate how spatial heterogeneity in ecological processes, agents of selection and environmental variables contributes to genetic divergence in nature. New and increasingly sophisticated studies of IBE in natural systems are poised to make significant contributions to our understanding of the role of ecology in genetic divergence and of modes of differentiation both within and between species. Here, we describe the underlying ecological processes that can generate patterns of IBE, examine its implications for a wide variety of disciplines and outline several areas of future research that can answer pressing questions about the ecological basis of genetic diversity. © 2014 John Wiley & Sons Ltd. Source


Cornell H.V.,University of California at Davis
Biological Reviews | Year: 2013

Two conflicting hypotheses have been proposed to explain large-scale species diversity patterns and dynamics. The unbounded hypothesis proposes that regional diversity depends only on time and diversification rate and increases without limit. The bounded hypothesis proposes that ecological constraints place upper limits on regional diversity and that diversity is usually close to its limit. Recent evidence from the fossil record, phylogenetic analysis, biogeography, and phenotypic disparity during lineage diversification suggests that diversity is constrained by ecological processes but that it is rarely asymptotic. Niche space is often unfilled or can be more finely subdivided and still permit coexistence, and new niche space is often created before ecological limits are reached. Damped increases in diversity over time are the prevalent pattern, suggesting the need for a new 'damped increase hypothesis'. The damped increase hypothesis predicts that diversity generally increases through time but that its rate of increase is often slowed by ecological constraints. However, slowing due to niche limitation must be distinguished from other possible mechanisms creating similar patterns. These include sampling artifacts, the inability to detect extinctions or declines in clade diversity with some methods, the distorting effects of correlated speciation-extinction dynamics, the likelihood that opportunities for allopatric speciation will vary in space and time, and the role of undetected natural enemies in reducing host ranges and thus slowing speciation rates. The taxonomic scope of regional diversity studies must be broadened to include all ecologically similar species so that ecological constraints may be accurately inferred. The damped increase hypothesis suggests that information on evolutionary processes such as time-for-speciation and intrinsic diversification rates as well as ecological factors will be required to explain why regional diversity varies among times, places and taxa. © 2012 Cambridge Philosophical Society. Source


Marcu L.,University of California at Davis
Journal of Biomedical Optics | Year: 2010

We review fluorescence lifetime techniques including timeresolved laser-induced fluorescence spectroscopy (TR-LIFS) and fluorescence lifetime imaging microscopy (FLIM) instrumentation and associated methodologies that allow for characterization and diagnosis of atherosclerotic plaques. Emphasis is placed on the translational research potential of TR-LIFS and FLIM and on determining whether intrinsic fluorescence signals can be used to provide useful contrast for the diagnosis of high-risk atherosclerotic plaque. Our results demonstrate that these techniques allow for the discrimination of important biochemical features involved in atherosclerotic plaque instability and rupture and show their potential for future intravascular applications. © 2010 Society of Photo-Optical Instrumentation Engineers. Source


Inoue K.,University of California at Davis
Trends in Plant Science | Year: 2011

The chloroplast is essential for the viability of plants. It is enclosed by a double-membrane envelope that originated from the outer and plasma membranes of a cyanobacterial endosymbiont. Chloroplast biogenesis depends on binary fission and import of nuclear-encoded proteins. Our understanding of the mechanisms and evolutionary origins of these processes has been greatly advanced by recent genetic and biochemical studies on envelope-localized multiprotein machines. Furthermore, the latest studies on outer envelope proteins have provided molecular insights into organelle movement and membrane lipid remodeling, activities that are vital for plant survival under diverse environmental conditions. Ongoing and future research on the chloroplast outer envelope should add to our knowledge of organelle biology and the evolution of eukaryotic cells. © 2011 Elsevier Ltd. Source


Hayward A.P.,Yale University | Dinesh-Kumar S.P.,University of California at Davis
Annual Review of Phytopathology | Year: 2011

Autophagy plays an established role in the execution of senescence, starvation, and stress responses in plants. More recently, an emerging role for autophagy has been discovered during the plant innate immune response. Recent papers have shown autophagy to restrict, and conversely, to also promote programmed cell death (PCD) at the site of pathogen infection. These initial studies have piqued our excitement, but they have also revealed gaps in our understanding of plant autophagy regulation, in our ability to monitor autophagy in plant cells, and in our ability to manipulate autophagic activity. In this review, we present the most pressing questions now facing the field of plant autophagy in general, with specific focus on autophagy as it occurs during a plant-pathogen interaction. To begin to answer these questions, we place recent findings in the context of studies of autophagy and immunity in other systems, and in the context of the mammalian immune response in particular. © 2011 by Annual Reviews. All rights reserved. Source


Frankel E.N.,University of California at Davis
Journal of Agricultural and Food Chemistry | Year: 2011

The nutritional benefits generally recognized for the consumption of extra virgin olive oil (EVOO) are based on a large number of dietary trials of several international populations and intervention studies. Unfortunately, many authors in this field used questionable analytical methods and commercial kits that were not validated scientifically to evaluate the complex bioactive constituents of EVOO and lipid oxidation and decomposition products. Many questionable antiradical methods were commonly used to evaluate natural polyphenolic antioxidants, including an indirect method to determine low-density lipoprotein (LDL) cholesterol. Extensive differences were observed in experimental design, diet control, populations of different ages and problems of compliance intervention, and questionable biomarkers of oxidative stress. Analyses in many nutritional studies were limited by the use of one-dimensional methods to evaluate multifunctional complex bioactive compounds and plasma lipid profiles by the common applications of commercial kits. Although EVOO contains polyphenolic compounds that exhibit significant in vitro antioxidant activity, much more research is needed to understand the absorption and in vivo activity. Many claims of in vivo human beneficial effects by the consumption of EVOO may be overstated. No distinctions were apparently made between in vivo studies based on general health effects in large populations of human subjects and smaller scale well-controlled feeding trials using either pure or mixtures of known phenolic constituents of EVOO. More reliable protocols and testing methods are needed to better validate the complex nutritional properties of EVOO. © 2011 American Chemical Society. Source


de Lartigue G.,University of California at Davis
Physiology and Behavior | Year: 2014

The vagus nerve is a major pathway by which information is communicated between the brain and peripheral organs. Sensory neurons of the vagus are located in the nodose ganglia. These vagal afferent neurons innervate the heart, the lung and the gastrointestinal tract, and convey information about peripheral signals to the brain important in the control of cardiovascular tone, respiratory tone, and satiation, respectively. Glutamate is thought to be the primary neurotransmitter involved in conveying all of this information to the brain. It remains unclear how a single neurotransmitter can regulate such an extensive list of physiological functions from a wide range of visceral sites. Many neurotransmitters have been identified in vagal afferent neurons and have been suggested to modulate the physiological functions of glutamate. Specifically, the anorectic peptide transmitters, cocaine and amphetamine regulated transcript (CART) and the orexigenic peptide transmitters, melanin concentrating hormone (MCH) are differentially regulated in vagal afferent neurons and have opposing effects on food intake. Using these two peptides as a model, this review will discuss the potential role of peptide transmitters in providing a more precise and refined modulatory control of the broad physiological functions of glutamate, especially in relation to the control of feeding. © 2014. Source


Sukumar N.,University of California at Davis
Computer Methods in Applied Mechanics and Engineering | Year: 2013

