Life Sciences Commons^™

Characterization Of Current And Historical Variations In Sediment Accretion And Carbon Dynamics At The Rice Rivers Center Kimages Creek Wetland Restoration, Melissa J. Davis, Christopher D. Gatens, Edward R. Crawford, Arif Sikder

Rice Rivers Center Research Symposium

Current research of freshwater wetland soils have assessed and reported smaller stocks of soil organic carbon in restored wetlands compared to reference natural wetlands. However, a majority of these studies focus on sites restored from agricultural draining of non-tidal depressional wetlands,whereas carbon and accretion dynamics in tidal freshwater wetlands restored via dam removal is poorly understood. The U.S. Army Corps of Engineers estimates over 80,000 dams greater than 6 feet and tens of thousands of smaller dams pepper the U.S., of which the majority are unsafe, old or no longer serve their intended purpose. Damming disrupts the natural flow of …

An Analysis Of Particulate Matter In Central Virginia, Elizabeth Garrett, Arif Sikder

Rice Rivers Center Research Symposium

Virginia is consistently rated as a state with high rates of asthma (Asthma and Allergy Foundation 2014). Although this respiratory disease has many causes, certain air pollutants can be a trigger. The EPA currently identifies, monitors, and regulates seven types of air pollutants. One of these pollutants, particulate matter, can occur both naturally and culturally. The primary anthropogenic cause of particulate matter is fly ash, which is formed during fossil fuel combustion. Different technology installed in the power plant can capture some of the fly ash but these methods are not entirely effective.

This study focused on estimating the ratio …

Assessing How Disruption Of Methanogenic Communities And Their Syntrophic Relationships In Tidal Freshwater Marshes Via Saltwater Intrusion May Affect Ch4 Emissions, David J. Berrier, Scott C. Neubauer, Rima B. Franklin

Rice Rivers Center Research Symposium

Tidal freshwater wetlands (TFW), which lie at the interface of saltwater and freshwater ecosystems, are predicted to experience moderate salinity increases due to sea level rise. Increases in salinity generally suppress CH4 production, but it is uncertain to what extent elevated salinity will affect CH4 cycling in TFW. It is also unknown whether CH4 production will resume when freshwater conditions return. The ability to produce CH4 is limited to a monophyletic group of the Euryarchaeota phylum called methanogens (MG), who are limited to a small number of substrates (e.g., acetate, H2, and formate) produced from the breakdown of fermentation products. …

Role Of The Calcium Plateau In The Neuronal Injury And Behavioral Morbidities Following Organophosphate Intoxication, Laxmikant S. Deshpande, Robert E. Blair, Kristin F. Phillips, Robert J. Delorenzo

Neurology Publications

Organophosphate (OP) chemicals include nerve agents and pesticides, and there is a growing concern of OP based chemical attacks against civilians. Current antidotes are essential in limiting immediate mortality associated with OP exposure. However, further research is needed to identify molecular mechanisms underlying long-term neurological deficits following survival of OP toxicity in order to develop effective therapeutics. We have developed rat survival models of OP induced status epilepticus (SE) that mimic chronic mortality and morbidity following OP intoxication. We have observed significant elevations in hippocampal calcium levels after OP SE that persisted for weeks following initial survival. Drugs inhibiting intracellular …

Cannabinoid Receptor Interacting Protein Suppresses Agonist-Driven Cb1 Receptor Internalization And Regulates Receptor Replenishment In An Agonist-Biased Manner, Lawrence C. Blumes, Sandra Leone-Kabler, Deborah J. Luessen, Glenn S. Marrs, Erica Lyons, Caroline E. Bass, Rong Chen, Dana E. Selley, Allyn C. Howlett

