Life Sciences Commons^™

The Relative Contribution Of Methanotrophs To Microbial Communities And Carbon Cycling In Soil Overlying A Coal-Bed Methane Seep, Christopher T. Mills, Gregpry F. Slater, Robert F. Dias, Stephanie A. Carr, Christopher M. Reddy, Raleigh Schmidt, Kevin W. Mandernack

Chemistry & Biochemistry Faculty Publications

Seepage of coal-bed methane (CBM) through soils is a potential source of atmospheric CH₄ and also a likely source of ancient (i.e. ¹⁴C-dead) carbon to soil microbial communities. Natural abundance ¹³C and ¹⁴C compositions of bacterial membrane phospholipid fatty acids (PLFAs) and soil gas CO₂ and CH₄ were used to assess the incorporation of CBM-derived carbon into methanotrophs and other members of the soil microbial community. Concentrations of type I and type II methanotroph PLFA biomarkers (16:1ω8c and 18:1ω8c, respectively) were elevated in CBM-impacted soils compared with a control site. Comparison …

Diatom Proteomics Reveals Unique Acclimation Strategies To Mitigate Fe Limitation, Brook L. Nunn, Jessica F. Faux, Anna A. Hippman, Maria T. Maldonado, H. Rodger Harvey, David R. Goodlett, Philip W. Boyd, Robert F. Strzepek

OES Faculty Publications

Phytoplankton growth rates are limited by the supply of iron (Fe) in approximately one third of the open ocean, with major implications for carbon dioxide sequestration and carbon (C) biogeochemistry. To date, understanding how alteration of Fe supply changes phytoplankton physiology has focused on traditional metrics such as growth rate, elemental composition, and biophysical measurements such as photosynthetic competence (Fv/Fm). Researchers have subsequently employed transcriptomics to probe relationships between changes in Fe supply and phytoplankton physiology. Recently, studies have investigated longer-term (i.e. following acclimation) responses of phytoplankton to various Fe conditions. In the present study, the coastal diatom, Thalassiosira pseudonana, …

Topical Gene Electrotransfer To The Epidermis Of Hairless Guinea Pig By Non-Invasive Multielectrode Array, Sigi Guo, Annelise L. Israel, Gaurav Basu, Amy Donate, Richard Heller

Bioelectrics Publications

Topical gene delivery to the epidermis has the potential to be an effective therapy for skin disorders, cutaneous cancers, vaccinations and systemic metabolic diseases. Previously, we reported on a non-invasive multielectrode array (MEA) that efficiently delivered plasmid DNA and enhanced expression to the skin of several animal models by in vivo gene electrotransfer. Here, we characterized plasmid DNA delivery with the MEA in a hairless guinea pig model, which has a similar histology and structure to human skin. Significant elevation of gene expression up to 4 logs was achieved with intradermal DNA administration followed by topical non-invasive skin gene electrotransfer. …

Cpg And Interleukin-15 Synergize To Enhance Ifn-Gamma Production By Activated Cd8(+) T Cells, Dustin Cobb, Sigi Guo, Ronald B. Smeltz

Bioelectrics Publications

Interleukin-15 (IL-15) regulates the development and maintenance of memory CD8(+) T cells. Paradoxically, we previously reported that IL-15 could enhance CD8(+) T-cell responses to IL-12, a proinflammatory cytokine required for optimal priming of effector CD8(+) T cells. To expand the physiological relevance of these findings, we tested IL-15 for its ability to enhance T-cell responses to bacterial CpG. Expectedly, CpG enhanced the production of IFN-gamma by CD8(+) T cells polyclonally activated with anti-CD3. However, addition of IL-15 to CpG-stimulated cultures led to a striking increase in IFN-gamma production. The effect of CpG and IL-15 was also evident with CD8(+) T …

Nanosecond Pulsed Electric Field (Nspef) Ablation As An Alternative Or Adjunct To Surgery For Treatment Of Cancer, Ru Chen, Xinhua Chen, Stephen J. Beebe

