Chicago Ridge, IL, United States
Chicago Ridge, IL, United States

Loyola University Chicago is a private Jesuit university located in Chicago, Illinois. It was founded by the Roman Catholic Society of Jesus in 1870 under the name of "St. Ignatius College", and has grown to be the largest Jesuit university in the United States with a total enrollment of 15,068 and over 150,000 alumni.Loyola University has six campuses throughout the Chicago metropolitan area, and it also has a permanent overseas campus in Rome, Italy and guest programs in Beijing, China and Ho Chi Minh City, Vietnam. Loyola has twelve undergraduate, graduate, and professional schools offering 71 undergraduate degrees, 85 master's degrees, 31 doctoral degrees, and 26 graduate-level certificate programs.The main campus, the Lake Shore Campus, is located in the Rogers Park and Edgewater neighborhoods of the City of Chicago, located along the shore of Lake Michigan. Loyola University Chicago's intercollegiate sports teams, commonly called the "Loyola Ramblers", compete in National Collegiate Athletic Association Division I and the Missouri Valley Conference. As of 2013, Loyola University is still the only Division I school in the State of Illinois to win a national championship in men's basketball. Wikipedia.


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Methods for modulating T-type calcium channel activity without directly targeting the T-type calcium channels are provided that include modulating kelch-like protein 1 (KLHL1) levels in a subject by providing a small hairpin RNA (shRNA) that targets a KLHL1 gene, and then administering the shRNA to the subject in an amount sufficient to modulate KLHL1 gene expression. The KLHL1 level directly effects current activity in T-type calcium channels and therefore modulation of KLHL1 gene expression indirectly modulates current activity in T-type calcium channels. The methods may be implemented with, for example, an shRNA molecule suitable for modulating a KLHL1 level in the subject which may be provided as a plasmid encoding the shRNA molecule or an adeno-associated virus vector encoding the shRNA molecule. Methods of identifying compounds that modulate current activity in T-type calcium channels by determining an effect of the compound on KLHL1 gene expression are also provided.


Campbell E.M.,Loyola University Chicago | Hope T.J.,Northwestern University
Nature Reviews Microbiology | Year: 2015

In a mature, infectious HIV-1 virion, the viral genome is housed within a conical capsid core made from the viral capsid (CA) protein. The CA protein and the structure into which it assembles facilitate virtually every step of infection through a series of interactions with multiple host cell factors. This Review describes our understanding of the interactions between the viral capsid core and several cellular factors that enable efficient HIV-1 genome replication, timely core disassembly, nuclear import and the integration of the viral genome into the genome of the target cell. We then discuss how elucidating these interactions can reveal new targets for therapeutic interactions against HIV-1. © 2015 Macmillan Publishers Limited. All rights reserved.


Gerding D.N.,Loyola University Chicago
Discovery Medicine | Year: 2013

We are in the midst of a resurgence of Clostridium difficile infection (CDI) in North America and Europe for which morbidity and mortality are higher than ever seen. C. difficile has risen in frequency to become the most common healthcare-associated infection pathogen, exceeding methicillin-resistant Staphylococcus aureus in many hospitals. Protection against CDI is thought to be mediated first by the normal bacterial microbiota, supplemented by an adaptive immune antibody response directed primarily at C. difficile toxins. Treatment of CDI is with antimicrobials that also further disrupt the protective bacterial microbiota leaving the patient susceptible to recurrent CDI. In addition, patients most susceptible to CDI, the advanced elderly, may already have a limited immune response and fail to increase their adaptive immune response with infection. The importance of both of these protective modalities has been demonstrated by 1) the success of fecal microbiota to restore "colonization resistance" for patients with multiple recurrences of CDI, and 2) the marked reduction in CDI recurrences with the use of intravenous monoclonal antibodies directed against toxin A and toxin B as an adjunct to antimicrobial treatment. Anti-toxin vaccines, passive monoclonal anti-toxin antibodies, and non-toxigenic C. difficile (to restore colonization resistance) are already undergoing patient clinical trials. The opportunity to prevent CDI is compelling and future research should focus on understanding the critical elements of the microbiota needed to restore colonization resistance and on development of novel immunologic strategies that include systemic and mucosal vaccines and passive immune modulators. © 2013, Discovery Medicine.


