Life Sciences Commons^™

Genome Sequences Of Mycobacteriophages Amgine, Amohnition, Bella96, Cain, Darthp, Hammy, Krueger, Lasthope, Peanam, Phelpsodu, Phrank, Sirphilip, Slimphazie, And Unicorn, Kirk R. Anders, Nazir Barekzi, Aaron A. Best, Gregory D. Frederick, Dmitri V. Mavrodi, Edwin Vasquez, Sea-Phages, Nana Yaa A. Amoh, Frederick N. Baliraine, William J. Buchser, Thomas P. Cast, Carmen E. Chamberlain, Hui-Min Chung, William A. D'Angelo, Christian T. Farris, Mariceli Fernandez-Martinez, Haley D. Fischman, Mark H. Forsyth, Anna G. Fortier, Kara F. Gallo, Greta J. Held, Miguel A. Lomas, Natalia Y. Maldonado-Vasquez, Claudia H. Moonsammy, Peace Namboote, Sudip Paudel, Sarah-Elizabeth Polley, Gabriella Reyes, Michael R. Rubin, Margaret S. Saha, Joseph Stukey, Tristan D. Tobias, Rebecca A. Garlena, Ty H. Stoner, Steven G. Cresawn, Deborah Jacobs-Sera, Welkin H. Pope, Daniel A. Russell, Graham F. Hatfull

Faculty Publications

We report the genome sequences of 14 cluster K mycobacteriophages isolated using Mycobacterium smegmatis mc²155 as host. Four are closely related to subcluster K1 phages, and 10 are members of subcluster K6. The phage genomes span considerable sequence diversity, including multiple types of integrases and integration sites.

Effects Of Trophic Relationships On Oyster Reef Restoration Success In The Mississippi Sound, Virginia Robin Fleer

Dissertations

Natural and anthropogenic changes resulting from altered hydrology, hurricanes, variable precipitation, and the BP oil spill have all taken their toll on oyster reefs in Mississippi. In response, oyster reef restoration efforts are currently underway within the Northern Gulf of Mexico. In order to understand why these efforts succeed or fail, it is crucial to consider predator-prey relationships within the context of the trophic dynamics of oyster reefs. Thus, for this dissertation study I integrated a multidisciplinary approach to understanding key trophic interactions affecting oyster recruitment, growth and survival, comprising field sampling, manipulative lab experiments, and individual-based modeling. Spat settlement …

Ecological And Oceanographic Influences On Leatherback Turtle Behavior And Scyphozoan Jellyfish Distributions In The Gulf Of Mexico, Katrina Aleksa

Dissertations

Leatherback turtles (Dermochelys coriacea) are a wide-ranging, oceanic species that feed exclusively on gelatinous zooplankton. Leatherback have been spotted in the Gulf of Mexico (GoM) for several decades and consistently had a high level of interactions with longline fisheries. However, no quantitative studies have been performed to address the spatiotemporal distribution of these turtles in the GoM. This research determines 1) leatherback movements and high-use areas in the GoM, 2) their association with oceanographic features, 3) the distribution and density of two abundant medusae in the northern GoM and any association with biophysical parameters, and 4) the body …

Msaabcr Operon Is Involved In Persister Cell Formation In Staphylococcus Aureus, Gyan S. Sahukhal, Shanti Pandey, Mohamed O. Elasri

Faculty Publications

Background

Persister cells comprise a phenotypic variant that shows extreme antibiotic tolerance resulting in treatment failures of bacterial infections. While this phenomenon has posed a great threat in public health, mechanisms underlying their formation in Staphylococcus aureus remain largely unknown. Increasing evidences of the presence of persister cells in recalcitrant infections underscores the great urgency to unravel the mechanism by which these cells develop. Previously, we characterized msaABCR operon that plays roles in regulation of virulence, biofilm development and antibiotic resistance. We also characterized the function of MsaB protein and showed that MsaB is a putative transcription factor that binds …

