Life Sciences Commons^™

Transcriptional Dynamics During Rhodococcus Erythropolis Infection With Phage Wc1, Dana Willner, Sudip Paudel, Andrew D. Halleran, Grace E. Solini, Veronica Gray, Margaret Saha

Arts & Sciences Articles

Background

Belonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, more rarely, in humans. Over 100 phages that infect Rhodococcus species have been isolated but despite their importance for Rhodococcus ecology and biotechnology applications, little is known regarding the molecular genetic interactions between phage and host during infection. To address this need, we report RNA-Seq analysis of a novel Rhodococcus erythopolis phage, WC1, analyzing both the phage and host transcriptome at various stages throughout the infection process.

Results

By five …

The Helicobacter Pylori Methylome Is Acid-Responsive Due To Regulation By The Two-Component System Arsrs And The Type I Dna Methyltransferase Hsdm1 (Hp0463), Elise H. Zimmerman, Erin L. Ramsey, Katherine E. Hunter, Sarah M. Villadelgado, Celeste M. Phillips, Ryan T. Shipman, Mark H. Forsyth

Arts & Sciences Articles

In addition to its role in genome protection, DNA methylation can regulate gene expression. In this study, we characterized the impact of acidity, phase variation, and the ArsRS TCS on the expression of the Type I m6A DNA methyltransferase HsdM1 (HP0463) of Helicobacter pylori 26695 and their subsequent effects on the methylome. Transcription of hsdM1 increases at least fourfold in the absence of the sensory histidine kinase ArsS, the major acid-sensing protein of H. pylori. hsdM1 exists in the phase-variable operon hsdR1-hsdM1. Phase-locking hsdR1 (HP0464), the restriction endonuclease gene, has significant impacts on the transcription of hsdM1. To determine the …

Seasonal Trends In Lysogeny In An Appalachian Oak-Hickory Forest Soil, Melaina L. Jacoby, Graham D. Hogg, Madelein R. Assaad, Kurt E. Williamson

Arts & Sciences Articles

Since 1989, investigations into viral ecology have revealed how bacteriophages can influence microbial dynamics within ecosystems at global scales. Most of the information we know about temperate phages, which can integrate themselves into the host genome and remain dormant via a process called lysogeny, has come from research in aquatic ecosystems. Soil environments remain under-studied, and more research is necessary to fully understand the range of impacts phage infections have on the soil bacteria they infect. The aims of this study were to compare the efficacy of different prophage-inducing agents and to elucidate potential temporal trends in lysogeny within a …

Host Defense Peptide Piscidin And Yeast-Derived Glycolipid Exhibit Synergistic Antimicrobial Action Through Concerted Interactions With Membranes, Fei Liu, Alexander I. Greenwood, Yawei Xiong, Et Al., Myriam L. Cotten

Arts & Sciences Articles

Developing new antimicrobials as alternatives to conventional antibiotics has become an urgent race to eradicate drug-resistant bacteria and to save human lives. Conventionally, antimicrobial molecules are studied independently even though they can be cosecreted in vivo. In this research, we investigate two classes of naturally derived antimicrobials: sophorolipid (SL) esters as modified yeast-derived glycolipid biosurfactants that feature high biocompatibility and low production cost; piscidins, which are host defense peptides (HDPs) from fish. While HDPs such as piscidins target the membrane of pathogens, and thus result in low incidence of resistance, SLs are not well understood on a mechanistic level. Here, …

Is Diversity Dammed? Analysis Of Fish Diversity In Dammed And Undammed Estuary Streams Within The Virginia Peninsula Using Environmental Dna (Edna), Melinda Ann Spence

Dissertations, Theses, and Masters Projects

Anthropogenic activities are the leading cause to biodiversity decline worldwide. It has been well documented that large dams disrupt dispersal and alter local habitat often leading to less diverse aquatic systems. Yet, it is not well known how much more numerous smaller dams impact fish communities in estuary systems where dispersal is a critical part of the ecosystem, or how dams affect variation in species composition across sites (beta diversity). Coastal waterways of Virginia are impounded by hundreds of small dams. Here we used eDNA (environmental DNA) to assess the alpha, beta, and gamma diversity of fish species within the …

Population Genetics Of Transposable Element Load: A Mechanistic Account Of Observed Overdispersion, Gregory Conradi Smith, Ron D. Smith, Joshua Puzey

