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Old Dominion University

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2017

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Articles 1 - 30 of 72

Full-Text Articles in Life Sciences

Ticks, Ixodes Scapularis, Feed Repeatedly On White-Footed Mice Despite Strong Inflammatory Response: An Expanding Paradigm For Understanding Tick-Host Interactions, Jennifer M. Anderson, Ian N. Moore, Bianca M. Nagata, José M.C. Ribeiro, Jesus G. Valenzuela, Daniel E. Sonenshine Dec 2017

Ticks, Ixodes Scapularis, Feed Repeatedly On White-Footed Mice Despite Strong Inflammatory Response: An Expanding Paradigm For Understanding Tick-Host Interactions, Jennifer M. Anderson, Ian N. Moore, Bianca M. Nagata, José M.C. Ribeiro, Jesus G. Valenzuela, Daniel E. Sonenshine

Biological Sciences Faculty Publications

Ticks transmit infectious agents including bacteria, viruses and protozoa. However, their transmission may be compromised by host resistance to repeated tick feeding. Increasing host resistance to repeated tick bites is well known in laboratory animals, including intense inflammation at the bite sites. However, it is not known whether this also occurs in wild rodents such as white-footed mice, Peromyscus leucopus, and other wildlife, or if it occurs at all. According to the "host immune incompetence" hypothesis, if these mice do not have a strong inflammatory response, they would not reject repeated tick bites by Ixodes scapularis. To test …

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Distributions Of Krill And Antarctic Silverfish And Correlations With Environmental Variables In The Western Ross Sea, Antarctica, L. Brynn Davis, Eileen E. Hofmann, John M. Klinck, Andrea Piñones, Michael S. Dinniman Dec 2017

Distributions Of Krill And Antarctic Silverfish And Correlations With Environmental Variables In The Western Ross Sea, Antarctica, L. Brynn Davis, Eileen E. Hofmann, John M. Klinck, Andrea Piñones, Michael S. Dinniman

CCPO Publications

Antarctic krill Euphausia superba, crystal krill E. crystallorophias, and Antarctic silverfish Pleuragramma antarctica are key mid-trophic level species in the Ross Sea, connecting primary production to the upper trophic levels. Distributions of these species were constructed from observations made in the western Ross Sea from 1988 to 2004. Distributions of environmental conditions were obtained from a 5-km resolution circulation model (temperature, mixed layer depth, surface speed) and satellite-derived observations (chlorophyll, sea ice cover). A hierarchy of statistical methods determined correlations and relationships between species and environmental conditions. Each species occupies a localized habitat defined by different environmental characteristics. …

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Molecular Geometries And Other Properties Of H2o⋯Agi And H3n⋯Agi As Characterised By Rotational Spectroscopy And Ab Initio Calculations, Chris Medcraft, Eva Gougoula, Dror M. Bittner, John C. Mullaney, Susana Blanco, David P. Tew, Nicholas R. Walker, Anthony C. Legon Dec 2017

Molecular Geometries And Other Properties Of H2o⋯Agi And H3n⋯Agi As Characterised By Rotational Spectroscopy And Ab Initio Calculations, Chris Medcraft, Eva Gougoula, Dror M. Bittner, John C. Mullaney, Susana Blanco, David P. Tew, Nicholas R. Walker, Anthony C. Legon

Chemistry & Biochemistry Faculty Publications

The rotational spectra of H3N⋯AgI and H2O⋯AgI have been recorded between 6.5 and 18.5 GHz by chirped-pulse Fourier-transform microwave spectroscopy. The complexes were generated through laser vaporisation of a solid target of silver or silver iodide in the presence of an argon gas pulse containing a low concentration of the Lewis base. The gaseous sample subsequently undergoes supersonic expansion which results in cooling of rotational and vibrational motions such that weakly bound complexes can form within the expanding gas jet. Spectroscopic parameters have been determined for eight isotopologues of H3N⋯AgI and six isotopologues of …

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High-Throughput Single-Molecule Telomere Characterization, Jennifer Mccaffrey, Eleanor Young, Katy Lassahn, Justin Sibert, Steven Pastor, Harold Riethman, Ming Xiao Nov 2017

High-Throughput Single-Molecule Telomere Characterization, Jennifer Mccaffrey, Eleanor Young, Katy Lassahn, Justin Sibert, Steven Pastor, Harold Riethman, Ming Xiao

