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2006

Faculty Publications

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Articles 1 - 30 of 79

Full-Text Articles in Life Sciences

Computational Promoter Analysis Of Mouse, Rat, And Human Antimicrobial Peptide-Coding Genes, Chin-Yo Lin, Manisha Brahmachary, Christian Schonbach, Liang Yang, Enli Huang, Sin Lam Tan, Rajesh Chowdhary, S. P. T. Krishnan, David A. Hume, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B. Bajic Dec 2006

Computational Promoter Analysis Of Mouse, Rat, And Human Antimicrobial Peptide-Coding Genes, Chin-Yo Lin, Manisha Brahmachary, Christian Schonbach, Liang Yang, Enli Huang, Sin Lam Tan, Rajesh Chowdhary, S. P. T. Krishnan, David A. Hume, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B. Bajic

Faculty Publications

Mammalian antimicrobial peptides (AMPs) are effectors of the innate immune response. A multitude of signals coming from pathways of mammalian pathogen/pattern recognition receptors and other proteins affect the expression of AMP-coding genes (AMPcgs). For many AMPcgs the promoter elements and transcription factors that control their tissue cell-specific expression have yet to be fully identified and characterized. Results- Based upon the RIKEN full-length cDNA and public sequence data derived from human, mouse and rat, we identified 178 candidate AMP transcripts derived from 61 genes belonging to 29 AMP families. However, only for 31 mouse genes belonging to 22 AMP families ...


Amyloid-Β-Induced Pathological Behaviors Are Suppressed By Ginkgo Biloba Extract Egb 761 And Ginkgolides In Transgenic Caenorhabditis Elegans, Yanjue Wu, Zhixin Wu, Peter Butko, Yves Christen, Mary P. Lambert, William L. Klein, Christopher D. Link, Yuan Luo Dec 2006

Amyloid-Β-Induced Pathological Behaviors Are Suppressed By Ginkgo Biloba Extract Egb 761 And Ginkgolides In Transgenic Caenorhabditis Elegans, Yanjue Wu, Zhixin Wu, Peter Butko, Yves Christen, Mary P. Lambert, William L. Klein, Christopher D. Link, Yuan Luo

Faculty Publications

Amyloid-β (Aβ) toxicity has been postulated to initiate synaptic loss and subsequent neuronal degeneration seen in Alzheimer's disease (AD). We previously demonstrated that the standardized Ginkgo biloba extract EGb 761, commonly used to enhance memory and by AD patients for dementia, inhibits Aβ-induced apoptosis in neuroblastoma cells. In this study, we use EGb 761 and its single constituents to associate Aβ species with Aβ-induced pathological behaviors in a model organism, Caenorhabditis elegans. We report that EGb 761 and one of its components, ginkgolide A, alleviates Aβ-induced pathological behaviors, including paralysis, and reduces chemotaxis behavior and 5-HT hypersensitivity in a ...


Development Of Computations In Bioscience And Bioinformatics And Its Application: Review Of The Symposium Of Computations In Bioinformatics And Bioscience (Scbb06), Youping Deng, Jun Ni, Chaoyang Zhang Dec 2006

Development Of Computations In Bioscience And Bioinformatics And Its Application: Review Of The Symposium Of Computations In Bioinformatics And Bioscience (Scbb06), Youping Deng, Jun Ni, Chaoyang Zhang

Faculty Publications

The first symposium of computations in bioinformatics and bioscience (SCBB06) was held in Hangzhou, China on June 21-22, 2006. Twenty-six peer-reviewed papers were selected for publication in this special issue of BMC Bioinformatics. These papers cover a broad range of topics including bioinformatics theories, algorithms, applications and tool development. The main technical topics contain gene expression analysis, sequence analysis, genome analysis, phylogenetic analysis, gene function prediction, molecular interaction and system biology, genetics and population study, immune strategy, protein structure prediction and proteomics.


Svm Classifier: A Comprehensive Java Interface For Support Vector Machine Classification Of Microarray Data, Mehdi Pirooznia, Youping Deng Dec 2006

Svm Classifier: A Comprehensive Java Interface For Support Vector Machine Classification Of Microarray Data, Mehdi Pirooznia, Youping Deng

Faculty Publications

Motivation

Graphical user interface (GUI) software promotes novelty by allowing users to extend the functionality. SVM Classifier is a cross-platform graphical application that handles very large datasets well. The purpose of this study is to create a GUI application that allows SVM users to perform SVM training, classification and prediction.

