Life Sciences Commons^™

Fish Sound Production: The Swim Bladder, Michael L. Fine, Eric Parmentier

Biology Publications

Analogous to the syrinx in birds and larynx in mammals, the swim bladder is a major sound-producing organ in fishes. It also functions in hearing and is responsible for most returns from sonar. Historically, the swim bladder has been modeled as an underwater resonant bubble, whereas we provide evidence for a forced-response model in which viscous damping of the bladder wall inhibits resonance of the internal bubble. Further experimental work on the shape, wall structure, and mechanical behavior of the swim bladder is required.

An Investigation Of Bubble Resonance And Its Implications For Sound Production By Deepwater Fishes, Mark W. Sprague, Michael L. Fine, Timothy M. Cameron

Biology Publications

Although the continental slope and abyss comprise the largest habitat on earth, the absence of documented fish sounds from deep waters is striking. Fishes with sexually dimorphic muscles attached to their swim bladders suggests that sounds are likely used in male courtship on the upper, mid and lower continental slope. To investigate the effects of environmental extremes on fish sound production, the acoustic behavior of a driven bubble is examined. This study is also relevant to target strength of sonar returns from fish and hearing in auditory specialist fishes. A bubble is a classic, if imperfect, model for swim bladder …

Qualitative And Quantitative Characterization Of Epithelial Cell Mixtures Using Hormone Antibody Probes And Flow Cytometry, Luke Baldridge

Master of Science in Forensic Science Directed Research Projects

“Touch” DNA is evidence that consists of epidermal cells deposited by handling objects and it is becoming more common in evidence samples processed in crime labs. Because “touch” DNA evidence samples may be low-template DNA and are often mixtures, there is a need to both nondestructively estimate the amount of DNA present prior to DNA purification and to identify and characterize mixtures prior to DNA typing. The purpose of this study was to test the use of FITC-labeled anti-testosterone antibodies as a potential tool to estimate the number of contributors in two-, three-, and four-person mixtures of epidermal skin cells, …

Quantitative Pcr And Sanger Sequencing Of Mitochondrial Dna Recovered From Waterlogged Bone, Kailey Babcock

Master of Science in Forensic Science Directed Research Projects

In forensic contexts, samples containing heavily fragmented DNA are commonly encountered. Compromised biological samples are especially prevalent in instances where human remains have been submerged in an aqueous environment for extended periods of time. Nuclear DNA is particularly vulnerable to the prolonged exposure to heat, moisture, and bacterial degradation that are prevalent in aquatic settings. Paired with the difficulty of recovering DNA from skeletal remains, which are often the only remaining component after the soft tissues have been stripped away, mitochondrial DNA (mtDNA) analysis serves as an invaluable alternative. In this multifaceted study, mtDNA analysis was performed on waterlogged bone …

Identification Of Compounds Causing Cellular Autofluorescence In Touch Samples, Elora C. Wall

Master of Science in Forensic Science Directed Research Projects

As DNA analysis has advanced and produced tests with higher sensitivities, attention has turned toward obtaining DNA profiles from cells left with fingermarks. Recent studies have reported that cells deposited within fingermarks can exhibit differences in autofluorescence emission in the ‘red’ region of the visible spectrum (e.g., between 650-670 nm), which can be used to differentiate contributor cell population and separate them before DNA profiles. Interestingly, this emission was not consistent to the individual day-to-day and likely not a genetically-controlled attribute of the contributor. Instead, this emission signature results from extended exposure of the skin to certain materials such as …

Decreased Temperature Variance Associated With Biotic Composition Enhances Coastal Shrub Encroachment, Lauren K. Wood, Spencer Hays, Julie C. Zinnert

Biology Publications

Regime shift from grasslands to shrub-dominated landscapes occur worldwide driven by altered land-use and climate change, affecting landscape function, biodiversity, and productivity. Warming winter temperatures are a main driver of expansion of the native, evergreen shrub, Morella cerifera, in coastal landscapes. Shrub establishment in these habitats alters microclimate, but little is known about seasonal differences and microclimate variance. We assessed influence of shrubs on microclimate variance, community composition, and community physiological functioning across three vegetation zones: grass, transitional, and shrub in a coastal grassland. Using a novel application of a time-series analysis, we interpret microclimatic variance modification and elucidate …

Topography And Disturbance Influence Trait‐Based Composition And Productivity Of Adjacent Habitats In A Coastal System, Joseph K. Brown, Julie C. Zinnert