Neurology Publications

Cannabinoid receptor interacting protein 1a (CRIP1a) is a CB1 receptor (CB1R) distal C-terminus-associated protein that modulates CB1R signaling via G proteins, and CB1R down-regulation but not desensitization (Blume et al. [2015] Cell Signal., 27, 716-726; Smith et al. [2015] Mol. Pharmacol., 87, 747-765). In this study, we determined the involvement of CRIP1a in CB1R plasma membrane trafficking. To follow the effects of agonists and antagonists on cell surface CB(1)Rs, we utilized the genetically homogeneous cloned neuronal cell line N18TG2, which endogenously expresses both CB1R and CRIP1a, and exhibits a well-characterized endocannabinoid signaling system. We developed stable CRIP1a-over-expressing and CRIP1a-siRNA-silenced knockdown …

Effects Of Olfactory Cues On The Foraging Behavior Of A Carabid Beetle, Calosoma Wilcoxi, A Predator Of A Forest Defoliator., Kennesha J. Myrick-Bragg, Karen Kester, Derek M. Johnson

Rice Rivers Center Research Symposium

Arthropod predators use environmental cues such as kairomones to locate herbivore prey. Several species have been shown to be attracted to volatiles emitted by herbivore host plants, as well as olfactory cues produced by the herbivore. Calosoma wilcoxi is a voracious predator that specializes on lepidopteran larvae often found in the forest canopy, showing a preference for the fall cankerworm. It is unknown whether C. wilcoxi uses olfactory cues associated with prey or their host plants to locate foraging sites.

The objective of this study is to use fall cankerworm frass, caterpillars, damaged oak leaves, and conspecifics to determine if …

The Interactome Of Streptococcus Pneumoniae And Its Bacteriophages Show Highly Specific Patterns Of Interactions Among Bacteria And Their Phages, Rachelle Mariano, Stefan Wuchty, Maria G. Vizoso-Pinto, Roman Häuser, Peter Uetz

Study of Biological Complexity Publications

Although an abundance of bacteriophages exists, little is known about interactions between their proteins and those of their bacterial hosts. Here, we experimentally determined the phage-host interactomes of the phages Dp-1 and Cp-1 and their underlying protein interaction network in the host Streptococcus pneumoniae. We compared our results to the interaction patterns of E. coli phages lambda and T7. Dp-1 and Cp-1 target highly connected host proteins, occupy central network positions, and reach many protein clusters through the interactions of their targets. In turn, lambda and T7 targets cluster to conserved and essential proteins in E. coli, while such …

Network Topology Analysis Of Post-Mortem Brain Microarrays Identifies More Alzheimer’S Related Genes And Micrornas And Points To Novel Routes For Fighting With The Disease, Sreedevi Chandrasekaran, Danail Bonchev

Study of Biological Complexity Publications

Network-based approaches are powerful and beneficial tools to study complex systems in their entirety, elucidating the essential factors that turn the multitude of individual elements into a functional system. In this study we used critical network topology descriptors and guilt-by-association rule to explore and understand the significant molecular players, drug targets and underlying biological mechanisms of Alzheimer’s disease. Analyzing two post-mortem brain gene microarrays (GSE4757 and GSE28146) with Pathway Studio software package we constructed and analyzed a set of protein-protein interaction, as well as miRNA-target networks. In a 4-step procedure the expression datasets were normalized using Robust Multi-array Average approach, …

In Silico Identification Of Essential Proteins In Corynebacterium Pseudotuberculosis Based On Protein-Protein Interaction Networks, Edson Luiz Folador, Paulo Vinícius Sanches Daltro De Carvalho, Wanderson Marques Silva, Rafaela Salgado Ferreira, Artur Silva, Michael Gromiha, Preetam Ghosh, Debmalya Barh, Vasco Azevedo, Richard Röttger

Biology Publications

Background

Corynebacterium pseudotuberculosis (Cp) is a gram-positive bacterium that is classified into equi and ovis serovars. The serovar ovis is the etiological agent of caseous lymphadenitis, a chronic infection affecting sheep and goats, causing economic losses due to carcass condemnation and decreased production of meat, wool, and milk. Current diagnosis or treatment protocols are not fully effective and, thus, require further research of Cp pathogenesis.

