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2015

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Articles 1081 - 1110 of 1751

Full-Text Articles in Biology

Systematics And Biogeography Of Orthaea Kloztsch (Ericaceae: Vaccinieae), Nelson Salinas Feb 2015

Systematics And Biogeography Of Orthaea Kloztsch (Ericaceae: Vaccinieae), Nelson Salinas

Dissertations, Theses, and Capstone Projects

In the first chapter a study of the distribution patterns of the neotropical Vaccinieae (Ericaceae) is presented. Five areas of endemism were recovered: Central America, northern Chocó, southern Chocó, eastern Ecuador, and Yungas. Divergence times estimations indicate that the Andean clade of Vaccinieae migrated to South America during the Late Oligocene or Early Miocene (28.9-17.84 MA), and most of the subsequent diversification took place during the Tertiary. The Yungas was the first Andean area to be colonized, and several dispersals towards the north expanded their distribution range. Both areas of endemism and dispersal events were influenced by geological processes, such …

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Population Genomic Inference Of Ecology, Conservation, Evolution, And Demographic History Of Atlantic Seahorses And Pipefishes (Syngnathidae), Joel Thomas Boehm Feb 2015

Population Genomic Inference Of Ecology, Conservation, Evolution, And Demographic History Of Atlantic Seahorses And Pipefishes (Syngnathidae), Joel Thomas Boehm

Dissertations, Theses, and Capstone Projects

In the Atlantic Ocean powerful directional ocean currents can play a significant role in the formation and persistence of marine species. Syngnathidae fishes have a sparse fossil record, high morphological plasticity, and many of these species are difficult to observe in the wild, therefore they frequently lack life history information and the status of regional lineages and species designations are often obscure. In this dissertation I explore the ecology, evolution, and conservation of primarily Atlantic seahorses (Hippocampus) and pipefish (Syngnathus) in four core chapters, using differing genetic datasets ranging from mitochondrial DNA to genome-wide RAD sequences. Most Synganthids have the …

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E Pluribus Unum: What Individual Whales Can Tell Us About Enigmatic Species Distribution And Social Organization, Tanya Marie Lubansky Jan 2015

E Pluribus Unum: What Individual Whales Can Tell Us About Enigmatic Species Distribution And Social Organization, Tanya Marie Lubansky

Dissertations

Large whales have historically been difficult to study and many aspects of their ecology remain unknown especially at the long -term population level. The ability to identify individual whales based on natural markings provides the opportunity to track individuals over time and space; this data may offer more insight into the ecology of whales than previously imagined. This study demonstrates use of photo-identification data to model both social structure and habitat selection, minimizing the need for invasive research and greatly increasing the sample size used in such endeavors. A conditional logistic model is written for a 20-year sightings dataset on …

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Marz: An Algorithm To Combinatorially Analyze Gapped N-Mer Models Of Transcription Factor Binding, Rowan G. Zellers, Robert A. Drewell, Jacqueline M. Dresch Jan 2015

Marz: An Algorithm To Combinatorially Analyze Gapped N-Mer Models Of Transcription Factor Binding, Rowan G. Zellers, Robert A. Drewell, Jacqueline M. Dresch

Biology

Background: A key challenge in understanding the molecular mechanisms that control gene regulation is the characterization of the specificity with which transcription factor proteins bind to specific DNA sequences. A number of computational approaches have been developed to examine these interactions, including simple mononucleotide and dinucleotide position weight matrix models. Results: Here we develop a novel, unbiased computational algorithm, MARZ, that systematically analyzes all possible gapped matrices across a fixed number of nucleotides. In addition, to evaluate the ability of these matrix models to predict in vivo binding sites, we utilize a new scoring system and, in combination with established …

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In Situ Nitrogen Mineralization, Nitrification, And Ammonia Volatilization In Maize Field Fertilized With Urea In Huanghuaihai Region Of Northern China, Xuelin Zhang, Qun Wang, Jun Xu, Frank S. Gilliam, Nicolas Tremblay, Chaohai Li Jan 2015