Arts & Sciences Articles

In an empirical analysis of transposable element (TE) abundance within natural populations of Mimulus guttatus and Drosophila melanogaster, we found a surprisingly high variance of TE count (e.g., variance-to-mean ratio on the order of 10 to 300). To obtain insight regarding the evolutionary genetic mechanisms that underlie the overdispersed population distributions of TE abundance, we developed a mathematical model of TE population genetics that includes the dynamics of element proliferation and purifying selection on TE load. The modeling approach begins with a master equation for a birth-death process and extends the predictions of the classical theory of TE dynamics in …

Use Of Nest Web Cameras And Citizen Science To Quantify Osprey Prey Delivery Rate And Nest Success, Michael H. Academia, Harmony J. Dalgleish

Arts & Sciences Articles

Ospreys (Pandion haliaetus) are obligate piscivores and their nesting success depends on sufficient amounts of fish delivered to the nests during the breeding season. Nests are considered successful when pairs raise a minimum of one young to fledging or near-fledging age. Through web cameras and online broadcasts of Osprey nests, citizen scientists quantified daily number of fish deliveries, nest survival, and nest success. We received and analyzed curated data (one to seven seasons, 2014–2020) from citizen scientist groups representing 19 Osprey web cameras from four countries in North America and Europe. We compared the average and the coefficient …

Carrying Capacity Of Cultured Bivalves In Cherrystone Inlet, Va, And The Implications Of Spatial Distribution And Environmental Change, Sophia Chirico

Undergraduate Honors Theses

Aquaculture is a growing industry internationally. In the United States, aquaculture of bivalves occurs throughout the Chesapeake Bay. Cherrystone Inlet, a tidal inlet on the Virginia Eastern Shore, is the location of intensive hard clam culture, and recently oyster aquaculture has become common there as well. Given the intensive culture in Cherrystone and similar systems in the Chesapeake, it is important to understand the carrying capacity of the respective bivalves and how they can be grown together. Carrying capacity is defined here as the largest population of individuals that can be supported that allows individuals to reach a harvestable size …

The Characterization Of The Type I Dna Methyltransferase Hsdm1 (Hp0463) In Helicobacter Pylori, Elise Zimmerman

Undergraduate Honors Theses

Helicobacter pylori is a gram-negative spiral-shaped bacterium that colonizes the gastric epithelium and is the leading cause of gastric adenocarcinoma globally. For both H. pylori and many other bacterial species, there is an increasing body of evidence that methylation by restriction-modification systems regulates gene expression in addition to its traditional role in genome protection. The study aimed to further elucidate the mechanisms through which H. pylori achieves methylome plasticity. We demonstrated that the Type I DNA methyltransferase hsdM1 (HP0463) is regulated by the main acid sensing mechanism of H. pylori, the two-component system (TCS) ArsRS. ArsRS induces hsdM1 …

Climate Change And Conservation Of Milkweed: Evidence Of Extensive Admixture Between Common Milkweed And Poke Milkweed, Elizabeth Davies

Undergraduate Honors Theses

Global climate change can drive many changes in species interactions. One primary way it affects species is by changing climates, causing species to expand their ranges and allowing them to interact with species from whom they were previously isolated. In plants, new species interactions can result in hybridization – the creation of hybrid offspring between two separate species. This hybridization can increase gene flow between the species and lead to introgression, the transfer of genetic material from one species to another through hybrid backcrossing with the parent species. My thesis investigates hybridization in the model system Asclepias (milkweed) by analyzing …

Honey As A Biomonitor For Air Pollutant Deposition In The Eastern United States Using Ion Chromatography And Scanning Electron Microscopy, Cole Cochran

Undergraduate Honors Theses

Anthropogenic activities generate metal, acid, and particulate air pollutants which negatively impact human and ecological health. In the United States, power plant, industrial, and vehicle emissions are leading causes of air pollution, however, the measurement of air pollution at high-resolution spatial regimes remains a challenge. Honey has emerged as a powerful biomonitoring tool to effectively quantify contaminants without the need for a large array of monitoring instruments. I hypothesized that honey could be used to effectively measure and map modern air pollutant spatiotemporal relationships over the Eastern U.S. Using ion chromatography with sulfate as an indicator for air pollution and …

Transcriptomes Of Electrophysiologically Recorded Dbx1-Derived Respiratory Neurons Of The Prebötzinger Complex In Neonatal Mice, Prajkta S. Kallurkar, Maria Cristina D. Picardo, Yae K. Sugimura, Margaret Saha, Gregory D. Conradi Smith, Christopher A. Del Negro

