Life Sciences Commons^™

Feature Selection And Classification Of Maqc-Ii Breast Cancer And Multiple Myeloma Microarray Gene Expression Data, Qingzhong Liu, Andrew H. Sung, Zhongxue Chen, Jianzhong Liu, Xudong Huang, Youping Deng

Faculty Publications

Microarray data has a high dimension of variables but available datasets usually have only a small number of samples, thereby making the study of such datasets interesting and challenging. In the task of analyzing microarray data for the purpose of, e.g., predicting gene-disease association, feature selection is very important because it provides a way to handle the high dimensionality by exploiting information redundancy induced by associations among genetic markers. Judicious feature selection in microarray data analysis can result in significant reduction of cost while maintaining or improving the classification or prediction accuracy of learning machines that are employed to sort …

Environmental Dna Sequencing Primers For Eutardigrades And Bdelloid Rotifers, Byron J. Adams, Jeremy Whiting, Elizabeth K. Costello, Kristen R. Freeman, Andrew P. Martin, Michael S. Robeson, Steve K. Schmidt

Faculty Publications

Background: The time it takes to isolate individuals from environmental samples and then extract DNA from each individual is one of the problems with generating molecular data from meiofauna such as eutardigrades and bdelloid rotifers. The lack of consistent morphological information and the extreme abundance of these classes makes morphological identification of rare, or even common cryptic taxa a large and unwieldy task. This limits the ability to perform large-scale surveys of the diversity of these organisms. Here we demonstrate a culture-independent molecular survey approach that enables the generation of large amounts of eutardigrade and bdelloid rotifer sequence data directly …

Heterologous Expression Studies Of Saccharomyces Cerevisiae Reveal Two Distinct Trypanosomatid Caax Protease Activities And Identify Their Potential Targets, David Z. Mokry, Surya P. Manandhar, Kristen A. Chicola, George M. Santangelo, Walter K. Schmidt

Faculty Publications

The CaaX tetrapeptide motif typically directs three sequential posttranslational modifications, namely, isoprenylation, proteolysis, and carboxyl methylation. In all eukaryotic systems evaluated to date, two CaaX proteases (Rce1 and Ste24/Afc1) have been identified. Although the Trypanosoma brucei genome also encodes two putative CaaX proteases, the lack of detectable T. brucei Ste24 activity in trypanosome cell extracts has suggested that CaaX proteolytic activity within this organism is solely attributed to T. brucei Rce1 (J. R. Gillespie et al., Mol. Biochem. Parasitol. 153: 115-124. 2007). In this study, we demonstrate that both T. brucei Rce1 and T. brucei Ste24 are enzymatically active when …

Water Uptake Threshold Of Rabbiteye (Vaccinium Ashei) Blueberries And Its Influence On Fruit Splitting, Donna A. Marshall-Shaw, James M. Spiers, Kenneth J. Curry

Faculty Publications

Split-resistant and split-susceptible rabbiteye blueberry fruit were evaluated at all stages of development to determine ''water uptake thresholds'' by soaking in distilled water. Weight increase after soaking was measured, and percent weight gain was calculated to take into consideration the weight increase of the fruit from development. The ratio of percent increase in volume to weight increase resulting from water uptake was calculated. Ratios of percent water uptake to weight increase between splitsusceptible 'Tifblue' and split-resistant 'Premier' blueberries were found to be similar. The split-susceptible 'Tifblue' had a 1.6 g/50 fruit increase with a 1.7% water uptake and a ratio …

Sensitivity Of The Carbon Cycle In The Arctic To Climate Change, A. David Mcguire, Leif G. Anderson, Torben R. Christensen, Scott Dallimore, Laodong Guo, Daniel J. Hayes, Martin Heimann, Robie W. Macdonald, Nigel Roulet