Bottom-Up Control Of Parasites, David S. Johnson, Richard W. Heard

Faculty Publications

Parasitism is a fundamental ecological interaction. Yet we understand relatively little about the ecological role of parasites compared to the role of free-living organisms. Bottom-up theory predicts that resource enhancement will increase the abundance and biomass of free-living organisms. Similarly, parasite abundance and biomass should increase in an ecosystem with resource enhancement. We tested this hypothesis in a landscape-level experiment in which salt marshes (60,000 m2 each) received elevated nutrient concentrations via flooding tidal waters for 11 yr to mimic eutrophication. Nutrient enrichment elevated the densities of the talitrid amphipod, Orchestia grillus, and the density and biomass of its trematode …

Effects Of Tectonics And Large Scale Climatic Changes On The Evolutionary History Of Hyalomma Ticks, Arthur F. Sands, Dmitry A. Apanaskevich, Sonja Matthee, Ivan G. Horak, Alan Harrison, Shahid Karim, Mohammad K. Mohammad, Kosta Y. Mumcuoglu, Rupika S. Rajakaruna, Maria M. Santos-Silva, Joshua Kamani, Conrad A. Matthee

Faculty Publications

Hyalomma Koch, 1844 are ixodid ticks that infest mammals, birds and reptiles, to which 27 recognized species occur across the Afrotropical, Palearctic and Oriental regions. Despite their medical and veterinary importance, the evolutionary history of the group is enigmatic. To investigate various taxonomic hypotheses based on morphology, and also some of the mechanisms involved in the diversification of the genus, we sequenced and analysed data derived from two mtDNA fragments, three nuclear DNA genes and 47 morphological characters. Bayesian and Parsimony analyses based on the combined data (2242 characters for 84 taxa) provided maximum resolution and strongly supported the monophyly …

Connecting The Dots: Stopover Strategies Of An Intercontinental Migratory Songbird In The Context Of The Annual Cycle, Kristina Paxton, Frank R. Moore

Faculty Publications

The phases of the annual cycle for migratory species are inextricably linked. Yet, less than five percent of ecological studies examine seasonal interactions. In this study, we utilized stable hydrogen isotopes to geographically link individual black-and-white warblers (Mniotilta varia) captured during spring migration with breeding destinations to understand a migrant's stopover strategy in the context of other phases of the annual cycle. We found that stopover strategy is not only a function of a bird's current energetic state, but also the distance remaining to breeding destination and a bird's time-schedule, which has previously been linked to habitat conditions experienced …

Ethanol-Induced Stress Response Of Staphylococcus Aureus, Jasmine M. Pando, Richard F. Pfeltz, Jesus A. Cuaron, Vijayaraj Nagarajan, Mukti N. Mishra, Nathaniel J. Torres, Mohamed O. Elasri, Brian J. Wilkinson, John E. Gustafson

Faculty Publications

Transcriptional profiles of 2 unrelated clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates were analyzed following 10% (v/v) ethanol challenge (15 min), which arrested growth but did not reduce viability. Ethanol-induced stress (EIS) resulted in differential gene expression of 1091 genes, 600 common to both strains, of which 291 were upregulated. With the exception of the downregulation of genes involved with osmotic stress functions, EIS resulted in the upregulation of genes that contribute to stress response networks, notably those altered by oxidative stress, protein quality control in general, and heat shock in particular. In addition, genes involved with …

Amblyomma Maculatum Secis Binding Protein 2 And Putative Selenoprotein P Are Indispensable For Pathogen Replication And Tick Fecundity, Khemraj Budachetri, Gary Crispell, Shahid Karim

Faculty Publications

Selenium, a vital trace element, is incorporated into selenoproteins to produce selenocysteine. Our previous studies have revealed an adaptive co-evolutionary process that has enabled the spotted fever-causing tick-borne pathogen Rickettsia parkeri to survive by manipulating an antioxidant defense system associated with selenium, which includes a full set of selenoproteins and other antioxidants in ticks. Here, we conducted a systemic investigation of SECIS binding protein 2 (SBP2) and putative selenoprotein P (SELENOP) by transcript silencing in adult female Gulf-coast ticks (Amblyomma maculatum). Knockdown of the SBP2 and SELENOP genes depleted the respective transcript levels of these tick selenogenes, and …

Listeria Occurrence In Poultry Flocks: Detection And Potential Implications, Michael J. Rothrock Jr., Morgan L. Davis, Aude Locatelli, Aaron Bodie, Tori G. Mcintosh, Janet R. Donaldson, Steven C. Ricke

