Life Sciences Commons^™

Patterns Of Gene Expression From Human Costal Cartilage In Relation To The Chest Wall Deformity Pectus Carinatum, Janna E. Grubbs

Biological Sciences Theses & Dissertations

Cartilage deformities within the human chest wall, specifically pectus excavatum (PE) and pectus carinatum (PC) are common (1/400-1/1000) and yet, despite their clinical significance, are some of the least studied disorders pertaining to cartilage [1]. The costal cartilage connecting "false ribs" 8-10 to the sternum is often abnormally grown and can lead to formation of a severely sunken "funnel" chest (PE) or push outwards to form a "pigeon" chest (PC). Both conditions can have impact on the diaphragm, heart, lungs, and psychological function. An established ratio of PE and PC in males to females is 4:1, indicating a sex-linked male …

Basin Isolation And Oceanographic Features Influencing Lineage Divergence In The Humbug Damselfish (Dascyllus Aruanus) In The Coral Triangle, Jeremy M. Raynal

Biological Sciences Theses & Dissertations

The Coral Triangle (CT) is a hotspot for marine species diversity as well as for intraspecific genetic diversity. Here, nuclear RAG2 and mitochondrial D-Loop genes were used to identify deep genetic divergence among Dascyllus aruanus (Linnaeus, 1758) populations across relatively short scales within the CT. Mitochondrial clades different by greater than 20 mutational steps were geographically isolated from one another across the distance between Java and the Lesser Sunda Islands, and also east and west across the Philippines. Evidence for population structure in the Sulu Sea and at the Lesser Sunda Islands is also identified. The results suggest that the …

Comparative Phylogeography Of The Emperor Snappers Lethrinus Lentjan And Lethrinus Harak (Lethrinidae: Percoidei) In The Coral Triangle, Andrew B. Hines

Biological Sciences Theses & Dissertations

Many questions remain regarding the origins of the well-known peak in marine biodiversity found in the Coral Triangle. Barriers to gene flow may promote lineage diversification and provide the potential for speciation contributing to the high biodiversity in this area. Population structure was examined in two species of Emperor Snappers (Lethrinidae), Lethrinus harak and Lethrinus lentjan. These species were selected because they share similar life-history traits and geographic distributions, but differ in their habitat preferences. Specimens were collected from within the Coral Triangle as well as other localities across the Indo-Pacific. To investigate phylogeographic patterns and structure a hypervariable …

Uncoupling Between Dinitrogen Fixation And Primary Productivity In The Eastern Mediterranean Sea, Eyal Rahav, Barak Herut, Noga Stambler, Edo Bar-Zeev, Margaret R. Mulholland

OES Faculty Publications

In the nitrogen (N)-impoverished photic zones of many oceanic regions, prokaryotic organisms fixing atmospheric dinitrogen (N₂; diazotrophs) supply an essential source of new nitrogen and fuel primary production. We measured dinitrogen fixation and primary productivity (PP) during the thermally stratified summer period in different water regimes of the oligotrophic eastern Mediterranean Sea, including the Cyprus Eddy and the Rhodes Gyre. Low N₂ fixation rates were measured (0.8-3.2μmol N m-2 d-1) excluding 10-fold higher rates in the Rhodes Gyre and Cyprus Eddy (~20μmol N m^-2 d^-1). The corresponding PP increased from east to west (200-2500μmol …

Undergraduate Research In Biology: Field Studies, Eric Walters

Undergraduate Research Symposium

Chair: Eric Walters, Department of Biological Sciences

Undergraduate Research In Biology: Ticks, Holly Gaff

Undergraduate Research Symposium

Chair: Dr. Holly Gaff, Department of Biological Sciences

Undergraduate Research In Biology: Aquatic, David Gauthier

Undergraduate Research Symposium

Chair: Dr. David Gauthier, Department of Biological Sciences

Systematic Ichthyofaunal Surveys In Urban And Non-Urban Watersheds, Eugene G. Maurakis, David V. Grimes, Amanda Schutt, Suzy Short