Faculty Publications

The recent warming in the Arctic is affecting a broad spectrum of physical, ecological, and human/cultural systems that may be irreversible on century time scales and have the potential to cause rapid changes in the earth system. The response of the carbon cycle of the Arctic to changes in climate is a major issue of global concern, yet there has not been a comprehensive review of the status of the contemporary carbon cycle of the Arctic and its response to climate change. This review is designed to clarify key uncertainties and vulnerabilities in the response of the carbon cycle of …

The Pentameric Vertex Proteins Are Necessary For The Icosahedral Carboxysome Shell To Function As A Co2 Leakage Barrier, Fei Cai, Balaraj B. Menon, Gordon C. Cannon, Kenneth J. Curry, Jessup M. Shively, Sabine Heinhorst

Faculty Publications

Background

Carboxysomes are polyhedral protein microcompartments found in many autotrophic bacteria; they encapsulate the CO₂ fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) within a thin protein shell and provide an environment that enhances the catalytic capabilities of the enzyme. Two types of shell protein constituents are common to carboxysomes and related microcompartments of heterotrophic bacteria, and the genes for these proteins are found in a large variety of bacteria.

Methodology/Principal Findings

We have created a Halothiobacillus neapolitanus knockout mutant that does not produce the two paralogous CsoS4 proteins thought to occupy the vertices of the icosahedral carboxysomes and related microcompartments. Biochemical …

An Intertidal Sea Star Adjusts Thermal Inertia To Avoid Extreme Body Temperatures, Sylvain Pincebourde, Eric Sanford, Brian Helmuth

Faculty Publications

The body temperature of ectotherms is influenced by the interaction of abiotic conditions, morphology, and behavior. Although organisms living in different thermal habitats may exhibit morphological plasticity or move from unfavorable locations, there are few examples of animals adjusting their thermal properties in response to short-term changes in local conditions. Here, we show that the intertidal sea star Pisaster ochraceus modulates its thermal inertia in response to prior thermal exposure. After exposure to high body temperature at low tide, sea stars increase the amount of colder than-air fluid in their coelomic cavity when submerged during high tide, resulting in a …

Nutrition Literacy Status And Preferred Nutrition Communication Channels Among Adults In The Lower Mississippi Delta, Jamie Zoellner, Carol L. Connell, Wendy Bounds, Lashaundrea Crook, M. Kathleen Yadrick

Faculty Publications

Introduction

The objective of this cross-sectional study was to examine the nutrition literacy status of adults in the Lower Mississippi Delta.

Methods

Survey instruments included the Newest Vital Sign and an adapted version of the Health Information National Trends Survey. A proportional quota sampling plan was used to represent educational achievement of residents in the Delta region. Participants included 177 adults, primarily African Americans (81%). Descriptive statistics, X(2) analysis, analysis of variance, and multivariate analysis of covariance tests were used to examine survey data.

Results

Results indicated that 24% of participants had a high likelihood of limited nutrition literacy, 28% …

It's Time To Check The Nets: Research And Conservation Of Rafinesque Big-Eared Bats In East Texas, Christopher E. Comer

Faculty Publications

No abstract provided.

A Method Of Successive Corrections Of The Control Subspace In The Reduced-Order Variational Data Assimilation, Max Yaremchuk, Dmitri A. Nechaev, Gleb Panteleev

Faculty Publications

A version of the reduced control space four-dimensional variational method (R4DVAR) of data assimilation into numerical models is proposed. In contrast to the conventional 4DVAR schemes, the method does not require development of the tangent linear and adjoint codes for implementation. The proposed R4DVAR technique is based on minimization of the cost function in a sequence of low-dimensional subspaces of the control space. Performance of the method is demonstrated in a series of twin-data assimilation experiments into a nonlinear quasigeostrophic model utilized as a strong constraint. When the adjoint code is stable, R4DVAR's convergence rate is comparable to that of …

Complex Evolution Of A Highly-Conserved Microsatellite Locus In Several Fish Species, J.-X. Liu, Bert Ely

Faculty Publications

The evolutionary dynamics of a highly conserved microsatellite locus (Dla 11) were studied in several fish species. The data indicated that multiple types of compound microsatellites arose through point mutations that were sometimes followed by expansion of the derived motif. Furthermore, extensive length variation was detected among species in the regions immediately flanking the repeat region.

