Life Sciences Commons^™

Detection And Verification Of Mammalian Mirtrons By Northern Blotting, Mohammad Farid Zia, Alex S. Flynt

Faculty Publications

microRNAs (miRNAs) have vital roles in regulating gene expression—contributing to major diseases like cancer and heart disease. Over the last decade, thousands of miRNAs have been discovered through high throughput sequencing-based annotation. Different classes have been described, as well as a great dynamic range of expression levels. While sequencing approaches provide insight into biogenesis and allow confident identification, there is a need for additional methods for validation and characterization. Northern blotting was one of the first techniques used for studying miRNAs, and remains one of the most valuable as it avoids enzymatic manipulation of miRNA transcripts. Blotting can also provide …

Msab And Cody Interact To Regulate Staphylococcus Aureus Capsule In A Nutrient-Dependent Manner, Justin Batte, Gyan S. Sahukhal, Mohamed O. Elasri

Faculty Publications

Staphylococcus aureus has a complex regulatory network for controlling the production of capsule polysaccharide. In S. aureus, capsule production is controlled by several regulators in response to various environmental stimuli. Previously, we described MsaB as a new regulator that specifically binds to the cap promoter in a growth-phase or nutrient-dependent manner. In addition to MsaB, several other regulators have also been shown to bind the same region. In this study, we examined the interactions between MsaB and other nutrient-sensing regulators (CodY and CcpE) with respect to binding to the cap promoter in a nutrient-dependent manner. We observed that msaABCR …

Stability, Persistence And Habitat Associations Of The Pearl Darter Percina Aurora In The Pascagoula River System, Southeastern Usa, Scott R. Clark, William T. Slack, Brian Kreiser, Jacob F. Schaefer, Mark A. Dugo

Faculty Publications

The southeastern United States represents one of the richest collections of aquatic biodiversity worldwide; however, many of these taxa are under an increasing threat of imperilment, local extirpation, or extinction. The pearl darter Percina aurora is a small-bodied freshwater fish endemic to the Pearl and Pascagoula river systems of Mississippi and Louisiana (USA). The last collected specimen from the Pearl River drainage was taken in 1973, and it now appears that populations in this system are likely extirpated. This reduced the historical range of this species by approximately 50%, ultimately resulting in federal protection under the US Endangered Species Act …

Honey Bee Survival And Pathogen Prevalence: From The Perspective Of Landscape And Exposure To Pesticides, Mohamed Alburaki, Deniz Chen, John A. Skinner, William G. Meikle, David R. Tarpy, John Adamczyk, Scott D. Stewart

Faculty Publications

In order to study the in situ effects of the agricultural landscape and exposure to pesticides on honey bee health, sixteen honey bee colonies were placed in four different agricultural landscapes. Those landscapes were three agricultural areas with varying levels of agricultural intensity (AG areas) and one non-agricultural area (NAG area). Colonies were monitored for different pathogen prevalence and pesticide residues over a period of one year. RT-qPCR was used to study the prevalence of seven different honey bee viruses as well as Nosema sp. in colonies located in different agricultural systems with various intensities of soybean, corn, sorghum, and …

Exposure To Crude Oil And Chemical Dispersant May Impact Marine Microbial Biofilm Composition And Steel Corrosion, Jennifer Salerno, Brenda Little, Jason Lee, Leila J. Hamdan

Faculty Publications

The release of hydrocarbons and chemical dispersant in marine environments may disrupt benthic ecosystems, including artificial reefs, formed by historic steel shipwrecks, and their associated organisms. Experiments were performed to determine the impacts of crude oil, dispersed crude oil, and dispersant on the community structure and function of microorganisms in seawater (SW) and biofilms formed on carbon steel, a common ship hull construction material. Steel corrosion was also monitored to illustrate how oil spills may impact preservation of steel shipwrecks. Microcosms were filled with seawater (SW) and incubated at 4°C. Carbon steel disks (CSDs) were placed in each tank, and …