Biology Publications

Coastal systems experience frequent disturbance and multiple environmental stressors over short spatial and temporal scales. Investigating functional traits in coastal systems has the potential to inform how variation in disturbance frequency and environmental variables influence differences in trait‐based community composition and ecosystem function. Our goals were to (1) quantify trait‐based communities on two barrier islands divergent in topography and long‐term disturbance response and (2) determine relationships between community trait‐based composition and ecosystem productivity. We hypothesized that locations documented with high disturbance would have habitats with similar environmental conditions and trait‐based communities, with the opposite relationship in low‐disturbance locations. Furthermore, we …

Seasonal Facilitative And Competitive Trade‐Offs Between Shrub Seedlings And Coastal Grasses, Michael N. Sinclair, Natasha N. Woods, Julie C. Zinnert

Biology Publications

Shrub expansion is occurring in grasslands globally and may be impacted by the balance of competition and facilitation with existing grasses. Along the mid‐Atlantic and Gulf coasts, the native shrub Morella cerifera (wax myrtle) is rapidly expanding and displacing other native coastal species. Recent research suggests that much of this expansion is due to warming winter temperatures, as temperatures below −15°C kill M. cerifera. The objective of this project was to understand the importance of species interactions with grasses on the growth and physiology of M. cerifera at the seedling life stage through both field and laboratory experiments. In …

The Utilization Of Sex Hormone Antibodies For Screening And Separation Of Trace Biological Mixtures, Kristin N. Jones

Master of Science in Forensic Science Directed Research Projects

Touch or trace evidence consists of epidermal cells deposited by contact with items such as handled objects, touched surfaces, or worn clothes. This type of evidence has surpassed most other sample types submitted to forensic labs and typically consists of low quantities of DNA and multiple contributors. In this study epithelial skin cells, i.e., “touch/trace evidence,” were used as they are estimated to constitute approximately half of the casework evidence items submitted for DNA analysis. For the optimization of antibody staining, male and female skin epithelial samples from donors were incubated and hybridized with antibodies of various concentrations of Alexa …

Non-Destructive, Rapid Differentiation Of Cell Types Relevant To Sexual Assault Investigations Utilizing Morphological And Autofluorescence Signatures, Taylor R. Moldenhauer

Master of Science in Forensic Science Directed Research Projects

Current methods for confirming the presence of spermatozoa in sexual assault samples can be time-consuming and often lack sensitivity; however, this remains the most definitive test for the presence of semen. Additionally, male DNA can be deposited without the presence of intact sperm as may be the case with seminal fluid from vasectomized individuals or sexual activity where seminal fluid is not recovered (e.g., perpetrator wears a condom, penetration without ejaculation, etc.). The ability to detect bodily fluids, as well as quantify their presence in a sample, could aid in forensic DNA analysis by limiting the amount of time performing …

The Utilization Of Eukaryotic Cell Types In Microbiomes For Semen, Vaginal Fluid, And Menstrual Blood Identification Using 18s Rdna, Ines Benaissa

Master of Science in Forensic Science Directed Research Projects

The accurate identification of body fluids is vital for crime scene investigation and forensic analysis. While many body fluids can be presumptively identified, there is a lack of confirmatory testing for verification. Therefore, the purpose of this study was to determine if body fluids (menstrual blood, vaginal fluid, and semen) could be differentiated based on their eukaryotic microbial communities. The target area of interest was the V9 hyper-variable region of 18S ribosomal DNA (18S rDNA). The samples were extracted, barcoded using a duel-index strategy, and PCR amplified before undergoing high throughput sequencing using the Illumina Miseq FGx instrument. The samples …

Application Of Optical Trapping To Obtain Single-Source Str Profiles From Forensically Relevant Body Fluid Mixtures With Modified Dna Analysis Workflow, Benjamin J. O'Brien

Master of Science in Forensic Science Directed Research Projects

Current methods of mixture separation in forensic DNA laboratories typically deconvolute the mixture after analysis using statistical analysis or probabilistic genotyping. To save time and effort of labs already backlogged, a method to separate mixtures on a cellular level before analysis needs to be developed. Optical trapping is a method that uses a focused 1064 nm laser to manipulate cells. Previous research has shown that approximately 50 spermatozoa or 15 leukocytes from a liquid sample are required to produce a full STR DNA profile. It was found that the number of spermatozoa required remains constant when the method of sample …

Development Of A Quantitative Pcr (Qpcr) Based Method For Studying Temporal Dna Degradation In Waterlogged Bone, Isis Thornton

