Life Sciences Commons^™

Discrete Diffusion Models To Study The Effects Of Mg2+ Concentration On The Phopq Signal Transduction System, Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal K. Das, Chaoyang Zhang

Faculty Publications

Background: The challenge today is to develop a modeling and simulation paradigm that integrates structural, molecular and genetic data for a quantitative understanding of physiology and behavior of biological processes at multiple scales. This modeling method requires techniques that maintain a reasonable accuracy of the biological process and also reduces the computational overhead. This objective motivates the use of new methods that can transform the problem from energy and affinity based modeling to information theory based modeling. To achieve this, we transform all dynamics within the cell into a random event time, which is specified through an information domain …

Measured And Estimated Ground Reaction Forces For Multi-Segment Foot Models, Dustin A. Bruening, Kevin M. Cooney, Frank L. Buczek

Faculty Publications

Accurate measurement of ground reaction forces under discrete areas of the foot is important in the development of more advanced foot models, which can improve our understanding of foot and ankle function. To overcome current equipment limitations, a few investigators have proposed combining a pressure mat with a single force platform and using a proportionality assumption to estimate subarea shear forces and free moments. In this study, two adjacent force platforms were used to evaluate the accuracy of the proportionality assumption on a three segment foot model during normal gait. Seventeen right feet were tested using a targeted walking approach, …

A New Approach To Construct Pathway Connected Networks And Its Application In Dose Responsive Gene Expression Profiles Of Rat Liver Regulated By 2,4dnt, Sudhir Chowbina, Youping Deng, Junmei Ai, Xiaogang Wu, Xin Guan, Mitchell S. Wilbanks, Barbara Lynn Escalon, Edward J. Perkins, Jake Y. Chen

Faculty Publications

Background: Military and industrial activities have lead to reported release of 2,4-dinitrotoluene (2,4DNT) into soil, groundwater or surface water. It has been reported that 2,4DNT can induce toxic effects on humans and other organisms. However the mechanism of 2,4DNT induced toxicity is still unclear. Although a series of methods for gene network construction have been developed, few instances of applying such technology to generate pathway connected networks have been reported.

Results: Microarray analyses were conducted using liver tissue of rats collected 24h after exposure to a single oral gavage with one of five concentrations of 2,4DNT. We observed …

Systematic Approach To Electrostatically Induced 2d Crystallization Of Nanoparticles At Liquid Interfaces, Sumit Kewalramani, Suntao Wang, Yuan Lin, Huong Giang Nguyen, Qian Wang, Masafumi Fukuto, Lin Yang

Faculty Publications

We report an experimental demonstration of a strategy for inducing two-dimensional (2D)crystallization of charged nanoparticles on oppositely charged fluid interfaces. This strategy aims to maximize the interfacial adsorption of nanoparticles, and hence their lateral packing density, by utilizing a combination of weakly charged particles and a high surface charge density on the planar interface. In order to test this approach, we investigated the assembly of cowpea mosaic virus (CPMV) on positively charged lipid monolayers at the aqueous solution surface, by means of in situX-ray scattering measurements at the liquid–vapor interface. Theassembly was studied as a function of the solution …

Nucleosome Structure Incorporated Histone Acetylation Site Prediction In Arabidopsis Thaliana, Chen Zhao, Hui Liu, Youping Deng, Tieliu Shu

Faculty Publications

Background

Acetylation is a crucial post-translational modification for histones, and plays a key role in gene expression regulation. Due to limited data and lack of a clear acetylation consensus sequence, a few researches have focused on prediction of lysine acetylation sites. Several systematic prediction studies have been conducted for human and yeast, but less for Arabidopsis thaliana.

Results

Concerning the insufficient observation on acetylation site, we analyzed contributions of the peptide-alignment-based distance definition and 3D structure factors in acetylation prediction. We found that traditional structure contributes little to acetylation site prediction. Identified acetylation sites of histones in Arabidopsis thaliana …

Global Protein Interactome Exploration Through Mining Genome-Scale Data In Arabidopsis Thaliana, Feng Xu, Guang Li, Chen Zhao, Yuhua Li, Peng Li, Jian Cui, Youping Deng, Tieliu Shi

Faculty Publications

Background

Many essential cellular processes, such as cellular metabolism, transport, cellular metabolism and most regulatory mechanisms, rely on physical interactions between proteins. Genome-wide protein interactome networks of yeast, human and several other animal organisms have already been established, but this kind of network reminds to be established in the field of plant.

