Claremont, CA, United States
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Angielczyk K.D.,Integrative Research Center | Schmitz L.,Pitzer and Scripps Colleges
Proceedings of the Royal Society B: Biological Sciences | Year: 2014

Nocturnality is widespread among extant mammals and often considered the ancestral behavioural pattern for all mammals. However, mammals are nested within a larger clade, Synapsida, and non-mammalian synapsids comprise a rich phylogenetic, morphological and ecological diversity. Even though non-mammalian synapsids potentially could elucidate the early evolution of diel activity patterns and enrich the understanding of synapsid palaeobiology, data on their diel activity are currently unavailable. Using scleral ring and orbit dimensions, we demonstrate that nocturnal activity was not an innovation unique to mammals but a character that appeared much earlier in synapsid history, possibly several times independently. The 24 Carboniferous to Jurassic non-mammalian synapsid species in our sample featured eye morphologies consistent with all major diel activity patterns, with examples of nocturnality as old as the Late Carboniferous (ca 300 Ma). Carnivores such as Sphenacodon ferox and Dimetrodon milleri, but also the herbivorous cynodont Tritylodon longaevus were likely nocturnal, whereas most of the anomodont herbivores are reconstructed as diurnal. Recognizing the complexity of diel activity patterns in non-mammalian synapsids is an important step towards a more nuanced picture of the evolutionary history of behaviour in the synapsid clade. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Price S.A.,University of California at Davis | Schmitz L.,Pitzer and Scripps Colleges
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2016

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research.We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. © 2016 The Author(s) Published by the Royal Society. All rights reserved.

Robins C.R.,Pitzer and Scripps Colleges | Brock-Hon A.L.,University of Tennessee at Chattanooga | Buck B.J.,University of Nevada, Las Vegas
Soil Science Society of America Journal | Year: 2012

We use the very old, extant, Stage VI Mormon Mesa petrocalcic soil profile in southern Nevada to: (i) present a conceptual model summarizing known spatial and temporal relationships among authigenic calcite (or low-Mg calcite), palygorskite and/or sepiolite, and amorphous silica and (ii) adapt a second model to describe the occurrence of pedogenic barite and the effect of climate oscillations on soil mineralogy at Mormon Mesa. These conceptual models, one compiled from previous research, one built from new data in this study, directly address the importance of dust to soil genesis, especially the control of salt flux and high pH on Ba, Si, and Al mobility in alkaline soil solutions. Authigenesis of calcite and palygorskite/sepiolite creates positive feedbacks with soil solution chemistry that drives further mineralogical development. We explain the occurrence of pedogenic barite at Mormon Mesa based on higher Ba solubility and translocation into the soil profile with increased concentrations of Cl and Mg in soil solutions during interpluvial climates. Development of integrated, mineral development models illustrates individual system components and/or processes that should be targeted for future chemical, biological, geochronologic, or micromorphological study, and provides a basis for comparison of calcic soil genesis from disparate sites around the world. © Soil Science Society of America.

Tambara K.,University of Cambridge | Olsen J.-C.,Indiana University Kokomo | Hansen D.E.,Pitzer and Scripps Colleges | Pantos G.D.,University of Bath
Organic and Biomolecular Chemistry | Year: 2014

The mechanism and thermodynamic functions of the self-assembly of a family of covalently linked oligomeric naphthalenediimides (NDIs) were investigated through variable-temperature NMR and CD studies. The NDIs were shown to self-assemble into helical supramolecular nanotubes via an isodesmic polymerisation mechanism, and regardless of the oligomer length a surprising entropy-enthalpy compensation was observed. This journal is © The Royal Society of Chemistry.

In eukaryotes, abnormally circularized chromosomes, known as ‘rings,’ can be mitotically unstable. Some rings derived from a compound X-Y chromosome induce mitotic abnormalities during the embryonic cleavage divisions and early death in Drosophila melanogaster, but the underlying basis is poorly understood. We recently demonstrated that a large region of 359-bp satellite DNA, which normally resides on the X chromosome, prevents sister ring chroma-tids from segregating properly during these divisions. Cytogenetic comparisons among 3 different X-Y rings with varying levels of lethality showed that all 3 contain similar amounts of 359-bp DNA, but the repetitive sequences surrounding the 359-bp DNA differ in each case. This finding suggests that ring misbehavior results from novel heterochromatin position effects on the 359-bp satellite. The purpose of this view is to explore possible explanations for these effects with regard to heterochromatin formation and replication of repetitive sequences. Also discussed are similarities of this system to a satellite-based hybrid incompatibility and potential influences on genome evolution. © 2014 Landes Bioscience.

Friedman E.J.,University of California at Berkeley | Landsberg A.S.,Pitzer and Scripps Colleges
Chaos | Year: 2013

We show that in networks with a hierarchical architecture, critical dynamical behaviors can emerge even when the underlying dynamical processes are not critical. This finding provides explicit insight into current studies of the brain's neuronal network showing power-law avalanches in neural recordings, and provides a theoretical justification of recent numerical findings. Our analysis shows how the hierarchical organization of a network can itself lead to power-law distributions of avalanche sizes and durations, scaling laws between anomalous exponents, and universal functions-even in the absence of self-organized criticality or critical points. This hierarchy-induced phenomenon is independent of, though can potentially operate in conjunction with, standard dynamical mechanisms for generating power laws. © 2013 American Institute of Physics.

