Life Sciences Commons^™

Smoq: A Tool For Predicting The Absolute Residue-Specific Quality Of A Single Protein Model With Support Vector Machine, Renzhi Cao, Zheng Wang, Yiheng Wang, Jianlin Cheng

Faculty Publications

Background: It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein model is rare, yet particularly needed for using, ranking and refining protein models.

Results: We developed a machine learning tool (SMOQ) that can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines (SVM) with protein sequence and structural features (i.e. basic feature set), including amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts to …

Designing And Evaluating The Multicom Protein Local And Global Model Quality Prediction Methods In The Casp10 Experiment, Renzhi Cao, Zheng Wang, Jianlin Cheng

Faculty Publications

Background: Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we developed and tested four automated methods (MULTICOM-REFINE, MULTICOM-CLUSTER, MULTICOM-NOVEL, and MULTICOM-CONSTRUCT) that predicted both local and global quality of protein structural models.

Results: MULTICOM-REFINE was a clustering approach that used the average pairwise structural similarity between models to measure the global quality and the average Euclidean distance between a model and several top ranked models to measure the local quality. MULTICOM-CLUSTER and MULTICOM-NOVEL were two new support vector machine-based …

Transcriptional Activation Of Antioxidants May Compensate For Selenoprotein Deficiences In Amblyomma Maculatum (Acari: Ixodidae) Injected With Selk- Or Selm- Dsrna, S. Adamson, R. Browning, P. Singh, S. Nobles, A. Villareal, Shahid Karim

Faculty Publications

The Gulf‐Coast tick, Amblyomma maculatum, possesses an elaborate set of selenoproteins, which prevent the deleterious effects from oxidative stress that would otherwise occur during feeding. In the current work, we examined the role of selenoprotein K (SelK) and selenoprotein M (SelM) in feeding A. maculatum by bioinformatics, transcriptional gene expression, RNA interference and antioxidant assays. The transcriptional expression of SelK did not vary significantly in salivary glands or midguts throughout the bloodmeal. However, there was a 58‐fold increase in transcript levels of SelM in tick midguts. Ticks injected with selK‐dsRNA or selM‐dsRNA did not reveal any observable …

Improvements In Blood Pressure Among Undiagnosed Hypertensive Participants In A Community-Based Lifestyle Intervention, Mississippi, 2010, Jamie M. Zoellner, Jessica L. Thomson, Alicia S. Landry, Charkarra Anderson-Lewis, Carol Connell, Elaine Fontenot Molaison, Kathleen Yadrick

Faculty Publications

Introduction

Effective strategies are needed to reach and treat people who lack awareness of or have uncontrolled hypertension. We used data from a community-based participatory research initiative, Hub City Steps, to quantify the prevalence of undiagnosed hypertension and determine the relationship between hypertension status at baseline and postintervention improvements in blood pressure and health-related quality of life.

Methods

Hub City Steps was a 6-month preintervention–postintervention lifestyle intervention targeting hypertension risk factors. Outcome measures were collected at baseline, 3 months, and 6 months. Generalized linear mixed models were used to test for effects by time and hypertension status.

Results

Of the …

Hub City Steps: A 6-Month Lifestyle Intervention Improves Blood Pressure Among A Primarily African-American Community, Jamie M. Zoellner, Carol Connell, Michael B. Modson, Jessica L. Thomson, Alicia S. Landry, Elaine Fontenot Molaison, Vickie Blakely Reed, Kathleen Yadrick

Faculty Publications

The effectiveness of community-based participatory research (CBPR) efforts to address the disproportionate burden of hypertension among African Americans remains largely untested. The objective of this 6-month, noncontrolled, pre-/post-experimental intervention was to examine the effectiveness of a CBPR intervention in achieving improvements in blood pressure, anthropometric measures, biological measures, and diet. Conducted in 2010, this multicomponent lifestyle intervention included motivational enhancement, social support provided by peer coaches, pedometer diary self-monitoring, and monthly nutrition and physical activity education sessions. Of 269 enrolled participants, 94% were African American and 85% were female. Statistical analysis included generalized linear mixed models using maximum likelihood estimation. …

