Animal Sciences Commons^™

High Quality Draft Genomes Of The Mycoplasma Mycoides Subsp. Mycoides Challenge Strains Afadé And B237, Anne Fischer, Ivette Santana-Cruz, Jan Hegerman, Hadrien Gourlé, Elise Schieck, Mathieu Lambert, Suvarna Nadendla, Hezron Wesonga, Rachel A. Miller, Sanjay Vashee, Johann Weber, Jochen Meens, Joachim Frey, Joerg Jores

All Peer-Reviewed Publications

Members of the Mycoplasma mycoides cluster' represent important livestock pathogens worldwide. Mycoplasma mycoides subsp. mycoides is the etiologic agent of contagious bovine pleuropneumonia (CBPP), which is still endemic in many parts of Africa. We report the genome sequences and annotation of two frequently used challenge strains of Mycoplasma mycoides subsp. mycoides, Afadé and B237. The information provided will enable downstream 'omics' applications such as proteomics, transcriptomics and reverse vaccinology approaches. Despite the absence of Mycoplasma pneumoniae like cyto-adhesion encoding genes, the two strains showed the presence of protrusions. This phenotype is likely encoded by another set of genes.

Factors Influencing The Choice Of A Safe Haven For Offloading Illegally Caught Fish: A Comparative Analysis Of Developed And Developing Economies, Nerea Marteache, Julie S. Viollaz, Gohar A. Petrossian

Publications and Research

Using data from 72 countries, this study focuses on factors that affect illegal, unreported, and unregulated (IUU) fishing vessels’ choice of country to offload their catch, with a specific emphasis on the differences between developed and developing economies. The concept of choice-structuring properties is applied to analyze whether the following factors influence the selection of a country: concealability of vessels and illegally caught fish; convenience of the ports; strength of fisheries monitoring, control, and surveillance measures; effectiveness of country governance; and commitment to wildlife protection regulations. Results indicate that, rather than a country’s level of development, situational factors play a …

Antioxidant Effect Of Spent, Ground, And Lyophilized Brew From Roasted Coffee In Frozen Cooked Pork Patties, Katrina Maryse Malixi Jully, Criselda Toto, Lilian Were

Food Science Faculty Articles and Research

The ability of light and dark roasted coffee (1 g/kg) in varying application forms (spent ground [SCG], whole ground [WGC], or lyophilized brew [LBC]) to inhibit lipid and protein oxidation in cooked pork patties stored at −18 °C was monitored over 3 months. Malondialdehyde (MDA) for the negative control (NC) increased from 0.31 to 1.11 mg MDA/kg pork over 3 months, while pork with coffee or rosemary oleoresin had lower values at month 3 (0.054–0.40 mg MDA/kg pork). The NC had the highest values for hexanal, octanal, and nonanal (2.59, 0.10, and 0.13 mg/kg pork, respectively), while light and dark …

The First Whole Genome And Transcriptome Of The Cinereous Vulture Reveals Adaptation In The Gastric And Immune Defense Systems And Possible Convergent Evolution Between The Old And New World Vultures, Oksung Chung, Seondeok Jin, Yun Sung Cho, Jeongheui Lim, Hyunho Kim, Sungwoong Jho, Hak-Min Kim, Jehoon Jun, Hyejin Lee, Alvin Chon, Junsu Ko, Jeremy Edwards, Jessica A. Weber, Kyudong Han, Stephen J. O'Brien, Andrea Manica, Jong Bhak, Woon Kee Paek

Biology Faculty Articles

Background: The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.

