Life Sciences Commons^™

Reproductive Function For A C-Terminus Extended, Male-Transmitted Cytochrome C Oxidase Subunit Ii Protein Expressed In Both Spermatozoa And Eggs, Rumela Chakrabarti, Jennifer M. Walker, E.G. Chapman, S.P. Shepardson, R.J. Trdan, J.P. Curole, G.T. Watters, D.T. Stewart, S. Vijayaraghavan, W.R. Hoeh

Faculty Publications

Our previous study documented expression of a male-transmitted cytochrome c oxidase subunit II protein (MCOX2), with a C-terminus extension (MCOX2e), in unionoidean bivalve testes and sperm mitochondria. Here, we present evidence demonstrating that MCOX2 is seasonally expressed in testis, with a peak shortly before fertilization that is independent of sperm density. MCOX2 is localized to the inner and outer sperm mitochondrial membranes and the MCOX2 antibody’s epitope is conserved across >65 million years of evolution. We also demonstrate the presence of male-transmitted mtDNA and season-specific MCOX2 spatial variation in ovaries. We hypothesize …

Cloning, Analysis And Functional Annotation Of Expressed Sequence Tags From The Earthworm Eisenia Fetida, Mehdi Pirooznia, Ping Gong, Xin Guan, Laura S. Inouye, Kuan Yang, Edward J. Perkins, Youping Deng

Faculty Publications

Background

Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR.

Results

A total of 3144 good quality ESTs (GenBank dbEST accession number EH669363–EH672369 and EL515444–EL515580) were obtained from the raw clone …

Comparison Of Probabilistic Boolean Network And Dynamic Bayesian Network Approaches For Inferring Gene Regulatory Networks, Peng Li, Chaoyang Zhang, Edward J. Perkins, Ping Gong, Youping Deng

Faculty Publications

Background: The regulation of gene expression is achieved through gene regulatory networks (GRNs) in which collections of genes interact with one another and other substances in a cell. In order to understand the underlying function of organisms, it is necessary to study the behavior of genes in a gene regulatory network context. Several computational approaches are available for modeling gene regulatory networks with different datasets. In order to optimize modeling of GRN, these approaches must be compared and evaluated in terms of accuracy and efficiency.

Results: In this paper, two important computational approaches for modeling gene regulatory networks, …

Sammd: Staphylococcus Aureus Microarray Meta-Database, Vijayaraj Nagarajan, Mohamed O. Elasri

Faculty Publications

Background

Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation …

Algal Regulation Of Extracellular Enzyme Activity In Stream Microbial Communities Associated With Inert Substrata And Detritus, Steven T. Rier, Kevin A. Kuehn, Steven N. Francoeur

Faculty Publications

We tested the hypothesis that algae influence the activities of extracellular enzymes involved in mineralization processes within microbial assemblages in streams. We tested the prediction that the factors that influence algal biomass and photosynthesis (i.e., diel fluctuations in photosynthetically active radiation [PAR], long-term variations in light regime, and community development stage) would have a corresponding effect on extracellular enzyme activities. We also tested the prediction that algae would influence enzyme activities on inorganic substrata and in detrital communities where they ultimately would influence plant litter decomposition rates. We allowed microbial communities to develop on inert substrata (glass-fiber filters) or on …

A Multi-Scale Examination Of Stopover Habitat Use By Birds, Jeffrey J. Buler, Frank R. Moore, Stefan Woltmann

Faculty Publications

Most of our understanding of habitat use by migrating land birds comes from studies conducted at single, small spatial scales, which may overemphasize the importance of intrinsic habitat factors, such as food availability, in shaping migrant distributions. We believe that a multi-scale approach is essential to assess the influence of factors that control en route habitat use. We determined the relative importance of eight variables, each operating at a habitat-patch, landscape, or regional spatial scale, in explaining the differential use of hardwood forests by Nearctic-Neotropical land birds during migration. We estimated bird densities through transect surveys at sites near the …

Variability In The Bulk Composition And Abundance Of Dissolved Organic Matter In The Lower Mississippi And Pearl Rivers, Shuiwang Duan, Thomas S. Bianchi, Alan M. Shiller, Karl Dria, Patrick G. Hatcher, Kevin R. Carman