In this paper, we present the development of quadratic serendipity shape functions on planar convex and nonconvex polygons. Drawing on the work of Bompadre et al. (2012) [1] and Hormann and Sukumar (2008) [2], we adopt a relative entropy measure for signed (positive or negative) shape functions, with nodal prior weight functions that have the appropriate zero-set on the boundary of the polygon. We maximize the objective functional subject to the constraints for quadratic completeness proposed by Rand et al. (2013) [3]. Along an edge of a polygon, the approximation is identical to univariate Bernstein polynomials: the choice of the nodal prior weight function ensures that the shape functions satisfy a weak Kronecker-delta property on each edge. The shape functions are well-defined for arbitrary planar polygons without self-intersections. On using a modified numerical integration scheme, we show that the quadratic patch test is passed on polygonal meshes with convex and nonconvex elements. Numerical tests for the Poisson equation on self-similar trapezoidal meshes and quasiuniform polygonal meshes are presented, which reveal the sound accuracy of the method, and optimal rates of convergence in the L2 norm and the H1 seminorm are established. © 2013. Source


Yang Y.,University of California at Davis
Decision Support Systems | Year: 2010

In this paper, we propose a simple, yet powerful approach to profile users' web browsing behavior for the purpose of user identification. The importance of being able to identify users can be significant given a wide variety of applications in electronic commerce, such as product recommendation, personalized advertising, etc. We create user profiles capturing the strength of users' behavioral patterns, which can be used to identify users. Our experiments indicate that these profiles can be more accurate at identifying users than decision trees when sufficient web activities are observed, and can achieve higher efficiency than Support Vector Machines. The comparisons demonstrate that profile-based methods for user identification provide a viable and simple alternative to this problem. © 2010 Elsevier B.V. All rights reserved. Source


Baskett M.L.,University of California at Davis | Waples R.S.,National Oceanic and Atmospheric Administration
Conservation Biology | Year: 2013

Artificial propagation strategies often incur selection in captivity that leads to traits that are maladaptive in the wild. For propagation programs focused on production rather than demographic contribution to wild populations, effects on wild populations can occur through unintentional escapement or the need to release individuals into natural environments for part of their life cycle. In this case, 2 alternative management strategies might reduce unintended fitness consequences on natural populations: (1) reduce selection in captivity as much as possible to reduce fitness load (keep them similar), or (2) breed a separate population to reduce captive-wild interactions as much as possible (make them different). We quantitatively evaluate these 2 strategies with a coupled demographic-genetic model based on Pacific salmon hatcheries that incorporates a variety of relevant processes and dynamics: selection in the hatchery relative to the wild, assortative mating based on the trait under selection, and different life cycle arrangements in terms of hatchery release, density dependence, natural selection, and reproduction. Model results indicate that, if natural selection only occurs between reproduction and captive release, the similar strategy performs better. However, if natural selection occurs between captive release and reproduction, the different and similar strategies present viable alternatives to reducing unintended fitness consequences because of the greater opportunity to purge maladaptive individuals. In this case, the appropriate approach depends on the feasibility of each strategy and the demographic goal (e.g., increasing natural abundance, or ensuring that a high proportion of natural spawners are naturally produced). In addition, the fitness effects of hatchery release are much greater if hatchery release occurs before (vs. after) density-dependent interactions. Given the logistical challenges to achieving both the similar and different strategies, evaluation of not just the preferred strategy but also the consequences of failing to achieve the desired target is critical. © 2012 Society for Conservation Biology. Source


Adaptive phenotypic plasticity and adaptive genetic differentiation enable plant lineages to maximize their fitness in response to environmental heterogeneity. The spatial scale of environmental variation relative to the average dispersal distance of a species determines whether selection will favor plasticity, local adaptation, or an intermediate strategy. Habitats where the spatial scale of environmental variation is less than the dispersal distance of a species are fine grained and should favor the expression of adaptive plasticity, while coarse-grained habitats, where environmental variation occurs on spatial scales greater than dispersal, should favor adaptive genetic differentiation. However, there is relatively little information available characterizing the link between the spatial scale of environmental variation and patterns of selection on plasticity measured in the field. I examined patterns of spatial environmental variation within a serpentine mosaic grassland and selection on an annual plant (Erodium cicutarium) within that landscape. Results indicate that serpentine soil patches are a significantly finer-grained habitat than non-serpentine patches. Additionally, selection generally favored increased plasticity on serpentine soils and diminished plasticity on non-serpentine soils. This is the first empirical example of differential selection for phenotypic plasticity in the field as a result of strong differences in the grain of environmental heterogeneity within habitats. © 2011 by The University of Chicago. Source


Breast-fed infants and young children need complementary foods with a very high nutrient density (particularly for iron andzinc), especially at ages 6-12 mo. However, in low-income countries, their diet is usually dominated by cereal-based porridges with low nutrient density and poor mineral bioavailability. Complementary feeding diets typically fall short in iron andzinc and sometimes in other nutrients. These gaps in nutritional adequacy of infant diets have likely been a characteristic of human diets since the agricultural revolution ~10,000 y ago. Estimates of nutrient intakes before then, based on hypothetical diets of preagricultural humans, suggest that infants had much higher intakes of key nutrients than is true today and would have been able to meet their nutrient needs from the combination of breast milk and premasticated foods provided by their mothers. Strategies for achieving adequate nutrition for infants and young children in modern times must address the challenge of meeting nutrient needs from largely cereal-based diets. © 2013 American Society for Nutrition. Source


Cummings B.P.,University of California at Davis
Diabetes, Obesity and Metabolism | Year: 2013

There is a pressing need for new effective therapeutic strategies for addressing the epidemic of type 2 diabetes. Leptin has been shown to reduce hyperglycaemia in rodent models of type 1 diabetes and has recently been shown to normalize fasting plasma glucose concentrations in a rodent model of polygenic obesity and type 2 diabetes. Overall, these findings suggest that leptin may be an effective therapeutic option for both type 1 and type 2 diabetes. However, short-term human clinical studies in overweight and obese patients with recently diagnosed type 2 diabetes have reported minimal efficacy of leptin administration to lower blood glucose levels. Herein, the role of leptin in the maintenance of glucose homeostasis and the potential use of leptin in the treatment of type 2 diabetes are discussed. © 2012 Blackwell Publishing Ltd. Source


Plant cells assemble the bipolar spindle and phragmoplast microtubule (MT) arrays in the absence of the centrosome structure. Our recent findings in Arabidopsis thaliana indicated that AUGMIN subunit3 (AUG3), a homolog of animal dim γ-tubulin 3, plays a critical role in γ-tubulin-dependent MT nucleation and amplification during mitosis. Here, we report the isolation of the entire plant augmin complex that contains eight subunits. Among them, AUG1 to AUG6 share low sequence similarity with their animal counterparts, but AUG7 and AUG8 share homology only with proteins of plant origin. Genetic analyses indicate that the AUG1, AUG2, AUG4, and AUG5 genes are essential, as stable mutations in these genes could only be transmitted to heterozygous plants. The sterile aug7-1 homozygous mutant in which AUG7 expression is significantly reduced exhibited pleiotropic phenotypes of seriously retarded vegetative and reproductive growth. The aug7-1 mutation caused delocalization of γ-tubulin in the mitotic spindle and phragmoplast. Consequently, spindles were abnormally elongated, and their poles failed to converge, as MTs were splayed to discrete positions rendering deformed arrays. In addition, the mutant phragmoplasts often had disorganized MT bundles with uneven edges. We conclude that assembly of MT arrays during plant mitosis depends on the augmin complex, which includes two plant-specific subunits. Source


