Life Sciences Commons^™

Topographic Effects On The Path And Evolution Of Loop Current Eddies, Kyung Hoon Hyun, Patrick J. Hogan

Faculty Publications

Eddy-topography (ET) interactions are important in determining the path and evolution of oceanic eddies, including Loop Current Eddies (LCE) in the Gulf of Mexico (GOM). We use the Hybrid Coordinate Ocean Model and satellite altimetry data to investigate the ET interactions and the impact on LCE pathway evolution in the GOM. Satellite altimetry reveals that LCEs translate dominantly westward in the central GOM and strongly collide and reflect against topography near the continental slope in the northern and western GOM. The result is the frequent generation of an anticyclone-cyclone (AC) pair in conjunction with the LCEs. In the absence of …

The Role Of Msa In Staphylococcus Aureus Biofilm Formation, Karthik Sambanthamoorthy, Antony Schwartz, Vijayaraj Nagarajan, Mohamed O. Elasri

Faculty Publications

Background

Staphylococcus aureus is an important pathogen that forms biofilms. The global regulator sarA is essential for biofilm formation. Since the modulator of sarA (msa) is required for full expression of sarA and regulates several virulence factors, we examined the capacity of the msa mutant to form biofilm.

Results

We found that mutation of msa results in reduced expression of sarA in biofilm and that the msa mutant formed a weak and unstable biofilm. The msa mutant is able to adhere to surfaces and begins to form biofilm but fails to mature indicating that the defect of the …

Biological Invasions And Biocultural Diversity: Linking Ecological And Cultural Systems, Jeanine Pfeiffer, Robert Voeks

Faculty Publications

Study of the ecological and economic effects of invasive species has paralleled their progressively pervasive influence worldwide, yet their cultural impacts remain largely unexamined and therefore unrecognized. Unlike biological systems, where the ecological consequences of biological invasions are primarily negative, from an ethnoscientific standpoint, invasive species' impacts on cultural systems span a range of effects. Biological invasions affect cultural groups in myriad, often unpredictable and at times contradictory ways. This review groups case studies into a conceptual matrix suggesting three categorically different cultural impacts of invasive species. Culturally impoverishing invasive species precipitate the loss or replacement of culturally important native …

Gene Order Phylogeny Of The Genus Prochlorococcus, Haiwei Luo, Jian Shi, William Arndt, Jijun Tang, Robert Friedman

Faculty Publications

Background
Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. This character was used to resolve the evolutionary history within the genus Prochlorococcus, a group of marine cyanobacteria.

Methodology/Principal Findings
Orthologous gene sets and their genomic positions were identified from 12 species of Prochlorococcus and 1 outgroup species of Synechococcus. From this data, inversion and breakpoint distance-based phylogenetic trees were computed by GRAPPA and FastME. Statistical support of the resulting topology was obtained by application of a 50% jackknife resampling technique. The result was consistent and congruent with nucleotide sequence-based and gene-content based …

Using Sport Science To Improve Coaching: A Case Study Of The American Record Holder In The Women’S Hammer Throw, Iain Hunter, Erin Gilreath, Larry W. Judge

Faculty Publications

Conclusions from biomechanical data can make a significant difference in the performance of athletes in the hammer throw if properly understood by coaches. By utilizing this scientific approach to the hammer throw event, the throws coach will be able to determine more accurate adjustments and devise training stimuli to better accommodate the athlete. In this case study, we have attempted to bridge the gap between the researcher and the coach in our approach to teaching the hammer throw, by integrating biomechanical analysis. We have employed the use of video analysis as an essential part of our coaching/teaching system. This USATF …

Leucon (Crymoleucon) Rossi, A New Species (Crustacea: Cumacea: Leuconidae) From The Shelf Waters Of The Ross Sea (Antarctica), With A Key To The Genus Leucon South Of 60°S, Peter Rehm, Richard W. Heard

Faculty Publications

A new leuconid cumacean, Leucon (Crymoleucon) rossi n. sp., is described from depths of 84 to 458 m in the Ross Sea off the Victoria Land coast. Leucon rossi n. sp. is distinguished from other members of the genus by a combination of characters including 1) a blunt, horizontally directed pseudorostrum) Without a distinctly protruding siphon; 2) strongly developed antennal notch; 3) entire dorsomedian margin of carapace appearing serrate, armed with 14 to 19 anteriorly Curved spines in female (up to 21 in subadult males); 4) a small, but distinct, spine behind the frontal lobe; and 5) the uropodal peduncle …

A Simple, Anatomically Based Correction To The Conventional Ankle Joint Center, Dustin A. Bruening, Ashlie N. Crewe, Frank L. Buczek

Faculty Publications

Background

Conventional motion analysis studies define the ankle joint center as the midpoint between the most medial and lateral aspects of the malleoli, yet research points toward a more distal joint center location. The purpose of this study was to develop and evaluate an anatomically based correction that would move the conventional ankle joint center to a more accurate location.