Master of Science in Forensic Science Directed Research Projects

Human activities are often centered around the presence of water, thus it is not surprising that there are many water-related human deaths. Accumulated degree days (ADD), and other aquatic variables may affect DNA retrieval from waterlogged bone. Calcium and collagen in bone can inhibit the PCR necessary to produce an STR profile; the current solution is a time-consuming organic extraction. While there are examples of research on DNA degradation in terrestrial bone over time, there has been little work done on submerged bone samples and they are usually limited to case studies. The major aim of this study was to …

Interaction Of Seed Dispersal And Environmental Filtering Affects Woody Encroachment Patterns In Coastal Grassland, Natasha N. Woods, Benjamin L. Dows, Evan B. Goldstein, Laura J. Moore, Donald R. Young, Julie C. Zinnert

Biology Publications

Encroachment of woody plants into grasslands has occurred worldwide and includes coastal ecosystems. This conversion process is mediated by seed dispersal patterns, environmental filtering, and biotic interactions. As spatiotemporally heterogeneous, harsh environments, barrier islands present a unique set of challenges for dispersal and establishment. Environmental conditions act as filters on dispersed seeds, thereby influencing encroachment and distribution patterns. Seldom have patterns of propagule dispersal been considered in the context of woody encroachment. We quantified dispersal and post‐dispersal processes of an encroaching woody population of Morella cerifera relative to directional rate of encroachment and observed distribution patterns on an Atlantic coastal …

Evolutionary Relationships Of Courtship Songs In The Parasitic Wasp Genus, Cotesia (Hymenoptera: Braconidae), Justin P. Bredlau, Karen M. Kester

Biology Publications

Acoustic signals play an important role in premating isolation based on sexual selection within many taxa. Many male parasitic wasps produce characteristic courtship songs used by females in mate selection. In Cotesia (Hymenoptera: Braconidae: Microgastrinae), courtship songs are generated by wing fanning with repetitive pulses in stereotypical patterns. Our objectives were to sample the diversity of courtship songs within Cotesia and to identify underlying patterns of differentiation. We compared songs among 12 of ca. 80 Cotesia species in North America, including ten species that have not been recorded previously. For Cotesia congregata, we compared songs of wasps originating from …

Effect Of Tidal Cycling Rate On The Distribution And Abundance Of Nitrogen-Oxidizing Bacteria In A Bench-Scale Fill-And-Drain Bioreactor, Joseph M. Battistelli, Rima B. Franklin, Aaron L. Mills

Biology Publications

Most domestic wastewater can be effectively treated for secondary uses by engineered biological systems. These systems rely on microbial activity to reduce nitrogen (N) content of the reclaimed water. Such systems often employ a tidal-flow process to minimize space requirements for the coupling of aerobic and anaerobic metabolic processes. In this study, laboratory-scale tidal-flow treatment systems were studied to determine how the frequency and duration of tidal cycling may impact reactor performance. Fluorescent in situ hybridization and epifluorescence microscopy were used to enumerate the key functional groups of bacteria responsible for nitrification and anaerobic ammonium oxidation (anammox), and N-removal efficiency …

Mechanisms Of Surviving Burial: Dune Grass Interspecific Differences Drive Resource Allocation After Sand Deposition, Joseph K. Brown, Julie C. Zinnert

Biology Publications

Sand dunes are important geomorphic formations of coastal ecosystems that are critical in protecting human populations that live in coastal areas. Dune formation is driven by ecomorphodynamic interactions between vegetation and sediment deposition. While there has been extensive research on responses of dune grasses to sand burial, there is a knowledge gap in understanding mechanisms of acclimation between similar, coexistent, dune-building grasses such as Ammophila breviligulata (C₃), Spartina patens (C₄), and Uniola paniculata (C₄). Our goal was to determine how physiological mechanisms of acclimation to sand burial vary between species. We hypothesize that (1) …

Investigation Into The Role Of Manganese In The Growth Of The Opportunistic Pathogen Streptococcus Sanguinis, Brittany Spivey

Auctus: The Journal of Undergraduate Research and Creative Scholarship

While Streptococcus sanguinis plays a beneficial role in the oral cavity as a competitor of Streptococcus mutans and Streptococcus sobrinus, the bacteria that produce dental caries, it can cause deadly infective endocarditis if given the opportunity to colonize the vegetations that form over damaged endocardial tissue. Pre-existing heart conditions, surgery, and intravenous drug use predispose individuals to endocarditis. S. sanguinis growth and consequential virulence is significantly impeded by restriction to manganese. This is due to the resulting overwhelming oxidative stress and formation of reactive oxygen species which damage DNA and other cellular components. Manganese is essential for S. sanguinis proteins …

