Digital Commons Network^™

Sex-Differences In Adiponectin Levels And Body Fat Distribution: Longitudinal Observations In Afro-Jamaicans, Michael S. Boyne, Nadia R. Bennett, Richard S. Cooper, Tamika Y. Royal-Thomas, Franklyn I. Bennett, Amy Luke, Rainford J. Wilks, Terrence E. Forrester

Faculty Publications

We longitudinally explored the relationship of body size and adiponectin levels in 393 community-dwelling Afro-Jamaicans. Adiponectin levels were greater in women, increased with age and declined with abdominal adiposity. Multivariate regression analyses suggest that subcutaneous fat in women may contribute significantly to the variance in their adiponectin levels. © 2010 Elsevier Ireland Ltd.

Behavioral Flexibility And Species Invasions: The Adaptive Flexibility Hypothesis, T. F. Wright, J. R. Eberhard, E. A. Hobson, M. L. Avery, M. A. Russello

Faculty Publications

Behavioral flexibility is an important adaptive response to changing environments for many animal species. Such plasticity may also promote the invasion of novel habitats by introduced species by providing them with the ability to expand or change their ecological niche, a longstanding idea with recent empirical support. At the individual level, flexibility may arise through innovation, in which an individual invents a new behavior, or through social learning, in which an individual adopts a behavior used by others. There is increasing evidence that the adaptive value of these two modes of learning, and the overall expression of behavioral flexibility, may …

Effects Of Hurricane Katrina And Salvage Logging On Bachman's Sparrow, Matthew E. Brooks, Philip C. Stouffer

Faculty Publications

In the southeastern U. S., longleaf pine savannas, important habitat for grassland birds, are subject to hurricanes and subsequent management. The intensity of tropical storms is predicted to increase with climate change, heightening the importance of understanding the effects of storm disturbance and salvage logging on species of concern such as Bachman's Sparrow (Peucaea aestivalis), a pine-savanna specialist. To determine how Bachman's Sparrow occupancy varies with the age and salvage history of pine stands, and to identify the vegetation and post-hurricane habitat features influencing stand occupancy, we surveyed Bachman's Sparrows in Mississippi savannas affected by Hurricane Katrina. Our point counts …

Structures Of Human Thymidylate Synthase R163k With Dump, Fdump And Glutathione Show Asymmetric Ligand Binding, Lydia M. Gibson, Lesa R. Celeste, Leslie L. Lovelace, Lukasz Lebioda

Faculty Publications

Thymidylate synthase (TS) is a well validated target in cancer chemotherapy. Here, a new crystal form of the R163K variant of human TS (hTS) with five subunits per asymmetric part of the unit cell, all with loop 181-197 in the active conformation, is reported. This form allows binding studies by soaking crystals in artificial mother liquors containing ligands that bind in the active site. Using this approach, crystal structures of hTS complexes with FdUMP and dUMP were obtained, indicating that this form should facilitate high-throughput analysis of hTS complexes with drug candidates. Crystal soaking experiments using oxidized glutathione revealed that …

More Collaboration - More Power In Combating Ill Health, Ilkka Vuori, Steven N. Blair, Fiona C. Bull, Peter T. Katzmarzyk

Faculty Publications

This symposium highlighted the position of physical activity as one of the most important factors causally related to common non-communicable diseases (NCDs), and discussed the need for including physical activity in comprehensive prevention strategies and policies to combat the major NCDs. Lifestyle factors such as smoking, physical inactivity, and obesity are all major risk factors for ischemic heart disease, cerebrovascular disease, and several cancers, and physical inactivity globally ranks as the fourth leading risk factor for mortality. Despite the solid evidence that physical activity is related to several NCDs, stronger advocacy actions are required because physical activity is not viewed …

The Mathematics Of Animal Behavior: An Interdisciplinary Dialogue, Shandelle M. Henson, James L. Hayward

Faculty Publications

No abstract provided.

