Other Genetics and Genomics Commons^™

Highly Targeted Metabolomics Coupled With Gene Expression Analysis By Rt–Qpcr Improves Beef Separation Based On Grass, Grain, Or Grape Supplemented Diet, Lucas Krusinski, Chloe Castanon, Rosalee S. Hellberg, Isabella C. F. Maciel, Muhammad Ahsin, Stephan Van Vliet, Jason E. Rowntree, Jennifer I. Fenton

Food Science Faculty Articles and Research

The objective of this study was to use a multi-omics (i.e., gene expression quantification, metabolomics, and fatty acid [FA] profiling) approach to separate and authenticate beef from three different dietary groups. In this 2-year study, Red Angus steers (n = 54) were randomly allocated to one of three treatments: (1) complex biodiverse pasture (GRASS), (2) total mixed ration (TMR) in feedlot (GRAIN), or (3) TMR in feedlot supplemented with 5% (dry matter) grapeseed extract for the last 30 days (GRAPE). FAs were measured by gas chromatography-mass spectrometry (GC–MS), secondary metabolites were identified using ultra-high-performance liquid chromatography tandem mass spectrometry …

Karyotyping As A Method To Verify Phylogenetic Relationships Among The Enneacanthus Species, Ophelia A. Anderson

Theses and Dissertations

The Enneacanthus genus consists of three species of freshwater fish endemic to eastern North America: E. obesus (Banded Sunfish), E. gloriosus (Blue Spotted Sunfish), and E. chaetodon (Black Banded Sunfish). Previous studies using molecular data suggest that E. obesus and E. gloriosus are more closely related, with E. chaetodon as the most distantly related species in the genus. This study investigates the phylogenetic relationship among the Enneacanthus species, using karyotype characteristics - chromosome number, morphology and fundamental number - as comparative metrics. Chromosome spreads were obtained from scale and gill epithelium samples collected between 1993 and 1994. Prepared slides …

Omani Camels From A Cultural And Genomics Perspective, Al Muatasim Al Zadjali

Electronic Theses and Dissertations

The Dromedarian camel, Camelus dromedarius, is native to the Arabian Peninsula, including the Sultanate of Oman. These camels are used for food, milk, as well as show and racing competitions. Despite their economic and cultural importance research on camels in Oman is limited. The goal of this study was to examine their genomic variation, relationship with camels in other parts of the Arabian Peninsula, and to determine if selective breeding has led to the establishment of distinct breeds in Oman. Information was compiled from multiple sources to produce a comprehensive review on the breeding, management, economic and cultural use, …

Documenting The Southern Range Terminus Of The Wood Frog (Lithobates Sylvaticus) In North America, Christian Braswell

Theses

The Wood Frog (Lithobates sylvaticus) holds a remarkable position in North American amphibian biology, with its range extending from the Arctic Circle down to the near sub-tropical southeastern United States. This thesis presents a novel quantitative polymerase chain reaction analysis (qPCR) primer specific to L. sylvaticus and a survey effort regarding the southernmost distribution and detection of this species in Alabama through the application of environmental DNA (eDNA) sampling techniques. By investigating historical data and employing advanced genetic methodologies, this research provides insights into the contemporary status and distribution of the Wood Frog. This research is important to …

Genome Editing Using Crispr-Cas9 In Annual Killifish Species, Keria Moritsugu-Vandehey

University Honors Theses

CRISPR-Cas9 genome editing has been used successfully to knock out genes in model organisms such as zebrafish, turquoise killifish, and cichlid fish. CRISPR-Cas9 genome editing has not been verified in the annual killifish, Austrofundulus limnaeus. We hypothesize that targeted editing of the tyrosinase gene in embryos of A. limnaeus will lead to fish without the ability to produce black pigment. Embryos at the 1-cell stage were injected with a Cas9 cocktail containing a mix of guide RNA molecules that target the genomic sequence of the tyrosinase gene and either an mRNA coding for the Cas9 protein or Cas9 protein. …