Methods

Lower extremity radiographs from 30 pediatric patients were analyzed retrospectively. An offset between the conventional and more accurate ankle joint centers was measured and correlated to other common anatomical measures based on conventional skin mounted marker positions. The best …

Timing Of Supplementation Of Selenium And Isoflavones Determines Prostate Cancer Risk Factor Reduction In Rats, Merrill J. Christensen, Jessica R. Tolman, Edwin D. Lephart, Dennis L. Eggett, Kenneth Setchell

Faculty Publications

High dietary intake of selenium or isoflavones reduces risk factors for prostate cancer. We tested whether combined supplementation of these two dietary components would reduce prostate cancer risk factors in rats more than supplementation of each component individually. Methods Male Noble rat pups were exposed from conception to diets containing an adequate (0.33-0.45 mg/kg diet) or high (3.33-3.45 mg/kg) concentration of selenium as Se-methylselenocysteine and a low (10 mg/kg) or high (600 mg/kg) level of isoflavones in a 2 x 2 factorial design. Pups consumed their respective diets until sacrifice at 35, 100, or 200 days. Male Noble rat breeders, …

Multi-Break Rearrangements And Breakpoint Re-Uses: From Circular To Linear Genomes, Max A. Alekseyev

Faculty Publications

Multi-break rearrangements break a genome into multiple fragments and further glue them together in a new order. While 2-break rearrangements represent standard reversals, fusions, fissions, and translocations, 3-break rearrangements represent a natural generalization of transpositions. Alekseyev and Pevzner (2007a, 2008a) studied multi-break rearrangements in circular genomes and further applied them to the analysis of chromosomal evolution in mammalian genomes. In this paper, we extend these results to the more difficult case of linear genomes. In particular, we give lower bounds for the rearrangement distance between linear genomes and for the breakpoint re-use rate as functions of the number and proportion …

Improving Reversal Median Computation Using Commuting Reversals And Cycle Information, William Arndt, Jijun Tang

Faculty Publications

In the past decade, genome rearrangements have attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. Methods for reconstructing phylogeny from genome rearrangements include distance-based methods, MCMC methods, and direct optimization methods. The latter, pioneered by Sankoff and extended with the software suites GRAPPA and MGR, is the most accurate approach, but is very limited due to the difficulty of its scoring procedure—it must solve multiple instances of the reversal median problem to compute the score of a given tree. The reversal median problem is known to be NP-hard and all …

Infant-Feeding Practices Of Low-Income Vietnamese American Women, Yashmi Mistry, Marjorie Freedman, Kathleen Sweeney, Clarie Hollenbeck

Faculty Publications

Healthy People 2010 breastfeeding goals include 50% exclusive breastfeeding at 6 months. In California, US, Santa Clara County Women, Infants, and Children (SCCWIC) data indicated Asian participants had low (5.6%) 6-month breastfeeding rates. To examine infant-feeding practices, Vietnamese breastfeeding peer counselors surveyed 133 Vietnamese SCCWIC participants (≥ 18 years old, nonpregnant, < 28 months postpartum) using a structured questionnaire regarding intentions, attitudes, and subjective norms toward breastfeeding. Results indicated that 75% initiated breastfeeding in the hospital (33% exclusively, 42% partially), and 25% exclusively formula fed. At survey time, 49% had terminated breastfeeding (average duration 4.4 months). Feeding intentions during pregnancy predicted feeding method used (P < .001). Most prenatal advice was from SCCWIC employees, friends, and doctors who supported breastfeeding. Most postnatal advice was from nurses who supported breastfeeding and bottle-feeding equally. Stronger control beliefs, peer counseling, and education were correlated with breastfeeding (P < .001). Improved postdelivery hospital advice may further increase breastfeeding initiation and duration.

