Physical Sciences and Mathematics Commons^™

Overlap Matrix Completion For Predicting Drug-Associated Indications, Menhyun Yang, Huimin Luo, Yaohang Li, Fang-Xiang Wu, Jianxin Wang

Computer Science Faculty Publications

Identification of potential drug-associated indications is critical for either approved or novel drugs in drug repositioning. Current computational methods based on drug similarity and disease similarity have been developed to predict drug-disease associations. When more reliable drug- or disease-related information becomes available and is integrated, the prediction precision can be continuously improved. However, it is a challenging problem to effectively incorporate multiple types of prior information, representing different characteristics of drugs and diseases, to identify promising drug-disease associations. In this study, we propose an overlap matrix completion (OMC) for bilayer networks (OMC2) and tri-layer networks (OMC3) to predict potential drug-associated …

Growth Phase Proteomics Of The Heterotrophic Marine Bacterium Ruegeria Pomeroyi, Dasha Krayushkina, Emma Timmins-Schiffman, Jessica Faux, Damon H. May, Michael Riffle, H. Rodger Harvey, Brook L. Nunn

OES Faculty Publications

The heterotrophic marine bacterium, Ruegeria pomeroyi, was experimentally cultured under environmentally realistic carbon conditions and with a tracer-level addition of ¹³C-labeled leucine to track bacterial protein biosynthesis through growth phases. A combination of methods allowed observation of real-time bacterial protein production to understand metabolic priorities through the different growth phases. Over 2000 proteins were identified in each experimental culture from exponential and stationary growth phases. Within two hours of the ¹³C-labeled leucine addition, R. pomeroyi significantly assimilated the newly encountered substrate into new proteins. This dataset provides a fundamental baseline for understanding growth phase differences in molecular …

Seaflow Data V1, High-Resolution Abundance, Size And Biomass Of Small Phytoplankton In The North Pacific, François Ribalet, Chris Berthiaume, Annette Hynes, Jarred Swalwell, Michael Carlson, Sophie Clayton, Gwenn Hennon, Camille Poirier, Eric Shimabukuro, Angelicque White, E. Virginia Armhurst

OES Faculty Publications

SeaFlow is an underway flow cytometer that provides continuous shipboard observations of the abundance and optical properties of small phytoplankton (μm in equivalent spherical diameter, ESD). Here we present data sets consisting of SeaFlow-based cell abundance, forward light scatter, and pigment fluorescence of individual cells, as well as derived estimates of ESD and cellular carbon content of picophytoplankton, which includes the cyanobacteria Prochlorococcus, Synechococcus and small-sized Crocosphaera (μm ESD), and picophytoplankton and nanophytoplankton (2–5 μm ESD). Data were collected in surface waters (≈5 m depth) from 27 oceanographic cruises carried out in the Northeast Pacific Ocean between 2010 and 2018. …

How Oxygen Availability Affects The Antimicrobial Efficacy Of Host Defense Peptides: Lessons Learned From Studying The Copper-Binding Peptides Piscidins 1 And 3, Adenrele Oludiran, David S. Courson, Malia D. Stuart, Anwar R. Radwan, John C. Putsma, Myriam L. Cotten, Erin B. Purcell

Chemistry & Biochemistry Faculty Publications

The development of new therapeutic options against Clostridioides difficile (C. difficile) infection is a critical public health concern, as the causative bacterium is highly resistant to multiple classes of antibiotics. Antimicrobial host-defense peptides (HDPs) are highly effective at simultaneously modulating the immune system function and directly killing bacteria through membrane disruption and oxidative damage. The copper-binding HDPs piscidin 1 and piscidin 3 have previously shown potent antimicrobial activity against a number of Gram-negative and Gram-positive bacterial species but have never been investigated in an anaerobic environment. Synergy between piscidins and metal ions increases bacterial killing aerobically. Here, we …

Closing The Oxygen Mass Balance In Shallow Coastal Ecosystems, Matthew H. Long, Jennie E. Rheuban, Daniel C. Mccorkle, David J. Burdige, Richard C. Zimmerman

