Biology Commons^™

Long-Read Assembly Of A Great Dane Genome Highlights The Contribution Of Gc-Rich Sequence And Mobile Elements To Canine Genomes, Julia V. Halo, Amanda L. Pendleton, Feichen Shen, Aurélien J. Doucet, Thomas Derrien, Christophe Hitte, Laura E. Kirby, Bridget Myers, Elzbieta Sliwerska, Sarah Emery, John V. Moran, Adam R. Boyko, Jeffrey M. Kidd

Biological Sciences Faculty Publications

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of …

Effect Of Cultivation Parameters On Fermentation And Hydrogen Production In The Phylum, Mariamichela Lanzilli, Nunzia Esercizio, Marco Vastano, Zhaohui Xu, Genoveffa Nuzzo, Carmela Gallo, Emiliano Manzo, Angelo Fontana, Giuliana D'Ippolito

Biological Sciences Faculty Publications

The phylum is composed of a single class (), 4 orders (), 5 families (), and 13 genera. They have been isolated from extremely hot environments whose characteristics are reflected in the metabolic and phenotypic properties of the species. The metabolic versatility of members leads to a pool of high value-added products with application potentials in many industry fields. The low risk of contamination associated with their extreme culture conditions has made most species of the phylum attractive candidates in biotechnological processes. Almost all members of the phylum, especially those in the order , can produce bio-hydrogen from a variety …

Activated Protein Kinase C (Pkc) Is Persistently Trafficked With Epidermal Growth Factor (Egf) Receptor, Carol A. Heckman, Tania Biswas, Douglas M. Dimick, Marilyn L. Cayer

Biological Sciences Faculty Publications

Protein kinase Cs (PKCs) are activated by lipids in the plasma membrane and bind to a scaffold assembled on the epidermal growth factor (EGF) receptor (EGFR). Understanding how this complex is routed is important, because this determines whether EGFR is degraded, terminating signaling. Here, cells were preincubated in EGF-tagged gold nanoparticles, then allowed to internalize them in the presence or absence of a phorbol ester PKC activator. PKC colocalized with EGF-tagged nanoparticles within 5 min and migrated with EGFR-bearing vesicles into the cell. Two conformations of PKC-epsilon were distinguished by different primary antibodies. One, thought to be enzymatically active, was …

Multivariate Analysis Of Open Field Exploration Identifies Latent Spatial And Social Behavioral Axes In Domestic Dogs, Budhaditya Chowdhury, Moira Van Staaden, Robert Huber

Biological Sciences Faculty Publications

Recent methodological advances in studying large scale animal movements have let researchers gather rich datasets from behaving animals. Often collected in small sample sizes due to logistical constraints, these datasets are however, ideal for multivariate explorations into behavioral complexity. In behavioral studies of domestic dogs, although automated data loggers have recently seen increasing use, a comprehensive framework to identify complex behavioral axes is lacking. Dog behavioral studies frequently rely on subjective ratings, despite demonstrable evidence that these are insufficient for identifying behavioral variables. Taking advantage of dogs' innate running abilities and readily available GPS data loggers, we extracted latitude-longitude coordinates …

The Complicated And Confusing Ecology Of Microcystis Blooms, Steven W. Wilhelm, George S. Bullerjahn, R Michael Mckay

Biological Sciences Faculty Publications

Blooms of the toxin-producing cyanobacterium are increasing globally, leading to the loss of ecosystem services, threats to human health, as well as the deaths of pets and husbandry animals. While nutrient availability is a well-known driver of algal biomass, the factors controlling "who" is present in fresh waters are more complicated. possesses multiple strategies to adapt to temperature, light, changes in nutrient chemistry, herbivory, and parasitism that provide a selective advantage over its competitors. Moreover, its ability to alter ecosystem pH provides it a further advantage that helps exclude many of its planktonic competitors. While decades of nutrient monitoring have …

Metatranscriptomic And Metagenomic Analysis Of Biological Diversity In Subglacial Lake Vostok (Antarctica), Colby Gura, Scott O. Rogers

