Digital Commons Network^™

Fine Tuning A Well-Oiled Machine: Influence Of Nk1.1 And Nkg2d On Nkt Cell Development And Function, Sunil K. Joshi, Mark L. Lang

Bioelectrics Publications

Natural killer T cells (NKT) represent a group of CD1d-restricted T-lineage cells that provide a functional interface between innate and adaptive immune responses in infectious disease, cancer, allergy and autoimmunity. There have been remarkable advances in understanding the molecular events that underpin NKT development in the thymus and in the complex array of functions in the periphery. Most functional studies have focused on activation of T cell antigen receptors expressed by NKT cells and their responses to CD1d presentation of glycolipid and related antigens. Receiving less attention has been several molecules that are hallmarks of Natural Killer (NK) cells, but …

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.

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 …

Arsenic And Phosphorus Biogeochemistry In The Ocean: Arsenic Species As Proxies For P-Limitation, Oliver Wurl, Louise Zimmer, Gregory A. Cutter

OES Faculty Publications

Arsenic and phosphorus are biochemically very similar, and hence arsenate (As⁵⁺) is toxic by interfering with the energy metabolism, in particular during P limitation. However, many phytoplankton detoxify As by reducing arsenate to arsenite (As³⁺), and/or methylating it to mono and dimethyl As. Such As detoxification becomes operative in oligotrophic waters when phosphate concentrations are below those for As; therefore, we evaluated the potential use of these detoxification products as indicators of P-limitation by measuring As speciation during the US GEOTRACES North Atlantic transect. The distribution of As³⁺ concentrations in surface waters is similar to …

Intercalibraton In Chemical Oceanography-- Getting The Right Number, Gregory A. Cutter

OES Faculty Publications

Intercalibration has a strict metrological definition, but in brief, it's an open sharing of methods and results between laboratories to achieve the most accurate data with the fewest random and systematic errors. In the field of chemical oceanography where concentrations of many constituents can be in the nano- to picomolar range, the salt water matrix can be difficult to analyze, and knowing the exact concentrations, or even chemical forms, of biologically required elements is essential, intercalibration is a very relevant and needed tool. Implementing it is not simple because errors can occur at any step in the process of taking …

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 …

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 …

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, …

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 …

Wintering Eiders Acquire Exceptional Se And Cd Burdens In The Bering Sea: Physiological And Oceanographic Factors, James R. Lovvorn, Merl F. Raisbeck, Lee W. Cooper, Gregory A. Cutter, Micah W. Miller, Marjorie L. Brooks, Jacqueline M. Grebmeier, Angela C. Matz, Cortney M. Schaefer

OES Faculty Publications

During late winter (March) in the Bering Sea, levels of Se in livers and Cd in kidneys of spectacled eiders Somateria fischeri were exceptionally high (up to 489 and 312 µg g⁻¹ dry mass, respectively). Comparison of organ and blood samples during late winter, early spring migration, and breeding suggests that the eiders’ high Se and Cd burdens were accumulated at sea, with highest exposure during winter. High exposure may have resulted from high metabolic demands and food intake, as well as concentrations in food. In the eiders’ remote wintering area, their bivalve prey contained comparable Se levels and …

Distributions Of Particulate Heme B In The Atlantic And Southern Oceans- Implications For Electron Transport In Phytoplankton, Martha Gledhill, Eric P. Achterberg, David J. Honey, Maria C. Nielsdottir, Micha J.A. Rijkenberg

OES Faculty Publications

Concentrations of heme b, the iron-containing component of b-type hemoproteins, ranged from b concentrations were enhanced in the photic zone and decreased with depth. Heme b concentrations correlated positively with chlorophyll a (chl a) in the TNA (r=0.41, pb did not correlate with chl a in the IB or SS. In the IB and SS, stations with high-chlorophyll and low-nutrient (Fe and/or Si) concentrations exhibited low heme bconcentrations relative to particulate organic carbon (< 0.1 μmolmol^-1, and high chl a:heme b ratios (> 500). High chl a:heme b ratios resulted from relative decreases in …

