Life Sciences Commons^™

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …

Genetic Characteristics Required In Dairy And Beef Cattle For Temperate Grazing Systems, F. Buckley, C. Holmes, M. G. Keane

IGC Proceedings (1997-2023)

Key points

1. Only about 10% of the world’s milk is produced from grazing systems. Consequently the majority of dairy cattle have not been selected under grazing, nor on seasonal systems. This is not true for beef cattle, for which the majority, especially the dams, are managed under seasonal grazing systems.

2. In grazing systems daily feed intake is limited to lower levels than are achievable on concentrate plus conserved forage rations. Consequently, cows most suited to grazing environments are likely to have a lower genetic potential for milk production than cows selected in high concentrate systems, to minimise their relative energy …

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Dfhic: A Dilated Full Convolution Model To Enhance The Resolution Of Hi-C Data, Bin Wang, Kun Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Hi-C technology has been the most widely used chromosome conformation capture(3C) experiment that measures the frequency of all paired interactions in the entire genome, which is a powerful tool for studying the 3D structure of the genome. The fineness of the constructed genome structure depends on the resolution of Hi-C data. However, due to the fact that high-resolution Hi-C data require deep sequencing and thus high experimental cost, most available Hi-C data are in low-resolution. Hence, it is essential to enhance the quality of Hi-C data by developing the effective computational methods.

Results: In this work, we propose …

Utilizing Markov Chains To Estimate Allele Progression Through Generations, Ronit Gandhi

Honors Theses

All populations display patterns in allele frequencies over time. Some alleles cease to exist, while some grow to become the norm. These frequencies can shift or stay constant based on the conditions the population lives in. If in Hardy-Weinberg equilibrium, the allele frequencies stay constant. Most populations, however, have bias from environmental factors, sexual preferences, other organisms, etc. We propose a stochastic Markov chain model to study allele progression across generations. In such a model, the allele frequencies in the next generation depend only on the frequencies in the current one.

We use this model to track a recessive allele …

Genomic Tools Reveal Complex Social Organization Of An Invasive Large Mammal (Sus Scrofa), Chelsea L. Titus, Courtney F. Bowden, Timothy J. Smyser, Stephen L. Webb, James C. Beasley

USDA Wildlife Services: Staff Publications

A comprehensive understanding of sociality in wildlife is vital to optimizing conservation and management efforts. However, sociality is complicated, especially for widely distributed species that exhibit substantive behavioral plasticity. Invasive wild pigs (Sus scrofa), often representing hybrids of European wild boar and domestic pigs, are among the most adaptable and widely distributed large mammals. The social structure of wild pigs is believed to be similar to European wild boar, consisting of matriarchal groups (sounders) and solitary males. However, wild pig social structure is understudied and largely limited to visual observations. Using a hierarchical approach, we incorporated genomic tools …

Genetic Structure Of Urban White-Tailed Deer In West Michigan, Jacob David Brand

Masters Theses

In urban areas, green spaces are used by humans and wildlife. The proximity between them can lead to both positive and negative interactions, which can make managing urban wildlife difficult. Managers are challenged due to conflicts between wildlife population sizes that can be naturally supported versus those that are socially tolerable. White-tailed deer (Odocoileus virginianus) thrive in urban environments because their habitat requirements are met within green spaces and backyard vegetation. Matrilineal groups of urban white-tailed deer live within the same areas, at times forming high densities that can lead to the spread of diseases or environmental pests, including hemlock …

Development And Validation Of An Edna Protocol For Monitoring Endemic Asian Spiny Frogs In The Himalayan Region Of Pakistan, Muhammad Saeed, Muhammad Rais, Ayesha Akram, Maggie R. Williams, Kenneth F. Kellner, Syed A. Hashsham, Drew R. Davis

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

Wildlife monitoring programs are instrumental for the assessment of species, habitat status, and for the management of factors affecting them. This is particularly important for species found in freshwater ecosystems, such as amphibians, as they have higher estimated extinction rates than terrestrial species. We developed and validated two species-specific environmental DNA (eDNA) protocols and applied them in the field to detect the Hazara Torrent Frog (Allopaa hazarensis) and Murree Hills Frog (Nanorana vicina). Additionally, we compared eDNA surveys with visual encounter surveys and estimated site occupancy. eDNA surveys resulted in higher occurrence probabilities for both A. …

