Life Sciences Commons^™

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 transgenic …

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

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 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 μm by …

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 …

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 …

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 in white skeletal …

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 …

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 its function. …

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 …

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

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 …

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)). They were at the early stages of sexual maturity, and their condition …

Source And Transport Of Terrigenous Organic Matter In The Upper Yukon River: Evidence From Isotope (𝛿c-13, Δc-14, And 𝛿n-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 +/- 8% …

Summer Transport Estimates Of The Kamchatka Current Derived As A Variational Inverse Of Hydrophysical And Surface Drifter Data, G.G. Panteleev, P. Stabeno, V.A. Luchin, Dmitri A. Nechaev, M. Ikeda

Faculty Publications

The quasistationary summer Bering Sea circulation is reconstructed as a variational inverse of the hydrographic and atmospheric climatologies, transport estimates through the Bering Strait, and surface drifter data. Our results indicate the splitting of the Kamchatka Current in the vicinity of the Shirshov Ridge. This branching is in agreement with independent ARGO drifter observations. It was also found, that transport of the Kamchatka Current gradually increases downstream from 14 Sv in the Olyutorsky Gulf to 24 Sv in the Kamchatka Strait, which is twice higher than previous estimates.

The Total And Specific Dimensions Of Self Concept Related To Female Participation In Collegiate Athletics, Dane Bradford Beary

Dissertations

The purpose of this study was to determine if differences existed between female collegiate sport participation and non-participation, as well as female collegiate individual and team sport participation on the total, the specific dimensions of self-concept and supplementary scores as rendered by the Tennessee Self-Concept Scale Second Edition TSCS:2 (Fitts & Warren, 1996). A subject pool of N=190 participants were used. All subjects included in data analysis were female undergraduate students. A multivariate analysis of variance (M ANOVA) was utilized to evaluate effects of sports participation versus non-participation and individual versus team sports participation on self-concept. On sports participation versus …

Phylogeny And Androecial Evolution In Schisandraceae, Inferred From Sequences Of Nuclear Ribosomal Dna Its And Chloroplast Dna TrnL-F Regions, Zhong Liu, Gang Hao, Yi-Bo Luo, Leonard B. Thien, Samuel W. Rosso, An-Ming Lu, Zhi-Duan Chen

Faculty Publications

Sequences of nuclear ribosomal DNA ITS and chloroplast trnL‐F regions were used to construct a phylogeny of Schisandraceae. The results show that there are two major clades in Schisandraceae. One is composed entirely of Schisandra species; the other contains a mixture of Schisandra and Kadsura species. Molecular data place Smith’s sect. Sphaerostema of Schisandra prominently within Kadsura, and thus neither Schisandra nor Kadsura is monophyletic, refuting the traditional division of the family into two genera based on morphological characters of mature fruits. The sister relationship between S. glabra (North America) and S. bicolor (China) and the monophyly of …

Vittatispora, A New Melanosporaceous Genus From Indian Soil, Preeti Chaudhary, Jinx Campbell, David L. Hawksworth, Kedarnath N. Sastry

Faculty Publications

Vittatispora coorgii gen. sp. nov., isolated from soil in India, is described and illustrated. The fungus has morphological characteristics of the genera Melanospora, Sphaerodes and Syspastospora. The most striking feature is the presence of a thick hyaline ridge along the vertical axis of the lemonshaped ascospores wall. Perithecia also have a long neck composed of adhering hyphae, similar to that of Syspatospora. Phylogenetic studies on the 28S rDNA indicate it is closely related to Melanospora and Sphaerodes and belongs in the Ceratostomataceae. The new genus is based on the distinctive morphology and phylogenetic analyses. The fungus grew in culture only …

Antiestrogens Inhibit Xenoestrogen-Induced Brain Aromatase Activity But Do Not Prevent Xenoestrogen-Induced Feminization In Japanese Medaka (Oryzias Latipes), Adam J. Kuhl, Marius Brouwer

Faculty Publications

In fish, exposure to estrogen or estrogen-mimicking chemicals (xenoestrogeus)during a critical period of development can irreversibly invert sex differentiation. In medaka, a male-to-female reversal upon exposure to a xenoestrogen is accompanied by an increase in brain aromatase expression and activity. However, whether this increase is the direct cause of sex reversal is unknown. In this study we further examined the role brain aromatase plays in genesis of developmental abnormalities in response to endocrine-disrupting chemicals (EDCs). Further, the effects of a mixture of apparent antagonistic environmentally relevant EDCs on development were examined to determine if their combined actions could lessen each …