Bioelectrics Publications

Surgery as resection or transplantation remains a fundamental means for cancer treatment and often offers an opportunity for a cure. However, surgery is not always possible because of tumor proximity to blood vessels or ducts or when a patient is not healthy enough to undergo surgery. Application of nanosecond pulsed electric fields (nsPEFs) is a new approach to treat cancer using pulse power technology that was originally designed for military purposes. This novel approach deposits extremely short pulses of high power, low energy electric fields into malignant tissues using electrodes to encompass tumors. Pre-clinical studies show that treatments are effective …

Response To "Sodium Current Inhibition By Nanosecond Pulsed Electric Field (Nspef) - Fact Or Artifact?" By Verkerk Et Al, Andrei G. Pakhomov

Bioelectrics Publications

It was nice to learn that our studies of nanosecond pulsed electric field (nsPEF) effects on membrane currents [Nesin et al., 2012; Nesin and Pakhomov, 2012] gained the attention of scientists outside the immediate field of bioelectromagnetics.

Study Of Charge-Dependent Transport And Toxicity Of Peptide-Functionalized Silver Nanoparticles Using Zebrafish Embryos And Single Nanoparticle Plasmonic Spectroscopy, Kerry J. Lee, Lauren M. Browning, Prakash D. Nallathamby, Xiao-Hong Nancy Xu

Chemistry & Biochemistry Faculty Publications

Nanomaterials possess unusually high surface area-to-volume ratios and surface-determined physicochemical properties. It is essential to understand their surface-dependent toxicity in order to rationally design biocompatible nanomaterials for a wide variety of applications. In this study, we have functionalized the surfaces of silver nanoparticles (Ag NPs, 11.7 ±+2.7 nm in diameter) with three biocompatible peptides (CALNNK, CALNNS, CALNNE) to prepare positively (Ag-CALNNK NPs^+ζ), negatively (Ag-CALNNS NPs^−2ζ), and more negatively charged NPs (Ag-CALNNE NPs^−4ζ), respectively. Each peptide differs in a single amino acid at its C-terminus, which minimizes the effects of peptide sequences and serves as …

Phytoplankton In Virginia Lakes And Reservoirs, Harold G. Marshall

Virginia Journal of Science

This study involves a phytoplankton summer/autumn survey in 46 Virginia lakes and reservoirs during 2010-2012. A total of 307 taxa were identified which included several filamentous and colonial cyanabacteria in bloom concentrations. With the exception of one natural lake, the other sites sampled represent impoundments created decades ago, with the majority presently classified as meso- or eutrophic. Among the cyanobacteria were 6 known toxin producers (Anabaena circinalis, Anabaena spiroides, Aphanizomenon flos-aquae, Cylindrospermopsis raciborskii, Limnothrix redekei, and Microcystis aeruginosa). The study characterizes phytoplankton populations in these aging freshwater habitats taken from a large number …

First Record Of Pond Sliders (Trachemys Scripta Scripta And T. S. Elegans) At Fredericksburg, Virginia With Observations On Population Size, Age And Growth, Werner Wieland, Yoshinori Takeda

Virginia Journal of Science

We conducted a turtle mark-recapture program within a 160 m stretch of the Fredericksburg Canal with standard, baited hoop nets from May to July 2012 to determine if a population of the introduced Red-eared Slider (Trachemys scripta elegans) and Yellow-bellied Slider (Trachemys s. scripta) are established in this area. We captured and marked nine Red-eared Sliders (1 male, 8 females) and estimated a population size of 23 individuals. Most were reproductively mature. The established population in the canal may be a source of introduction into the Rappahannock River.