Results

Here, we mapped known protein-protein interactions (PPI) from various species to nine Cp strains to reconstruct parts of the potential Cp interactome and to identify potentially essential proteins serving as putative drug …

Using The Past To Restore The Future: Quantifying Historical Vegetation To Assist In Tidal Freshwater Wetland Restoration, Christopher D. Gatens, Richard Ward, Edward R. Crawford

Rice Rivers Center Research Symposium

Wetlands have been providing humans with critical natural ecosystem services throughout our time on Earth. Nevertheless, these invaluable ecosystems have been habitually altered as a cost of human progression. Two of the most common alterations to wetlands are hydrologic, in the form of damming, and filling. Both occurred along Kimages Creek in Charles City County, VA during the 19th and 20th centuries. In 2010 the Lake Charles dam was partially removed, restoring the creek's tidal communication with the James River and beginning tidal forested freshwater wetland restoration. Upon the recession of the body of water, numerous woody stumps were revealed.

Greenhouse Gas Emissions Over A Tidal Cycle In A Freshwater Wetland, Joseph C. Morina, Rima B. Franklin

Rice Rivers Center Research Symposium

Tidal freshwater wetlands are located at the interface of non-tidal freshwater riverine systems and estuarine tidal systems. These habitats experience freshwater tides, creating unique redoximorphic soil characteristics while simultaneously presenting an opportunity for hydrologic nutrient transport into the system. Because of this periodic flooding and draining, tidal freshwater wetlands are systems of intense biogeochemical transformations, which are microbially mediated. Several microbial transformations (e.g., methanogenesis, incomplete denitrification, and nitrification) result in the production of greenhouse gases (CO2, CH4, and N2O) at globally-significant levels. For example, wetlands are one of the greatest sources of methane on Earth, accounting for 20-33% of the …

Foraging And Song Rate Of Prothonotary Warblers In High And Low Density Breeding Sites, Denney Turner, Amanda Mcghee, Lesley Bulluck

Rice Rivers Center Research Symposium

Foraging observations can be used as an indicator of habitat quality and food availability. Previous studies with song rate have had conflicting results. Song rate increases with abundance (male-­‐male interac=ons) (Warren et. al 2013) and with high quality habitats (Stehelin and Lein 2013). Unmated males sing twice as often as mated males (Robins et. al 2009), expected in poor quality habitats. Few studies have assessed foraging and song rate behaviors in high and low density systems. Prothonotary Warblers (PROW) are excellent study species because they nest in boxes and we can manipulate density. The objective of this study was to …

Simba: A Web Tool For Managing Bacterial Genome Assembly Generated By Ion Pgm Sequencing Technology, Diego C. B. Mariano, Felipe L. Pereira, Edgar L. Aguiar, Letícia C. Oliveira, Leandro Benevides, Luís C. Guimarães, Edson L. Folador, Thiago J. Sousa, Preetam Ghosh, Debmalya Barh, Henrique C. P. Figueiredo, Artur Silva, Rommel T. J. Ramos, Vasco A. C. Azevedo

Biology Publications

Background

The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects.

Results …

Prothonotary Warbler Nestling Growth And Condition Inresponse To Variation In Aquatic And Terrestrial Preyavailability, Jenna C. Dodson, Nicholas J. Moy, Lesley P. Bulluck

Biology Publications

Aquatic prey subsidies entering terrestrial habitats are well documented, but little is known about the degree to which these resources provide fitness benefits to riparian consumers. Riparian species take advantage of seasonal pulses of both terrestrial and aquatic prey, although aquatic resources are often over-looked in studies of how diet influences the reproductive ecology of these organisms. Ideally, the timing of resource pulses should occur at the time of highest reproductive demand. This study investigates the availability of aquatic(mayfly) and terrestrial (caterpillar) prey resources as well as the nestling diet of the prothonotary warbler (Protonotaria citrea) at two sites along …