Dairy Cattle Genetics By Environment Interaction Mismatch Contributes To Poor Mitigation And Adaptation Of Grazing Systems To Climate Change Actions In The Peruvian High Andes: A Review, V. M. Velez Marroquin, J. Manhire, R. Garcia Ticllacuri, J. L. Bernal Madrid, C. S. Pinares-Patino

IGC Proceedings (1997-2023)

The high Andes of Peru includes fragile ecosystems. Nevertheless, it plays important ecosystem functions (e.g., biodiversity, water supply for the lowlands, CO₂ sinks in soil, etc). More than 80% of the livestock population of Peru is farmed in this area, supporting the livelihood of approximately 1’400,000 poor families, who are vulnerable to climate change (CC). Climate change in the high Andes is occurring at accelerated rates, compared to lowlands regions. Prevalent factors in the high Andes, such as hypoxia, high UV radiation, climatic extremes, large variation between maximum and minimum temperatures, seasonality in rainfall (determining highly seasonal forage growth) …

Achievements And Perspectives In The Breeding Of Tropical Grasses And Legumes, John W. Miles

IGC Proceedings (1997-2023)

Pasture and forage plant breeding is complicated by the perennial nature of the plants, the diversity of environments in which improved cultivars will be used, and the complex criteria of merit involved, criteria that necessarily include some measure of impact on the efficiency of animal production. While pasture plant breeding in the temperate zone is a demonstrably productive activity, the record of success for the tropical species -- "success" measured by release and adoption of bred cultivars -- is less convincing, in spite of four decades of activity in numerous public sector breeding programs and a large published literature. The …

Alfalfa, J. H. Bouton

IGC Proceedings (1997-2023)

Cultivated alfalfa or lucerne (Medicago sativa spp. sativa) is the most important forage legume in the world with approximately 32 million hectares cultivated mainly in the temperate regions of both the northern and southern hemispheres. Intensive research has been conducted on the management and physiology of the crop and a major seed industry has developed world wide. Since insect and disease pests are numerous in alfalfa, development of cultivars with the proper fall dormancy and a broad genetic base for pest resistance has been pursued in order to provide increased adaptation, persistence, and yield. There has been a …

Population Genetic Analyses Of Arctic Char (Salvelinus Alpinus) Life History Types In Nettilling Lake & Amadjuak River Ecosystem: A Test Of Reproductive Isolation, Chen Liu

Electronic Theses and Dissertations

A great number of studies have identified strong genetic differences between sympatric anadromous and resident populations of Salmonidae. However, Arctic char (Salvelinus alpinus) migratory phenotypes in the Nettilling Lake and Amadjuak River ecosystem in Nunavut, Canada have not been genetically characterized, and it remains unclear if distinct genotypes and phenotypes associated with migratory life history differences are maintained through reproductive isolation, and they have been assumed to be sympatric populations, or co-occurring populations. Co-occurring Arctic char (n=225) were sampled from eleven sites along the Amadjuak River in 2014 and 2015. Twelve microsatellite loci were used to quantify genetic variation among …

A Timeline Of Discovery And Current Research On Primary Open-Angle Glaucoma And Emergence Of Potentially Permanent Treatment Solutions, Yonosuke Dejesus, Guadalupe Moreno Ceballos

Spectra Undergraduate Research Journal

This research examines the timeline of the discovery and research of Primary Open-Angle Glaucoma (POAG). By reviewing the literature on genetic and molecular mechanisms, we aim to emphasize a long-term treatment solution (iSTENT) to mitigate intraocular pressure (IOP) related to POAG etiology and disease progression. POAG is a multifactorial, autosomal dominant, adult-onset eye disease wherein the optic nerve cells become damaged due to a buildup of excess aqueous humor, resulting in increased IOP. Consequently, POAG leads to progressive loss of peripheral vision and is the leading cause of blindness in the US. Due to the multifactorial nature of glaucoma’s inheritance …