Medical Diagnostics & Translational Sciences Faculty Publications

We have developed a novel method that enables global subtelomere and haplotype-resolved analysis of telomere lengths at the single-molecule level. An in vitro CRISPR/Cas9 RNA-directed nickase system directs the specific labeling of human (TTAGGG) n DNA tracts in genomes that have also been barcoded using a separate nickase enzyme that recognizes a 7bp motif genome-wide. High-throughput imaging and analysis of large DNA single molecules from genomes labeled in this fashion using a nanochannel array system permits mapping through subtelomere repeat element (SRE) regions to unique chromosomal DNA while simultaneously measuring the (TTAGGG) n tract length at the end of each …

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Human Rickettsial Pathogen Modulates Arthropod Organic Anion Transporting Polypeptide And Tryptophan Pathway For Its Survival In Ticks, Vikas Taank, Shovan Dutta, Amrita Dasgupta, Durland Fish, John F. Anderson, Hameeda Sultana, Girish Neelakanta Oct 2017

Human Rickettsial Pathogen Modulates Arthropod Organic Anion Transporting Polypeptide And Tryptophan Pathway For Its Survival In Ticks, Vikas Taank, Shovan Dutta, Amrita Dasgupta, Durland Fish, John F. Anderson, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

The black-legged tick Ixodes scapularis transmits the human anaplasmosis agent, Anaplasma phagocytophilum. In this study, we show that A. phagocytophilum specifically up-regulates I. scapularis organic anion transporting polypeptide, isoatp4056 and kynurenine amino transferase (kat), a gene involved in the production of tryptophan metabolite xanthurenic acid (XA), for its survival in ticks. RNAi analysis revealed that knockdown of isoatp4056 expression had no effect on A. phagocytophilum acquisition from the murine host but affected the bacterial survival in tick cells. Knockdown of the expression of kat mRNA alone or in combination with isoatp4056 mRNA significantly affected A. phagocytophilum survival …

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Activation Of The Phospholipid Scramblase Tmem16f By Nanosecond Pulsed Electric Field (Nspef) Facilitates Its Diverse Cytophysiological Effects, Claudia Muratori, Andrei G. Pakhomov, Elena Gianulis, Jade Meads, Maura Casciola, Peter A. Mollica, Olga N. Pakhomova Oct 2017

Activation Of The Phospholipid Scramblase Tmem16f By Nanosecond Pulsed Electric Field (Nspef) Facilitates Its Diverse Cytophysiological Effects, Claudia Muratori, Andrei G. Pakhomov, Elena Gianulis, Jade Meads, Maura Casciola, Peter A. Mollica, Olga N. Pakhomova

Bioelectrics Publications

Nanosecond pulsed electric fields (nsPEF) are emerging as a novel modality for cell stimulation and tissue ablation. However, the downstream protein effectors responsible for nsPEF bioeffects remain to be established. Here we demonstrate that nsPEF activate TMEM16F (or Anoctamin 6), a protein functioning as a Ca2+-dependent phospholipid scramblase and Ca2+-activated chloride channel. Using confocal microscopy and patch clamp recordings, we investigated the relevance of TMEM16F activation for several bioeffects triggered by nsPEF, including phosphatidylserine (PS) externalization, nanopore-conducted currents, membrane blebbing, and cell death. In HEK 293 cells treated with a single 300-ns pulse of 25.5 kV/cm, …

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Delayed Hypersensitivity To Nanosecond Pulsed Electric Field In Electroporated Cells, Sarah D. Jensen, Vera A. Khorokhorina, Claudia Muratori, Andrei G. Pakhomov, Olga N. Pakhomova Sep 2017

Delayed Hypersensitivity To Nanosecond Pulsed Electric Field In Electroporated Cells, Sarah D. Jensen, Vera A. Khorokhorina, Claudia Muratori, Andrei G. Pakhomov, Olga N. Pakhomova

Bioelectrics Publications

We demonstrate that conditioning of mammalian cells by electroporation with nanosecond pulsed electric field (nsPEF) facilitates their response to the next nsPEF treatment. The experiments were designed to unambiguously separate the electroporation-induced sensitization and desensitization effects. Electroporation was achieved by bursts of 300-ns, 9 kV/cm pulses (50 Hz, n = 3–100) and quantified by propidium dye uptake within 11 min after the nsPEF exposure. We observed either sensitization to nsPEF or no change (when the conditioning was either too weak or too intense, or when the wait time after conditioning was too short). Within studied limits, conditioning never caused desensitization. …