In Situ Nitrogen Mineralization, Nitrification, And Ammonia Volatilization In Maize Field Fertilized With Urea In Huanghuaihai Region Of Northern China, Xuelin Zhang, Qun Wang, Jun Xu, Frank S. Gilliam, Nicolas Tremblay, Chaohai Li

Biological Sciences Faculty Research

Nitrogen (N) fertilization potentially affects soil N mineralization and leaching, and can enhance NH3 volatilization, thus impacting crop production. A fertilizer experiment with five levels of N addition (0, 79, 147, 215 and 375 kg N ha-1) was performed in 2009 and 2010 in a maize field in Huanghuaihai region, China, where > 300 kg N ha-1 has been routinely applied to soil during maize growth period of 120 days. Responses of net N mineralization, inorganic N flux (0–10cm), NH3 volatilization, and maize yield to N fertilization were measured. During the growth period, net N mineralization …

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Status Of A Translocated Florida Sand Skink Population After Six Years: Establishing And Evaluating Criteria For Success, Adam Ryan Emerick Jan 2015

Status Of A Translocated Florida Sand Skink Population After Six Years: Establishing And Evaluating Criteria For Success, Adam Ryan Emerick

USF Tampa Graduate Theses and Dissertations

The translocation of organisms is becoming a frequently used tool in conservation biology. There are, however, a disproportionate number of unsuccessful attempts translocating populations of herpetofauna. Logistical and temporal limits of monitoring, combined with ambiguous metrics concerning "success," have led to few advances regarding reptile translocations. Successfully established and persistent populations are those in which both the founding population and subsequent generations show consistent or positive levels of survival and reproduction. A small population of the threatened Florida Sand Skink (Plestiodon reynoldsi) was translocated in 2007. Data collected from 2007 to 2009 confirmed survival and reproduction among the founding individuals, …

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On The Analysis Of Phylogenetically Paired Designs, Jennifer L. Funk, Cyril Rakovski, J. Michael Macpherson Jan 2015

On The Analysis Of Phylogenetically Paired Designs, Jennifer L. Funk, Cyril Rakovski, J. Michael Macpherson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

As phylogenetically controlled experimental designs become increasingly common in ecology, the need arises for a standardized statistical treatment of these datasets. Phylogenetically paired designs circumvent the need for resolved phylogenies and have been used to compare species groups, particularly in the areas of invasion biology and adaptation. Despite the widespread use of this approach, the statistical analysis of paired designs has not been critically evaluated. We propose a mixed model approach that includes random effects for pair and species. These random effects introduce a “two-layer” compound symmetry variance structure that captures both the correlations between observations on related species within …

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Mapping Legume Roots Can Determine Best Performing Crops, Frédérique C. Guinel Jan 2015

Mapping Legume Roots Can Determine Best Performing Crops, Frédérique C. Guinel

Clear Language Summaries

Legume plants have a mutually beneficial relationship with bacteria. These beneficial bacteria live in nodules found on plant roots. Until recently there was no way to systematically measure the roots the nodules are found on and to place accurately the nodules on these roots. The research team created software and a method to measure multiple root parameters which were not available previously. This allows different plant varieties to be compared with precise measurements of the root structure in order to figure out which plants will grow better.

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Trehalose Is A Chemical Attractant In The Establishment Of Coral Symbiosis, M. Hagedorn, V. Carter, N. Zuchowicz, M. Phillips, C. Penfield, B. Shamenek, Elizabeth A. Vallen, F. W. Kleinhans, K. Peterson, M. White, P. H. Yancey Jan 2015

Trehalose Is A Chemical Attractant In The Establishment Of Coral Symbiosis, M. Hagedorn, V. Carter, N. Zuchowicz, M. Phillips, C. Penfield, B. Shamenek, Elizabeth A. Vallen, F. W. Kleinhans, K. Peterson, M. White, P. H. Yancey