The Small Mammals Of Two Dune Communities In Southeastern Virginia, Robert K. Rose, Justin L. Sweitzer

Virginia Journal of Science

Small mammals were surveyed using live and pitfall traps between the primary and secondary dunes at two locations on the shores of the Chesapeake Bay near the Atlantic Ocean: Little Creek Amphibious Base in Norfolk and Joint Expeditionary Base Fort Story in Virginia Beach, Virginia. Captures were dominated by house mice (Mus musculus) in interdunal habitats with sparse grass, whereas white-footed mice (Peromyscus leucopus) were found primarily in shrubby live-oak thickets on the tops of dunes. Hispid cotton rats (Sigmodon hispidus) were present only at Fort Story, and then only in patches of dense …

2013 Undergraduate Research Awards

Virginia Journal of Science

Information about the 2013 Undergraduate Research award-winners. Includes photos.

Recruitment Of The Intracellular Ca2+ By Ultrashort Electric Stimuli: The Impact Of Pulse Duration, Iurii Semenov, Shu Xiao, Olga N. Pakhomova, Andrei G. Pakhomov

Bioelectrics Publications

Nanosecond-duration electric stimuli are distinguished by the ability to permeabilize intracellular membranes and recruit Ca²⁺ from intracellular stores. We quantified this effect in non-excitable cells (CHO) using ratiometric Ca²⁺ imaging with Fura-2. In a Ca²⁺-free medium, 10-, 60-, and 300-ns stimuli evoked Ca2⁺ transients by mobilization of Ca²⁺ from the endoplasmic reticulum. With 2 mM external Ca²⁺, the transients included both extra- and intracellular components. The recruitment of intracellular Ca²⁺ increased as the stimulus duration decreased. At the threshold of 200–300 nM, the transients were amplified by calcium-induced calcium release. We …

Primary Pathways Of Intracellular Ca2+ Mobilization By Nanosecond Pulsed Electric Field, Iurii Semenov, Shu Xiao, Andrei G. Pakhomov

Bioelectrics Publications

Permeabilization of cell membranous structures by nanosecond pulsed electric field (nsPEF) triggers transient rise of cytosolic Ca²⁺ concentration ([Ca²⁺]_i), which determines multifarious downstream effects. By using fast ratiometric Ca²⁺ imaging with Fura-2, we quantified the external Ca²⁺ uptake, compared it with Ca²⁺ release from the endoplasmic reticulum (ER), and analyzed the interplay of these processes. We utilized CHO cells which lack voltage-gated Ca²⁺ channels, so that the nsPEF-induced [Ca²⁺]_i changes could be attributed primarily to electroporation. We found that a single 60-ns pulse caused fast [Ca2+]_i increase …

Innovative Applications Of Genetic Algorithms To Problems In Accelerator Physics, Alicia Hofler, Balša Terzić, Matthew Kramer, Anton Zvezdin, Vasiliy Morozov, Yves Roblin, Fanglei Lin, Colin Jarvis

Physics Faculty Publications

The genetic algorithm (GA) is a powerful technique that implements the principles nature uses in biological evolution to optimize a multidimensional nonlinear problem. The GA works especially well for problems with a large number of local extrema, where traditional methods (such as conjugate gradient, steepest descent, and others) fail or, at best, underperform. The field of accelerator physics, among others, abounds with problems which lend themselves to optimization via GAs. In this paper, we report on the successful application of GAs in several problems related to the existing Continuous Electron Beam Accelerator Facility nuclear physics machine, the proposed Medium-energy Electron-Ion …

Real-Time In Vivo Imaging Of Size-Dependent Transport And Toxicity Of Gold Nanoparticles In Zebrafish Embryos Using Single Nanoparticle Plasmonic Spectroscopy, Lauren M. Browning, Tao Huang, Xiao-Hong Nancy Xu

Chemistry & Biochemistry Faculty Publications

Noble metal nanoparticles (NPs) show distinctive plasmonic optical properties and superior photostability, enabling them to serve as photostable multicoloured optical molecular probes and sensors for real-time in vivo imaging. To effectively study biological functions in vivo, it is essential that the NP probes are biocompatible and can be delivered into living organisms non-invasively. In this study, we have synthesized, purified and characterized stable (non-aggregated) gold (Au) NPs (86.2 +/- 10.8 nm). We have developed dark-field single NP plasmonic microscopy and spectroscopy to study their transport into early developing zebrafish embryos (cleavage stage) and their effects on embryonic development …