Microbially Induced Sedimentary Structures Recording An Ancient Ecosystem In The Ca. 3.48 Billion-Year-Old Dresser Formation, Pilbara, Western Australia, Nora Noffke, Daniel Christian, David Wacey, Robert M. Hazen

OES Faculty Publications

Microbially induced sedimentary structures (MISS) result from the response of microbial mats to physical sediment dynamics. MISS are cosmopolitan and found in many modern environments, including shelves, tidal flats, lagoons, riverine shores, lakes, interdune areas, and sabkhas. The structures record highly diverse communities of microbial mats and have been reported from numerous intervals in the geological record up to 3.2 billion years (Ga) old. This contribution describes a suite of MISS from some of the oldest well-preserved sedimentary rocks in the geological record, the early Archean (ca. 3.48 Ga) Dresser Formation, Western Australia. Outcrop mapping at the meter to …

Combined Effects Of Co2 And Light On Large And Small Isolates Of The Unicellular N2-Fixing Cyanobacterium Crocosphaera Watsonii From The Western Tropical Atlantic Ocean, Nathan S. Garcia, Fei-Xue Fu, Cynthia L. Breene, Elizabeth K. Yu, Peter W. Bernhardt, Margaret R. Mulholland, David A. Hutchins

OES Faculty Publications

We examined the combined effects of light and pCO₂ on growth, CO₂-fixation and N₂-fixation rates by strains of the unicellular marine N₂-fixing cyanobacterium Crocosphaera watsonii with small (WH0401) and large (WH0402) cells that were isolated from the western tropical Atlantic Ocean. In low-pCO₂-acclimated cultures (190ppm) of WH0401, growth, CO₂-fixation and N₂-fixation rates were significantly lower than those in cultures acclimated to higher (present-day approximate to 385ppm, or future approximate to 750ppm) pCO² treatments. Growth rates were not significantly different, however, in low-pCO₂-acclimated cultures of …

Development And Deployment Of A Point-Source Digital Inline Holographic Microscope For The Study Of Plankton And Particles To A Depth Of 6000 M, Alexander B. Bochdansky, Manfred H. Jericho, Gerhard J. Herndl

OES Faculty Publications

Bochdansky, A. B., Jericho, M. H., & Herndl, G. J. (2013). Development and deployment of a point-source digital inline holographic microscope for the study of plankton and particles to a depth of 6000 m. Limnology and Oceanography: Methods, 11, 28-40. doi: 10.4319/lom.2013.11.28

Stromatolites And Miss—Differences Between Relatives, N. Noffke, S. M. Awramik

OES Faculty Publications

Benthic microorganisms form highly organized communities called “biofilms.” A biofilm consists of the individual cells plus their extracellular polymeric substances (EPS). In marine and non-marine environments, benthic microbial communities interact with the physical sediment dynamics and other factors in the environment in order to survive. This interaction can produce distinctive sedimentary structures called microbialites. Binding, biostabilization, baffling, and trapping of sediment particles by microorganisms result in the formation of microbially induced sedimentary structures (MISS); however, if carbonate precipitation occurs in EPS, and these processes happen in a repetitive manner, a multilayered build-up can form—stromatolites. Stromatolites and MISS are first found …

Bacterial Colonization And Extinction On Marine Aggregates: Stochastic Model Of Species Presence And Abundance, Andrew M. Kramer, M. Maille Lyons, Fred C. Dobbs, John M. Drake

OES Faculty Publications

Organic aggregates provide a favorable habitat for aquatic microbes, are efficiently filtered by shellfish, and may play a major role in the dynamics of aquatic pathogens. Quantifying this role requires understanding how pathogen abundance in the water and aggregate size interact to determine the presence and abundance of pathogen cells on individual aggregates. We build upon current understanding of the dynamics of bacteria and bacterial grazers on aggregates to develop a model for the dynamics of a bacterial pathogen species. The model accounts for the importance of stochasticity and the balance between colonization and extinction. Simulation results suggest that while …