Biology Faculty Works

Coral reefs have evolved with a crucial symbiosis between photosynthetic dinoflagellates (genus Symbiodinium) and their cnidarian hosts (Scleractinians). Most coral larvae take up Symbiodinium from their environment; however, the earliest steps in this process have been elusive. Here we demonstrate that the disaccharide trehalose may be an important signal from the symbiont to potential larval hosts. Symbiodinium freshly isolated from Fungia scutaria corals constantly released trehalose (but not sucrose, maltose or glucose) into seawater, and released glycerol only in the presence of coral tissue. Spawning Fungia adults increased symbiont number in their immediate area by excreting pellets of Symbiodinium, and …

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The Candidate Cancer Gene Database: A Database Of Cancer Driver Genes From Forward Genetic Screens In Mice, Kenneth L. Abbott, Erik T. Nyre, Juan Abrahante, Yen Yi Ho, Rachel Isaksson Vogel, Timothy K. Starr Jan 2015

The Candidate Cancer Gene Database: A Database Of Cancer Driver Genes From Forward Genetic Screens In Mice, Kenneth L. Abbott, Erik T. Nyre, Juan Abrahante, Yen Yi Ho, Rachel Isaksson Vogel, Timothy K. Starr

Faculty Publications

Identification of cancer driver gene mutations is crucial for advancing cancer therapeutics. Due to the overwhelming number of passenger mutations in the human tumor genome, it is difficult to pinpoint causative driver genes. Using transposon mutagenesis in mice many laboratories have conducted forward genetic screens and identified thousands of candidate driver genes that are highly relevant to human cancer. Unfortunately, this information is difficult to access and utilize because it is scattered across multiple publications using different mouse genome builds and strength metrics. To improve access to these findings and facilitate metaanalyses, we developed the Candidate Cancer Gene Database (CCGD, …

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Low-Severity Fire Increases Tree Defense Against Bark Beetle Attacks, Sharon Metzger Hood, Anna Sala, Emily K. Heyerdahl, Marion Boutin Jan 2015

Low-Severity Fire Increases Tree Defense Against Bark Beetle Attacks, Sharon Metzger Hood, Anna Sala, Emily K. Heyerdahl, Marion Boutin

Biological Sciences Faculty Publications

Induced defense is a common plant strategy in response to herbivory. Although abiotic damage, such as physical wounding, pruning, and heating, can induce plant defense, the effect of such damage by large-scale abiotic disturbances on induced defenses has not been explored and could have important consequences for plant survival facing future biotic disturbances. Historically, low-severity wildfire was a widespread, frequent abiotic disturbance in many temperate coniferous forests. Native Dendroctonus and Ips bark beetles are also a common biotic disturbance agent in these forest types and can influence tree mortality patterns after wildfire. Therefore, species living in these disturbance-prone environments with …

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The Body Size Dependence Of Trophic Cascades, John Delong, Benjamin Gilbert, Jonathan B. Shurin, Van M. Savage, Brandon T. Barton, Christopher F. Clements, Anthony I. Dell, Hamish S. Greig, Christopher D.G. Harley, Pavel Kratina, Kevin S. Mccann, Tyler D. Tunney, David A. Vasseur, Mary I. O’Connor Jan 2015

The Body Size Dependence Of Trophic Cascades, John Delong, Benjamin Gilbert, Jonathan B. Shurin, Van M. Savage, Brandon T. Barton, Christopher F. Clements, Anthony I. Dell, Hamish S. Greig, Christopher D.G. Harley, Pavel Kratina, Kevin S. Mccann, Tyler D. Tunney, David A. Vasseur, Mary I. O’Connor

School of Biological Sciences: Faculty Publications

Trophic cascades are indirect positive effects of predators on resources via control of intermediate consumers. Larger-bodied predators appear to induce stronger trophic cascades (a greater rebound of resource density toward carrying capacity), but how this happens is unknown because we lack a clear depiction of how the strength of trophic cascades is determined. Using consumer-resource models, we first show that the strength of a trophic cascade has an upper limit set by the interaction strength between the basal trophic group and its consumer and that this limit is approached as the interaction strength between the consumer and its predator increases. …

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A Structure-Function Approach To Understanding The Dual Functions Of The Plant Mechanosensitive Ion Channel Msl10, Grigory Maksaev, Kira M. Veley, Elizabeth S. Haswell Jan 2015