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A Synergistic Approach For Evaluating Climate Model Output For Ecological Applications, Rachel D. Cavanagh, Eugene J. Murphy, Thomas J. Bracegirdle, John Turner, Cheryl A. Knowland, Stuart P. Corney, Walker O. Smith Jr., Claire M. Waluda, Nadine M. Johnston, Richard G. J. Bellerby, Eileen E. Hofmann Sep 2017

A Synergistic Approach For Evaluating Climate Model Output For Ecological Applications, Rachel D. Cavanagh, Eugene J. Murphy, Thomas J. Bracegirdle, John Turner, Cheryl A. Knowland, Stuart P. Corney, Walker O. Smith Jr., Claire M. Waluda, Nadine M. Johnston, Richard G. J. Bellerby, Eileen E. Hofmann

CCPO Publications

Increasing concern about the impacts of climate change on ecosystems is prompting ecologists and ecosystem managers to seek reliable projections of physical drivers of change. The use of global climate models in ecology is growing, although drawing ecologically meaningful conclusions can be problematic. The expertise required to access and interpret output from climate and earth system models is hampering progress in utilizing them most effectively to determine the wider implications of climate change. To address this issue, we present a joint approach between climate scientists and ecologists that explores key challenges and opportunities for progress. As an exemplar, our focus …

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Damage-Free Peripheral Nerve Stimulation By 12-Ns Pulsed Electric Field, Maura Casciola, Shu Xiao, Andrei G. Pakhomov Sep 2017

Damage-Free Peripheral Nerve Stimulation By 12-Ns Pulsed Electric Field, Maura Casciola, Shu Xiao, Andrei G. Pakhomov

Bioelectrics Publications

Modern technologies enable deep tissue focusing of nanosecond pulsed electric field (nsPEF) for non-invasive nerve and muscle stimulation. However, it is not known if PEF orders of magnitude shorter than the activation time of voltage-gated sodium channels (VGSC) would evoke action potentials (APs). One plausible scenario requires the loss of membrane integrity (electroporation) and resulting depolarization as an intermediate step. We report, for the first time, that the excitation of a peripheral nerve can be accomplished by 12-ns PEF without electroporation. 12-ns stimuli at 4.1-11 kV (3.3-8.8 kV/cm) evoked APs similarly to conventional stimuli (100-250 mus, 1-5 V, 103-515 V/m), …

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Controllable Moderate Heating Enhances The Therapeutic Efficacy Of Irreversible Electroporation For Pancreatic Cancer, Chelsea M. Edelblute, James Hornef, Niculina I. Burcus, Thomas Norman, Stephen J. Beebe, Karl Schoenbach, Richard Heller, Chunqi Jiang, Sigi Guo Sep 2017

Controllable Moderate Heating Enhances The Therapeutic Efficacy Of Irreversible Electroporation For Pancreatic Cancer, Chelsea M. Edelblute, James Hornef, Niculina I. Burcus, Thomas Norman, Stephen J. Beebe, Karl Schoenbach, Richard Heller, Chunqi Jiang, Sigi Guo

Bioelectrics Publications

Irreversible electroporation (IRE) as a non-thermal tumor ablation technology has been studied for the treatment of pancreatic carcinoma and has shown a significant survival benefit. We discovered that moderate heating (MH) at 43°C for 1-2 minutes significantly enhanced ex vivo IRE tumor ablation of Pan02 cells by 5.67-fold at 750 V/cm and by 1.67-fold at 1500 V/cm. This amount of heating alone did not cause cell death. An integrated IRE system with controllable laser heating and tumor impedance monitoring was developed to treat mouse ectopic pancreatic cancer. With this novel IRE system, we were able to heat and maintain the …

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Microbial Invasion Vs. Tick Immune Regulation, Daniel E. Sonenshine, Kevin R. Macaluso Sep 2017

Microbial Invasion Vs. Tick Immune Regulation, Daniel E. Sonenshine, Kevin R. Macaluso

Biological Sciences Faculty Publications

Ticks transmit a greater variety of pathogenic agents that cause disease in humans and animals than any other haematophagous arthropod, including Lyme disease, Rocky Mountain spotted fever, human granulocytic anaplasmosis, babesiosis, tick-borne encephalitis, Crimean Congo haemorhagic fever, and many others (Gulia-Nuss et al., 2016). Although diverse explanations have been proposed to explain their remarkable vectorial capacity, among the most important are their blood feeding habit, their long term off-host survival, the diverse array of bioactive molecules that disrupt the host's natural hemostatic mechanisms, facilitate blood flow, pain inhibitors, and minimize inflammation to prevent immune rejection (Hajdušek et al., 2013). Moreover, …

