Life Sciences Commons^™

Deep Learning Architectures For Multi-Label Classification Of Intelligent Health Risk Prediction, Andrew Maxwell, Runzhi Li, Bei Yang, Heng Weng, Aihua Ou, Huixiao Hong, Zhaoxian Zhou, Ping Gong, Chaoyang Zhang

Faculty Publications

No abstract provided.

Deep Experimental Profiling Of Microrna Diversity, Deployment, And Evolution Across The Drosophila Genus, Jaaven Mohammed, Alex S. Flynt, Alexandra M. Panzarino, Md Mosharrof Hossain Mondal, Matthew Decruz, Adam Siepel, Eric C. Lai

Faculty Publications

To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death …

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.

A Neuroprotective Role For Mir-1017, A Non-Canonical Mirna, Matthew De Cruz

Master's Theses

miRNAs are post-transcriptional regulators of gene expression, with numerous being involved in neurobiology. Within the human genome a quarter of the identified miRNA loci derive from a class of miRNAs termed tailed mirtrons. Despite the identification of this large population of miRNA, no functional studies have been conducted to identify their role. In this study we examined the highly expressed and deeply conserved Drosophila 3’ tail mirtron, miR-1017, as a candidate to elucidate tailed mirtron functionality. We identified acetylcholine receptor transcripts, Da5 and Da2, as bona fide targets for miR-1017. Interestingly, Da2 is also the host transcript for miR-1017. We …

Impacts Of Oil Exposure During Early Life Development Stages In Sheepshead Minnows (Cyprinodon Variegatus) Under Different Environmental Factors, Danielle Simning

Master's Theses

The release of approximately 5 million barrels of crude oil into the northern Gulf of Mexico during the 2010 Deepwater Horizon oil spill jeopardized estuarine ecosystem health from Texas to Florida. These estuarine habitats, which serve as nurseries for many important fisheries are also prone to rapid fluctuations in environmental stressors such as oxygen concentration, and salinity. The consequence of combined exposure to crude oil and suboptimal environmental factors during early life stage development of fish is still largely unknown. The objective of this project was to investigate the impacts of exposure to crude oil in combination with varying environmental …

Effects Of Temperature On Growth And Molting In Blue Crabs (Callinectes Sapidus) And Lesser Blue Crabs (Callinectes Similis), Abigail Ann Kuhn

Master's Theses

Temperature can exert impacts on many processes in ectotherms. With global temperatures rising due to climate change, many ectothermic species may exhibit changes in growth rates and size at maturity, and these changes can have population-level effects. Predicting responses of species to climate change will require not only knowledge of thermal tolerance limits, but also effects of temperature change on growth rates and other life history parameters. For arthropods that exhibit discontinuous growth (i.e., molting), this includes both intermolt period and growth per molt. Previous laboratory and field experiments suggest that temperature affects both intermolt period (IMP) and growth per …

Combined Effects Of Dissolved Oxygen And Temperature On Aerobic Respiration And Respiratory Recovery Responses Of The Spioniform Polychaete, Streblospio Gynobranchiata, In Relation To Body Size, Alyssa Bennett

Master's Theses

Elevated surface temperatures exacerbate the threat of hypoxia within coastal ecosystems. These two primary stressors likely interact as they elicit opposing physiological responses from marine organisms. Metabolic depression is typically associated with hypoxia, while metabolic rates increase with temperature. Moreover, physiological effects of combined stressors may not be additive. In light of increasing pressures from hypoxia, elevated ocean temperatures, and other stressors within coastal regions, studies need to examine effects of multiple stressors on physiology of coastal organisms.

Mass-specific aerobic respiration (V_O2) was characterized as a proxy for metabolic cost of Streblospio gynobranchiata, at combined levels of …

Morphological, Genetic, And Environmental Characterization Of An Unusual Population Of Isoetes (Isoetaceae, Lycopodiophyta), Shannon L. Walker

Honors Theses

A large and unusual population of Isoetes (Isoetaceae, Lycopodiophyta) in the DeSoto National Forest, Wayne County, Mississippi, was studied to determine if the individuals there represent a new species or if they represent part of the variation of the one primary species of the longleaf pine belt of Mississippi, Isoetes louisianensis, which it most closely resembles. The unusual population and specimens of known Isoetes louisianensis were examined comparatively based on morphology, megaspore ornamentation, examination of habitat characteristics, and phylogenetic analysis of DNA sequence data from the nuclear internal transcribed spacer 1 and 2 (ITS) and the 5.8S ribosomal gene. No …

An Examination Of The Influence Of Social Physique Anxiety On Effort And Exercise Participation In College Students, Trellony M. Irwin

