Digital Commons Network^™

Normal-Mode-Analysis-Guided Investigation Of Crucial Intersubunit Contacts In The Camp-Dependent Gating In Hcn Channels, Farzana Marni, Shengjun Wu, Gaurav M. Shah, Xin-Ping Xu, Amber R. Hackett, Changan Xie, Sabisha Shrestha, Lin Liu, Qinglian Liu, Lei Zhou

Physiology and Biophysics Publications and Presentations

Abstract

Protein structures define a complex network of atomic interactions in three dimensions. Direct visualization of the structure and analysis of the interaction potential energy are not straightforward approaches to pinpoint the atomic contacts that are crucial for protein function. We used the tetrameric hyperpolarization-activated cAMP-regulated (HCN) channel as a model system to study the intersubunit contacts in cAMP-dependent gating. To obtain a systematic survey of the contacts between each pair of residues, we used normal-mode analysis, a computational approach for studying protein dynamics, and constructed the covariance matrix for C-α atoms. The significant contacts revealed by covariance analysis …

Stateless Babies & Adoption Scams: A Bioethical Analysis Of International Commercial Surrogacy, Seema Mohapatra

Faculty Scholarship

Truth is often stranger than fiction, and nowhere is this more evident than when examining the real stories related to international commercial surrogacy that have occurred in the last few years. This Article utilizes these recent cases to analyze this industry using a bioethical lens. Bioethicists use stories effectively to demonstrate how theory and normative ideals apply to real world situations. By detailing examples of some of the unique scenarios that have arisen in far-flung cities of India, the United States, and the Ukraine, this Article highlights some of the bioethical dilemmas such stories raise. This Article examines these stories …

Lotteries And Public Policy In American Law, Stephen J. Leacock

Faculty Scholarship

No abstract provided.

Co-Cultures Of Pseudomonas Aeruginosa And Roseobacter Denitrificans Reveal Shifts In Gene Expression Levels Compared To Solo Cultures, Crystal A. Conway, Nwadiuto Esiobu, Jose V. Lopez

Marine & Environmental Sciences Faculty Articles

Consistent biosynthesis of desired secondary metabolites (SMs) from pure microbial cultures is often unreliable. In a proof-ofprinciple study to induce SM gene expression and production, we describe mixed “co-culturing” conditions and monitoring of messages via quantitative real-time PCR (qPCR). Gene expression of model bacterial strains (Pseudomonas aeruginosa PAO1 and Roseobacter denitrificans Och114) was analyzed in pure solo and mixed cocultures to infer the effects of interspecies interactions on gene expression in vitro, Two P. aeruginosa genes (PhzH coding for portions of the phenazine antibiotic pathway leading to pyocyanin (PCN) and the RhdA gene for thiosulfate: cyanide sulfurtransferase …

Characterizing And Determining The Extent Of Coral Reefs And Associated Resources In Southeast Florida Through The Acquisition Of High-Resolution Bathymetry And Benthic Habitat Mapping, Brian K. Walker, Amanda Costaregni, Ian Rodericks, Greg Lewis, Nick Gadbois

Marine & Environmental Sciences Faculty Reports

Effective marine resource management begins with knowing the distribution of resources within the region. Minimal data, and thus limited knowledge, exists about the reef resources of Martin County. The marine benthic habitats in Martin County need to be mapped to characterize and quantify the distribution of its coral and other benthic communities, therefore, the Florida Department of Environmental Protection – Coral Reef Conservation Program, FL Fish and Wildlife Research Institute and the National Coral Reef Institute at Nova Southeastern University have partnered to expand upon previous mapping efforts to identify and classify the benthic habitats in the southeast Florida region …

Bayesian Approach To Zero-Inflated Bivariate Ordered Probit Regression Model, With An Application To Tobacco Use, Shiferaw Gurmu, Getachew A. Dagne

Epidemiology and Biostatistics Faculty Publications

This paper presents a Bayesian analysis of bivariate ordered probit regression model with excess of zeros. Specifically, in the context of joint modeling of two ordered outcomes, we develop zero-inflated bivariate ordered probit model and carry out estimation using Markov Chain Monte Carlo techniques. Using household tobacco survey data with substantial proportion of zeros, we analyze the socioeconomic determinants of individual problem of smoking and chewing tobacco. In our illustration, we find strong evidence that accounting for excess zeros provides good fit to the data. The example shows that the use of a model that ignores zero-inflation masks differential effects …