Biological Sciences Faculty Publications

A combined metatranscriptomic and metagenomic study of Vostok (Antarctica) ice core sections from glacial, basal, and lake water accretion ice yielded sequences that indicated a wide variety of species and possible conditions at the base of the glacier and in subglacial Lake Vostok. Few organisms were in common among the basal ice and accretion ice samples, suggesting little transmission of viable organisms from the basal ice meltwater into the lake water. Additionally, samples of accretion ice, each of which originated from water in several locations of the shallow embayment, exhibit only small amounts of mixing of species. The western-most portion …

Statin Drugs Plus Th1 Cytokines Potentiate Apoptosis And Ras Delocalization In Human Breast Cancer Lines And Combine With Dendritic Cell-Based Immunotherapy To Suppress Tumor Growth In A Mouse Model Of Her-2 Disease, Crystal M. Oechsle, Loral E. Showalter, Colleen M. Novak, Brain J. Czerniecki, Gary K. Koski

Biological Sciences Faculty Publications

A dendritic cell-based, Type 1 Helper T cell (Th1)-polarizing anti-Human Epidermal Growth Factor Receptor-2 (HER-2) vaccine supplied in the neoadjuvant setting eliminates disease in up to 30% of recipients with HER-2-positive (HER-2) ductal carcinoma in situ (DCIS). We hypothesized that drugs with low toxicity profiles that target signaling pathways critical for oncogenesis may work in conjunction with vaccine-induced immune effector mechanisms to improve efficacy while minimizing side effects. In this study, a panel of four phenotypically diverse human breast cancer lines were exposed in vitro to the combination of Th1 cytokines Interferon-gamma (IFN-γ) and Tumor Necrosis Factor-alpha (TNF-α) and lipophilic …

The Role Of Demographic History And Selection In Shaping Genetic Diversity Of The Galápagos Penguin (Spheniscus Mendiculus), Gabriella Arauco-Shapiro, Katelyn I. Schumacher, Dee Boersma, Juan L. Bouzat

Biological Sciences Faculty Publications

Although many studies have documented the effects of demographic bottlenecks on the genetic diversity of natural populations, there is conflicting evidence of the roles that genetic drift and selection may play in driving changes in genetic variation at adaptive loci. We analyzed genetic variation at microsatellite and mitochondrial loci in conjunction with an adaptive MHC class II locus in the Galápagos penguin (Spheniscus mendiculus), a species that has undergone serial demographic bottlenecks associated with El Niño events through its evolutionary history. We compared levels of variation in the Galápagos penguin to those of its congener, the Magellanic penguin (Spheniscus magellanicus), …

Loci Encoding Compounds Potentially Active Against Drug-Resistant Pathogens Amidst A Decreasing Pool Of Novel Antibiotics, Joseph Basalla, Payel Chatterjee, Elizabeth Burgess, Mahnur Khan, Emily Verbrugge, Daniel D. Wiegmann, John J. Lipuma, Hans Wildschutte

Biological Sciences Faculty Publications

Since the discovery of penicillin, microbes have been a source of antibiotics that inhibit the growth of pathogens. However, with the evolution of multidrug-resistant (MDR) strains, it remains unclear if there is an abundant or limited supply of natural products to be discovered that are effective against MDR isolates. To identify strains that are antagonistic to pathogens, we examined a set of 471 globally derived environmental strains (env-Ps) for activity against a panel of 65 pathogens including spp., spp., , and spp. isolated from the lungs of cystic fibrosis (CF) patients. From more than 30,000 competitive interactions, 1,530 individual inhibitory …

Metatranscriptomic Analyses Of Diel Metabolic Functions During A Microcystis Bloom In Western Lake Erie (United States), Emily J. Davenport, Michelle J. Neudeck, Paul G. Matson, George S. Bullerjahn, Timothy W. Davis, Steven W. Wilhelm, Maddie K. Denney, Lauren E. Krausfeldt, Joshua M. Stough, Kevin A. Meyer, Gregory J. Dick, Thomas H. Johengen, Erika Lindquist, Susannah G. Tringe, Robert Michael Mckay