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Advances In Developing Therapies To Combat Zika Virus: Current Knowledge And Future Perspectives, Ashok Munjal, Rekha Khandia, Kuldeep Dharma, Swati Sachan, Kumaragurubaran Karthik, Ruchi Tiwari, Yashpal S. Malik, Deepak Kumar, Raj K. Singh, Hafiz M. N. Iqbal, Sunil K. Joshi Aug 2017

Advances In Developing Therapies To Combat Zika Virus: Current Knowledge And Future Perspectives, Ashok Munjal, Rekha Khandia, Kuldeep Dharma, Swati Sachan, Kumaragurubaran Karthik, Ruchi Tiwari, Yashpal S. Malik, Deepak Kumar, Raj K. Singh, Hafiz M. N. Iqbal, Sunil K. Joshi

Bioelectrics Publications

Zika virus (ZIKV) remained largely quiescent for nearly six decades after its first appearance in 1947. ZIKV reappeared after 2007, resulting in a declaration of an international “public health emergency” in 2016 by the World Health Organization (WHO). Until this time, ZIKV was considered to induce only mild illness, but it has now been established as the cause of severe clinical manifestations, including fetal anomalies, neurological problems, and autoimmune disorders. Infection during pregnancy can cause congenital brain abnormalities, including microcephaly and neurological degeneration, and in other cases, Guillain-Barré syndrome, making infections with ZIKV a substantial public health concern. Genomic and …

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Anaplasma Phagocytophilum Infection Modulates Expression Of Megakaryocyte Cell Cycle Genes Through Phosphatidylinositol-3-Kinase Signaling, Supreet Khanal, Hameeda Sultana, John D. Catravas, Jason A. Carlyon, Girish Neelakanta Aug 2017

Anaplasma Phagocytophilum Infection Modulates Expression Of Megakaryocyte Cell Cycle Genes Through Phosphatidylinositol-3-Kinase Signaling, Supreet Khanal, Hameeda Sultana, John D. Catravas, Jason A. Carlyon, Girish Neelakanta

Biological Sciences Faculty Publications

Anaplasma phagocytophilum, the agent of human granulocytic anaplasmosis infects neutrophils and other cells from hematopoietic origin. Using human megakaryocytic cell line, MEG-01, we show that expression of cell cycle genes in these cells are altered upon A. phagocytophilum infection. Expression of several cell cycle genes in MEG-01 cells was significantly up regulated at early and then down regulated at later stages of A. phagocytophilum infection. Lactate dehydrogenase (LDH) assays revealed reduced cellular cytotoxicity in MEG-01 cells upon A. phagocytophilum infection. The levels of both PI3KCA (p110 alpha, catalytic subunit) and PI3KR1 (p85, regulatory subunit) of Class …

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Large Marine Protected Areas Represent Biodiversity Now And Under Climate Change, T. E. Davies, S. M. Maxwell, K. Kaschner, C. Garilao, N. C. Ban Aug 2017

Large Marine Protected Areas Represent Biodiversity Now And Under Climate Change, T. E. Davies, S. M. Maxwell, K. Kaschner, C. Garilao, N. C. Ban

Biological Sciences Faculty Publications

Large marine protected areas (>30,000 km2) have a high profile in marine conservation, yet their contribution to conservation is contested. Assessing the overlap of large marine protected areas with 14,172 species, we found large marine protected areas cover 4.4% of the ocean and at least some portion of the range of 83.3% of the species assessed. Of all species within large marine protected areas, 26.9% had at least 10% of their range represented, and this was projected to increase to 40.1% in 2100. Cumulative impacts were significantly higher within large marine protected areas than outside, refuting the …

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Nanosecond Electric Pulses Differentially Affect Inward And Outward Currents In Patch Clamped Adrenal Chromaffin Cells, Lisha Yang, Gale L. Craviso, P. Thomas Vernier, Indira Chatterjee, Normand Leblanc Jul 2017

Nanosecond Electric Pulses Differentially Affect Inward And Outward Currents In Patch Clamped Adrenal Chromaffin Cells, Lisha Yang, Gale L. Craviso, P. Thomas Vernier, Indira Chatterjee, Normand Leblanc

Bioelectrics Publications

This study examined the effect of 5 ns electric pulses on macroscopic ionic currents in whole-cell voltage-clamped adrenal chromaffin cells. Current-voltage (I-V) relationships first established that the early peak inward current was primarily composed of a fast voltage-dependent Na+ current (INa), whereas the late outward current was composed of at least three ionic currents: a voltage-gated Ca2+ current (ICa), a Ca2+-activated K+ current (IK(Ca)), and a sustained voltage-dependent delayed rectifier K+ current (IKV). A constant-voltage step protocol was next used to monitor peak inward and late …