Results: We sequenced the genome of a cinereous vulture, and mapped it to the bald …

Interaction Of Isoflavones And Endophyte-Infected Tall Fescue Seed Extract On Vasoactivity Of Bovine Mesenteric Vasculature, Yang Jia, David L. Harmon, Michael D. Flythe, James L. Klotz

Animal and Food Sciences Faculty Publications

It was hypothesized that isoflavones may attenuate ergot alkaloid-induced vasoconstriction and possibly alleviate diminished contractility of vasculature after exposure to ergot alkaloids. The objective of this study was to determine if prior incubation of bovine mesenteric vasculature with the isoflavones formononetin (F), biochanin A (B), or an ergovaline-containing tall fescue seed extract (EXT) and their combinations affect ergotamine (ERT)-induced contractility. Multiple segments of mesenteric artery and vein supporting the ileal flange of the small intestine were collected from Angus heifers at slaughter (n = 5, bodyweight = 639 ± 39 kg). Duplicates of each vessel …

Laterality Enhances Numerical Skills In The Guppy, Poecilia Reticulata, Marco Dadda, Christian Agrillo, Angelo Bisazza, Culum Brown

Sentience Collection

It has been hypothesized that cerebral lateralization can significantly enhance cognition and that this was one of the primary selective forces shaping its wide-spread evolution amongst vertebrate taxa. Here, we tested this hypothesis by examining the link between cerebral lateralization and numerical discrimination. Guppies, Poecilia reticulata, were sorted into left, right and non-lateralized groups using a standard mirror test and their numerical discrimination abilities tested in both natural shoal choice and abstract contexts. Our results show that strongly lateralized guppies have enhanced numerical abilities compared to non-lateralized guppies irrespective of context. These data provide further credence to the notion that …

Maturity Characteristics Of Pacific Saury During Fishing Season In The Northwest Pacific, Wen-Bin Huang, Yu-Chun Huang

Journal of Marine Science and Technology–Taiwan

Pacific saury is a commercially important fish in the Northwest Pacific. This study examined the maturity characteristics, gonadosomatic index (GSI), condition factor (CF), and ovarian developmental stage of the saury stock in three months of the fishing season (from May to December) in the Northwest Pacific. The maturity characteristics of saury varied among these three months (May, July, and October) in 2009. In May, large GSI and CF values with advanced ovarian developmental stages but small knob lengths (KnL) and body weights (BW) were found. Also in this month, the large-sized saury (> 29 cm) possessed large GSI values and …

Cytokine Gene Expression In The Maternal-Fetal Interface In Somatic Cell Nuclear Transfer Pregnancies In Small Ruminants, Heloisa M. Rutigliano, Amanda Wilhelm, Justin Hall, Bi Shi, Qinggang Meng, Rusty Stott, Tom D. Bunch, Kenneth L. White, Christopher J. Davies, Irina A. Polejaeva

Animal, Dairy, and Veterinary Science Faculty Publications

The present retrospective study investigates pregnancy rates, incidence of pregnancy losses and large offspring syndrome (LOS), and immune-related gene expression of sheep and goat somatic cell nuclear transfer (SCNT) pregnancies. We hypothesized that significantly higher pregnancy losses observed in sheep SCNT pregnancies compared to goats are due to the increased amounts of T-helper 1 cytokines and pro-inflammatory mediators at the maternal-fetal interface. Sheep and goat SCNT pregnancies were generated using the same procedure. Control pregnancies were established by natural breeding. Although SCNT pregnancy rates at 45 days were similar in both species, pregnancy losses between 45 and 60 days and …

The Broad-Spectrum Antiviral Favipiravir Protects Guinea Pigs From Lethal Lassa Virus Infection Post-Disease Onset, David Safronetz, Kyle Rosenke, Jonna B. Westover, Cynthia Martellaro, Atsushi Okumura, Yousuke Furuta, Joan Geisbert, Greg Saturday, Takashi Komeno, Thomas W. Geisbert, Heinz Feldmann, Brian B. Gowen

Plants, Soils, and Climate Faculty Publications

With up to 500,000 infections annually, Lassa virus (LASV), the cause of Lassa fever, is one of the most prevalent etiological agents of viral hemorrhagic fever (VHF) in humans. LASV is endemic in several West African countries with sporadic cases and prolonged outbreaks observed most commonly in Sierra Leone, Liberia, Guinea and Nigeria. Additionally several cases of Lassa fever have been imported into North America, Europe and Asia making LASV a global threat to public health. Despite this, currently no approved therapeutic or vaccine exists to treat or prevent LASV infections. Here, using a passaged strain of LASV that is …