Faculty Publications

[1] In this study, we examined the temporal and spatial variability of dissolved organic matter (DOM) abundance and composition in the lower Mississippi and Pearl rivers and effects of human and natural influences. In particular, we looked at bulk C/N ratio, stable isotopes (delta N-15 and delta C-13) and C-13 nuclear magnetic resonance (NMR) spectrometry of high molecular weight (HMW; 0.2 mu m to 1 kDa) DOM. Monthly water samples were collected at one station in each river from August 2001 to 2003. Surveys of spatial variability of total dissolved organic carbon (DOC) and nitrogen ( DON) were also conducted …

Revision Of The Nonequilibrium Thermal Dissociation And Stringent Washing Approaches For Identification Of Mixed Nucleic Acid Targets By Microarrays, Alex E. Pozhitkov, Robert D. Stedtfeld, Syed A. Hashsham, Peter A. Noble

Faculty Publications

Microarray experiments typically involve washing steps that remove hybridized nonspecific targets with the purpose of improving the signal- to- noise ratio. The quality of washing ultimately affects downstream analysis of the microarray and interpretation. The paucity of fundamental studies directed towards understanding the dissociation of mixed targets from microarrays makes the development of meaningful washing/ dissociation protocols difficult. To fill the void, we examined activation energies and preexponential coefficients of 47 perfect match ( PM) and double- mismatch ( MM) duplex pairs to discover that there was no statistical difference between the kinetics of the PM and MM duplexes. Based …

Fecundity And Survival Of The Calanoid Copepod Acartia Tonsa Fed Isochrysis Galeana (Tahitian Strain) And Chaetoceros Mulleri, Angelos Apeitos

Master's Theses

Historically, red snapper (Lutjanus campechanus) larviculture at the Gulf Coast Research Lab (GCRL) used 25 ppt artificial salt water and mixed, wild zooplankton composed primarily of Acartia tonsa, a calanoid copepod. Acartia tonsa was collected from the estuarine waters of Davis Bayou and bloomed in outdoor tanks from which it was harvested and fed to red snapper larvae. We are developing a more controlled copepod mass culture system to support finfish larviculture. To that end, I examined the effect of single species versus mixed species of algae as food for the copepods. Wild A. tonsa were isolated and reared in …

Upper-Ocean Response To Hurricane Ivan In A 1/25 Degrees Nested Gulf Of Mexico Hycom, T. G. Prasad, Patrick J. Hogan

Faculty Publications

[ 1] A 20-layer, 1/25 degrees nested Gulf of Mexico (GoM) Hybrid Coordinate Ocean Model (HYCOM) has been employed to examine the evolving three-dimensional ocean response to Hurricane Ivan during 14 - 16 September 2004. Results from several combinations of numerical experiments with and without assimilation of satellite-altimetry sea-surface height (SSH) are being analyzed and compared for the September 2004 hurricane period. A comparison of simulated zonal and meridional velocities using data assimilation shows improved agreement with profiler observations. The amplitude of the cold wake ( similar to 6 degrees C) produced by these simulations compared reasonably well with the …

Investigation Of The Summer Kara Sea Circulation Employing A Variational Data Assimilation Technique, G. Panteleev, A. Proshutinsky, M. Kulakov, Dmitri A. Nechaev, W. Maslowski

Faculty Publications

[ 1] The summer circulations and hydrographic fields of the Kara Sea are reconstructed for mean, positive and negative Arctic Oscillation regimes employing a variational data assimilation technique which provides the best fit of reconstructed fields to climatological data and satisfies dynamical and kinematic constraints of a quasi-stationary primitive equation ocean circulation model. The reconstructed circulations agree well with the measurements and are characterized by inflow of 0.63, 0.8, 0.51 Sv through Kara Gate and 1.18, 1.1, 1.12 Sv between Novaya Zemlya and Franz Josef Land, for mean climatologic conditions, positive and negative AO indexes, respectively. The major regions of …

First Record Of A Sleeper Shark In The Western Gulf Of Mexico And Comments On Taxonomic Uncertainty Within Somniosus (Somniosus), George W. Benz, Eric R. Hoffmayer, William B. Driggers, Dan Allen, Lougan E. Bishop, David A. Brown

Faculty Publications

A sleeper shark, Somniosus (Somniosus) sp., is reported from Alaminos Canyon in the western Gulf of Mexico at a depth of about 2647 m based on observations made using a remotely operated vehicle. This is the first record of a sleeper shark (Somniosus, Somniosidae) from the western Gulf of Mexico and deepest record of any shark from the Gulf of Mexico. Despite claims to the contrary in the literature, no taxonomic character has been identified to date that can be used to unequivocally identify all representatives of Somniosus (Somniosus), and as a result, some species records must be considered dubious.