Membrane Surface Charges Attracted Protons Are Not Relevant To Proton Motive Force, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

[First Paragraph] Only a half-century ago, British scientist Peter Mitchell proposed the conceptual scheme known as "chemiosmotic theory" that identified the role of proton coupling in the formation of ATP in cells [1,2]. Mitchell's delocalized proton-coupling chemiosmotic theory was initially quite controversial. But it would win for him the Nobel Prize in Chemistry in 1978. However, questions about Mitchell's chemiosmotic hypothesis have never gone away and a number of credible studies indicated the full extent of Mitchell's idea didn't always hold up to experience.

Experiences Of Kenyan Healthcare Workers Providing Services To Men Who Have Sex With Men: Qualitative Findings From A Sensitivity Training Programme, Elise M. Van Der Elst, Evans Gichuru, Anisa Omar, Jennifer Kanungi, Zoe Duby, Miriam Midoun, Sylvia Shangani, Susan M. Graham, Adrian D. Smith, Eduard J. Sanders, Don Operario

Community & Environmental Health Faculty Publications

Introduction

Men who have sex with men (MSM) in Kenya are at high risk for HIV and may experience prejudiced treatment in health settings due to stigma. An on-line computer-facilitated MSM sensitivity programme was conducted to educate healthcare workers (HCWs) about the health issues and needs of MSM patients.

Methods

Seventy-four HCWs from 49 ART-providing health facilities in the Kenyan Coast were recruited through purposive sampling to undergo a two-day MSM sensitivity training. We conducted eight focus group discussions (FGDs) with programme participants prior to and three months after completing the training programme. Discussions aimed to characterize HCWs’ challenges in …

Monarch, Jim Raper (Editor)

Monarch Magazine

Winter 2013 issue of Monarch, the Old Dominion University Magazine.

Subtitled: Facebook Philosopher

Dinosolve: A Protein Disulfide Bonding Prediction Server Using Context-Based Features To Enhance Prediction Accuracy, Ashraf Yaseen, Yaohang Li

Computer Science Faculty Publications

Background: Disulfide bonds play an important role in protein folding and structure stability. Accurately predicting disulfide bonds from protein sequences is important for modeling the structural and functional characteristics of many proteins.

Methods: In this work, we introduce an approach of enhancing disulfide bonding prediction accuracy by taking advantage of context-based features. We firstly derive the first-order and second-order mean-force potentials according to the amino acid environment around the cysteine residues from large number of cysteine samples. The mean-force potentials are integrated as context-based scores to estimate the favorability of a cysteine residue in disulfide bonding state as well as …

Image-Level And Group-Level Models For Drosophila Gene Expression Pattern Annotation, Quian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart Newfeld, Sudhir Kumar, Jieping Ye

Computer Science Faculty Publications

Background: Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment …

Estimating Loop Length From Cryoem Images At Medium Resolutions, Andrew Mcknight, Dong Si, Kamal Al Nasr, Andrey Chemikov, Nikos Chrisochoides, Jing He

Computer Science Faculty Publications

Background: De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein.

Results: We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was …

Computational Genetic Neuroanatomy Of The Developing Mouse Brain: Dimensionality Reduction, Visualization, And Clustering, Shuiwang Ji

Computer Science Faculty Publications

Background: The structured organization of cells in the brain plays a key role in its functional efficiency. This delicate organization is the consequence of unique molecular identity of each cell gradually established by precise spatiotemporal gene expression control during development. Currently, studies on the molecular-structural association are beginning to reveal how the spatiotemporal gene expression patterns are related to cellular differentiation and structural development.