Galt R.E.,University of California at Davis
Antipode | Year: 2013

Through empirical analysis and theory, this paper critiques technocratic regimes of protection vis à vis pesticide use, which are efforts limited to technical rationality and didactic communication of pesticide risks that model pesticide users as self-responsible individuals (ie Homo economicus). Data reveal that knowledge of pesticide risk does not translate into greater protective gear use, within the Costa Rican case presented and more broadly. This circumstance, across first and third world contexts, leads me to develop a more holistic conceptualization of farmers' subjectivities that highlights numerous constraints-informational, political economic, cultural, individual, and environmental-to which farmers are subject. This conceptualization reveals the inadequacy of most efforts to address farmers' protective gear use, and leads me to propose a multi-tiered solution to pesticide problems, including an industrial hygiene approach and fostering subjectivities through participatory research involving pesticide users. © 2012 The Author. Antipode. © 2012 Antipode Foundation Ltd. Source


Wingfield J.C.,University of California at Davis
Frontiers in Neuroendocrinology | Year: 2015

The Earth has always been a changeable place but now warming trends shift seasons and storms occur with greater frequency, intensity and duration. This has prompted reference to the modern era as the Anthropocene caused by human activity. This era poses great challenges for all life on earth and important questions include why and how some organisms can cope and others cannot? It is of heuristic value to consider a framework for types of environmental signals and how they might act. This is especially important as predictable changes of the environment (seasonality) are shifting rapidly as well as unpredictable changes (perturbations) in novel ways. What we need to know is how organisms perceive their environment, transduce that information into neuroendocrine signals that orchestrate morphological, physiological and behavioral responses. Given these goals we can begin to address the questions: do neuroendocrine systems have sufficient flexibility to acclimate to significant change in phenology, are genetic changes leading to adaptation necessary, or both? © 2014 Elsevier Inc. Source


Yellowlees P.M.,University of California at Davis
Telemedicine journal and e-health : the official journal of the American Telemedicine Association | Year: 2013

To examine the feasibility and diagnostic reliability of asynchronous telepsychiatry (ATP) consultations in Spanish and ATP consultation with Spanish-to-English translation. Twenty-four interviews of Spanish-speaking patients were videorecorded by a bilingual clinician who also collected patient history data and gave the Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I) to each patient. The ATP data (video of the interview and patient history) were forwarded for psychiatric consultation and a diagnostic assessment by the investigators. The ATP data were then examined separately by two Spanish-speaking psychiatrists, before being translated into English and then re-examined by two English-speaking psychiatrists. Agreement between the expert diagnoses of the investigators and the diagnoses from the Spanish consultations, the Spanish-to-English translated consultations, and the SCID-I results was assessed using kappa statistics. We found acceptable levels of agreement for major diagnostic groupings among the Spanish- and English-speaking psychiatrists. Kappa values for diagnostic agreement between the expert and the translated consultations, the original language consultations, and the SCID-I were at least 0.52 (percentage agreement, 79%) and higher. ATP consultations in Spanish, and those translated from Spanish to English, are feasible, and broad diagnostic reliability was achieved. The ATP process allows for rapid language translation. This approach could be useful across national boundaries and in numerous ethnic groups. Cross-language ATP may also offer significant benefits over the use of real-time interpreting services and has the potential to improve the quality of care by allowing for the addition of culturally relevant information. Source


Bloom A.J.,University of California at Davis
Current Opinion in Plant Biology | Year: 2015

Many studies of plant nitrogen relations assess only the total amount of the element available from the soil and the total amount of the element within the plant. Nitrogen, however, is a constituent of diverse compounds that participate in some of the most energy-intensive reactions in the biosphere. The following characterizes some of these reactions, especially those that involve ammonium and nitrate, and highlights the importance of distinguishing both among the nitrogen sources available to plants and among the nitrogen forms within plants when considering plant responses to rising atmospheric CO2 concentrations. © 2015 Elsevier Ltd. Source


Lubell M.,University of California at Davis
Current Opinion in Environmental Sustainability | Year: 2015

Collaborative partnerships exist in the context of complex institutional systems that feature multiple institutions and actors interacting in the context of interconnected collective-action problems within ecosystems. How collaborative partnerships contribute to the overall capacity of complex institutional systems to sustainability govern natural resources remains an open question. This article reviews several theoretical approaches for studying complex institutional systems, and discusses how collaborative partnerships would be viewed from these perspectives. The approaches covered include neo-institutional economics, polycentric governance, complex adaptive systems, and evolutionary models of institutional change. The conclusion calls for synthetic theoretical frameworks that integrate many of these ideas, and identifies the research on social-ecological systems as a promising direction. © 2014 Published by Elsevier Ltd. Source


Jee M.J.,University of California at Davis
Astrophysical Journal | Year: 2010

Intracluster light (ICL) is believed to originate from the stars stripped from cluster galaxies. They are no longer gravitationally bound to individual galaxies, but to the cluster, and their smooth distribution potentially makes them serve as much denser tracers of the cluster dark matter than the sparsely distributed cluster galaxies. We present our study of the ICL in the galaxy cluster Cl 0024+17 using both Advanced Camera for Surveys (ACS) and Subaru data, where we previously reported the discovery of a ring-like dark matter structure with gravitational lensing. The ACS images provide much lower sky levels than ground-based data, and enable us to measure relative variation of surface brightness reliably. This analysis is repeated with the Subaru images to examine if consistent features are recovered despite a different reduction scheme and different instrumental characteristics. We find that the ICL profile clearly resembles the peculiar mass profile, which stops decreasing at r ∼50″ (∼265 kpc) and slowly increases until it turns over at r ∼ 75″ (∼397 kpc). This feature is seen in both ACS and Subaru images for nearly all available passband images while the features are in general stronger in red filters. The consistency across different filters and instruments strongly rules out the possibility that the feature might come from any residual, uncorrected calibration errors. In addition, our re-analysis of the cluster X-ray data shows that the peculiar mass structure is also indicated by a non-negligible (3.7σ in Chandra and 2.4σ in XMM-Newton) bump in the intracluster gas profile when the geometric center of the dark matter ring, not the peak of the X-ray emission, is chosen as the center of the radial bin. The location of the gas ring is closer to the center by ∼15″ (∼80 kpc), raising an interesting possibility that the ring-like structure is expanding and the gas ring is lagging behind perhaps because of the ram pressure if both features in mass and gas share the same dynamical origin. © 2010. The American Astronomical Society. Source


Hart B.L.,University of California at Davis
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2011

No other theme in animal biology seems to be more central than the concept of employing strategies to survive and successfully reproduce. In nature, controlling or avoiding pathogens and parasites is an essential fitness strategy because of the ever-present disease-causing organisms. The disease-control strategies discussed here are: physical avoidance and removal of pathogens and parasites; quarantine or peripheralization of conspecifics that could be carrying potential pathogens; herbal medicine, animal style, to prevent or treat an infection; potentiation of the immune system; and care of sick or injured group members. These strategies are seen as also encompassing the pillars of human medicine: (i) quarantine; (ii) immune-boosting vaccinations; (iii) use of medicinal products; and (iv) caring or nursing. In contrast to animals, in humans, the disease-control strategies have been consolidated into a consistent and extensive medical system. A hypothesis that explains some of this difference between animals and humans is that humans are sick more often than animals. This increase in sickness in humans leading to an extensive, cognitively driven medical system is attributed to an evolutionary dietary transition from mostly natural vegetation to a meat-based diet, with an increase in health-eroding free radicals and a dietary reduction of free-radical-scavenging antioxidants. © 2011 The Royal Society. Source


Chen B.,Michigan Technological University | Cheng H.H.,University of California at Davis
IEEE Transactions on Intelligent Transportation Systems | Year: 2010