Can Edna Be Used To Locate Shawnee Hills Cavefish Forbesichthys Papilliferus?, Megan Brandt, Timothy Spier Phd, Gary Zeruth Phd

Murray State Theses and Dissertations

Traditional stream fish sampling methods, such as seining and electrofishing, are time consuming, expensive, and limited to short stretches of stream. However, the analysis of environmental DNA (eDNA) from water samples promises to be a quick, inexpensive method for detecting fish. The streams of the Land Between the Lakes Recreational Area (LBL) are unique, undisturbed streams which contain many interesting fish species for which little information exists. One such rare species is the Shawnee Hills Cavefish Forbesichthys papilliferus, which is known to exist in a few LBL streams. However, the complete distribution of the Shawnee Hills Cavefish in LBL …

Determining Population Structure In Kentucky Parascaris Univalens Specimens, Constance Finnerty

Theses and Dissertations--Veterinary Science

Parascaris univalens is a highly pathogenic nematode that affects the gastrointestinal system of young horses. When unaddressed, this parasite causes severe intestinal impactions and even death. Parascaris univalens is also found to have an emergence of anthelmintic resistances, causing a concern for horse owners. Despite its clinical significance, very little work has been done on Parascaris univalens to identify its population structure. This study aimed to determine the population structure of Parascaris univalens through Illumina next generation sequencing (NGS) on three hierarchical categorizations: within a horse, within an isolated herd, and within horses in the state of Kentucky. A total …

Multi-Omics Reveals Largely Distinct Transcript- And Protein-Level Responses To The Environment In An Intertidal Mussel, Lani U. Gleason, Florian J. Fekete, Richelle L. Tanner, W. Wesley Dowd

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Organismal responses to stressful environments are influenced by numerous transcript- and protein-level mechanisms, and the relationships between expression changes at these levels are not always straightforward. Here, we used paired transcriptomic and proteomic datasets from two previous studies from gill of the California mussel, Mytilus californianus, to explore how simultaneous transcript and protein abundance patterns may diverge under different environmental scenarios. Field-acclimatized mussels were sampled from two disparate intertidal sites; individuals from one site were subjected to three further treatments (common garden, low-intertidal or high-intertidal outplant) that vary in temperature and feeding time. Assessing 1519 genes shared between …

Genetic Considerations For The Conservation Of The Red Junglefowl, Courtney Lee Mcpheron

University Honors Theses

The undomesticated wild populations of our domestic species deserve heightened consideration when it comes to their conservation. Not only do they carry significant socio-cultural and economic roles, but they offer an exceptionally unique case study for population genetics. The red junglefowl (Gallus gallus) of southern and south-eastern Asia is considered to be the living ancestor and progenitor of the domestic chicken. This literature review examines how published research has evaluated its genetic relationship with the chicken and implications for its conservation. A special emphasis is given to the threat of genetic introgression with domestic and feral chicken populations …

American Eel (Anguilla Rostrata) And Other Fishes As Surveyed By Environmental Dna In The Bronx River And Hudson River Watershed, Sam C. Chin

Dissertations, Theses, and Capstone Projects

Mounting an effective response to the threats faced by freshwater fish may require expansions to aquatic biomonitoring in excess of what is feasible using the capture-based survey techniques currently relied upon by natural resource managers. Methods for analyzing environmental DNA (eDNA) are emerging as a minimally invasive and cost-effective approach for surveying fish and other organisms. By detecting taxon-specific DNA sequences recovered from environmental samples (e.g. water, sediment), eDNA methods are able to infer species presence from samples that can be collected rapidly with simple equipment. In many cases, eDNA detection rates of fish species have been shown to meet …

The Effect Of Infection Risk On Female Blood Transcriptomics, Brenna M. G. Gormally, Patricia C. Lopes