Wolfe A.J.,Loyola University Chicago
Current Opinion in Microbiology | Year: 2010

Recent reports support the long-standing hypothesis that acetyl phosphate, a physiologically relevant small molecule, can serve as a phosphoryl donor to a subset of two-component response regulators that regulate diverse cellular processes. Since acetyl phosphate is a central metabolite, this ability would link nutritional status to global signaling. This review will first introduce acetyl phosphate and its pathway. It will then summarize the most compelling evidence supporting the hypothesis and list predicted properties of an acetyl phosphate-sensitive pathway. Next, it will describe emerging evidence that acetyl phosphate and/or its pathway can influence diverse cellular processes across a broad spectrum of bacteria. Finally, the review will explore the possibility that other metabolites can function in a capacity similar to acetyl phosphate. © 2010 Elsevier Ltd. All rights reserved.


Marchese A.,Loyola University Chicago
Current Opinion in Cell Biology | Year: 2014

Chemokine receptors belong to the super family of G protein-coupled receptors (GPCRs). The cognate ligands for chemokine receptors are small circulating proteins known as chemokines. Upon binding to their cognate chemokines, receptors are rapidly desensitized, internalized onto early endosomes and sorted either into a recycling pathway or degradative pathway. Chemokine receptor trafficking is essential because it limits the magnitude and duration of signaling by removing receptors from the cell surface thereby limiting access to their ligands, but it also delivers bound chemokines to lysosomes for degradation. Receptor sorting into the recycling pathway contributes to resensitization of receptor signaling, whereas sorting into the degradative pathway leads to long-term attenuation of signaling. Recent studies have revealed some key information regarding the molecular determinants mediating chemokine receptor internalization and have shed light on the mechanisms dictating sorting into either the recycling or degradative pathways. Here I discuss our current understanding of the mechanisms mediating chemokine receptor trafficking with a focus primarily on recent findings for the chemokine receptor CXCR4. © 2013.


Grant
Agency: NSF | Branch: Standard Grant | Program: | Phase: ENVIRONMENTAL ENGINEERING | Award Amount: 600.00K | Year: 2016

Accumulation of man-made trash in the oceans has received much public attention. Human trash includes plastic, fishing debris, and metal, which have negative effects on marine resources. For example, some trash can be ingested by organisms including birds and turtles, and plastic can break down into small particles that have unique toxic properties. The study of the origins, movement, and consumption of trash in the ocean has provided information about ocean currents and food webs. Research by this investigator has shown that trash in rivers can reach similar densities as in the oceans. However, the sources, movements, and influences on biological systems of human trash in rivers are unknown, and are needed to develop efficient prevention strategies and policies. Also, studying the ecology of trash in rivers may reveal previously unexplored controls on ecosystem structure and function. This study will be conducted in Chicago- and Baltimore-area rivers, and include students from high school, undergraduate, and graduate levels. Trash removal will be used by student teachers to develop lessons for teaching the scientific method across grade levels.

This research will examine the ecosystem role of anthropogenic litter (AL) in 3 size classes by adapting fundamental tools used to measure communities of organisms and movement of organic matter. First, the role of large AL will be measured. Urban rivers typically have reduced channel complexity due to straightening and flood management. Large AL may act as an ?artificial reef,? providing habitat complexity and organic matter retention that is otherwise lacking, and thereby enhance biodiversity. Researchers will measure stream organism abundance at naturally occurring debris dams (i.e., wood) and at those generated by large AL. Next, this research will quantify interactions between AL and microbes. Bacteria, fungi, and algae carry out important biological activities in rivers, removing excess nutrients and providing food for insects and fish. Initial studies showed AL has unique microbial communities compared to natural surfaces. Experiments will test how microbes are affected by the structural and chemical properties of AL surfaces. Last, movement of intermediate-sized (e.g., shopping bags), and small AL (e.g., microplastic) will be examined. Initial research showed that AL in rivers is abundant and mobile, with some portion always moving downstream. Because AL attracts common toxic chemicals, its movement may be an overlooked pathway for delivery of toxins downstream and into food webs. This work will quantify inputs, outputs, and re-distribution of toxins on litter surfaces in urban streams.