Results

We first predicted the protein protein interaction in Arabidopsis thaliana with methods, including ortholog, SSBP, gene fusion, gene neighbor, phylogenetic profile, coexpression, protein domain, and used Naïve Bayesian approach next to integrate the results of these methods and text mining data to build a genome-wide protein interactome …

Geolite, An Arcgis Extension To Assist In Lidar Data Processing, Yanli Zhang, Jason Grogan, I-Kuai Hung, Ramanathan Sugumaran

Faculty Publications

No abstract provided.

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 …

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

Faculty Publications

No abstract provided.

Feasibility Of Re-Using Pete Soda Bottles To Exclude Oxygen During Storage Of Low Moisture Foods, Sarah Broderick, Michelle A. Lloyd, Lynn V. Ogden, Oscar A. Pike

Faculty Publications

Many consumers are beginning to store grain on their own creating a need for easy disinfestation methods that can be accomplished in the home. Oxygen deprivation has proven to be an effective method for grain disinfestation when kept below 1% for 12 days. Re-using PETE soda bottles is an easy way many consumers can store their grains. The purpose of this study was to determine if using oxygen absorber packets in used PETE soda bottles will keep the oxygen percent low enough to disinfest the grain stored in them. Experiments were carried out to determine how long oxygen absorber packets …

Can Grain Be Disinfested In 5-Gal Hdpe Buckets Containing Oxygen Absorber Packets?, Lynn V. Ogden, C. Griffin

Faculty Publications

Effective methods of grain disinfestation include freezing, the use of carbon dioxide gas, and the use of pesticides. Oxygen deprivation has also been shown to be an effective method of disinfestation when the oxygen content is held below 1% for at least 12 days (d). High Density Polyethylene (HDPE) 5 gallon (gal) buckets have become a popular and convenient storage container for dry foods such as wheat, rice and beans. Oxygen absorber packets are an effective way to remove the oxygen in high-barrier sealed containers to prolong the life of many of these foods. It is hypothesized that sealed HDPE …

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 …

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 …

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 …

Repression Of Wnt Signaling By A Fer-Type Nonreceptor Tyrosine Kinase, Aaron P. Putzke, Joel H. Rothman

Faculty Publications

The Wnt signaling pathway must be properly modulated to ensure an appropriate output: pathological conditions result from either insufficient or excessive levels of Wnt signal. For example, hyperactivation of the Wnt pathway is associated with various cancers and subnormal Wnt signaling can lead to increased invasiveness of tumor cells. We found that the Caenorhabditis elegans ortholog of the Fer nonreceptor tyrosine kinase, FRK-1, limits Wnt signaling by preventing the adhesion complex-associated beta-catenin, HMP-2, from participating in Wnt-dependent specification of the endoderm during embryogenesis. Removal of FRK-1 function results in relocalization of HMP-2 to the nucleus of epidermal cells, and allows …

Glutamine Synthetase Partitioning In Native And Introduced Salt Marsh Grasses, Eric L.G. Hazelton, Thomas J. Knight Phd, Theresa A. Theodose Phd

Faculty Publications

Plants with higher glutamine synthetase (GS) activity in photosynthetic tissues than below-ground structures (high leaf:root [L:R] GS activity) show growth advantages over plants with a low L:R GS activity ratio. The benefits of a high L:R GS activity ratio are well documented in agricultural systems, but little is known about the ecology of GS partitioning in natural systems. To determine the ecological significance of GS partitioning, we measured above- and below-ground GS activity in Spartina grasses field-collected from a Maine salt marsh and others raised in a growth chamber from seed. The more stress-tolerant, faster growing S. alterniflora had a …

A “Healthy Pizza Kitchen” Nutrition Education Program At A Children's Health Museum, Marjorie Freedman

Faculty Publications

For nutrition education to be successful in changing behavior, schools, families, and communities must participate in or provide a variety of diverse, creative, accessible, and culturally appropriate programs. One venue for provision of nutrition education is a health and science education center that has exhibits and special programs not found in an average school. Establishing relationships with these organizations could greatly enhance a school health curriculum.1 Although nutrition information, displays, and programming are often found in these centers, studies examining whether provision of nutrition education in these venues increases knowledge or changes behavior are lacking. The purpose of this study, …