OES Faculty Publications

The oxygen concentration in marine ecosystems is influenced by production and consumption in the water column and fluxes across both the atmosphere-water and benthic-water boundaries. Each of these fluxes has the potential to be significant in shallow ecosystems due to high fluxes and low water volumes. This study evaluated the contributions of these three fluxes to the oxygen budget in two contrasting ecosystems, a Zostera marina (eelgrass) meadow in Virginia, U.S.A., and a coral reef in Bermuda. Benthic oxygen fluxes were evaluated by eddy covariance. Water column oxygen production and consumption were measured using an automated water incubation system. Atmosphere-water …

Monarch Science Observer, Volume 1, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Fall 2019, issue of Monarch Science Observer, ODU Colleges of Sciences Newsletter.

Global Conservation Status And Threat Patterns Of The World’S Most Prominent Forage Fishes (Teleostei, Clupeiformes), Tiffany L. Birge

Biological Sciences Theses & Dissertations

Conserving biodiversity is one of the greatest ethical responsibilities and challenges humans face. Understanding the conservation status of taxonomic groups provides a systematic way to prioritize efforts to combat biodiversity loss. The 405 species within the order Clupeiformes are the herrings, shads, sardines, anchovies, menhadens and relatives that include many of the most important marine forage fishes. These small, schooling fishes are economically, ecologically and culturally significant globally. Despite their contribution to global fisheries and our increasing reliance on these fishes for food and industrial commodities, they are generally poorly known with limited information regarding basic biology and population trends. …

Tick Control Methods For Amblyomma Americanum In Virginia: Applications And Modeling, Alexis Lynn White

Biological Sciences Theses & Dissertations

Tick-borne diseases continue to increase in the United States, and yet no comprehensive method of tick control currently exists. The lone star tick, Amblyomma americanum, is an aggressive human-biting tick and vector of several pathogens which effect both humans and other animals. Standard control methods do not work as well for A. americanum as they do for the more commonly studied blacklegged tick, Ixodes scapularis. TickBot, a tick-killing robot, is a potential method to control A. americanum that lures ticks to its path with carbon dioxide and the ticks die from contact with a permethrin-treated cloth that is …

Acute Systemic Inflammatory Response To Lipopolysaccharide Stimulation In Pigs Divergently Selected For Residual Feed Intake, Haibo Liu, Kristina M. Feye, Yet T. Nguyen, Anoosh Rakhshandeh, Crystal L. Loving, Jack C. M. Sekkers, Nicholas K. Gabler, Christopher K. Tuggle

Mathematics & Statistics Faculty Publications

Background: It is unclear whether improving feed efficiency by selection for low residual feed intake (RFI) compromises pigs’ immunocompetence. Here, we aimed at investigating whether pig lines divergently selected for RFI had different inflammatory responses to lipopolysaccharide (LPS) exposure, regarding to clinical presentations and transcriptomic changes in peripheral blood cells.

Results: LPS injection induced acute systemic inflammation in both the low-RFI and high-RFI line (n = 8 per line). At 4 h post injection (hpi), the low-RFI line had a significantly lower (p= 0.0075) mean rectal temperature compared to the high-RFI line. However, no significant differences in complete blood count …

Odu Launches Open Seas Technology Innovation Hub, News @ Odu

News Items

No abstract provided.

Nutrient Controls Over Cyanobacterial Synthesis Of The Neurotoxin Β-N-Methylamino-L-Alanine (Bmaa) And Its Potential Accumulation In The Blue Crab (Callinectes Sapidus), Madeline M. Hummel

OES Theses and Dissertations

Cyanobacteria are known to produce a variety of toxins that negatively impact both aquatic and terrestrial organisms. One putative neurotoxic compound is the non-protein amino acid β-N-methylamino-L-alanine (BMAA), which has epidemiological linkages to the development of several human neurological diseases. Three cyanobacterial species thought to produce BMAA —Microcystis aeruginosa, Synechococcus bacillaris, and Nostoc sp. —were grown in nutrient replete cultures to examine its synthesis and cellular distribution over a growth cycle. Production of BMAA was also examined in nutrient (nitrogen and phosphorus) deplete cultures of Microcystis aeruginosa. In addition, natural assemblages of phytoplankton dominated by …

