Other Genetics and Genomics Commons^™

50 Whys To Look For Genes: Pros And Complications, Peter J. Taylor

Working Papers on Science in a Changing World

“Treating the audience as capable of thinking about the complexities that surround the application of genetic knowledge” was the tagline of a series of daily blog posts made over seven weeks in the fall of 2014, posts that included extended quotes from the recently published Nature-Nurture? No (Taylor 2014). This working paper is a compilation of those posts.

Dalla Traccia Di Sangue All'identikit Facciale, Charles E. Maclean

Charles E. MacLean

Assessment of dilemmas inherent in using DNA phenotyping methods to generate a physical likeness of a crime suspect based only on DNA shed at the crime scene.

Differential Methylation Methods In Multi-Context Organisms, Douglas Baumann, Yuqing Su, Iranga Mendis, Gayla R. Olbricht

Conference on Applied Statistics in Agriculture

DNA methylation is an epigenetic modification that has the ability to alter gene expression without any change in the DNA sequence. DNA methylation occurs when a methyl chemical group attaches to cytosine bases on the DNA sequence. In mammals, DNA methylation primarily occurs at CG sites, when a cytosine is followed by a guanine in the DNA sequence. In plants, DNA methylation can also occur in other cytosine sequences, such as when a cytosine is not followed directly by a guanine. Many of the statistical methods that have been developed to estimate methylation levels and test differential methylation in whole-genome …

Steps In Metagenomics: Let’S Avoid Garbage In And Garbage Out, Jacques Izard

Department of Food Science and Technology: Faculty Publications

Is metagenomics a revolution or a new fad? Metagenomics is tightly associated with the availability of next-generation sequencing in all its implementations. The key feature of these new technologies, moving beyond the Sanger-based DNA sequencing approach, is the depth of nucleotide sequencing per sample.¹ Knowing much more about a sample changes the traditional paradigms of “What is the most abundant?” or “What is the most significant?” to “What is present and potentially sig­nificant that might influence the situation and outcome?” Let’s take the case of identifying proper biomarkers of disease state in the context of chronic disease prevention. Prevention …

Functional Characterization Of Rai1 In Zebrafish, Joshua S. Beach

Theses and Dissertations

Smith-Magenis Syndrome (SMS; OMIM #182290) is a multiple congenital abnormality and intellectual disability (ID) disorder caused by either an interstitial deletion of the 17p11.2 region containing the retinoic acid induced-1 (RAI1) gene or a mutation of the RAI1 gene. Individuals diagnosed with SMS typically present characteristics such as ID, self-injurious behavior, sleep disturbance, ocular and otolaryngological abnormalities, craniofacial and skeletal abnormalities, neurological and behavioral abnormalities, as well as other systemic defects and manifestations. Previous work by Vyas in 2009 showed temporal expression of rai1 in zebrafish embryos as early as 9 hpf. We hypothesize that there is maternal …

Metagenomics For Microbiology: Preface, Jacques Izard, Maria C. Rivera

Department of Food Science and Technology: Faculty Publications

It is well known that only a small fraction of extant microbial life has been identified. Metagenomics, the direct sequencing and characterization of genes and genomes present in complex microbial ecosystems (e.g., metagenomes), has revolutionized the practice of microbiology by bypassing the hurdle of pure culture isolation. Metagenomics shows promise of advancing our understanding of the diversity, function, and evolution of the uncultivated majority.

Metagenomics as a field arose in the 1990s after the application of molecular biology techniques to genomic material directly extracted from microbial assemblages present in diverse habitats, including the human body. The application of metagenomic approaches …

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 …

Promises And Prospects Of Microbiome Studies, Maria C. Rivera, Jacques Izard

Department of Food Science and Technology: Faculty Publications

Since Anthony van Leeuwenhoek, first microscopic observations of the unseen microbiota and the more recent realization that little of the microbes in the biosphere are known, humans have developed a deep curiosity to fully understand the inner workings of the microbial realm. Our ability to characterize the complexity of microbial communities in their natural habitats has dramatically improved over the past decade thanks to advances in high-throughput methodologies. By eliminating the need to isolate and culture individual species, metagenomics approaches have removed many of the obstacles that hindered research in the ecology of mixed microbial consortia, providing valuable information about …

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, …

Cloning Of Ribosomal Its Pcr Products Creates Frequent, Non-Random Chimeric Sequences – A Test Involving Heterozygotes Between Gymnopus Dichrous Taxa I And Ii., Karen Hughes, Samuel D. Morris, Ana L. Reboredo-Segovia