Cognitive Impact Of Genetic Variation Of The Serotonin Transporter In Primates Is Associated With Differences In Brain Morphology Rather Than Serotonin Neurotransmission, Hank P. Jedema, Peter J. Gianaros, Phillip J. Greer, Dustin D. Kerr, Shijing Liu, James Dee Higley, Stephen J. Suomi, Adam S. Olsen, Jessica N. Porter, Brian J. Lopresti, Ahmad R. Hariri, Charles W. Bradberry

Faculty Publications

A powerful convergence of genetics, neuroimaging and epidemiological research has identified biological pathways mediating individual differences in complex behavioral processes and related risk for disease. Orthologous genetic variation in non-human primates represents a unique opportunity to characterize the detailed molecular and cellular mechanisms which bias behaviorally- and clinically-relevant brain function. We report that a rhesus macaque orthologue of a common polymorphism of the serotonin transporter gene (rh5-HTTLPR) has strikingly similar effects on behavior and brain morphology to those in humans. Specifically, the rh5- HTTLPR Short allele broadly impacts cognitive choice behavior and brain morphology without observably affecting 5-HT transporter or …

A Map Of Human Genome Variation From Population-Scale Sequencing, David L. Altshuler, Richard M. Durbin, Gonçalo R. Abecasis, David R. Bentley, Aravinda Chakravarti, Andrew G. Clark, Francis S. Collins, Francisco M. De La Vega, Peter Donnelly, Michael Egholm, Paul Flicek, Stacey B. Gabriel, Richard A. Gibbs, Bartha M. Knoppers, Eric S. Lander, Hans Lehrach, Elaine R. Mardis, Gil A. Mcvean, Debbie A. Nickerson, Leena Peltonen, Alan J. Schafer, Stephen T. Sherry, Jun Wang, Richard K. Wilson, David Deiros, Mike Metzker, Donna Muzny, Jeff Reid, David Wheeler, Shenzhen Jun Wang, Jingxiang Li, Min Jian, Guoqing Li, Ruiqiang Li

Faculty Publications

The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and …

Identification And Optimization Of Classifier Genes From Multi-Class Earthworm Microarray Dataset, Ying Li, Nan Wang, Chaoyang Zhang, Ping Gong

Faculty Publications

Monitoring, assessment and prediction of environmental risks that chemicals pose demand rapid and accurate diagnostic assays. A variety of toxicological effects have been associated with explosive compounds TNT and RDX. One important goal of microarray experiments is to discover novel biomarkers for toxicity evaluation. We have developed an earthworm microarray containing 15,208 unique oligo probes and have used it to profile gene expression in 248 earthworms exposed to TNT, RDX or neither. We assembled a new machine learning pipeline consisting of several well-established feature filtering/selection and classification techniques to analyze the 248-array dataset in order to construct classifier models that …

Dated Molecular Phylogenies Indicate A Miocene Origin For Arabidopsis Thaliana, Mark A. Beilstein, Nathalie S. Nagalingum, Mark D. Clements, Steven R. Manchester, Sarah Mathews

Faculty Publications

Dated molecular phylogenies are the basis for understanding species diversity and for linking changes in rates of diversification with historical events such as restructuring in developmental pathways, genome doubling, or dispersal onto a new continent. Valid fossil calibration points are essential to the accurate estimation of divergence dates, but for many groups of flowering plants fossil evidence is unavailable or limited. Arabidopsis thaliana, the primary genetic model in plant biology and the first plant to have its entire genome sequenced, belongs to one such group, the plant family Brassicaceae. Thus, the timing of A. thaliana evolution and the history of …

Comprehensive Structural And Functional Characterization Of The Human Kinome By Protein Structure Modeling And Ligand Virtual Screening, Michal Brylinski, Jeffrey Skolnick

Faculty Publications

The growing interest in the identification of kinase inhibitors, promising therapeutics in the treatment of many diseases, has created a demand for the structural characterization of the entire human kinome. At the outset of the drug development process, the lead-finding stage, approaches that enrich the screening library with bioactive compounds are needed. Here, protein structure based methods can play an important role, but despite structural genomics efforts, it is unlikely that the three-dimensional structures of the entire kinome will be available soon. Therefore, at the proteome level, structure-based approaches must rely on predicted models, with a key issue being their …

