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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 ( …

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; …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

Long-Term Monitoring Of A Successful Recovery Program Of Peregrine Falcons In Virginia, B. D. Watts, Mitchell A. Byrd, E. K. Mojica, S. Padgett, S. R. Harding, C. A. Koppie

Arts & Sciences Articles

The Peregrine Falcon (Falco peregrinus anatum) was believed to be extirpated as a breeding species in Virginia by the early 1960s. An aggressive restoration program was initiated in 1978 that involved the release of captive-reared birds totaling 115 on the Coastal Plain (1978–1985) and 127 in the Mountain physiographic region (1985–1993). The first occupied territory was established and the first breeding attempt was documented in 1979 and 1982, respectively. We have monitored the size, distribution, reproductive rate, and substrate use of the resulting breeding population (1979–2016). The population proceeded through an establishment phase (1979–1993) driven by releases with an average …

Predator-Induced Plasticity In Egg Capsule Deposition In The Mud Snail, Tritia Obsoleta, Emily A. Harmon, Jonathan D. Allen

Arts & Sciences Articles

Most marine invertebrates develop in the plankton, where microscopic offspring can avoid abundant benthic predators until settlement. However, at least four phyla of marine invertebrates (Annelida, Mollusca, Nemertea, and Platyhelminthes) deposit benthic egg capsules or masses. Often, these animals possess additional means to protect their young, including chemical or morphological defenses or nonrandom selection of deposition sites. Egg capsule deposition is the dominant reproductive strategy among gastropod molluscs, including the mud snail, Tritia obsoleta. In intertidal and shallow subtidal habitats in New England, the mud snail preferentially deposits egg capsules on blades of eelgrass (Zostera marina), a substrate that stands …

Subgenome Dominance In An Interspecific Hybrid, Synthetic Allopolyploid, And A 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower, Patrick P. Edger, Ronald Smith, Micheal R. Mckain, (...), Gregory D. Conradi Smith, Joshua R. Puzey

Arts & Sciences Articles

Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant, having retained more genes and being more highly expressed, a phenomenon termed subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of emergence of subgenome dominance, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural, <140-year-old allopolyploid (Mimulus peregrinus), a resynthesized interspecies triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and progenitor species (M. guttatus …

Mapping Bald Eagle Activity Shadows Around Communal Roosts, B. D. Watts, Courtney Turrin

Arts & Sciences Articles

We assessed diurnal activity patterns associated with communal roosts (n = 26) by tracking nonbreeding bald eagles (Haliaeetus leucocephalus; n = 58) within the upper Chesapeake Bay, USA, 2008-2013. We used daytime locations (n = 54,165) to map activity shadows (using home range analytics, 90% kernel) around communal roosts, to evaluate the spatial structure and to delineate diurnal activity centers. We overlaid a range (100-3,200 m) of buffers around the perimeter of each roost to estimate the benefits of management scenarios in extending protection to daytime activities. Activity shadows around roosts varied from 1.5 km(2) to 116 km(2) ((x) over …

Correlation Between Investment In Sexual Traits And Valve Sexual Dimorphism In Cyprideis Species (Ostracoda), Maria João Fernandes Martins, Gene Hunt, Rowan Lockwood, John P. Swaddle, David J. Horne

Arts & Sciences Articles

Assessing the long-term macroevolutionary consequences of sexual selection has been hampered by the difficulty of studying this process in the fossil record. Cytheroid ostracodes offer an excellent system to explore sexual selection in the fossil record because their readily fossilized carapaces are sexually dimorphic. Specifically, males are relatively more elongate than females in this superfamily. This sexual shape difference is thought to arise so that males carapaces can accommodate their very large copulatory apparatus, which can account for up to one-third of body volume. Here we test this widely held explanation for sexual dimorphism in cytheroid ostracodes by correlating investment …

Obligate Planktotrophy In The Götte's Larva Of Stylochus Ellipticus (Platyhelminthes), Jonathan D. Allen, A. M. L. Klompen, E. J. Alpert, A. J. Reft

Arts & Sciences Articles

Polyclad flatworms are a diverse and emerging model system for developmental biologists, yet development remains poorly understood for many species. One limitation of polyclads as a model system has been the lack of reliable methods for culturing planktotrophic polyclad larvae to metamorphosis. There are conflicting statements in the literature about which types of polyclad larvae require food to complete development. We developed simple methods for rearing planktotrophic flatworms to metamorphosis and tested the effects of food type and concentration on their development. The flatworm Stylochus ellipticus develops from small (~65 μm) eggs into an obligately planktotrophic Götte’s larva. In this …