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Defenses against pathogens can take on many forms. For instance, behavioral avoidance of diseased conspecifics is widely documented. Interactions with these infectious conspecifics can also, however, lead to physiological changes in uninfected animals, an effect that is much less well understood. These changes in behavior and physiology are particularly important to study in a reproductive context, where they can impact reproductive decisions and offspring quality. Here, we studied how an acute (3 h) exposure to an immune-challenged male affected female blood transcriptomics and behavior. We predicted that females paired with immune-challenged males would reduce eating and drinking behaviors (as avoidance …

Genetic Protocols For Dna Extraction From White-Tailed Deer Cast Antlers To Confirm Individuality, Zach Carter, Brian C. Peterson, Casey W. Schoenebeck, Kimberly A. Carlson

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

White-tailed deer (Odocoileus virginianus) are the most sought-after deer species in America. The antlers of mammals, such as deer, are one of the fastest regenerative tissues in the world and are grown and naturally cast every year. Research on cast antlers have been used for a variety of purposes including population comparisons and impacts of deer health due to climatic stressors. When investigating cast antlers, it is important to confirm individuality of match sets in addition to antlers of the same individual between years. Therefore, individuality must be confirmed genetically, and protocols must be developed and established to …

Climate-Assisted Persistence Of Tropical Fish Vagrants In Temperate Marine Ecosystems, Laura Gajdzik, Thomas M. Decarlo, Adam Koziol, Mahsa Mousavi-Derazmahalleh, Megan Coghlan, Matthew W. Power, Michael Bunce, David Fairclough, Michael J. Travers, Glenn I. Moore, Joseph D. Dibattista

Fisheries Research Articles

Rising temperatures and extreme climate events are propelling tropical species into temperate marine ecosystems, but not all species can persist. Here, we used the heatwave-driven expatriation of tropical Black Rabbitfish (Siganus fuscescens) to the temperate environments of Western Australia to assess the ecological and evolutionary mechanisms that may entail their persistence. Population genomic assays for this rabbitfish indicated little genetic differentiation between tropical residents and vagrants to temperate environments due to high migration rates, which were likely enhanced by the marine heatwave. DNA metabarcoding revealed a diverse diet for this species based on phytoplankton and algae, as well …

Dietary Development And Nutritional Ontogeny In Gorilla Beringei : A Multi-Layered, -Omics Approach, Emma C. Cancelliere

Dissertations, Theses, and Capstone Projects

In species who consume folivorous diets, immature individuals must contend with the challenges of extracting nutrients from fibrous foods before dietary adaptations and strategies are fully developed. Additionally, immatures have distinct nutritional needs to support their stage-specific metabolic and biophysiological requirements. To meet these stage-specific needs, while constrained by underdeveloped feeding strategies and digestive capacities, immatures may adopt distinct diets better suited to their specific developmental context. However, where dietary modification is constrained by low dietary diversity or landscape homogeneity, it is unclear how immature individuals compensate through alternative strategies. In turn, little is known about the nutritional and life …

Wild Mice With Different Social Network Sizes Vary In Brain Gene Expression, Patricia C. Lopes, Barbara König

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background

Appropriate social interactions influence animal fitness by impacting several processes, such as mating, territory defense, and offspring care. Many studies shedding light on the neurobiological underpinnings of social behavior have focused on nonapeptides (vasopressin, oxytocin, and homologues) and on sexual or parent-offspring interactions. Furthermore, animals have been studied under artificial laboratory conditions, where the consequences of behavioral responses may not be as critical as when expressed under natural environments, therefore obscuring certain physiological responses. We used automated recording of social interactions of wild house mice outside of the breeding season to detect individuals at both tails of a distribution …

Spatial And Temporal Genetic Structure Of Winter-Run Steelhead (Oncorhynchus Mykiss) Returning To The Mad River, California, Steven R. Fong

Cal Poly Humboldt theses and projects

Distinct populations of steelhead in the wild are in decline. The propagation of steelhead in hatcheries has been used to boost population numbers for recreational fisheries and for use in conservation. However, hatchery breeding practices of steelhead can result in changes in genetic structure. I investigated the genetic structure of winter-run steelhead (Oncorhynchus mykiss) returning to the Mad River, California, where a hatchery has been used enhance production for recreational fisheries since 1971. Genetic variability in Mad River steelhead was evaluated using 96 single nucleotide polymorphisms (SNPs) among 4203 individuals, including the Mad River and nearby locations, and …

Crispr-Mediated Gene Editing: Scientific And Ethical Issues, Jarrod Bailey

Genetics Collection

There remains substantial evidence to warrant great concern over the poor efficiency and specificity of clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genetic modification (GM), despite relatively minor improvements compared to other GM methods. These issues cause persistent, adverse, ethical, and scientific consequences for GM animals, which may never be sufficiently resolvable.