Results

The GUI provides user-friendly access to state-of-the-art SVM methods embodied in the LIBSVM implementation of Support Vector Machine. We implemented the java interface using standard swing libraries.

We used a sample data from a breast cancer study for testing classification accuracy. We achieved 100% accuracy in classification among the ...


A Phylogeny Of Belonolaimus Populations In Florida Inferred From Dna Sequences, Byron J. Adams, U. Gozel, K. B. Nguyen, R. N. Inserra, R. M. Giblin-Davis Dec 2006

A Phylogeny Of Belonolaimus Populations In Florida Inferred From Dna Sequences, Byron J. Adams, U. Gozel, K. B. Nguyen, R. N. Inserra, R. M. Giblin-Davis

Faculty Publications

The D2-D3 and ITS regions of rDNA from 33 Florida populations of Belonolaimus spp. were sequenced and subjected to phylogenetic analysis. Our objective was to derive a theoretical evolutionary framework for interpreting phenotypic differences as they relate to the taxonomy of the genus. The most striking aspect of the phylogenetic analysis is that none of the three nominal species (B. longicaudatus, B. euthychilus, and B. gracilis) are monophyletic. Additionally, two taxa appear to have discordant ITS and LSU sequences. Three major clades of B. longicaudatus exhibited discernible, overlapping, geographic foci from east to west across the peninsula. Morphological character states ...


A Review Of Polylekithum Arnold, 1934 And Its Familial Affinities Using Morphological And Molecular Data, With Description Of Polylekithum Catahoulensis Sp Nov., Stephen S. Curran, Vasyl V. Tkach, Robin M. Overstreet Dec 2006

A Review Of Polylekithum Arnold, 1934 And Its Familial Affinities Using Morphological And Molecular Data, With Description Of Polylekithum Catahoulensis Sp Nov., Stephen S. Curran, Vasyl V. Tkach, Robin M. Overstreet

Faculty Publications

The type material of Polylekithum ictaluri, P. halli, and Maculifer chandleri was examined from the United States National Parasite Museum, and we determined that the material was conspecific, making P. halli and M. chandleri junior subjective synonyms of P. ictaluri. Polylekithum catahoulensis sp. nov. was described from material collected from catfishes at the Catahoula Wildlife Refuge, LaSalle Parish, Louisiana, USA, and compared with P. ictaluri collected from catfishes in Reelfoot Lake, Obion County, Tennessee, USA, and the Pearl River, Hancock County, Mississippi, USA. Polylekithum catahoulensis had smaller eggs (77–88 μm long by 51–63 μm wide vs. 94–108 ...


Linking Bacterioplankton Community Structures To Environmental State Variables And Phytoplankton Assemblages In Two South Carolina Salt Marsh Estuaries, Wes Johnson, Alan J. Lewitus, Madilyn Fletcher Nov 2006

Linking Bacterioplankton Community Structures To Environmental State Variables And Phytoplankton Assemblages In Two South Carolina Salt Marsh Estuaries, Wes Johnson, Alan J. Lewitus, Madilyn Fletcher

Faculty Publications

Microorganisms are among the most important organisms to the ecology of salt marsh estuaries; however, fundamental questions regarding their distribution, environmental controls, and interactions with phytoplankton remain unanswered. We used denaturing gradient gel electrophoresis (DGGE) of bacterial rRNA genes and high performance liquid chromatography (HPLC) of phytoplankton photopigments to characterize planktonic communities from the Ashepoo, Combahee, and Edisto (ACE) Basin and North Inlet (NI) estuaries on the South Carolina coast, USA. Multivariate comparisons of the planktonic community profiles revealed that the 2 estuaries supported distinct bacterial communities. Furthermore, bacterial communities in both systems were partitioned into separate particle-associated (PA) and ...