Faculty Publications

Foodborne pathogens such as Salmonella, Campylobacter, Escherichia coli, and Listeria are a major concern within the food industry due to their pathogenic potential to cause infection. Of these, Listeria monocytogenes, possesses a high mortality rate (approximately 20%) and is considered one of the most dangerous foodborne pathogens. Although the usual reservoirs for Listeria transmission have been extensively studied, little is known about the relationship between Listeria and live poultry production. Sporadic and isolated cases of listeriosis have been attributed to poultry production and Listeria spp. have been isolated from all stages of poultry production and processing. Farm studies …

Oviposition Preference And Offspring Performance In Container Breeding Mosquitoes: Evaluating The Effects Of Organic Compounds And Laboratory Colonisation, David W. Allgood, Donald A. Yee

Faculty Publications

1. The preference–performance hypothesis (PPH) predicts that organisms lacking parental care should oviposit in habitats that optimise offspring performance. Preference–performance relationships were investigated for the Asian tiger mosquito (Aedes albopictus Skuse) and the southern house mosquito (Culex quinquefasciatus Say) (Diptera: Culicidae), two medically important container-breeding species, in response to an organic chemical blend mimicking decaying plant matter. Additionally, the effects of long-term laboratory colonisation of Cx. quinquefasciatus using wild and laboratory strains were evaluated.

2. Oviposition bioassays were conducted by releasing gravid mosquitoes into field enclosures with automobile tires containing low and high concentrations of the chemical blend, …

Effects Of Wave Action On The Structure Of Fish Assemblages Across An Exposure Gradient, Lauren Liddon

Master's Theses

Disturbance affects the function and diversity of ecosystems. Increased wave exposure to salt marsh can disturb sediments and cause a loss of habitat. The purpose of this study was to explore the effects of increased wave exposure on diversity, abundance, and functional ecology of estuarine fishes. If increased wave exposure is acting as a disturbance to these habitats, ecological theory (Intermediate Disturbance Hypothesis) predicts that diversity will peak at intermediate frequencies and intensities of disturbance. Fish were sampled from 10 sites monthly for 6 years. The sites were assigned to different exposure categories (Open, Intermediate, and Sheltered) using an exposure …

An Ecological Examination Of Johnson Bayou (Pass Christian, Ms) With A Reproductive Histological Analysis Of Rangia Cuneata, And A Comparative Morphological Study Of The Foot And Shell Of Rangia Cuneata And Polymesoda Caroliniana, Brandon Drescher

Dissertations

Johnson Bayou is an estuarine system located in Pass Christian, MS. Research involved a biotic and abiotic examination of Johnson Bayou, resulting in the identification of numerous species of plants and animals, including Rangia cuneata (Mactridae) and Polymesoda caroliniana (Cyrenidae), sympatric species of infaunal bivalves. Environmental factors (e.g., water temperature, salinity) were measured over three years to describe the system from an abiotic standpoint, and used in a qualitative and quantitative reproductive histological study on R. cuneata. Results revealed differences in timing of gamete production and spawning between three subpopulations of this species. Sediment samples taken from the study …

Solution Of Pdes For First-Order Photobleaching Kinetics Using Krylov Subspace Spectral Methods, Somayyeh Sheikholeslami

Dissertations

We solve the first order reaction-diffusion equations which describe binding-diffusion kinetics using a photobleaching scanning profile of a confocal laser scanning microscope approximated by a Gaussian laser profile. We show how to solve these equations with prebleach steady-state initial conditions using a time-domain method known as a Krylov Subspace Spectral (KSS) method. KSS methods are explicit methods for solving time- dependent variable-coefficient partial differential equations (PDEs). KSS methods are advantageous compared to other methods because of their stability and their superior scalability. These advantages are obtained by applying Gaussian quadrature rules in the spectral domain developed by Golub and Meurant. …

Draft Genome Sequences Of Strains Salinicola Socius Smb35T, Salinicola Sp. Mh3r3-1 And Chromohalobacter Sp. Smb17 From The Verkhnekamsk Potash Mining Region Of Russia, Björn E. Olsson, Ekaterina S. Korsakova, Lyudmila N. Anan'ina, Anna A. Pyankova, Olga V. Mavrodi, Elena G. Plotnikova, Dmitri V. Mavrodi