The Enigmatic Ichnofossil Tisoa Siphonalis And Widespread Authigenic Seep Carbonate Formation During The Late Pliensbachian In Southern France, B. Van De Schootbrugge, D. Harazim, K. Sorichter, W. Oschmann, J. Fiebig, W. Püttmann, M. Peinl, F. Zanella, B. M.A. Teichert, J. Hoffmann, A. Stadnitskaia, Y. Rosenthal

Faculty Publications

Tubular carbonate concretions of up to 1 m in length and perpendicular to bedding, occur abundantly in the Upper Pliensbachian (upper Amaltheus margaritatus Zone, Gibbosus Subzone) in outcrops (Fontaneilles section) in the vicinity of Riviére-sûr-Tarn, southern France. Stable isotope analyses of these concretions show negative δ13C values that decrease from the rim to the center from -18.8‰ to -25.7‰ (V-PDB), but normal marine δ18O values (-1.8‰). Carbon isotope analyses of Late Pliensbachian bulk carbonate (matrix) samples from the Fontaneilles section show clearly decreasing C-isotope values across the A. margaritatus Zone, from +1‰ to -3‰ (V-PDB). Isotope analyses of coeval belemnite …

Characterization Of Subsurface Polycyclic Aromatic Hydrocarbons At The Deepwater Horizon Site, Arne Diercks, Raymond C. Highsmith, Vernon L. Asper, Dongjoo Joung, Zhengzhen Zhou, Laodong Guo, Alan M. Shiller, Andreas P. Teske, Norman Guinasso, Terry L. Wade, Steven E. Lohrenz

Faculty Publications

Here, we report the initial observations of distributions of polycyclic aromatic hydrocarbons (PAH) in subsurface waters near the Deepwater Horizon oil well site (also referred to as the Macondo, Mississippi Canyon Block 252 or MC252 well). Profiles of in situ fluorescence and beam attenuation conducted during 9-16 May 2010 were characterized by distinct peaks at depths greater than 1000 m, with highest intensities close to the wellhead and decreasing intensities with increasing distance from the wellhead. Gas chromatography/mass spectrometry (GC/MS) analyses of water samples coinciding with the deep fluorescence and beam attenuation anomalies confirmed the presence of polycyclic aromatic hydrocarbons …

The Sll0606 Protein Is Required For Photosystem Ii Assembly/Stability In The Cyanobacterium Synechocystis Sp. Pcc 6803, Shulu Zhang, Laurie K. Frankel, Terry M. Bricker

Faculty Publications

An insertional transposon mutation in the sll0606 gene was found to lead to a loss of photoautotrophy but not photoheterotrophy in the cyanobacterium Synechocystis sp. PCC 6803. Complementation analysis of this mutant (Tsll0606) indicated that an intact sll0606 gene could fully restore photoautotrophic growth. Gene organization in the vicinity of sll0606 indicates that it is not contained in an operon. No electron transport activity was detected in Tsll0606 using water as an electron donor and 2,6-dichlorobenzoquinone as an electron acceptor, indicating that Photosystem II (PS II) was defective. Electron transport activity using dichlorophenol indolephenol plus ascorbate as an electron donor …

The Effect Of Typhoon On Particulate Organic Carbon Flux In The Southern East China Sea, C. C. Hung, G. C. Gong, W. C. Chou, C. C. Chung, M. A. Lee, Y. Chang, H. Y. Chen, S. J. Huang, Y. Yang, W. R. Yang, W. C. Chung, W. C. Li, E. Laws

Faculty Publications

Severe tropical storms play an important role in triggering phytoplankton blooms, but the extent to which such storms influence biogenic carbon flux from the euphotic zone is unclear. In 2008, typhoon Fengwong provided a unique opportunity to study the in situ biological responses including phytoplankton blooms and particulate organic carbon fluxes associated with a severe storm in the southern East China Sea (SECS). After passage of the typhoon, the sea surface temperature (SST) in the SECS was markedly cooler (∼25 to 26 °C) than before typhoon passage (∼28 to 29 °C). The POC flux 5 days after passage of the …