The Construction Of Belief : Reflections On The Thought Of Mohammed Arkoun, Abdou Filali-Ansari, Aziz Esmail

Independent Volumes

Mohammed Arkoun was one of the most prominent and influential Arab intellectuals of his day. During a career spanning more than thirty years, he was revered as an outstanding research scholar, a bold critic of the theoretical tensions embedded within Islamic studies and an outspoken public figure, upholding political, social and cultural modernism.

This festschrift honours Mohammed Arkoun’s scholarship, bringing together the contributions of eleven distinguished scholars of history, religious studies and philosophy. It offers a comprehensive selection of critical engagements with Arkoun’s work, reflecting on his considerable influence on contemporary thinking about Islam and its ideological, philosophical and theological …

A Saving Grace - The Impact Of The Fostering Connections To Success And Increasing Adoptions Act On America's Older Foster Youth, May Shin

UC Law Journal of Race and Economic Justice

This note examines the struggles of youths who must leave state foster care systems (called "aging out" of foster care) upon turning eighteen years old. Thousands of young people age out of foster care systems each year. Foster care systems have traditionally abandoned children upon their eighteenth birthday, without providing aged-out youth real assistance in obtaining employment, health services, or basic shelter. Most commonly, these young adults do not have sufficient resources or support to allow them to transition into safe and stable lives. The majority of these older youths either get incarcerated, become homeless, or are forced to depend …

Medicine@Yale March 2012 Volume 8, Issue 1, Yale School Of Medicine Office Of Communications

Medicine@Yale - development newsletter

Medicine@Yale : advancing biomedical science, education and health care was a print and online newsletter which published news about academics, research and philanthropy for alumni, donors, faculty, students and the general public. It was initially published 6 times a year and then changed to a quarterly schedule. The first issue came out June/Jul. 2005. The final issue was published in May/June 2022, vol. 17, issue 1. Published by Yale School of Medicine, Office of Communications.

Review Of Storytelling Globalization: From The Chaco And Beyond, Jeremy M. Campbell

Arts & Sciences Faculty Publications

No abstract provided.

Flow Structure And Transport Characteristics Of Feeding And Exchange Currents Generated By Upside-Down Cassiopea Jellyfish, Arvind Santhanakrishnan, Makani Dollinger, Christina L. Hamlet, Sean Colin, Laura A. Miller

Arts & Sciences Faculty Publications

Quantifying the flows generated by the pulsations of jellyfish bells is crucial for understanding the mechanics and efficiency of their swimming and feeding. Recent experimental and theoretical work has focused on the dynamics of vortices in the wakes of swimming jellyfish with relatively simple oral arms and tentacles. The significance of bell pulsations for generating feeding currents through elaborate oral arms and the consequences for particle capture are not as well understood. To isolate the generation of feeding currents from swimming, the pulsing kinematics and fluid flow around the benthic jellyfish Cassiopea spp. were investigated using a combination of videography, …

Wisconsin's League Against Nuclear Dangers: The Power Of Informed Citizenship, Nancy Unger

History

Wisconsin's League Against Nuclear Dangers (LAND), a loose organization active in the 1970s and 1980s, was predominantly made up of white middle-aged and middle-class homemakers with minimal formal education in the sciences. The story of LAND is a powerful lesson in what people can accomplish when they take their rights as citizens seriously and commit themselves to learning a complex subject in depth in order to be knowledgeable and persuasive.

Annual Report, 2011-2012, University Of Arkansas, Fayetteville. College Of Education And Health Professions

College of Education and Health Professions Annual Reports

Beginning in 2004/2005- issued in online format only

Export Controls And Economic Sanctions, John Boscariol, Steven Brotherton, Matthew A. Goldstein, David T. Hardin, Valentin A. Povarchuk, Nicholas M. Roegner

The International Lawyer

No abstract provided.

West Virginia And Regional History Collection Newsletter Twenty-Year Index, Volume 1-Volume 20, Spring 1985-Spring 2005, Anna M. Schein

West Virginia & Regional History Center Newsletters

Index of articles and photographs appearing in the WVRHC Newsletter over a 20 year period.