Cytochrome P4501a Is Induced In Endothelial Cell Lines From The Kidney And Lung Of The Bottlenose Dolphin, Tursiops Truncatus, Rita Anne Garrick, Bruce R. Woodin, Joanna Y. Wilson, Bobby L. Middlebrooks, John J. Stegman

Faculty Publications

Marine mammals respond to the presence of polycyclic and planar halogenated aromatic hydrocarbons (PAH or PHAH) with the induced expression in endothelium of cytochrome P4501A1, regulated through the aryl hydrocarbon receptor (AHR) transcription factor. Physiological responses in other animals, such as edema and inflammation indicate that the endothelium may be compromised by exposure to AHR agonists, which are ubiquitous in the marine environment. In other mammals and fish the cellular and molecular consequences of exposure to AHR agonists have been elucidated in cultured endothelial cells. We have cultured and characterized cetacean endothelial cells (EC) and used them in induction studies. …

Zonal Patterns Of Delta C-13, Delta N-15 And Po-210 In The Tropical And Subtropical North Pacific, Min Chen, Laodong Guo, Qiang Ma, Yusheng Qiu, Run Zhang, E Lv, Yipu Huang

Faculty Publications

Nitrogen fixation process may supply a significant fraction of bioavailable nitrogen to surface waters, increase the oceanic sequestration of atmospheric CO2, and alter the distribution of geochemical parameters. We report a zonal pattern of delta N-15 and delta C-13 in particulate organic matter (POM), and ratios of particulate Po-210 to dissolved Po-210 along a transect through the subtropical and tropical North Pacific. Both N-15 and Po-210 signals indicated an enhanced N-2 fixation in the northwestern subtropical North Pacific. The eastward decrease of N-2 fixation along this transect testified the role of aeolian Fe and P in controlling marine N-2 fixation. …

Parallelization Of Multicategory Support Vector Machines (Pmc- Svm) For Classifying Microarray Data, Chaoyang Zhang, Peng Li, Arun Rajendran, Youping Deng, Dequan Chen

Faculty Publications

Background: Multicategory Support Vector Machines (MC-SVM) are powerful classification systems with excellent performance in a variety of data classification problems. Since the process of generating models in traditional multicategory support vector machines for large datasets is very computationally intensive, there is a need to improve the performance using high performance computing techniques.

Results: In this paper, Parallel Multicategory Support Vector Machines (PMC-SVM) have been developed based on the sequential minimum optimization-type decomposition method for support vector machines (SMO-SVM). It was implemented in parallel using MPI and C++ libraries and executed on both shared memory supercomputer and Linux cluster …

Benthic Nutrient Flux In A Small Estuary In Northwestern Florida (Usa), Guy T. Didonato, Emile M. Lores, Michael C. Murrell, Lisa M. Smith, Jane M. Caffrey

Gulf and Caribbean Research

Benthic nutrient fluxes of ammonium (NH₄⁺), nitrite/nitrate (NO₂^- + NO₃^-), phosphate (PO₄^-3), and dissolved silica (DSi) were measured in Escambia Bay, an estuary within the larger Pensacola Bay system of northwestern Florida (USA). Our study occurred during a severe drought which reduced riverine inputs to Escambia Bay. Laboratory incubations of field-collected cores were conducted on 8 dates between June and October 2000 to estimate nutrient flux, and cores were collected from locations exhibiting a range of sediment organic matter content. NH₄⁺ flux ranged from – 48.1 to …

Feeding Habits Of Common Snook, Centropomus Undecimalis, In Charlotte Harbor, Florida, David A. Blewett, Rebecca A. Hensley, Philip W. Stevens

Gulf and Caribbean Research

We examined the feeding habits, ontogenetic and seasonal diet variations, and predator size–prey size relationships of common snook, Centropomus undecimalis, in Charlotte Harbor, Florida, through stomach contents analysis. A total of 694 stomachs were extracted from common snook (300–882 mm standard length [SL]) during a 24-month period (March 2000–February 2002); 432 stomachs contained prey items. At least 37 prey taxa were identified, including 19 that had not been previously reported. Fishes made up 71% of the prey by number and 90% by weight. Three prey items made up almost 50% of the diet numerically—Lagodon rhomboides, Anchoa spp., …

Comparison Of Fish Assemblages And Water Quality In Two Marinas In The British Virgin Islands, Brian Gratwicke, Martin R. Speight