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Population-Level Coordination Of Pigment Response In Individual Cyanobacterial Cells Under Altered Nitrogen Levels, Jaclyn Murton, Aparna Nagarajan, Amelia Y. Nguyen, Michelle Liberton, Harmony A. Hancock, Himadri B. Pakrasi, Jerilyn A. Timlin Jul 2017

Population-Level Coordination Of Pigment Response In Individual Cyanobacterial Cells Under Altered Nitrogen Levels, Jaclyn Murton, Aparna Nagarajan, Amelia Y. Nguyen, Michelle Liberton, Harmony A. Hancock, Himadri B. Pakrasi, Jerilyn A. Timlin

Biological Sciences Faculty Publications

Cyanobacterial phycobilisome (PBS) pigment-protein complexes harvest light and transfer the energy to reaction centers. Previous ensemble studies have shown that cyanobacteria respond to changes in nutrient availability by modifying the structure of PBS complexes, but this process has not been visualized for individual pigments at the single-cell level due to spectral overlap. We characterized the response of four key photosynthetic pigments to nitrogen depletion and repletion at the subcellular level in individual, live Synechocystis sp. PCC 6803 cells using hyperspectral confocal fluorescence microscopy and multivariate image analysis. Our results revealed that PBS degradation and re-synthesis comprise a rapid response to …

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Perspective: The Physics, Diagnostics, And Applications Of Atmospheric Pressure Low Temperature Plasma Sources Used In Plasma Medicine, M. Laroussi Jul 2017

Perspective: The Physics, Diagnostics, And Applications Of Atmospheric Pressure Low Temperature Plasma Sources Used In Plasma Medicine, M. Laroussi

Electrical & Computer Engineering Faculty Publications

Low temperature plasmas have been used in various plasma processing applications for several decades. But it is only in the last thirty years or so that sources generating such plasmas at atmospheric pressure in reliable and stable ways have become more prevalent. First, in the late 1980s, the dielectric barrier discharge was used to generate relatively large volume diffuse plasmas at atmospheric pressure. Then, in the early 2000s, plasma jets that can launch cold plasma plumes in ambient air were developed. Extensive experimental and modeling work was carried out on both methods and much of the physics governing such sources …

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A Variant Pfcrt Isoform Can Contribute To Plasmodium Falciparum Resistance To The First-Line Partner Drug Piperaquine, Satish K. Dhingra, Devasha Redhi, Jill M. Combrinck, Tomas Yeo, John Okombo, Philipp P. Henrich, Annie N. Cowell, Purva Gupta, Matthew L. Stegman, Jonathan M. Hoke, Roland A. Cooper, Elizabeth Winzeler, Sachel Mok, Timothy J. Egan, David A. Fidock May 2017

A Variant Pfcrt Isoform Can Contribute To Plasmodium Falciparum Resistance To The First-Line Partner Drug Piperaquine, Satish K. Dhingra, Devasha Redhi, Jill M. Combrinck, Tomas Yeo, John Okombo, Philipp P. Henrich, Annie N. Cowell, Purva Gupta, Matthew L. Stegman, Jonathan M. Hoke, Roland A. Cooper, Elizabeth Winzeler, Sachel Mok, Timothy J. Egan, David A. Fidock

Biological Sciences Faculty Publications

Current efforts to reduce the global burden of malaria are threatened by the rapid spread throughout Asia of Plasmodium falciparum resistance to artemisinin-based combination therapies, which includes increasing rates of clinical failure with dihydroartemisinin plus piperaquine (PPQ) in Cambodia. Using zinc finger nuclease-based gene editing, we report that addition of the C101F mutation to the chloroquine (CQ) resistance-conferring PfCRT Dd2 isoform common to Asia can confer PPQ resistance to cultured parasites. Resistance was demonstrated as significantly higher PPQ concentrations causing 90% inhibition of parasite growth (IC90) or 50% parasite killing (50% lethal dose [LD50]). This mutation …

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Ebola Virus - Epidemiology, Diagnosis, And Control: Threat To Humans, Lessons Learnt, And Preparedness Plans - An Update On Its 40 Year's Journey, Raj Kumar Singh, Kuldeep Dhama, Yashpal Singh Malik, Muthannan Andavar Ramakrishnan, Kumaragurubaran Karthik, Rekha Khandia, Ruchi Tiwari, Ashok Munjal, Mani Saminathan, Perumal Arumugam, Sunil Kumar Joshi Apr 2017