The Broad-Spectrum Antiviral Favipiravir Protects Guinea Pigs From Lethal Lassa Virus Infection Post-Disease Onset, David Safronetz, Kyle Rosenke, Cynthia Martellaro, Heinz Feldmann, Jonna B. Westover, Brian B. Gowen, Atsushi Okumura, Yousuke Furuta, Takashi Komeno, Greg Saturday, Joan Geisbert, Thomas W. Geisbert

Animal, Dairy, and Veterinary Science Faculty Publications

With up to 500,000 infections annually, Lassa virus (LASV), the cause of Lassa fever, is one of the most prevalent etiological agents of viral hemorrhagic fever (VHF) in humans. LASV is endemic in several West African countries with sporadic cases and prolonged outbreaks observed most commonly in Sierra Leone, Liberia, Guinea and Nigeria. Additionally several cases of Lassa fever have been imported into North America, Europe and Asia making LASV a global threat to public health. Despite this, currently no approved therapeutic or vaccine exists to treat or prevent LASV infections. Here, using a passaged strain of LASV that is …

A Tail Of Two Phages: Genomic And Functional Analysis Of Listeria Monocytogenes Phages Vb_Lmos_188 And Vb_Lmos_293 Reveal The Receptor-Binding Proteins Involved In Host Specificity, Aidan Casey, Kieran Jordan, Horst Neve, Aidan Coffey, Olivia Mcauliffe

Department of Biological Sciences Publications

The physical characteristics of bacteriophages establish them as viable candidates for downstream development of pathogen detection assays and biocontrol measures. To utilize phages for such purposes, a detailed knowledge of their host interaction mechanisms is a prerequisite. There is currently a wealth of knowledge available concerning Gram-negative phage-host interaction, but little by comparison for Gram-positive phages and Listeria phages in particular. In this research, the lytic spectrum of two recently isolated Listeria monocytogenes phages (vB_LmoS_188 and vB_LmoS_293) was determined, and the genomic basis for their observed serotype 4b/4e host-specificity was investigated using comparative genomics. The late tail genes of these …

Gene Loss, Adaptive Evolution And The Co-Evolution Of Plumage Coloration Genes With Opsins In Birds, Rui Borges, Imran Khan, Warren E. Johnson, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O'Brien, Agostinho Antunes

Biology Faculty Articles

Background: The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems.

Results: We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal …

Using An Agent-Based Model To Study The Effect Of Reproductive Skew On Mongoose Populations, Stacy Lee Mowry

Theses and Dissertations

Reproductive skew is the name given to the unequal partitioning of breeding

within social groups. Within these groups a mating hierarchy emerges wherein one dominant mating pair holds an unproportional majority of the group's reproductive benefit, while other members mate infrequently, yet allocate energy and resources toward the offspring of the dominant group members. In this paper, we use an agent-based model, which mimics dwarf and banded mongoose populations, to investigate how reproductive skew aftects the speed natural selection, and thus how reproductive skew affects fitness. The results of the model show that due to the geometric structure of skewed …

Métodos Cuantitativos Para La Conservación De Los Vertebrados, Michael J. Conroy, John P. Carroll, Juan Carlos Senar, Jeffrey J. Thompson

School of Natural Resources: Faculty Publications

Este libro es destinado para el uso por biólogos del campo y otras personas, incluso biólogos de campo en el futuro que podrían estar en un curso de la universidad y trabajando en estudios y conservación de animales. Nuestro objetivo es que los biólogos usen este libro como (haciendo apología a nuestro colega Evan Cooch) una “introducción suave” al campo de la ecología cuantitativa. Esperamos convencer a los lectores que los métodos y aproximaciones del libro no son solo para los matemáticos, estadísticos y programadores de computadoras, sino que de hecho son herramientas esenciales para practicar la conservación en el …