Replicating Adenovirus-Simian Immunodeficiency Virus (Siv) Vectors Efficiently Prime Siv-Specific Systemic And Mucosal Immune Responses By Targeting Myeloid Dendritic Cells And Persisting In Rectal Macrophages, Regardless Of Immunization Route, L. Jean Patterson, Seraphin Kuate, Mara Daltabuit-Test, Qingsheng Li, Peng Xiao, Katherine Mckinnon, Janet Dipasquale, Anthony Cristillo, David Venzon, Ashley Haase, Marjorie Robert-Guroff

United States Public Health Resources

Although priming with replicating adenovirus type 5 host range mutant (Ad5hr)-human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) recombinants, followed by HIV/SIV envelope boosting, has proven highly immunogenic, resulting in protection from SIV/simian-human immunodeficiency virus (SHIV) challenges, Ad5hr recombinant distribution, replication, and persistence have not been examined comprehensively in nonhuman primates. We utilized Ad5hr-green fluorescent protein and Ad5hr-SIV recombinants to track biodistribution and immunogenicity following mucosal priming of rhesus macaques by the intranasal/intratracheal, sublingual, vaginal, or rectal route. Ad recombinants administered by all routes initially targeted macrophages in bronchoalveolar lavage (BAL) fluid and rectal tissue, later extending to myeloid dendritic cells …

Nitrogen Loss From Soil Through Anaerobic Ammonium Oxidation Coupled To Iron Reduction, Wendy H. Yang, Karrie A. Weber, Whendee L. Silver

Department of Earth and Atmospheric Sciences: Faculty Publications

The oxidation of ammonium is a key step in the nitrogen cycle, regulating the production of nitrate, nitrous oxide and dinitrogen. In marine and freshwater ecosystems, anaerobic ammonium oxidation coupled to nitrite reduction, termed anammox, accounts for up to 67% of dinitrogen production. Dinitrogen production through anaerobic ammonium oxidation has not been observed in terrestrial ecosystems, but the anaerobic oxidation of ammonium to nitrite has been observed in wetland soils under iron-reducing conditions. Here, we incubate tropical upland soil slurries with isotopically labelled ammonium and iron(iii) to assess the potential for anaerobic ammonium oxidation coupled to iron(iii) reduction, otherwise known …

Ecological Regime Shifts In Lake Kälksjön, Sweden, In Response To Abrupt Climate Change Around The 8.2 Ka Cooling Event, Linda Randsalu-Wendrup, Daniel J. Conley, Jacob Carstensen, Ian Snowball, Catherine Jessen, Sherilyn C. Fritz

Department of Earth and Atmospheric Sciences: Faculty Publications

A detailed diatom record from Lake Kälksjön, westcentral Sweden, reveals two periods of abrupt ecological change correlative with the 8.2 ka cooling event. Using a combination of abrupt step changes and piece-wise linear regressions, the diatom data were analyzed for change points over time, and two sudden and large events that are described as regime shifts were detected. During the first event at c. 8040 cal. y BP, a doubling in diatom biomass took place over 5–10 years. This increase in primary productivity can be connected to an erosion event in the catchment that resulted in an abrupt increase in …

Effects Of Glycerol And Creatine Hyperhydration On Doping-Relevant Blood Parameters, Thelma P. Polyviou, Chris Easton, Lukas Beis, Dalia Malkova, Pantazis Takas, Cathertine Hambly, John R. Speakman, Karsten Koehler, Yannis P. Pitsiladis

Department of Nutrition and Health Sciences: Faculty Publications

Glycerol is prohibited as an ergogenic aid by the World Anti-Doping Agency (WADA) due to the potential for its plasma expansion properties to have masking effects. However, the scientific basis of the inclusion of Gly as a “masking agent” remains inconclusive. The purpose of this study was to determine the effects of a hyperhydrating supplement containing Gly on doping-relevant blood parameters. Nine trained males ingested a hyperhydrating mixture twice per day for 7 days containing 1.0 g·kg⁻¹ body mass (BM) of Gly, 10.0 g of creatine and 75.0 g of glucose. Blood samples were collected and total hemoglobin (Hb) …