Cadherin-2 Is Required Cell Autonomously For Collective Migration Of Facial Branchiomotor Neurons, Jane K. Rebman, Kathryn E. Kirchoff, Gregory S. Walsh

Biology Publications

Collective migration depends on cell-cell interactions between neighbors that contribute to their overall directionality, yet the mechanisms that control the coordinated migration of neurons remains to be elucidated. During hindbrain development, facial branchiomotor neurons (FBMNs) undergo a stereotypic tangential caudal migration from their place of birth in rhombomere (r)4 to their final location in r6/7. FBMNs engage in collective cell migration that depends on neuron-to-neuron interactions to facilitate caudal directionality. Here, we demonstrate that Cadherin-2-mediated neuron-to-neuron adhesion is necessary for directional and collective migration of FBMNs. We generated stable transgenic zebrafish expressing dominant-negative Cadherin-2 (Cdh2ΔEC) driven by the islet1 promoter. …

Single-Locus Versus Multilocus Patterns Of Local Adaptation To Climate In Eastern White Pine (Pinus Strobus, Pinaceae), Om P. Rajora, Andrew J. Eckert, John W. R. Zinck

Biology Publications

Natural plant populations are often adapted to their local climate and environmental conditions, and populations of forest trees offer some of the best examples of this pattern. However, little empirical work has focused on the relative contribution of single-locus versus multilocus effects to the genetic architecture of local adaptation in plants/forest trees. Here, we employ eastern white pine (Pinus strobus) to test the hypothesis that it is the inter-genic effects that primarily drive climate-induced local adaptation. The genetic structure of 29 range-wide natural populations of eastern white pine was determined in relation to local climatic factors using both …

Pharmacological Blockade Of The Calcium Plateau Provides Neuroprotection Following Organophosphate Paraoxon Induced Status Epilepticus In Rats, Laxmikant S. Deshpande, Robert E. Blair, Beverly A. Huang, Kristin F. Phillips, Robert J. Delorenzo

Neurology Publications

Organophosphate (OP) compounds which include nerve agents and pesticides are considered chemical threat agents. Currently approved antidotes are crucial in limiting OP mediated acute mortality. However, survivors of lethal OP exposure exhibit delayed neuronal injury and chronic behavioral morbidities. In this study, we investigated neuroprotective capabilities of dantrolene and carisbamate in a rat survival model of paraoxon (POX) induced status epilepticus (SE). Significant elevations in hippocampal calcium levels were observed 48-h post POX SE survival, and treatment with dantrolene (10 mg/kg, i.m.) and carisbamate (90 mg/kg, i.m.) lowered these protracted calcium elevations. POX SE induced delayed neuronal injury …

Tower-Based Greenhouse Gas Fluxes In A Restored Tidal Freshwater Wetland: A Shared Resource For Research And Teaching., Ellen J. Stuart-Haëntjens, Scott C. Neubauer, Christopher M. Gough

Rice Rivers Center Research Symposium

The goals of this study are: 1) to use an eddy-covariance system to continuously measure wetland-atmosphere CO2 and CH4 exchange in a restored forested wetland, 2) to quantity C sequestration in plant biomass and soils in restored (Kimages Creek watershed) and old-growth (Harris Creek watershed) forested wetlands, and 3) to establish a shared long-term, shared research and teaching platform centered on eddy-covariance tower measurements. Since the old-growth forest wetland has had longer to accumulate C, the current C stocks are likely much larger than those of the restored wetland; however, the rate of C accumulation (i.e., C sequestration or net …

Wood Frog And Spotted Salamander Abundance Across Pool Types And Wetland Networks At Fort A.P. Hill, Va, Logan Mcdonald, Will Fields, Katelyn Horn, James R. Vonesh, Kristine Grayson