Silver Nanoparticles Induce Developmental Stage-Specific Embryonic Phenotypes In Zebrafish, Kerry J. Lee, Lauren M. Browning, Prakash D. Nallathamby, Christopher J. Osgood, Xiao-Hong Nancy Xu

Chemistry & Biochemistry Faculty Publications

Much is anticipated from the development and deployment of nanomaterials in biological organisms, but concerns remain regarding their biocompatibility and target specificity. Here we report our study of the transport, biocompatibility and toxicity of purified and stable silver nanoparticles (Ag NPs, 13.1 ± 2.5 nm in diameter) upon the specific developmental stages of zebrafish embryos using single NP plasmonic spectroscopy. We find that single Ag NPs passively diffuse into five different developmental stages of embryos (cleavage, early-gastrula, early-segmentation, late-segmentation, and hatching stages), showing stage-independent diffusion modes and diffusion coefficients. Notably, the Ag NPs induce distinctive stage and dose-dependent phenotypes and …

Using Ammonium Pore Water Profiles To Assess Stoichiometry Of Deep Remineralization Processes In Methanogenic Continental Margin Sediments, David J. Burdige, Tomoko Komada

OES Faculty Publications

In many continental margin Sediments, a deep reaction zone exists which is separated from remineralization processes near the sediment surface. Here, methane diffuses upward to a depth where it is oxidized by downwardly diffusing sulfate. However, the methane sources that drive this anaerobic oxidation of methane (AOM) in the sulfate-methane transition zone (SMT) may vary among sites. In particular, these sources can be thought of as either (i) "internal" sources from in situ methanogenesis (regardless of where it occurs in the sediment column) that are ultimately coupled to organic matter deposition and burial, or (ii) "external" sources such as hydrocarbon …

Dinitrogen Fixation In Aphotic Oxygenated Marine Environments, Eyal Rahav, Edo Bar-Zeev, Sarah Ohayon, Hila Elifantz, Natalia Belkin, Barak Herut, Margaret R. Mulholland, Iiana Berman-Frank

OES Faculty Publications

We measured N₂ fixation rates from oceanic zones that have traditionally been ignored as sources of biological N₂fixation; the aphotic, fully oxygenated, nitrate (NO¯₃)-rich, waters of the oligotrophic Levantine Basin (LB) and the Gulf of Aqaba (GA). N₂ fixation rates measured from pelagic aphotic waters to depths up to 720 m, during the mixed and stratified periods, ranged from 0.01 nmol N L^-1 d^-1 to 0.38 nmol N L^-1 d^-1. N₂ fixation rates correlated significantly with bacterial productivity and heterotrophic diazotrophs were identified from aphotic as well as …

Effect Of Laser Ablation Depth In Otolith Life History Scans, Renée R. Hoover, Cynthia M. Jones

OES Faculty Publications

Life history scans of fish otoliths are bringing new insight into the structure, connectivity, and movement of fish populations. Data obtained from such scans, however, possess in-herent limitations that have not yet been fully addressed or understood. For example, several investigators have noted delays in otolith elemental uptake that do not appear to reflect habitat exposure. We hypothesized that the 3-dimensional structure of otoliths may produce sampling artifacts in the results obtained from laser ablation scans. To test this hypothesis, we sampled sagittal otoliths from juvenile Atlantic croaker Micropogonias undulatus with laser ablation inductively coupled plasma mass spectrometry to obtain …

Phosphorus Cycling In The Sargasso Sea: Investigation Using The Oxygen Isotopic Composition Of Phosphate, Enzyme-Labeled Fluorescence, And Turnover Times, Karen Mclaughlin, Jill A. Sohm, Gregory A. Cutter, Michael W. Lomas, Adina Paytan