Red Tides In The Gulf Of Mexico: Where, When, And Why?, J. J. Walsh, J. K. Jolliff, B. P. Darrow, J. M. Lenes, S.P. Milroy, A. Remsen, D.A. Dieterle, K.L. Carder, F.R. Chen, F.R. Chen, G.A. Vargo, R.H. Weisberg, K.A. Fanning, F.E. Muller-Karger, E. Shinn, K.A. Steidinger, C.A. Heil, C.R. Tomas, J.S. Prospero, T.N. Lee, G.J. Kirkpatrick, T.E. Whitledge, D.A. Stockwell, T.A. Villareal, A.E. Jochens, P.S. Bontempi Nov 2006

Red Tides In The Gulf Of Mexico: Where, When, And Why?, J. J. Walsh, J. K. Jolliff, B. P. Darrow, J. M. Lenes, S.P. Milroy, A. Remsen, D.A. Dieterle, K.L. Carder, F.R. Chen, F.R. Chen, G.A. Vargo, R.H. Weisberg, K.A. Fanning, F.E. Muller-Karger, E. Shinn, K.A. Steidinger, C.A. Heil, C.R. Tomas, J.S. Prospero, T.N. Lee, G.J. Kirkpatrick, T.E. Whitledge, D.A. Stockwell, T.A. Villareal, A.E. Jochens, P.S. Bontempi

Faculty Publications

Independent data from the Gulf of Mexico are used to develop and test the hypothesis that the same sequence of physical and ecological events each year allows the toxic dinoflagellate Karenia brevis to become dominant. A phosphorus-rich nutrient supply initiates phytoplankton succession, once deposition events of Saharan iron-rich dust allow Trichodesmium blooms to utilize ubiquitous dissolved nitrogen gas within otherwise nitrogen-poor sea water. They and the co-occurring K. brevis are positioned within the bottom Ekman layers, as a consequence of their similar diel vertical migration patterns on the middle shelf. Upon onshore upwelling of these near-bottom seed populations to CDOM-rich ...


The Role Of A Conserved Serine Residue Within Hydrogen Bonding Distance Of Fad In Redox Properties And The Modulation Of Catalysis By Ca2+/Calmodulin Of Constitutive Nitric-Oxide Synthases, Satya Prakash Panda, Ying Tong Gao, Linda J. Roman, Pavel Marta´Sek, John C. Salerno, Bettie Masters Nov 2006

The Role Of A Conserved Serine Residue Within Hydrogen Bonding Distance Of Fad In Redox Properties And The Modulation Of Catalysis By Ca2+/Calmodulin Of Constitutive Nitric-Oxide Synthases, Satya Prakash Panda, Ying Tong Gao, Linda J. Roman, Pavel Marta´Sek, John C. Salerno, Bettie Masters

Faculty Publications

The crystal structure of the neuronal nitric-oxide synthase (nNOS) NADPH/FAD binding domain indicated that Ser-1176 is within hydrogen bonding distance of Asp-1393 and the O4 atom of FAD and is also near the N5 atom of FAD (3.7Å). This serine residue is conserved in most of the ferredoxin-NADP+ reductase family of proteins and is important in electron transfer. In the present study, the homologous serines of both nNOS (Ser-1176) and endothelial nitric-oxide synthase (eNOS) (Ser-942) were mutated to threonine and alanine. Both substitutions yielded proteins that exhibited decreased rates of electron transfer through the flavin domains, in the ...


Changes In Understory Vegetation Of A Ponderosa Pine Forest In Northern Arizona 30 Years After A Wildfire, Amanda L. Bataineh, Brian P. Oswald, Mohammad M. Bataineh, Hans M. Williams, Dean W. Coble Nov 2006

Changes In Understory Vegetation Of A Ponderosa Pine Forest In Northern Arizona 30 Years After A Wildfire, Amanda L. Bataineh, Brian P. Oswald, Mohammad M. Bataineh, Hans M. Williams, Dean W. Coble

Faculty Publications

Wildland fires can cause shifts in understory species composition and production. Many studies have examined short-term changes in understory vegetation following a wildfire; however, very few long term studies are available. The objective of this study was to examine changes in understory (herb and shrub) species composition and production since the 1972 Rattle Burn wildfire on the Coconino National Forest near Flagstaff, Arizona. Understory species composition and production were originally sampled in 1972, 1974, and 1980 and were re-sampled during July and August of 2002 and 2003 on 30 plots in each of four sites: high severity burn, low severity ...