A Structure-Function Approach To Understanding The Dual Functions Of The Plant Mechanosensitive Ion Channel Msl10, Grigory Maksaev, Kira M. Veley, Elizabeth S. Haswell

Biology Faculty Research

MscS‐Like (MSL) 10 is a member of the MscS superfamily of mechanosensitive ion channels and one of 10 MSL proteins in the model flowering plant Arabidopsis thaliana. Unlike Escherichia coli MscS, MSL10 contains 6 transmembrane helices, and only its C‐terminal TM helix shows homology with EcMscS's pore‐lining domain. MSL10 has been shown to provide a mechanosensitive activity in plant cells and Xenopus oocytes. However, its structural organization and function in plants are just beginning to be elucidated.

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Determining Best Practices For Freshwater Mussel Relocation Using Burrowing And Behavior, Lindsey Marie Griffin Jan 2015

Determining Best Practices For Freshwater Mussel Relocation Using Burrowing And Behavior, Lindsey Marie Griffin

Biology Theses

Of the 302 freshwater mussel species in North America, 70% are listed as imperiled or threatened. The increase in habitat impairments and reduction in mussel fauna has increased interest in relocations in regard to the Endangered Species Act of 1973. The most common time to conduct mussel relocations is July to September, when it is speculated that the least amount of reproductive stress will occur and the metabolic rate is high enough for reburying. Because summer is the most common time to relocate threatened or endangered freshwater mussels, the effects of extreme temperature differences (27°C to over 49°C) on burrowing …

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Galapagos Seabirds' Lice Community: Host Hetero-Specific Interactions And Parasite Evolution, Jose Luis Rivera Jan 2015

Galapagos Seabirds' Lice Community: Host Hetero-Specific Interactions And Parasite Evolution, Jose Luis Rivera

Dissertations

My dissertation focused on understanding the factors behind host-parasite specificity and parasite diversification, using Galapagos seabirds and their ectoparasites as the study system. This system comprised the seabird hosts (magnificent and great frigatebirds, Nazca, blue-footed and red-footed boobies) and nine species of ectoparasitic lice (one Pectinopygus ischnoceran louse species infecting each host, two species of Colpocephalum amblyceran lice, one on each frigatebird species, and two shared amblyceran lice, Eidmanniella albescens found on Nazca and blue-footed boobies and Fregatiella aurifasciata found on the two frigatebirds). Using as focal species Eidmanniella albescens and Fregatiella aurifasciata, which infect multiple hosts, I analyzed how …

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Vesicle Biomechanics In A Time-Varying Magnetic Field, Hui Ye, Austen Curcuru Jan 2015

Vesicle Biomechanics In A Time-Varying Magnetic Field, Hui Ye, Austen Curcuru

Biology: Faculty Publications and Other Works

Background Cells exhibit distortion when exposed to a strong electric field, suggesting that the field imposes control over cellular biomechanics. Closed pure lipid bilayer membranes (vesicles) have been widely used for the experimental and theoretical studies of cellular biomechanics under this electrodeformation. An alternative method used to generate an electric field is by electromagnetic induction with a time-varying magnetic field. References reporting the magnetic control of cellular mechanics have recently emerged. However, theoretical analysis of the cellular mechanics under a time-varying magnetic field is inadequate. We developed an analytical theory to investigate the biomechanics of a modeled vesicle under a …

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Gene Expression Patterns That Support Novel Developmental Stress Buffering In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Josiah T. Wagner, Jason E. Podrabsky Jan 2015

Gene Expression Patterns That Support Novel Developmental Stress Buffering In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Josiah T. Wagner, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Background: The cellular signaling mechanisms and morphogenic movements involved in axis formation and gastrulation are well conserved between vertebrates. In nearly all described fish, gastrulation and the initial patterning of the embryonic axis occur concurrently with epiboly. However, annual killifish may be an exception to this norm. Annual killifish inhabit ephemeral ponds in South America and Africa and permanent populations persist by the production of stress-tolerant eggs. Early development of annual killifish is unique among vertebrates because their embryonic blastomeres disperse randomly across the yolk during epiboly and reaggregate several days later to form the embryo proper. In addition, annual …