Biological Sciences Faculty Publications

This study examined diel shifts in metabolic functions of spp. during a 48-h Lagrangian survey of a toxin-producing cyanobacterial bloom in western Lake Erie in the aftermath of the 2014 Toledo Water Crisis. Transcripts mapped to the genomes of recently sequenced lower Great Lakes isolates showed distinct patterns of gene expression between samples collected across day (10:00 h, 16:00 h) and night (22:00 h, 04:00 h). Daytime transcripts were enriched in functions related to Photosystem II (e.g., ), nitrogen and phosphate acquisition, cell division (), heat shock response (, ), and uptake of inorganic carbon (, ). Genes transcribed during …

Editorial: Invertebrate Models Of Natural And Drug-Sensitive Reward, Moira J. Van Staaden, Robert Huber

Biological Sciences Faculty Publications

The relationship between insects and humans is a complex one, characterized biotically as commensalism, mutualism, or parasitism. This collection of papers reveals yet another dimension, in which shared history invests invertebrate models with the power to interrogate critical challenges to the human reward system. As humans we take pride in approaching a given scenario rationally, in considering the possible options, assigning them values, and then choosing that which maximizes one's individual outcomes. So, why do drug addicts make choices that inevitably lead to ruinous consequences? Fundamentally, addiction appears to impair the very ability to form considered judgments, as it strips …

Origin And Recent Expansion Of An Endogenous Gammaretroviral Lineage In Domestic And Wild Canids, Julia V. Halo, Amanda L. Pendleton, Abigail S. Jarosz, Robert J. Gifford, Malika L. Day, Jeffrey M. Kidd

Biological Sciences Faculty Publications

BACKGROUND: Vertebrate genomes contain a record of retroviruses that invaded the germlines of ancestral hosts and are passed to offspring as endogenous retroviruses (ERVs). ERVs can impact host function since they contain the necessary sequences for expression within the host. Dogs are an important system for the study of disease and evolution, yet no substantiated reports of infectious retroviruses in dogs exist. Here, we utilized Illumina whole genome sequence data to assess the origin and evolution of a recently active gammaretroviral lineage in domestic and wild canids.

RESULTS: We identified numerous recently integrated loci of a canid-specific ERV-Fc sublineage within …

Predator Water Balance Alters Intraguild Predation In A Streamsidefood Web, Israel L. Leinbach, Kevin E. Mccluney, John L. Sabo

Biological Sciences Faculty Publications

Previous work suggests that animal water balance can influence trophic interactions, with predators increasing their consumption of water-laden prey to meet water demands.But it is unclear how the need for water interacts with the need for energy to drive trophic interactions under shifting conditions. Using manipulative field experiments, we show that water balance influences the effects of top predators on prey with contrasting ratios of water and energy, altering the frequency of intraguild predation. Water-stressed top predators (large spiders) negatively affect water-laden basal prey (crickets), especially male prey with higher water content, whereas alleviation of water limitation causes top predators …

Differential Sensitivity Of Bees To Urbanization-Driven Changes In Body Temperature And Water Content, Justin D. Burdine, Kevin E. Mccluney

Biological Sciences Faculty Publications

Predicting how species will respond to climate change and land use modification is essential for conserving organisms and maintaining ecosystem services. Thermal tolerances have been shown to have strong predictive power, but the potential importance of desiccation tolerances have been less explored in some species. Here, we report measurements of thermal and desiccation tolerances and safety margins across a gradient of urbanization, for three bee species: silky striped sweat bees (Agapostemon sericeus), western honeybees (Apis mellifera), and common eastern bumblebees (Bombus impatiens). We found significant differences in thermal tolerances, measured as critical thermal maximum …

Mass-Length Relationships For 3 Bee Species In Northwest Ohio, Justin D. Burdine, Erin Plummer, Melissa Seidel, Kevin E. Mccluney

