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Articles 1 - 15 of 15
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
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 we …
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
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 …
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
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 average kinetic energy is …
Warming Up With An Ice Vest: Core Body Temperature Before And After Cross-Country Racing, J. Ty Hopkins, Iain Hunter, Douglas J. Casa
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 75%) …
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
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 platforms …
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
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 …
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
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 …
Quality Of Cornmeal Stored Long-Term In A Low Oxygen Atmosphere, Megan L. Bingham, Heather F. Pahulu, Lynn V. Ogden, Oscar A. Pike
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
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 history …
Steeplechase Barriers Affect Women Less Than Men, Tyler D. Bushnell, Iain Hunter
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 the …
Mechanisms Imposing The Vbeta Bias Of V14a Natural Killer T Cells And Consequences For Microbial Glycolipid Recognition, Paul B. Savage, Dasten G. Wei, Shane A. Curran, Luc Teyton, Albert Bendelac
Mechanisms Imposing The Vbeta Bias Of V14a Natural Killer T Cells And Consequences For Microbial Glycolipid Recognition, Paul B. Savage, Dasten G. Wei, Shane A. Curran, Luc Teyton, Albert Bendelac
Faculty Publications
Mouse and human natural killer T (NKT) cells recognize a restricted set of glycosphingolipids presented by CD1d molecules, including self iGb3 and microbial alpha-glycuronosylceramides. The importance of the canonical Valpha 14-Jalpha18 TCR alphachain for antigen recognition by NKT cells is well recognized, but the mechanisms underlying the Vbeta8, Vbeta7, and Vbeta2 bias in mouse have not been explored. To study the influences of thymic selection and the constraints of pairing with Valpha 14-Jalpha 18, we have created a population of mature T cells expressing Valpha 14-Jalpha 18 TCRalpha chain in CD1d-deficient mice and studied its recognition properties in vitro and …
Erratum: "Hard Sphere Radial Distribution Function Again", Andrij Trokhymchuk, Douglas Henderson, Ivo Nezbeda, Jan Jirsak
Erratum: "Hard Sphere Radial Distribution Function Again", Andrij Trokhymchuk, Douglas Henderson, Ivo Nezbeda, Jan Jirsak
Faculty Publications
Some misprints have been found for parameters given by Eqs. 29 and 30 and the relevant equations in the Appendix.
A Hydrothermal After-Ripening Time Model For Seed Dormancy Loss In Bromus Tectorum L., Phil S. Allen, Necia B. Bair
A Hydrothermal After-Ripening Time Model For Seed Dormancy Loss In Bromus Tectorum L., Phil S. Allen, Necia B. Bair
Faculty Publications
After-ripening, the loss of dormancy under dry conditions, is associated with a decrease in mean base water potential for germination of Bromus tectorum L. seeds. After-ripening rate is a linear function of temperature above a base temperature, so that dormancy loss can be quantified using a thermal after-ripening time (TAR) model. To incorporate storage water potential into TAR, we created a hydrothermal after-ripening time (HTAR) model. Seeds from two B. tectorum populations were stored under controlled temperatures (20 or 30° C) and water potentials (400 to 40MPa). Subsamples were periodically removed from each storage treatment and incubated at 15 or …
Evolution Of The Nanog Pseudogene Family In The Human And Chimpanzee Genomes, Daniel J. Fairbanks, Peter J. Maughan
Evolution Of The Nanog Pseudogene Family In The Human And Chimpanzee Genomes, Daniel J. Fairbanks, Peter J. Maughan
Faculty Publications
The NANOG gene is expressed in mammalian embryonic stem cells where it maintains cellular pluripotency. An unusually large family of pseudogenes arose from it with one unprocessed and ten processed pseudogenes in the human genome. This article compares the NANOG gene and its pseudogenes in the human and chimpanzee genomes and derives an evolutionary history of this pseudogene family. Results: The NANOG gene and all pseudogenes except NANOGP8 are present at their expected orthologous chromosomal positions in the chimpanzee genome when compared to the human genome, indicating that their origins predate the human-chimpanzee divergence. Analysis of flanking DNA sequences demonstrates …
Patterns Of Habitat Use By Bats Along A Riparian Corridor In Northern Utah, Duke S. Rogers, Mark C. Belk, Malinda W. González, Brent L. Coleman
Patterns Of Habitat Use By Bats Along A Riparian Corridor In Northern Utah, Duke S. Rogers, Mark C. Belk, Malinda W. González, Brent L. Coleman
Faculty Publications
We examined patterns of habitat use within a community of bats along the Provo River in Heber Valley, Utah. The landscape was divided into 5 habitat categories: riparian forest, wetland, agricultural field, edge, and a habitat restoration site. We used Anabat II bat detectors to record the number of echolocation calls per night within each habitat type as an index of bat activity. Echolocation calls were classified into foraging guilds based on acoustic traits, and we analyzed activity by entire community and by the 4 guilds related to habitat type and environmental variables. Activity was not significantly related to moon …