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The Evolving International Grassland Congress, L R. Humphreys

IGC Proceedings (1997-2023)

The locations of the International Grassland Congresses are listed. Analysis of the disciplinary themes of papers presented at five Congresses from 1937 to 1993 indicated a considerable homeostasis of content. The plant genetic base for grassland improvement received most attention, and this, together with plant physiology, plant ecology and soil science contributed 52 to 57 per cent of the subject matter at all five Congresses. Emergent topics are mentioned.

Dispersal And Population Structure Of Euchlanis Chihuahuaensis Via Anemochory In The Chihuahuan Desert, Tristan Chavez-Poeschel

Open Access Theses & Dissertations

Desert ecosystems present challenges for aquatic organisms as habitats are fragmented, both in space and time; however, diapausing stages of rotifers can travel hundreds of kilometers during wind events. I used the rotifer Euchlanis chihuahuaensis as a model species to investigate the influence of wind dispersal on gene flow and population genetics in Chihuahuan Desert populations. I hypothesized that anemochory facilitates gene flow from source populations in the Northern Chihuahuan Desert in Mexico and the western United States to habitats in the Trans-Pecos region via delineated wind corridors. To test this hypothesis, the genetic diversity of populations from both inside …

Bayesian Statistical Modeling Of Spatially Resolved Transcriptomics Data, Xi Jiang

Statistical Science Theses and Dissertations

Spatially resolved transcriptomics (SRT) quantifies expression levels at different spatial locations, providing a new and powerful tool to investigate novel biological insights. As experimental technologies enhance both in capacity and efficiency, there arises a growing demand for the development of analytical methodologies.

One question in SRT data analysis is to identify genes whose expressions exhibit spatially correlated patterns, called spatially variable (SV) genes. Most current methods to identify SV genes are built upon the geostatistical model with Gaussian process, which could limit the models' ability to identify complex spatial patterns. In order to overcome this challenge and capture more types …

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 …

Mechanobiology As A Tool For Addressing The Genotype-To- Phenotype Problem In Microbiology, Merrill E. Asp, Minh-Tri Ho Thanh, Subarna Dutta, Jessica A. Comstock, Roy D. Welch, Alison E. Patteson

Physics - All Scholarship

The central hypothesis of the genotype–phenotype relationship is that the phenotype of a developing organism (i.e., its set of observable attributes) depends on its genome and the environment. However, as we learn more about the genetics and biochemistry of living systems, our understanding does not fully extend to the complex multiscale nature of how cells move, interact, and organize; this gap in understanding is referred to as the genotype-to-phenotype problem. The physics of soft matter sets the background on which living organisms evolved, and the cell environment is a strong determinant of cell phenotype. This inevitably leads to challenges as …

A Mathematical Model For Mosquito Population Dynamics, Christian Evans, Jemal Mohammed-Awel, Andreas Lazari

Georgia Journal of Science

In this study, a deterministic mathematical model for mosquito population dynamics is presented. The use of chemical insecticide to control population is incorporated into the model. It is assumed that there is insecticide sensitive (sensitive-type) and insecticide resistant (resistant-type) mosquitoes in the environment. Conditions for the existence and stability of four equilibria of the model have been established. Numerical simulations are carried out to confirm the analytical results and the implications, in terms of mosquito control in the environment, are discussed.

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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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 …

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 …

The Application Of Statistical Modeling To Identify Genetic Associations With Mild Traumatic Brain Injury Outcomes, Caroline Schott

Masters Theses

"Traumatic brain injury (TBI) is a growing health concern, with millions of TBI diagnoses in the United States each year. The vast majority of TBI diagnoses are mild traumatic brain injuries (mTBI), which can be challenging to manage due to variation in symptoms and outcomes. Most individuals with mTBI successfully recover quickly, but a small subset has a delayed recovery. Although the factors that contribute to this variation in recovery are not clearly understood, it is possible that genetic differences may play a role. Very few studies have investigated the association between single nucleotide polymorphisms (SNPs) with mTBI outcomes and …

Mathematics Model Of Inheritance Three Different Traits In Genetics With Matrix Approach, Jufra Jufra, Asrul Sani, Sardin Sardin