Lipid Biomarkers Of Bering And Chukchi Sea Euphausiids And Their Application To Diet History, Rachel L. Pleuthner

OES Theses and Dissertations

In the eastern Bering Sea, Thysanoessa raschii are the most abundant krill species and a keystone trophic member that serve as both an important grazer and link to upper level consumers. In this system krill experience large annual variation in food resources, especially during ice advance and retreat; multiple lipid classes are used to temper the effects of those fluctuations, as well as to fuel reproduction and growth. Two shipboard feeding experiments that occurred during late spring and early summer of 2010, respectively, monitored the lipid retention in adult T. raschii and examined the fluctuation of specific lipid biomarkers under …

Protocol Measuring Horizontal Gene Transfer From Algae To Non-Photosynthetic Organisms, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Horizontal gene transfer (HGT) is a natural process for an organism to transfer genetic material to another organism that is a completely different species, for example, from a blue-green alga to a non-photosynthetic bacterium. The phenomenon of HGT is not only of an interest to the science of molecular genetics and biology, but also to the biosafety issue of genetic engineering. The novel protocol reported here for the first time teaches how to measure HGT from a genetically engineered (GE) blue-green alga (gene donor) to wild-type E. coli (recipient). This novel protocol can be used to measure HGT frequency for …

Coupling Metaproteomics With Taxonomy To Determine Responses Of Bacterioplankton To Organic Perturbations In The Western Arctic Ocean, Molly P. Mikan

OES Theses and Dissertations

Understanding how the functionality of marine microbial communities change over time and space, and which taxonomic groups dominate distinct metabolic pathways, are essential to understanding the ecology of these microbiomes and the factors contributing to their regulation of elemental cycles in the oceans. The primary goal of this dissertation was to investigate the community metabolic and taxonomic responses and the degradation potential of two compositionally distinct marine microbiomes within the shallow shelf ecosystem of the Chukchi Sea after rapid fluctuations in algal organic matter availability. Novel bioinformatics tools were collaboratively developed and used together with community proteomics (metaproteomics) to characterize …

Study Of The Effects Of Silver Ions And Silver Nanoparticles On Embryonic Development, Martha Sharisha Johnson

Biomedical Sciences Theses & Dissertations

This dissertation focuses on the study of the toxicity of metal nanoparticles (NPs) and their ions on the development of zebrafish embryos, aiming to understand unique biological effects of NPs and ions, and design new in vivo assays to characterize the toxicity of these metal NPs and metal ions. Currently, the underlying molecular mechanisms of biological effects of nanomaterials are partially understood. Some studies assume that the toxic effects of NPs can be attributed to the release of their ions. We investigate the effects of silver NPs (Ag NPs) and silver ions (Ag+ ions) on the embryonic development of zebrafish …

Cryptic Herbivorous Invertebrates Restructure The Composition Of Degraded Coral Reef Communities In The Florida Keys, Florida, Usa, Angelo Jason Spadaro

Biological Sciences Theses & Dissertations

Coral reefs have been on a trajectory of decline for nearly a century due to a variety of factors that have contributed to the shift in these communities away from dominance by reef-building corals, with commensurate changes on community composition and function. Florida’s reefs are a compelling example of a degraded system that has undergone a phase shift, and thus offered an excellent model system for my study of the effects of grazing by cryptic herbivores on community composition and their potential restoration value. I had four major objectives: (1) determine the suitability of Maguimithrax spinosissimus for manipulating grazing intensity …

Sponge Community Biocomplexity, Competition, And Functional Significance In Hard-Bottom Habitats Of The Florida Keys, Fl (Usa), Marla Maxine Valentine