Genetics Of Pediatric Musculoskeletal Disorders, Lilian Antunes

Arts & Sciences Electronic Theses and Dissertations

Pediatric musculoskeletal disorders are an extremely broad category of diseases that are often inherited. While individually rare, collectively these disorders are common, affecting around 3% of live births in the US. Despite the mounting clinical and molecular evidence for a genetic etiology, the cause for many patients with pediatric musculoskeletal disorders remain largely unknown. Major challenges in rare pediatric diseases include recruiting large numbers of patients and determining the significance and functional impacts of variants associated with disease within individuals or families. Whole exome sequencing (WES) is a powerful tool to identify coding variants that are associated with rare pediatric …

Analysis Of Subtelomeric Rextal Assemblies Using Quast, Tunazzina Islam, Desh Ranjan, Mohammad Zubair, Eleanor Young, Ming Xiao, Harold Riethman

Computer Science Faculty Publications

Genomic regions of high segmental duplication content and/or structural variation have led to gaps and misassemblies in the human reference sequence, and are refractory to assembly from whole-genome short-read datasets. Human subtelomere regions are highly enriched in both segmental duplication content and structural variations, and as a consequence are both impossible to assemble accurately and highly variable from individual to individual. Recently, we developed a pipeline for improved region-specific assembly called Regional Extension of Assemblies Using Linked-Reads (REXTAL). In this study, we evaluate REXTAL and genome-wide assembly (Supernova) approaches on 10X Genomics linked-reads data sets partitioned and barcoded using the …

Introduction To Neutrosophic Genetics, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

Neutrosophic Genetics is the study of genetics using neutrosophic logic, set, probability, statistics, measure and other neutrosophic tools and procedures. In this paper, based on the Neutrosophic Theory of Evolution (that includes degrees of Evolution, Neutrality (or Indeterminacy), and Involution) – as extension of Darwin’s Theory of Evolution, we show the applicability of neutrosophy in genetics, and we present within the frame of neutrosophic genetics the following concepts: neutrosophic mutation, neutrosophic speciation, and neutrosophic coevolution.

Connections In The Underworld: A Morphological And Molecular Study Of Diversity And Connectivity Among Anchialine Shrimp., Robert Eugene Ditter

FIU Electronic Theses and Dissertations

This research investigates the distribution and population structure of crustaceans, endemic to anchialine systems in the tropical western Atlantic focusing on cave-dwelling shrimp from the family Barbouriidae. Taxonomic and molecular tools (genetic and genomic) are utilized to examine population dynamics and the presence of phenotypic hypervariation (PhyV) of the critically endangered species Barbouria cubensis (von Martens, 1872). The presence of PhyV and its geographic distribution is investigated among anchialine populations of B. cubensis from 34 sites on Abaco, Eleuthera, and San Salvador, Bahamas. Examination of 54 informative morphological characters revealed PhyV present in nearly 90% (n=463) of specimens with no …

An Investigation Into Multi-View Error Correcting Output Code Classifiers Applied To Organ Tissue Classification, Daniel Alvarez

UNLV Theses, Dissertations, Professional Papers, and Capstones

Large amounts of data is being generated constantly each day, so much data that it is difficult to find patterns in order to predict outcomes and make decisions for both humans and machines alike. It would be useful if this data could be simplified using machine learning techniques. For example, biological cell identity is dependent on many factors tied to genetic processes. Such factors include proteins, gene transcription, and gene methylation. Each of these factors are highly complex mechanism with immense amounts of data. Simplifying these can then be helpful in finding patterns in them. Error-Correcting Output Codes (ECOC) does …

Genetic Studies Of Wildlife, Brittaney L. Buchanan

School of Natural Resources: Dissertations, Theses, and Student Research

Genetic techniques are being more frequently used to understand the biology and management of wildlife species. The wild turkey is one species of genetic interest because the correct identification of individuals to the subspecies level is difficult using traditional methods. Currently phenotypic differences in plumage, especially the upper tail coverts, are used to assign individuals to subspecies. To hunters wanting to complete a “grand slam,” identification of birds’ subspecies is important. This study focuses on the five extant subspecies: Eastern (M. g. silvestris), Osceola (M. g. osceola), Rio Grande (M. g. intermedia), Merriam’s ( …