Feeding Patterns Of Two Commercially Important Fish Species Scomberoides Commersonnianus And S. Tol In The Northern Arabian Sea Coast Of Pakistan, Nazia Qamar, Sher Khan Panhwar, Ralf Riedel

Faculty Publications

Port landing of Scomberoides commersonnianus and S. tol were obtained between July 2013 and June 2015 for stomach content analysis. Analysis of prey composition was done using permutational analysis of variance (permanova), with species, life stage (juvenile and adults), gender, and weather (rainy and dry season) as factors. Patterns of empty stomachs were investigated to estimate feeding intensity. Feeding intensity was estimated with logistic regression, using the same independent variables as above. Prey importance was also investigated. Prey importance was assessed using a Wilcox Rank Correlation analysis on the Index of Relative Importance (IRI) by species and life-stage. Permanova analysis …

Assessing Natural Infection With Zika Virus In The Southern House Mosquito, Culex Quinquefasciatus, During 2016 In Puerto Rico, Donald A. Yee, Rebeca De Jesus Crespo, Fiona F. Hunter, Fengwei Bai

Faculty Publications

The epidemic of Zika in the Western hemisphere has led to intense investigations of all species important in the transmission of Zika virus (ZikV), including putative mosquito vectors. Although evidence points to Stegomyia (= Aedes) (Diptera: Culicidae) mosquitoes as the primary vectors in nature among humans, there remains the possibility that other common mosquito species may be implicated in the rapid spread of the virus. Herein, field-caught Culex quinquefasciatus (Diptera: Culicidae) collected during June 2016 in different neighbourhoods in San Juan, Puerto Rico were examined for the presence of natural infection with ZikV. Stegomyia aegypti (= Aedes aegypti) …

The Effect Of Light Conditions On Interpreting Oil Composition Engineering In Arabidopsis Seeds, Nischal Karki, Philip D. Bates

Faculty Publications

Arabidopsis thaliana is the most developed and utilized model plant. In particular, it is an excellent model for proof‐of‐concept seed oil engineering studies because it accumulates approximately 37% seed oil by weight, and it is closely related to important Brassicaceae oilseed crops. Arabidopsis can be grown under a wide variety of conditions including continuous light; however, the amount of light is strongly correlated with total seed oil accumulation. In addition, many attempts to engineer novel seed oil fatty acid compositions in Arabidopsis have reported significant reductions in oil accumulation; however, the relative reduction from the nontransgenic controls varies greatly within …

Toxicity Of Selected Acaricides To Honey Bees (Apis Mellifera) And Varroa (Varroa Destructor Anderson And Trueman) And Their Use In Controlling Varroa Within Honey Bee Colonies, Aleš Gregorc, Mohamed Alburaki, Blair Sampson, John Adamczyk

Faculty Publications

The efficacies of various acaricides in order to control a parasitic mite, the Varroa mite, Varroa destructor, of honey bees, were measured in two different settings, namely, in laboratory caged honey bees and in queen-right honey bee colonies. The Varroa infestation levels before, during, and after the acaricide treatments were determined in two ways, namely: (1) using the sugar shake protocol to count mites on bees and (2) directly counting the dead mites on the hive bottom inserts. The acaricides that were evaluated were coumaphos, tau-fluvalinate, amitraz, thymol, and natural plant compounds (hop acids), which were the active ingredients. The …

Physical Processes Dictate Early Biogeochemical Dynamics Of Soil Pyrogenic Organic Matter In A Subtropical Forest Ecosystem, Jason Stuart, Russell Anderson, Patrick Lazzarino, Kevin A. Kuehn, Omar R. Harvey