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Integrated Survival Analysis Using An Event-Time Approach In A Bayesian Framework, Daniel P. Walsh, Victoria J. Dreitz, Dennis M. Heisey Jan 2015

Integrated Survival Analysis Using An Event-Time Approach In A Bayesian Framework, Daniel P. Walsh, Victoria J. Dreitz, Dennis M. Heisey

Wildlife Biology Faculty Publications

Event-time or continuous-time statistical approaches have been applied throughout the bio-statistical literature and have led to numerous scientific advances. However, these techniques have traditionally relied on knowing failure times. this has limited application of these analyses, particularly, within the ecological field where fates of marked animals may be unknown. To address these limitations, we developed in integrated approach within a Bayesian framework to estimate hazard rates in the face of unknown fates. We combine failure/survival times from individuals whose fates are known and times of which are interval-censored with information from those whose fates are unknown, and model the process …

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Assessing Infection Patterns In Chinese Mystery Snails From Wisconsin, Usa Using Field And Laboratory Approaches, Brittany Harried, Kyle Fischer, Kathryn E. Perez, Gregory J. Sandland Jan 2015

Assessing Infection Patterns In Chinese Mystery Snails From Wisconsin, Usa Using Field And Laboratory Approaches, Brittany Harried, Kyle Fischer, Kathryn E. Perez, Gregory J. Sandland

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

The success of invasive species establishment in new habitats depends, in part, on interactions with other members of the invaded community. Cipangopaludina chinensis, the Chinese mystery snail (CMS), is an exotic, invasive snail in North America. Since its introduction in the 1890s, CMS have spread to a number of watersheds across the United States and parts of Canada. This invasion has generated questions about the snail’s capacity to serve as a host for parasites within local habitats, including parasites with conservation implications. To begin addressing these questions, we necropsied 147 wild-caught snails from 22 lakes across Wisconsin, finding only two …

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The Global Distribution Of Diet Breadth In Insect Herbivores, Robert Marquis, Matthew Forister, Vojtech Novotny, Anna Panorska, Leontine Baje, Yves Basset, Philip Butterill, Lukas Cizek, Phyllis Coley, Francesca Dem, Ivone Diniz, Pavel Drozd, Mark Fox, Andrea Glassmire, Rebecca Hazen, Jan Hrcek, Joshua Jahner, Ondrej Kaman, Tomasz Kozubowski, Thomas Kursar, Owen Lewis, John Lill, Scott Miller, Helena Morais, Masashi Murakami, Herbert Nickel, Nicholas Pardikes, Robert Ricklefs, Michael Singer, Angela Smilanich, John Stireman, Santiago Villamarín-Cortez, Stepan Vodka, Martin Volf, David Wagner, Thomas Walla, George Weiblen, Lee Dyer Jan 2015

The Global Distribution Of Diet Breadth In Insect Herbivores, Robert Marquis, Matthew Forister, Vojtech Novotny, Anna Panorska, Leontine Baje, Yves Basset, Philip Butterill, Lukas Cizek, Phyllis Coley, Francesca Dem, Ivone Diniz, Pavel Drozd, Mark Fox, Andrea Glassmire, Rebecca Hazen, Jan Hrcek, Joshua Jahner, Ondrej Kaman, Tomasz Kozubowski, Thomas Kursar, Owen Lewis, John Lill, Scott Miller, Helena Morais, Masashi Murakami, Herbert Nickel, Nicholas Pardikes, Robert Ricklefs, Michael Singer, Angela Smilanich, John Stireman, Santiago Villamarín-Cortez, Stepan Vodka, Martin Volf, David Wagner, Thomas Walla, George Weiblen, Lee Dyer

Biology Department Faculty Works

Understanding variation in resource specialization is important for progress on issues that include coevolution, community assembly, ecosystem processes, and the latitudinal gradient of species richness. Herbivorous insects are useful models for studying resource specialization, and the interaction between plants and herbivorous insects is one of the most common and consequential ecological associations on the planet. However, uncertainty persists regarding fundamental features of herbivore diet breadth, including its relationship to latitude and plant species richness. Here, we use a global dataset to investigate host range for over 7,500 insect herbivore species covering a wide taxonomic breadth and interacting with more than …

