Life Sciences Commons^™

Design Of Drug Nano-Carriers For Study Of Multidrug Resistance In Single Live Cells, Pavan Kumar Cherukuri

Chemistry & Biochemistry Theses & Dissertations

Multidrug resistance (MDR) exists in both prokaryotic and eukaryotic cells. MDR is responsible for ineffective treatment of a wide range of diseases, such as infections and cancer. The ATP-binding cassette (ABC) membrane transporters (efflux pumps) are one of the largest and most diverse super-families of membrane proteins found in all living organisms, ranging from bacteria to humans. All ABC transporters share a common structure of four core domains; two transmembrane domains (TMD) with variable sequence and topology and two nucleotide-binding domains (NBD) with conserved sequences. Conventional methods for the study of the efflux functions are radioactively labeled substrates and fluorescent …

Abiotic Factors Contributing To The Survival Of Three Tick Species In Southeastern Virginia, Amblyomma Americanum (Lone Star Tick), Dermacentor Variabilis (American Dog Tick), And Amblyomma Maculatum (Gulf Coast Tick), Lindsey A. Bidder

Biological Sciences Theses & Dissertations

Amblyomma americanum, Amblyomma maculatum, and Dermacentor variabilis are hard-bodied ticks in the Hampton Roads area of southeastern Virginia. This study consisted of two field projects focused on these tick species. To estimate the off-host survival of local tick species, a capture-mark-recapture (CMR) study was performed. An environmental survival study was performed to quantify the ability of these three tick species to survive in situ. Four field sites were used in the Hampton Roads region covering a variety of habitat types and vegetation; specifically two drier, upland field sites and two flood-prone sites. CMR was conducted from May through …

Coarse Root Biomass And Architecture: Applications Of Ground Penetrating Radar, John Claude Bain

Biological Sciences Theses & Dissertations

The effectiveness of ground penetrating radar (GPR) to identify and quantify coarse roots was tested in a mixed-oak forest in Southeastern Virginia using experimental pits and locally excavated root segments. GPR was found to be highly dependent on low soil moisture levels as it is unable to differentiate root structures if they possess similar moisture content as their surrounding soil. Likewise, GPR was unable to identify simulated dead roots. This does not alter the effectiveness of GPR to measure living coarse root biomass, but does present the potential for underestimation of carbon storage in coarse root structures, as a dead …

Regional Extinction Risk And Conservation Priorities For Persian Gulf Marine Bony Fishes, Jack Ryan Buchanan

Biological Sciences Theses & Dissertations

Around the world, protected areas are the primary conservation measure used to combat biodiversity loss; however, these are often established without comprehensive species-specific information, leading to placement in areas that often do not address the processes that threaten biodiversity. To address this, International Union for Conservation of Nature Red List assessments are being utilized to determine species-specific threats and population status at the global and sub-global levels. This study examines the regional extinction risk for all known marine bony fishes of the Persian Gulf. About 8.3% of the 471 marine bony fishes assessed are at elevated risk of regional extinction. …

Cloning, Characteristics, And Functional Analysis Of Rabbit Nadph Oxidase 5, Feng Chen, Caiyong Yin, Christiana Dimitropoulou, David J.R. Fulton

Bioelectrics Publications

Background: Nox5 was the last member of the Nox enzyme family to be identified. Functionally distinct from the other Nox isoforms, our understanding of its physiological significance has been hampered by the absence of Nox5 in mouse and rat genomes. Nox5 is present in the genomes of other species such as the rabbit that have broad utility as models of cardiovascular disease. However, the mRNA sequence, characteristics, and functional analysis of rabbit Nox5 has not been fully defined and were the goals of the current study.

Methods: Rabbit Nox5 was amplified from rabbit tissue, cloned, and sequenced. COS-7 cells were …

Hotspots, Extinction Risk And Conservation Priorities Of Greater Caribbean And Gulf Of Mexico Marine Bony Shorefishes, Christi Linardich

Biological Sciences Theses & Dissertations

Understanding the status of species is important for allocation of resources to redress biodiversity loss. Regional organizations tasked with managing threats to the 1,360 marine bony shorefishes of the Caribbean and Gulf of Mexico would benefit from a delineation of conservation priorities. However, prior to this study, conservation status was known for only one quarter of these shorefishes. Extinction risk assessment under IUCN Red List Criteria is a widely-used, objective method to communicate species-specific conservation needs. Data were collated on each species’ distribution, population, habitats and threats and experts at three Red List workshops assigned a global level extinction risk …

Section Abstracts: Natural History And Biodiversity

Virginia Journal of Science

Abstracts of the Natural History and Biodiversity Section for the 94th Annual Virginia Academy of Science Meeting, May 18-20, 2016, at University of Mary Washington, Fredericksburg, VA.