OES Faculty Publications

Dissolved inorganic phosphorus (DIP) concentrations in surface water of vast areas of the ocean are extremely low (<10 nM) and phosphorus (P) availability could limit primary productivity in these regions. We explore the use of oxygen isotopic signature of dissolved phosphate (δ¹⁸O_PO4) to investigate biogeochemical cycling of P in the Sargasso Sea, Atlantic Ocean. Additional techniques for studying P dynamics including ³³P-based DIP turnover time estimates and percent of cells expressing alkaline phosphatase (AP) activity as measured by enzyme-labeling fluorescence are also used. In surface waters, δ¹⁸O_PO4 values were lower than equilibrium by 3–6%, indicative of dissolved organic phosphorous (DOP) remineralization by extracellular enzymes. An isotope mass balance model using a variety of possible combinations of …

How Do Shellfisheries Influence Genetic Connectivity In Metapopulations? A Modeling Study Examining The Role Of Lower Size Limits In Oyster Fisheries, Daphne M. Munroe, Eileen E. Hofmann, Eric N. Powell, John M. Klinck

CCPO Publications

Fisheries can potentially alter evolutionary processes such as genetic connectivity and lead to genotypic changes in stocks. Using an individual-based metapopulation genetics model, we examined the possible influence of oyster (Crassostrea virginica) fisheries on genetic connectivity. We simulated a range of realistic fishing pressures, with and without a minimum size limit (limit = 63.5 mm), over a range of fishing scenarios including single-area and stock-wide fisheries. Movement of a neutral marker gene provided an indicator of gene transfer between populations. Simulations showed that fishing may alter genetic connectivity. Increasing fishing pressure tended to decrease potential for fished populations …

The Big Blue Test: Effects Of 14 Minutes Of Physical Activity On Blood Glucose Levels, Sheri R. Colberg, Manuel J. Hernandez

Human Movement Sciences & Special Education Faculty Publications

[First paragraph] For most with diabetes, physical activity has a blood glucose lowering effect (1). Hypoglycemia (i.e., blood glucose < 65 mg/dL) resulting from exercise is a concern, particularly for insulin users (2).

Blood Glucose Responses To Type, Intensity, Duration, And Timing Of Exercise, Sheri R. Colberg, Manuel J. Hernandez, Fatima Shahzad

Human Movement Sciences & Special Education Faculty Publications

[First Paragraph] The Big Blue Test (BBT) is an annual initiative by the Diabetes Hands Foundation to raise awareness of the importance of physical activity in managing diabetes. Individuals with diabetes voluntarily exercise and record self-monitored blood glucose levels. During the 2012 BBT, 5,157 diabetic participants (~90% insulin users) anonymously entered exercise type, intensity, duration, time elapsed since last meal, and blood glucose readings before and after one or more bouts of exercise separately through www.BigBlueTest.org or an Iphone app.

Development And Validation Of A Predictive Model Of Acute Glucose Response To Exercise In Individuals With Type 2 Diabetes, Bryan S. Gibson, Sheri R. Colberg, Paul Poirier, Denise Maria Martins Vancea, Jason Jones, Robin Marcus

Human Movement Sciences & Special Education Faculty Publications

Background: Our purpose was to develop and test a predictive model of the acute glucose response to exercise in individuals with type 2 diabetes.

Design and methods: Data from three previous exercise studies (56 subjects, 488 exercise sessions) were combined and used as a development dataset. A mixed-effects Least Absolute Shrinkage Selection Operator (LASSO) was used to select predictors among 12 potential predictors. Tests of the relative importance of each predictor were conducted using the Lindemann Merenda and Gold (LMG) algorithm. Model structure was tested using likelihood ratio tests. Model accuracy in the development dataset was assessed by leave-one-out cross-validation. …

Prescribing Physical Activity To Prevent And Manage Gestational Diabetes, Sheri R. Colberg, Kristin Castorino, Lois Jovanovič