Reducing Portion Size Reduces Food Intake And Plate Waste, Marjorie Freedman, Carolina Brochado

Faculty Publications

As portion size (PS) increases, so does food intake. The effect of decreasing PS on food intake in a nonlaboratory setting is unknown. This 5-week study sought to determine whether decreasing PS resulted in decreased intake of the same food, and if so, at what point further PS reductions might lack benefit. It also assessed effects of PS reduction on food production and waste in a university all-you-can-eat dining facility (DF). Subjects were primarily freshmen who regularly ate lunch at the DF, and self-selected French fries (FF) presented in individual paper bags, portioned originally at 88 g, and decreased ∼15 …

Integrating Concepts And Technologies To Advance The Study Of Bird Migration, W. Douglas Robinson, Melissa Bowlin, Isabelle Bisson, Judy Shamoun-Barnes, Kasper Thorup, Robert H. Diehl, Thomas H. Kunz, Sarah Mabey, David W. Winkler

Faculty Publications

Recent technological innovation has opened new avenues in migration research - for instance, by allowing individual migratory animals to be followed over great distances and long periods of time, as well as by recording physiological information. Here, we focus on how technology - specifically applied to bird migration - has advanced our knowledge of migratory connectivity, and the behavior, demography, ecology, and physiology of migrants. Anticipating the invention of new and smaller tracking devices, in addition to the ways that technologies may be combined to measure and record the behavior of migratory animals, we also summarize major conceptual questions that …

Evaluating Tiffs (Toolbox For Lidar Data Filtering And Forest Studies) In Deriving Forest Measurements From Lidar Data, John Chapman, I-Kuai Hung, Jeff Tippen

Faculty Publications

Recent advances in LiDAR (Light Detection and Ranging) technology have allowed for the remote sensing of important forest characteristics to be more reliable and commercially available. Studies have shown that this technology can adequately estimate forest characteristics such as individual tree locations, tree heights, and crown diameters. These values are then used to estimate biophysical properties of forests, such as basal area and timber volume. This study assessed the capability of a commercially available program, Tiffs (Toolbox for Lidar Data Filtering and Forest Studies), to accurately estimate forest characteristics, as compared to data collected at the plot level using traditional …

Incorporating Genomics And Bioinformatics Across The Life Sciences Curriculum, Jayna L. Ditty, Christopher A. Kvaal, Brad Goodner, Sharyn K. Freyermuth, Cheryl Bailey, Robert A. Britton, Stuart G. Gordon, Sabine Heinhorst, Kelyenne Reed, Zhaohui Xu, Erin R. Sanders-Lorenz, Seth Axen, Edwin Kim, Mitrick Johns, Kathleen Scott, Cheryl A. Kerfeld

Faculty Publications

No abstract provided.

Soil Viewer Extension Brings Soil Data To Your Gis, Jason Grogan, I-Kuai Hung, Yanli Zhang

Faculty Publications

No abstract provided.

Alteration Of Microbial Communities Colonizing Leaf Litter In A Temperate Woodland Stream By Growth Of Trees Under Conditions Of Elevated Atmospheric Co2, John J. Kelly, Amit Bansal, Jonathan Winkelman, Lori R. Janus, Shannon Hell, Marie Wencel, Patricia Belt, Kevin A. Kuehn, Steven T. Rier, Nancy C. Tuchman

Faculty Publications

Elevated atmospheric CO₂ can cause increased carbon fixation and altered foliar chemical composition in a variety of plants, which has the potential to impact forested headwater streams because they are detritus-based ecosystems that rely on leaf litter as their primary source of organic carbon. Fungi and bacteria play key roles in the entry of terrestrial carbon into aquatic food webs, as they decompose leaf litter and serve as a source of nutrition for invertebrate consumers. This study tested the hypothesis that changes in leaf chemistry caused by elevated atmospheric CO₂ would result in changes in the size and …

Weeds In The Flower Garden: An Exploration Of Plagiarism In Graduate Students’ Research Proposals And Its Connection To Enculturation, Esl, And Contextual Factors, Joanna Gilmore, Denise Strickland, Briana Eileen Timmerman, Michelle Maher, David Feldon