Section Abstracts: Biology

Virginia Journal of Science

Abstracts of the Biology Section for the 94th Annual Virginia Academy of Science Meeting, May 18-20, 2016, at University of Mary Washington, Fredericksburg, VA.

Naturalization Of Salt Marsh Restoration Sites In The Elizabeth River, Virginia, Assessed By Feeding Activity And Trophic Level Of Mummichogs (Fundulus Heteroclitus), Moriah Anne Good

Biological Sciences Theses & Dissertations

Recent efforts to mitigate environmental issues within the Southern Branch of the Elizabeth River, Virginia, designated a “Region of Concern” by the Chesapeake Bay Program, include several salt marsh restorations. By examining gut contents and stable isotopes values (δ13C and δ15N) from mummichogs (Fundulus heteroclitus), the functional equivalency of restored salt marshes compared to natural marshes was measured. In July 2013 I collected mummichogs from three restored and three reference salt marshes in the Southern Branch. Fish were collected for gut content analysis and were analyzed for stable isotopes (δ13C and δ15N).

I removed gut contents from 16 fish per …

Characterization Of Soundscapes In Shallow Water Habitats Of The Florida Keys (Usa) And Their Influence On The Settlement Of Larval Fish And Invertebrates, John R. Butler

Biological Sciences Theses & Dissertations

In recent decades, changes in climate and water quality in Florida Bay and the Florida Keys (FL, USA) caused expansive cyanobacteria blooms that in turn precipitated massive sponge die-offs that drastically altered sponge-dominated hard-bottom communities in south-central Florida Bay. This area served as a model system to explore the effect of ecosystem change and habitat restoration on underwater soundscapes and larval recruitment. I had four main objectives: (1) characterize the underwater soundscapes of three near-shore, benthic habitats: mangrove islands, seagrass meadows, and hard-bottom (Chapter 2); (2) quantify larval settlement within healthy, degraded, and restored hard-bottom areas to test whether habitat …

A Hitchhiker’S Guide To Invasion Biology: Describing The Ecological Mechanisms Underlying The Range Expansions Of Two Ixodid Tick Species, Robyn M. Nadolny

Biological Sciences Theses & Dissertations

Increasing incidence of many tick-borne diseases have been linked to recent expansions of tick species distributions. Many tick species are expanding their ranges because of anthropogenic changes in the landscape, shifting climatic variables, and increasing populations of suitable host species and tick habitat. Few empirical studies have been performed, however, investigating the ecological mechanisms underlying these range expansions. Ticks are parasitic organisms that disperse across landscape by hitchhiking on hosts, but must then survive in the environment for long periods of time between bloodmeals. Two species of ixodid tick, Ixodes affinis and Amblyomma maculatum, are simultaneously expanding their ranges throughout …

Anti-Predator Responses Of Squid Throughout Ontogeny, Carly Anne York

Biological Sciences Theses & Dissertations

Multiple sensory modalities and a complex array of escape behaviors have evolved as components of anti-predator responses in squids. The goals of this study include: (1) examine the role of the lateral line analogue and vision in successful predator evasion; (2) measure kinematics of escape jetting; (3) document how chromatic patterning, posturing and inking in squid change in response to predators; and (4) investigate escape jet hydrodynamics of squid. Given that squids undergo considerable morphological, ecological, and behavioral changes throughout ontogeny, the goals above were all investigated across different life history stages. To test the respective roles of vision and …

Non-Thermal Atmospheric-Pressure Plasma For Sterilization Of Surfaces And Biofilms, Johanna Ursula Neuber