Biological Sciences Theses & Dissertations

Sponges can have powerful effects on ecosystem processes in shallow, tropical marine ecosystems and are an integral component of the bentho-pelagic cycle of nutrients, via filtering of dissolved and particulate organic matter from the water column. The diversity of marine communities is thought to play a determining role in intensity of ecosystem processes; thus the loss of taxa alters community function and by extension ecosystem processes. Coastal sponge populations worldwide are increasingly exposed to declining water quality that in several regions has resulted in mass sponge mortalities and reduced sponge diversity. In the Florida Keys (Florida, USA), for example, frequent …

Highly Accurate Fragment Library For Protein Fold Recognition, Wessam Elhefnawy

Computer Science Theses & Dissertations

Proteins play a crucial role in living organisms as they perform many vital tasks in every living cell. Knowledge of protein folding has a deep impact on understanding the heterogeneity and molecular functions of proteins. Such information leads to crucial advances in drug design and disease understanding. Fold recognition is a key step in the protein structure discovery process, especially when traditional computational methods fail to yield convincing structural homologies. In this work, we present a new protein fold recognition approach using machine learning and data mining methodologies.

First, we identify a protein structural fragment library (Frag-K) composed of a …

Does Helping-At-The-Nest Help? The Case Of The Acorn Woodpecker, Walter D. Koenig, Eric L. Walters, Sahas Barve

Biological Sciences Faculty Publications

Cooperative breeding groups often involve "helpers-at-the-nest"; indeed, such behavior typically defines this intriguing breeding system. In few cases, however, has it been demonstrated that feeding nestlings by helpers, rather than some other behavior associated with helpers' presence, leads to greater reproductive success. One prediction of the hypothesis that feeding behavior per se is responsible for the fitness benefits conferred by helpers is that there should be close congruence between the patterns of helping-at-the-nest and the fitness effects of helpers. Here we look for such a relationship in the cooperatively breeding acorn woodpecker (Melanerpes formicivorus) in order to begin …

Bomb Radiocarbon Age Validation For The Long-Lived, Unexploited Arctic Fish Species Coregonus Clupeaformis, John M. Casselman, Cynthia M. Jones, Steven E. Campana

OES Faculty Publications

The growth rates of freshwater fish in the Arctic would be expected to be very low, but some previous studies of lake whitefish (Coregonus clupeaformis) have reported relatively rapid growth and longevity estimates of less than 15 years. We used bomb radiocarbon chronologies to validate an ageing method based on otolith sections for lake whitefish in both an unexploited Arctic lake (MacAlpine Lake; longevity 50 years) and a lightly exploited temperate population (Lake Simcoe; longevity 49 years). Our results confirm previous suggestions that other ageing methods can seriously underestimate lake whitefish age after ~5–8 years. A Chapman–Robson estimate …

Dinitrogen Fixation Across Physico-Chemical Gradients Of The Eastern Tropical North Pacific Oxygen Deficient Zone, C. R. Selden, M. R. Mulholland, P.W. Bernhardt, B. Widner, A. Macías-Tapia, Q. Ji, A. Jayakumar

OES Faculty Publications

The Eastern Tropical North Pacific Ocean hosts one of the world's largest oceanic oxygen deficient zones (ODZs). Hot spots for reactive nitrogen (N_r) removal processes, ODZs generate conditions proposed to promote N_r inputs via dinitrogen (N₂) fixation. In this study, we quantified N₂ fixation rates by ¹⁵N tracer bioassay across oxygen, nutrient, and light gradients within and adjacent to the ODZ. Within subeuphotic oxygen‐deplete waters, N₂ fixation was largely undetectable; however, addition of dissolved organic carbon stimulated N₂ fixation in suboxic (μmol/kg O₂) waters, suggesting that diazotroph communities are …

A Full-Ocean-Depth Rated Modular Lander And Pressure-Retaining Sampler Capable Of Collecting Hadal-Endemic Microbes Under In Situ Conditions, Logan M. Peoples, Matthew Norenberg, David Price, Madeline Mcgoldrick, Mark Novotny, Alexander Bochdansky, Douglas H. Bartlett