Virginia Journal of Science

Objectives were to model fish species richness relative to natural and anthropogenic variables in Quantico Creek, a forested undisturbed stream environment, and Cameron Run, a highly disturbed urban stream environment in the lower Piedmont-Fall Line region of the Potomac River watershed. Species richness in all stream orders (e.g. avg. range=2.5-9.65 in 1st-3rd orders) of Quantico Creek were significantly higher than those (e.g. avg. range=2.1- 7.6 in 1st -4th orders) of Cameron Run. Fish species richness in Quantico Creek watershed can be modeled by eight factors: season, stream order, elevation, river km, stream width and depth, watershed size, and percent of …

Applications For Pulse Power Using Nanosecond Pulsed Electric Fields (Nspefs) In Cell Biology And Cancer Treatment, Stephen J. Beebe

Bioelectrics Publications

No abstract provided.

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 …

Intensity-Based Skeletonization Of Cryoem Gray-Scale Images Using A True Segmentation-Free Algorithm, Kamal Al Nasr, Chunmei Liu, Mugizi Rwebangira, Legand Burge, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viruses and ribosomes. At medium resolution, the positions of the atoms are not visible and the process cannot proceed. The medium-resolution images produced by cryo-electron microscopy are used to derive the atomic structure of the proteins in de novo modeling. The skeletons of the 3D gray-scale images are used to interpret important information that is helpful in de novo modeling. Unfortunately, not all features of the …

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 …

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 …

The Use Of Metagenomic Approaches To Analyze Changes In Microbial Communities, Girish Neelakanta, Hameeda Sultana

Biological Sciences Faculty Publications

Microbes are the most abundant biological entities found in the biosphere. Identification and measurement of microorganisms (including viruses, bacteria, archaea, fungi, and protists) in the biosphere cannot be readily achieved due to limitations in culturing methods. A non-culture based approach, called “metagenomics”, was developed that enabled researchers to comprehensively analyse microbial communities in different ecosystems. In this study, we highlight recent advances in the field of metagenomics for analyzing microbial communities in different ecosystems ranging from oceans to the human microbiome. Developments in several bioinformatics approaches are also discussed in context of microbial metagenomics that include taxonomic systems, sequence databases, …

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 …

Habitat Availability And Heterogeneity And The Indo-Pacific Warm Pool As Predictors Of Marine Species Richness In The Tropical Indo-Pacific, Jonnell C. Sanciangco, Kent E. Carpenter, Peter J. Etnoyer, Fabio Moretzsohn

Biological Sciences Faculty Publications

Range overlap patterns were observed in a dataset of 10,446 expert-derived marine species distribution maps, including 8,295 coastal fishes, 1,212 invertebrates (crustaceans and molluscs), 820 reef-building corals, 50 seagrasses, and 69 mangroves. Distributions of tropical Indo-Pacific shore fishes revealed a concentration of species richness in the northern apex and central region of the Coral Triangle epicenter of marine biodiversity. This pattern was supported by distributions of invertebrates and habitat-forming primary producers. Habitat availability, heterogeneity, and sea surface temperatures were highly correlated with species richness across spatial grains ranging from 23,000 to 5,100,000 km(2) with and without correction for autocorrelation. The …

Corrected Numbers For Fish On Red List, Bruce B. Collette, Beth Polidoro, Kent Carpenter

Biological Sciences Faculty Publications

(First paragraph) Kelly Swing gives inaccurate numbers for marine fish species on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. He also mistakenly conflates the scientific process of species assessment for the Red List with the separate political process of IUCN member voting (Nature 494, 314; 2013).