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The Quest For Ash Resistance To Eab: Towards A Mechanistic Understanding, Daniel A. Herms, Don Cipollini, K. S. Knight, J. L. Koch, T. M. Poland, Chad Michael Rigsby, Justin G.A. Whitehill, Pierluigi Bonello Jan 2015

The Quest For Ash Resistance To Eab: Towards A Mechanistic Understanding, Daniel A. Herms, Don Cipollini, K. S. Knight, J. L. Koch, T. M. Poland, Chad Michael Rigsby, Justin G.A. Whitehill, Pierluigi Bonello

Biological Sciences Faculty Publications

Since emerald ash borer (EAB), Agrilus planipennis, was discovered in North America in 2002, it has killed many millions of ash trees in North America, and ash mortality now exceeds 99% near the epicenter of the invasion in southeast Michigan (Klooster et al. 2014). The development of EAB-resistant ash trees will be critical for restoration of ash in natural and urban forests. Goals of our collaboration are to identify, breed and screen ash germplasm for EAB resistance and silvicultural traits; and identify mechanisms of EAB resistance to facilitate breeding and screening.

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Recent Origin Of Low Trabecular Bone Density In Modern Humans, Habiba Chirchir Phd, Tracy L. Kivell, Christopher B. Ruff, Jean-Jacques Hublin, Kristian J. Carlson, Bernhard Zipfel, Brian G. Richmond Jan 2015

Recent Origin Of Low Trabecular Bone Density In Modern Humans, Habiba Chirchir Phd, Tracy L. Kivell, Christopher B. Ruff, Jean-Jacques Hublin, Kristian J. Carlson, Bernhard Zipfel, Brian G. Richmond

Biological Sciences Faculty Research

Humans are unique, compared with our closest living relatives (chimpanzees) and early fossil hominins, in having an enlarged body size and lower limb joint surfaces in combination with a relatively gracile skeleton (i.e., lower bone mass for our body size). Some analyses have observed that in at least a few anatomical regions modern humans today appear to have relatively low trabecular density, but little is known about how that density varies throughout the human skeleton and across species or how and when the present trabecular patterns emerged over the course of human evolution. Here, we test the hypotheses that (i) …

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Lineage Sorting In Multihost Parasites: Eidmanniella Albescens And Fregatiella Aurifasciata On Seabirds From The Galapagos Islands, Jose Rivera-Parra, Iris Levin, Kevin Johnson, Patricia Parker Jan 2015

Lineage Sorting In Multihost Parasites: Eidmanniella Albescens And Fregatiella Aurifasciata On Seabirds From The Galapagos Islands, Jose Rivera-Parra, Iris Levin, Kevin Johnson, Patricia Parker

Biology Department Faculty Works

Parasites comprise a significant percentage of the biodiversity of the planet and are useful systems to test evolutionary and ecological hypotheses. In this study, we analyze the effect of host species identity and the immediate local species assemblage within mixed species colonies of nesting seabirds on patterns of genetic clustering within two species of multihost ectoparasitic lice. We use three genetic markers (one mitochondrial, COI, and two nuclear, EF1‐α and wingless) and maximum likelihood phylogenetic trees to test whether (1) parasites show lineage sorting based on their host species; and (2) switching of lineages to the alternate host species depends …

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Insects In Fluctuating Thermal Environments., Hervé Colinet, Brent J Sinclair, Philippe Vernon, David Renault Jan 2015

Insects In Fluctuating Thermal Environments., Hervé Colinet, Brent J Sinclair, Philippe Vernon, David Renault

Biology Publications

All climate change scenarios predict an increase in both global temperature means and the magnitude of seasonal and diel temperature variation. The nonlinear relationship between temperature and biological processes means that fluctuating temperatures lead to physiological, life history, and ecological consequences for ectothermic insects that diverge from those predicted from constant temperatures. Fluctuating temperatures that remain within permissive temperature ranges generally improve performance. By contrast, those which extend to stressful temperatures may have either positive impacts, allowing repair of damage accrued during exposure to thermal extremes, or negative impacts from cumulative damage during successive exposures. We discuss the mechanisms underlying …