Work-Type Influences Perceived Livestock Herding Success In Australian Working Kelpies, Jonathan B. Early, Elizabeth R. Arnott, Lisa J. Mascord, Diane Van Rooy, Paul Mcgreevy, Claire M. Wade

Genetics Collection

Background

Working dog handlers and breeders have very different behavioural requirements in the animals that they employ for managing livestock. The Australian Working Kelpie breed may be used in several working contexts, notably yards, paddocks and a combination of both. The working context influences the skillsets required and gives rise to three corresponding work-types: Yard, Paddock and Utility Kelpies. In particular, dogs used for working stock in the confines of yards and trucks interact with stock more forcefully than those mustering in larger areas (paddocks) where they can herd stock effectively from a greater distance. This article explores owner assessments …

Genomic Data Reveal A Loss Of Diversity In Two Species Of Tuco-Tucos (Genus Ctenomys) Following A Volcanic Eruption, Jeremy L. Hsu, Jeremy Chase Crawford, Mauro N. Tammone, Uma Ramakrishnan, Eileen A. Lacey, Elizabeth A. Hadly

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Marked reductions in population size can trigger corresponding declines in genetic variation. Understanding the precise genetic consequences of such reductions, however, is often challenging due to the absence of robust pre- and post-reduction datasets. Here, we use heterochronous genomic data from samples obtained before and immediately after the 2011 eruption of the Puyehue-Cordón Caulle volcanic complex in Patagonia to explore the genetic impacts of this event on two parapatric species of rodents, the colonial tuco-tuco (Ctenomys sociabilis) and the Patagonian tuco-tuco (C. haigi). Previous analyses using microsatellites revealed no post-eruption changes in genetic variation in C. …

Genomic Signatures Of Local Adaptation Reveal Source-Sink Dynamics In A High Gene Flow Fish Species, Katherine Cure, Luke Thomas, Jean-Paul A. Hobbs, David V. Fairclough, Winn Jason Kennington

Fisheries Research Articles

Understanding source-sink dynamics is important for conservation management, particularly when climatic events alter species’ distributions. Following a 2011 ‘marine heatwave’ in Western Australia, we observed high recruitment of the endemic fisheries target species Choerodon rubescens, towards the cooler (southern) end of its distribution. Here, we use a genome wide set of 14 559 single-nucleotide polymorphisms (SNPs) to identify the likely source population for this recruitment event. Most loci (76%) showed low genetic divergence across the species’ range, indicating high levels of gene flow and confirming previous findings using neutral microsatellite markers. However, a small proportion of loci showed strong …

A Population Genetic Investigation Of The Reticulated Flatwoods Salamander (Ambystoma Bishopi) On Eglin Air Force Base, Alexander S. Wendt

College of Graduate Studies: Theses & Dissertations

The reticulated flatwoods salamander (RFS) is an endangered salamander with a unique life history. One of the largest known, best studied refuges for RFS is found on Eglin Air Force Base, and these RFS have been sampled and managed extensively since 2010. My thesis seeks to better understand RFS by using genetic techniques to address several unknowns, including: 1) determining the population structuring of RFS and the manageable units for species conservation, 2) estimating the size and status of populations, 3) understanding dispersal of RFS and factors that influence this, 4) exploring the breeding biology and recruitment patterns of RFS …

Sheep Updates 2016, Mick Keogh, David Cornish, Michael Chilvers, Gerry Hinkley, Danielle England, Rosemary Bartle, Brad Wooldridge, Norm Santich, John Young, Ashley Herbert, Jamie Heinrich, Graeme Howie, Bruce Mullan