Grant
Agency: NSF | Branch: Continuing grant | Program: | Phase: AISL | Award Amount: 366.47K | Year: 2015

Nationally, there is tremendous interest in enhancing participation in science, technology, engineering, and mathematics (STEM). Providing rich opportunities for engagement in science and engineering practices may be key to developing a much larger cadre of young people who grow up interested in and pursue future STEM education and career options. One particularly powerful way to engage children in exploration and playful experimentation may be through learning experiences that call for tinkering with real objects and tools to make and remake things. Tinkering is an important target for research and educational practice for at least two reasons: (1) tinkering experiences are frequently social, involving children interacting with educators and family members who can support STEM-relevant tinkering in various ways and (2) tinkering is more open-ended than many other kinds of building experiences (e.g., puzzles, making a model airplane), because it is the participants own unique questions and objectives that guide the activity. Thus, tinkering provides a highly accessible point of entry into early STEM learning for children and families from a variety of backgrounds, interests and levels of expertise. This Research-in-Service to Practice project is funded by the Advancing Informal STEM Learning (AISL) program which seeks to advance new approaches to, and evidence-based understanding of, the design and development of STEM learning in informal environments.

The project will take place in the Tinkering Lab exhibit at Chicago Childrens Museum. The research will investigate how reflective interactions between parents and children (ages 6-8) during tinkering activities ultimately impact child engagement in STEM. Design-based research (DBR) is well-suited to the iterative and contextually-rich process of tinkering. Using a DBR approach, researchers and museum facilitators will be trained to prompt variations of simple reflection strategies at different time points between family members as a way to strengthen childrens engagement with, and memory of these shared tinkering events. Through progressive refinement, each cycle of testing will lead to new hypotheses that can be tested in the subsequent round of observations. The operationalization of study constructs and their measurement will come organically from families activities in the Tinkering Lab and will be developed in consultation with members of the advisory board. Data collection strategies will include observation and interviews; a series of coding schemes will be used to make sense of the data. The research will result in theoretical and practical understanding of ways to enhance STEM engagement and learning by young children and their families through tinkering. A diverse group of at least 350 children and their families will be involved.

The project will provide much needed empirical results on how to promote STEM engagement and learning in informal science education settings. It will yield useful information and resources for informal science learning practitioners, parents, and other educators who look to advance STEM learning opportunities for children. This research will be conducted through a partnership among researchers at Loyola University of Chicago and Northwestern University and museum staff and educators at the Chicago Childrens Museum.


Grant
Agency: NSF | Branch: Standard Grant | Program: | Phase: PHYLOGENETIC SYSTEMATICS | Award Amount: 690.70K | Year: 2015

Islands are natural laboratories for studying the evolutionary and ecological processes of how species colonize and diversify in novel environments. The island of Madagascar is a biodiversity hotspot that is renowned for its distinctive avifauna -- an exceptional diversity of bird species found nowhere else. This project uses Madagascar as a model to address a fundamental question in biology: why some groups become much more diverse than others over time. The current bird fauna of Madagascar is the result of several independent colonizations from surrounding regions over historical time. Despite arriving in Madagascar millions of years ago, only half the native lineages have subsequently speciated within this large island. This project will focus on a comprehensive investigation of the poorly-studied bird diversity on Madagascar to determine what causes some groups to diversify while others fail to speciate. The study will produce a more accurate assessment of species diversity and diversification patterns, which is crucial for subsequent conservation measures in this highly threatened landscape. This project will promote international collaborations, education and training from high-school to postdoctoral stages, conservation policy, and public outreach activities.

With a strong collaboration of international scientists of diverse backgrounds and expertise, this project will examine all 43 endemic terrestrial avian lineages, including 14 independent radiations, using phylogenetic, biogeographic, and phenotypic data. This study has three main objectives. First, a robust foundation of systematic and biogeographic information for Malagasy avian lineages and their close relatives will be developed to provide more accurate assessments of species diversity within Madagascar, as well as insight into the timing and routes of colonizations. Second, analyses of how and why lineages change in ecology and morphology upon colonization of novel environments will be conducted. These analyses will include large-scale characterization of morphology, plumage, and climatic niche across Malagasy endemic species and their continental relatives to determine the importance of shared and clade-specific evolutionary responses to common environmental settings. Third, predictability of within-island speciation and adaptive radiation will be determined. The research will investigate the probability of radiation after colonization as a function of numerous predictors, including evolutionary lability of trophic morphology, environmental tolerance, and the intrinsic speciation potential of individual clades. This project is a novel approach towards a comprehensive analysis of a biota and has broad implications for understanding the disparity in species richness across the evolutionary tree of life.