Periodic Boundary Condition Induced Breakdown Of The Equipartition Principle And Other Kinetic Effects Of Finite Sample Size In Classical Hard-Sphere Molecular Dynamics Simulation, Randall B. Shirts, Scott R. Burt, Aaron M. Johnson Oct 2006

Periodic Boundary Condition Induced Breakdown Of The Equipartition Principle And Other Kinetic Effects Of Finite Sample Size In Classical Hard-Sphere Molecular Dynamics Simulation, Randall B. Shirts, Scott R. Burt, Aaron M. Johnson

Faculty Publications

We examine consequences of the non-Boltzmann nature of probability distributions for one-particle kinetic energy, momentum, and velocity for finite systems of classical hard spheres with constant total energy and nonidentical masses. By comparing two cases, reflecting walls (NVE or microcanonical ensemble) and periodic boundaries (NVEPG or molecular dynamics ensemble), we describe three consequences of the center-of-mass constraint in periodic boundary conditions: the equipartition theorem no longer holds for unequal masses, the ratio of the average relative velocity to the average velocity is increased by a factor of [N/(N–1)]^1/2, and the ratio of average collision energy to ...


Analysis And Functional Annotation Of Expressed Sequence Tags From The Fall Armyworm Spodoptera Frugiperda, Youping Deng, Yinghua Dong, Venkata Thodima, Rollie J. Clem, A. Lorena Passareli Oct 2006

Analysis And Functional Annotation Of Expressed Sequence Tags From The Fall Armyworm Spodoptera Frugiperda, Youping Deng, Yinghua Dong, Venkata Thodima, Rollie J. Clem, A. Lorena Passareli

Faculty Publications

Background

Little is known about the genome sequences of lepidopteran insects, although this group of insects has been studied extensively in the fields of endocrinology, development, immunity, and pathogen-host interactions. In addition, cell lines derived from Spodoptera frugiperda and other lepidopteran insects are routinely used for baculovirus foreign gene expression. This study reports the results of an expressed sequence tag (EST) sequencing project in cells from the lepidopteran insect S. frugiperda, the fall armyworm.

Results

We have constructed an EST database using two cDNA libraries from the S. frugiperda-derived cell line, SF-21. The database consists of 2,367 ESTs ...


Warming Up With An Ice Vest: Core Body Temperature Before And After Cross-Country Racing, J. Ty Hopkins, Iain Hunter, Douglas J. Casa Oct 2006

Warming Up With An Ice Vest: Core Body Temperature Before And After Cross-Country Racing, J. Ty Hopkins, Iain Hunter, Douglas J. Casa

Faculty Publications

Context: Athletes running in a hot, humid environment may have an increased risk of heat illness. In the 2004 Olympic Games, American and Australian athletes were provided with ice vests designed to cool their bodies before performance. The vest appeared to be effective in keeping body temperatures down and improving the performance of the marathoners. However, body temperatures have not been reported when the vest was used before an actual competition. Objective: To determine if wearing the Nike Ice-Vest decreased core temperature (Tc) before and during athletic performance in warm (26°C to 27°C), humid (relative humidity = 50% to ...


Effects Of Long-Term Hypoxia On Enzymes Of Carbohydrate Metabolism In The Gulf Killifish, Fundulus Grandis, Mery L. Mártinez, Christie Landry, Ryan Boehm, Steve Manning, Bernard B. Rees Oct 2006

Effects Of Long-Term Hypoxia On Enzymes Of Carbohydrate Metabolism In The Gulf Killifish, Fundulus Grandis, Mery L. Mártinez, Christie Landry, Ryan Boehm, Steve Manning, Bernard B. Rees

Faculty Publications

The goal of the current study was to generate a comprehensive, multi-tissue perspective of the effects of chronic hypoxic exposure on carbohydrate metabolism in the Gulf killifish Fundulus grandis. Fish were held at approximately 1.3 mg l(-1) dissolved oxygen (similar to 3.6 kPa) for 4 weeks, after which maximal activities were measured for all glycolytic enzymes in four tissues (white skeletal muscle, liver, heart and brain), as well as for enzymes of glycogen metabolism (in muscle and liver) and gluconeogenesis (in liver). The specific activities of enzymes of glycolysis and glycogen metabolism were strongly suppressed by hypoxia ...


A Fourier Transformation Based Method To Mine Peptide Space For Antimicrobial Activity, Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, Mohamed O. Elasri, Youping Deng Sep 2006

A Fourier Transformation Based Method To Mine Peptide Space For Antimicrobial Activity, Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, Mohamed O. Elasri, Youping Deng

Faculty Publications

Background

Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of every living organism, it is possible to discover new candidate peptides using the available genomic and proteomic data. High throughput computational techniques could also be used to virtually scan the entire peptide space for discovering out new candidate antimicrobial peptides.