Biological Sciences Faculty Publications

The ability to accurately estimate bee mass through measurements of intertegular distance (ITD) is an important tool for field biologists. ITD is the distance between the bases of the 2 wing tegulae on the bee’s thorax. However, the relationship between ITD and bee mass can vary based on species and sampling region. A collection of 92 bees—representing 3 species—was examined to assess the accuracy of ITD in estimating dry mass for bees in northwest Ohio. The focus was on 3 species: silky striped sweat bees (Agapostemon sericeus), honey bees (Apis mellifera), and common eastern bumble bees (Bombus impatiens). Overall, there …

Water Availability Influences Arthropod Water Demand, Hydration And Community Composition On Urban Trees, Kevin E. Mccluney, Thomas George, Steven D. Frank

Biological Sciences Faculty Publications

The drive for animals to regulate their water content can have significant consequences for food webs in xeric ecosystems. But the importance of animal water balance (gains vs losses) for mesic food webs has not been explored. Impervious surfaces in cities absorb and re-radiate solar radiation, raising local temperatures. Higher temperatures lead to greater rates of organismal water loss. Thus, urbanization of mesic regions may lead to greater likelihood of desiccation, with consequences for food webs. We tested the effects of animal water balance on a mesic urban food web by supplementing animal-available water (but not plant) within trees in …

Urbanization Alters Communities Of Flying Arthropods In Parks And Gardens Of A Medium-Sized City, Edward Lagucki, Justin D. Burdine, Kevin E. Mccluney

Biological Sciences Faculty Publications

Urbanization transforms undeveloped landscapes into built environments, causing changes in communities and ecological processes. Flying arthropods play important roles in these processes as pollinators, decomposers, and predators, and can be important in structuring food webs. The goal of this study was to identify associations between urbanization and the composition of communities of flying (and floating) arthropods within gardens and parks in a medium-sized mesic city. We predicted that flying arthropod abundance and diversity would respond strongly to percent impervious surface and distance to city center, measurements of urbanization. Flying arthropods were sampled from 30 gardens and parks along an urbanization …

Variation In Arthropod Hydration Across Us Cities With Distinct Climate, Kevin E. Mccluney, Justin D. Burdine, Steven D. Frank

Biological Sciences Faculty Publications

Increasing evidence suggests that altered environmental conditions within cities (e.g. temperature) can have strong effects on the biology and ecology of animals. Moreover, multiple abiotic (e.g. soil moisture, distributions of water bodies) and biotic factors (e.g. plant and animal communities) may be more similar among cities in distinct climate regions as compared to outside cities. But the mechanisms behind these patterns are unclear. We suggest that animal physiological condition responds to urbanization and may become more similar with urbanization among cities. As a first attempt at assessing this possibility, we measured hydration (water content) of field-collected arthropods, across variation in …

Implications Of Animal Water Balance For Terrestrial Food Webs, Kevin E. Mccluney

Biological Sciences Faculty Publications

Recent research has documented shifts in per capita trophic interactions and food webs in response to changes in environmental moisture, from the top-down (consumers to plants), rather than solely bottom-up (plants to consumers). These responses may be predictable from effects of physiological, behavioral, and ecological traits on animal water balance, although predictions could be modified by energy or nutrient requirements, the risk of predation, population-level responses, and bottom-up effects. Relatively little work has explicitly explored food web effects of changes in animal water balance, despite the likelihood of widespread relevance, including during periodic droughts in mesic locations, where taxa may …

Animal Water Balance Drives Top-Down Effects In A Riparian Forest-Implications For Terrestrial Trophic Cascades, Kevin E. Mccluney, John L. Sabo

Biological Sciences Faculty Publications

Despite the clear importance of water balance to the evolution of terrestrial life, much remains unknown about the effects of animal water balance on food webs. Based on recent research suggesting animal water imbalance can increase trophic interaction strengths in cages, we hypothesized that water availability could drive top-down effects in open environments, influencing the occurrence of trophic cascades. We manipulated large spider abundance and water availability in 20 × 20 m open-air plots in a streamside forest in Arizona, USA, and measured changes in cricket and small spider abundance and leaf damage. As expected, large spiders reduced both cricket …