The agent computing paradigm is rapidly emerging as one of the powerful technologies for the development of large-scale distributed systems to deal with the uncertainty in a dynamic environment. The domain of traffic and transportation systems is well suited for an agent-based approach because transportation systems are usually geographically distributed in dynamic changing environments. Our literature survey shows that the techniques and methods resulting from the field of agent and multiagent systems have been applied to many aspects of traffic and transportation systems, including modeling and simulation, dynamic routing and congestion management, and intelligent traffic control. This paper examines an agent-based approach and its applications in different modes of transportation, including roadway, railway, and air transportation. This paper also addresses some critical issues in developing agent-based traffic control and management systems, such as interoperability, flexibility, and extendibility. Finally, several future research directions toward the successful deployment of agent technology in traffic and transportation systems are discussed. © 2010 IEEE. Source


Carlip S.,University of California at Davis
Journal of High Energy Physics | Year: 2011

I rederive the Kerr/CFT correspondence without first taking the near-horizon extremal Kerr limit. This method extends easily to nonextremal black holes, for which the temperature and central charge behave poorly at the horizon but the entropy remains finite. A computation yields one-half of the standard Bekenstein-Hawking entropy, with hints that the other half may be related to a conformal field theory at the inner horizon. I then present an alternative approach, based on a stretched Killing horizon, in which the full entropy is obtained and the temperature and central charge remain well-behaved even in the nonextremal case. © SISSA 2011. Source


A group of 22 treatments from 6 experiments in which lactating dairy cows were fed diets with different ingredient compositions, and in which the amino acid (AA) profile of their duodenal protein was measured with the same techniques and methodologies, were assembled. Correlative statistics were used to assess relationships between proportions of various crude protein (CP) sources in the diet and the proportion of methionine and lysine in duodenal protein. Changes in the percentages of dietary CP coming from several classes of feeds had some impact on the lysine and methionine proportions of duodenal CP, but changes were generally modest either when predicted by simple (i.e., increased diet canola CP increased, and increased corn CP decreased, lysine in duodenal digesta CP, while increased diet canola and barley/wheat CP increased, and increased corn CP and grass/legume CP decreased, methionine in duodenal digesta) or multiple correlation analysis (i.e., increased legume/grass, canola, linseed and blood increased, and increased corn and canola decreased, lysine in duodenal digesta, while increased corn and barley/wheat decreased lysine in duodenal digesta and increased dietary CP from barley/wheat, canola, linseed and fish meal increased methionine in duodenal digesta). Feeding experiments that used lactating Holstein cows, from peer review publications since 1984, were then used to determine the ability to predict production responses of lactating dairy cows to feeding ruminally protected (RP) methionine, lysine or lysine/methionine combinations based upon the composition of their diets. The 54 published experiments included 54 comparisons of a control diet to one supplemented with RP methionine, 12 to RP lysine and 47 to a combination of both AA. Differences among the three treatments (i.e., RP methionine, RP lysine, RP lysine/methionine addition to the diets) in the characteristics of the cows and diets assigned to the control treatments, as well as their responsiveness to AA addition, were analyzed using a systematic review of the literature with a model that considered each experiment to be an observation. There were differences in the ingredient and chemical characteristics of the control diets utilized to evaluate responses to RP methionine, lysine and methionine/lysine combinations. RP methionine supplementation increased milk energy output as well as milk protein and fat percentages, while increasing the proportion of dietary N captured as milk N. RP lysine supplementation decreased dry matter (DM) intake and increased the milk/DM intake ratio. RP lysine and methionine combinations increased milk and milk energy yield, milk protein percentage as well as increased the proportion of dietary N captured as milk N and the milk/DM intake ratio. However these changes were judged to be small (i.e., the largest was a 3.9% increase in capture of dietary N as milk N for lysine and methionine combinations) and largely not predictable based upon characteristics of the control cows and diets among studies. This review provides strong evidence that levels of lysine and methionine in duodenal protein do change with source of dietary proteins, and that manipulation of the lysine and methionine proportions of duodenal protein by feeding RP methionine or lysine/methionine combinations does have modest impacts on dairy cow performance, although RP lysine alone has a negative impact. However these differences are small and relatively unpredictable in practice making their utility as a practical means to improve the productivity and/or reduce the environmental impact of dairy cows on commercial dairy farms very limited. © 2009 Elsevier B.V. All rights reserved. Source


Burke A.,University of California at Davis
International Journal of Energy Research | Year: 2010

This paper focuses on ultracapacitors (electrochemical capacitors) as energy storage in vehicle applications and thus evaluates the present state-of-the-art of ultracapacitor technologies and their suitability for use in electric and hybrid drivelines of various types of vehicles. A key consideration in determining the applicability of ultracapacitors for a particular vehicle application is the proper assessment of the energy storage and power requirements. For hybrid-electric vehicles, the key issues are the useable energy requirement and the maximum pulse power at high efficiency. For a Prius size vehicle, if the useable energy storage is about 125 Wh and needed efficiency is 90-95%, analysis shown in this paper indicate that vehicles can be designed using carbon ultracapacitors (both carbon/carbon and hybrid carbon) that yield high fuel economy improvements for all driving cycles and the cost of the ultracapacitors can be competitive with lithium-ion batteries for high volume production and carbon prices of less than $20 kg-1. The use of carbon/carbon devices in micro-hybrids is particularly attractive for a control strategy (sawtooth) that permits engine operation near its maximum efficiency using only a 6 kW electric motor. Vehicle projects in transit buses and passenger cars have shown that ultracapacitors have functioned as expected and significant fuel economy improvements have been achieved that are higher than would have been possible using batteries because of the higher round-trip efficiencies of the ultracapacitors. Ultracapacitors have particular advantages for use in fuel cell powered vehicles in which it is likely they can be used without interface electronics. Development of hybrid carbon devices is continuing showing energy densities of 12 Wh kg-1 and a high efficiency power density of about 1000 W kg-1 Vehicle simulations using those devices have shown that increased power capability in such devices is needed before full advantage can be taken of their increased energy density compared with carbon/carbon devices in some vehicle applications. Energy storage system considerations indicate that combinations of ultracapacitors and advanced batteries (Wh kg-1 >200) are likely to prove advantageous in the future as such batteries are developed. This is likely to be the case in plug-in hybrids with high-power electric motors for which it may be difficult to limit the size and weight of the energy storage unit even using advanced batteries. © 2009 John Wiley & Sons, Ltd. Source


Baum W.M.,University of California at Davis
Journal of the experimental analysis of behavior | Year: 2012

The concept of reinforcement is at least incomplete and almost certainly incorrect. An alternative way of organizing our understanding of behavior may be built around three concepts: allocation, induction, and correlation. Allocation is the measure of behavior and captures the centrality of choice: All behavior entails choice and consists of choice. Allocation changes as a result of induction and correlation. The term induction covers phenomena such as adjunctive, interim, and terminal behavior-behavior induced in a situation by occurrence of food or another Phylogenetically Important Event (PIE) in that situation. Induction resembles stimulus control in that no one-to-one relation exists between induced behavior and the inducing event. If one allowed that some stimulus control were the result of phylogeny, then induction and stimulus control would be identical, and a PIE would resemble a discriminative stimulus. Much evidence supports the idea that a PIE induces all PIE-related activities. Research also supports the idea that stimuli correlated with PIEs become PIE-related conditional inducers. Contingencies create correlations between "operant" activity (e.g., lever pressing) and PIEs (e.g., food). Once an activity has become PIE-related, the PIE induces it along with other PIE-related activities. Contingencies also constrain possible performances. These constraints specify feedback functions, which explain phenomena such as the higher response rates on ratio schedules in comparison with interval schedules. Allocations that include a lot of operant activity are "selected" only in the sense that they generate more frequent occurrence of the PIE within the constraints of the situation; contingency and induction do the "selecting." Source