Hepatocellular Cancer Genome And Transcriptome Analysis Validates Clinically Significant Mutational Signatures With The Tgf-𝛃 Pathway, Shuyun Rao, Jian Chen, Kazufumi Ohshiro, Shoujun Gu, Sobia Zaidi, Wilma S. Jogunoori, Jon White, Nagarajan Pattabiraman, Raja Mazumder, Anelia Horvath, Ray-Chang Wu, Shulin Li, Chuxia Deng, Bibhuti Mishra, Rehan Akbanni, The Tcga Cancer Network, Lopa Mishra

Hepatobiliary Cancers: Pathobiology and Translational Advances

No abstract provided.

Aggregate Stability And Water Retention Near Saturation Characteristics As Affected By Soil Texture, Aggregate Size And Polyacrylamide Application, Amrakh I. Mamedov, Chi-Hua Huang, Fazil A. Aliev, Guy J. Levy

Biology Publications

Understanding the effects of soil intrinsic properties and extrinsic conditions on aggregate stability is essential for the development of effective soil and water conservation practices. Our objective was to evaluate the combined role of soil texture, aggregate size and application of a stabilizing agent on aggregate and structure stability indices (composite structure index [SI], the and n parameters of the VG model and the S-index) by employing the high energy (0-5.0 J kg(-1)) moisture characteristic (HEMC) method. We used aggregates of three sizes (0.25-0.5, 0.5-1.0 and 1.0-2.0 mm) from four semi-arid soils treated with polyacrylamide (PAM). An increase in SI …

Variation In Growth And Developmental Responses To Supraoptimal Temperatures Near Latitudinal Range Limits Of Gypsy Moth Lymantria Dispar (L.), An Expanding Invasive Species, Lily M. Thompson, Trevor M. Faske, Nana Banahene, Dominique Grim, Salvatore J. Agosta, Dylan Parry, Patrick C. Tobin, Derek M. Johnson, Kristine L. Grayson

Biology Publications

Variation in thermal performance within and between populations provides the potential for adaptive responses to increasing temperatures associated with climate change. Organisms experiencing temperatures above their optimum on a thermal performance curve exhibit rapid declines in function and these supraoptimal temperatures can be a critical physiological component of range limits. The gypsy moth, Lymantria dispar (L.) (Lepidoptera: Erebidae), is one of the best-documented biological invasions and factors driving its spatial spread are of significant ecological and economic interest. The present study examines gypsy moth sourced from different latitudes across its North American range for sensitivity to high temperature in constant …

Individually Mark–Mass Release–Resight Study Elucidates Effects Of Patch Characteristics And Distance On Host Patch Location By An Insect Herbivore, Zeynep Sezen, Derek M. Johnson, Katriona Shea

Biology Publications

1. How organisms locate their hosts is of fundamental importance in a variety of basic and applied ecological fields, including population dynamics, invasive species management and biological control. However, tracking movement of small organisms, such as insects, poses significant logistical challenges.

2. Mass-release and individual–mark–recapture techniques were combined in an individually mark–mass release–resight (IMMRR) approach to track the movement of over 2000 adult insects in an economically important plant–herbivore system. Despite its widespread use for the biological control of the invasive thistle Carduus nutans, the host-finding behaviour of the thistle head weevil Rhinocyllus conicus has not previously been studied. …

Functional Responses Can’T Unify Invasion Ecology, James Vonesh, Mike Mccoy, Res Altwegg, Pietro Landi, John Measey

Biology Publications

Dick et al. (Biol Invasions, 2017) propose that the comparative functional response framework provides a unifying approach for the study of invasive species. We agree that functional responses are an important and powerful quantitative description of consumer effects on resources, and co-opting classical ecological theory to better predict invasive species impacts is a laudable move for invasion biology. However, we fear that the early successes of select examples of the comparative functional response (CFR) approach has led Dick et al. to exaggerate the generality of its utility, and about its ability to unify the field. Further, they fail to provide …

Nerve Conduction Through Dendrites Via Proton Hopping, Lemont B. Kier

Biology Publications

Background: In our previous studies of nerve conduction conducted by proton hopping, we have considered the axon, soma, synapse and the nodes of Ranvier. The role of proton hopping described the passage of information through each of these units of a typical nerve system. The synapse projects information from the axon to the dendrite and their associated spines.