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Satrat: Staphylococcus Aureus Transcript Regulatory Network Analysis Tool, Tamilselvi Gopal, Vijayaraj Nagarajan, Mohamed O. Elasri Jan 2015

Satrat: Staphylococcus Aureus Transcript Regulatory Network Analysis Tool, Tamilselvi Gopal, Vijayaraj Nagarajan, Mohamed O. Elasri

Faculty Publications

Staphylococcus aureus is a commensal organism that primarily colonizes the nose of healthy individuals. S. aureus causes a spectrum of infections that range from skin and soft-tissue infections to fatal invasive diseases. S. aureus uses a large number of virulence factors that are regulated in a coordinated fashion. The complex regulatory mechanisms have been investigated in numerous high-throughput experiments. Access to this data is critical to studying this pathogen. Previously, we developed a compilation of microarray experimental data to enable researchers to search, browse, compare, and contrast transcript profiles. We have substantially updated this database and have built a novel …

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Finding Our Way Through Phenotypes, Andrew R. Deans, Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, Laurel D. Cooper, Mélanie Courtot, Sándor Csösz, Hong Cui, Wasila Dahdul, Sandip Das, T. Alexander Dececchi, Agnes Dettai, Rui Diogo, Robert E. Druzinsky, Michel Dumontier, Nico M. Franz, Frank Friedrich, George V. Gkoutos, Melissa Haendel, Luke J. Harmon, Terry F Hayamizu, Yongqun He, Heather M. Hines, Nizar Ibrahim, Laura M. Jackson, Pankaj Jaiswal, Christina James-Zorn, Sebastian Köhler, Guillaume Lecointre, Hilmar Lapp, Carolyn J. Lawrence, Nicolas Le Novère, John G. Lundberg, James Macklin, Austin R. Mast, Peter E. Midford, István Mikó, Christopher J. Mungall, Anika Oellrich, David Osumi-Sutherland, Helen Parkinson, Martín J. Ramírez, Stefan Richter, Peter N. Robinson, Alan Ruttenberg, Katja S. Schulz, Erik Segerdell, Katja C. Seltmann, Michael Sharkey, Aaron D. Smith, Barry Smith, Chelsea D. Specht, R. Burke Squires, Robert W. Thacker, Anne Thessen, Jose Fernandez-Triana, Mauno Vihinen, Peter D. Vize, Lars Vogt, Christine E. Wall, Ramona L. Walls, Monte Westerfeld, Robert A. Wharton, Christian S. Wirkner, James B. Woolley, Matthew J. Yoder, Aaron M. Zorn, Paula Mabee Jan 2015

Finding Our Way Through Phenotypes, Andrew R. Deans, Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, Laurel D. Cooper, Mélanie Courtot, Sándor Csösz, Hong Cui, Wasila Dahdul, Sandip Das, T. Alexander Dececchi, Agnes Dettai, Rui Diogo, Robert E. Druzinsky, Michel Dumontier, Nico M. Franz, Frank Friedrich, George V. Gkoutos, Melissa Haendel, Luke J. Harmon, Terry F Hayamizu, Yongqun He, Heather M. Hines, Nizar Ibrahim, Laura M. Jackson, Pankaj Jaiswal, Christina James-Zorn, Sebastian Köhler, Guillaume Lecointre, Hilmar Lapp, Carolyn J. Lawrence, Nicolas Le Novère, John G. Lundberg, James Macklin, Austin R. Mast, Peter E. Midford, István Mikó, Christopher J. Mungall, Anika Oellrich, David Osumi-Sutherland, Helen Parkinson, Martín J. Ramírez, Stefan Richter, Peter N. Robinson, Alan Ruttenberg, Katja S. Schulz, Erik Segerdell, Katja C. Seltmann, Michael Sharkey, Aaron D. Smith, Barry Smith, Chelsea D. Specht, R. Burke Squires, Robert W. Thacker, Anne Thessen, Jose Fernandez-Triana, Mauno Vihinen, Peter D. Vize, Lars Vogt, Christine E. Wall, Ramona L. Walls, Monte Westerfeld, Robert A. Wharton, Christian S. Wirkner, James B. Woolley, Matthew J. Yoder, Aaron M. Zorn, Paula Mabee