Health Insurance Status, Psychological Processes, And Older African Americans' Use Of Preventive Care, Catherine Walker O'Neal, Kandauda A.S. Wickrama, Penny A. Ralston, Jasminka Z. Elich, Cynthia M. Harris, Catherine Coccia, Iris Young-Clark, Jennifer Lemacks

Faculty Publications

The current study examined the influence of health insurance, psychological processes (i.e. psychological competency and vulnerability), and the interaction of these two constructs on older African Americans' utilization of five preventive care services (e.g. cholesterol screening and mammogram/prostate examination) using data from 211 older African Americans (median age = 60). In addition to direct effects, the influence of health insurance sometimes varied depending on respondents' psychological competency and/or vulnerability. Policies and interventions to increase older African Americans' use of preventive health services should consider structural (e.g. health insurance) and psychological (e.g. psychological competency and vulnerability) factors along with the interaction …

Concentrations And Sources Of Polycyclic Aromatic Hydrocarbons In Surface Coastal Sediments Of The Northern Gulf Of Mexico, Zucheng Wang, Zhanfei Liu, Kehui Xu, Lawrence M. Mayer, Zulin Zhang, Alexander S. Kolker, Wei Wu

Faculty Publications

Background: Coastal sediments in the northern Gulf of Mexico have a high potential of being contaminated by petroleum hydrocarbons, such as polycyclic aromatic hydrocarbons (PAHs), due to extensive petroleum exploration and transportation activities. In this study we evaluated the spatial distribution and contamination sources of PAHs, as well as the bioavailable fraction in the bulk PAH pool, in surface marsh and shelf sediments (top 5 cm) of the northern Gulf of Mexico. Results: PAH concentrations in this region ranged from 100 to 856 ng g(-1), with the highest concentrations in Mississippi River mouth sediments followed by marsh sediments and then …

Drosophila Snap-29 Is An Essential Snare That Binds Multiple Proteins Involved In Membrane Traffic, Hao Xu, Mahmood Mohtashami, Bryan Stewart, Gabrielle Boulianne, William S. Trimble

Faculty Publications

Each membrane fusion event along the secretory and endocytic pathways requires a specific set of SNAREs to assemble into a 4-helical coiled-coil, the so-called trans-SNARE complex. Although most SNAREs contribute one helix to the trans-SNARE complex, members of the SNAP-25 family contribute two helixes. We report the characterization of the Drosophila homologue of SNAP-29 (dSNAP-29), which is expressed throughout development. Unlike the other SNAP-25 like proteins in fruit fly (i.e., dSNAP-25 and dSNAP-24), which form SDS-resistant SNARE complexes with their cognate SNAREs, dSNAP-29 does not participate in any SDS-resistant complexes, despite its interaction with dsyntaxin1 and dsyntaxin 16 in vitro. …

Structural And Functional Analyses Of A Glutaminyl Cyclase From Ixodes Scapularis Reveal Metal-Independent Catalysis And Inhibitor Binding, Kai-Fa Huang, Hui-Ling Hsu, Shahid Karim, Andrew H.-J. Wang

Faculty Publications

Glutaminyl cyclases (QCs) from mammals and Drosophila are zinc-dependent enzymes that catalyze N-terminal pyroglutamate formation of numerous proteins and peptides. These enzymes have been found to be critical for the oviposition and embryogenesis of ticks, implying that they are possible physiological targets for tick control. Here, 1.10–1.15 Å resolution structures of a metal-independent QC from the black-legged tick Ixodes scapularis (Is-QC) are reported. The structures exhibit the typical scaffold of mammalian QCs but have two extra disulfide bridges that stabilize the central β-­sheet, resulting in an increased thermal stability. Is-QC contains ∼0.5 stoichiometric zinc ions, which could …

Priming In The Microbial Landscape: Periphytic Algal Stimulation Of Litter-Associated Microbial Decomposers, Kevin A. Kuehn, Steven N. Francoeur, Robert H. Findlay, Robert K. Neely