Sample Preparation Of Mycobacterium Tuberculosis Extracts For Nuclear Magnetic Resonance Metabolomic Studies, Denise Zinniel, Robert J. Fenton, Steven M. Halouska, Robert Powers, Raul G. Barletta

Robert Powers Publications

Mycobacterium tuberculosis is a major cause of mortality in human beings on a global scale. The emergence of both multi- (MDR) and extensively-(XDR) drug-resistant strains threatens to derail current disease control efforts. Thus, there is an urgent need to develop drugs and vaccines that are more effective than those currently available. The genome of M. tuberculosis has been known for more than 10 years, yet there are important gaps in our knowledge of gene function and essentiality. Many studies have since used gene expression analysis at both the transcriptomic and proteomic levels to determine the effects of drugs, oxidants, and …

Trans-10, Cis-12 Conjugated Linoleic Acid Decreases De Novo Lipid Synthesis In Human Adipocytes, Thomas Obsen, Nils J. Faergeman, Soonkyu Chung, Kristina Martinez, Semone Gobern, Olivier Loreau, Martin Wabitsch, Susanne Mandrup, Michael Mcintosh

Department of Nutrition and Health Sciences: Faculty Publications

Conjugated linoleic acid (CLA) reduces adiposity in vivo. However, mechanisms mediating these changes are unclear. Therefore, we treated cultures of human adipocytes with trans-10, cis-12 (10,12) CLA, cis-9, trans-11 (9,11) CLA, or other trans fatty acids (FA) and measured indices of lipid metabolism. The lipid-lowering effects of 10,12 CLA were unique, as other trans FA did not reduce TG content to the same extent. Using low levels of [14C]-CLA isomers, it was shown that both isomers were readily incorporated into acylglycerols and phospholipids, albeit at lower levels than [14C]-oleic or [14C]-linoleic acids. When using [14C]-acetic acid and [14C]-pyruvic acid as …

Two Approaches To Teaching Young Children Science Concepts, Vocabulary, And Scientific Problem-Solving Skills, Soo-Young Hong, Karen E. Diamond

Nebraska Center for Research on Children, Youth, Families, and Schools: Faculty Publications

The present study examined the efficacy of two different approaches to teaching designed to facilitate children’s learning about science concepts and vocabulary related to objects’ floating and sinking and scientific problem-solving skills: responsive teaching (RT) and the combination of responsive teaching and explicit instruction (RT + EI). Participants included 104 children (51 boys) aged four to five years.Small groups of children were randomly assigned to one of the two intervention groups (RT, RT + EI) or to a control group. Responsive teaching (RT) reflects a common approach to teaching young children, and the combination approach (RT + EI) includes explicit …

Dissecting Mammalian Replication-Independent Chromatin Assembly — Biochemical And Structural Studies On The H3.3-Specific Histone Chaperones Hira And Daxx, Simon Elsässer

Student Theses and Dissertations

Histones are architectural proteins that wrap approximately two turns of DNA around their octameric core structure, constituting the fundamental packaging unit of eukaryotic chromatin — the nucleosome. Beyond their structural role, they regulate virtually all processes that act on or depend on DNA, such as replication, gene expression and maintenance of centromeres and telomeres. Despite the high conservation of the four core histones, H3, H4, H2A and H2B, throughout all eukaryotes, histone variants have emerged with variable degree of divergence from their canonical counterparts. These variants are thought to expand the regulatory repertoire of chromatin. The histone replacement variant H3.3 …

Genetic Variation In Neurotransmitter Receptors Generates Behavioral Diversity, Andres Bendesky

Student Theses and Dissertations

Variation in behavior among individuals is both remarkable and of great significance to society. People differ in locomotor skills, in sleep patterns, in their willingness to take risks, and in how they relate to other people. Whereas diversity enriches society, extreme behavioral deviations can be pathological, so it is important to identify the causes of behavioral variability. It is clear that both the environment and genetics contribute to behavioral diversity in all animals, but the nature of the specific genes involved is only beginning to emerge. The nematode worm Caenorhabditis elegans is a good animal model to study the genetic …

Efforts Toward Production Of Novel Natural Products From Uncultured Soil Microbes, Jacob Joseph Banik

