Digital Commons Network^™

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 …

An Overview Of The Near-Death Experience Phenomenon, David San Filippo Ph.D.

Faculty Publications

Near-death experiences appear to be universal phenomena that have been reported for centuries. A near-death encounter is defined as an event in which the individual could very easily die or be killed, or may have already been considered clinically dead, but nonetheless survives, and continue his or her physical life. Reports of near-death experiences date back to the Ice Age. There are cave paintings, in France and Spain that depict possible after life scenes that are similar to reported scenes related to near-death experiences. Plato's Republic presents the story of a near-death experience of a Greek soldier named Er. In …

Sines Of A Nearly Perfect Character, David A. Ray, Jinchuan Xing, Abdel Halim Salem, Mark A. Batzer

Faculty Publications

Mobile elements have been recognized as powerful tools for phylogenetic and population-level analyses. However, issues regarding potential sources of homoplasy and other misleading events have been raised. We have collected available data for all phylogenetic and population level studies of primates utilizing Alu insertion data and examined them for potentially homoplasious and other misleading events. Very low levels of each potential confounding factor in a phylogenetic or population analysis (i.e., lineage sorting, parallel insertions, and precise excision) were found. Although taxa known to be subject to high levels of these types of events may indeed be subject to problems when …

Improved Cryopreservation Of Sperm Of Paddlefish (Polyodon Spathula), Ákos Horváth, Béla Urbányi, Steven D. Mims, William B. Bean, Boris Gomelsky, Terrence R. Tiersch

Faculty Publications

Experiments were performed to improve protocols for sperm cryopreservation of paddlefish (Polyodon spathula), a species for which there has been limited study. The first experiment was conducted to investigate the effects of two extenders (modified Tsvetkova's extender: mT and modified Hanks'balanced salt solution: mHBSS) in combination with methanol (MeOH) and dimethyl sulfoxide in two concentrations (5 and 10%) on the postthaw motility and fertilization rates of cryopreserved sperm. The highest postthaw motility (85 ± 5%) was observed when sperm were frozen using mT extender with 10% MeOH as cryoprotectant. Extenders (P = 0.0018) and cryoprotectants (P = 0.0040) each had …

A Novel Account Of Scientific Anomaly: Help For The Dispute Over Low-Dose Biochemical Effects, Kevin C. Elliott

Faculty Publications

The biological effects of low doses of toxic and carcinogenic chemicals are currently a matter of significant scientific controversy. This paper argues that philosophers of science can contribute to alleviating this controversy by examining it with the aid of a novel account of scientific anomaly. Specifically, analysis of contemporary research on chemical hormesis (i.e.. alleged beneficial biological effects produced by low doses of substances that are harmful at higher doses) suggests that scientists may initially describe anomalous phenomena in terms of multiple distinct '"characterizations," each
of which is compatible with current empirical evidence. By focusing attention on this feature of …

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 …

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 …

Culturally Adapted Mental Health Interventions: A Meta-Analytic Review, Timothy B. Smith, Derek Griner

Faculty Publications

There is a pressing need to enhance the availability and quality of mental health services provided to persons from historically disadvantaged racial and ethnic groups. Many previous authors have advocated that traditional mental health treatments be modified to better match clients? cultural contexts. Numerous studies evaluating culturally adapted interventions have appeared, and the present study used meta-analytic methodology to summarize these data. Across 76 studies the resulting random effects weighted average effect size was d = .45, indicating a moderately strong benefit of culturally adapted interventions. Interventions targeted to a specific cultural group were four times more effective than interventions …

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 …

Emergence Of Primate Genes By Retrotransposon-Mediated Sequence Transduction, Jinchuan Xing, Hui Wang, Victoria P. Belancio, Richard Cordaux, Prescott L. Deininger, Mark A. Batzer

Faculty Publications

Gene duplication is one of the most important mechanisms for creating new genes and generating genomic novelty. Retrotransposon-mediated sequence transduction (i.e., the process by which a retrotransposon carries flanking sequence during its mobilization) has been proposed as a gene duplication mechanism. L1 exon shuffling potential has been reported in cell culture assays, and two potential L1-mediated exon shuffling events have been identified in the genome. SVA is the youngest retrotransposon family in primates and is capable of 3′ flanking sequence transduction during retrotransposition. In this study, we examined all of the full-length SVA elements in the human genome to assess …