The Effects Of Salinity And Ph On Fertilization, Early Development And Hatching In The Crown-Of-Thorns Seastar, Jonathan D. Allen, Kharis R. Schrage, Shawna A. Foo, Sue-Ann Watson, Maria Byrne

Arts & Sciences Articles

Understanding the influence of environmental factors on the development and dispersal of crown-of-thorns seastars is critical to predicting when and where outbreaks of these coral-eating seastars will occur. Outbreaks of the crown-of-thorns seastars are hypothesized to be driven by terrestrial runoff events that increase nutrients and the phytoplankton food for the larvae. In addition to increasing larval food supply, terrestrial runoff may also reduce salinity in the waters where seastars develop. We investigated the effects of reduced salinity on the fertilisation and early development of seastars, up to and including their hatching from the fertilisation envelope. We also tested the …

Utilization Probability Map For Migrating Bald Eagles In Northeastern North America: A Tool For Siting Wind Energy Facilities And Other Flight Hazards, Elizabeth K. Mojica, B. D. Watts, Courtney L. Turrin

Arts & Sciences Articles

Collisions with anthropogenic structures are a significant and well documented source of mortality for avian species worldwide. The bald eagle (Haliaeetus leucocephalus) is known to be vulnerable to collision with wind turbines and federal wind energy guidelines include an eagle risk assessment for new projects. To address the need for risk assessment, in this study, we 1) identified areas of northeastern North America utilized by migrating bald eagles, and 2) compared these with high wind-potential areas to identify potential risk of bald eagle collision with wind turbines. We captured and marked 17 resident and migrant bald eagles in the northern …

Nuclear Import Of The Thyroid Hormone Receptor Α1 Is Mediated By Importin 7, Importin Β1, And Adaptor Importin Α1, Vincent R. Roggero, Jibo Zhang, Laura E. Parente, Yazdi Doshi, Lizabeth A. Allison

Arts & Sciences Articles

The thyroid hormone receptor a1 (TRa1) is a nuclear receptor for thyroid hormone that shuttles rapidly between the nucleus and cytoplasm. Our prior studies showed that nuclear import of TRa1 is directed by two nuclear localization signals, one in the N-terminal A/B domain and the other in the hinge domain. Here, we showed using in vitro nuclear import assays that TRa1 nuclear localization is temperature and energy-dependent and can be reconstituted by the addition of cytosol. In HeLa cells expressing green fluorescent protein (GFP)-tagged TRa1, knockdown of importin 7, importin B1 and importin a1 by RNA interference, or treatment with …

Use Of Esi-Fticr-Ms To Characterize Dissolved Organic Matter In Headwater Streams Draining Forest-Dominated And Pasture-Dominated Watersheds, Randolph Chambers

Arts & Sciences Articles

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) has proven to be a powerful technique revealing complexity and diversity of natural DOM molecules, but its application to DOM analysis in grazing-impacted agricultural systems remains scarce. In the present study, we presented a case study of using ESI-FTICR-MS in analyzing DOM from four headwater streams draining forest- or pasture-dominated watersheds in Virginia, USA. In all samples, most formulas were CHO compounds (71.8–87.9%), with other molecular series (CHOS, CHON, CHONS, and CHOP (N, S)) accounting for only minor fractions. All samples were dominated by molecules falling in the lignin-like region …

Landfill Use By Bald Eagles In The Chesapeake Bay Region, Courtney Turrin, B. D. Watts, Elizabeth K. Mojica

Arts & Sciences Articles

We examined patterns in the use of landfills (rubbish dumps) in the Chesapeake Bay by Bald Eagles (Haliaeetus leucocephalus). Sites of solid waste landfills (n  =  72) were located using state databases. Satellite tracking data from 64 eagles were used to track eagle movements hourly during daylight and once at midnight to determine roosting locations (2007–2012). Landfill use varied significantly with age class, with hatch-year birds using landfills six times more often than adults and twice as often as third- and fourth-year birds. Hatch-year birds spent significantly more time at landfills than expected based on landfill area …

Seasonal Variation In Space Use By Nonbreeding Bald Eagles Within The Upper Chesapeake Bay, B. D. Watts, Elizabeth K. Mojica, B. J. Paxton

Arts & Sciences Articles

Access to food resources is essential to self-maintenance and reproduction and, for species of conservation concern, foraging areas are considered critical habitat. Human disturbance is an important factor restricting access to prey resources for Bald Eagles (Haliaeetus leucocephalus) and guidelines in the Chesapeake Bay have been developed to mitigate its impact. However, our ability to implement such guidelines has been limited by a lack of information on important foraging areas. We used Brownian bridge movement modeling to develop a population-wide utilization probability surface for Bald Eagles along shorelines within the upper Chesapeake Bay. We used locations (n …