Faculty Publications

Quantifying links between pyOM dynamics, environmental factors and processes is central to predicting ecosystem function and response to future perturbations. In this study, changes in carbon (TC), nitrogen (TN), pH, and relative recalcitrance (R50) for pineand cordgrass-derived pyOM were measured at 3–6 weeks intervals throughout the first year of burial in the soil. Objectives were to (1) identify key environmental factors and processes driving early-stage pyOM dynamics, and (2) develop quantitative relationships between environmental factors and observed changes in pyOM properties. The study was conducted in sandy soils of a forested ecosystem within the Longleaf pine range of the United …

The Ethical Justification Of Equal Candidacy For Organ Transplantation In Alcoholic Patients, Peter A. Depergola Ii

Journal of Health Ethics

An increasingly blurred understanding of the distinctive challenges posed to transplantation medicine and, by extension, public health, by the debilitating reality of alcoholism suggests a critical need to revisit the relationship between causality, candidacy, and culpability in light of substance addiction. This essay grounds its arguments in two, straightforward premises: (i) compassionate medical practice - understood as the sympathetic willingness to enter into the existential suffering of another in order to ameliorate the anguish invoked by disease - rests on the fiduciary relationship shared between provider and patient; and (ii) allocating medical goods according to moral desert rather than existential …

Does Interest Equal Success? Evaluating Student Perceptions Of The Study Of Biology And Their Effects On Student Success In An Introductory Biology Course, Courtney Irene Barlow

Honors Theses

As instructors begin to devote more time to improving student perceptions of biology, the validity of these efforts should be determined. Do students possessing favorable views of biology regularly perform on a higher level than those with less favorable impressions, or would class time be better spent without exercises intended to increase student interest? The goal of this project was to address the research questions “How do students view the study of biology?”, “How do student perceptions of the subject area affect their performance in an Introductory Biology course?”, and “How does a student’s chosen area of study affect their …

Effects Of Acorns On Populations Of Aedes Mosquitoes, Rachel Rogers

Honors Theses

Aedes albopictus (Asian tiger mosquito) and Aedes aegypti (yellow fever mosquito) are two mosquito species that are non-native to North America and are of medical importance. Both species can be found in aquatic container habitats, such as discarded tires and tree holes. In container habitats, the influx of detritus from the outside environment is essential to mosquito production and can include a variety of plant and animal material. Seeds from oak trees (acorns) can seasonally contribute to the detritus of these container habitats. This study examined the effect of acorns from the southern live oak (Quercus virginiana) on the performance …

Lead, Copper, And Iron In University Tap Water, Alison Mclendon

Honors Theses

This study observed concentrations of lead, copper, and iron in university tap water over an eight-week span during and between the summer and fall semesters. First draw and 30s flush samples were taken after overnight stagnation from the Honor House, College Hall, J. B. George Building, and International Center bathrooms and analyzed with an inductively-coupled plasma mass spectrometer (ICPMS). There was no obvious correlation between time in the semester and metal concentrations. Relative iron levels rose and fell at the same time in all buildings, but there was little correlation between buildings for lead and copper concentrations. The Honor House …

The Characterization Of The Transcription Factor Msab And Its Role In Staphylococcal Virulence, Justin Batte

Dissertations

Staphylococcus aureus is a common human pathogen that is responsible for a wide range of infections, ranging from relative minor skin infections to life-threatening disease such as bacteremia, septicemia, and endocarditis. S. aureus possesses many different virulent factors that aid in its ability to cause this wide array of infections. One major virulence factor includes the production of capsular polysaccharide (CP). The production of CP plays a major role in the virulence response during infection specifically by providing S. aureus an antiphagocytic mechanism that allows the pathogen to evade phagocytosis during an infection. S. aureus has developed complex genetic regulatory …

Regional Variation In Migratory Behavior And Reproductive Output Of The Gulf Of Mexico Blue Crab Spawning Stock, Adam Kemberling