Complex Systems Analysis In Selected Domains: Animal Biosecurity & Genetic Expression, Luke Trinity

Graduate College Dissertations and Theses

I first broadly define the study of complex systems, identifying language to describe and characterize mechanisms of such systems which is applicable across disciplines. An overview of methods is provided, including the description of a software development methodology which defines how a combination of computer science, statistics, and mathematics are applied to specified domains. This work describes strategies to facilitate timely completion of robust and adaptable projects which vary in complexity and scope. A biosecurity informatics pipeline is outlined, which is an abstraction useful in organizing the analysis of biological data from cells. This is followed by specific applications of …

9th Annual Postdoctoral Science Symposium, University Of Texas Md Anderson Cancer Center Postdoctoral Association

Annual Postdoctoral Science Symposium Abstracts

The mission of the Annual Postdoctoral Science Symposium (APSS) is to provide a platform for talented postdoctoral fellows throughout the Texas Medical Center to present their work to a wider audience. The MD Anderson Postdoctoral Association convened its inaugural Annual Postdoctoral Science Symposium (APSS) on August 4, 2011.

The APSS provides a professional venue for postdoctoral scientists to develop, clarify, and refine their research as a result of formal reviews and critiques of faculty and other postdoctoral scientists. Additionally, attendees discuss current research on a broad range of subjects while promoting academic interactions and enrichment and developing new collaborations.

Hierarchical Modeling And Differential Expression Analysis For Rna-Seq Experiments With Inbred And Hybrid Genotypes, Andrew Lithio, Dan Nettleton

Dan Nettleton

The performance of inbred and hybrid genotypes is of interest in plant breeding and genetics. High-throughput sequencing of RNA (RNA-seq) has proven to be a useful tool in the study of the molecular genetic responses of inbreds and hybrids to environmental stresses. Commonly used experimental designs and sequencing methods lead to complex data structures that require careful attention in data analysis. We demonstrate an analysis of RNA-seq data from a split-plot design involving drought stress applied to two inbred genotypes and two hybrids formed by crosses between the inbreds. Our generalized linear modeling strategy incorporates random effects for whole-plot experimental …

Genetic Sequencing For Measuring Biodiversity In Recent And Ancient Marine Sediments, Lauren Judge

Celebration of Learning

Taxonomic biodiversity, measured by counting the number of species present in a given area, is the most common method of capturing ecosystem biodiversity in recent and ancient environments. While this method is widely accepted, it is limited by poor preservation and identification of many individuals, making it impossible to include every species within an ecosystem and resulting in the loss of some diversity information. To address this issue, we measured the genetic biodiversity (in which species are determined based on sequencing of their DNA) of shallow marine ecosystems by extracting and sequencing the 18S ribosomal gene from bulk carbonate sediment …

What Can We Do? Puzzling Over The Interpretation Of Heredity And Variation From Galton To Genetic Engineering, Peter J. Taylor

Working Papers on Science in a Changing World

First six chapters of a book motivated as follows: When I had mentioned to colleagues that I was exploring some significant issues overlooked by both sides in nature-nurture debates, the typical response was “we know, of course, that nature and nurture are intertwined”; they never asked “which nature-nurture science are you referring to?” It occurred to me that, in the long history of nature-nurture debates, opposing sides had always assumed or implied that these different scientific approaches were speaking to the same issues. If that were the case, then the challenge—something I was already puzzling over—was how best to draw …

Application And Refinement Of Molecular Ecology Techniques For Amphibian Conservation, Stephanie Marie Burgess

Electronic Theses and Dissertations

Wildlife conservation has become increasingly difficult due to habitat loss habitat fragmentation and land use change. Thus conservationists have embraced advances in molecular ecology such as landscape genetics and microbial bioinformatics that employ genetic techniques to further understand the relationship between individuals and their environment. In landscape genetics model inferences can be used to identify features that facilitate or resist gene flow providing a framework for anticipating the impacts of land use changes on a species’ ability to disperse. However the factors that affect the transferability of landscape genetics inferences are poorly understood and little is known about the effect …

Genome-Wide Systems Genetics Of Alcohol Consumption And Dependence, Kristin Mignogna

Theses and Dissertations

Widely effective treatment for alcohol use disorder is not yet available, because the exact biological mechanisms that underlie this disorder are not completely understood. One way to gain a better understanding of these mechanisms is to examine the genetic frameworks that contribute to the risk for developing this disorder. This dissertation examines genetic association data in combination with gene expression networks in the brain to identify functional groups of genes associated with alcohol consumption and dependence.