Electrical & Computer Engineering Theses & Dissertations

Bacterial resistance to antimicrobial methods is a critical issue in many fields of medicine. This work describes the studies performed to characterize and optimize the bacterial inactivation effects of a non-thermal atmospheric-pressure plasma brush and plasma jet on a laminate surface inoculated with Acinetobacter baumannii and Staphylococcus aureus, and a cultivated Enterococcus faecalis biofilm, respectively. These treatments are pilot studies for eventual application to surface sterilization in hospitals and root canal disinfection. To evaluate bacterial inactivation, after treatment and recovery, the bacterial colony forming units (CFUs) are counted. Several different methods are used to optimize the antimicrobial effect. For the …

Calcification Rates Indicate Thermal Stress Tolerance In Belize “Backreef” Corals, David D. Jones

Undergraduate Research Symposium

Reef-building corals host symbiotic algae known as zooxanthellae living within their tissues. Exposure to prolonged elevated temperature can cause corals to expel their symbionts and lead to coral bleaching. In this study, corals from Florida and Belize inshore reefs (high temperature variability) and offshore reefs (low temperature variability) were subjected to a 6-week-long heat stress experiment to determine if inshore corals displayed higher stress tolerance than offshore samples. Measurements of calcification rates suggested that Belize’s inshore or “BackReef” corals demonstrated the greatest growth and stress tolerance. Ongoing symbiont density measurements will provide further clues to stress tolerance.

Damsels In Distress: A Preliminary Assessment Of Pomacentridae Extinction Risk, Allison Roberts

Undergraduate Research Symposium

The family Pomacentridae is among the most diverse of the perciformes, boasting 400 different species of damselfish. These fish are found in coral reefs of varying depths around the world, most of which risk great damage due to climate change. In addition, many species are key components of the ornamental aquarium trade. Considering these threats, the importance of examining the state of Pomacentridae is paramount in examining the health of our oceans. Using IUCN Red List methods, preliminary data suggests some species of damselfish are at elevated risk of extinction.

Local Avian Density Influences Risk Of Mortality From Window Strikes, Ann M. Sabo, Natasha D.G. Hagemeyer, Ally S. Lahey, Eric L. Walters

Biological Sciences Faculty Publications

Up to a billion birds die per year in North America as a result of striking windows. Both transparent and reflective glass panes are a cause for concern, misleading birds by either acting as invisible, impenetrable barriers to desired resources, or reflecting those resources over a large surface area. A high number of window strikes occur during migration, but little is known about the factors of susceptibility, or whether particular avian taxa are more vulnerable than others. We report on a study of window strikes and mist-netting data at the Virginia Zoological Park (Norfolk, Virginia, USA), conducted in the autumn …

Tick Genome Assembled: New Opportunities For Research On Tick-Host-Pathogen Interactions, Jose De La Fuente, Robert M. Waterhouse, Daniel E. Sonenshine, R. Michael Roe, Jose M. Ribeiro, David B. Sattelle, Catherine A. Hill

Biological Sciences Faculty Publications

As tick-borne diseases are on the rise, an international effort resulted in the sequence and assembly of the first genome of a tick vector. This result promotes research on comparative, functional and evolutionary genomics and the study of tick-host-pathogen interactions to improve human, animal and ecosystem health on a global scale.

Genomic Insights Into The Ixodes Scapularis Tick Vector Of Lyme Disease, Monika Gulia-Nuss, Andrew B. Nuss, Jason M. Meyer, Daniel E. Sonenshine, R. Michael Roe, Robert M. Waterhouse, David B. Sattelle, Jose De La Fuente, Jose M. Ribeiro, Karine Megy

Biological Sciences Faculty Publications

Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ~57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle …

A Genetically Distinct Hybrid Zone Occurs For Two Globally Invasive Mosquito Fish Species With Striking Phenotypic Resemblance, Rebecca J. Wilk, Lisa Horth

Biological Sciences Faculty Publications

Hybrid zones allow for the investigation of incipient speciation and related evolutionary processes of selection, gene flow, and migration. Interspecific dynamics, like competition, can impact the size, shape, and directional movement of species in hybrid zones. Hybrid zones contribute to a paradox for the biological species concept because interbreeding between species occurs while parental forms remain distinct. A long‐standing zone of intergradation or introgression exists for eastern and western mosquito fish (Gambusia holbrooki and G. affinis) around Mobile Bay, AL. The region has been studied episodically, over decades, making it perfect for addressing temporal dynamics and for providing …

Selective Mutation Accumulation: A Computational Model Of The Paternal Age Effect, Eoin C. Whelan, Alexander C. Nwala, Christopher Osgood, Stephan Olariu

Biological Sciences Faculty Publications

Motivation: As the mean age of parenthood grows, the effect of parental age on genetic disease and child health becomes ever more important. A number of autosomal dominant disorders show a dramatic paternal age effect due to selfish mutations: substitutions that grant spermatogonial stem cells (SSCs) a selective advantage in the testes of the father, but have a deleterious effect in offspring. In this paper we present a computational technique to model the SSC niche in order to examine the phenomenon and draw conclusions across different genes and disorders.