The Use And Perceptions Of Concept Mapping As A Learning Tool By Dietetic Internship Students And Preceptors, Elaine Fontenot Molaison, Kimberly Taylor, Dawn Erickson, Carol Connell

Faculty Publications

Critical thinking and problem solving skills are currently emphasis areas in the education of allied health professionals. Use of concept maps to teach these skills have been utilized primarily in nursing and medical education, but little has been published about their use in dietetics education. Therefore the purpose of this study was to evaluate the potential efficacy of concept mapping as a learning tool for nutrition assessment among dietetic interns and its acceptability by internship preceptors. Nineteen dietetic interns and 31 preceptors participated in a quasi-experimental pre-/post-design in which the concept mapping strategy was taught as a replacement for the …

Transcriptome Analysis Of Frog Virus 3, The Type Species Of The Genus Ranavirus, Family Iridoviridae, Sai Majji, V. Thodima, R. Sample, D. Whitley, Y. Deng, J. Mao, V. Gregory Chinchar

Faculty Publications

Frog virus 3 is the best characterized species within the genus Ranavirus, family Iridoviridae. FV3's large (similar to 105 kbp) dsDNA genome encodes 98 putative open reading frames (ORFs) that are expressed in a coordinated fashion leading to the sequential appearance of immediate early (IE), delayed early (DE) and late (L) viral transcripts. As a step toward elucidating molecular events in FV3 replication, we sought to identify the temporal Class Of Viral messages. To accomplish this objective an oligonucleotide microarray containing 70-mer probes corresponding to each of the 98 FV3 ORFs was designed and used to examine viral gene expression. …

Mouse Embryonic Stem Cells Lacking P38Α And P38Δ Can Differentiate To Endothelial Cells, Smooth Muscle Cells, And Epithelial Cells, Samujjwal Chakraborty, Baobin Kang, Faqing Huang, Yan-Lin Guo

Faculty Publications

The p38 mitogen-activated protein (MAP) kinases (p38) are important signaling molecules that regulate various cellular processes. Four isoforms of p38 family, p38α, p38β, p38γ, and p38δ, have been identified in mammalian cells. Previous studies have shown that p38α knockout is embryonic lethal in mice. At the cellular level, p38α is abundantly expressed in mouse embryonic stem cells (ESCs), but p38α knockout (p38α-/-) ESCs can differentiate to endothelial cells (ECs), smooth muscle cells (SMCs), and neurons. We speculate that the lost function of p38α in p38α-/- ESCs may be compensated for by the redundant function of other isoforms. To test this …

Sibship Reconstruction Demonstrates The Extremely Low Effective Population Size Of Striped Bass Morone Saxatilis In The Santee-Cooper System, South Carolina, Usa, Jin-Xian Liu, Bert Ely

Faculty Publications

For organisms with great fecundity and high mortality in early life stages, such as shellfish or fishes, the need to match reproductive activity with environmental conditions conducive to spawning, fertilization, larval development and recruitment may result in extreme variance in reproductive success among individuals. The main objective of this study was to investigate evidence of large variance in the reproductive success of the striped bass Morone saxatilis in the Santee-Cooper system, South Carolina, USA. Seven microsatellite loci were analysed in 603 recruits representing three yearly cohorts from 1992 to 1994, and a group analysis was performed to identify full-sib families. …

Evaluation Of Cay-1, An Experimental, Natural Fungicide, For Control Of Strawberry Pathogens, Kenneth J. Curry, Maritza Abril, Anthony J. Delucca, Stephen M. Boue, Barbara J. Smith, David E. Wedge