Seasonal Variability In Air-Sea Fluxes Of Co2 In A River-Influenced Coastal Margin, Steven E. Lohrenz, Wei-Jun Cai, Fengwei Cai, Xiaogang Chen, Merritt Tuel

Faculty Publications

Recent studies in the northern Gulf of Mexico and elsewhere have demonstrated that enhanced biological production in large river plumes may contribute to a net surface influx of atmospheric CO2. However, large rivers also deliver significant amounts of terrestrial carbon into continental margin waters; hence, the potential for large and variable signals in carbon flux exist in these regions. Here, we used a combination of satellite and ship-based observations to examine variability in surface pCO(2) and air-sea flux of carbon dioxide in relation to variations in river discharge and seasonal environmental conditions. Underway surface pCO(2) showed large seasonal differences based …

Bedrock Erosion By Root Fracture And Tree Throw: A Coupled Biogeomorphic Model To Explore The Humped Soil Production Function And The Persistence Of Hillslope Soils, Emmanuel Gabet, Simon Mudd

Faculty Publications

In 1877, G. K. Gilbert reasoned that bedrock erosion is maximized under an intermediate soil thickness and declines as soils become thinner or thicker. Subsequent analyses of this “humped” functional relationship proposed that thin soils are unstable and that perturbations in soil thickness would lead to runaway thinning or thickening of the soil. To explore this issue, we developed a numerical model that simulates the physical weathering of bedrock by root fracture and tree throw. The coupled biogeomorphic model combines data on conifer population dynamics, rootwad volumes, tree throw frequency, and soil creep from the Pacific Northwest (USA). Although not …

Quail Genomics: A Knowledgebase For Northern Bobwhite, Arun Rawat, Kurt A. Gust, Mohamed O. Elasri, Edward J. Perkins

Faculty Publications

Background

The Quail Genomics knowledgebase (http://www.quailgenomics.info) has been initiated to share and develop functional genomic data for Northern bobwhite (Colinus virginianus). This web-based platform has been designed to allow researchers to perform analysis and curate genomic information for this non-model species that has little supporting information in GenBank.

Description

A multi-tissue, normalized cDNA library generated for Northern bobwhite was sequenced using 454 Life Sciences next generation sequencing. The Quail Genomics knowledgebase represents the 478,142 raw ESTs generated from the sequencing effort in addition to assembled nucleotide and protein sequences including 21,980 unigenes annotated with meta-data. A …

Time Lagged Information Theoretic Approaches To The Reverse Engineering Of Gene Regulatory Networks, Vijender Chaitankar, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng, Chaoyang Zhang

Faculty Publications

Background: A number of models and algorithms have been proposed in the past for gene regulatory network (GRN) inference; however, none of them address the effects of the size of time-series microarray expression data in terms of the number of time-points. In this paper, we study this problem by analyzing the behaviour of three algorithms based on information theory and dynamic Bayesian network (DBN) models. These algorithms were implemented on different sizes of data generated by synthetic networks. Experiments show that the inference accuracy of these algorithms reaches a saturation point after a specific data size brought about by …

Dynamics Of Protofibril Elongation And Association Involved In Aβ42 Peptide Aggregation In Alzheimer's Disease, Preetam Ghosh, Amit Kumar, Bhaswati Datta, Vijayaraghavan Rangachari

Faculty Publications

Background: The aggregates of a protein called, ‘Aβ’ found in brains of Alzheimer’s patients are strongly believed to be the cause for neuronal death and cognitive decline. Among the different forms of Aβ aggregates, smaller aggregates called ‘soluble oligomers’ are increasingly believed to be the primary neurotoxic species responsible for early synaptic dysfunction. Since it is well known that the Aβ aggregation is a nucleation dependant process, it is widely believed that the toxic oligomers are intermediates to fibril formation, or what we call the ‘on-pathway’ products. Modeling of Aβ aggregation has been of intense investigation during the last …