Arts & Sciences Articles

Breathing depends on interneurons in the preBötzinger complex (preBötC) derived from Dbx1-expressing precursors. Here we investigate whether rhythm- and pattern-generating functions reside in discrete classes of Dbx1 preBötC neurons. In a slice model of breathing with ~ 5 s cycle period, putatively rhythmogenic Type-1 Dbx1 preBötC neurons activate 100–300 ms prior to Type-2 neurons, putatively specialized for output pattern, and 300–500 ms prior to the inspiratory motor output. We sequenced Type-1 and Type-2 transcriptomes and identified differential expression of 123 genes including ionotropic receptors (Gria3, Gabra1) that may explain their preinspiratory activation profiles and Ca2+ signaling ( …

Ecosystem Enriching And Efficient Solar Energy: Exploring The Effects Of Pollinator-Friendly Solar Facilities On Ecosystem Function And Solar Panel Efficiency, Jordan Martin

Dissertations, Theses, and Masters Projects

As the solar energy industry grows, many hundreds of thousands of acres of land will be transformed into solar panel facilities. With this large change in land use, there is the opportunity to promote biodiversity and support pollinators by using pollinator-friendly management practices at the solar facilities. This paper explores the ecological and economic effects of a pollinator-friendly solar facility compared to a turfgrass solar facility.

I hypothesized that a pollinator-friendly solar facility would be functionally equivalent in pollinator support and overall insect diversity to a pollinator-friendly non-solar field and that both sites would have far greater pollinator support and …

Find The Bullseye: Targeting Conservation In The Candy Darter, Jemelyn Grace P. Baldisimo

Reports

Grade: 7th grade, ability to scale up to high school Biology Subject: Life Science

Determining a species’ risk of extinction using available data and spreading awareness for conservation of an endemic species.

The Annual Cycle For Whimbrel Populations Using The Western Atlantic Flyway, B. D. Watts, F. Smith, C. Hines, L. Duval, Et Al.

Arts & Sciences Articles

Many long-distance migratory birds use habitats that are scattered across continents and confront hazards throughout the annual cycle that may be population-limiting. Identifying where and when populations spend their time is fundamental to effective management. We tracked 34 adult whimbrels (Numenius phaeopus) from two breeding populations (Mackenzie Delta and Hudson Bay) with satellite transmitters to document the structure of their annual cycles. The two populations differed in their use of migratory pathways and their seasonal schedules. Mackenzie Delta whimbrels made long (22,800 km) loop migrations with different autumn and spring routes. Hudson Bay whimbrels made shorter (17,500 km) …

Intertidal Zonation Of Hemichordates In Soft Sediments, Kharis R. Schrage, Juselyn D. Tupik, Jonathan D. Allen

Arts & Sciences Articles

Intertidal zonation of organisms is well studied on rocky shores but less so in soft sediment communities. On rocky shores, communities are two dimensional, with biotic factors such as competition and predation setting the lower bound of a zone, whereas abiotic factors such as desiccation set the upper bound. In soft sediment communities, these patterns persist, but with a dynamic three-dimensional ecosystem occupied by mobile infaunal organisms, zonation can be more difficult to quantify and detect. Hemichordate worms, however, deposit fecal casts at the surface, which can be easily identified and counted, making them a potential model system for identifying …

Whimbrel Populations Differ In Trans-Atlantic Pathways And Cyclone Encounters, B. D. Watts, F. M. Smith, C. Hines, L. Duval, Et Al.

Arts & Sciences Articles

Each year hundreds of millions of birds cross the Atlantic Ocean during the peak of tropical cyclone activity. The extent and consequences of migrant-storm interactions remain unknown. We tracked whimbrels from two populations (Mackenzie Delta; Hudson Bay) to examine overlap between migration routes and storm activity and both the frequency and consequence of storm encounters. Here we show that Mackenzie Delta and Hudson Bay whimbrels follow different routes across the ocean and experience dramatically different rates of storm encounters. Mackenzie Delta whimbrels departed North America from Atlantic Canada, made long (x¯" role="presentation" style="box-sizing: inherit; display: inline; line-height: normal; word-spacing: normal; …

Mysteries And Uncertainties In Tracing Cryptic Viral Infections, Melaina Jacoby

Undergraduate Honors Theses

Viruses are the most abundant biological entities on Earth. Viral impacts are evident from the level of individual cells and population all the way up to ecosystems and global elemental cycles. Since bacteriophages (viruses that infect bacteria) were first identified in the early twentieth century, the study of these fascinating entities has shown how viral dynamics within ecosystems can influence microbially-mediated processes at a large scale. Viral infections can impact hosts and host-mediated processes in in multiple ways, one of which is through cryptic infections. This state, in which a bacterium may harbor a cryptic phage infection, is known as …