Faculty Publications

CAY-1 is an experimental, natural product being tested as a potential fungicide. This saponin isolated from Capsicum frutescens interacts with membrane sterols causing leakage of cell components and ultimately cell death in a variety of fungi. CAY-1 and the commercial fungicide captan were tested in an in vitro doseresponse dilution-broth assay. They caused at least 85% growth inhibition of the fungal pathogens Colletotrichum acutatum, C fragariae and C. gloeosporioides when tested at 3.0 μM. Even though CAY-1 strongly reduced the growth of these fungal pathogens in laboratory assays and prevented anthracnose development in detached leaf assays, it did not …

Remote Sensing And Mapping Of Tamarisk Along The Colorado River, Usa: A Comparative Use Of Summer-Acquired Hyperion, Thematic Mapper And Quickbird Data, Gregory A. Carter, Kelly L. Lucas, Gabriel A. Blossom, Cheryl L. Lassitter, Dan M. Holiday, David S. Mooneyhan, Danielle R. Fastring, Tracy R. Holcombe, Jerry A. Griffith

Faculty Publications

Tamarisk (Tamarix spp., saltcedar) is a well-known invasive phreatophyte introduced from Asia to North America in the 1800s. This report compares the efficacy of Landsat 5 Thematic Mapper (TM5), QuickBird (QB) and EO-1 Hyperion data in discriminating tamarisk populations near De Beque, Colorado, USA. As a result of highly correlated reflectance among the spectral bands provided by each sensor, relatively standard image analysis methods were employed. Multispectral data at high spatial resolution (QB, 2.5 m Ground Spatial Distance or GSD) proved more effective in tamarisk delineation than either multispectral (TM5) or hyperspectral (Hyperion) data at moderate spatial resolution (30 m …

Detecting Proteins In Highly Autofluorescent Cells Using Quantum Dot Antibody Conjugates, Karen M. Orcutt, Shanshan Ren, Kjell Gundersen

Faculty Publications

We have applied quantum dot (Qdot) antibody conjugates as a biomolecular probe for cellular proteins important in biogeochemical cycling in the sea. Conventional immunological methods have been hampered by the strong autofluorescence found in cyanobacteria cells. Qdot conjugates provide an ideal alternative for studies that require long-term imaging of cells such as detection of low abundance cellular antigens by fluorescence microscopy. The advantage of Qdot labeled probes over conventional immunological methods is the photostability of the probe. Phycoerythrin bleaches in cyanobacterial cells under prolonged UV or blue light excitation, which means that the semiconducting nanocrystal probe, the Qdot, can yield …

The Tbx20 Homologs Midline And H15 Specify Ventral Fate In The Drosophila Melanogaster Leg, Pia C. Svendson, Ann Formaz-Preston, Sandra M. Leal, William J. Brook

Faculty Publications

Regional fates in the developing limbs of Drosophila melanogaster are controlled by selector gene transcription factors. Ventral fate in the fly leg is specified by the expression of the ligand Wingless. We present evidence that midline and H15, members of the Tbx20 class of T-box transcription factors, are key mediators of the Wingless signal in the formation of the ventral region of the fly leg. midline and H15 are restricted to identical ventral domains of expression through activation by Wingless and repression by the dorsal signal Decapentaplegic. midline and H15 function redundantly and cell autonomously in the formation of …

Interaction Of Fish Aryl Hydrocarbon Receptor Paralogs (Ahr1 And Ahr2) With The Retinoblastoma Protein, Rebeka R. Merson, Sibel I. Karchner, Mark E. Hahn

Faculty Publications

The aryl hydrocarbon receptor (AHR) mediates the toxic effects of 2,3,7,8-tetrachlorodibenzo-pdioxin (TCDD) and related compounds. In some mammalian cell lines, TCDD induces G1 cell cycle arrest, which depends on an interaction between the AHR and the retinoblastoma tumor suppressor (RB). Mammals possess one AHR, whereas fishes possess two or more AHR paralogs that differ in the domains important for AHR-RB interactions in mammals. To test the hypothesis that fish AHR paralogs differ in their ability to interact with RB, we cloned RB cDNA from Atlantic killifish, Fundulus heteroclitus, and studied the interactions of killifish RB protein with killifish AHR1 and …