Establishment Of Cecidochares Connexa (Diptera: Tephritidae) In Guam And Its Effect On The Growth Of Chromolaena Odorata (Asteraceae), Z. T. Cruz, R. Muniappan, G. V.P. Reddy

Faculty Publications

The gall fly Cecidochares connexa (Macquart) (Diptera: Tephritidae) was imported from Indone ia into Guam in 1998. It was field-established at one location in north central Guam, and its spatial and temporal spread in Guam was monitored. The biology of the gall fly is presented. No relationship between the number of larvae in a gall and the dimensions of the gall (length and width) existed. Three pupae per gall was the most frequent density with a range of 1-7. The sex ratio of flies emerging from galls was 1:1 irrespective of number of larvae per gall. C. connexa-induced galls established …

Electrophile-Induced Ether Transfer: A New Approach To Polyketide Structural Units, Kai Liu, Richard E. Taylor, Rendy Kartika

Faculty Publications

A strategically novel approach to the formation of syn-1,3-diol mono- and diethers through electrophilic activation of homoallylic alkoxymethyl ethers has been developed. The resulting polyketide-like synthetic fragments are generated in good yield and with excellent stereocontrol. A chairlike transition state is proposed to account for the high stereoselectivity. Varying the conditions of the reaction workup results in the efficient generation of mono- and diether containing structural units common to polyketide natural products. © 2006 American Chemical Society.

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 …

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 …

A Molecular Phylogenetic Analysis Of Strombid Gastropod Morphological Diversity, Jared M. Latiolais, Michael S. Taylor, Kaustuv Roy, Michael E. Hellberg

Faculty Publications

The shells of strombid gastropods show a wide variety of forms, ranging from small and fusiform to large and elaborately ornamented with a strongly flared outer lip. Here, we present the first species-level molecular phylogeny for strombids and use the resulting phylogenetic framework to explore relationships between species richness and morphological diversity. We use portions of one nuclear (325 bp of histone H3) and one mitochondrial (640 bp of cytochrome oxidase I, COI) gene to infer relationships within the two most species-rich genera in the Strombidae: Strombus and Lambis. We include 32 species of Strombus, representing 10 of 11 extant …

Estradiol Interactions With Dopamine Antagonists In Mares: Prolactin Secretion And Reproductive Traits, K. K. Kelley, D. L. Thompson, W. A. Storer, P. B. Mitcham, R. M. Gilley, P. J. Burns

Faculty Publications

Two experiments studied the effects of pretreatment with estradiol benzoate before treatment with a dopamine antagonist on prolactin secretion and reproductive traits in mares during (1) the seasonal anovulatory period and (2) the normal breeding season. Experiment 1 was performed in winter with 17 mares selected for low follicular activity. Nine mares received estradiol benzoate injections every other day for a total of 10 injections; 8 mares received similar injections of vehicle. Ten days after onset of injections, all mares were placed on daily injections of sulpiride (250 mg) for 35 days or until ovulation. Plasma prolactin concentrations were higher …

An Organic White Light-Emitting Fluorophore, Youjun Yang, Mark Lowry, Corin M. Schowalter, Sayo O. Fakayode, Jorge O. Escobedo, Xiangyang Xu, Huating Zhang, Timothy J. Jensen, Frank R. Fronczek, Isiah M. Warner, Robert M. Strongin

Faculty Publications

The synthesis of new benzo[a]- and [b]xanthene dye frameworks is described. A unique benzo[a]xanthene, seminaphtho[a]fluorone (SNAFR-1), is studied in a variety of media. The optimization of solution parameters and excitation wavelengths allows SNAFR-1 to display red, green, and blue emission bands of approximately equal intensities and also to produce white light. Ratiometric red (anion) and green (neutral) emissions are observed upon varying solution pH. A pH-independent violet-blue emission band is due to the addition of nucleophiles to the benzylic carbon of SNAFR-1. © 2006 American Chemical Society.