Honors Theses

The purpose of this study was to investigate whether an individual’s perception of others influenced exercise participation and effort in women and men participants involved in exercise classes in a campus recreation facility. The study consists of a survey that utilizes the Social Physique Anxiety Scale, the Ratings of Perceived Exertion (RPE) Scale, and demographic information. Results revealed that participants’ social physique anxiety accounted for roughly 30% of the variance in self-reported physical activity. However, when it came to participant effort during the group exercise classes, there was only roughly 2% variance between social physique anxiety and RPE. Further, the …

Salinity Tolerance Of Gambusia Affinis, Sarah Rubelowsky

Honors Theses

Developmental plasticity refers to changes during development as a result of environmental contributions. Salinity is a varying environmental condition in freshwater and estuarine habitats that can mediate developmental plasticity in Gambusia affinis, which can increase their tolerances as an invasive species. For my study, estuarine and freshwater populations of Gambusia affinis were sampled in March of 2017 using dip nets. Both populations were then brought back to the laboratory where pregnant females were acclimated to three different salinities (0‰, 15‰, 25‰) until they gave birth. I predicted that the estuarine population of Gambusia affinis would have a greater salinity tolerance …

Development, Evaluation, And Application Of A Novel Error Correction Method For Next Generation Sequencing Data, Isaac Akogwu

Dissertations

Tremendous evolvement in sequencing technologies and the vast availability of data due to decreasing cost of Next-Generation-Sequencing (NGS) has availed scientists the opportunity to address a wide variety of evolutionary and biological issues. NGS uses massively parallel technology to accelerate the process at the expense of accuracy and read length in comparison to earlier Sanger methods. Therefore, computational limitations exist in how much analysis and information can be gleaned from the data without performing some form of error correction.

Error correction process is laborious and consumes a lot of computational resources. Despite the existence of many NGS data error correction …

Development Of Innate Immunity During In Vitro Differentiation Of Mouse Embryonic Stem Cells, William D'Angelo

Dissertations

Embryonic stem cells (ESCs) hold enormous promise for the goals of regenerative medicine and tissue engineering, and extraordinary progress has been made in defining conditions for differentiation to desired cell types. However, an often overlooked aspect of ESC biology is innate immunity, the ability of cells to detect and respond to pathogens and inflammatory cytokines. A number of recent studies by our lab and others have established that ESCs and other types of pluripotent cells from both mice and humans do not mount typical immune responses to viral or bacterial stimuli. There are also indications that various cell types differentiated …

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 …

Signature Whistle Production During A Bottlenose Dolphin Group Integration, Megan S. Broadway

Dissertations

Bottlenose dolphins are an important species of interest because they possess a variety of abilities that are relatively rare in the animal kingdom, one being complex acoustic communication. Signature whistles - distinctive calls that are unique for each individual – are one of the most studied call types, but we know little about how these calls are used in various contexts, such as during an introduction. Looking at the socio-behavioral context in which signature whistles are used is likely the best way of learning how these whistles are used in a particular context (Caldwell, Caldwell, & Tyack, 1990). For this …

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 …

Historical Change Of Seagrasses In The Mississippi And Chandeleur Sounds, Linh Thuy Pham

Dissertations

Seagrasses are important coastal resources facing numerous stressors, and losses have been documented from local to global assessments. Under the broad theme of habitat loss and fragmentation, a study of historical change in total area and landscape configuration of seagrasses in the Mississippi and Chandeleur Sounds was conducted. Mapping data was collated from a multitude of previous projects from 1940 to 2011.

Comparisons of seagrass area among various studies that used different mapping methods can result in overestimation of area change and misleading conclusions of change over time. The vegetated seagrass area (VSA) data were generalized to a common resolution …

Evaluating Social Network Dynamics Of Bigg’S Killer Whales (Orcinus Orca) And Vessel Traffic Within A Transboundary Region: Implications For Conservation Management, Courtney Smith

Dissertations

The social lives of animals are defined by group dynamics based on the nature and strength of associations and movements between individuals, often resulting in highly complex and interconnected social networks. However, understanding of how environmental variables may shape this structure is poorly understood. Within the inland waters of Washington State and southern Vancouver Island, British Columbia, mammal-eating Bigg’s (transient) killer whales occur in relatively small, but stable social groups. Group size and occurrence in recent years has increased, coinciding with a growing whale watching industry. Given the central importance of the social network within killer whale population dynamics, such …

Escorting Of Mother-Calf Pairs Of Humpback Whales (Megaptera Novaeangliae) In The Colombian Pacific During The Breeding Season, Natalia Botero Acosta