Faculty Publications

Microbial communities associated with submerged detritus in aquatic ecosystems often comprise a diverse mixture of autotrophic and heterotrophic microbes, including algae, bacteria, protozoa, and fungi. Recent studies have documented increased rates of plant litter mass loss when periphytic algae are present. We conducted laboratory and field experiments to assess potential metabolic interactions between natural autotrophic and heterotrophic microbial communities inhabiting submerged decaying plant litter of Typha angustifolia and Schoenoplectus acutus. In the field, submerged plant litter was either exposed to natural sunlight or placed under experimental canopies that manipulated light availability and growth of periphytic algae. Litter was collected …

Culture Of Lobotes Surinamensis (Tripletail), Eric Saillant, Jason T. Lemus, James S. Franks

Faculty Publications

No abstract provided.

Effects Of Coastal Urbanization On Salt-Marsh Faunal Assemblages In The Northern Gulf Of Mexico, Michael R. Lowe, Mark S. Peterson

Faculty Publications

Coastal landscapes in the northern Gulf of Mexico, specifically the Mississippi coast, have undergone rapid urbanization that may impact the suitability of salt-marsh ecosystems for maintaining and regulating estuarine faunal communities. We used a landscape ecology approach to quantify the composition and configuration of salt-marsh habitats and developed surfaces at multiple spatial scales surrounding three small, first-order salt-marsh tidal creeks arrayed along a gradient of urbanization in two river-dominated estuaries. From May 3 to June 4, 2010, nekton and macroinfauna were collected weekly at all six sites. Due to the greater abundance of grass shrimp Palaemonetes spp., brown shrimp Farfantepenaeus …

Effects Of Landscape Composition And Configuration On Migrating Songbirds: Inference From An Individual-Based Model, Emily B. Cohen, Scott M. Pearson, Frank R. Moore

Faculty Publications

The behavior of long-distance migrants during stopover is constrained by the need to quickly and safely replenish energetic reserves. Replenishing fuel stores at stopover sites requires adjusting to unfamiliar landscapes with little to no information about the distribution of resources. Despite their critical importance to the success of songbird migration, the effects of landscape composition and configuration on fuel deposition rates (FDR [g/d]), the currency of migration, has not been tested empirically. Our objectives were to understand the effects of heterogeneous landscapes on FDR of forest-dwelling songbirds during spring migration. The results of field experiments were used to parameterize a …

Interspecific Competition Of A New Invasive Mosquito, Culex Coronator, And Two Container Mosquitoes, Aedes Albopictus And Cx. Quinquefasciatus (Diptera: Culicidae), Across Different Detritus Environments, D. A. Yee, J. F. Skiff

Faculty Publications

The mosquito Culex coronator (Dyar and Knab) (Diptera: Culicidae) has undergone rapid range expansion in the United States since 2003, with its historical distribution in the southwest expanding eastward to the Atlantic coast. Although Cx. coronator nominally use small natural aquatic habitats for development, the use of containers (e.g., tires) makes it potentially important as container invasive. To determine the potential ecological effects of Cx. coronator on resident container species, we conducted a laboratory experiment to assess its competitive ability with two common tire-inhabiting species, Aedes albopictus (Skuse) and Culex quinquefasciatus (Say) (Diptera: Culicidae). Larvae were reared under a factorial …

Importation Of Exotic Ticks And Tick-Borne Spotted Fever Group Rickettsiae Into The United States By Migrating Songbirds, Nabanita Mukherjee, Lorenza Beati, Michael Sellers, Laquita Burton, Steven Adamson, Richard G. Robbins, Frank Moore, Shahid Karim

Faculty Publications

Birds are capable of carrying ticks and, consequently, tick-transmitted microorganisms over long distances and across geographical barriers such as oceans and deserts. Ticks are hosts for several species of spotted fever group rickettsiae (SFGR), which can be transmitted to vertebrates during blood meals. In this study, the prevalence of this group of rickettsiae was examined in ticks infesting migratory songbirds by using polymerase chain reaction (PCR). During the 2009 and 2010 spring migration season, 2064 northward-migrating passerine songbirds were examined for ticks at Johnson Bayou, Louisiana. A total of 91 ticks was removed from 35 individual songbirds for tick species …