The first study took advantage of the behavioral complexity of human samples, and experimental capabilities provided by mouse models, by co-analyzing gene expression networks …

Adam And Eve, Designed Diversity, And Allele Frequencies, John C. Sanford, Robert W. Carter, Wes Brewer, John Baumgardner, Bruce Potter, Jon Potter

Proceedings of the International Conference on Creationism

Theistic evolutionists present multiple genetic arguments against a literal Adam and Eve. One key argument asserts it would be impossible for a single human couple to give rise to the genetic diversity seen in the modern human population. This implicitly assumes Adam and Eve would have been created without internal genetic diversity. If this were true, all observed variations would have to arise recently via random mutations. This would require incredibly high mutation rates, logically leading to rapid extinction.

Yet, Adam and Eve could have been created massively heterozygous. We have argued for over a decade that they could have …

The Role Of Reproductive Timing As A Driver Of Genetic Differentiation In Populations Of Pacific Herring, Eleni L. Petrou, Todd Sandell, Dayv Lowry, Lorenz Hauser

Salish Sea Ecosystem Conference

There is growing recognition that maintaining diversity in life history traits contributes to the sustainable management of wild populations. One important life history characteristic is reproductive phenology, and it has been shown that differences in the timing of reproduction can act as a barrier to gene flow between populations. If the difference in reproductive timing determines the level of connectivity, one would expect that genetic differentiation between populations would increase as a function of difference in reproductive date. This pattern, known as “isolation by time” (IBT), has been observed in wild populations of salmonids containing early and late runs. Pacific …

Unseen Science: Modern Discoveries Too Far Away Or Tiny For Human Eyes, Lucy Huang

Capstones

As science has progressed, scientists have realized that evidence goes beyond the realms of physical sight. Whether it is too small or difficult to find, scientists have developed different ways to get around this problem. We see this in cancer genomics and in extrasolar planetary research. Scientists use what they know and what they measure to validate their work.

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Impact Of Home Visit Capacity On Genetic Association Studies Of Late-Onset Alzheimer's Disease, David W. Fardo, Laura E. Gibbons, Shubhabrata Mukherjee, M. Maria Glymour, Wayne Mccormick, Susan M. Mccurry, James D. Bowen, Eric B. Larson, Paul K. Crane

Biostatistics Faculty Publications

INTRODUCTION—Findings for genetic correlates of late-onset Alzheimer's disease (LOAD) in studies that rely solely on clinic visits may differ from those with capacity to follow participants unable to attend clinic visits.

METHODS—We evaluated previously identified LOAD-risk single nucleotide variants in the prospective Adult Changes in Thought study, comparing hazard ratios (HRs) estimated using the full data set of both in-home and clinic visits (n = 1697) to HRs estimated using only data that were obtained from clinic visits (n = 1308). Models were adjusted for age, sex, principal components to account for ancestry, and additional health indicators.

RESULTS …

Consequences Of Severe Habitat Fragmentation On Density, Genetics, And Spatial Capture-Recapture Analysis Of A Small Bear Population, Sean Mccarthy Murphy, Ben C. Augustine, Wade Allen Ulrey, Joseph Maddox Guthrie, Brian K Scheick, J. Walter Mccown, John J. Cox

Forestry and Natural Resources Faculty Publications

Loss and fragmentation of natural habitats caused by human land uses have subdivided several formerly contiguous large carnivore populations into multiple small and often isolated subpopulations, which can reduce genetic variation and lead to precipitous population declines. Substantial habitat loss and fragmentation from urban development and agriculture expansion relegated the Highlands-Glades subpopulation (HGS) of Florida, USA, black bears (Ursus americanus floridanus) to prolonged isolation; increasing human land development is projected to cause ≥ 50% loss of remaining natural habitats occupied by the HGS in coming decades. We conducted a noninvasive genetic spatial capture-recapture study to quantitatively describe the …