Commercial Evaluation Of A Continuous Micronutrient Fortification Process For Nixtamal Tortillas, Michael L. Dunn, Sergio O. Serna-Saldivar, Diana Sanchez-Hernandez, Robert W. Griffin

Faculty Publications

The corn tortilla plays an integral role in the Mexican diet and is an ideal vehicle for micronutrient fortification. Approximately 60% of corn tortillas in Mexico are produced from nixtamal, with the remainder prepared from masa flour. A process for continuous fortification of nixtamal tortillas was evaluated in two commercial mills in Mexico. A commercial powder dosifier was used to add micronutrient premix containing iron, zinc, folic acid, niacin, riboflavin, and thiamin to nixtamal (1 g/kg) as it was milled. After training and preliminary sampling, mills produced fortified tortillas unassisted for four weeks. Masa flow rates over a four-day period …

A Competitive Hybridization Model Predicts Probe Signal Intensity On High Density Dna Microarrays, Shuzhao Li, Alex Pozhitkov, Marius Brouwer

Faculty Publications

A central, unresolved problem of DNA microarray technology is the interpretation of different signal intensities from multiple probes targeting the same transcript. We propose a competitive hybridization model for DNA microarray hybridization. Our model uses a probe-specific dissociation constant that is computed with current nearest neighbor model and existing parameters, and only four global parameters that are fitted to Affymetrix Latin Square data. This model can successfully predict signal intensities of individual probes, therefore makes it possible to quantify the absolute concentration of targets. Our results offer critical insights into the design and data interpretation of DNA microarrays.

Calculating Expected Dna Remnants From Ancient Founding Events In Human Population Genetics, Nathan C. Sheffield, Keith A. Crandall, Andrew Stacey

Faculty Publications

Background- Recent advancements in sequencing and computational technologies have led to rapid generation and analysis of high quality genetic data. Such genetic data have achieved wide acceptance in studies of historic human population origins and admixture. However, in studies relating to small, recent admixture events, genetic factors such as historic population sizes, genetic drift, and mutation can have pronounced effects on data reliability and utility. To address these issues we conducted genetic simulations targeting influential genetic parameters in admixed populations. Results- We performed a series of simulations, adjusting variable values to assess the affect of these genetic parameters on current …

Body Mass Index And Health Related Quality Of Life In Elementary School Children: A Pilot Study, Lei Zhang, Peter J. Fos, William D. Johnson, Vafa Kamali, Reagan G. Cox, Miguel A. Zuniga, Theresa Kittle

Faculty Publications

Background: We investigated the relationship between Body Mass Index (BMI) and health-related quality of life (HRQOL) indicated by baseline health status in elementary school children. Methods: Data were obtained via parents whose children enrolled in an elementary school, kindergarten to fourth grade, in southern Mississippi in spring 2004. Parents completed the SF-10 for Children (TM), a brief 10-item questionnaire designed to measure children's HRQOL on a voluntary basis. Results: A total of 279 parents completed the questionnaires for their children. On average, physical and psychosocial summary scores, major indicators for HRQOL, were significantly higher among the elementary school children in …

Conservation And Conflict Between Endangered Desert Fishes, Jennifer M. Gumm, Jennifer L. Snekser, Murray Itzkowitz

Faculty Publications

Conservation of naturally sympatric endangered species requires unique considerations. While impacts of invasive species garner much attention, interactions between endangered species must also be managed. The endangered Leon Springs pupfish, Cyprinodon bovinus, has suffered a population decline due to decreasing natural habitat. As breeding habitat is lost, C. bovinus is also adversely affected by the sympatric, endangered Pecos gambusia, Gambusia nobilis. Here, we document interactions between these species, finding significantly more G. nobilis accumulated at pupfish spawning events than randomly distributed on breeding grounds in the absence of spawning. As a known egg predator, our results suggest that G. nobilis …

Black Bears On The Way Back, Christopher E. Comer

Faculty Publications

No abstract provided.

Red-Cockaded Woodpeckers And Hurricanes, Zoe Hoyle

Faculty Publications

No abstract provided.