An Insight Into The Microbiome Of The Amblyomma Maculatum(Acari: Ixodidae), Khemraj Budachetri, Rebecca E. Browning, Steven W. Adamson, Scot E. Dowd, Chien-Chung Chao, Wei-Mei Ching, Shahid Karim

Faculty Publications

The aim of this study was to survey the bacterial diversity of Amblyomma maculatum Koch, 1844, and characterize its infection with Rickettsia parkeri. Pyrosequencing of the bacterial 16S rRNA was used to determine the total bacterial population in A. maculatum. Pyrosequencing analysis identified Rickettsia in A. maculatum midguts, salivary glands, and saliva, which indicates successful trafficking in the arthropod vector. The identity of Rickettsia spp. was determined based on sequencing the rickettsial outer membrane protein A (rompA) gene. The sequence homology search revealed the presence of R. parkeri, Rickettsia amblyommii, and Rickettsia endosymbiont of …

The Status Of Plethodon Ainsworthi Lazell: Extinct, Extant, Or Nonexistent?, John G. Himes, David C. Beckett

Faculty Publications

Plethodon ainsworthi Lazell was described as a new species in the slimy salamander (Plethodon glutinosus [Northern Slimy Salamander]) complex from two specimens collected in Jasper County, MS, in 1964. Prior to their designation as the type and paratype of the newly described species in 1998, both specimens were presumably stored in strong formalin for 26 years and thus were in poor condition. Plethodon ainsworthi is distinguished from the sympatric Plethodon mississippi (Mississippi Slimy Salamander) by a more attenuated body, as evidenced by a higher snout-vent length (SVL)/head width (HW) ratio, and shorter limbs. Despite numerous searches between 1991 and …

Cross Amplification Of Microsatellite Loci Developed For Atractosteus Spatula In Atractosteus Tropicus, Sandra Bohn, Enrique Barraza, Caleb Mcmahan, Brian Kreiser

Faculty Publications

Due to recent population declines in tropical gar (Atractosteus tropicus), a greater understanding of its population structure is needed. A key step in gaining this understanding is the development of microsatellite loci for use in this species. For this purpose, 33 microsatellite loci from alligator gar (A. spatula) were screened in 52 individuals from a population in Zanjón del Chino, El Salvador. Twenty-five of these loci successfully amplified in this species, and 9 of those loci were polymorphic in this population. These loci should provide a useful tool for genotyping A. tropicus, both in studying …

Age, Growth, Mortality, And The Effects Of Trawling On Mortality Of The Longspine Porgy, Stenotomus Caprinus, Cher Marie Newman

Master's Theses

Stenotomus caprinus (Longspine Porgy) is one of the most abundant bycatch species caught in trawl fisheries in the northern Gulf of Mexico (GOM). Biological data of length, weight, and abundance have been collected since 1972 on the Southeast Area Monitoring and Assessment Program (SEAMAP) surveys with a variety of GOM species, including Longspine Porgy, using trawl nets during groundfish surveys. In 2010-2011 five Longspine Porgy were obtained from Groundfish and Pelagic surveys at each station for further analysis. Age distribution was determined through von Bertalanffy length and weight-age models. The samples were separated into two regions of the GOM to …

Assessing Respiration Rates And Nutrient Dynamics Of Aritifical Reef Biofilms And Bacterioplankton In The Mississippi Sound, Lynn Elizabeth Wilking

Master's Theses

Artificial reefs are primarily used to provide a suitable habitat for target fish populations, but the structures can also improve water quality and benefit non-target organisms. Laboratory incubation experiments were conducted in the presence of biofilm on rubble and in its absence to examine bacterial growth, community respiration, and nutrient dynamics at four artificial reef habitats in the Mississippi Sound. Biofilm samples were also collected from settlement plates deployed at each site and were analyzed for 813C and 81sN stable isotope content. Respiration rates were always higher in the presence of biofilm but bacterial abundance often declined over time, and …