Carlip S.,University of California at Davis
Classical and Quantum Gravity | Year: 2015

Results from a number of different approaches to quantum gravity suggest that the effective dimension of spacetime may drop to d = 2 at small scales. I show that two different dimensional estimators in causal set theory display the same behavior, and argue that a third, the spectral dimension, may exhibit a related phenomenon of 'asymptotic silence.' © 2015 IOP Publishing Ltd. Source


Oteiza P.I.,University of California at Davis
Free Radical Biology and Medicine | Year: 2012

Zinc, a redox-inactive metal, has been long viewed as a component of the antioxidant network, and growing evidence points to its involvement in redox-regulated signaling. These actions are exerted through several mechanisms based on the unique chemical and functional properties of zinc. Overall, zinc contributes to maintaining the cell redox balance through various mechanisms including: (i) the regulation of oxidant production and metal-induced oxidative damage; (ii) the dynamic association of zinc with sulfur in protein cysteine clusters, from which the metal can be released by nitric oxide, peroxides, oxidized glutathione, and other thiol oxidant species; (iii) zinc-mediated induction of the zinc-binding protein metallothionein, which releases the metal under oxidative conditions and acts per se as a scavenging oxidant; (iv) the involvement of zinc in the regulation of glutathione metabolism and of the overall protein thiol redox status; and (v) a direct or indirect regulation of redox signaling. Findings of oxidative stress, altered redox signaling, and associated cell/tissue dysfunction in cell and animal models of zinc deficiency highlight the relevant role of zinc in the preservation of cell redox homeostasis. However, although the participation of zinc in antioxidant protection, redox sensing, and redox-regulated signaling is accepted, the molecules, targets, and mechanisms involved are still partially known and the subject of active research. © 2012 Elsevier Inc. All rights reserved. Source


Celli J.,Washington State University | Tsolis R.M.,University of California at Davis
Nature Reviews Microbiology | Year: 2015

The unfolded protein response (UPR) is a cytoprotective response that is aimed at restoring cellular homeostasis following physiological stress exerted on the endoplasmic reticulum (ER), which also invokes innate immune signalling in response to invading microorganisms. Although it has been known for some time that the UPR is modulated by various viruses, recent evidence indicates that it also has multiple roles during bacterial infections. In this Review, we describe how bacteria interact with the ER, including how bacteria induce the UPR, how subversion of the UPR promotes bacterial proliferation and how the UPR contributes to innate immune responses against invading bacteria. © 2015 Macmillan Publishers Limited. All rights reserved. Source


Powell J.S.,University of California at Davis
Journal of Thrombosis and Haemostasis | Year: 2015

Hemophilia, when severe, leads to spontaneous life-threatening bleeding episodes. Current therapy requires frequent intravenous infusions. Most patients must limit their physical activities to avoid bleeding when the factor activity levels are below normal. In 2014, new therapeutic factor VIII and IX products were approved in Canada and the U.S. Over the next couple of years, other new factor products will likely be approved. These new factors have been engineered to have improved pharmacokinetic properties, including extended half-life in circulation, thus providing major therapeutic advances for patients with hemophilia. In the completed clinical trials, over 700 patients have successfully used these longer acting products regularly for more than one year. These promising new therapies should allow patients with hemophilia to use fewer infusions to prevent spontaneous bleeding or to treat bleeding episodes, and to provide appropriate clotting factor levels for different physical activities. © 2015 International Society on Thrombosis and Haemostasis. Source


A pilot scheme uses upper air data from a few extreme hottest days to identify those and other extreme hottest days measured by 3 stations sampling the California Central Valley (CV). Prior work showed that CV extreme heat wave onsets have characteristic large scale patterns in many upper-air variables; those patterns also occur for the hottest days. A pilot scheme uses areas of two upper-air variables with high significance and consistency to forecast extreme surface temperatures. The scheme projects key parts of composite patterns for one or more variables onto daily weather maps of the corresponding variables resulting in a 'circulation index' for each day. The circulation index measures how similar the pattern on that day is to the composite patterns in areas dynamically relevant to a CV extremely hot day, with a larger value for a stronger match and larger amplitude. The scheme is tested on the development period (1979-1988) and on the subsequent 18 year 'independent' period (1989-2006). The pilot scheme captures about half of the rare events in the development period, with similar skill for the independent period. Based only on 16 days of extreme heat in the first 10 years, the scheme is not intended to represent the general distribution; however the circulation index has similar kurtosis, variance, and skewness as the observed maximum temperatures. Properties of the high end tail of the distribution are notably improved by adding the second predictor. The scheme outperforms simply using 850 hPa temperature above the CV. © 2011 The Author(s). Source


Kayhanian M.,University of California at Davis
Environmental Pollution | Year: 2012

This study presents the results of lead (Pb) concentrations from both highway runoff and contaminated soil along 32 and 23 highway sites, respectively. In general, the Pb concentration on topsoil (0-15 cm) along highways was much higher than the Pb concentration in subsurface soil (15-60 cm). The Pb deposited on soil appears to be anthropogenic and a strong correlation was found between the Pb concentration in surface soil and highway runoff in urban areas. The concentration of Pb measured during 1980s from highways runoff throughout the world was up to 11 times higher than the measured values in mid 1990s and 2000s. The current Pb deposited on soil near highways appears to be a mixture of paint, tire weight balance and old leaded gasoline combustion. Overall, the Pb phase-out regulation reduced the Pb deposits in the environment and consequently lowered Pb loading into receiving waters. © 2011 Elsevier Ltd. All rights reserved. Source


Amitani I.,University of California at Davis
Methods in enzymology | Year: 2010

In traditional biochemical experiments, the behavior of individual proteins is obscured by ensemble averaging. To better understand the behavior of proteins that bind to and/or translocate on DNA, we have developed instrumentation that uses optical trapping, microfluidic solution delivery, and fluorescent microscopy to visualize either individual proteins or assemblies of proteins acting on single molecules of DNA. The general experimental design involves attaching a single DNA molecule to a polystyrene microsphere that is then used as a microscopic handle to manipulate individual DNA molecules with a laser trap. Visualization is achieved by fluorescently labeling either the DNA or the protein of interest, followed by direct imaging using high-sensitivity fluorescence microscopy. We describe the sample preparation and instrumentation used to visualize the interaction of individual proteins with single molecules of DNA. As examples, we describe the application of these methods to the study of proteins involved in recombination-mediated DNA repair, a process essential for the maintenance of genomic integrity. Copyright 2010 Elsevier Inc. All rights reserved. Source


Saucerman J.J.,University of Virginia | Bers D.M.,University of California at Davis
Journal of Molecular and Cellular Cardiology | Year: 2012

Calmodulin (CaM) acts as a common Ca 2+ sensor for many signaling pathways, transducing local Ca 2+ signals into specific cellular outcomes. Many of CaM's signaling functions can be explained by its unique biochemical properties, including high and low affinity Ca 2+-binding sites with slow and fast kinetics, respectively. CaM is expected to have a limited spatial range of action, emphasizing its role in local Ca 2+ signaling. Interactions with target proteins further fine-tune CaM signal transduction. Here, we focus on only three specific cellular targets for CaM signaling in cardiac myocytes: the L-type Ca 2+ channel, the ryanodine receptor, and the IP 3 receptor. We elaborate a working hypothesis that each channel is regulated by two distinct functional populations of CaM: dedicated CaM and promiscuous CaM. Dedicated CaM is typically tethered to each channel and directly regulates channel activity. In addition, a local pool of promiscuous CaM appears poised to sense local Ca 2+ signals and trigger downstream pathways such as Ca 2+/CaM dependent-protein kinase II and calcineurin. Understanding how promiscuous CaM coordinates multiple distinct signaling pathways remains a challenge, but is aided by the use of mathematical modeling and a new generation of fluorescent biosensors. This article is part of a special issue entitled "Local Signaling in Myocytes.". © 2011 Elsevier Ltd. Source