Results: In this article, we aim at a global, data-driven study of the relationship between gene expressions and neuroanatomy in the developing mouse brain. To enable visual explorations of the high-dimensional data, we map the in …

Resilience Governance Through Serious Energy Gaming, Adrian V. Gheorghe, Dan V. Vamanu

Engineering Management & Systems Engineering Faculty Publications

Physical analogies emphasizing cooperative behavior in systems are explored and integrated into so called 'serious energy games', to contribute in a better understanding, monitoring and good governance of some of the complex security issues confronting the evolvement of contemporary energy systems. It is believed that such exercises might be supportive in the necessary attempt, by the many stakeholders and actors / agents involved, to bring balance to prevailing policies of which seems to be “Go change yourself - in a resilient fashion!” An extrapolation of several findings to other than energy systems tempted to implement drastic changes based on substantial …

The Population Dynamics Of Two Rodents In Two Coastal Marshes In Virginia, Robert K. Rose, John A. March

Virginia Journal of Science

The communities of small mammals were evaluated for 13 months with capture-mark-recapture methods in two Spartina-Juncus marshes of the Atlantic coast in Northampton County, Virginia. Small mammals were trapped for three days each month using live traps placed on floats on two study grids. Two rodents were numerically dominant (~90% of small mammals) there: marsh rice rat, Oryzomys palustris, and meadow vole, Microtus pennsylvanicus. Monthly estimates of population density were greater for rice rats (peak: 45/ha) than for those of meadow voles (peak: 30/ha). Survival rates were generally low, especially for rice rats, indicating highly vagile populations. Both …

Public Philosophy Of Technology, Dylan E. Wittkower, Evan Selinger, Lucinda Rush

Philosophy Faculty Publications

Philosophers of technology are not playing the public role which our own theoretical perspectives motivate us to take. A great variety of theories and perspectives within philosophy of technology, including those of Marcuse, Feenberg, Borgmann, Ihde, Michelfelder, Bush, Winner, Latour, and Verbeek, either support or directly call for various sorts of intervention—a call that we have failed to adequately heed. Barriers to such intervention are discussed, and three proposals for reform are advanced: (1) post-publication peer-reviewed reprinting of public philosophy, (2) increased emphasis on true open access publication, and (3) increased efforts to publicize and adapt traditional academic research.

Vitamin D And Biomarkers Of Sex Steroid Hormones Are Non-Linearly And Inversely Related To All-Cause Mortality: Results From Nhanes Iii, Hind A. Beydoun, Shaker M. Eid, Hueiwang Anna Jeng, Alan B. Zonderman, May A. Beydoun

Community & Environmental Health Faculty Publications

Background: In men, hypovitaminosis D as well as high and low testosterone levels have been linked to adverse events, including death. A biological interaction has been previously suggested between vitamin D and androgens. In a cohort study using Third National Health and Nutrition Examination Survey data, we simultaneously investigated circulating vitamin D and biomarkers of sex steroid hormones as predictors of all-cause mortality.

Methods: Age-adjusted and fully-adjusted Cox regression models were constructed to estimate hazard ratios (HR) and their 95% confidence intervals (CI). Whereas the vitamin D sufficient group (25(OH)D3 ≥30 ng/ml) was selected as a referent, biomarkers of sex …

Production Mechanisms, Number Concentration, Size Distribution, Chemical Composition, And Optical Properties Of Sea Spray Aerosols, Nicholas Meskhidze, Markus D. Petters, Kostas Tsigaridis, Tim Bates, Colin O'Dowd, Jeff Reid, Ernie R. Lewis, Brett Gantt, Magdalena D. Anguelova, Prakash V. Bhave, Andrew Wozniak

Chemistry & Biochemistry Faculty Publications

(First paragraph)

The impact of sea spray aerosols on global climate remains one of the most uncertain components of the aerosol–radiation–climate problem, but has received less attention than the impacts of terrestrial and anthropogenic aerosols. The last decade has produced a large body of information regarding the sources and composition of marine aerosols, resulting in a reassessment of the complex role that sea spray particles play in climate and various geophysical phenomena. As sea spray aerosol contributes substantially to the preindustrial, natural background which provides the baseline on top of which anthropogenic forcing should be quantified, and because the ocean …

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 …