Connecting The Dots: Understanding Migration In The Context Of Other Periods Of The Annual Cycle, Kristina Lee Paxton

Dissertations

Migration is a fundamental characteristic of the life history of many organisms. Large-scale seasonal movements expose migratory species to an array of differing environmental conditions such that the ecology, behavior, and life history strategies of migratory species must balance selection pressures associated with each phase of the annual cycle. Therefore, scientists increasingly realize that to understand the ecology of a migratory species in any one phase of the annual cycle requires an understanding of how other phases may interact with and influence the period of interest. That said, following individuals throughout the year poses a serious challenge.

The focus of …

Racial Differences In Self-Efficacy Expectations For Exercise, Selena P. Smith

Honors Theses

This project examined the link between race and self-efficacy. Self-efficacy pertains to an individual’s confidence in ability to complete or engage in a particular task or activity (Bandura, 1986). Prior research shows that self-efficacy has a great influence on exercise initiation and adherence (Bandura, 1986; Dishman, 1982; Rodgers and Sullivan, 2001). Research also supports that Caucasians are more likely to participate in exercise than African Americans (Centers for Disease Control and Prevention, 2000).

Participants included 51 females, 31 Caucasians and 20 African Americans, between the ages of 18 and 50 years old. The women were recruited from local fitness gyms, …

Knockdown Of Selenocysteine-Specific Elongation Factor In Amblyomma Maculatum Alters The Pathogen Burden Of Rickettsia Parkeri With Epigenetic Control By The Sin3 Histone Deacetylase Corepressor Complex, Steven W. Adamson, Rebecca E. Browning, Khemraj Budachetri, José M.C. Ribeiro, Shahid Karim

Faculty Publications

Selenocysteine is the 21st naturally-occurring amino acid. Selenoproteins have diverse functions and many remain uncharacterized, but they are typically associated with antioxidant activity. The incorporation of selenocysteine into the nascent polypeptide chain recodes the TGA stop codon and this process depends upon a number of essential factors including the selenocysteine elongation factor (SEF). The transcriptional expression of SEF did not change significantly in tick midguts throughout the blood meal, but decreased in salivary glands to 20% at the end of the fast feeding phase. Since selenoprotein translation requires this specialized elongation factor, we targeted this gene for knockdown by RNAi …

The Glucose Signaling Network In Yeast, Jeong-Ho Kim, Adhiraj Roy, David Jouandot Ii, Kyu Hong Cho

Faculty Publications

Background

Most cells possess a sophisticated mechanism for sensing glucose and responding to it appropriately. Glucose sensing and signaling in the budding yeast Saccharomyces cerevisiae represent an important paradigm for understanding how extracellular signals lead to changes in the gene expression program in eukaryotes.

Scope of review

This review focuses on the yeast glucose sensing and signaling pathways that operate in a highly regulated and cooperative manner to bring about glucose-induction of HXT gene expression.

Major conclusions

The yeast cells possess a family of glucose transporters (HXTs), with different kinetic properties. They employ three major glucose signaling pathways—Rgt2/Snf3, …

Morphological Divergence And Flow-Induced Phenotypic Plasticity In A Native Fish From Anthropogenically Altered Stream Habitats, Nathan R. Franssen, Laura K. Stewart, Jacob F. Schaefer

Faculty Publications

Understanding population-level responses to human-induced changes to habitats can elucidate the evolutionary consequences of rapid habitat alteration. Reservoirs constructed on streams expose stream fishes to novel selective pressures in these habitats. Assessing the drivers of trait divergence facilitated by these habitats will help identify evolutionary and ecological consequences of reservoir habitats. We tested for morphological divergence in a stream fish that occupies both stream and reservoir habitats. To assess contributions of genetic-level differences and phenotypic plasticity induced by flow variation, we spawned and reared individuals from both habitats types in flow and no flow conditions. Body shape significantly and consistently …