Rice Rivers Center Research Symposium

Effective management of pond breeding amphibians requires identifying suitable breeding habitat and its use by different species. Suitable breeding habitat is largely characterized by pool type, physical habitat, and position within the landscape. Parameters such as vegetative cover, hydrology, and water chemistry are known to influence amphibian occupancy of vernal pools. While seasonal vernal pools have been the focus of conservation efforts, pools that are an artifact of anthropogenic disturbance, such as road ruts, may be an important component of the landscape for amphibians. The role of wetland isolation within a landscape has been well studied, but less consideration has …

Bacterial Forensics: Revolutionizing Biochemical Analysis, Caitlin Cain

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

Eva Childrey is a junior forensic science and chemistry double major working in Dr. Eh- rhardt’s research laboratory at VCU. The main goal of the research conducted in this laboratory is to explore the lipid profiles of different bacterial species.

Homo Heidelbergensis: The Tool To Our Success, Alexander Burkard

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

Homo heidelbergensis, a physiological variant of the species Homo sapien, is an extinct species that existed in both Europe and parts of Asia from 700,000 years ago to roughly 300,000 years ago (carbon dating). This “subspecies” of Homo sapiens, as it is formally classified, is a direct ancestor of anatomically modern humans, and is understood to have many of the same physiological characteristics as those of anatomically modern humans while still expressing many of the same physiological attributes of Homo erectus, an earlier human ancestor. Since Homo heidelbergensis represents attributes of both species, it has therefore earned the classification as …

Potential For Aerobic Exercise To Release Growth Factors To Induce Cognitive Changes In Children With Autism Spectrum Disorder, Maya Harrington

UROP Posters

Autism Spectrum Disorder (ASD) is becoming increasingly prevalent among adolescents, and while the number of individuals diagnosed with the disorder grows, there continues to be no cure or even a clear treatment path for ASD. This study analyzes the biological stimulations that create cognitive changes—which are induced by intensive aerobic exercise—within the brains of individuals ages 8-18 diagnosed with autism. I studied journal articles on the current treatments available for ASD, the increasing prevalence of the disease, the cognitive alterations of the autistic brain relative to the brains of individuals without the disease, the release of growth factors due to …

The Impact Of Urbanization On Mosquito-Borne Viruses, Nikhita Puthuveetil

UROP Posters

Mosquito-borne diseases such as yellow fever, dengue, and West Nile are rapidly emerging across the globe. Their emergence is often aided by the growth of their vector population, or the organisms that transmit the virus to the host. Urbanization and land use often destroys the habitat of the virus and its vector. However, the virus and its vector often survive despite the changes to its environment. The goal of this paper is to find out exactly how urbanization and changes in land use affect mosquito-borne viruses and how these viruses survive despite the destruction of their habitats. To understand how …

Forensic Signatures For Production Conditions Of Bacillus Thuringiensis (Str. Hd1) Spore Cultures, Dani Jabado, Cristina Stanciu, Christopher Ehrhardt

UROP Posters

Chemical signatures that can indicate growth medium recipes or other key aspects of the production conditions are an important goal for forensic and biodefense agencies. In this study, Fatty Acid Methyl Ester (FAME) profiles were analyzed from Bacillus thuringiensis spores grown five different published medium recipes. B. thuringiensis was chosen due to its biochemical, structural, and genetic similarity to B. anthracis, a Biosafety Level III select agent and the organisms used in the Amerithrax attacks in 2001. The relative abundance of 13 different fatty acid biomarkers, spanning four structure classes, was compared across all spore samples. Differences in the …

Exploring Pharmacological And Behavioral Mechanisms Involved In Alcohol Dependence During Adolescence, Rabha Mousa Younis