Phytoplankton In Virginia Lakes And Reservoirs, Harold G. Marshall

Biological Sciences Faculty Publications

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 …

Pronounced Genetic Structure In A Highly Mobile Coral Reef Fish, Caesio Cuning, In The Coral Triangle, Amanda S. Ackiss, Shinta Pardede, Eric D. Crandall, Ma Carmen A. Ablan-Lagman, Ambariyanto, November Romena, Paul H. Barber, Kent E. Carpenter

Biological Sciences Faculty Publications

The redbelly yellowtail fusilier Caesio cuning has a tropical Indo-West Pacific range that straddles the Coral Triangle, a region of dynamic geological history and the highest marine biodiversity on the planet. Previous genetic studies in the Coral Triangle indicate the presence of multiple limits to connectivity. However, these studies have focused almost exclusively on benthic, reef-dwelling species. Schooling, reef-associated fusiliers (Perciformes: Caesionidae) account for a sizable portion of the annual reef catch in the Coral Triangle, yet to date, there have been no indepth studies on the population structure of fusiliers or other mid-water, reef-associated planktivores across this region. We …

Thalassiosira Spp. Community Composition Shifts In Response To Chemical And Physical Forcing In The Northeast Pacific Ocean, P. Dreux Chappell, Leann P. Whitney, Traci L. Haddock, Susanne Menden-Deuer, Eric G. Roy, Mark L. Wells, Bethany D. Jenkins

Biological Sciences Faculty Publications

Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a 3-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA) method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., …

Heritable Melanism And Parasitic Infection Both Result In Black-Spotted Mosquitofish, Lisa Horth, David Gauthier, Wolfgang Vogelbein

Biological Sciences Faculty Publications

Male Gamhusia holhrooki (Eastern Mosquitofish) express a heritable pigmentation polymorphism approximate to 99% of males are silver, and only approximate to 1% have a melanic, black-spotted pattern. Sex-linkage, an autosomal modifier, and temperature control the expression of this heritable melanism. In many teleosts, melanin also accumulates around the site of parasitic invasion. We have identified black-spot disease in wild mosquitofish from their native habitat. Here, we demonstrate convergence upon the black-pigmented phenotype through two means: 1) heritable melanism, and 2) melanic spotting on the silver genotype that results from infection with immature encysted trematodes. Females are silver and express greater …

Chemical Defense Of An Asian Snake Reflects Local Availability Of Toxic Prey And Hatchling Diet, D. A. Hutchinson, A. H. Savitzky, G. M. Burghardt, C. Nguyen, J. Meinwald, F. C. Schroeder, A. Mori

Biological Sciences Faculty Publications

Species that sequester toxins from prey for their own defense against predators may exhibit population-level variation in their chemical arsenal that reflects the availability of chemically defended prey in their habitat. Rhabdophis tigrinus is an Asian snake that possesses defensive glands in the skin of its neck (nuchal glands'), which typically contain toxic bufadienolide steroids that the snakes sequester from consumed toads. In this study, we compared the chemistry of the nuchal gland fluid of R.tigrinus from toad-rich and toad-free islands in Japan and determined the effect of diet on the nuchal gland constituents. Our findings demonstrate that captive-hatched juveniles …

Identifying Requirements For The Invasion Of A Tick Species And Tick-Borne Pathogen Through Ticksim, Holly Gaff, Robyn Nadolny

Biological Sciences Faculty Publications

Ticks and tick-borne diseases have been on the move throughout the United State over the past twenty years. We use an agent-based model, TICKSIM, to identify the key parameters that determine the success of invasion of the tick and if that is successful, the success of the tick-borne pathogen. We find that if an area has competent hosts, an initial population of ten ticks is predicted to always establish a new population. The establishment of the tick-borne pathogen depends on three parameters: the initial prevalence in the ten founding ticks, the probability that a tick infects the longer-lived hosts and …

The Role Of P38 Mapk In The Aetiopathogenesis Of Psoriasis And Psoriatic Arthritis, Athanasios Mavropoulos, Eirini I. Rigopoulou, Christos Liaskos, Dimitrios P. Bogdanos, Lazaros I. Sakkas

Biological Sciences Faculty Publications

The pathogenetic mechanisms responsible for the induction of immune-mediated disorders, such as psoriasis, remain not well characterized. Molecular signaling pathways are not well described in psoriasis, as well as psoriatic arthritis, which is seen in up to 40% of patients with psoriasis. Signaling pathway defects have long been hypothesized to participate in the pathology of psoriasis, yet their implication in the altered psoriatic gene expression still remains unclear. Emerging data suggest a potential pathogenic role for mitogen activated protein kinases p38 (p38 MAPK) extracellular signal-regulated kinase 1/2 (ERK1/2), and c-Jun N-terminal kinase (JNK) in the development of psoriasis. The data …

