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, …

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 …

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 ( …

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; …

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 …

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 …

A Simple Method For Sphingolipid Analysis Of Tissues Embedded In Optimal Cutting Temperature Compound, Timothy Rohrbach, April E. Boyd, Pamela J. Grizzard, Sarah Speigel, Jeremy Allegood, Santiago Lima

Richard Bland Faculty Works

MS-assisted lipidomic tissue analysis is a valuable tool to assess sphingolipid metabolism dysfunction in disease. These analyses can reveal potential pharmacological targets or direct mechanistic studies to better understand the molecular underpinnings and influence of sphingolipid metabolism alterations on disease etiology. But procuring sufficient human tissues for adequately powered studies can be challenging. Therefore, biorepositories, which hold large collections of cryopreserved human tissues, are an ideal retrospective source of specimens. However, this resource has been vastly underutilized by lipid biologists, as the components of OCT compound used in cryopreservation are incompatible with MS analyses. Here, we report results indicating that …

Role Of Synaptic Inhibition In The Coupling Of The Respiratory Rhythms That Underlie Eupnea And Sigh Behaviors, Daniel S. Borrus, Cameron J. Grover, Gregory D. Conradi Smith, Christopher A. Del Negro

Arts & Sciences Articles

The preBötzinger complex (preBötC) gives rise to two types of breathing behavior under normal physiological conditions: eupnea and sighing. Here, we examine the neural mechanisms that couple their underlying rhythms. We measured breathing in awake intact adult mice and recorded inspiratory rhythms from the preBötC in neonatal mouse brainstem slice preparations. We show previously undocumented variability in the temporal relationship between sigh breaths or bursts and their preceding eupneic breaths or inspiratory bursts. Investigating the synaptic mechanisms for this variability in vitro, we further show that pharmacological blockade of chloride-mediated synaptic inhibition strengthens inspiratory-to-sigh temporal coupling. These findings contrast …

Fty720/Fingolimod Decreases Hepatic Steatosis And Expression Of Fatty Acid Synthase In Diet-Induced Nonalcoholic Fatty Liver Disease In Mice, Timothy D. Rohrbach, Amon Asgharpour, Melizza A. Maczis, David Montefusco, Ashley Cowart, Pierre Bedossa, Arun J. Sanyal, Sarah Spiegel

Richard Bland Faculty Works

Nonalcoholic fatty liver disease (NAFLD), a leading cause of liver dysfunction, is a metabolic disease that begins with steatosis. Sphingolipid metabolites, particularly ceramide and sphingosine-1-phosphate (S1P), have recently received attention for their potential roles in insulin resistance and hepatic steatosis. FTY720/fingolimod, a prodrug for the treatment of multiple sclerosis, is phosphorylated in vivo to its active phosphorylated form by sphingosine kinase 2 and has been shown to interfere with the actions of S1P and to inhibit ceramide biosynthesis. Therefore, in this study we investigated the effects of FTY720 in a diet-induced animal model of NAFLD (DIAMOND) that recapitulates the hallmarks …

Baseline Bird Surveys Of Plum Trees Islands National Wildlife Refuge: 2017, 2018 And 2019 Seasons Final Results, B. D. Watts, B. J. Paxton

CCB Technical Reports

No abstract provided.

Investigation Of Red-Cockaded Woodpeckers In Virginia: Year 2019 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 2019 breeding season, Piney Grove Preserve supported 15 potential breeding groups (including …

A Likelihood Ratio Test For Changes In Homeolog Expression Bias, Ronald D. Smith, Taliesin J. Kinser, Gregory D. Conradi Smith, Joshua R. Puzeyn

Arts & Sciences Articles

Background

Gene duplications are a major source of raw material for evolution and a likely contributor to the diversity of life on earth. Duplicate genes (i.e., homeologs, in the case of a whole genome duplication) may retain their ancestral function, sub- or neofunctionalize, or be lost entirely. A primary way that duplicate genes evolve new functions is by altering their expression patterns. Comparing the expression patterns of duplicate genes gives clues as to whether any of these evolutionary processes have occurred.

Results

We develop a likelihood ratio test for the analysis of the expression ratios of duplicate genes across two …

Trpm4 Ion Channels In Pre-Bo¨Tzinger Complex Interneurons Are Essential For Breathing Motor Pattern But Not Rhythm, Marina Cristina D. Picardo, Yae K. Sugimura, Kaitlyn E. Dorst, Prajkta S. Kallurkar, Victoria T. Akins, Xingru Ma, Ryoichi Teruyama, Romaine Guinamard, Kaiwen Kam, Margaret Saha, Christopher A. Del Negro

Arts & Sciences Articles

Inspiratory breathing movements depend on pre-Bötzinger complex (preBötC) interneurons that express calcium (Ca2+)-activated nonselective cationic current (ICAN) to generate robust neural bursts. Hypothesized to be rhythmogenic, reducing ICAN is predicted to slow down or stop breathing; its contributions to motor pattern would be reflected in the magnitude of movements (output). We tested the role(s) of ICAN using reverse genetic techniques to diminish its putative ion channels Trpm4 or Trpc3 in preBötC neurons in vivo. Adult mice transduced with Trpm4-targeted short hairpin RNA (shRNA) progressively decreased the tidal volume of breaths yet surprisingly increased breathing frequency, often followed by gasping and …

One Fish, Two Fish, Red Fish, Whose Fish? Subjects: Life Science, Environmental Science, Marine / Ocean Science, Shelby White

Reports

This activity invites students to assume the role of various stakeholders in fisheries management and actively discuss the influence of economics, ecology and human interactions in decision-making.

Students will demonstrate their argument for/against a certain regulation by participating as a specific stakeholder (i.e. commercial fisher, recreational fisher, scientists/researcher, environmental group, management agency, and citizen). Students will recognize that stakeholders tend to advocate based on their individual needs, often making it difficult for proposed policies to satisfy the needs of all stakeholders and achieve sustainability goals.

Expedition Sediments: Mud's Journey Through The Watershed. Subjects: Earth Science / Environmental Science Grades: 9-12, Jessie Turner

Reports

Expedition Sediments is a game-in-a-lesson that allows students to explore the movement of sediments through watersheds by moving around the classroom. This lesson explores how grains of estuarine mud and sand move throughout estuaries and coastal regions, with a focus on processes surrounding a highly populated estuary such as the Chesapeake Bay. By the end of the lesson, students will be able to explain how sediments are transported through an estuary, graph sediment residence times in different locations, and compare the timescales of different sediment transport processes.