Gunbas G.,University of California at Davis | Gunbas G.,Middle East Technical University | Toppare L.,Middle East Technical University
Chemical Communications | Year: 2012

Polymer electrochromism has been considered one of the liveliest branches of conducting polymer research, a tradition continued in the last decade. We have witnessed numerous significant advances, making commercial applications closer than ever. This feature article highlights these advances by separating them into 3 sections. The material design section emphasizes the new molecular structures that have been utilized as electrochromic materials and their promising results. The color control of polymeric electrochromics section focuses on the recent achievements towards realization of full color electrochromic display devices, lastly the advances en route commercial applications section demonstrates how some of the major drawbacks towards commercialization have been successfully addressed. © The Royal Society of Chemistry 2012. Source


The suppression of high p T hadrons in 200 GeV Au + Au collisions at RHIC has been seen as a signature for a partonic medium being formed. The evolution of this key QGP signature is a powerful tool for studying the QCD phase structure in the RHIC Beam Energy Scan. In these proceedings, we present measurements of identified π +, K +, and p, as well as unidentified charged particles in Au + Au collisions at √sNN=7.7,11.5,19.6,27,39,and62.4GeV. We report nuclear modification factors R C P and R A A where published p + p references are available. These results offer insight into the sNN dependence of high p T suppression in nuclear collisions. © 2013. Source


Carlip S.,University of California at Davis
Classical and Quantum Gravity | Year: 2015

Several recent results have hinted that black hole thermodynamics in loop quantum gravity simplifies if one chooses an imaginary Barbero-Immirzi parameter γ = i. This suggests a connection with SL(2, ℂ) or SL(2, ℝ) conformal field theories at the 'boundaries' formed by spin network edges intersecting the horizon. I present a bit of background regarding the relevant conformal field theories, along with some speculations about how they might be used to count black hole states. I show, in particular, that a set of unproven but plausible assumptions can lead to a boundary conformal field theory whose density of states matches the Bekenstein-Hawking entropy. © 2015 IOP Publishing Ltd. Source


Schumann C.M.,University of California at Davis
Acta neuropathologica communications | Year: 2014

BACKGROUND: Abnormal connectivity across brain regions underlies many neurological disorders including multiple sclerosis, schizophrenia and autism, possibly due to atypical axonal organization within white matter. Attempts at investigating axonal organization on post-mortem human brains have been hindered by the availability of high-quality, morphologically preserved tissue, particularly for neurodevelopmental disorders such as autism. Brains are generally stored in a fixative for long periods of time (often greater than 10 years) and in many cases, already frozen and sectioned on a microtome for histology and immunohistochemistry. Here we present a method to assess the quality and quantity of axons from long-term fixed and frozen-sectioned human brain samples to demonstrate their use for electron microscopy (EM) measures of axonal ultrastructure.RESULTS: Six samples were collected from white matter below the superior temporal cortex of three typically developing human brains and prepared for EM analyses. Five samples were stored in fixative for over 10 years, two of which were also flash frozen and sectioned on a freezing microtome, and one additional case was fixed for 3 years and sectioned on a freezing microtome. In all six samples, ultrastructural qualitative and quantitative analyses demonstrate that myelinated axons can be identified and counted on the EM images. Although axon density differed between brains, axonal ultrastructure and density was well preserved and did not differ within cases for fixed and frozen tissue. There was no significant difference between cases in axon myelin sheath thickness (g-ratio) or axon diameter; approximately 70% of axons were in the small (0.25 μm) to medium (0.75 μm) range. Axon diameter and g-ratio were positively correlated, indicating that larger axons may have thinner myelin sheaths.CONCLUSION: The current study demonstrates that long term formalin fixed and frozen-sectioned human brain tissue can be used for ultrastructural analyses. Axon integrity is well preserved and can be quantified using the methods presented here. The ability to carry out EM on frozen sections allows for investigation of axonal organization in conjunction with other cellular and histological methods, such as immunohistochemistry and stereology, within the same brain and even within the same frozen cut section. Source


LaSalle J.M.,University of California at Davis
Epigenetics | Year: 2011

The etiologic paradigm of complex human disorders such as autism is that genetic and environmental risk factors are independent and additive, but the interactive effects at the epigenetic interface are largely ignored. Genomic technologies have radically changed perspective on the human genome and how the epigenetic interface may impact complex human disorders. Here, I review recent genomic, environmental and epigenetic findings that suggest a new paradigm of "integrative genomics" in which genetic variation in genomic size may be impacted by dietary and environmental factors that influence the genomic saturation of DNA methylation. Human genomes are highly repetitive, but the interface of large-scale genomic differences with environmental factors that alter the DNA methylome such as dietary folate is under-explored. In addition to obvious direct effects of some environmental toxins on the genome by causing chromosomal breaks, nonmutagenic toxin exposures correlate with DNA hypomethylation that can lead to rearrangements between repeats or increased retrotransposition. Since human neurodevelopment appears to be particularly sensitive to alterations in epigenetic pathways, a further focus will be on how developing neurons may be particularly impacted by even subtle alterations to DNA methylation and proposing new directions towards understanding the quixotic etiology of autism by integrative genomic approaches. © 2011 Landes Bioscience. Source


Grismer M.E.,University of California at Davis
Hydrological Processes | Year: 2013

Estimates of groundwater volumes available in semiarid regions that rely on water balance calculations require the determination of both surface to groundwater lag times and volumes from irrigation or rainfall initiated recharge. Subsurface geologic material hydraulic properties (e.g. hydraulic conductivities, water retention functions) necessary for unsaturated flow modelling are rarely available as are the instrumented field tests that might determine such lag times. Here we develop a simple two-parameter (specific yield, Sy, and pore-size distribution index, λ), one-dimensional unsaturated flow model from simplifications of the Richards equation (using the Brooks-Corey relationships) to determine lag times from agricultural deep drainage associated with the irrigation of alfalfa hay and various row crops in the Antelope Valley of California, USA. Model-predicted lag times to depths of 85m bgs (below ground surface) were similar to that measured in a 2-year ponded recharge field trial, slightly overestimating that measured by approximately 15% (0.51 vs 0.44years). Lag time estimates were most sensitive to estimated deep percolation rates and roughly equally sensitive to the model hydraulic parameters. Generally, as subsurface material textures coarsen towards larger Sy and λ values for all Sy >10%, lag times progressively increase; however, at Sy <10%, lag times decrease substantially suggesting that particular combinations of Sy and λ values that may be associated with similarly textured materials can result in the prediction of different lag times for Sy approximately 10%. Overall, lag times of 1-3years to a depth of 69m bgs were estimated from deep drainage of agricultural irrigation across a variety of irrigation schedules and subsurface materials. © 2012 John Wiley & Sons, Ltd. Source


Dumit J.,University of California at Davis
Frontiers in Human Neuroscience | Year: 2014

Drawing on Allan Newell's "You can't play 20 questions with nature and win," this article proposes that neuroscience needs to go beyond binary hypothesis testing and design experiments that follow what neurons care about. Examples from Lettvin et. al. are used to demonstrate that one can experimentally play with neurons and generate surprising results. In this manner, brains are not confused with persons, rather, persons are understood to do things with their brains. © 2014 Dumit. Source