Morphological Deformities As Biomarkers In Fish From Contaminated Rivers In Taiwan, Peter Lin Sun, William E. Hawkins, Robin M. Overstreet, Nancy J. Brown-Peterson

Faculty Publications

Tilapia (Oreochromis spp.) were collected seasonally from four contaminated rivers in southwestern Taiwan for studies of morphological deformities that could be used as biomarkers of contamination. Morphological deformities found in tilapia were separated into 15 categories. Overall, the prevalence of deformities such as split fins, lower lip extension and gill deformities were significantly related to various water quality parameters, including low DO and high ammonium, lead and zinc concentrations. The persistence of tilapia in polluted waters and the development of a suite of morphological deformities suggest that tilapia can be used as sentinels of non-point source pollution in rivers.

Differential Mortality Drives Life-History Evolution And Population Dynamics In The Fish Brachyrhaphis Rhabdophora, Jerald B. Johnson, J. Jaime Zuniga-Vega

Faculty Publications

Life-history theory predicts that populations experiencing different levels of extrinsic mortality will evolve divergent reproductive strategies. Previous work in the live bearing fish Brachyrhaphis rhabdophora shows that individuals from populations that occur with piscivorous fish mature earlier and at smaller sizes and have more and smaller offspring than fish from populations without predators. However, until now, there have been no data to demonstrate that differences in mortality rates actually exist between predator and predator free sites. Here we present the results of a serial mark-recapture field study designed to estimate mortality rates in natural populations of B. rhabodophora from Costa …

Odontometric Patterns In The Radiation Of Extant Ground-Dwelling Squirrels Within Marmotini (Sciuridae: Xjrini), H. Thomas Goodwin

Faculty Publications

I document odontometry variation across ground-dwelling squirrels of the Holarctic tribe Marmotini. Dental size, which correlates well with published average body mass values across species, accounts for most odontometric variation across the clade. Dental shape variation primarily reflects relative size of P3 (upper cheek teeth) and relative width of p4-ml + length of m3 (lower cheek teeth). Shape variables and relative tooth crown height covary significantly across species, suggesting a common functional complex or shared genetic control. When dental morphology is mapped on published DNA-based phytogenies, Sciurotamias (Chinese rock squirrels), Ammospermophilus (antelope squirrels), and basal subgenera within Spermophilus (ground squirrels …

Chemical And Isotopic Characterization Of Size-Fractionated Organic Matter From Cryoturbated Tundra Soils, Northern Alaska, Chunhao Xu, Laodong Guo, Chien-Lu Ping, Daniel M. White, Thomas D. Lorenson

Faculty Publications

Recent studies indicate a second layer of organic matter often accumulates in the lower active layer and upper permafrost in arctic tundra soils as a result of cryoturbation. In this study, cryoturbated organic matter was characterized using a combination of physical size fractionation and modern analytical techniques for elemental composition (C and N), stable isotopes (delta(13) C and delta(15)N), radiocarbon content (Delta(14)C), and molecular fingerprinting (pyrolysis-gas chromatography/mass spectrometry, Py-GC/MS). The results indicated that cryoturbated organic matter could be highly bioavailable. Soil organic matter (SOM) associated with fine sand particles was considered to be the organic carbon pool most sensitive to …

Developmental Emergence Of Power-Law Wake Behavior Depends Upon The Functional Integrity Of The Locus Coeruleus, Andrew J. Gall, Badal Joshi, Janet Best, Virginia R. Florang, Jonathan A. Doorn, Mark S. Blumberg

Faculty Publications

STUDY OBJECTIVES:

Daily amounts of sleep and wakefulness are accumulated in discrete bouts that exhibit distinct statistical properties. In adult mammals, sleep bout durations follow an exponential distribution whereas wake bout durations follow a power-law distribution. In infant Norway rats, however, wake bouts initially follow an exponential distribution and only transition to a power-law distribution beginning around postnatal day 15 (P15). Here we test the hypothesis that the locus coeruleus (LC), one of several wake-active nuclei in the brainstem, contributes to this developmental transition.