Master's Theses

The overarching goal of this research was to better understand the structure and boundaries of the blue crab stock(s) in the Gulf of Mexico, focusing on large-scale movements of spawning female crabs. Because spawning location is a primary determinant of larval transport pathways, understanding spawning locations and offshore movements of female blue crabs can inform stock identification and potentially clarify the somewhat conflicting population genetic information available for blue crabs. A large-scale mark-recapture study was conducted through the partnership of state/federal management agencies, the commercial fishing industry, recreational fisherman, tourists, and numerous academic institutions to shed light on the timing …

The Role And Contribution Of Saprotrophic Fungi During Standing Litter Decomposition Of Two Perennial Grass Species, Schizachyrium Scoparium And Schizachyrium Tenerum, Matthew Lodato

Master's Theses

In terrestrial ecosystems, most of the plant biomass produced enters the detrital pool, where microbial decomposers colonize, enzymatically degrade, and assimilate plant litter carbon and nutrients in amounts sufficient to bring about the decomposition of plant litter. Here, I estimated the biomass and production of fungi and microbial respiration associated with decaying Schizachyrium scoparium and Schizachyrium tenerum leaf litter, and constructed a partial organic matter budget estimating C flow into and through fungal decomposers. Significant losses in S. scoparium (57%) and S. tenerum (68%) leaf mass was observed during litter decomposition along with concomitant increases in fungal biomass, which reached …

Linkages Between Marsh Fragmentation, Prey Availability, And Blue Crab (Callinectes Sapidus) Abundance And Mortality, Lennah Shakeri

Master's Theses

Coastal marshes are important nursery habitats for many commercially important invertebrate species, yet these marshes are being lost worldwide at an unprecedented rate due to subsidence, erosion, climate change, and human activity. As marsh is lost, it creates the opportunity for submerged aquatic vegetation (SAV) colonization and establishment in newly created open water areas. Blue crabs, Callinectes sapidus, use both marsh edge and SAV habitat during the juvenile stages and support one of the largest fisheries in the Gulf of Mexico, worth over $70 million in 2015. This thesis studied the linkages between habitat type, SAV cover, benthic prey …

Vocalizations Of North American River Otters (Lontra Canadensis) In Two Human Care Populations, Sarah Walkley

Master's Theses

There is a dearth of information regarding the vocal repertoire of North American river otters (Lontra canadensis). This indicator species is cosmopolitan yet elusive, making recordings methodologically difficult in the wild. Therefore, this exploratory study uses video and audio recordings of two populations of North American river otters in human care to broaden the known vocal repertoire of river otters in various social contexts. The populations consist of a male-female pair at the Stamford Museum and Nature Center and a male-male pair at The Maritime Aquarium at Norwalk. This study is the first to examine the vocalizations produced …

Spatial Variation In Basal Resources And Trophic Position Of Selected Fishes Of The North-Central Gulf Of Mexico, Christopher Fleming

Master's Theses

The North-central Gulf of Mexico is a complex hydrologic environment with freshwater influx that varies on spatial and temporal scales. Freshwater input exerts influence on the isotope values of organisms living in coastal ecosystems. The objectives of this study were to determine relationships between total length and isotope value, estimate basal resource usage and trophic position of target species from Mississippi Sound, reef, and pelagic environments, and identify differences and similarities in spatial patterns of collection. Muscle tissue samples were collected from October 2014 through September 2015. Stable isotope analysis identified a trophic gradient extending from nearshore to offshore, with …

Impact Of Prolonged Sitting On Central Hemodynamics: Role Of Intermittent Pneumatic Compression Therapy, Anna Kayleigh Downey

Master's Theses

Prolonged sitting (3-6 hours) negatively impacts peripheral vascular health. Whether sitting similarly impacts central cardiovascular hemodynamics and vascular stiffness is unknown. Purpose: Determine if prolonged sitting increases central blood pressure, aortic pulse wave reflection and vascular stiffness. Methods: In 10 subjects (Age=22±2 yrs, BMI=28±4kg/m², 3 females), brachial artery pulse wave analysis was performed before (baseline-BL), during, and after 3 hours of sitting. Aortic pulse wave velocity (PWV) was examined before and after sitting using carotid applanation tonometry coupled with oscillometry performed on left upper-thigh. For mechanistic insight, intermittent pneumatic compression (IPC) was applied during sitting (i.e., 3, 120 …