Ebola Virus - Epidemiology, Diagnosis, And Control: Threat To Humans, Lessons Learnt, And Preparedness Plans - An Update On Its 40 Year's Journey, Raj Kumar Singh, Kuldeep Dhama, Yashpal Singh Malik, Muthannan Andavar Ramakrishnan, Kumaragurubaran Karthik, Rekha Khandia, Ruchi Tiwari, Ashok Munjal, Mani Saminathan, Perumal Arumugam, Sunil Kumar Joshi

Bioelectrics Publications

Ebola virus (EBOV) is an extremely contagious pathogen and causes lethal hemorrhagic fever disease in man and animals. The recently occurred Ebola virus disease (EVD) outbreaks in the West African countries have categorized it as an international health concern. For the virus maintenance and transmission, the non-human primates and reservoir hosts like fruit bats have played a vital role. For curbing the disease timely, we need effective therapeutics/prophylactics, however, in the absence of any approved vaccine, timely diagnosis and monitoring of EBOV remains of utmost importance. The technologically advanced vaccines like a viral-vectored vaccine, DNA vaccine and virus-like particles are …

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Management Strategy Evaluation For The Atlantic Surfclam (Spisula Solidissima) Using A Spatially Explicit, Vessel-Based Fisheries Model, Kelsey M. Kuykendall, Eric N. Powell, John M. Klink, Paula T. Moreno, Robert T. Leaf Apr 2017

Management Strategy Evaluation For The Atlantic Surfclam (Spisula Solidissima) Using A Spatially Explicit, Vessel-Based Fisheries Model, Kelsey M. Kuykendall, Eric N. Powell, John M. Klink, Paula T. Moreno, Robert T. Leaf

CCPO Publications

The commercially valuable Atlantic surfclam (Spisula solidissima) is harvested along the northeastern continental shelf of the United States. Its range has contracted and shifted north, driven by warmer bottom water temperatures. Declining landings per unit of effort (LPUE) in the Mid-Atlantic Bight (MAB) is one result. Declining stock abundance and LPUE suggest that overfishing may be occurring off New Jersey. A management strategy evaluation (MSE) for the Atlantic surfclam is implemented to evaluate rotating closures to enhance Atlantic surfclam productivity and increase fishery viability in the MAB. Active agents of the MSE model are individual fishing vessels with …

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Computing Spatiotemporal Heat Maps Of Lipid Electropore Formation: A Statistical Approach, Willy Wriggers, Frederica Castellani, Julio A. Kovacs, P. Thomas Vernier Apr 2017

Computing Spatiotemporal Heat Maps Of Lipid Electropore Formation: A Statistical Approach, Willy Wriggers, Frederica Castellani, Julio A. Kovacs, P. Thomas Vernier

Mechanical & Aerospace Engineering Faculty Publications

We extend the multiscale spatiotemporal heat map strategies originally developed for interpreting molecular dynamics simulations of well-structured proteins to liquids such as lipid bilayers and solvents. Our analysis informs the experimental and theoretical investigation of electroporation, that is, the externally imposed breaching of the cell membrane under the influence of an electric field of sufficient magnitude. To understand the nanoscale architecture of electroporation, we transform time domain data of the coarse-grained interaction networks of lipids and solvents into spatial heat maps of the most relevant constituent molecules. The application takes advantage of our earlier graph-based activity functions by accounting for …

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A Balanced Approach To Adaptive Probability Density Estimation, Julio Kovacs, Cailee Helmick, Willy Wriggers Apr 2017

A Balanced Approach To Adaptive Probability Density Estimation, Julio Kovacs, Cailee Helmick, Willy Wriggers

Mechanical & Aerospace Engineering Faculty Publications

Our development of a Fast (Mutual) Information Matching (FIM) of molecular dynamics time series data led us to the general problem of how to accurately estimate the probability density function of a random variable, especially in cases of very uneven samples. Here, we propose a novel Balanced Adaptive Density Estimation (BADE) method that effectively optimizes the amount of smoothing at each point. To do this, BADE relies on an efficient nearest-neighbor search which results in good scaling for large data sizes. Our tests on simulated data show that BADE exhibits equal or better accuracy than existing methods, and visual tests …

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Quantitative Limits On Small Molecule Transport Via The Electropermeome - Measuring And Modeling Single Nanosecond Perturbations, Esin B. Sözer, Zachary A. Levine, P. Thomas Vernier Mar 2017