Brock-Hon A.L.,University of Tennessee at Chattanooga | Robins C.R.,Pitzer and Scripps Colleges | Buck B.J.,University of Nevada, Las Vegas
Geoderma | Year: 2012

Barite crystals are identified in stage VI petrocalcic horizons at Mormon Mesa, Nevada. Their presence is significant because barite is not typically associated with arid soil processes. Barite is identified through backscatter SEM/EDS as bright white crystals with EDS peaks of high Ba, S, and O. Barite crystals are euhedral, tabular to acicular crystals ranging in size from 1 to 50μm in length and 1-20μm in diameter, and as small (2-4μm) tabular-ovoid crystals. Forty-one percent of the barite in SEM images is associated with fibers of palygorskite and/or sepiolite. Barite crystals are also associated with linear voids, circular pores, and within micropores between fibers of silicate clays. The formation of barite at Mormon Mesa is attributed to: (i) The dissolution of Ba and SO 4 ions from detrital minerals and dust that are flushed into the soil profile and precipitate as barite; and/or (ii) Biomineralization of barite in micro-environments suitable for bacteria or other organisms within the petrocalcic horizon. © 2012 Elsevier B.V..

Chapman D.E.,Pitzer and Scripps Colleges | Steck J.K.,Pitzer and Scripps Colleges | Nerenberg P.S.,Pitzer and Scripps Colleges
Journal of Chemical Theory and Computation | Year: 2014

The quality of molecular dynamics (MD) simulations relies heavily on the accuracy of the underlying force field. In recent years, considerable effort has been put into developing more accurate dihedral angle potentials for MD force fields, but relatively little work has focused on the nonbonded parameters, many of which are two decades old. In this work, we assess the accuracy of protein-protein van der Waals interactions in the AMBER ff9x/ff12 force field. Across a test set of 44 neat organic liquids containing the moieties present in proteins, we find root-mean-square (RMS) errors of 1.26 kcal/mol in enthalpy of vaporization and 0.36 g/cm3 in liquid densities. We then optimize the van der Waals radii and well depths for all of the relevant atom types using these observables, which lowers the RMS errors in enthalpy of vaporization and liquid density of our validation set to 0.59 kcal/mol (53% reduction) and 0.019 g/cm3 (46% reduction), respectively. Limitations in our parameter optimization were evident for certain atom types, however, and we discuss the implications of these observations for future force field development. © 2013 American Chemical Society.

Wenzel A.G.,Pitzer and Scripps Colleges | Blake G.,Pitzer and Scripps Colleges | Vandervelde D.G.,California Institute of Technology | Grubbs R.H.,California Institute of Technology
Journal of the American Chemical Society | Year: 2011

The reaction of the phosphonium alkylidene [(H2IMes)RuCl 2=CHP(Cy)3)]+ BF4 - with propene, 1-butene, and 1-hexene at -45 ° affords various substituted, metathesis-active ruthenacycles. These metallacycles were found to equilibrate over extended reaction times in response to decreases in ethylene concentrations, which favored increased populations of α-monosubstituted and α,α′-disubstituted (both cis and trans) ruthenacycles. On an NMR time scale, rapid chemical exchange was found to preferentially occur between the β-hydrogens of the cis and trans stereoisomers prior to olefin exchange. Exchange on an NMR time scale was also observed between the α- and β-methylene groups of the monosubstituted ruthenacycle (H 2IMes)Cl2Ru(CHRCH2CH2) (R = CH 3, CH2CH3, (CH2)3CH 3). EXSY NMR experiments at -87 ° were used to determine the activation energies for both of these exchange processes. In addition, new methods have been developed for the direct preparation of metathesis-active ruthenacyclobutanes via the protonolysis of dichloro(1,3-bis(2,4,6- trimethylphenyl)-2-imidazolidinylidene)(benzylidene) bis(pyridine)ruthenium(II) and its 3-bromopyridine analogue. Using either trifluoroacetic acid or silica-bound toluenesulfonic acid as the proton source, the ethylene-derived ruthenacyclobutane (H2IMes)Cl2Ru(CH2CH 2CH2) was observed in up to 98% yield via NMR at -40 °. On the basis of these studies, mechanisms accounting for the positional and stereochemical exchange within ruthenacyclobutanes are proposed, as well as the implications of these dynamics toward olefin metathesis catalyst and reaction design are described. © 2011 American Chemical Society.

Liguori N.,Third University of Rome | Nerenberg P.S.,Pitzer and Scripps Colleges | Head-Gordon T.,University of California at Berkeley
Biophysical Journal | Year: 2013

Using a coarse-grained lipid and peptide model, we show that the free energy stabilization of amyloid-β in heterogeneous lipid membranes is predicted to have a dependence on asymmetric distributions of cholesterol compositions across the membrane leaflets. We find that a highly asymmetric cholesterol distribution that is depleted on the exofacial leaflet but enhanced on the cytofacial leaflet of the model lipid membrane thermodynamically favors membrane retention of a fully embedded Aβ peptide. However, in the case of cholesterol redistribution that increases concentration of cholesterol on the exofacial layer, typical of aging or Alzheimer's disease, the free energy favors peptide extrusion of the highly reactive N-terminus into the extracellular space that may be vulnerable to aggregation, oligomerization, or deleterious oxidative reactivity. © 2013 Biophysical Society.

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