Faculty Publications

Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This study addresses this gap by presenting draft genomes of Salinicola socius SMB35T, Salinicola sp. MH3R3–1 and Chromohalobacter sp. SMB17, which were isolated from potash mine tailings in the Verkhnekamsk salt deposit area of Russia. The analysis of these genomes confirmed the importance of ectoines and quaternary amines to the …

Osteopontin Facilitates West Nile Nirus Neuroinvasion Via Neutrophil "Trojan Horse" Transport, Amber M. Paul, Dhiraj Acharya, Laurel Duty, E. Ashley Thompson, Linda Le, Dobrivoje S. Stokic, A. Arturo Leis, Fengwei Bai

Faculty Publications

West Nile virus (WNV) can cause severe human neurological diseases including encephalitis and meningitis. The mechanisms by which WNV enters the central nervous system (CNS) and host-factors that are involved in WNV neuroinvasion are not completely understood. The proinflammatory chemokine osteopontin (OPN) is induced in multiple neuroinflammatory diseases and is responsible for leukocyte recruitment to sites of its expression. In this study, we found that WNV infection induced OPN expression in both human and mouse cells. Interestingly, WNV-infected OPN deficient (Opn −/−) mice exhibited a higher survival rate (70%) than wild type (WT) control mice (30%), suggesting OPN plays a …

A Study Of Ticks And Tick-Borne Livestock Pathogens In Pakistan, Shahid Karim, Khemraj Budachetri, Nabanita Mukherjee, Jaclyn Williams, Asma Kausar, Muhammad Jawadul Hassan, Steven W. Adamson, Scot E. Dowd, Dmitry Apanskevich, Abdullah Arijo, Zia Uddin Sindhu, Muhammad Azam Kakar, Raja Muhammad Dilpazir Khan, Shafiq Ullah, Muhammad Sohail Sajid, Abid Ali, Zafar Iqbal

Faculty Publications

Background

As obligate blood-feeding arthropods, ticks transmit pathogens to humans and domestic animals more often than other arthropod vectors. Livestock farming plays a vital role in the rural economy of Pakistan, and tick infestation causes serious problems with it. However, research on tick species diversity and tick-borne pathogens has rarely been conducted in Pakistan. In this study, a systematic investigation of the tick species infesting livestock in different ecological regions of Pakistan was conducted to determine the microbiome and pathobiome diversity in the indigenous ticks.

Methodology/Principal findings A total of 3,866 tick specimens were morphologically identified as 19 different tick …

Genetic Bottlenecks In Pristis Sawfishes In Northern Australian Waters, Nicole M. Phillips, Annemarie Fearing, David L. Morgan

Faculty Publications

Northern Australia has been identified as the last stronghold for the dwarf sawfish Pristis clavata, green sawfish P. zijsron, and largetooth sawfish P. pristis, making these populations key in global conservation efforts for each species. This research assesses the levels of genetic diversity in these 3 sawfishes in Australian waters, testing for the presence of population bottlenecks using data at microsatellite loci. Levels of observed heterozygosity in each species from the west coast of Australia and the north-eastern Gulf of Carpentaria were generally high. M ratio tests suggest that assemblages of P. zijsron and P. pristis on …

Effects Of Marsh Fragmentation And Patch Area On Fish And Nekton Assemblages In Mississippi, Jennifer R. Main

Honors Theses

Fragmentation divides continuous habitat into smaller patches. Fragmentation can also produce smaller populations of species, because fragmentation can split a population into smaller groups. Both terrestrial and aquatic ecosystems suffer from fragmentation. There are a variety of fishes that live along marsh, each depending upon the marsh for protection, food, and sometimes even competition. Species richness of fishes can be altered due to marsh fragmentation. I predict islands with a larger patch index should have a higher species richness of fishes. For this study, fish assemblages at 20 islands of marsh were sampled in the months of June and July …

Use Of A Novel Oleaginous Microorganism As A Potential Source Of Lipids For Weanling Pigs, Jeffery A. Carroll, Ty B. Schmidt, T.R. Callaway, J.G. Wilson, Janet R. Donaldson