Modeling The Daily Activities Of Breeding Colonial Seabirds: Dynamic Occupancy Patterns In Multiple Habitat Patches, Andrea L. Moore, Smruti P. Damania, Shandelle M. Henson, James L. Hayward

Faculty Publications

We constructed differential equation models for the diurnal abundance and distribution of breeding glaucous-winged gulls (Larus glaucescens) as they moved among nesting and non-nesting habitat patches. We used time scale techniques to reduce the differential equations to algebraic equations and connected the models to field data. The models explained the data as a function of abiotic environmental variables with R2=0.57. A primary goal of this study is to demonstrate the utility of a methodology that can be used by ecologists and wildlife managers to understand and predict daily activity patterns in breeding seabirds.

Lis1 And Ndel1 Influence The Timing Of Nuclear Envelope Breakdown In Neural Stem Cells, Sachin Hebbar, Mariano T. Mesngon, Aimee M. Guillotte, Bhavim Desai, Ramses Ayala, Deanna S. Smith

Faculty Publications

Lis1 and Ndel1 are essential for animal development. They interact directly with one another and with cytoplasmic dynein. The developing brain is especially sensitive to reduced Lis1 or Ndel1 levels, as both proteins influence spindle orientation, neural cell fate decisions, and neuronal migration. We report here that Lis1 and Ndel1 reduction in a mitotic cell line impairs prophase nuclear envelope (NE) invagination (PNEI). This dyneindependent process facilitates NE breakdown (NEBD) and occurs before the establishment of the bipolar spindle. Ndel1 phosphorylation is important for this function, regulating binding to both Lis1 and dynein. Prophase cells in the ventricular zone (VZ) …

Seasonal Variations In Nutrient Concentrations And Speciation In The Chena River, Alaska, Yihua Cai, Laodong Guo, Thomas A. Douglas, Terry E. Whitledge

Faculty Publications

To better understand the seasonal controls on nutrient abundances, speciation, and fluxes in a watershed underlain by discontinuous permafrost, we collected water samples biweekly from the Chena River during 2005-2006 to measure inorganic and organic N, P, and Si in dissolved and particulate phases. Nitrate concentrations were low (8-14 mu M) during the winter and summer dry seasons but were elevated during the spring freshet (15-24 mu M). Ammonium varied from 8 to 13 mu M during the winter but dropped dramatically during the ice-open season to 0.1-3 mM. Phosphate was very low throughout the year (ranging from 0.03 to …

Oriented Cell Growth On Self-Assembled Bacteriophage M13 Thin Films, Jianhua Rong, L. Andrew Lee, Kai Li, Brandon Harp, Charlene M. Mello, Zhongwei Niu, Qian Wang

Faculty Publications

Fibrillar M13 bacteriophages were used as basic building blocks to generate thin films with aligned nanogrooves, which, upon chemical grafting with RGD peptides, guide cell alignment and orient the cell outgrowth along defined directions.

Light-Dependant Biostabilisation Of Sediments By Stromatolite Assemblages, David M. Paterson, Rebecca J. Aspden, Pieter T. Visscher, Mireille Consalvey, Miriam S. Andres, Alan W. Decho, John Stolz, R. Pamela Reid

Faculty Publications

For the first time we have investigated the natural ecosystem engineering capacity of stromatolitic microbial assemblages. Stromatolites are laminated sedimentary structures formed by microbial activity and are considered to have dominated the shallows of the Precambrian oceans. Their fossilised remains are the most ancient unambiguous record of early life on earth. Stromatolites can therefore be considered as the first recognisable ecosystems on the planet. However, while many discussions have taken place over their structure and form, we have very little information on their functional ecology and how such assemblages persisted despite strong eternal forcing from wind and waves. The capture …

Many Species In One: Dna Barcoding Overestimates The Number Of Species When Nuclear Mitochondrial Pseudogenes Are Coamplified, Michael F. Whiting, Hojun Song, Keith A. Crandall, Jennifer E. Buhay

Faculty Publications

Nuclear mitochondrial pseudogenes (numts) are nonfunctional copies of mtDNA in the nucleus that have been found in major clades of eukaryotic organisms.