Differential Reconstructed Gene Interaction Networks For Deriving Toxicity Threshold In Chemical Risk Assessment, Yi Yang, Andrew Maxwell, Xiaowei Zhang, Nan Wang, Edward J. Perkins, Chaoyang Zhang, Ping Gong

Faculty Publications

Background: Pathway alterations reflected as changes in gene expression regulation and gene interaction can result from cellular exposure to toxicants. Such information is often used to elucidate toxicological modes of action. From a risk assessment perspective, alterations in biological pathways are a rich resource for setting toxicant thresholds, which may be more sensitive and mechanism-informed than traditional toxicity endpoints. Here we developed a novel differential networks (DNs) approach to connect pathway perturbation with toxicity threshold setting.

Methods: Our DNs approach consists of 6 steps: time-series gene expression data collection, identification of altered genes, gene interaction network reconstruction, differential …

Molecular Characterization Of Tick Salivary Gland Glutaminyl Cyclase, Steven W. Adamson, Rebecca E. Browning, Chien-Chung Chao, Robert C. Bateman Jr., Wei-Mei Ching, Shahid Karim

Faculty Publications

Glutaminyl cyclase (QC) catalyzes the cyclization of N-terminal glutamine residues into pyroglutamate. This post-translational modification extends the half-life of peptides and, in some cases, is essential in binding to their cognate receptor. Due to its potential role in the post-translational modification of tick neuropeptides, we report the molecular, biochemical and physiological characterization of salivary gland QC during the prolonged blood feeding of the black-legged tick (Ixodes scapularis) and the gulf-coast tick (Amblyomma maculatum). QC sequences from I. scapularis and A. maculatum showed a high degree of amino acid identity to each other and other arthropods and …

Penetration Of Uv-Visible Solar Radiation In The Global Oceans: Insights From Ocean Color Remote Sensing, Zhongping Lee, Chuanmin Hu, Shaoling Shang, Keping Du, Marlon Lewis, Robert Arnone, Robert Brewin

Faculty Publications

Penetration of solar radiation in the ocean is determined by the attenuation coefficient (K-d()). Following radiative transfer theory, K-d is a function of angular distribution of incident light and water's absorption and backscattering coefficients. Because these optical products are now generated routinely from satellite measurements, it is logical to evolve the empirical K-d to a semianalytical K-d that is not only spectrally flexible, but also the sun-angle effect is accounted for explicitly. Here, the semianalytical model developed in Lee et al. (2005b) is revised to account for the shift of phase function between molecular and particulate scattering from the short …

Jellyfish Body Plans Provide Allometric Advantages Beyond Low Carbon Content, Kylie A. Pitt, Carlos M. Duarte, Cathy H. Lucas, Kelly R. Sutherland, Robert H. Condon, Hermes Mianzan, Jennifer E. Purcell, Kelly L. Robinson, Shin-Ichi Uye

Faculty Publications

Jellyfish form spectacular blooms throughout the world's oceans. Jellyfish body plans are characterised by high water and low carbon contents which enables them to grow much larger than non-gelatinous animals of equivalent carbon content and to deviate from non-gelatinous pelagic animals when incorporated into allometric relationships. Jellyfish have, however, been argued to conform to allometric relationships when carbon content is used as the metric for comparison. Here we test the hypothesis that differences in allometric relationships for several key functional parameters remain for jellyfish even after their body sizes are scaled to their carbon content. Data on carbon and nitrogen …

Developmental Expression Profile Of Bric Á Brac 2, Midline And H15 In The Developing Eye And Central Nervous System Of Drosophila Melanogaster, Petra Visic

Honors Theses

Aberrant activity of a single gene can lead towards development of cancerous cells. Drosophila melanogaster is a useful model system to study cancer because there is high degree of evolutionary conservation in signaling pathways between humans and flies that play major roles in regulating cell proliferation and growth (Miles et al., 2011). At The University of Southern Mississippi (USM), Dr. Leal’s lab has gathered evidence suggesting that bab1 and bab2 interact with the T-box gene midline (mid) and its paralog H15, while the early developmental function of bab1 and bab2 remains unknown. That is why elucidating the early …