Human Movement Sciences & Special Education Faculty Publications

Gestational diabetes mellitus (GDM) is the most prevalent metabolic disorder during pregnancy. Women diagnosed with GDM have a substantially greater risk of developing type 2 diabetes within 5-10 years after delivery, and the risk is increased by excess body weight. Uncontrolled hyperglycemia during pregnancy is potentially harmful to both mother and fetus, resulting in a greater need for Caesarian-section deliveries, delivery of larger infants with more excess body fat, a greater risk of infant death and stillbirth, and an elevated risk of infant hypoglycemia immediately after birth. Fortunately, engaging in physical activity prior to and during pregnancy may lower the …

Nocturnal Diaphoresis Secondary To Mild Obstructive Sleep Apnea In A Patient With A History Of Two Malignancies, Robert Daniel Vorona, Mariana Szklo-Coxe, Mark Fleming, J. Catesby Ware

Community & Environmental Health Faculty Publications

Numerous medical disorders, including obstructive sleep apnea, may cause nocturnal diaphoresis. Previous work has associated severe obstructive sleep apnea with nocturnal diaphoresis. This case report is of import as our patient with severe nocturnal diaphoresis manifested only mild sleep apnea, and, for years, his nocturnal diaphoresis was ascribed to other causes, i.e., first prostate cancer and then follicular B-cell lymphoma. Additionally, it was the nocturnal diaphoresis and not more common symptoms of obstructive sleep apnea, such as snoring, that led to the definitive diagnosis of his sleep apnea and then to treatment with a gratifying resolution of his onerous symptom.

Higher Food Prices May Threaten Food Security Status Among American Low-Income Households With Children, Qi Zhang, Sonya Jones, Christopher J. Ruhm, Margaret Andrews

Community & Environmental Health Faculty Publications

Children in food-insecure households are more likely to experience poorer health function and worse academic achievement. To investigate the relation between economic environmental factors and food insecurity among children, we examined the relation between general and specific food prices (fast food, fruits and vegetables, beverages) and risk of low (LFS) and very low food security (VLFS) status among low-income American households with children. Using information for 27,900 child-year observations from the Early Childhood Longitudinal Study-Kindergarten Class of 1998 1999 linked with food prices obtained from the Cost of Living Data of the Council for Community and Economic Research, formerly known …

Nucleic Acid Oxidation In Human Health And Disease, Mu-Rong Chao, Pavel Rossner Jr., Siamak Haghdoost, Hueiwang Anna Jeng, Chiung-Wen Hu

Community & Environmental Health Faculty Publications

No abstract provided.

Next-Peak: A Normal-Exponential Two-Peak Model For Peak-Calling In Chip-Seq Data, Nak-Kyeong Kim, Rasika V. Jayatillake, John L. Spouge

Mathematics & Statistics Faculty Publications

Background: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) can locate transcription factor binding sites on genomic scale. Although many models and programs are available to call peaks, none has dominated its competition in comparison studies.

Results: We propose a rigorous statistical model, the normal-exponential two-peak (NEXT-peak) model, which parallels the physical processes generating the empirical data, and which can naturally incorporate mappability information. The model therefore estimates total strength of binding (even if some binding locations do not map uniquely into a reference genome, effectively censoring them); it also assigns an error to an estimated binding location. The comparison study …

Conus: First Comprehensive Conservation Red List Assessment Of A Marine Gastropod Mollusc Genus, Howard Peters, Bethan C. O'Leary, Julie P. Hawkins, Kent E. Carpenter, Callum M. Roberts

Biological Sciences Faculty Publications

Marine molluscs represent an estimated 23% of all extant marine taxa, but research into their conservation status has so far failed to reflect this importance, with minimal inclusion on the authoritative Red List of the International Union for the Conservation of Nature (IUCN). We assessed the status of all 632 valid species of the tropical marine gastropod mollusc, Conus (cone snails), using Red List standards and procedures to lay the groundwork for future decadal monitoring, one of the first fully comprehensive global assessments of a marine taxon. Three-quarters (75.6%) of species were not currently considered at risk of extinction owing …