Gulf and Caribbean Research

Eutrophication is a widespread problem in tropical marine environments that leads to the increase of nutrients in a water body, usually nitrate and phosphate, and is usually associated with the discharge of untreated sewage, intensive farming or fertilizer-enriched agricultural runoff (Wu 1999). Common symptoms are increased N and P levels, increased macroalgal production in shallow areas, reduced dissolved oxygen, loss of seagrass and coral habitats and changes in the fish community (Hallock and Schlager 1986, Granelli et al. 1990, Valiela 1995, Hemminga and Duarte 2000). Direct chemical testing to establish pollution levels can be difficult because of sharp pollution gradients, …

Body Size Of The Endosymbiotic Pea Crab Tumidotheres Maculatus: Larger Hosts Hold Larger Crabs, Karen Kane, Gregory S. Farley

Gulf and Caribbean Research

The endosymbiotic pea crab, Tumidotheres maculatus, uses a broad range of host taxa, including several bivalve species, in the northern Gulf of Mexico. Because shelter size affects the size of other, free-living crab species, we hypothesized that pea crabs living in larger bivalve hosts should attain larger sizes. Crabs and hosts collected from 3 field sites in northern Florida show this trend. We examined crabs living in a large host, the pen shell Atrina rigida, and found them to be larger than pea crabs living in a small host, the bay scallop Argopecten irradians. Moreover, this trend …

Marionia Tedi Ev. Marcus, 1983 (Nudibranchia, Tritoniidae) In The Gulf Of Mexico: First Record Of An Opisthobranch Mollusk From Hydrocarbon Cold Seeps, Angel Valdes

Gulf and Caribbean Research

Cold seeps in the Gulf of Mexico contain relatively diverse molluscan assemblages primarily composed of species that support chemoautotrophic symbionts, such as vesicomyid and mytilid bivalves, but also numerous species of shelled gastropods, bivalves, monoplacophorans, and polyplacophorans (Cordes 2004).

Recent exploration of hydrocarbon seep sites in the Mississippi Canyon and the Vioska Knoll revealed the presence of an unidentified species of nudibranch. The present paper describes the single specimen collected, which constitutes the first published record of an opisthobranch mollusk from a cold seep. The material examined is deposited at the Field Museum of Natural History (FMNH).

New Records For Cubanocuma Gutzui Băcescu And Muradian, 1977 (Crustacea: Cumacea: Nannastacidae) From The Western Atlantic, Richard W. Heard, Joel W. Martin, Thomas J. Hansknecht, Donald B. Cadien

Gulf and Caribbean Research

Because the original description and many subsequent records for Cubanocuma gutzui have appeared in a Romanian journal, Travaux du Muséum d’Histoire naturelle “Grigore Antipa,” which has limited distribution in the west, many workers studying tropical western Atlantic crustaceans still remain unaware of both the genus and species. Also, the species may have gone unrecognized (recorded as an odd specimen of Campylaspis, for instance) or may have been overlooked because of its small size. As part of an ongoing survey of the marine invertebrates of Guana Island, British Virgin Islands (BVI) (led by T.L. Zimmerman and J.W. Martin), numerous specimens …

Baseline Mapping Of Phragmites Australis (Common Reed) In Three Coastal Mississippi Estuarine Basins, Mark S. Peterson, Melissa L. Partyka

Faculty Publications

Over the last two decades, the northern Gulf of Mexico has undergone tremendous growth and development that has resulted in extensive and ongoing habitat modification. We had the opportunity to survey the main channels and bayous of three coastal estuarine basins for the presence and coverage of the invasive Phragmites australis (common reed). The occurrence and area of P. australis was highly variable among the lower Pascagoula River, Back Bay of Biloxi, and St. Louis Bay basins, with the largest amount of coverage (0.489 km(2)) found within the lower Pascagoula River basin and the smallest in Back Bay of Biloxi …

Nomenclatural Innovations In Neotropical Salicaeeae, Mac H. Alford

Faculty Publications

Macrothumia M. H. Alford is described as a new genus of Salicaceae based on Neosprucea kuhlmannii Steamer from Brazil. The deciduous perianth, papillate leaf teeth, presence of receptacular disk glands, and analyses of plastid DNA data Suggest that the new genus is more closely related to Ahernia Merrill and Pleuranthodendron. L. O. Williams than to Banara Aublet or Neosprucea Sleuruer. The monotypic genus Aphaerema Miers of Brazil and Argentina is transferred to Abatia Ruiz & Pavon, based on analyses of plastid DNA sequences and on the lack of morphological discontinuities between the genera. Because the name Abatia spicata (Turczaninow) …