Multiple Ca2+-Dependent Mechanisms Regulate L-Type Ca 2+ Current In Retinal Amacrine Cells, Merve Tekmen, Evanna Gleason

Faculty Publications

Understanding the regulation of L-type voltage-gated Ca2+ current is an important component of elucidating the signaling capabilities of retinal amacrine cells. Here we ask how the cytosolic Ca2+ environment and the balance of Ca2+-dependent effectors shape native L-type Ca2+ channel function in these cells. To achieve this, whole cell voltage clamp recordings were made from cultured amacrine cells under conditions that address the contribution of mitochondrial Ca2+ uptake (MCU), Ca2+/calmodulin (CaM)-dependent channel inactivation (CDI), protein kinase A (PKA), and Ca2+-induced Ca2+ release (CICR). Under control conditions, repeated activation of the L-type channels produces a progressive enhancement of the current. Inhibition …

Hras1 And Lass1 With Apoe Are Associated With Human Longevity And Healthy Aging, S. Michal Jazwinski, Sangkyu Kim, Jianliang Dai, Li Li, Xiuhua Bi, James C. Jiang, Jonathan Arnold, Mark A. Batzer, Jerilyn A. Walker, David A. Welsh, Christina M. Lefante, Julia Volaufova, Leann Myers, L. Joseph Su, Dorothy B. Hausman, Michael V. Miceli, Eric Ravussin, Leonard W. Poon, Katie E. Cherry, Michael A. Welsch

Faculty Publications

The search for longevity-determining genes in human has largely neglected the operation of genetic interactions. We have identified a novel combination of common variants of three genes that has a marked association with human lifespan and healthy aging. Subjects were recruited and stratified according to their genetically inferred ethnic affiliation to account for population structure. Haplotype analysis was performed in three candidate genes, and the haplotype combinations were tested for association with exceptional longevity. An HRAS1 haplotype enhanced the effect of an APOE haplotype on exceptional survival, and a LASS1 haplotype further augmented its magnitude. These results were replicated in …

Genetypes: A Concept To Help Integrate Molecular Phylogenetics And Taxonomy, Prosanta Chakrabarty

Faculty Publications

No abstract provided.

Song Divergence By Sensory Drive In Amazonian Birds, Joseph A. Tobias, Job Aben, Robb T. Brumfield, Elizabeth P. Derryberry, Wouter Halfwerk, Hans Slabbekoorn, Nathalie Seddon

Faculty Publications

Visual signals are shaped by variation in the signaling environment through a process termed sensory drive, sometimes leading to speciation. However, the evidence for sensory drive in acoustic signals is restricted to comparisons between highly dissimilar habitats, or single-species studies in which it is difficult to rule out the influence of undetected ecological variables, pleiotropic effects, or chance. Here we assess whether this form of sensory drive-often termed " acoustic adaptation" -can generate signal divergence across ecological gradients. By studying avian communities in two Amazonian forest types, we show that songs of 17 " bamboo-specialist" bird species differ in predictable …

Evaluation Of Cryoprotectant And Cooling Rate For Sperm Cryopreservation In The Euryhaline Fish Medaka Oryzias Latipes, Huiping Yang, Michelle Norris, Richard Winn, Terrence R. Tiersch

Faculty Publications

Medaka Oryzias latipes is a well-recognized biomedical fish model because of advantageous features such as small body size, transparency of embryos, and established techniques for gene knockout and modification. The goal of this study was to evaluate two critical factors, cryoprotectant and cooling rate, for sperm cryopreservation in 0.25-ml French straws. The objectives were to: (1) evaluate the acute toxicity of methanol, 2-methoxyethanol (ME), dimethyl sulfoxide (Me2SO), N,N-dimethylacetamide (DMA), N,N-dimethyl formamide (DMF), and glycerol with concentrations of 5%, 10%, and 15% for 60min of incubation at 4°C; (2) evaluate cooling rates from 5 to 25°C/min for freezing and their interaction …