Root Dynamics Of Crop Plants In A High Carbon Dioxide World: Effects Of Elevated Versus Ambient Carbon Dioxide Levels And No-Till Versus Conventional Agricultural Management, Charlotte Barker

Dissertations

Due to the continuing increases is atmospheric carbon dioxide levels and its potential effect on food sources, there is an interest in evaluating the effect of elevated CO₂ concentration versus ambient CO₂ concentration in agricultural crop plants although more studies have focused on the aboveground portions of plants rather than the roots. Additionally, the conservation agricultural method, no-till, has been widely suggested as a possible method of increasing soil organic carbon and increasing soil moisture in a hotter world.

This research involves two major agricultural plants, Sorghum bicolor (sorghum), and Glycine max (soybean) grown under four conditions including …

A Mechanistic Understanding Of Self-Propagating Amyloid-Β Oligomer Conformations In Alzheimer Disease, Dexter Nathanael Dean

Dissertations

Alzheimer disease (AD) is a fatal neurodegenerative disorder characterized by the widespread deposition of proteinaceous plaques abundant in amyloid-β (Aβ) aggregates. Although the plaques mainly contain high molecular weight, insoluble Aβ fibrils, the low molecular weight soluble aggregates called oligomers have been shown as the primary toxic species responsible for synaptic dysfunction and neuronal loss in AD. The process of aggregation is nucleation-dependent, but also highly stochastic and inhomogeneous resulting in biophysically diverse assemblies. Recent advances in the field indicate a potential correlation between the phenotypic diversity observed in AD subtypes and aggregate polymorphism. Therefore, understanding the molecular mechanisms which …

Personality In California Sea Lions (Zalophus Californianus) And Harbor Seals (Phoca Vitulina): Methodological Convergence And Species-Specific Emotional Repertoires, Amber De Vere

Dissertations

Despite the wide acceptance of animal personality as a valid area of study, research on marine mammal personality remains remarkably scarce. What literature does exist predominantly focuses on bottlenose dolphins (Frick, 2016; Highfill & Kuczaj, 2007; Kuczaj, Highfill & Byerly, 2012; Lilley, de Vere, Yeatre & Kuczaj, 2018; Moreno, Highfill & Kuczaj, 2017). There is also strong evidence for individual differences in grey seals (Robinson et al., 2015; Twiss & Franklin, 2010; Twiss, Culloch & Pomeroy, 2011; Twiss, Cairns, Culloch, Richards & Pomeroy, 2012), and preliminary research has provided evidence of broad personality factors in pinniped species using behavioral coding …

Factors Affecting The Regrowth Of Ilex Glabra In A Routinely Burned Longleaf Forest, Jaybus Price

Master's Theses

This study examines the effects of historical management by use of prescribed fire on Ilex glabra stems/m² and factors affecting the regrowth of I. glabra after a prescribed burn to gain beneficial knowledge for management purposes. Environmental factors and morphological parameters of I. glabra were sampled before and after a prescribed burn of the Longleaf Trace Nature Preserve in September 2016. The study site is located in Lamar County, Mississippi, just west of Hattiesburg, MS. Stem densities of I. glabra were collected once before the prescribed burn and twice after the prescribed burn at 2 month and 9 month …

Life-History Characteristics And Fishery Dynamics Of Red Drum (Sciaenops Ocellatus), In The North-Central Gulf Of Mexico, Corbin Bennetts