Result

We have identified a unique indexing method based on biologically distinct characteristic features of known antimicrobial peptides. Analysis of the entries in the antimicrobial peptide databases, based on our indexing method, using Fourier transformation ...


Multiplatform Genome-Wide Identification And Modeling Of Functional Human Estrogen Receptor Binding Sites, Chin-Yo Lin, Vinsensius B. Vega, Koon Siew Lai, Li Say Kong, Min Xie, Xiaodi Su, Huey Fang The, Jane S. Thomsen, Ai Li Yeo, Wing Kin Sung, Guillaume Bourque, Edison T. Liu Sep 2006

Multiplatform Genome-Wide Identification And Modeling Of Functional Human Estrogen Receptor Binding Sites, Chin-Yo Lin, Vinsensius B. Vega, Koon Siew Lai, Li Say Kong, Min Xie, Xiaodi Su, Huey Fang The, Jane S. Thomsen, Ai Li Yeo, Wing Kin Sung, Guillaume Bourque, Edison T. Liu

Faculty Publications

Transcription factor binding sites (TFBS) impart specificity to cellular transcriptional responses and have largely been defined by consensus motifs derived from a handful of validated sites. The low specificity of the computational predictions of TFBSs has been attributed to ubiquity of the motifs and the relaxed sequence requirements for binding. We posited that the inadequacy is due to limited input of empirically verified sites, and demonstrated a multiplatform approach to constructing a robust model. Results: Using the TFBS for the estrogen receptor (ER)alpha (estrogen response element [ERE]) as a model system, we extracted EREs from multiple molecular and genomic ...


Two Glucose-Sensing Pathways Converge On Rgt1 To Regulate Expression Of Glucose Transporter Genes In Saccharomyces Cerevisiae, Jeong-Ho Kim, Mark Johnston Sep 2006

Two Glucose-Sensing Pathways Converge On Rgt1 To Regulate Expression Of Glucose Transporter Genes In Saccharomyces Cerevisiae, Jeong-Ho Kim, Mark Johnston

Faculty Publications

The yeast Saccharomyces cerevisiae deploys two different types of glucose sensors on its cell surface that operate in distinct glucose signaling pathways: the glucose transporter-like Snf3 and Rgt2 proteins and the Gpr1 receptor that is coupled to Gpa2, a G-protein α subunit. The ultimate target of the Snf3/Rgt2 pathway is Rgt1, a transcription factor that regulates expression of HXT genes encoding glucose transporters. We have found that the cAMP-dependent protein kinase A (PKA), which is activated by the Gpr1/Gpa2 glucose-sensing pathway and by a glucose-sensing pathway that works through Ras1 and Ras2, catalyzes phosphorylation of Rgt1 and regulates ...


Co-Variation In Soil Biodiversity And Biogeochemistry In Northern And Southern Victoria Land, Antarctica, Byron J. Adams, J. E. Barrett, Ross A. Virginia, Diana H. Wall, S. C. Cary, A. L. Hacker, J. M. Aislabie Sep 2006

Co-Variation In Soil Biodiversity And Biogeochemistry In Northern And Southern Victoria Land, Antarctica, Byron J. Adams, J. E. Barrett, Ross A. Virginia, Diana H. Wall, S. C. Cary, A. L. Hacker, J. M. Aislabie

Faculty Publications

Data from six sites in Victoria Land (72-77degrees S) investigating co-variation in soil communities (microbial and invertebrate) with biogeochemical properties show the influence of soil properties on habitat suitability varied among local landscapes as well as across climate gradients. Species richness of metazoan invertebrates (Nematoda, Tardigrada and Rotifera) was similar to previous descriptions in this region, though identification of three cryptic nematode species of Eudorylaimus through DNA analysis contributed to the understanding of controls over habitat preferences for individual species. Denaturing Gradient Gel Electrophoresis profiles revealed unexpectedly high diversity of bacteria. Distribution of distinct bacterial communities was associated with specific ...