DESIGN:

At P7, rats were injected subcutaneously with saline or DSP-4, a neurotoxin that targets noradrenergic …

Guatemala's Green Revolution: Synthetic Fertilizer, Public Health, And Economic Autonomy In The Mayan Highland, David Carey

Faculty Publications

Despite extensive literature both supporting and critiquing the Green Revolution, surprisingly little attention has been paid to synthetic fertilizers' health and environmental effects or indigenous farmers' perspectives. The introduction of agrochemicals in the mid-twentieth century was a watershed event for many Mayan farmers in Guatemala. While some Maya hailed synthetic fertilizers' immediate effectiveness as a relief from famines and migrant labor, others lamented the long-term deterioration of their public health, soil quality, and economic autonomy. Since the rising cost of agrochemicals compelled Maya to return to plantation labor in the 1970s, synthetic fertilizers simply shifted, rather than alleviated, Mayan dependency …

Aintegumenta And Aintegumenta-Like6 Act Redundantly To Regulate Arabidopsis Floral Growth And Patterning, Beth A. Krizek

Faculty Publications

An Arabidopsis (Arabidopsis thaliana) flower consists of four types of organs arranged in a stereotypical pattern. This complex floral structure is elaborated from a small number of floral meristem cells partitioned from the shoot apical meristem during reproductive development. The positioning of floral primordia within the periphery of the shoot apical meristem depends on transport of the phytohormone auxin with floral anlagen arising at sites of auxin maxima. An early marker of lateral organ fate is the AP2/ERF-type transcription factor AINTEGUMENTA (ANT), which has been proposed to act downstream of auxin in organogenic growth. Here, I show that …

On The Mechanisms Of Episodic Salinity Outflow Events In The Strait Of Hormuz, Prasad G. Thoppil, Patrick J. Hogan

Faculty Publications

Observations in the Strait of Hormuz (26.26 degrees N, 56.08 degrees E) during 1997-98 showed substantial velocity fluctuations, accompanied by episodic changes in the salinity outflow events with amplitude varying between 1 and 2 psu on time scales of several days to a few weeks. These events are characterized by a rapid increase in salinity followed by an abrupt decline. The mechanisms behind these strong pulses of salinity events are investigated with a whigh-resolution (similar to 1 km) Hybrid Coordinate Ocean Model (HYCOM) with particular reference to the year 2005. In accordance with the observations, the simulated salinity events are …

Gene Order Phylogeny And The Evolution Of Methanogens, Haiwei Luo, Zhiyi Sun, William Arndt, Jian Shi, Robert Friedman, Jijun Tang

Faculty Publications

Methanogens are a phylogenetically diverse group belonging to Euryarchaeota. Previously, phylogenetic approaches using large datasets revealed that methanogens can be grouped into two classes, “Class I” and “Class II”. However, some deep relationships were not resolved. For instance, the monophyly of “Class I” methanogens, which consist of Methanopyrales, Methanobacteriales and Methanococcales, is disputable due to weak statistical support. In this study, we use MSOAR to identify common orthologous genes from eight methanogen species and a Thermococcale species (outgroup), and apply GRAPPA and FastME to compute distance-based gene order phylogeny. The gene order phylogeny supports two classes of methanogens, but it …

My Two Boots ... A Walk Through The Wetlands. An Annual Outing For 700 Middle School Students, Julie Cwikla, Mark Lasalle, Sybil Wilner

Faculty Publications

No abstract provided.