Grant
Agency: NSF | Branch: Standard Grant | Program: | Phase: Molecular Biophysics | Award Amount: 640.00K | Year: 2016

ADP-glucose pyrophosphorylase is central to starch synthesis in plants and glycogen synthesis in bacteria and other organisms, serving as carbon storage polymers. It is a common biotechnology target and an informed understanding of its regulation has implications for starch/glycogen synthesis in a host of organisms. Allosteric control of ADP-glucose pyrophosphorylase activity is an important but poorly understood regulatory mechanism. Presently it is unclear how the enzyme is allosterically activated and how that activation signal is transmitted structurally within the enzyme. The goal of this project is to perform computational, structural and biochemical studies to understand and characterize the allosteric signals and the interaction of the allosteric effectors on ADP-glucose pyrophosphorylase activity in bacteria as a model for plants. The PIs predict the presence of a common structural element that works as a switch but also the presence of an alternative allosteric signal binding site. This project will also contribute to education by training undergraduate and graduate students, establish international collaborations, and foster participation of underrepresented minorities in research by supporting programs such as McNair-SROP. This project will also support an international course on protein science that includes elements of the research, providing a unique training opportunity for undergraduate and graduate students.

Plant starch and bacterial glycogen biosynthetic pathways provide models for the structure and evolution of allosteric regulatory functions of the enzyme ADP-glucose pyrophosphorylase. Despite the importance of these pathways, the allosteric mechanism that controls the activity of this enzyme is largely unknown. The project comprises computational, structural, and biochemical studies to understand and characterize the transmission of the allosteric signal and the interaction of the allosteric effectors in the ADP-glucose pyrophosphorylase family. It is predicted there is both a common structural element that works as a switch and an alternative allosteric signal guided by a secondary site. Three main research objectives will be pursued: 1) screen several enzyme forms from diverse branches of the phylogenetic tree for the presence of a dual allosteric mechanism; 2) obtain crystal structures of allosteric mutants (switched off) in several different conditions with different ligands to test the hypothesis that certain residues form a conserved allosteric switch in ADP-glucose pyrophosphorylases; and 3) perform computational studies (molecular dynamics, correlated movement analysis, and network pathway analysis) to predict the signaling pathways of activation from each putative allosteric site.


Grant
Agency: NSF | Branch: Standard Grant | Program: | Phase: APPLIED MATHEMATICS | Award Amount: 363.00K | Year: 2015

Transport problems involve the study of the movement of mass from one location to another. Optimal transport is the study of exactly how to do this so that the cost of transportation is the smallest it can be. This is a very broad field with many applications, from the planning of urban transportation networks to molecular transport. The present project considers several important generalizations of the classical optimal transport problem which have not been previously studied. For example, a natural question to consider is what happens if there are two or more entities transporting the same initial mass to another location, each having its own costs to minimize. This is the game theoretic version of the optimal transport problem. Another problem deals with time-dependent transportation costs. This considers various cases when moving objects is more or less expensive depending on the time of movement. Overtime payments or transport in congested periods fall into this category. Transport problems in which one seeks to minimize the worst possible costs (instead of some average cost) are also important in applications and are considered here. Since optimal transport arises in many economic, biological, engineering, and other scientific areas, the mathematical theory developed for the problems considered in this project could have a significant practical impact. In addition, the project will study several new mathematical models arising in image processing and in understanding the motion of frontal boundaries due to flame or plasma propagation.

The relaxed version of the optimal transport problem involves finding a measure, called a transport plan, that minimizes the integral of a given cost density, subject to the constraint that the transport plan has given marginals. This is a one-player transport problem. Several generalizations of this much studied problem will be considered in this project. For example, if there are two players, each with their own cost density and each choosing their own transport plan, then they are coupled through the cost densities and, more importantly, through the given marginals. Another generalization of the original problem is to consider cost densities that depend on time. When that happens, the transport plan and map will also depend on time. Yet another line of investigation is driven by issues in the emerging area of L-infinity optimal transport, where the cost to be minimized is represented as the essential supremum of a cost function rather than the integral of a cost density. Optimal transport differential equations for the transport maps in the game model should lead to generalized Monge-Ampere systems. Dynamic programming of the time-dependent and perhaps the game-theoretic transport problem should lead to Hamilton-Jacobi equations in measure spaces. Existence of a generalized Nash equilibrium in the non-zero-sum case will be established. Finally, several PDE models arising in the study of quasiconvex functions and in the theory of stochastic differential games will be analyzed. The techniques used to tackle the problems proposed in this project will involve nonlinear functional analysis, game theory, and nonlinear partial differential equations arising from dynamic programming, as well as the theory of viscosity solutions for first and second order partial differential equations and modern methods in the calculus of variations.

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