Sheep Updates

This session covers eleven papers from different authors:

1. Forward, Dr Bruce Mullan, Director Sheep Industry Development, Department of Agriculture and Food Western Australia

2. The Australian sheep industry in 2025, Mick Keogh, Australian Farm Institute

3. Decision making in a risky environment, David Cornish, Cornish Consulting

4. Business Transitioning, Michael Chilvers, Nile Tasmania

5. Advisory Boards in WA Agriculture - making life 'easier' for everyone, Gerry Hinkley, Producer, Tincurrin and Danielle England, Aginnovate

6. Principles of Successful Family Business Succession Strategies, Rosemary Bartle, Succession Planning Facilitator, Rabobank

7. Diversifying the Feedbase...is the …

Sheep Updates 2015 - Katanning, Bruce Mullan, Kate Pritchett, Kimbal Curtis, Chris Wilcox, Mike Hyder, Leigh Sonnerman, Lynne Bradshaw, Geoff Lindon, Katherine Davies, Joe Young, Stephen Lee, Ian Robertson, Lucy Anderton, Hayley Norman, Ed Barrett-Lennard, Jackie Jarvis, Ben Patrick

Sheep Updates

This session covers fourteen papers from different authors:

1. The Sheep Industry Business Innovation project, Bruce Mullan, Sheep Industry Development Director, Department of Agriculture and Food, Western Australia

2. Western Australian sheep stocktake, Kate Pritchett and Kimbal Curtis, Research Officers, Department of Agriculture and Food, Western Australia

3. Wool demand and supply - short term volatility, long term opportunities, Chris Wilcox, Principal of Poimena Analysis

4. Lifetime management for maternal ewes, Mike Hyder, Research Officer, Department of Agriculture and Food, Western Australia

5. National Livestock Identification System (NLIS) for sheep and goats - what is the NLIS database? Leigh Sonnermann, …

Developing Microbial Biomarkers To Non-Invasively Assess Health In Wild Elk (Cervus Canadensis) Populations, Samuel B. Pannoni

Undergraduate Theses, Professional Papers, and Capstone Artifacts

The composition of the intestinal bacterial community (intestinal microbiome) of mammals is associated with changes in diet, stress, disease and physical condition of the animal. The relationship between health and the microbiome has been extensively demonstrated in studies of humans and mice; this provides strong support for its potential utility in wildlife. When managing elk (Cervus canadensis), federal and state agencies currently must rely on invasive sampling and coarse demographic data on which to base their decisions. By developing microbiome-based biomarkers that vary as a function of elk body condition and disease (i.e. microbial biomarkers), we hope to …

Assessing The Contributions Of Two Stocked Strains On A Minnesota-Wisconsin Border Water, Douglas Zentner

Journal of Earth and Life Science

Stocking has long been used as a management tool in the United States even though many of its effects remain cryptic. Past comparisons between stocked strains were generally based on the survival and growth rates of physically marked individuals. More recently the use of genetic markers to assess contributions of stocked individuals has been employed by fisheries managers. Using 13 microsatellite markers we assessed the contributions of two muskellunge (Esox masquinongy) strains (Wisconsin and Leech) stocked into the St. Louis River Estuary. Ancestry in the adult samples remained relatively constant with differences only observed between the 2008 and …

A Genetic Based Approach To Management And Stocking Of Muskellunge, Douglas Zentner

Journal of Earth and Life Science

Fish stocking has long been used as a management tool among fisheries biologists and continues to be met with popular public opinion. Despite perceived simplicity, the full effects of stocking remain cryptic for many fish populations. Stocking has frequently been used to maintain or establish successful muskellunge (Esox masquinongy) populations. Coupled with other management practices the Minnesota Department of Natural Resources (MNDNR) has established Minnesota as a premier muskellunge fishery. From 1958 to 2012 the MNDNR stocked three strains of muskellunge in Big Mantrap Lake, MN. The first from Shoepack Lake, MN (hereafter Shoepack-strain) was used until the …