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Gymnopus dichrous exists in the southern Appalachians as two distinct entities with essentially identical nuclear ribosomal ITS1 sequences but differing ITS2 and LSU sequences (for convenience, called G. dichrous I and II). F₁ ITS heterozygotes between the two are routinely collected from nature. Cloning of ITS PCR products from F₁ heterozygotes produced sequences of both parental haplotypes but also numerous chimeric sequences (21.9%). The location of template switching was non-random leading to recovery of the same chimera several times and the chimeric region varied from 45bp to 300bp. By comparison, single-basidiospore isolates from heterozygote F₁ fruitbodies showed …

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 …

Proof-Of-Concept Of Environmental Dna Tools For Atlantic Sturgeon Management, Jameson Hinkle

Theses and Dissertations

Abstract

The Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus, Mitchell) is an anadromous species that spawns in tidal freshwater rivers from Canada to Florida. Overfishing, river sedimentation and alteration of the river bottom have decreased Atlantic Sturgeon populations, and NOAA lists the species as endangered. Ecologists sometimes find it difficult to locate individuals of a species that is rare, endangered or invasive. The need for methods less invasive that can create more resolution of cryptic species presence is necessary. Environmental DNA (eDNA) is a non-invasive means of detecting rare, endangered, or invasive species by isolating nuclear or mitochondrial DNA (mtDNA) from 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, …

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 Genetic Ancestry Of African Americans, Latinos, And European Americans Across The United States, Katarzyna Bryc, Eric Y. Durand, J. Michael Macpherson, David Reich, Joanna Mountain

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans (brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differences reflect historical …

Genetic Parameter Estimates And Breed Effects For Calving Difficulty And Birth Weight In A Multi-Breed Population, Cashley Ahlberg

Department of Animal Science: Dissertations, Theses, and Student Research

There are multiple breeds of beef cattle available to utilize in breeding systems to maximize production and economics. Calving difficulty (dystocia) is a significant cost to beef production and is more prevalent in first-calf heifers. The objectives of this study were to estimate genetic parameters and breed differences for calving difficulty and birth weight as a first step towards the development of across-breed adjustment factors for calving difficulty.

Two models were employed to analyze birth weight (BWT) and calving difficulty (CD) recorded on 4,579 first parity females from the Germplasm Evaluation program at the U.S. Meat Animal Research Center (USMARC). …

Peroxisome Proliferator-Activated Receptor-Γ Coactivator 1-Α (Ppargc1a) Genetic Associations With Type 2 Diabetes In Three Ethnicities, Amanpreet K. Cheema

FIU Electronic Theses and Dissertations

Genetic heterogeneity, lifestyle factors, gene-gene or gene-environment interactions are the determinants of T2D which puts Hispanics and populations with African ancestry at higher risk of developing T2D. In this dissertation, the genetic associations of PPARGC1A polymorphisms with T2D and its related phenotypes (metabolic markers) in Haitian Americans (cases=110, controls=116), African Americans (cases=120, controls=124) and Cuban Americans (cases=160, controls=181) of South Florida were explored. Five single nucleotide polymorphisms of gene PPARGC1A were evaluated in each ethnicity for their disease association. In Haitian Americans, rs7656250 (OR= 0.22, pp=0.03) had significant protective association with T2D but had risk association in African Americans …

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 …

Investigating The Role Of Micrornas In The Response To Nitrogen Deprivation In The Green Alga Chlamydomonas Reinhardtii, Adam Voshall

School of Biological Sciences: Dissertations, Theses, and Student Research

Microalgae are gaining attention as a potential feedstock for the production of biodiesel, mainly derived from triacylglycerols (TAG). In many algae, TAG synthesis increases dramatically upon certain stresses but this is often accompanied by growth retardation. Rational improvements to strain productivity are limited by the scant knowledge on algal lipid metabolism and gene regulatory mechanisms. In this context, systems-level approaches aimed at understanding and modeling metabolic and regulatory networks may enable hypothesis-driven genetic engineering strategies. The green microalga Chlamydomonas reinhardtii accumulates significant amounts of TAGs under nutrient starvation and provides a genetically tractable model for manipulating biosynthetic pathways. In order …

The Effects Of Sugar Consumption And Race On Satisfaction With Body Size And Weight, Diego Rubalcava

Undergraduate Research Conference

No abstract provided.