Results: We used a Markov chain to model the probabilities of …

Accessible Bioprinting: Adaptation Of A Low-Cost 3d-Printer For Precise Cell Placement And Stem Cell Differentiation, John A. Reid, Peter A. Mollica, Garett D. Johnson, Roy C. Ogle, Robert D. Bruno, Patrick C. Sachs

School of Medical Diagnostics & Translational Sciences Faculty Publications

The precision and repeatability offered by computer-aided design and computer-numerically controlled techniques in biofabrication processes is quickly becoming an industry standard. However, many hurdles still exist before these techniques can be used in research laboratories for cellular and molecular biology applications. Extrusion-based bioprinting systems have been characterized by high development costs, injector clogging, difficulty achieving small cell number deposits, decreased cell viability, and altered cell function post-printing. To circumvent the high-price barrier to entry of conventional bioprinters, we designed and 3D printed components for the adaptation of an inexpensive 'off-the-shelf' commercially available 3D printer. We also demonstrate via goal based …

Electrosensitization Assists Cell Ablation By Nanosecond Pulsed Electric Field In 3d Cultures, Claudia Muratori, Andrei G. Pakhomov, Shu Xiao, Olga N. Pakhomova

Bioelectrics Publications

Previous studies reported a delayed increase of sensitivity to electroporation (termed "electrosensitization") in mammalian cells that had been subjected to electroporation. Electrosensitization facilitated membrane permeabilization and reduced survival in cell suspensions when the electric pulse treatments were split in fractions. The present study was aimed to visualize the effect of sensitization and establish its utility for cell ablation. We used KLN 205 squamous carcinoma cells embedded in an agarose gel and cell spheroids in Matrigel. A local ablation was created by a train of 200 to 600 of 300-ns pulses (50 Hz, 300-600 V) delivered by a two-needle probe with …

Red List Of Marine Bony Fishes Of The Eastern Central Atlantic, Beth Polidoro, Gina Ralph, Kyle Strongin, Michael Harvey, Kent Carpenter, Titus Ayo Adeofe, Rachel Arnold, Paul Bannerman, Jean Noel Bibang Bi Nguema, Jack Buchanan, Khairdine Mohamed Abdallahi Camara, Youssouf Hawa Camara, Kadiatou Cissoko, Bruce B. Collette, Mia T. Comeros-Raynal, Godefroy De Bruyne, Madeleine Diouf, Roger Djiman, Mathieu Ducrocq, Ofer Gon, Antony S. Harold, Heather Harwell, Craig Hilton-Taylor, Andrew Hines, P. Alexander Hulley, Tomio Iwamoto, Steen Knudsen, Jean De Dieu Lewembe, Christi Linardich, Ken Lindeman, Ebou Mass Mbye, Jean Egard Mikolo, Vanda Monteiro, Jean Bernard Mougoussi, Thomas Munroe, Jean Hervé Mve Beh, Francis K.E. Nunoo, Caroline Pollock, Stuart Poss, Richmond Quartey, Barry Russell, Alphonse Sagna, Catherine Sayer, Aboubacar Sidibe, William Smith-Vaniz, Emilie Stump, Mor Sylla, Luis Tito De Morais, Jean-Christophe Vié, Akanbi Williams

Biological Sciences Faculty Publications

The Red List of marine bony fishes of the Eastern Central Atlantic (ECA) is a review of the conservation status of all native marine bony fishes in ECA according to the global Categories and Criteria of the IUCN Red List of Threatened Species. It identifies those species that are threatened with extinction at the global level and occur within the ECA region. This comprehensive assessment, which is the first of its kind in the ECA, aims to provide improved knowledge of species presence and extinction risk status for the purposes of guiding conservation actions and improved policies for these species …