Dissertations

Humpback whales (Megaptera novaeangliae) belonging to the “breeding G-stock” annually migrate from the Antarctic Peninsula and southern Chile to the southeastern Pacific to reproduce. Associations between mother-calf pairs and escorts were examined in the Gulf of Tribugá, northern Colombian Pacific, using photo-identification and behavioral/spatial sampling. Research hypotheses included: 1. The association between cows and escorts is short-lived, consistent with a male reproductive strategy, 2. The presence of escort(s) elicits a behavioral response from mother-calf pairs and, 3. The patterns of spatial distribution reflect the spatial segregation of maternal females. Groups were classified as mother-calf pairs (Mc), mother, calf …

Brachylicoa Lui, A New Species Of Parapseudid Tanaidacean (Crustacea: Peracarida: Apseudomorpha), From The Hawaiian Islands, With A Taxonomic Key, Andrés G. Morales-Núñez, Sterling Ulrich, Richard W. Heard

Faculty Publications

Brachylicoa lui sp. n. is described from the coastal waters of the Hawaiian island of O‘ahu. It is distinguished from the other four nominal members of Brachylicoa by a combination of characters including (1) an incised margin between base of rostrum and carapace, (2) mandible palp article-1 with cluster of 20–25 simple setae, (3) maxillule biarticulate palp ending in eight “cleaning’ setae, (4) maxilliped inner sub-distal margin with two stout spiniform seta, and (5) pereopod-6 with carpus having three plumose setae on mid-dorsal margin. Brachylicoa (=Apseudes) babelmandebensis sensu Guţu is tentatively transferred to the genus Saltipedis Guţu sensu …

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 …

Swainson's Thrushes Do Not Show Strong Wing Selectivity Prior To Crossing The Gulf Of Mexico, Rachel T. Bolus, Robert H. Diehl, Frank R. Moore, Jill L. Deppe, Michael P. Ward, Jaclyn Smolinsky, Theodore J. Zenzal Jr.

Faculty Publications

During long-distance fall migrations, nocturnally migrating Swainson’s Thrushes often stop on the northern Gulf of Mexico coast before flying across the Gulf. To minimize energetic costs, trans-Gulf migrants should stop over when they encounter crosswinds or headwinds, and depart with supportive tailwinds. However, time constrained migrants should be less selective, balancing costs of headwinds with benefits of continuing their migrations. To test the hypotheses that birds select supportive winds and that selectivity is mediated by seasonal time constraints, we examined whether local winds affected Swainson’s Thrushes’ arrival and departure at Ft. Morgan, Alabama, USA at annual, seasonal, and nightly time …

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 …

Thresholds Of Sea-Level Rise Rate And Sea-Level Rise Acceleration Rate In A Vulnerable Coastal Wetland, Wei Wu, Patrick D. Biber, Matthew Bethel

Understanding the Trajectory of Mississippi Coastal Salt Marsh Structure Function, and Processes in the face of Sea Level Rise: Data and Information Repository

Feedbacks among inundation, sediment trapping, and vegetation productivity help maintain coastal wetlands facing sea-level rise (SLR). However, when the SLR rate exceeds a threshold, coastal wetlands can collapse. Understanding the threshold helps address key challenges in ecology—nonlinear response of ecosystems to environmental change, promotes communication between ecologists and resource managers, and facilitates decision-making in climate change policies. We studied the threshold of SLR rate and developed a new threshold of SLR acceleration rate on sustainability of coastal wetlands as SLR is likely to accelerate due to enhanced anthropogenic forces. Deriving these two thresholds depends on the temporal scale, the interaction …

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 …

In Vivo Cloning Of Up To 16 Kb Plasmids In E. Coli Is As Simple As Pcr, Faqing Huang, Joseph Rankin Spengler, Allen Yang Huang

Faculty Publications

The precise assembly of defined DNA sequences into plasmids is an essential task in bioscience research. While a number of molecular cloning techniques have been developed, many methods require specialized expensive reagents or laborious experimental procedure. Not surprisingly, conventional cloning techniques based on restriction digestion and ligation are still commonly used in routine DNA cloning. Here, we describe a simple, fast, and economical cloning method based on RecA- and RecET-independent in vivo recombination of DNA fragments with overlapping ends using E. coli. All DNA fragments were prepared by a 2-consecutive PCR procedure with Q5 DNA polymerase and used …

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 …

Egg Quality Traits And Predictors Of Embryo And Fry Viability In Red Snapper Lutjanus Campechanus, Agnés Bardon-Albaret, Eric Saillant

Faculty Publications

The quality of red snapper eggs is highly variable and unpredictable in aquaculture, leading to high mortality during early larval rearing. In this work, the viability of red snapper eggs was monitored from fertilization until unfed larvae expired because of exhaustion of vitelline reserves to determine egg quality traits in this species. The spawns were obtained via strip spawning wild-caught females following hormonal induction with chorionic gonadotropin. Females were induced immediately after capture (wild group, n = 17) or held captive for the entire maturation period prior to induction (captive group, n = 7). Candidate predictors of egg quality measured …