Economic Contribution Of Agriculture And Food To Arkansas' Gross Domestic Product 1997-2013, Leah English, Jennie Popp, Wayne Miller

AAES Research Reports and Research Bulletins

Agricultural production, processing, and retail industries are major contributors to the Arkansas economy in terms of GDP. Agriculture contributes to the economy through direct agricultural production, value-added processing, and agricultural retail activities, and it also plays an important role through its interactions with other sectors. The use of non-agricultural goods and services as inputs into the agricultural sector promotes diversified growth in Arkansas’ economy; thus agriculture remains a vital part of Arkansas’ economy. This report: 1) compares the relative size of the Agriculture and Food Sector in Arkansas with those of neighboring states; 2) provides an overview of Arkansas’ economy …

Viewing The Status Of Virginia’S Environment Through The Lens Of Freshwater Fishes, Paul L. Angermeier, Michael J. Pinder

Virginia Journal of Science

We summarize a range of topics related to the status of Virginia’s freshwater fishes, their reflection of environmental quality, and their contribution to human wellbeing. Since 1994 the list of extant Virginia fishes has lengthened from 210 species to 227 species, mostly due to taxonomic reorganizations. Virginia’s list of Species of Greatest Conservation Need currently contains 96 fish species, predominated by darters (32 species) and minnows (28 species). Increasing trends in species rarity and threats to fishes suggest that Virginia’s aquatic environment is becoming less hospitable for fishes. Prevailing anthropogenic threats to fishes include agriculture, urban development, mineral extraction, forestry, …

The Examination Of Enrichment Using Space And Food For African Elephants (Loxodonta Africana) At The San Diego Zoo Safari Park, Charlotte Hacker

Masters Theses & Specialist Projects

Concern for elephant welfare in zoological facilities has prompted a number of exhibit and management modifications, including those involving enrichment. Knowledge of how these changes impact measures of health and wellbeing, such as elephant movement and behavior, is crucial as the effects of multiple enrichment types and their interactions are largely understudied. The present study used observations and GPS unit collected data to determine the effects of space and food on the walking distance and behavior of thirteen African elephants, whose dominance structure was ascertained by the handlers at the San Diego Zoo Safari Park (SDZSP). This facility has two …

Ua24 Mcicsl Newsletter - October 2015, Shannon R. Trimboli Education Coordinator

MCICSL Newsletter

This issue includes the following:

Mercy Academy Begins Study of Mammoth Cave’s Aquatic Habitat

National Network of Research Learning Centers Releases New Strategic Framework

as well as education and research highlights, MCICSL symposium information and FY16 Education report

Virginia’S Land Mammals: Past And Present, With Some Thoughts About Their Possible Future, John F. Pagels, Nancy D. Moncrief

Virginia Journal of Science

Mammals encountered today in Virginia’s forests and fields include native and nonnative species, feral populations, and free-ranging pets. We examine factors that have influenced Virginia’s terrestrial mammal fauna since the arrival of European colonists in the 1600s and some of the factors that are shaping the fauna today. We look in depth at changes since Handley and Patton’s (1947) first complete monograph on Virginia mammals and augment Linzey’s (1998) book, The Mammals of Virginia. We include current nomenclature, baseline information, and references to comprehensive literature. We discuss some of the current and developing anthropogenic factors that have impacted, or that …

Breeding Birds Of Virginia, Bryan D. Watts

Virginia Journal of Science

Virginia supports a diverse community of breeding birds that has been the focus of investigation for more than 400 years. The avifauna reflects the latitudinal position of the state and the fact that the border extends from the Atlantic Ocean to the Appalachian Mountains. A total of 224 species have been recorded breeding in Virginia, 214 of which are extant. Twenty species have colonized the state since 1900 including 14 since 1950. Of all extant species, 102 (48%) are considered common at least somewhere in the state and 64 (30%) are rare to very rare. Diversity varies by physiographic region …