Wang G.,University of California at Davis
Journal of Power Sources | Year: 2011

Advanced vehicles and alternative fuels could play an important role in reducing oil use and changing the economy structure. We developed the Costs for Advanced Vehicles and Energy (CAVE) model to investigate a vehicle portfolio scenario in California during 2010-2030. Then we employed a computable general equilibrium model to estimate macroeconomic impacts of the advanced vehicle scenario on the economy of California. Results indicate that, due to slow fleet turnover, conventional vehicles are expected to continue to dominate the on-road fleet and gasoline is the major transportation fuel over the next two decades. However, alternative fuels could play an increasingly important role in gasoline displacement. Advanced vehicle costs are expected to decrease dramatically with production volume and technological progress; e.g., incremental costs for fuel cell vehicles and hydrogen could break even with gasoline savings in 2028. Overall, the vehicle portfolio scenario is estimated to have a slightly negative influence on California's economy, because advanced vehicles are very costly and, therefore, the resulting gasoline savings generally cannot offset the high incremental expenditure on vehicles and alternative fuels. Sensitivity analysis shows that an increase in gasoline price or a drop in alternative fuel prices could offset a portion of the negative impact. © 2010 Elsevier B.V. Source


Feske S.,New York University | Wulff H.,University of California at Davis | Skolnik E.Y.,New York University
Annual Review of Immunology | Year: 2015

Ion channels and transporters mediate the transport of charged ions across hydrophobic lipid membranes. In immune cells, divalent cations such as calcium, magnesium, and zinc have important roles as second messengers to regulate intracellular signaling pathways. By contrast, monovalent cations such as sodium and potassium mainly regulate the membrane potential, which indirectly controls the influx of calcium and immune cell signaling. Studies investigating human patients with mutations in ion channels and transporters, analysis of gene-targeted mice, or pharmacological experiments with ion channel inhibitors have revealed important roles of ionic signals in lymphocyte development and in innate and adaptive immune responses. We here review the mechanisms underlying the function of ion channels and transporters in lymphocytes and innate immune cells and discuss their roles in lymphocyte development, adaptive and innate immune responses, and autoimmunity, as well as recent efforts to develop pharmacological inhibitors of ion channels for immunomodulatory therapy. © 2015 by Annual Reviews. All rights reserved. Source


Pedersen N.C.,University of California at Davis
Veterinary Journal | Year: 2014

This review is concerned with what has been learned about feline infectious peritonitis (FIP) diagnostics and therapeutics since the publication of an extensive overview of literature covering the period 1963-2009. Although progress has been made in both areas, obtaining a definitive diagnosis of FIP remains a problem for those veterinarians and/or cat owners who require absolute certainty. This review will cover both indirect and direct diagnostic tests for the disease and will emphasize their limitations, as well as their specificity and sensitivity. There is still no effective treatment for FIP, although there are both claims that such therapies exist and glimmers of hope coming from new therapies that are under research. FIP has also been identified in wild felids and FIP-like disease is now a growing problem among pet ferrets. © 2014 The Author. Source


Borowsky A.D.,University of California at Davis
Cold Spring Harbor perspectives in biology | Year: 2011

Genetically engineered mice are critical experimental models for the study of breast cancer biology. Transgenic mice, employing strong mammary epithelial promoters to drive oncogenes, develop carcinomas with phenotypes corresponding to the molecular pathway activated. Gene-targeted (knockout) mice, in which tumor suppressors are deleted, develop mammary neoplasms with phenotypes primarily including patterns seen in spontaneous mouse mammary tumors, albeit at higher rates. Improved genetic engineering, using inducible gene expression, somatic gene transduction, conditional alleles, and crossbreeding for combined/compound genetic engineering yields precise molecular models with exquisite experimental control and phenotypes with comparative pathologic validity. Mammary gland transplantation technology adds a practical and validated method for assessing biologic behavior of selected mammary tissues. Overall, the many mouse models available are a rich resource for experimental biology with phenocopies of breast cancer subtypes, and a variety of practical advantages. The challenge is matching the model to the experimental question. Source


Delye C.,CNRS Agroecology Lab | Jasieniuk M.,University of California at Davis | Le Corre V.,CNRS Agroecology Lab
Trends in Genetics | Year: 2013

Resistance to herbicides in arable weeds is increasing rapidly worldwide and threatening global food security. Resistance has now been reported to all major herbicide modes of action despite the development of resistance management strategies in the 1990s. We review here recent advances in understanding the genetic bases and evolutionary drivers of herbicide resistance that highlight the complex nature of selection for this adaptive trait. Whereas early studied cases of resistance were highly herbicide-specific and largely under monogenic control, cases of greatest concern today generally involve resistance to multiple modes of action, are under polygenic control, and are derived from pre-existing stress response pathways. Although 'omics' approaches should enable unraveling the genetic bases of complex resistances, the appearance, selection, and spread of herbicide resistance in weed populations can only be fully elucidated by focusing on evolutionary dynamics and implementing integrative modeling efforts. © 2013 Elsevier Ltd. Source


Baumgarth N.,University of California at Davis
Immunological Reviews | Year: 2013

Influenza virus infection induces robust and highly protective B-cell responses. Knowledge gained from the analysis of such protective humoral responses can provide important clues for the design of successful vaccines and vaccination approaches and also provides a window into the regulation of fundamental aspects of B-cell responses that may not be at play when responses to non-replicating agents are studied. Here, I review features of the B-cell response to viruses, with emphasis on influenza virus infection, a highly localized infection of respiratory tract epithelial cells, and a response that is directed against a virus that continuously undergoes genetic changes to its surface spike protein, a major target of neutralizing antibodies. Two aspects of the B-cell response to influenza are discussed here, namely polyreactive natural antibodies and the role and function of germinal center responses. Both these features of the B-cell response raise the question of how important antibody fine-specificity is for long-term protection from infection. As outlined, the pathogenesis of influenza virus and the nature of the antiviral B-cell response seem to emphasize repertoire diversity over affinity maturation as driving forces behind the influenza-specific B-cell immunity. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd. Source


Telander D.G.,University of California at Davis
Seminars in Ophthalmology | Year: 2011

Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly. The cause of AMD is complex and many risk factors have been implicated including age, family history (genetics), diet, smoking, and other environmental risk factors. Over the past decade, studies has found that inflammation play a large role in the pathogenesis of age-related macular degeneration (AMD). In fact, the main genetic changes (polymorphism) associated with AMD were found to be genes that regulate inflammation, most notably complement Factor H. This review ties together many studies done over the past decade to give us new insight into the role inflammation plays in the development of AMD. © 2011 Informa Healthcare USA, Inc. Source


Submersed macrophytes have important ecological functions in many streams, but fostering growth of beneficial native species while suppressing weedy invasives may be challenging. Two approaches commonly used in management of terrestrial plant communities may be useful in this context: (1) altering resource availability and (2) establishing desirable species before weeds can invade (priority effects). However, these approaches are rarely used in aquatic systems, despite widespread need for sustainable solutions to aquatic weed problems. In artificial stream channels in California, USA, I conducted experiments with asexual propagules of non-native invasive Myriophyllum spicatum (Eurasian watermilfoil) and native Elodea nuttallii (western waterweed) to address the questions: (1) How does light availability affect relative performance of the two species?; (2) Does planting the native earlier than the invasive decrease survival or growth rate of the invasive?; and (3) Do light level and priority effects interact? The relative performance between E. nuttallii and M . spicatum had an interesting and unexpected pattern: M. spicatum had higher growth rates than E. nuttallii in the zero and medium shade levels, but had similar performance in the low and high shade levels. This pattern is most likely the result of E. nutallii's sensitivity to both very low and very high light, and M . spicatum ' s sensitivity to very low light only. Native priority did not significantly affect growth rate or survival of M. spicatum, possibly because of unexpectedly poor growth of the E. nuttallii planted early. This study suggests that altering light levels could be effective in reducing growth of an invasive macrophyte, and for changing the competitive balance between a native and a non-native species in the establishment phase. Further investigations into the use of priority effects and resource alteration for submersed macrophyte management are warranted, given their mixed results in other (limited) studies. © 2015 Emily P. Zefferman. Source