Characterizing The Microbiome Of Floral Nectar Of Asclepias Syriaca And Other Asclepias Species, Heather Natterer

Undergraduate Honors Theses

In recent decades, Danaus plexippus (the monarch butterfly) has experienced a drastic decrease in population size due to urbanization, climate change, and habitat loss. The primary habitat and food source of D. plexippus is plant species that are within the genus Asclepias (milkweed). The preservation and propagation of Asclepias spp. is necessary to combat D. plexippus’s population declines. A plant’s reproductive success is dependent upon its ability to attract pollinators, which is linked to the plant’s nectar qualities. We propose that, in turn, these nectar qualities may be influenced by the nectar microbiome. This study aims to better understand the …

Field Testing An "Acoustic Lighthouse": Combined Acoustic And Visual Cues Provide A Multimodal Solution That Reduces Avian Collision Risk With Tall Human-Made Structures, Timothy James Boycott, J. P. Swaddle, Sally Mullis, Brandon E. Jackson

Peer-Reviewed Publications

Billions of birds fatally collide with human-made structures each year. These mortalities have consequences for population viability and conservation of endangered species. This source of human-wildlife conflict also places constraints on various industries. Furthermore, with continued increases in urbanization, the incidence of collisions continues to increase. Efforts to reduce collisions have largely focused on making structures more visible to birds through visual stimuli but have shown limited success. We investigated the efficacy of a multimodal combination of acoustic signals with visual cues to reduce avian collisions with tall structures in open airspace. Previous work has demonstrated that a combination of …

The Regulatory Network For Petal Anthocyanin Pigmentation Is Shaped By The Myb5a/Negan Transcription Factor In Mimulus, Xingyu Zheng, Kuenzang Om, Kimmy A. Stanton, (...), Gregory D. Conradi Smith, Joshua R. Puzeyn, Et Al.

Arts & Sciences Articles

Much of the visual diversity of angiosperms is due to the frequent evolution of novel pigmentation patterns in flowers. The gene network responsible for anthocyanin pigmentation, in particular, has become a model for investigating how genetic changes give rise to phenotypic innovation. In the monkeyflower genus Mimulus, an evolutionarily recent gain of petal lobe anthocyanin pigmentation in M. luteus var. variegatus was previously mapped to genomic region pla2. Here, we use sequence and expression analysis, followed by transgenic manipulation of gene expression, to identify MYB5a—orthologous to the NEGAN transcriptional activator from M. lewisii—as the gene responsible …

Investigation Of Red-Cockaded Woodpeckers Within The Great Dismal Swamp National Wildlife Refuge: 2020 Report, B. D. Watts, C. Hines, L. Duval, B. J. Paxton

CCB Technical Reports

No abstract provided.

Comparison Of Nutrient Accrual In Constructed Living Shoreline And Natural Fringing Marshes, Randolph Chambers, A. L. Gorsky, Robert Isdell, Molly Mitchell, Donna Marie Bilkovic

Arts & Sciences Articles

Living shoreline marshes are coastal wetlands constructed as alternatives to “hardened shorelines” (e.g., bulkheads, riprap) to mitigate erosion and to allow for landward migration of intertidal habitat as sea level rises. Living shorelines are designed to mimic natural fringing marshes and over time should be sinks for carbon and other nutrients. We collected soil cores and aboveground plant material from 13 pairs of natural fringing marshes and living shoreline marshes of different ages and degree of isolation from more extensive marsh shorescapes to compare nutrient pools and accrual. Although the nutrient content of plants was similar within and between marsh …

Bird-Window Collisions And Reflection As A Daytime Risk Factor, Lauren Celeste Emerson

Dissertations, Theses, and Masters Projects

Bird-window collisions account for millions of bird deaths annually in the United States. Despite many correlative studies citing the potential influence of reflective glass on daytime collision risk, few studies have explicitly tested this hypothesis. We aimed to determine whether reflection from a window influences daytime collision risk by manipulating the lighting conditions on exterior and interior window surfaces. We conducted this research within a flight tunnel in which domesticated zebra finches (Taeniopygia guttata) flew towards a window structure with two windows situated behind a mist-net. We assessed collision risk and flight velocity through 3D videography. We predicted that risk …