Entomology Faculty Publications

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of …

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Evolution And Ecology Of Two Iconic Australian Clades: The Meliphagidae (Birds) And The Hakeinae (Plants), Eliot Trimarchi Miller Jan 2015

Evolution And Ecology Of Two Iconic Australian Clades: The Meliphagidae (Birds) And The Hakeinae (Plants), Eliot Trimarchi Miller

Dissertations

The first part of this dissertation explores the evolution of two iconic groups of species through Australian climate space: the Meliphagidae, or honeyeaters, which are primarily nectar-feeding birds, and the Hakeinae, a section of the plant family Proteaceae. Both groups are inferred to have had their origins in Gondwanan rainforests that were widespread across Australia 45 million years ago and then diversified into more arid environments as the continent’s climate became more arid. Accordingly, dry environments are inhabited by closely related (phylogenetically clustered) sets of species, although, in contrast to the honeyeaters, Hakeinae communities are characterized by more localized diversification. …

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Drift Algae In New Haven Harbor And Impacts On Benthic Communities, Roman Zajac, Andrea Mccarthy Jan 2015

Drift Algae In New Haven Harbor And Impacts On Benthic Communities, Roman Zajac, Andrea Mccarthy

Biology and Environmental Science Faculty Publications

In 2009 the University of New Haven initiated studies to develop a contemporary database and assessment of the benthic ecology of New Haven Harbor. Previous studies were last conducted in the 1970s and 1980s (e.g. McCusker, and Bosworth 1979, 1981, Rhoads and Germano 1982). Benthic populations and communities are excellent indicators of environmental conditions and are regularly used for environmental assessment in estuarine and coastal waters (e.g. Pearson and Rosenberg 1978, Rhoads et al. 1978, Zajac and Whitlatch 2001, Mangi 2003). Given the inherent ability of the benthos to integrate sediment and water quality, many environmental indicators and indices to …

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The Effects Of Parasites, Metals, And Environmental Conditions On Spotted Salamander (Ambystoma Maculatum) Populations Breeding In Northern Arkansas, Heather M. Demali Jan 2015

The Effects Of Parasites, Metals, And Environmental Conditions On Spotted Salamander (Ambystoma Maculatum) Populations Breeding In Northern Arkansas, Heather M. Demali

Student Theses and Dissertations

As more and more stressors impact amphibians worldwide, studies investigating multiple stressors currently affecting amphibians have increased. Novel to herpetological research is investigating parasites and metals of concern in spotted salamanders (Ambystoma maculatum) in northern Arkansas during the spotted salamander's breeding season. This study was conducted in Greene County and Stone County, Arkansas, during the spotted salamander's 2014 breeding season. Sublethal and lethal effects on Ceriodaphnia dubia were not observed; however, decrease in Pimephales promelas growth and survival suggest that other environmental stressors are affecting the vertebrate test organism in water from these ponds. Metal analysis showed that with increased …

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Single-Unit Turbines And Bat Mortality In Arkansas, Phillip Nathaniel Jordan Jan 2015

Single-Unit Turbines And Bat Mortality In Arkansas, Phillip Nathaniel Jordan

Student Theses and Dissertations

Wind power has become a substantial investment in the United States energy portfolio. It is approximated that by the year 2030, 30% of the world's energy will be produced by wind. An estimated 600,000 to 800,000 bats are killed in the United States every year by wind turbines. Using Anabat SD2, mist netting, fatalities searches, and two automatic-acoustic identifiers, I investigated six single-single unit turbines and their effects on bats in two ecoregions of Arkansas during the summers of 2012 and 2013. Netting effort totaled 30 nights with 94 bats captured during that time. I performed a combined 142 fatality …

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