Almario R.U.,University of California at Davis
Journal of the American College of Nutrition | Year: 2013

The omega-3 polyunsaturated fatty acid (n-3 PUFA) as well as lignan components of flaxseed (FLX) can have beneficial effects. In this 6-week-long, randomized, double-blinded, placebo-controlled study, we investigated the effects of FLX lignans on cardiovascular risk factors. Thirty-seven subjects (13 men and 24 women, age: 54±7 years, body mass index [BMI]: 29.7±1 kg/m2) consumed nutrition bars with similar macronutrient contents. The fatty acid composition and the lignan contents of the bars differed significantly. Two FLX bars both contained 3.0 g of alpha linolenic acid (ALA: 18:3 n-3) but different amount of lignans (0.15 g vs. 0.41 g). High-lignan FLX decreased total cholesterol (C) by 12% (p=0.044), LDL-C by 15% (p=0.022), and oxidized (Ox)-LDL by 25% (p=0.035). Regular FLX tended to increase Ox-LDL by 13% (p=0.051). The difference between the effects of high-lignan vs. regular lignan FLX on Ox-LDL was highly significant (p=0.004). High-lignan FLX has the unique property of decreasing Ox-LDL, which is an independent risk factor for cardiovascular disease. Source


Raychaudhuri S.P.,Sacramento Medical Center | Raychaudhuri S.P.,University of California at Davis
Clinical Reviews in Allergy and Immunology | Year: 2013

The role of T cell subpopulations in human disease is in a transition phase due to continuous discovery of new subsets of T cell, one of which is Th17, characterized by the production of signature cytokine IL-17. In the last couple of years, many articles are coming out on the role of Th17 and its signature cytokine IL-17 in different autoimmune diseases like rheumatoid arthritis, psoriasis, psoriatic arthritis (PsA), SLE and multiple sclerosis. Psoriasis and PsA are immune-mediated diseases, affecting the skin and joints, respectively. Initially, it was thought that psoriasis and PsA were Th1-mediated diseases; however, studies in knockout animal models (IL-17 knockout mice) as well as human experimental data indicate that Th17 and its signature cytokine IL-17 have a critical role in the pathogenesis of psoriatic disease. Th17 cells have been identified from the dermal extracts of psoriatic lesions. Subsequently, our research group has substantiated this observation that Th17 cells are enriched in the papillary dermis of psoriatic plaques and in freshly isolated effector T lymphocytes from the synovial fluid of PsA patients, and we have reported that the majority of these CD4 + IL-17+ T cells are of memory phenotype (CD4RO +CD45RA-CD11a+). Recent reports also suggest that the synovial tissue in psoriatic arthritis is enriched with IL-17R, and its most well recognized receptor IL-17RA is functionally active in psoriatic arthritis. In this review article, we have discussed the role of IL-17 in psoriatic disease and have narrated about the novel IL17/IL-17R antibodies currently in preparation for its therapeutic uses in autoimmune diseases. © 2012 Springer Science+Business Media, LLC (outside the USA). Source


Tiffin P.,University of Minnesota | Ross-Ibarra J.,University of California at Davis
Trends in Ecology and Evolution | Year: 2014

Local adaptation shapes species diversity, can be a stepping stone to ecological speciation, and can facilitate species range expansion. Population genetic analyses, which complement organismal approaches in advancing our understanding of local adaptation, have become widespread in recent years. We focus here on using population genetics to address some key questions in local adaptation: what traits are involved? What environmental variables are the most important? Does local adaptation target the same genes in related species? Do loci responsible for local adaptation exhibit trade-offs across environments? After discussing these questions we highlight important limitations to population genetic analyses including challenges with obtaining high-quality data, deciding which loci are targets of selection, and limits to identifying the genetic basis of local adaptation. © 2014 Elsevier Ltd. Source


Neale D.B.,University of California at Davis | Kremer A.,University of Bordeaux 1
Nature Reviews Genetics | Year: 2011

Over the past two decades, research in forest tree genomics has lagged behind that of model and agricultural systems. However, genomic research in forest trees is poised to enter into an important and productive phase owing to the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees and the need to mitigate the effects of climate change. Research on long-lived woody perennials is extending our molecular knowledge of complex life histories and adaptations to the environment - enriching a field that has traditionally drawn biological inference from a few short-lived herbaceous species. © 2011 Macmillan Publishers Limited. All rights reserved. Source


Mikulincer M.,The Interdisciplinary Center | Shaver P.R.,University of California at Davis
World Psychiatry | Year: 2012

In recent years, attachment theory, which was originally formulated to describe and explain infant-parent emotional bonding, has been applied to the study of adolescent and adult romantic relationships and then to the study of psychological processes, such as interpersonal functioning, emotion regulation, coping with stress, and mental health. In this paper, we offer a brief overview of the attachment perspective on psychopathology. Following a brief account of attachment theory, we go on to explain how the study of individual differences in adult attachment intersects with the study of psychopathology. Specifically, we review research findings showing that attachment insecurity is a major contributor to mental disorders, and that the enhancement of attachment security can facilitate amelioration of psychopathology. Source


Pedersen N.C.,University of California at Davis
Veterinary Journal | Year: 2014

Feline infectious peritonitis (FIP) continues to be one of the most researched infectious diseases of cats. The relatively high mortality of FIP, especially for younger cats from catteries and shelters, should be reason enough to stimulate such intense interest. However, it is the complexity of the disease and the grudging manner in which it yields its secrets that most fascinate researchers. Feline leukemia virus infection was conquered in less than two decades and the mysteries of feline immunodeficiency virus were largely unraveled in several years. After a half century, FIP remains one of the last important infections of cats for which we have no single diagnostic test, no vaccine and no definitive explanations for how virus and host interact to cause disease. How can a ubiquitous and largely non-pathogenic enteric coronavirus transform into a highly lethal pathogen? What are the interactions between host and virus that determine both disease form (wet or dry) and outcome (death or resistance)? Why is it so difficult, and perhaps impossible, to develop a vaccine for FIP? What role do genetics play in disease susceptibility? This review will explore research conducted over the last 5years that attempts to answer these and other questions. Although much has been learned about FIP in the last 5years, the ultimate answers remain for yet more studies. © 2014 The Author. Source


Boundy-Mills K.,University of California at Davis
Journal of Industrial Microbiology and Biotechnology | Year: 2012

The importance of selecting optimal yeast strains for research or industrial applications is often underestimated. For example, utilizing a strain background that already provides the desired stress tolerance or nutrient utilization profile can eliminate costly strain optimization. Yeast culture collections can provide not only the yeast strains but also data and curator expertise to help narrow the search for the optimal strain. While some collections are known for a broad range of cultures and services, other "boutique" collections can provide a broader selection of strains of certain categories, a surprising amount of characterization data, and assistance in selecting strains. This article provides information on dozens of yeast collections of the world, profiles of selected yeast culture collections, and the services that they provide: e.g., strain preservation for patent or safe deposit purposes, species identification servi