Methods: We have invoked the passage of protons via a hopping mechanism to illustrate the continuum of the impulse through the system, via the soma following the dendrites. This is proposed to be a continuum invoked by the proton hopping method.

Results: …

Minion™ Nanopore Sequencing Of Environmental Metagenomes: A Synthetic Approach, Bonnie L. Brown, Mick Watson, Samuel S. Minot, Maria C. Rivera, Rima B. Franklin

Biology Publications

Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1 × 104 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads. We tested the ability of sequence data produced by MinION (R7.3 flow cells) to correctly assign taxonomy in single bacterial species runs and in three types of low-complexity synthetic communities: …

Differential Response Of Barrier Island Dune Grasses To Species Interactions And Burial, April Harris, Julie C. Zinnert, Donald R. Young

Biology Publications

Barrier islands are at the forefront of storms and sea-level rise. High disturbance regimes and sediment mobility make these systems sensitive and dynamic. Island foredunes are protective structures against storm-induced overwash that are integrally tied to dune grasses via biogeomorphic feedbacks. Shifts in dune grass dominance could influence dune morphology and susceptibility to overwash, altering island stability. In a glasshouse study, two dune grasses, Ammophila breviligulata and Uniola paniculata, were planted together and subjected to a 20 cm burial to quantify morphological and physiological responses. Burial had positive effects on both plants as indicated by increased electron transport rate and …

Genetic Differentiation Of Spring-Spawning And Fall-Spawning Male Atlantic Sturgeon In The James River, Virginia, Matthew T. Balazik, Daniel J. Farrae, Tanya L. Darden, Greg C. Garman

Biology Publications

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus, Acipenseridae) populations are currently at severely depleted levels due to historic overfishing, habitat loss, and pollution. The importance of biologically correct stock structure for effective conservation and management efforts is well known. Recent improvements in our understanding of Atlantic sturgeon migrations, movement, and the occurrence of putative dual spawning groups leads to questions regarding the true stock structure of this endangered species. In the James River, VA specifically, captures of spawning Atlantic sturgeon and accompanying telemetry data suggest there are two discrete spawning groups of Atlantic sturgeon. The two putative spawning groups were …

Immediate Effects Of Microclimate Modification Enhance Native Shrub Encroachment, Joseph A. Thompson, Julie C. Zinnert, Donald R. Young

Biology Publications

Shrubs have become more dense and expanded beyond their range all over the world for a variety of reasons including increased temperatures, overgrazing, and alteration of historical fire regime. Native shrubs have been encroaching on Virginia barrier island grasslands for over half a century for unknown reasons. Species composition, soil nutrients, leaf area index (LAI), and ground and air temperature were recorded across the shrub to grass transition and at free-standing shrubs in a coastal grassland in order to determine the effect of shrub encroachment on plant community and microclimate. Species richness was significantly lower inside shrub thickets. Soil water …

Functional Traits Of Expanding, Thicket-Forming Shrubs: Contrasting Strategies Between Exotic And Native Species, Sheri A. Shiflett, Julie C. Zinnert, Donald R. Young

Biology Publications

Woody expansion has been documented for decades in many different systems globally, often yielding vast changes in ecosystem functioning. While causes and consequences of woody expansion have been well documented, few studies have addressed plant functional traits that promote dramatic and rapid expansion in range. Our objectives were to investigate plant functional traits that contribute to the colonization, rapid expansion, and thicket formation of an invasive, N-fixing shrub, Elaeagnus umbellata Thunb. (Elaeagnaceae), and a native, N-fixing shrub Morella cerifera (L.) Small (Myricaceae) and compare to native, sympatric, non-expanding shrub species. Quantified functional traits included morphological (e.g., specific leaf area, leaf …

Grunt Variation In The Oyster Toadfish Opsanus Tau: Effect Of Size And Sex, Michael L. Fine, Tyler D. Waybright

Biology Publications

As in insects, frogs and birds, vocal activity in fishes tends to be more developed in males than in females, and sonic swimbladder muscles may be sexually dimorphic, i.e., either larger in males or present only in males. Male oyster toadfish Opsanus tau L produce a long duration, tonal boatwhistle advertisement call, and both sexes grunt, a short duration more pulsatile agonistic call. Sonic muscles are present in both sexes but larger in males. We tested the hypothesis that males would call more than females by inducing grunts in toadfish of various sizes held in a net and determined incidence …