Sheep Updates 2015 - Ravensthorpe, Bruce Mullan, Kate Pritchett, Kimbal Curtis, Chris Wilcox, Mike Hyder, Leigh Sonnerman, Lynne Bradshaw, Geoff Lindon, Katherine Davies, Joe Young, Stephen Lee, Ian Robertson, Lucy Anderton, Hayley Norman, Ed Barrett-Lenard, Jackie Jarvis, Ben Patrick

Sheep Updates

This session covers fourteen papers from different authors:

1. The Sheep Industry Business Innovation project, Bruce Mullan, Sheep Industry Development Director, Department of Agriculture and Food, Western Australia

2. Western Australian sheep stocktake, Kate Pritchett and Kimbal Curtis, Research Officers, Department of Agriculture and Food, Western Australia

3. Wool demand and supply - short term volatility, long term opportunities, Chris Wilcox, Principal of Poimena Analysis

4. Lifetime management for maternal ewes, Mike Hyder, Research Officer, Department of Agriculture and Food, Western Australia

5. National Livestock Identification System (NLIS) for sheep and goats - what is the NLIS database? Leigh Sonnermann, …

Sheep Updates 2015 - Merredin, Bruce Mullan, Kate Pritchett, Kimbal Curtis, Chris Wilcox, Lynne Bradshaw, Geoff Lindon, Katherine Davies, Joe Young, Stephen Lee, Dawson Bradford, Khama Kelman, Lucy Anderton, Jaq Pearson, Jackie Jarvis, Ben Patrick

Sheep Updates

This session covers fourteen papers from different authors:

1. The Sheep Industry Business Innovation project, Bruce Mullan, Sheep Industry Development Director, Department of Agriculture and Food, Western Australia

2. Western Australian sheep stocktake, Kate Pritchett and Kimbal Curtis, Research Officers, Department of Agriculture and Food, Western Australia

3. Wool demand and supply - short term volatility, long term opportunities, Chris Wilcox, Principal of Poimena Analysis

4. Myths, Facts and the role of animal welfare in farming, Lynne Bradshaw, president, RSPCA WA

5. Latest research and development on breech strike prevention, Geoff Lindon, Manager Productivity and Animal Welfare, AWI

6. …

The Complexities Of Female Mate Choice And Male Polymorphisms: Elucidating The Role Of Genetics, Age, And Mate-Choice Copying, Kasey D. Fowler-Finn, Laura Sullivan-Beckers, Amy M. Runck, Eileen A. Hebets

Eileen Hebets Publications

Genetic, life history, and environmental factors dictate patterns of variation in sexual traits within and across populations, and thus the action and outcome of sexual selection. This study explores patterns of inheritance, diet, age, and mate-choice copying on the expression of male sexual signals and associated female mate choice in a phenotypically diverse group of Schizocosa wolf spiders. Focal spiders exhibit one of two male phenotypes: ‘ornamented’ males possess large black brushes on their forelegs, and ‘non-ornamented’ males possess no brushes. Using a quantitative genetics breeding design in a mixed population of ornamented/non-ornamented males, we found a strong genetic basis …

Dangerous Mating Systems: Signal Complexity, Signal Content And Neural Capacity In Spiders, Marie E. Herberstein, Anne E. Wignall, Eileen Hebets, Jutta M. Schneider

Eileen Hebets Publications

Spiders are highly efficient predators in possession of exquisite sensory capacities for ambushing prey, combined with machinery for launching rapid and determined attacks. As a consequence, any sexually motivated approach carries a risk of ending up as prey rather than as a mate. Sexual selection has shaped courtship to effectively communicate the presence, identity, motivation and/or quality of potential mates, which help ameliorate these risks. Spiders communicate this information via several sensory channels, including mechanical (e.g. vibrational), visual and/or chemical, with examples of multimodal signaling beginning to emerge in the literature. The diverse environments that spiders inhabit have further shaped …