Grass Shrimp (Palaemonetes Spp.) Play A Pivotal Trophic Role In Enhancing Ruppia Maritima, Donna Drury Mccall, Chet R. Rakocinski

Faculty Publications

Coupled trophic-engineer interactions are potentially important for maintaining habitat function and ecosystem services. As ephemeral submerged aquatic vegetation (SAV), Ruppia maritima has a short well-defined growth-senescence cycle and should benefit from any ecological interaction that enhances its physical condition and longevity. Grass shrimp (Palaemonetes spp.) are abundant facultative grazers of epiphytic algae and conveyors of nutrients in tidal marsh and SAV habitats. Grass shrimp addition consistently enhanced Ruppia biomass and shoot density in a series of three field experiments conducted in Grand Bay National Estuarine Research Reserve, Mississippi, USA. In two experiments, epiphyte grazing by grass shrimp enhanced Ruppia by …

Structure And Function Predictions Of The Msa Protein In Staphylococcus Aureus, Vijayaraj Nagarajan, Mohamed O. Elasri

Faculty Publications

Background

Staphylococcus aureus is a human pathogen that causes a wide variety of life-threatening infections using a large number of virulence factors. One of the major global regulators used by S. aureus is the staphylococcal accessory regulator (sarA). We have identified and characterized a new gene (modulator of sarA: msa) that modulates the expression of sarA. Genetic and functional analysis shows that msa has a global effect on gene expression in S. aureus. However, the mechanism of Msa function is still unknown. Function predictions of Msa are complicated by the fact that it does …

A Comparative Study Of Different Machine Learning Methods On Microarray Gene Expression Data, Mehdi Pirooznia, Jack Y. Yang, Mary Qu Yang, Youping Deng

Faculty Publications

Background

Several classification and feature selection methods have been studied for the identification of differentially expressed genes in microarray data. Classification methods such as SVM, RBF Neural Nets, MLP Neural Nets, Bayesian, Decision Tree and Random Forrest methods have been used in recent studies. The accuracy of these methods has been calculated with validation methods such as v-fold validation. However there is lack of comparison between these methods to find a better framework for classification, clustering and analysis of microarray gene expression results.

Results

In this study, we compared the efficiency of the classification methods including; SVM, RBF Neural Nets, …

A Hybrid Machine Learning-Based Method For Classifying The Cushing's Syndrome With Comorbid Adrenocortical Lesions, Jack Y. Yang, Mary Qu Yang, Zuojie Lao, Yan Ma, Jianling Li, Youping Deng, Xudong Huang

Faculty Publications

Background

The prognosis for many cancers could be improved dramatically if they could be detected while still at the microscopic disease stage. It follows from a comprehensive statistical analysis that a number of antigens such as hTERT, PCNA and Ki-67 can be considered as cancer markers, while another set of antigens such as P27KIP1 and FHIT are possible markers for normal tissue. Because more than one marker must be considered to obtain a classification of cancer or no cancer, and if cancer, to classify it as malignant, borderline, or benign, we must develop an intelligent decision system that can fullfill …

Improving Prediction Accuracy Of Tumor Classification By Reusing Genes Discarded During Gene Selection, Jack Y. Yang, Guo-Zheng Li, Hao-Hua Meng, Mary Qu Yang, Youping Deng

Faculty Publications

Background

Since the high dimensionality of gene expression microarray data sets degrades the generalization performance of classifiers, feature selection, which selects relevant features and discards irrelevant and redundant features, has been widely used in the bioinformatics field. Multi-task learning is a novel technique to improve prediction accuracy of tumor classification by using information contained in such discarded redundant features, but which features should be discarded or used as input or output remains an open issue.

Results

We demonstrate a framework for automatically selecting features to be input, output, and discarded by using a genetic algorithm, and propose two algorithms: GA-MTL …

Promoting Synergistic Research And Education In Genomics And Bioinformatics, Jack Y. Yang, Mary Qu Yang, Hamid R. Arabnia, Youping Deng

Faculty Publications

Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology.