Prediction Of Plant Height In Arabidopsis Thaliana Using Dna Methylation Data, Yaodong Hu, Gota Morota, Guilherme J. M. Rosa, Daniel Gianola

Department of Animal Science: Faculty Publications

Prediction of complex traits using molecular genetic information is an active area in quantitative genetics research. In the postgenomic era, many types of -omic (e.g., transcriptomic, epigenomic, methylomic, and proteomic) data are becoming increasingly available. Therefore, evaluating the utility of this massive amount of information in prediction of complex traits is of interest. DNA methylation, the covalent change of a DNA molecule without affecting its underlying sequence, is one quantifiable form of epigenetic modification. We used methylation information for predicting plant height (PH) in Arabidopsis thaliana nonparametrically, using reproducing kernel Hilbert spaces (RKHS) regression. Also, we used different criteria for …

Virginia’S Amphibians: Status, Threats And Conservation, Jennifer Sevin, John D. Kleopfer

Virginia Journal of Science

Virginia’s diverse environments support 84 amphibian species (anurans and caudates), making it the third highest state in terms of species richness. However, the Commonwealth matches the global trend in declining amphibian populations with over one-third of its amphibian species in conservation need. The Species of Greatest Conservation Need included in the most recent Virginia Wildlife Action Plan cut across amphibian families and ecoregions. It is challenging to ascertain the exact cause of most of the population declines. In one degree or another, all of the global threats to amphibians exist within Virginia’s borders. While an active research program on amphibians …

The Niehs Superfund Research Program: 25 Years Of Translational Research For Public Health, Philip J Landrigan, Robert O. Wright, Jose F. Cordero, David L. Eaton, Bernard D. Goldstein, Bernhard Hennig, Raina M. Maier, David M. Ozonoff, Martyn T. Smith, Robert H. Tukey

Animal and Food Sciences Faculty Publications

BACKGROUND: The Superfund Research Program (SRP) is an academically based, multidisciplinary, translational research program that for 25 years has sought scientific solutions to health and environmental problems associated with hazardous waste sites. SRP is coordinated by the National Institute of Environmental Health Sciences (NIEHS). It supports multi-project grants, undergraduate and postdoctoral training programs, individual research grants, and Small Business Innovation Research (SBIR) and Technology Transfer Research (STTR) grants.

RESULTS: SRP has had many successes: discovery of arsenic's toxicity to the developing human central nervous system; documentation of benzene toxicity to hematologic progenitor cells in human bone marrow; development …

Frog Diversity And Population Trends In Andasibe, Madagascar, Ryan Herman Herman, Alexandra Ulin

Independent Study Project (ISP) Collection

Facing immediate threats such as habitat loss, emerging infectious diseases, and climate change, the frog populations of the Madagascar rainforest, one of the richest amphibian diversity hotspots in the world, are an important focus for monitoring programs. This study focused on assessing the general diversity, key species population trends, and monitoring effectiveness of the Analamazaotra Forest Station’s amphibian community, a population of over forty species within Andasibe, Madagascar. Building on a long-term monitoring program that began in 2012, visual encounter surveys were conducted over a two-week period in November 2015 along the edge and within the interior of the forest …

The Impact Of The Queensland Shark Control Program On Local Populations Of Threatened Shark Species, 1962-2014, Carolyn Pushaw

Independent Study Project (ISP) Collection

Since 1962, the Queensland government has employed a shark control program consisting of shark nets and drum lines off the coast of popular beaches. This program is intended to protect beachgoers from shark interactions by fishing down local shark populations, reasoning that the fewer “large sharks that are present, all things being equal, the less chance of an attack occurring” (McPhee, 2012). In the current study, trends in Queensland Shark Control Program (QSCP) catch between 1962-2014 are examined for select threatened shark species; namely, Carcharodon carcharias, Carcharias taurus, and Sphyrna spp. For all focus species, significant and consistent …