Development Of Circadian Oscillators In Neurosphere Cultures During Adult Neurogenesis, Astha Malik, Roudabeh J. Jamasbi, Roman V. Kondratov, Michael Eric Geusz

Biological Sciences Faculty Publications

Circadian rhythms are common in many cell types but are reported to be lacking in embryonic stem cells. Recent studies have described possible interactions between the molecular mechanism of circadian clocks and the signaling pathways that regulate stem cell differentiation. Circadian rhythms have not been examined well in neural stem cells and progenitor cells that produce new neurons and glial cells during adult neurogenesis. To evaluate circadian timing abilities of cells undergoing neural differentiation, neurospheres were prepared from the mouse subventricular zone (SVZ), a rich source of adult neural stem cells. Circadian rhythms in mPer1 gene expression were recorded in …

Polychlorinated Biphenyl Exposure Alters Oxytocin Receptor Gene Expression And Maternal Behavior In Rat Model, E Nicole Dover, David E. Mankin, Howard C. Cromwell, Lee Meserve

Biological Sciences Faculty Publications

Polychlorinated biphenyl (PCB) is a persistent organic pollutant known to induce diverse molecular and behavioral alterations. Effects of PCB exposure could be transmitted to future generations via changes in behavior and gene expression. Previous work has shown that PCB-exposure can alter social behavior. The present study extends this work by examining a possible molecular mechanism for these changes. Pregnant rats (Sprague-Dawley) were exposed through diet to a combination of non-coplanar (PCB 47 - 2,20,4,40-tetrachlorobiphenyl) and coplanar (PCB 77 - 3,30,4,40- tetrachlorobiphenyl) congeners. Maternal care behaviors were examined by evaluating the rate and quality of nest building on the last 4 …

Sensitivity And Tolerance Of Riparian Arthropod Communities To Altered Water Resources Along A Drying River, Kevin E. Mccluney, John L. Sabo

Biological Sciences Faculty Publications

Rivers around the world are drying with increasing frequency, but little is known about effects on terrestrial animal communities. Previous research along the San Pedro River in southeastern AZ, USA, suggests that changes in the availability of water resources associated with river drying lead to changes in predator abundance, community composition, diversity, and abundance of particular taxa of arthropods, but these observations have not yet been tested manipulatively.

Darwin’S Diagram Of Divergence Of Taxa As A Causal Model For The Origin Of Species, Juan Luis Bouzat

Biological Sciences Faculty Publications

On the basis that Darwin's theory of evolution encompasses two logically independent processes (common descent and natural selection), the only figure in On the Origin of Species (the Diagram of Divergence of Taxa) is often interpreted as illustrative of only one of these processes: the branching patterns representing common ancestry. Here, I argue that Darwin's Diagram of Divergence of Taxa represents a broad conceptual model of Darwin's theory, illustrating the causal efficacy of natural selection in producing well-defined varieties and ultimately species. The Tree Diagram encompasses the idea that natural selection explains common descent and the origin of organic diversity, …

Riverine Macrosystems Ecology: Sensitivity, Resistance, And Resilience Of Whole River Basins With Human Alterations, Kevin E. Mccluney, N Leroy Poff, Margaret A. Palmer, James H. Thorp, Geoffrey C. Poole, Bradley S. Williams, Michael R. Williams, Jill S. Baron

Biological Sciences Faculty Publications

Riverine macrosystems are described here as watershed-scale networks of connected and interacting riverine and upland habitat patches. Such systems are driven by variable responses of nutrients and organisms to a suite of global and regional factors (eg climate, human social systems) interacting with finer-scale variations in geology, topography, and human modifications. We hypothesize that spatial heterogeneity, connectivity, and asynchrony among these patches regulate ecological dynamics of whole networks, altering system sensitivity, resistance, and resilience. Long-distance connections between patches may be particularly important in riverine macrosystems, shaping fundamental system properties. Furthermore, the type, extent, intensity, and spatial configuration of human activities …