Master's Theses

Red Drum (Sciaenops ocellatus) are highly targeted recreationally in the Gulf of Mexico, and support a small commercial fishery in Mississippi. Despite their popularity, the stock is assessed using data limited approaches that necessitate accurate life history information. I estimated the year-specific and year-aggregated escapement rates for the Mississippi stock (years 2004 to 2015), which were sensitive to mortality estimation methods; year-aggregated estimates were 6.9 to 28.2 % depending on the method, but temporal patterns were consistent. I then addressed concerns with previously estimated life-history characteristics by describing the sex-specific growth and reproductive dynamics. The three-parameter von Bertalanffy …

The Influence Of Conservation Tillage And Conventional Tillage On Soil Bacterial Diversity In Southern Illinois, Nasser Syed

Dissertations

Agriculture in the Midwest United States (Illinois, Indiana, Iowa, Michigan, Minnesota, Ohio, and Wisconsin) is a critically important component of the United States economy and also for world exports of food grain. This is well reflected in the 2012 Census of Agriculture which showed that these states had a market value of crop and livestock products sold in excess of $80,000,000,000 (USDA, 2012). Within the U.S. the three Midwest states, Illinois, Iowa, and Minnesota are ranked 2nd, 3rd, and 4th for the economic value of crops sold. This economic value of agriculture in the Midwest encompasses not only corn, soybeans, …

Detection, Activity Measurement And Phylogeny Of Ureolytic Bacteria Isolated From Elasmobranch Tissue, Yimu Yang

Master's Theses

Free-ranging marine elasmobranch tissue-associated micro-organisms were cultured from free-ranging Atlantic stingray (Dasyatis sabina) and Atlantic sharpnose sharks (Rhizoprionodon terraenovae). 16S rRNA gene phylogeny indicated bacteria community structure in both elasmobranchs were under phylum Proteobacteria, Firmicutes and Actinobacteria. By conducting split-plot ANOVA, we found the microbial richness is significantly different (P=0.0814) between two superorders of elasmobranch, which may largely due to their preferred habitats and feeding habits. Urease presentence and activity was detected in phylogenetically diverse bacterial strains. Species with high urea-hydrolyzing ability, such as Micrococcus luteus (shark blood isolate: 46.84 mU/mg protein; stingray blood isolate: 24.36 …

Interplay Of Dgat1, Pdat1 And Dgat2 Enzymes In Plant Triacylglycerol Assembly, Anushobha Regmi

Master's Theses

Acyl-CoA:diacylglycerol acyltransferase (DGAT) catalyzes the transesterification of fatty acid from acyl-CoA to diacylglycerol (DAG) forming triacylglycerol (TAG, a.k.a oils and fats). Most plants have at least two unrelated DGAT genes, DGAT1 and DGAT2. Plants predominantly express only one during oil synthesis; the reason, however is not clear. A few studies have indicated that each enzyme prefers DAG and acyl-CoA substrates with different fatty acid compositions. Industrially desirable seed oil composition can be obtained through genetic engineering by replacing the endogenous enzyme with one that has different substrate selectivity. In Arabidopsis thaliana, DGAT1 and another unrelated enzyme PDAT1 are essential …

Spatial Dynamics And Mixing Of Bluefin Tuna In The Atlantic Ocean And Mediterranean Sea Revealed Using Next-Generation Sequencing, Gregory N. Puncher, Alessia Cariani, Gregory E. Maes, Jeroen Van Houdt, Koen Herten, Rita Cannas, Naiara Rodriguez-Ezpeleta, Aitor Albania, Andone Estonba, Molly Lutcavage, Alex Hanke, Jay Rooker, James S. Franks, Joseph M. Quattro, Gualtiero Basilone, Igaratza Fraile, Urtzi Laconcha, Nicolas Goñi, Ai Kimoto, David Macías, Francisco Alemany, Simeon Deguara, Salem W. Zgozi, Fulvio Garibaldi, Isik K. Oray, Firdes Saadet Karakulak, Noureddine Abid, Miguel N. Santos, Piero Addis, Haritz Arrizabalaga, Fausto Tinti

Faculty Publications

The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species’ stock dynamics, a genomewide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young‐of‐the‐year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 …