Characteristics Of Geoffroy’S Tamarin (Saguinus Geoffroyi) Population, Demographics, And Territory Sizes In Urban Park Habitat (Parque Natural Metropolitano, Panama City, Panama), Caitlin Mcnaughton

Independent Study Project (ISP) Collection

Metropolitan parks are an important refuge for wildlife in developed areas. In the tropics, land conversion threatens rainforest habitat that holds some of the highest levels of biodiversity in the world. This study aims to investigate the characteristics of Geoffroy’s tamarin (Saguinus geoffroyi) population, demographics, and territory size in a highly urbanized forest habitat (Parque Natural Metropolitano (PNM), Panama City, Republic of Panamá). Studies of animal response to modified habitats are important as development continues worldwide. S. geoffroyi is an ideal species to study for this purpose due to the species’ tolerance to habitat disturbance. This particular park is …

Temporal Variability And Cooperative Breeding: Testing The Bet-Hedging Hypothesis In The Acorn Woodpecker, Walter D. Koenig, Eric L. Walters

Biological Sciences Faculty Publications

Cooperative breeding is generally considered an adaptation to ecological constraints on dispersal and independent breeding, usually due to limited breeding opportunities. Although benefits of cooperative breeding are typically thought of in terms of increased mean reproductive success, it has recently been proposed that this phenomenonmay be a bet-hedging strategy that reduces variance in reproductive success (fecundity variance) inpopulations living inhighly variable environments. We tested this hypothesis using long-term data on the polygynandrous acorn woodpecker (Melanerpes formicivorus). In general, fecundity variance decreased with increasing sociality, at least when controlling for annual variation in ecological conditions. Nonetheless, decreased fecundity variance …

Growing South Dakota (Fall 2015), College Of Agriculture &. Biological Sciences

Growing South Dakota (Publication of the College of Agriculture, Food and Environmental Sciences)

[Page] 2 Internships Lead to Career Opportunities
[Page] 4 Pre-Professional Prep: Peer Mentors. Anatomy Lab, Networking Opportunities Provide Students Strong Start
[Page] 7 Difference Maker: Range Science Grad Strives To Inspire Native American Youth
[Page] 8 Profiles In Leadership: Preparing Students For A Lifetime Of Learning And Opportunities
[Page] 9 Investing In The Future: Scholarship Donors Share Commitment To Supporting Student Success
[Page] 10 College News
[Page] 12 Economic Buzz: Real-World Applications Gained Through New e-Trading Lab & Student Organizations
[Page] 14 Lessons In Leadership Student Organizations Help Hone Array Of Skills [Page] 15 Little I - 93 Years Of …

The Effects Of Urbanization On Tick Parasitism Rates In Birds Of Southeastern Virginia, Erin Leigh Heller

Biological Sciences Theses & Dissertations

The coastal region of southeastern Virginia is one of the largest urban areas along one of North America’s migratory flyways. Because hundreds of avian species use this flyway, understanding factors affecting birds and their health is of paramount concern. Within this region, 14 species of ticks have been documented, all of which may serve as vectors of mammal (including human) pathogens. By sampling birds at sites of varying levels of urbanization within the coastal southeastern urban matrix, I studied the relationship between ticks and their avian hosts, and how this relationship varies seasonally. Mistnets were set-up at five permanent sites …

The Importance Of Bioacoustics For Dolphin Welfare: Soundscape Characterization With Implications For Management, Heather Ruth Spence

Dissertations, Theses, and Capstone Projects

Sound is the primary sensory modality for dolphins, yet policies mitigating anthropogenic sound exposure are limited in wild populations and even fewer noise policies or guidelines have been developed for governing dolphin welfare under human care. Concerns have been raised that dolphins under human care live in facilities that are too noisy, or are too acoustically sterile. However, these claims have not been evaluated to characterize facility soundscapes, and further, how they compare to wild soundscapes. The soundscape of a wild dolphin habitat off the coast of Quintana, Roo, Mexico was characterized based on Passive Acoustic Monitoring (PAM) recordings over …