Theses and Dissertations

Alcoholism is a serious illness that is marked by uncontrollable drinking and physical dependence to alcohol. Long-term alcoholism has been linked to many health concerns such as cirrhosis of the liver and cardiovascular disease. Alcohol is one of the most commonly used drugs among adolescent populations. Given that adolescence is a unique developmental stage during which alcohol has long-term effects on future drug-taking behavior; it is essential to understand how early exposure to alcohol during adolescence may affect the abuse liability of the drug later in life. Indeed, most alcohol users start during adolescence suggesting that exposure to alcohol during …

Genomic Comparisons And Genome Architecture Of Divergent Trypanosoma Species, Katie Bradwell

Theses and Dissertations

Virulent Trypanosoma cruzi, and the non-pathogenic Trypanosoma conorhini and Trypanosoma rangeli are protozoan parasites with divergent lifestyles. T. cruzi and T. rangeli are endemic to Latin America, whereas T. conorhini is tropicopolitan. Reduviid bug vectors spread these parasites to mammalian hosts, within which T. rangeli and T. conorhini replicate extracellularly, while T. cruzi has intracellular stages. Firstly, this work compares the genomes of these parasites to understand their differing phenotypes. Secondly, genome architecture of T. cruzi is examined to address the effect of a complex hybridization history, polycistronic transcription, and genome plasticity on this organism, and study its highly …

System Genetic Analysis Of Mechanisms Underlying Excessive Alcohol Consumption, Maren L. Smith

Theses and Dissertations

Increased alcohol consumption over time is one of the characteristic symptoms of Alcohol Use Disorder (AUD). The molecular mechanisms underlying this escalation in intake is still the subject of study. However, the mesocortical and mesolimbic dopamine pathways, and the extended amygdala, because of their involvement in reward and reinforcement are believed to play key roles in these behavioral changes. Multiple gene expression studies have shown that alcohol affects the expression of thousands of genes in the brain. The studies discussed in this document use the systems biology technique of co-expression network analysis to attempt to find

patterns within genome-wide expression …

A Pipeline For Creation Of Genome-Scale Metabolic Reconstructions, Shaun W. Norris

Theses and Dissertations

The decreasing costs of next generation sequencing technologies and the increasing speeds at which they work have lead to an abundance of 'omic datasets. The need for tools and methods to analyze, annotate, and model these datasets to better understand biological systems is growing. Here we present a novel software pipeline to reconstruct the metabolic model of an organism in silico starting from its genome sequence and a novel compilation of biological databases to better serve the generation of metabolic models. We validate these methods using five Gardnerella vaginalis strains and compare the gene annotation results to NCBI and the …

The Role Of E-Cadherin Force In The Maintenance Of Homeostasis In Epithelial Acini, Fnu Vani Narayanan

Theses and Dissertations

Numerous three-dimensional model systems have emerged for emulating the biochemical and physiological states of native tissue. Yet little is known about the effects of mechanical forces on cell behavior in the context of an organized tissue structure in three-dimensional cell-culture. Epithelial cells cultured in a three-dimensional environment comprised of extracellular matrix proteins form spheroids of polarized cells. Cellular responses to mechanical cues, generated from dynamic interactions with the extracellular matrix and neighboring cells, are known to influence cellular behavior to a great extent. Previous studies have shown that tumorigenic progression has been frequently linked to the down regulation of E-cadherin, …

Interactomics-Based Functional Analysis: Using Interaction Conservation To Probe Bacterial Protein Functions, J. Harry Caufield

Theses and Dissertations

The emergence of genomics as a discrete field of biology has changed humanity’s understanding of our relationship with bacteria. Sequencing the genome of each newly-discovered bacterial species can reveal novel gene sequences, though the genome may contain genes coding for hundreds or thousands of proteins of unknown function (PUFs). In some cases, these coding sequences appear to be conserved across nearly all bacteria. Exploring the functional roles of these cases ideally requires an integrative, cross-species approach involving not only gene sequences but knowledge of interactions among their products. Protein interactions, studied at genome scale, extend genomics into the field of …