Investigation Of Red-Cockaded Woodpeckers In Virginia: Year 2020 Report, B. D. Watts, C. Hines, L. Duval, B. J. Paxton

CCB Technical Reports

The Virginia population of red-cockaded woodpeckers is the northernmost throughout the species range and has been in eminent danger of extinction for more than 30 years. The Piney Grove Preserve represents a nucleus for recovery in the state and the focus of a multi-organizational partnership designed to increase the population to a sustainable level. The partnership has executed a program of aggressive habitat management, cavity-tree management and woodpecker population monitoring and management that has resulted in a quadrupling of the breeding population since the early 2000s. During the 2020 breeding season, Piney Grove Preserve supported 15 potential breeding groups (including …

Living Shorelines Achieve Functional Equivalence To Natural Fringe Marshes Across Multiple Ecological Metrics, Robert Isdell, Donna M. Bilkovic, Amanda Guthrie, Molly Mitchell, Randolph M. Chambers, Matthias Leu, Carl Hershner

VIMS Articles

Nature-based shoreline protection provides a welcome class of adaptations to promote ecological resilience in the face of climate change. Along coastlines, living shorelines are among the preferred adaptation strategies to both reduce erosion and provide ecological functions. As an alternative to shoreline armoring, living shorelines are viewed favorably among coastal managers and some private property owners, but they have yet to undergo a thorough examination of how their levels of ecosystem functions compare to their closest natural counterpart: fringing marshes. Here, we provide a synthesis of results from a multi-year, large-spatial-scale study in which we compared numerous ecological metrics (including …

Influence Of Introduced Peregrine Falcons On The Distribution Of Red Knots Within A Spring Staging Site, B. D. Watts, Barry R. Truitt

Arts & Sciences Articles

Predator recovery driven by single-species management approaches may lead to conservation conflicts between recovered predators and prey species of conservation concern. As part of an aggressive recovery plan, the Eastern Peregrine Falcon Recovery Team released (1975–1985) 307 captive-reared peregrine falcons (Falco peregrinus) and successfully established a breeding population within the mid-Atlantic Coastal Plain, a physiographic region with no historic breeding population and a critical spring staging area for migratory shorebirds. We examined the influence of resident falcons on the distribution of foraging red knots during spring migration. We conducted weekly aerial surveys (2006–2009) along the Virginia barrier islands …

Linking Monitoring And Data Analysis To Predictions And Decisions For The Range-Wide Eastern Black Rail Status Assessment, Conor P. Mcgowan, Nicole F. Angeli, Whitney A. Beisler, Et Al., F. M. Smith, B. D. Watts

Arts & Sciences Articles

The US Fish and Wildlife Service (USFWS) has initiated a re-envisioned approach for providing decision makers with the best available science and synthesis of that information, called the Species Status Assessment (SSA), for endangered species decision making. The SSA report is a descriptive document that provides decision makers with an assessment of the current and pre - dicted future status of a species. These analyses support all manner of decisions under the US Endangered Species Act, such as listing, reclassification, and recovery planning. Novel scientific analysis and predictive modeling in SSAs could be an important part of rooting conservation decisions …

Virginia Peregrine Falcon Monitoring And Management Program: Year 2020 Report, B. D. Watts, M. U. Watts

CCB Technical Reports

The peregrine falcon (Falco peregrinus) was believed to be extirpated as a breeding species in Virginia by the early 1960s. An aggressive restoration program was initiated in 1978 that included the release of 115 captive-reared birds on the Coastal Plain (1978-1985) and 127 birds in the mountains (1985-1993). This program resulted in the first breeding of the modern era in 1982. Since this time, the population has proceeded through a rapid establishment phase followed by a consolidation phase. However, more than 95% of all breeding activity over the past 30 years has occurred on the Coastal Plain with very limited …

Allostery In Oligomeric Receptor Models, Gregory D. Conradi Smith

Arts & Sciences Articles

We show how equilibrium binding curves of receptor homodimers can be expressed as rational polynomial functions of the equilibrium binding curves of the constituent monomers, without approximation and without assuming independence of receptor monomers. Using a distinguished spanning tree construction for reduced graph powers, the method properly accounts for thermodynamic constraints and allosteric interactions between receptor monomers (i.e. conformational coupling). The method is completely general; it begins with an arbitrary undirected graph representing the topology of a monomer state-transition diagram and ends with an algebraic expression for the equilibrium binding curve of a receptor oligomer composed of two or more …