Student Theses and Dissertations

The isolation of small molecule natural products from bacteria has led to the identification of many of the antibiotics currently in use today. Within the last 25 years, in fact, natural products (and their derivatives) account for almost three quarters of all antibiotic discoveries (Newman and Cragg). The discovery of novel natural product antibiotics, however, has witnessed a significant drop in numbers over this time period, suggesting that new sources of small molecules may be necessary to keep up with the need for new antibacterial compounds (Newman and Cragg). Due to the emergence of bacteria resistant to commonly used antibiotics, …

Analysis Of Behavior In Populations Of Swimming Microbes, David Jordan

Student Theses and Dissertations

This work describes our work developing an experimental biological system to study patterns of behavioral variability. We selected motility as the behavior of interest because it is common throughout biology and can be recorded and analyzed relatively easily. We chose to work with a microbe, Tetrahymena thermophila, as a model organism for these studies; it is easy to grow in the laboratory in controlled conditions, has a relatively short generation time, and is large enough to for its motions to be easily imaged. To achieve the imaging, we developed a set of low cost digital video microscopes. Concurrently, we wrote …

Phds, Stress, And Starvation: The Identification Of A New Rpd3 Deacetylase Complex Involved In The Yeast Oxidative Stress And Metabolism Pathways, Lindsey A. Baker

Student Theses and Dissertations

The cellular pathways that govern survival in the face of diverse stresses rely on gene expression changes as one mechanism to respond to or protect against internal and external threats. Because eukaryotic DNA is packaged into chromatin, these gene expression changes depend on the targeting of regulatory proteins to specific regions of the genome to alter chromatin structure, promoting or repressing transcription. One protein domain involved in targeting chromatin regulators is the plant homeodomain, or PHD finger, a module that preferentially interacts with either methylated or unmethylated lysines on histones, and has important functions in human health. Despite recent advances …

Develoment And Application Of Chemical Strategies To Study Protein Fatty-Acylation In Eukaryotes, Mingzi Zhang

Student Theses and Dissertations

Reversible S-palmitoylation confers spatiotemporal control of protein function by modulating protein stability, trafficking and activity as well as protein-protein and membrane-protein associations. While it is evident that palmitoylation is regulated in vivo, mechanisms that mediate cellular stimuli-driven changes of the lipid modification are not understood. Furthermore, the requirement for substrate specificity among the highly redundant palmitoyl acyltransferases (PATs) remains unresolved. To study the regulation of PATs and palmitoylomes, I developed bioorthogonal chemical strategies for improved analysis of dynamic palmitoylation in mammalian cells. I showed that alkyne-functionalized fatty acids, in conjunction with azido-fluorophores, provide the most sensitive detection of acylated proteins …

Chemical Reporters For Investigating Lipidated Proteins At The Host-Pathogen Interface, Guillaume Charron

Student Theses and Dissertations

Lipidation of proteins regulates many cellular processes such as signaling transduction and membrane sorting by modulating protein localization and proteinprotein interactions. As such, defects in protein lipidation can render host cells more susceptible to microbial infection and are also associated with a variety of human diseases ranging from cancer to neurological disorders. Moreover, viral and bacterial pathogens can exploit and modulate the host lipidation machinery to enhance infection. Robust biochemical methods for characterizing lipidated proteins are therefore important for understanding fundamental physiology and disease mechanisms. In this thesis, I report the development of alkyne-lipid chemical reporters that afford more sensitive …

Protein Phosphatase 1 At The Kinetochore Regulates Chromosome Segregation, Jessica Scott Rosenberg

Student Theses and Dissertations

Two regulatory mechanisms exist to ensure proper chromosome segregation in mitosis. First, improper kinetochore-microtubule attachments are destabilized through the error correction machinery. Second, the spindle assembly checkpoint (SAC) delays anaphase onset until all kinetochores have achieved bioriented microtubule attachments. Both of these mechanisms are mediated by several centromeric and kinetochore kinases, including Aurora B. Protein Phosphatase 1 (PP1) plays a counteracting role to Aurora B to stabilize kinetochore-microtubule attachments and silence the SAC. The regulation of PP1 to modulate these functions, however, remains enigmatic. Using the biochemical tools available in the Xenopus egg extract system, I show here that PP1 …