Siamese, A Plant-Specific Cell Cycle Regulator, Controls Endoreplication Onset In Arabidopsis Thaliana, Michelle L. Churchman, Matthew L. Brown, Naohiro Kato, Viktor Kirik, Martin Hülskamp, Dirk Inzé, Lieven De Veylder, Jason D. Walker, Ui Zheng, David G. Oppenheimer, Taylor Gwin, Jason Churchman, John C. Larkin

Faculty Publications

Recessive mutations in the SIAMESE (SIM) gene of Arabidopsis thaliana result in multicellular trichomes harboring individual nuclei with a low ploidy level, a phenotype strikingly different from that of wild-type trichomes, which are single cells with a nuclear DNA content of ∼16C to 32C. These observations suggested that SIM is required to suppress mitosis as part of the switch to endoreplication in trichomes. Here, we demonstrate that SIM encodes a nuclear-localized 14-kD protein containing a cyclin binding motif and a motif found in ICK/KRP (for interactors of Cdc2 kinase/Kip-related protein) cell cycle inhibitor proteins. Accordingly, SIM was found to associate …

The Saccharomyces Cerevisiae Rna Polymerase Iii Recruitment Factor Subunits Brf1 And Bdp1 Impose A Strict Sequence Preference For The Downstream Half Of The Tata Box, Nick D. Tsihlis, Anne Grove

Faculty Publications

Association of the TATA-binding protein (TBP) with its cognate site within eukaryotic promoters is key to accurate and efficient transcriptional initiation. To achieve recruitment of Saccharomyces cerevisiae RNA polymerase III, TBP is associated with two additional factors, Brf1 and Bdp1, to form the initiation factor TFIIIB. Previous data have suggested that the structure or dynamics of the TBP-DNA complex may be altered upon entry of Brf1 and Bdp1 into the complex. We show here, using the altered specificity TBP mutant TBPm3 and an iterative in vitro selection assay, that entry of Brf1 and Bdp1 into the complex imposes a strict …

Geographic Variation In Clonal Structure In A Reef-Building Caribbean Coral, Acropora Palmata, Iliana B. Baums, Margaret W. Miller, Michael E. Hellberg

Faculty Publications

Species that build the physical structure of ecosystems often reproduce clonally, both in terrestrial (e.g., grasses, trees) and marine (e.g., corals, seagrasses) environments. The degree of clonality may vary over a species' range in accordance with the relative success of sexual and asexual recruitment. High genotypic (clonal) diversity of structural species may promote the species diversity and resilience of ecosystems in the face of environmental extremes. Conversely, low genotypic diversity may indicate an asexual strategy to maintain resources and genetic variation during population decline. Here, we use microsatellite markers to assess geographic variation in clonality in the coral Acropora palmata …

Voluntary Participation And Informed Consent International Genetic Research, Patricia A. Marshall, Clement A. Adebamowo, Adebowale A. Adeyemo, Temidayo O. Ogundiran, Mirjana Vekich, Teri Strenski, Jie Zhou, T. Elaine Prewitt, Richard S. Cooper, Charles N. Rotimi

Faculty Publications

Objectives. We compared voluntary participation and comprehension of informed consent among individuals of African ancestry enrolled in similarly designed genetic studies of hypertension in the United States and Nigeria. Methods. Survey questionnaires were used to evaluate factors associated with voluntariness (the number of people volunteering) and understanding of the study's genetic purpose. A total of 655 individuals (United States: 348; Nigeria: 307) were interviewed after participation in the genetic studies. Results. Most US respondents (99%), compared with 72% of Nigerian respondents, reported being told the study purpose. Fewer than half of the respondents at both sites reported that the study …

Common Variants In The Enpp1 Gene Are Not Reproducibly Associated With Diabetes Or Obesity, Helen N. Lyon, Jose C. Florez, Todd Bersaglieri, Richa Saxena, Wendy Winckler, Peter Almgren, Ulf Lindblad, Tiinamaija Tuomi, Daniel Gaudet, Xiaofeng Zhu, Richard Cooper, Kristin G. Ardlie, Mark J. Daly, David Altshuler, Leif Groop, Joel N. Hirschhorn