Effects Of Polychlorinated Biphenyl (Pcb) Exposure On Response Perseveration And Ultrasonic Vocalization Emission In Rat During Development, Dena Krishnan, Howard C. Cromwell, Lee Meserve

Biological Sciences Faculty Publications

The 3 major symptoms of autistic spectrum disorders include 1) social behavioral alterations, 2) problems in communication and 3) higher-order motoric deficits of perseveration and stereotyped movements. Previous work has shown that early developmental exposure to polychlorinated biphenyls (PCBs) alters rat pup social motivation and juvenile rat social recognition/investigation. The present work extends this previous research by examining how perinatal PCB exposure alters motoric functions and communication abilities at different stages of development. Action perseveration was examined using performance measures from a T-maze environment. Communication abilities were evaluated by monitoring ultrasound emission in rat pups during a brief isolation from …

Natural Transformation Of Thermotoga Sp. Strain Rq7, Dongmei Han, Hui Xu, Rutika Puranik, Zhaohui Xu

Biological Sciences Faculty Publications

Background

Thermotoga species are organisms of enormous interest from a biotechnological as well as evolutionary point of view. Genetic modifications of Thermotoga spp. are often desired in order to fully release their multifarious potentials. Effective transformation of recombinant DNA into these bacteria constitutes a critical step of such efforts. This study aims to establish natural competency in Thermotoga spp. and to provide a convenient method to transform these organisms.

Results

Foreign DNA was found to be relatively stable in the supernatant of a Thermotoga culture for up to 6 hours. Adding donor DNA to T. sp. strain RQ7 at its …

Water As A Trophic Currency In Dryland Food Webs, Daniel C. Allen, Kevin E. Mccluney, Stephen R. Elser, John L. Sabo

Biological Sciences Faculty Publications

Water is essential for life on Earth, yet little is known about how water acts as a trophic currency, a unit of value in determining species interactions in terrestrial food webs. We tested the relative importance of groundwater and surface water in riparian food webs by manipulating their availability in dryland floodplains. Primary consumers (crickets) increased in abundance in response to added surface water and groundwater (contained in moist leaves), and predators (spiders and lizards) increased in abundance in response to added surface water, in spite of the presence of a river, an abundant water source. Moreover, the relative magnitude …

Subglacial Lake Vostok (Antarctica) Accretion Ice Contains A Diverse Set Of Sequences From Aquatic, Marine And Sediment-Inhabiting Bacteria And Eukarya, Scott O. Rogers, Yury M. Shtarkman, Zeynep A. Koçer, Robyn Edgar, Ram S. Veerapneni, Tom D'Elia, Paul F. Morris

Biological Sciences Faculty Publications

Lake Vostok, the 7th largest (by volume) and 4th deepest lake on Earth, is covered by more than 3,700 m of ice, making it the largest subglacial lake known. The combination of cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier), limited nutrients and complete darkness presents extreme challenges to life. Here, we report metagenomic/metatranscriptomic sequence analyses from four accretion ice sections from the Vostok 5G ice core. Two sections accreted in the vicinity of an embayment on the southwestern end of the lake, and the other two represented part of the southern main basin. We obtained 3,507 …

A New Method For Identifying Stem-Like Cells In Esophageal Cancer Cell Lines, Michael Eric Geusz, Taghreed N. Almanaa, Roudabeh J. Jamasbi

Biological Sciences Faculty Publications

Cancer stem cells (CSCs) appear to resist chemo-radiotherapy and initiate tumor recurrence in patients. Isolation and further characterization of this subpopulation is important for targeting CSCs. Flow cytometry using Aldefluor, a fluorescent substrate of aldehyde dehydrogenase, has been used to isolate CSCs from various cancer cell lines. However, newtechniques are needed to locate and identify CSCs in culture for live-cell analyses such as fluorescence microscopy without introducing artifacts during cell sorting and to observe CSC and non-CSC interactions. Previously, we characterized a distinct CSC subpopulation within human esophageal cancer cell lines (ESCC). In this study we introduce the attached-cell Aldefluor …