Rcd+: Fast Loop Modeling Server, José R. López-Blanco, Alejandro J. Canosa-Valis, Yaohang Li, Pablo Chacón

Computer Science Faculty Publications

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop …

Flexc: Protein Flexibility Prediction Using Context-Based Statistics, Predicted Structural Features, And Sequence Information, Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, Min Li, Jianxin Wang, Yaohang Li

Computer Science Faculty Publications

The fluctuation of atoms around their average positions in protein structures provides important information regarding protein dynamics. This flexibility of protein structures is associated with various biological processes. Predicting flexibility of residues from protein sequences is significant for analyzing the dynamic properties of proteins which will be helpful in predicting their functions.

The Small Mammals Of Southeastern Virginia As Revealed By Pitfall Trapping, Robert K. Rose

Biological Sciences Faculty Publications

Pitfall trapping is a poor method to catch small mammals but the only way to catch and study the Southeastern Shrew (Sorex longirostris), the primary mammal of interest in the field studies reported here. While learning much about its distribution and abundance, still more was learned about the other small mammals present in forests and fields of eastern Virginia. A total of 15 species was captured at 19 locations during the 1990-2013 period, including five shrews, two moles, and eight rodents, representing all but one of the common small mammals in eastern Virginia.

Are We Missing Important Areas In Pelagic Marine Conservation? Redefining Conservation Hotspots In The Ocean, Dana K. Briscoe, Sara M. Maxwell, Raphael Kudela, Larry B. Crowder

Biological Sciences Faculty Publications

The protection of biodiversity is one of the most important goals in terrestrial and marine conservation. Marine conservation approaches have traditionally followed the example of terrestrial initiatives. However, patterns, processes, habitats, and threats differ greatly between the 2 systems - and even within the marine environment. As a result, there is still a lack of congruence as to how to best identify and prioritize conservation approaches moving from the static terrestrial and nearshore realm into a more fluid, 3-dimensional pelagic realm. To address this problem, we investigate how the conservation science literature has been used to inform and guide management …

A Novel Method Of Microsatellite Genotyping-By-Sequencing Using Individual Combinatorial Barcoding, Salla Vartia, Jose L. Villanueva-Cañas, John Finarelli, Edward D. Farrell, Patrick C. Collins, Graham M. Hughes, Jeanette E.L. Carlson, David T. Gauthier, Philip Mcginnity, Thomas F. Cross, Richard D. Fitzgerald, Luca Mirimin, Fiona Crispie, Paul D. Cotter, Jens Carlsson

Biological Sciences Faculty Publications

This study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS …

Rnd3 As A Novel Target To Ameliorate Microvascular Leakage, Jerome W. Breslin, Dayle A. Daines, Travis M. Doggett, Kristine H. Kurtz, Flavia M. Souza-Smith, Xun E. Zhang, Mack H. Wu, Sarah Y. Yuan

Biological Sciences Faculty Publications

Background -Microvascular leakage of plasma proteins is a hallmark of inflammation that leads to tissue dysfunction. There are no current therapeutic strategies to reduce microvascular permeability. The purpose of this study was to identify the role of Rnd3, an atypical Rho family GTPase, in the control of endothelial barrier integrity. The potential therapeutic benefit of Rnd3 protein delivery to ameliorate microvascular leakage was also investigated.

Methods and Results-Using immunofluorescence microscopy, Rnd3 was observed primarily in cytoplasmic areas around the nuclei of human umbilical vein endothelial cells. Permeability to fluorescein isothiocyanate-albumin and transendothelial electrical resistance of human umbilical vein …

Draft Genome Sequences For Seven Streptococcus Parauberis Isolates From Wild Fish In The Chesapeake Bay, Ashley Haines, Emily Nebergall, Elvira Besong, Kimaya Council, Onaysha Lambert, David Gauthier

Biological Sciences Faculty Publications

Streptococcus parauberis is a pathogen of cattle and fish, closely related Streptococcus uberis and Streptococcus iniae. We report the genomes of seven S. parauberis strains recovered from striped bass (Morone saxatilis) in the Chesapeake Bay. The availability of these genomes will allow comparative genomic analysis of Chesapeake Bay S. parauberis strains versus S. parauberis cultured from other animal hosts and geographic regions.