Faculty Publications

Weanling pigs are at risk of succumbing to illness due to an immature immune system and insufficient supply of available energy at the time of weaning. This study was aimed at determining whether oleaginous bacteria could serve as a source of lipids to weanling pigs. Weanling pigs were provided a daily dose of 1×109 colony fomring unit (CFU) = kg−1 of the novel oleaginous Enterobacter cloacae strain JD6301 or JD8715 (which is a variant form of JD6301 capable of producing extracellular triglycerides) via oral gavage for 5 d. Serum was collected every 6 h and intestinal samples were collected at …

Relationships Between Root Pathogen Resistance, Abundance And Expression Of Pseudomonas Antimicrobial Genes, And Soil Properties In Representative Swiss Agricultural Soils, Nicola Imperiali, Francesca Dennert, Jana Schneider, Titouan Laessle, Christelle Velatta, Marie Fesselet, Michele Wyler, Fabio Mascher, Olga Mavrodi, Dmitri Mavrodi, Monika Maurhofer, Christoph Keel

Faculty Publications

Strains of Pseudomonas that produce antimicrobial metabolites and control soilborne plant diseases have often been isolated from soils defined as disease-suppressive, i.e., soils, in which specific plant pathogens are present, but plants show no or reduced disease symptoms. Moreover, it is assumed that pseudomonads producing antimicrobial compounds such as 2,4-diacetylphloroglucinol (DAPG) or phenazines (PHZ) contribute to the specific disease resistance of suppressive soils. However, pseudomonads producing antimicrobial metabolites are also present in soils that are conducive to disease. Currently, it is still unknown whether and to which extent the abundance of antimicrobials-producing pseudomonads is related to the general disease resistance …

The Molecular Basis For The Lack Of Inflammatory Responses In Mouse Embryonic Stem Cells And Their Differentiated Cells, William D'Angelo, Chandan Gurung, Dhiraj Acharya, Natalya Ortolano, Fengwei Bai, Yan-Lin Guo

Faculty Publications

We reported previously that mouse embryonic stem cells do not have a functional IFN-based antiviral mechanism. The current study extends our investigation to the inflammatory response in mouse embryonic stem cells and mouse embryonic stem cell–differentiated cells. We demonstrate that LPS, TNF-α, and viral infection, all of which induce robust inflammatory responses in naturally differentiated cells, failed to activate NF-κB, the key transcription factor that mediates inflammatory responses, and were unable to induce the expression of inflammatory genes in mouse embryonic stem cells. Similar results were obtained in human embryonic stem cells. In addition to the inactive state of NF-κB, …

Yeast Pro- And Paraprobiotics Have The Capability To Bind Pathogenic Bacteria Associated With Animal Disease, Gabriel A. Posadas, Paul R. Broadway, Justin A. Thornton, Jeffery A. Carroll, Amanda Lawrence, Jimmie R. Corley, Amber Thompson, Janet R. Donaldson

Faculty Publications

Live yeast probiotics and yeast cell wall components (paraprobiotics) may serve as an alternative to the use of antibiotics in prevention and treatment of infections caused by pathogenic bacteria. Probiotics and paraprobiotics can bind directly to pathogens, which limits binding of the pathogens to the intestinal cells and also facilitates removal from the host. However, knowledge of bacterial binding, specificity, and/or capability is limited with regard to probiotics or paraprobiotics. The goal of this study was to characterize the qualitative and quantitative nature of two Saccharomyces cerevisiae probiotics and three S. cerevisiae paraprobiotics to adhere to thirteen different pathogenic bacteria …

Distribution And Habitat Use Of The Golden Crab Chaceon Fenneri Off Eastern Florida Based On In Situ Submersible And Rov Observations And Potential For Impacts To Deep Water Coral/Sponge Habitat, John K. Reed, Stephanie Farrington, Charles Messing, Andrew David

Gulf and Caribbean Research

This study documents the distribution and habitat preferences of the golden crab, a commercially fished species, in relation to deep-sea coral/sponge ecosystems (DSCEs) at 200-900 m depths off eastern Florida. A total of 386 h of videotapes from 94 submersible and remotely operated vehicle (ROV) dives from 1999 to 2009, covering a total distance of 376 km, were reviewed and characterized for habitat type and presence of crabs. The DSCEs surveyed included Lophelia coral mounds, Miami Terrace, Pourtalès Terrace, and Tortugas Valleys. Video transect data also included environmental surveys of proposed deep-water routes for Liquid Natural Gas (LNG) pipelines, LNG …