High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and personalized healthcare. The impact of having the human sequence and personalized digital images in hand has also created tremendous demands of developing powerful supercomputing, statistical learning and artificial intelligence approaches to …

Iloop - A Web Application For Two-Channel Microarray Interwoven Loop Design, Mehdi Pirooznia, Ping Gong, Jack Y. Yang, Mary Qu Yang, Edward J. Perkins, Youping Deng

Faculty Publications

Microarray technology is widely applied to address complex scientific questions. However, there remain fundamental issues on how to design experiments to ensure that the resulting data enables robust statistical analysis. Interwoven loop design has several advantages over other designs. However it suffers in the complexity of design. We have implemented an online web application which allows users to find optimal loop designs for two-color microarray experiments. Given a number of conditions (such as treatments or time points) and replicates, the application will find the best possible design of the experiment and output experimental parameters. It is freely available from http://mcbc.usm.edu/iloop …

Batch Blast Extractor: An Automated Blastx Parser Application, Mehdi Pirooznia, Edward J. Perkins, Youping Deng

Faculty Publications

Motivation

BLAST programs are very efficient in finding similarities for sequences. However for large datasets such as ESTs, manual extraction of the information from the batch BLAST output is needed. This can be time consuming, insufficient, and inaccurate. Therefore implementation of a parser application would be extremely useful in extracting information from BLAST outputs.

Results

We have developed a java application, Batch Blast Extractor, with a user friendly graphical interface to extract information from BLAST output. The application generates a tab delimited text file that can be easily imported into any statistical package such as Excel or SPSS for further …

Genomics, Molecular Imaging, Bioinformatics, And Bio-Nano-Info Integration Are Synergistic Components Of Translational Medicine And Personalized Healthcare Research, Jack Y. Yang, Mary Qu Yang, Hamid R. Arabnia, Youping Deng

Faculty Publications

Supported by National Science Foundation (NSF), International Society of Intelligent Biological Medicine (ISIBM), International Journal of Computational Biology and Drug Design and International Journal of Functional Informatics and Personalized Medicine, IEEE 7th Bioinformatics and Bioengineering attracted more than 600 papers and 500 researchers and medical doctors. It was the only synergistic inter/multidisciplinary IEEE conference with 24 Keynote Lectures, 7 Tutorials, 5 Cutting-Edge Research Workshops and 32 Scientific Sessions including 11 Special Research Interest Sessions that were designed dynamically at Harvard in response to the current research trends and advances. The committee was very grateful for the IEEE Plenary Keynote Lectures …

Breeding Season And Molt Cycle Of The Fiddler Crab Uca Rapax (Brachyura, Ocypodidae) In A Subtropical Estuary, Brazil, South America, Daniela Da Silva Castiglioni, Maria Lucia Negreiros-Fransozo, Rosana Carina Flores Cardoso

Gulf and Caribbean Research

This is the first account of the breeding season and molt cycle of Uca rapax on the Brazilian coast during a one-year period (April 2001-March 2002). At 2 sites, the ltamambuca and Ubatumirim mangrove forests, 2 collectors captured crabs once a month at low tide far 15 minutes by the catch-per-unit-effort procedure, digging into the sediment and removing the crabs. The gonad-development stages of crabs of both sexes were determined by direct observation, and the molt stage was estimated from the hardness of the tegument. Crabs with developed gonads were found mostly in warmer seasons, with ovigerous females occurring mainly …

Large Pelagics In The Southern Section Of The Seaflower Marine Protected Area, San Andres Archipelago, Colombia: A Fishery In Expansion, Erick Castro, Heins Bent, Carlos Ballesteros, Martha Prada

Gulf and Caribbean Research

Isolated and sparse reef atolls comprising the southern section of the Seaflower MPA have been traditionally exploited by artisanal fishers using handlines. These practices have severely depleted the demersal fish stock and now fishers have shifted their efforts to the pelagic stock. The pelagic fishery included the extraction of more than 25 species, with Thunnus atlanticus, Acanthocybium solandri, Coryphaena hippurus, and Katsuwonus pelamis being the most common. Three years of fishery-dependent data (2004–2006) were used to describe traditional fishing methods and techniques, and to document, for the first time, a declining trend in the large pelagic stock. …

Habitat Use By Juvenile Gag, Mycteroperca Microlepis (Pisces: Serranidae), In Subtropical Charlotte Harbor, Florida (Usa), J. Patrick Casey, Gregg R. Poulakis, Philip W. Stevens