Distribution Of Isoflavones And Antioxidant Activities Of Soybean Cotyledon, Coat And Germ, Xiaohua Yue, Ahmed Moursy Abdallah, Zhimin Xu

Faculty Publications

Soy isoflavones in the cotyledon, coat and germ of four soybean varieties from the southern U.S.A. were determined and compared. Isoflavones with aglycone, daidzein, genistein, glycitein and aglycone, withβ-glucoside, genistin, daidzin and glycitin, were found in the four varieties. The range of total soy isoflavones in cotyledon, coat and germ extracts from the varieties was 2.73-9.71, 5.56-16.94 and 27.76-81.43 mg/g, respectively. Soy germ was the richest source of isoflavones among the three soybean parts. Distribution of the isoflavones in soy cotyledon was different from that in soy coat or germ. Daidzin and glycitin were the major isoflavones in the germ …

Brave New Eugenics: Regulating Assisted Reproductive Technologies In The Name Of Better Babies, Kerry L. Macintosh

Faculty Publications

Infertile men and women have been using assisted reproductive technologies (ART) to conceive children since the first "test-tube baby" was born in 1978. During the past decade, however, the federal government has begun to clamp down on ART, asserting safety concerns as grounds forbanning novel technologies such as cloning, nuclear transfer, and ooplasm transfer.

Some scholars and policymakers now want to extend governmental regulation to include conventional ART such as in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI). They claim children conceived through ART face an increased risk of birth defects and other health problems.

This Article examines the …

Biocompatibility Of Synthetic Poly(Ester Urethane)/Polyhedral Oligomeric Silsesquioxane Matrices With Embryonic Stem Cell Proliferation And Differentiation, Yan-Lin Guo, Wenshou Wang, Joshua U. Otaigbe

Faculty Publications

Incorporation of polyhedral oligomeric silsesquioxanes (POSS) into poly(ester urethanes) (PEU) as a building block results in a PEU/POSS hybrid polymer with increased mechanical strength and thermostability. An attractive feature of the new polymer is that it forms a porous matrix when cast in the form of a thin film, making it potentially useful in tissue engineering. In this study, we present detailed microscopic analysis of the PEU/POSS matrix and demonstrate its biocompatibility with cell culture. The PEU/POSS polymer forms a continuous porous matrix with open pores and interconnected grooves. From SEM image analysis, it is calculated that there are about …

Stable Isotope Analysis Reveals Detrital Resource Base Sources Of The Tree Hole Mosquito, Aedes Triseriatus, Michael G. Kaufman, Kirsten S. Pelz-Stelinski, Donald A. Yee, Steven A. Juliano, Peggy H. Ostrom, Edward D. Walker

Faculty Publications

1. Detritus that forms the basis for mosquito production in tree hole ecosystems can vary in type and timing of input. We investigated the contributions of plant‐ and animal‐derived detritus to the biomass of Aedes triseriatus (Say) pupae and adults by using stable isotope (¹⁵N and ¹³C) techniques in laboratory experiments and field collections.
2. Laboratory‐reared mosquito isotope values reflected their detrital resource base, providing a clear distinction between mosquitoes reared on plant or animal detritus.
3. Isotope values from field‐collected pupae were intermediate between what would be expected if a single (either plant or animal) detrital source dominated the …

Electronic Image Stabilization Using Optical Flow With Inertial Fusion, Michael J. Smith, Alexander J. Boxerbaum, Gilbert L. Peterson, Roger D. Quinn

Faculty Publications

When a camera is affixed on a dynamic mobile robot, image stabilization is the first step towards more complex analysis on the video feed. This paper presents a novel electronic image stabilization (EIS) algorithm for highly dynamic mobile robotic platforms. The algorithm combines optical flow motion parameter estimation with angular rate data provided by a strapdown inertial measurement unit (IMU). A discrete Kalman filter in feedforward configuration is used for optimal fusion of the two data sources. Performance evaluations are conducted using a simulated video truth model (capturing the effects of image translation, rotation, blurring, and moving objects), and live …