Faculty Publications

Existing literature provides insight into the nature and extent of plagiarism amongst undergraduate students (e.g., Ellery, 2008; Parameswaran & Devi, 2006; Selwyn, 2008). Plagiarism amongst graduate students is relatively unstudied, however, and the existing data are largely based on self-reports. This study investigated the rates and potential causes of plagiarism amongst graduate students in master’s and doctoral programmes in science, technology, engineering, mathematics, and science or mathematics education by examining actual research proposals written by graduate students. Results indicate that plagiarism is a prevalent issue at each of the three university sites sampled and across all of the investigated disciplines. …

Chemical Inhibition Of Caax Protease Activity Disrupts Yeast Ras Localization, Surya P. Mandahar, Emily R. Hildebrandt, William H. Jacobsen, George M. Santangelo, Walter K. Schmidt

Faculty Publications

Proteins possessing a C-terminal CaaX motif, such as the Ras GTPases, undergo extensive post-translational modification that includes attachment of an isoprenoid lipid, proteolytic processing and carboxylmethylation. Inhibition of the enzymes involved in these processes is considered a cancer-therapeutic strategy. We previously identified nine in vitro inhibitors of the yeast CaaX protease Rce1p in a chemical library screen (Manandhar et al., 2007). Here, we demonstrate that these agents disrupt the normal plasma membrane distribution of yeast GFP-Ras reporters in a manner that pharmacologically phenocopies effects observed upon genetic loss of CaaX protease function. Consistent with Rce1p being the in vivo target …

Comparison Of A Reduced Carbohydrate And Reduced Fat Diet For Ldl, Hdl, And Vldl Subclasses During 9-Months Of Weight Maintenance Subsequent To Weight Loss, James D. Lecheminant, Bryan K. Smith, Eric C. Westman, Mary C. Vernon, Joseph E. Donnelly

Faculty Publications

Objectives: This study compared LDL, HDL, and VLDL subclasses in overweight or obese adults consuming either a reduced carbohydrate (RC) or reduced fat (RF) weight maintenance diet for 9 months following significant weight loss. Methods: Thirty-five (21 RC; 14 RF) overweight or obese middle-aged adults completed a 1-year weight management clinic. Participants met weekly for the first six months and bi-weekly thereafter. Meetings included instruction for diet, physical activity, and behavior change related to weight management. Additionally, participants followed a liquid very low-energy diet of ~2092 kJ per day for the first three months of the study. Subsequently, participants followed …

Natural Selection On Testosterone Production In A Wild Songbird Population, Joel W. Mcglothlin, Danielle J. Whittaker, Sara E. Schrock, Nicole M. Gerlach, Jodie M. Jawor, Eric A. Snajdr, Ellen D. Ketterson

Faculty Publications

Because of their role in mediating life-history trade-offs, hormones are expected to be strongly associated with components of fitness; however, few studies have examined how natural selection acts on hormonal variation in the wild. In a songbird, the dark-eyed junco (Junco hyemalis), field experiments have shown that exogenous testosterone alters individuals' resolution of the survival-reproduction trade-off, enhancing reproduction at the expense of survival. Here we used standardized injections of gonadotropin-releasing hormone (GnRH) to assay variation in the testosterone production of males. Using measurements of annual survival and reproduction, we found evidence of strong natural selection acting on GnRH-induced …

Evaluating Ecosystem Response To Oyster Restoration And Nutrient Load Reduction With A Multispecies Bioenergetics Model, Richard S. Fulford, Denise L. Breitburg, Mark Luckenbach, Roger I.E. Newell

Faculty Publications

Many of the world's coastal ecosystems are impacted by multiple stressors each of which may be subject to different management strategies that may have overlapping or even conflicting objectives. Consequently, management results may be indirect and difficult to predict or observe. We developed a network simulation model intended specifically to examine ecosystem-level responses to management and applied this model to a comparison of nutrient load reduction and restoration of highly reduced stocks of bivalve suspension feeders (eastern oyster, Crassostrea virginica) in an estuarine ecosystem (Chesapeake Bay, USA). Model results suggest that a 50% reduction in nutrient inputs from the watershed …