Seasonal Dynamics Of Mesodinium Rubrum In Chesapeake Bay, Matthew D. Johnson, Doane K. Stoecker, Harold G. Marshall

Biological Sciences Faculty Publications

The photosynthetic ciliate Mesodinium rubrum is a common member of coastal phytoplankton communities that is well adapted to low-light, turbid ecosystems. It supports the growth of, or competes with, harmful dinoflagellate species for cryptophyte prey, as well as being a trophic link to copepods and larval fish. We have compiled data from various sources (n = 1063), on the abundance and distribution of M. rubrum in Chesapeake Bay and its tributaries. Because M. rubrum relies on obtaining organelles from cryptophyte algae to maintain rapid growth, we also enumerated cryptophyte algae in the portion of these samples that we collected …

Ontogenetic Shifts In Resource Allocation: Colour Change And Allometric Growth Of Defensive And Reproductive Structures In The Caribbean Spiny Lobster Panulirus Argus, Joshua R. Anderson, Angelo J. Spadaro, J. Antonio Baeza, Donald C. Behringer

Biological Sciences Faculty Publications

Resource allocation theory predicts a disproportionately large allocation of resources to defensive structures during early ontogeny in organisms that are subject to more intense predation at smaller than at larger body sizes. We tested this prediction on the Caribbean spiny lobster Panulirus argus, which exhibits a negative relationship between predation risk and body size with a high natural mortality of smaller individuals. Independent allometric growth analyses demonstrated that numerous defensive structures (e.g. orbital horns, segments supporting the antenna, the tail fan) display negative allometric growth throughout ontogeny. We interpret these findings as lobsters investing disproportionately more resources to defensive …

The Effects Of 11 Yr Of Co2 Enrichment On Roots In A Florida Scrub-Oak Ecosystem, Frank Day, Rachel E. Schroeder, Daniel B. Stover, Alisha L. P. Brown, John R. Butnor, John Dilustro, Bruce A. Hungate, Paul Dijkstra, Benjamn D. Duval, Troy J. Seiler

Biological Sciences Faculty Publications

• Uncertainty surrounds belowground plant responses to rising atmospheric CO₂ because roots are difficult to measure, requiring frequent monitoring as a result of fine root dynamics and long-term monitoring as a result of sensitivity to resource availability.
• We report belowground plant responses of a scrub-oak ecosystem in Florida exposed to 11yr of elevated atmospheric CO₂ using open-top chambers. We measured fine root production, turnover and biomass using minirhizotrons, coarse root biomass using ground-penetrating radar and total root biomass using soil cores.
• Total root biomass was greater in elevated than in ambient plots, and the absolute difference was larger than …

A Mesh Generation And Machine Learning Framework For Drosophila Gene Expression Pattern Image Analysis, Wenlu Zhang, Daming Feng, Rongjian Li, Andrey Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart Newfeld, Sudhir Kumar, Shuiwang Ji

Computer Science Faculty Publications

Background: Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide …

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 …

Cooperative Breeding And Long-Distance Dispersal: A Test Using Vagrant Records, Caroline L. Rusk, Eric L. Walters, Walter D. Koenig

Biological Sciences Faculty Publications

Cooperative breeding is generally associated with increased philopatry and sedentariness, presumably because short-distance dispersal facilitates the maintenance of kin groups. There are, however, few data on long-distance dispersal in cooperative breeders-the variable likely to be important for genetic diversification and speciation. We tested the hypothesis that cooperative breeders are less likely to engage in long-distance dispersal events by comparing records of vagrants outside their normal geographic range for matched pairs (cooperatively vs. non-cooperatively breeding) of North American species of birds. Results failed to support the hypothesis of reduced long-distance dispersal among cooperative breeders. Thus, our results counter the conclusion that …