Resulting Shifts In Percentile And Standard Placements After Comparison Of The Bod Pod And Dxa, Timothy Heden, Steve Shepard, John Smith, Kay Covington, James D. Lecheminant

Faculty Publications

Int J Exerc Sci 1(3) : 113-124, 2008. The purpose of this study was to determine the validity of the BOD POD® when compared to the DXA and if placement on a percentile chart and standard table is affected by any differences between the two measures. A total of 244 (27.7 ± 10.8 yrs, 77.3 ± 16.1 kg, 171.4 ± 10.1 cm, 26.31 ± 5.42 BMI) males and females between the ages of 18 and 52 were recruited to participate in this study. The participant’s body fat percentage (%BF) was tested in random order on the BOD POD® and DXA …

Phylogenetic Reconstruction From Transpositions, Feng Yue, Meng Zhang, Jijun Tang

Faculty Publications

Background
Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become possible to represent whole genomes as ordered lists of gene identifiers and to study the rearrangement of these entities through computational means. As a result, genome rearrangement data has attracted increasing attentions from both biologists and computer scientists as a new type of data for phylogenetic analysis. The main events of genome rearrangements include inversions, transpositions and transversions. To date, GRAPPA and MGR are the most accurate …

Novel Implementation Of Conditional Co-Regulation By Graph Theory To Derive Co-Expressed Genes From Microarray Data, Arun Rawat, Georg J. Seifert, Youping Deng

Faculty Publications

Background

Most existing transcriptional databases like Comprehensive Systems-Biology Database (CSB.DB) and Arabidopsis Microarray Database and Analysis Toolbox (GENEVESTIGATOR) help to seek a shared biological role (similar pathways and biosynthetic cycles) based on correlation. These utilize conventional methods like Pearson correlation and Spearman rank correlation to calculate correlation among genes. However, not all are genes expressed in all the conditions and this leads to their exclusion in these transcriptional databases that consist of experiments performed in varied conditions. This leads to incomplete studies of co-regulation among groups of genes that might be linked to the same or related biosynthetic pathway.

Results …

Decline In A Dominant Invertebrate Species Contributes To Altered Carbon Cycling In A Low-Diversity Soil Ecosystem, Byron J. Adams, J. E. Barrett, Ross A. Virginia, Diana H. Wall

Faculty Publications

Low-diversity ecosystems cover large portions of the Earth's land surface, yet studies of climate change on ecosystem functioning typically focus on temperate ecosystems, where diversity is high and the effects of individual species on ecosystem functioning are difficult to determine. We show that a climate-induced decline of an invertebrate species in a low-diversity ecosystem could contribute to significant changes in carbon © cycling. Recent climate variability in the McMurdo Dry Valleys of Antarctica is associated with changes in hydrology, biological productivity, and community composition of terrestrial and aquatic ecosystems. One of the greatest changes documented in the dry valleys is …

Satellite Assessment Of Bio-Optical Properties Of Northern Gulf Of Mexico Coastal Waters Following Hurricanes Katrina And Rita, Steven E. Lohrenz, Wei-Jun Cai, Xiaogang Chen, Merritt Tuel

Faculty Publications

The impacts of major tropical storms events on coastal waters include sediment resuspension, intense water column mixing, and increased delivery of terrestrial materials into coastal waters. We examined satellite imagery acquired by the Moderate Resolution Imaging Spectroradiometer (MODIS) ocean color sensor aboard the Aqua spacecraft following two major hurricane events: Hurricane Katrina, which made landfall on 29 August 2005, and Hurricane Rita, which made landfall on 24 September. MODIS Aqua true color imagery revealed high turbidity levels in shelf waters immediately following the storms indicative of intense resuspension. However, imagery following the landfall of Katrina showed relatively rapid return of …

Effect Of Iron Source On Color And Appearance Of Micronutrient-Fortified Corn Flour Tortillas, A. T. Richins, K. E. Burton, Heather F. Pahulu, Laura K. Jefferies, Michael L. Dunn

Faculty Publications

Iron deficiency anemia is a widespread occurrence. Consequently, iron is commonly added in cereal fortification programs. However, many iron sources cause undesirable sensory changes, especially color changes, in the food being fortified. This study evaluated the effect of different iron sources on CIE L*a*b* color values and sensory color perception in fortified corn tortillas. Corn masa flour was fortified with micronutrient premix containing vitamins, zinc, and one of eight iron compounds. Iron sources included ferrous fumarate (F), ferrous sulfate (S), ferric orthophosphate (OP), ferrous lactate (L), ferrous gluconate (G), ferric pyrophosphate (PP), sodium iron (III)-EDTA, and A-131 electrolytic iron (E), …