Dissolved Gallium In The Northwest Pacific And The South And Central Atlantic Oceans: Implications For Aeolian Fe Input And A Reconsideration Of Profiles, Alan M. Shiller, Gautam Raj Bairamadgi Aug 2006

Dissolved Gallium In The Northwest Pacific And The South And Central Atlantic Oceans: Implications For Aeolian Fe Input And A Reconsideration Of Profiles, Alan M. Shiller, Gautam Raj Bairamadgi

Faculty Publications

[1] The distribution of dissolved gallium, a less-reactive analogue of aluminum, has the potential to reveal information about the averaged dust input to the surface ocean and to complement studies using aluminum as a tracer. New data are presented here on the distribution of dissolved Ga, including six profiles in the south and central Atlantic as well as seven shallow and two deep profiles from the northwest Pacific. The Atlantic data allow for an estimate of Ga in Antarctic Bottom Water ( similar to 25 - 30 pmol kg(-1)) and show reasonably conservative behavior in deep waters. In the northwest Pacific ...


Interaction Of Ice Storms And Management Practices On Current Carbon Sequestration In Forests With Potential Mitigation Under Future Co2 Atmosphere, Heather R. Mccarthy, Ram Oren, Hyun-Seok Kim, Kurt H. Johnsen, Chris Maier, Seth G. Pritchard, Micheal Davis Aug 2006

Interaction Of Ice Storms And Management Practices On Current Carbon Sequestration In Forests With Potential Mitigation Under Future Co2 Atmosphere, Heather R. Mccarthy, Ram Oren, Hyun-Seok Kim, Kurt H. Johnsen, Chris Maier, Seth G. Pritchard, Micheal Davis

Faculty Publications

[1] Ice storms are disturbance events with potential impacts on carbon sequestration. Common forest management practices, such as fertilization and thinning, can change wood and stand properties and thus may change vulnerability to ice storm damage. At the same time, increasing atmospheric CO2 levels may also influence ice storm vulnerability. Here we show that a nonintensively managed pine plantation experienced a ∼250 g C m−2 reduction in living biomass during a single storm, equivalent to ∼30% of the annual net ecosystem carbon exchange of this ecosystem. Drawing on weather and damage survey data from the entire storm cell ...


Measuring The Effects Of Salinity Stress In The Red Mangrove, Rhizophora Mangle L., Patrick D. Biber Aug 2006

Measuring The Effects Of Salinity Stress In The Red Mangrove, Rhizophora Mangle L., Patrick D. Biber

Faculty Publications

The mangrove habitat exhibits many unique physical features, one of the most important of which is a salinity gradient. Photosynthetic rates, as measured by leaf stomatal conductance and leaf chlorophyll fluorescence induction, were tested as indicators of salinity stress in seedlings of the red mangrove, Rhizophora mangle, grown under five different salinity levels: 0, 15, 30, 45, and 60 parts per thousand. Photosynthetic gas exchange (measured by stomatal conductance), as well as the light reaction of photosynthesis (measured by chlorophyll fluorescence) were found to decrease as salinity increased. The use of leaf stomatal conductance and chlorophyll fluorescence as a measure ...


The Effect Of Protein Dielectric Coefficient On The Ionic Selectivity Of A Calcium Channel, Douglas Henderson, Dezso Boda, Monika Valisko, Bob Eisenberg, Wolfgang Nonner, Dirk Gillespie Jul 2006

The Effect Of Protein Dielectric Coefficient On The Ionic Selectivity Of A Calcium Channel, Douglas Henderson, Dezso Boda, Monika Valisko, Bob Eisenberg, Wolfgang Nonner, Dirk Gillespie

Faculty Publications

Calcium-selective ion channels are known to have carboxylate-rich selectivity filters, a common motif that is primarily responsible for their high Ca2+ affinity. Different Ca2+ affinities ranging from micromolar (the L-type Ca channel) to millimolar (the ryanodine receptor channel) are closely related to the different physiological functions of these channels. To understand the physical mechanism for this range of affinities given similar amino acids in their selectivity filters, we use grand canonical Monte Carlo simulations to assess the binding of monovalent and divalent ions in the selectivity filter of a model Ca channel. We use a reduced model where the electrolyte ...