Faculty Publications

The common missense single nucleotide polymorphism (SNP) K121Q in the ectoenzyme nucleotide pyrophosphate phosphodiesterase (ENPP1) gene has recently been associated with type 2 diabetes in Italian, U.S., and South-Asian populations. A three-SNP haplotype, including K121Q, has also been associated with obesity and type 2 diabetes in French and Austrian populations. We set out to confirm these findings in several large samples. We genotyped the haplotype K121Q (rs1044498), rs1799774, and rs7754561 in 8,676 individuals of European ancestry with and without type 2 diabetes, in 1,900 obese and 930 lean individuals of European ancestry from the U.S. and Poland, and in 1,101 …

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 …

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 …

Purification And Preconcentration Of Genomic Dna From Whole Cell Lysates Using Photoactivated Polycarbonate (Ppc) Microfluidic Chips, Małgorzata A. Witek, Shawn D. Llopis, Abigail Wheatley, Robin L. Mccarley, Steven A. Soper

Faculty Publications

We discuss the use of a photoactivated polycarbonate (PPC) microfluidic chip for the solid-phase, reversible immobilization (SPRI) and purification of genomic DNA (gDNA) from whole cell lysates. The surface of polycarbonate was activated by UV radiation resulting in a photo-oxidation reaction, which produced a channel surface containing carboxylate groups. The gDNA was selectively captured on this photoactivated surface in an immobilization buffer, which consisted of 3% polyethylene glycol, 0.4 M NaCl and 70% ethanol. The methodology reported herein is similar to conventional SPRI in that surface-confined carboxylate groups are used for the selective immobilization of DNA; however, no magnetic beads …

African-American Mitochondrial Dnas Often Match Mtdnas Found In Multiple African Ethnic Groups, Bert Ely, Jamie Lee Wilson, Fatimah Jackson, Bruce A. Jackson

Faculty Publications

Mitochondrial DNA (mtDNA) haplotypes have become popular tools for tracing maternal ancestry, and several companies offer this service to the general public. Numerous studies have demonstrated that human mtDNA haplotypes can be used with confidence to identify the continent where the haplotype originated. Ideally, mtDNA haplotypes could also be used to identify a particular country or ethnic group from which the maternal ancestor emanated. However, the geographic distribution of mtDNA haplotypes is greatly influenced by the movement of both individuals and population groups. Consequently, common mtDNA haplotypes are shared among multiple ethnic groups. We have studied the distribution of mtDNA …

Spatial Confidentiality And Gis: Re-Engineering Mortality Locations From Published Maps About Hurricane Katrina, Andrew J. Curtis, Jacqueline W. Mills, Michael Leitner

Faculty Publications

Background: Geographic Information System (GIS) can provide valuable insight into patterns of human activity. Online spatial display applications, such as Google Earth, can democratise this information by disseminating it to the general public. Although this is a generally positive advance for society, there is a legitimate concern involving the disclosure of confidential information through spatial display. Although guidelines exist for aggregated data, little has been written concerning the display of point level information. The concern is that a map containing points representing cases of cancer or an infectious disease, could be re-engineered back to identify an actual residence. This is …

Adulthood: New Terrain, E Michael Brady Phd

Faculty Publications

The article reviews the book Adulthood: New Terrain, edited by Mary Alice Wolf.

Liana Habitat Associations And Community Structure In A Bornean Lowland Tropical Forest, Saara J. Dewalt, Kalan Ickes, Reuben Nilus, Kyle E. Harms, David F.R.P. Burslem

Faculty Publications

Lianas (woody vines) contribute substantially to the diversity and structure of most tropical forests, yet little is known about the importance of habitat specialization in maintaining tropical liana diversity and the causes of variation among forests in liana abundance and species composition. We examined habitat associations, species diversity, species composition, and community structure of lianas at Sepilok Forest Reserve, Sabah, Malaysia in northeastern Borneo among three soil types that give rise to three distinct forest types of lowland tropical rain forest: alluvial, sandstone hill, and kerangas (heath) forest. Alluvial soils are more nutrient rich and have higher soil moisture than …