Quantitative Limits On Small Molecule Transport Via The Electropermeome - Measuring And Modeling Single Nanosecond Perturbations, Esin B. Sözer, Zachary A. Levine, P. Thomas Vernier

Bioelectrics Publications

The detailed molecular mechanisms underlying the permeabilization of cell membranes by pulsed electric fields (electroporation) remain obscure despite decades of investigative effort. To advance beyond descriptive schematics to the development of robust, predictive models, empirical parameters in existing models must be replaced with physics- and biology-based terms anchored in experimental observations. We report here absolute values for the uptake of YO-PRO-1, a small-molecule fluorescent indicator of membrane integrity, into cells after a single electric pulse lasting only 6 ns. We correlate these measured values, based on fluorescence microphotometry of hundreds of individual cells, with a diffusion-based geometric analysis of pore-mediated …

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Neurotrophic Factors Ngf, Gdnf And Ntn Selectively Modulate Hsv1 And Hsv2 Lytic Infection And Reactivation In Primary Adult Sensory And Autonomic Neurons, Andy Y. Yanez, Telvin Harrell, Heather J. Sriranganathan, Angela M. Ives, Andrea S. Bertke Mar 2017

Neurotrophic Factors Ngf, Gdnf And Ntn Selectively Modulate Hsv1 And Hsv2 Lytic Infection And Reactivation In Primary Adult Sensory And Autonomic Neurons, Andy Y. Yanez, Telvin Harrell, Heather J. Sriranganathan, Angela M. Ives, Andrea S. Bertke

Medical Diagnostics & Translational Sciences Faculty Publications

Herpes simplex viruses (HSV1 and HSV2) establish latency in peripheral ganglia after ocular or genital infection, and can reactivate to produce different patterns and frequencies of recurrent disease. Previous studies showed that nerve growth factor (NGF) maintains HSV1 latency in embryonic sympathetic and sensory neurons. However, adult sensory neurons are no longer dependent on NGF for survival, some populations cease expression of NGF receptors postnatally, and the viruses preferentially establish latency in different populations of sensory neurons responsive to other neurotrophic factors (NTFs). Thus, NGF may not maintain latency in adult sensory neurons. To identify NTFs important for maintaining HSV1 …

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Ticks Elicit Variable Fibrinogenolytic Activities Upon Feeding On Hosts With Different Immune Backgrounds, Ashish Vora, Vikas Taank, John F. Anderson, Durland Fish, Daniel E. Sonenshine, John D. Catravas, Hameeda Sultana, Girish Neelakanta Mar 2017

Ticks Elicit Variable Fibrinogenolytic Activities Upon Feeding On Hosts With Different Immune Backgrounds, Ashish Vora, Vikas Taank, John F. Anderson, Durland Fish, Daniel E. Sonenshine, John D. Catravas, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Ticks secrete several anti-hemostatic factors in their saliva to suppress the host innate and acquired immune defenses against infestations. Using Ixodes scapularis ticks and age-matched mice purchased from two independent commercial vendors with two different immune backgrounds as a model, we show that ticks fed on immunodeficient animals demonstrate decreased fibrinogenolytic activity in comparison to ticks fed on immunocompetent animals. Reduced levels of D-dimer (fibrin degradation product) were evident in ticks fed on immunodeficient animals in comparison to ticks fed on immunocompetent animals. Increased engorgement weights were noted for ticks fed on immunodeficient animals in comparison to ticks fed on …

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Turning Performance Of Brief Squid Lolliguncula Brevis During Attacks On Shrimp And Fish, Rachel A. Jastrebsky, Ian K. Bartol, Paul S. Krueger Mar 2017

Turning Performance Of Brief Squid Lolliguncula Brevis During Attacks On Shrimp And Fish, Rachel A. Jastrebsky, Ian K. Bartol, Paul S. Krueger

Biological Sciences Faculty Publications

Although squid are generally considered to be effective predators, little is currently known of how squid maneuver and position themselves during prey strikes. In this study, high-speed video and kinematic analyses were used to study attacks by the brief squid Lolliguncula brevis on both shrimp and fish. Squid attack successwas high (>80%) and three behavioral phases were identified: (1) approach, (2) strike and (3) recoil. Lolliguncula brevis demonstrated greater maneuverability (i.e. a smaller length-specific turning radius) and employed more body adjustments (i.e. mantle angle posturing) during approaches toward shrimp versus fish. Squid exhibited higher linear approach/strike velocities and accelerations …