Ecological Fitting As A Determinant Of The Community Structure Of Platyhelminth Parasites Of Anurans, Daniel R. Brooks, Virginia León-Règagnon, Deborah Mclennan, Derek Zelmer Jul 2006

Ecological Fitting As A Determinant Of The Community Structure Of Platyhelminth Parasites Of Anurans, Daniel R. Brooks, Virginia León-Règagnon, Deborah Mclennan, Derek Zelmer

Faculty Publications

Host–parasite associations are assumed to be ecologically specialized, tightly coevolved systems driven by mutual modification in which host switching is a rare phenomenon. Ecological fitting, however, increases the probability of host switching, creating incongruences between host and parasite phylogenies, when (1) specialization on a particular host resource is a shared characteristic of distantly related parasites, and (2) the resource being tracked by the parasite is widespread among many host species. We investigated the effect of ecological fitting on structuring the platyhelminth communities of anurans from a temperate forest and grassland in the United States and tropical dry and wet ...


Tissue Glycogen And Extracellular Buffering Limit The Survival Of Red-Eared Slider Turtles During Anoxic Submergence At 3°C, Daniel E. Warren, Scott A. Reese, Donald C. Jackson Jul 2006

Tissue Glycogen And Extracellular Buffering Limit The Survival Of Red-Eared Slider Turtles During Anoxic Submergence At 3°C, Daniel E. Warren, Scott A. Reese, Donald C. Jackson

Faculty Publications

The goal of this study was to identify the factors that limit the survival of the red-eared slider turtle Trachemys scripta during long-term anoxic submergence at 3°C. We measured blood acid-base status and tissue lactate and glycogen contents after 13, 29, and 44 d of submergence from ventricle, liver, carapace (lactate only), and four skeletal muscles. We also measured plasma Ca2+, Mg2+, Na+, K+, Cl-, inorganic phosphate (Pi), lactate, and glucose. After 44 d, one of the six remaining turtles died, while the other turtles were in poor condition and suffered from a severe acidemia (blood ...


Aintegumenta Contributes To Organ Polarity And Regulates Growth Of Lateral Organs In Combination With Yabby Genes, Staci Nole-Wilson, Beth A. Krizek Jul 2006

Aintegumenta Contributes To Organ Polarity And Regulates Growth Of Lateral Organs In Combination With Yabby Genes, Staci Nole-Wilson, Beth A. Krizek

Faculty Publications

Lateral organs in flowering plants display polarity along their adaxial-abaxial axis with distinct cell types forming at different positions along this axis. Members of three classes of transcription factors in Arabidopsis (Arabidopsis thaliana; the Class III homeodomain/leucine zipper [HD-ZIP] proteins, KANADI proteins, and YABBY proteins) are expressed in either the adaxial or abaxial domain of organ primordia where they confer these respective identities. Little is known about the factors that act upstream of these polarity-determining genes to regulate their expression. We have investigated the relationship between AINTEGUMENTA (ANT), a gene that promotes initiation and growth of lateral organ primordia ...


Steeplechase Barriers Affect Women Less Than Men, Tyler D. Bushnell, Iain Hunter Jun 2006

Steeplechase Barriers Affect Women Less Than Men, Tyler D. Bushnell, Iain Hunter

Faculty Publications

Women began contesting the 3000 m steeplechase during the 1990’s using barriers of different dimensions than men. Whenever a new event is introduced for women, consideration should be taken as to whether different technique or training methods should be utilized. This study investigated three aspects of hurdling technique: 1) Differences in the ratio of the landing step to the penultimate step between men and women around each non-water jump steeplechase barrier, 2) differences in step lengths between the four non-water jump barriers, and 3) changes in the step lengths around the barrier throughout the race. The step lengths around ...


Quality Of Cornmeal Stored Long-Term In A Low Oxygen Atmosphere, Megan L. Bingham, Heather F. Pahulu, Lynn V. Ogden, Oscar A. Pike Jun 2006

Quality Of Cornmeal Stored Long-Term In A Low Oxygen Atmosphere, Megan L. Bingham, Heather F. Pahulu, Lynn V. Ogden, Oscar A. Pike