OES Faculty Publications

The hadal zone remains one of the least studied environments because of its inaccessibility, in part because of hydrostatic pressures extending to 110 MPa. Few instruments are capable of sampling from such great depths. We have developed a full-ocean-depth-capable lander that can be fit with sampling packages for the collection of still images, video, motile megafauna, and hadal seawater. One payload includes a pressure-retaining sampler (PRS) able to maintain seawater samples under in situ pressure during recovery. We describe the technical specifications of the lander and the PRS and preliminary results from three deployments at depths in excess of 10,700 …

End-To-End Learning Via A Convolutional Neural Network For Cancer Cell Line Classification, Darlington A. Akogo, Xavier-Lewis Palmer

Electrical & Computer Engineering Faculty Publications

Purpose: Computer vision for automated analysis of cells and tissues usually include extracting features from images before analyzing such features via various machine learning and machine vision algorithms. The purpose of this work is to explore and demonstrate the ability of a Convolutional Neural Network (CNN) to classify cells pictured via brightfield microscopy without the need of any feature extraction, using a minimum of images, improving work-flows that involve cancer cell identification.

Design/methodology/approach: The methodology involved a quantitative measure of the performance of a Convolutional Neural Network in distinguishing between two cancer lines. In their approach, they trained, validated and …

Sponges Structure Water-Column Characteristics In Shallow Tropical Coastal Ecosystems, Marla M. Valentine, Mark J. Butler Iv

Biological Sciences Faculty Publications

Sponges can have powerful effects on ecosystem processes in shallow tropical marine ecosystems. They drive benthic-pelagic coupling by filtering dissolved and particulate organic matter from the water column, alter water chemistry in association with their symbiotic microorganisms, and increase habitat structural complexity. Anthropogenic degradation of coastal waters is widespread and can reduce the density and diversity of foundation species such as sponges, potentially diminishing their contributions to ecosystem processes. We used a novel mesocosm design that minimized artifacts associated with traditional single-species and closed-system filtration experiments to examine the effects of water turnover and sponge biomass on water-column properties. Using …

Modeling The Seasonal Cycle Of Iron And Carbon Fluxes In The Amundsen Sea Polynya, Antarctica, P. St-Laurent, P. L. Yager, R. M. Sherrell, H. Oliver, M. S. Dinniman, S. E. Stammerjohn

CCPO Publications

The Amundsen Sea Polynya (ASP) is distinguished by having the highest net primary production per unit area in the coastal Antarctic. Recent studies have related this high productivity to the presence of fast-melting ice shelves, but the mechanisms involved are not well understood. In this study we describe the first numerical model of the ASP to represent explicitly the ocean-ice interactions, nitrogen and iron cycles, and the coastal circulation at high resolution. The study focuses on the seasonal cycle of iron and carbon, and the results are broadly consistent with field observations collected during the summer of 2010–2011. The simulated …

Patterns Of Diatom Diversity Correlate With Dissolved Trace Metal Concentrations And Longitudinal Position In The Notheast Pacific Coastal Offshore Transition Zone, P. Dreux Chappell, E. Virginia Armbrust, Katherine A. Barbeau, Randelle M. Bundy, Jagruti Vedamati, Bethany D. Jenkins

OES Faculty Publications

Diatoms are important primary producers in the northeast Pacific Ocean, with their productivity closely linked to pulses of trace elements in the western high nitrate, low chlorophyll (HNLC) region of the oceanographic time series transect 'Line P.' Recently, the coastal-HNLC transition zone of the Line P transect was identified as a hotspot of phytoplankton productivity, potentially controlled by a combination of trace element and macronutrient concentrations. Here we describe diatom community composition in the eastern Line P transect, including the coastal- HNLC transition zone, with a method using high-throughput sequencing of diatom 18S gene amplicons. We identified significant correlations between …