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Characterization And Analysis Of Real-Time Capillary Convective Pcr Toward Commercialization, Xianbo Qiu, Shiyin Zhang, Lanju Mei, Di Wu, Ke Li, Shengxiang Ge, Xiangzhong Ye, Ningshao Xia, Michael G. Mauk Mar 2017

Characterization And Analysis Of Real-Time Capillary Convective Pcr Toward Commercialization, Xianbo Qiu, Shiyin Zhang, Lanju Mei, Di Wu, Ke Li, Shengxiang Ge, Xiangzhong Ye, Ningshao Xia, Michael G. Mauk

Mechanical & Aerospace Engineering Faculty Publications

Almost all the reported capillary convective polymerase chain reaction (CCPCR) systems to date are still limited to research use stemming from unresolved issues related to repeatability, reliability, convenience, and sensitivity. To move CCPCR technology forward toward commercialization, a couple of critical strategies and innovations are discussed here. First, single- and dual-end heating strategies are analyzed and compared between each other. Especially, different solutions for dual-end heating are proposed and discussed, and the heat transfer and fluid flow inside the capillary tube with an optimized dual-end heating strategy are analyzed and modeled. Second, real-time CCPCR is implemented with light-emitting diode and …

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Blubber Transciptome Response To Acute Stress Axis Activation Involves Transient Charges In Adipogenesis And Lipolysis In Fast-Adapted Marine Mammal, J. I. Khudyakov, C. D. Champagne, L. M. Meneghetti, D. E. Crocker Feb 2017

Blubber Transciptome Response To Acute Stress Axis Activation Involves Transient Charges In Adipogenesis And Lipolysis In Fast-Adapted Marine Mammal, J. I. Khudyakov, C. D. Champagne, L. M. Meneghetti, D. E. Crocker

Biological Sciences Faculty Publications

Stress can compromise an animal's ability to conserve metabolic stores and participate in energy-demanding activities that are critical for fitness. Understanding how wild animals, especially those already experiencing physiological extremes (e.g. fasting), regulate stress responses is critical for evaluating the impacts of anthropogenic disturbance on physiology and fitness, key challenges for conservation. However, studies of stress in wildlife are often limited to baseline endocrine measurements and few have investigated stress effects in fasting-adapted species. We examined downstream molecular consequences of hypothalamic-pituitary-adrenal (HPA) axis activation by exogenous adrenocorticotropic hormone (ACTH) in blubber of northern elephant seals due to the ease of …

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Experimental Impacts Of Climate Warming And Ocean Carbonation On Eelgrass Zostera Marina, Richard C. Zimmerman, Victoria J. Hill, Malee Jinuntuya, Billur Celebi, David Ruble, Miranda Smith, Tiffany Cedeno, W. Mark Swingle Feb 2017

Experimental Impacts Of Climate Warming And Ocean Carbonation On Eelgrass Zostera Marina, Richard C. Zimmerman, Victoria J. Hill, Malee Jinuntuya, Billur Celebi, David Ruble, Miranda Smith, Tiffany Cedeno, W. Mark Swingle

OES Faculty Publications

CO2 is a critical and potentially limiting substrate for photosynthesis of both terrestrial and aquatic ecosystems. In addition to being a climate-warming greenhouse gas, increasing concentrations of CO2 will dissolve in the oceans, eliciting both negative and positive responses among organisms in a process commonly known as ocean acidification. The dissolution of CO2 into ocean surface waters, however, also increases its availability for photosynthesis, to which the highly successful, and ecologically important, seagrasses respond positively. Thus, the process might be more accurately characterized as ocean carbonation. This experiment demonstrated that CO2 stimulation of primary production enhances …

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Multiple Mating By Females In The Chesapeake Bay Blue Crab Callinectes Sapidus Population, S. Wells, J. Mcconaugha, L. Horth Feb 2017

Multiple Mating By Females In The Chesapeake Bay Blue Crab Callinectes Sapidus Population, S. Wells, J. Mcconaugha, L. Horth

OES Faculty Publications

Mature females of the Chesapeake Bay (USA) blue crab Callinectes sapidus population mate multiple times. Microsatellite DNA analysis of sperm stored in the spermathecae has shown that virtually all (~97%, 104 out of 107) females collected in a 2009−2010 study mated with at least 2 males. Enumeration of stored sperm revealed that despite multiple mating, some females did not have enough sperm to fulfill their lifetime reproductive potential, suggesting that female blue crabs may experience varying levels of sperm limitation. This could result from multiple factors. The average body size of males in the population has decreased, which reduces the …

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