Faculty Publications

The U.S. Department of Homeland Security recommends food be included in efforts to be prepared for natural disasters and other emergencies. Cornmeal packaged in No. 10 cans with a low oxygen atmosphere has been available in the retail market for decades, but the effect of long-term storage on quality is unknown. This study assessed the quality of cornmeal stored up to 33 years at ambient temperatures in a low oxygen atmosphere. Sixteen samples of cornmeal packaged in No. 10 cans ranging in age from < 1 to 33 years were obtained from donors. The cornmeal and products made from the cornmeal (cornbread and cornmeal hot cereal) were evaluated by a 50-member consumer panel using a 9-point hedonic scale for attributes including appearance, aroma, flavor, texture, and overall acceptability. Acceptance for everyday use and emergency situations was also determined. Additional measurements included can headspace oxygen, can seam integrity, color, and water activity. There was no significant decrease over storage time in aroma, texture, flavor, and overall acceptability in cornmeal, cornbread or cornmeal cereal. Hedonic scores for cornmeal aroma and appearance ranged from 5.2 to 6.3 and 5.6 to 7.0, respectively. Hedonic scores for overall acceptability of cornmeal cereal and corn bread varied from 4.5 to 6.0 and 6.0 to 7.1, respectively. Acceptance of the cornmeal in a regular diet ranged from 44 to 76 % and emergency acceptance ranged from 90 to 99 %. Headspace oxygen ranged from 0.309 to 20.4%. CIE L*a*b* color values ranged from 82.0-86.6, 3.2-10.1, and 26.3-50.8, respectively. Cornmeal appearance hedonic scores correlated with CIE b* color values (r2=0.75). Water activity ranged from .28 to .58. Cornmeal, especially as an ingredient in a recipe, is capable of retaining a high percentage of consumer acceptance over long periods of time and can be included in long-term food storage efforts.


Effects Of Ankle Joint Cooling On Peroneal Short Latency Response, J. Ty Hopkins, Iain Hunter, Todd Mcloda Jun 2006

Effects Of Ankle Joint Cooling On Peroneal Short Latency Response, J. Ty Hopkins, Iain Hunter, Todd Mcloda

Faculty Publications

While cryotherapy has direct physiological effects on contractile tissues, the extent to which joint cooling affects the neuromuscular system is not well understood. The purpose of the study was to detect changes in ankle dynamic restraint (peroneal short latency response and muscle activity amplitude) during inversion perturbation following ankle joint cryotherapy. A 2x3 factorial design was used to compare reaction time and EMG amplitude data of treatment conditions (cryotherapy and control) across time (pre-treatment, post-treatment, and 30 min post-treatment). Thirteen healthy volunteers (age 23 ± 4 yrs, ht 1.76 ± 0.09 m, mass 78.8 ± 16.6 kg), with no ...


Growth, Feeding And Reproduction Of The Catfish Eremophilus Mutisii (Pisces : Trichomycteridae), From Artificial Reservoirs In Colombia, Gabriel Pinilla, Maritza Abril, Esperanza González Jun 2006

Growth, Feeding And Reproduction Of The Catfish Eremophilus Mutisii (Pisces : Trichomycteridae), From Artificial Reservoirs In Colombia, Gabriel Pinilla, Maritza Abril, Esperanza González

Faculty Publications

The catfish, Eremophilus mutisii, was cultured under different densities in artificial rainfall reservoirs at Caldas, Boyaca, Colombia. At capture, the average total length of the animals was 10 cm and the weight ranged between 9 and 10 g. These fish were in initial stages of sexual development. After a year in the reservoirs, they had increased in length and weight as follows (densities in parentheses): 5.22 cm and 27.23 g (0.5 individuals/m(2))); 1.98 cm and 8.79 g (1 individual/m(2)), and 2.45 cm and 0.82 g (2 individuals/m(2 ...


Source And Transport Of Terrigenous Organic Matter In The Upper Yukon River: Evidence From Isotope (Delta C-13, Delta C-14, And Delta N-15) Composition Of Dissolved, Colloidal, And Particulate Phases, Laodong Guo, Robie W. Macdonald May 2006

Source And Transport Of Terrigenous Organic Matter In The Upper Yukon River: Evidence From Isotope (Delta C-13, Delta C-14, And Delta N-15) Composition Of Dissolved, Colloidal, And Particulate Phases, Laodong Guo, Robie W. Macdonald

Faculty Publications

Natural organic matter was collected from the upper Yukon River and size fractionated into the (LMW-DOC), colloidal (COC, 1 kDa to 0.45 mu m) and particulate organic carbon (POC, > 0.45 mu m) phases for characterization of elemental (C and N) and isotopic (C-13, C-14 and N-15) composition to examine their sources and transport. Concentrations of total organic carbon (TOC) decreased from 3010 mu M in mid-May to 608 mu M in September, accompanying an increase in river water delta O-18 from the snowmelt to summer and early fall. COC was the predominant OC species, comprising, on average, 63 ...