Metaproteomics Reveal That Rapid Perturbations In Organic Matter Prioritize Functional Restructuring Over Taxonomy In Western Arctic Ocean Microbiomes, Molly P. Mikan, H. Rodger Harvey, Emma Timmins-Schiffman, Michael Riffle, Damon H. May, Ian Salter, William S. Noble, Brook L. Nunn

OES Faculty Publications

We examined metaproteome profiles from two Arctic microbiomes during 10-day shipboard incubations to directly track early functional and taxonomic responses to a simulated algal bloom and an oligotrophic control. Using a novel peptide-based enrichment analysis, significant changes (p-value < 0.01) in biological and molecular functions associated with carbon and nitrogen recycling were observed. Within the first day under both organic matter conditions, Bering Strait surface microbiomes increased protein synthesis, carbohydrate degradation, and cellular redox processes while decreasing C1 metabolism. Taxonomic assignments revealed that the core microbiome collectively responded to algal substrates by assimilating carbon before select taxa utilize and metabolize nitrogen intracellularly. Incubations of Chukchi Sea bottom water microbiomes showed similar, but delayed functional responses to identical treatments. Although 24 functional terms were shared between experimental treatments, the timing, and degree of the remaining responses were highly variable, showing that organic matter perturbation directs community functionality prior to alterations to the taxonomic distribution at the microbiome class level. The dynamic responses of these two oceanic microbial communities have important implications for timing and magnitude of responses to organic perturbations within the Arctic Ocean and how community-level functions may forecast biogeochemical gradients in oceans.

Ebullition Of Oxygen From Seagrasses Under Supersaturated Conditions, Matthew H. Long, Kevin Sutherland, Scott D. Wankel, David J. Burdige, Richard C. Zimmerman

OES Faculty Publications

Gas ebullition from aquatic systems to the atmosphere represents a potentially important fraction of primary production that goes unquantified by measurements of dissolved gas concentrations. Although gas ebullition from photosynthetic surfaces has often been observed, it is rarely quantified. The resulting underestimation of photosynthetic activity may significantly bias the determination of ecosystem trophic status and estimated rates of biogeochemical cycling from in situ measures of dissolved oxygen. Here, we quantified gas ebullition rates in Zostera marina meadows in Virginia, U.S.A. using simple funnel traps and analyzed the oxygen concentration and isotopic composition of the captured gas. Maximum hourly rates of …

Adaptive Signatures In Thermal Performance Of The Temperate Coral Astrangia Poculata, H. E. Aichelman, Richard C. Zimmerman, Daniel J. Barshis

Biological Sciences Faculty Publications

Variation in environmental characteristics and divergent selection pressures can drive adaptive differentiation across a species' range. Astrangia poculata is a temperate scleractinian coral that provides unique opportunities to understand the roles of phenotypic plasticity and evolutionary adaptation in coral physiological tolerance limits. A. poculata inhabits hard bottom ecosystems from the northwestern Atlantic to the Gulf of Mexico and withstands an annual temperature range up to 20° C. Additionally, A. poculata is facultatively symbiotic and co-occurs in both symbiotic ("brown") and aposymbiotic ("white") states. Here, brown and white A. poculata were collected from Virginia (VA) and Rhode Island (RI), USA and …

Condensation And Polymerization Explain The Humification Of Lignin Into Aliphatic And Aromatic Structures In Soil, Patrick G. Hatcher, Hongmei Chen, Seyyedhadi Khatami, Derek C. Waggoner

Chemistry & Biochemistry Faculty Publications

Soil organic matter (SOM) constitutes a global reservoir of carbon that is more than twice that of either atmospheric carbon or aquatic carbon; however, the manner in which it forms from degraded plant biomass is poorly understood. Some have recently questioned whether plant biomass is involved directly in SOM formation and suggest that it is microbial carbon that constitutes the main source of stable SOM. Such a view implies that above and below ground plant biomass is rapidly decomposed and mineralized. This view contrasts significantly with traditional ones that involve the transformation of plant biomass to recalcitrant humic materials fueled …