Gulf and Caribbean Research

Estuaries play a key role in the juvenile stage of gag (Myeteroperca microlepis). The use of estuarine habitats by juvenlle gag has been examined in temperate estuaries, which are at the northern limits of the range of this species, but the importance of subtropical estuaries during the early life history of this species has not been studied extensively. Gag were collected in subtropical Charlotte Harbor, Florida, during routine monthiy sampling from January 1996 to Decemher 2002. Juvenlle gag were collected using a 21.3-m seine, a 183-m haul seine, and a 183-m purse seine. A total of 738 individuals …

Abundance And Ecological Distribution Of The "Sete-Barbas" Shrimp Xiphopenaeus Kroyeri (Heller, 1862) (Decapoda: Penaeoidea) In Three Bays Of The Ubatuba Region, Southeastern Brazil, Rogerio C. Costa, Adilson Fransozo, Fulvio A.M. Freire, Antonio L. Castilho

Gulf and Caribbean Research

The influence of environmental factors on the abundance and spatial-temporal distribution of the shrimp Xiphopenaeus kroyeri was investigated in southeastern Brazil over 2 years. Monthly collections were conducted in Mar Virado, Ubatuba and Ubatumirim Bays using a commercial shrimp fishing boat equipped with 2 "double-rig" nets. Each bay was divided into 6 sampling stations, all of which were less than 25 m deep. The spatial distribution of X. kroyeri differed among Bays. Highest abundance values were recorded in areas where silt and clay comprised more than 70% of the bottom sediment. Abundance of X. kroyeri followed a seasonal trend, being …

Use Of Diadema Antillarum Spines By Juvenile Fish And Mysid Shrimp, Taryn Townsend, Paul A.X. Bologna

Gulf and Caribbean Research

This research has the following objectives: 1) identify the size structure of D. antillarum among 3 coastal bays of St. John, United States Virgin Islands and 2) determine relationships between urchin presence and spine utilization by fish and mysid shrimp.

Large Pelagic Fishes In The Caribbean Sea And The Gulf Of Mexico: Current Status And Integrated Management, Mark S. Peterson, Nancy J. Brown-Peterson, James S. Franks

Gulf and Caribbean Research

A symposium convened on 7 November 2006 in conjunction with the 59th annual meeting of the Gulf and Caribbean Fisheries Institute in Belize City, Belize.

Strategic Investments In Large Pelagic Research, Nancy B. Thompson, Eric D. Prince

Gulf and Caribbean Research

The Southeast Fisheries Science Center (SEFSC) of the US NOAA Fisheries provides much of the US science advice for the management of Highly Migratory Species (HMS) in the Atlantic, Gulf of Mexico and US Caribbean Sea. These stocks include the tunas, sharks, billfishes and swordfish all of which are targeted either commercially or recreationally or both in US waters. These species are managed internationally through membership to the International Commission for the Conservation of Atlantic Tunas (ICCAT); however, while the US is an ICCAT member, few Caribbean nations are members.

Large Pelagic Fishes In The Wider Caribbean And Northwest Atlantic Ocean: Movement Patterns Determined From Conventional And Electronic Tagging, Brian E. Luckhurst

Gulf and Caribbean Research

Conventional tagging data has documented long distance movements (including trans-Atlantic movements) in blue marlin (Makaira nigricans) and yellowfin tuna (Thunnus albacares) within the Atlantic. Swordfish (Xiphius gladius) have also been shown to move substantial distances, although primarily in a north-south direction. There is, however, a paucity of data for wahoo (Acanthocybium solandri). In the past several years, electronic archival (i.e., data recording) tags have significantly advanced our understanding of the behavior and movement patterns of large pelagic fishes. Data from electronic arcltival tags have generally corroborated conventional tagging data with respect to …

Distribution Of Molidae In The Northern Gulf Of Mexico, Gregory L. Fulling, Dagmar Fertl, Kevin Knight, Wayne Hoggard

Gulf and Caribbean Research

We compiled all available sighting, stranding and bycatch data for the Family Molidae (molas) in the northern Gulf of Mexico (NGOM) to assess spatial and temporal distribution. Overall, 483 records were collected from shipboard and aerial surveys, fisheries bycatch, and strandings. Molas were recorded year-round, with a ubiquitous distribution in both nearshore and offshore waters. Ocean sunfish (Mola mola) were sighted with greatest frequency during the winter (December thru April) in sea surface temperature < 24° C. Potential reasons for increased sightings during winter may be related to the lack of a well-defined thermocline in the NGOM; the species' "basking" behavior associated with thermoregulation; and oxygen replenishment after long, deep dives to oxygen-deficient depths.