PYTHAGORAS : Jurnal Matematika dan Pendidikan Matematika

Mathematical models can solve problems to find out which individuals are superior from crosses in the field of genetics. The matrix form of the mathematical model using the concept of matrix diagonalization can solve these problems. The general definition of matrix diagonalization is with the diagonalized matrix elements obtained from the probability of crossing the average parent and the recessive parent. The mathematical model of a cross between the average parent and recessive parent can be formulated as . The behavior of the solution from the cross is in the form of an explicit equation which can be formulated as …

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. …

Gene-Based Association Tests Using Gwas Summary Statistics And Incorporating Eqtl, Xuewei Cao, Xuexia Wang, Shuanglin Zhang, Qiuying Sha

Michigan Tech Publications

Although genome-wide association studies (GWAS) have been successfully applied to a variety of complex diseases and identified many genetic variants underlying complex diseases via single marker tests, there is still a considerable heritability of complex diseases that could not be explained by GWAS. One alternative approach to overcome the missing heritability caused by genetic heterogeneity is gene-based analysis, which considers the aggregate effects of multiple genetic variants in a single test. Another alternative approach is transcriptome-wide association study (TWAS). TWAS aggregates genomic information into functionally relevant units that map to genes and their expression. TWAS is not only powerful, but …

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) …

Mercury Methylation In Oxic Sub-Polar Marine Regions Linked With Nitrification, Marissa Collins Despins

Browse all Theses and Dissertations

Methylmercury (MeHg) is a neurotoxin that bioaccumulates to potentially harmful concentrations in Arctic marine wildlife and in those that consume them. Monitoring and modeling MeHg bioaccumulation and biogeochemical cycling in the ocean requires understanding of the mechanisms behind net mercury (Hg) methylation. The key functional gene for Hg methylation, hgcAB, is widely distributed throughout ocean basins and spans multiple microbial phyla. While multiple microbially-mediated anaerobic pathways for Hg methylation are known, in the ocean, the majority of hgcA homologs have been found in oxic subsurface waters, in contrast to other ecosystems. In particular, microaerophilic Nitrospina, a genera of nitrite-oxidizing bacteria …

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 …

Patterns And Drivers Of Introgression In Louisiana's Largemouth Bass (Micropterus Salmoides) Stocks, Colleen E. Walsh

LSU Master's Theses

In the southeastern U.S., populations of the popular sportfish Largemouth Bass (Micropterus salmoides; LMB) are often stocked with Florida Largemouth Bass (Micropterus salmoides floridanus; FLMB) to develop FLMB ancestry in systems north of its native peninsular Florida range, with the ultimate goal of creating trophy fisheries. Stock enhancement through introgression of FLMB ancestry can increase maximum potential size and growth in receiving populations, potentially through hybrid vigor of intergrade subspecies. We collected 60 fish and habitat data from six Louisiana lakes from 2018-2020 (N=360), quantified level of introgression of FLMB with fragment analysis at 12 microsatellite loci confirmed for subspecific …

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 …

Rm-Net: Rasterizing Markov Signals To Images For Deep Learning, Kajal Gupta

Theses

Statistical machine learning approaches are quite famous for processing Markov signal data. They can model unobserved states and learn certain characteristics particular to a signal with good accuracy. However, with the advent of Deep learning the novice ways of solving a problem has shifted towards this more sophisticated algorithm, which is much better, powerful and more accurate. Specifically, Convolutional Neural Nets (CNN) have shown many promising results on images and videos. Here we illustrate how CNN can be applied to a 1D numeric signal using signal rasterization technique. We start by rasterizing a 1D numeric Markov signal into an image …

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 …

Development And Assessment Of An Environmental Dna (Edna) Assay For The Rio Grande Siren And Review Of Edna Metabarcoding Applications, Krista M. Ruppert

Theses and Dissertations

Environmental DNA (eDNA) assays have become a major aspect of amphibian surveys in the past decade. These methods are highly sensitive, making them well-suited for monitoring rare and cryptic species. Current efforts to study the Rio Grande Siren in south Texas have been hampered due to the cryptic nature of these aquatic salamanders. Arid conditions further add to the difficulty in studying this species, as many water bodies they inhabit are ephemeral, sometimes constraining sampling efforts to a short window after heavy rain. Additionally, sirens are known to cease activity and reside underground when ponds begin to dry or as …

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 …

A Study Of The Efficacy Of Machine Learning For Diagnosing Obstructive Coronary Artery Disease In Non-Diabetic Patients, Demond Larae Handley

Theses and Dissertations

According to the Centers for Disease Control and Prevention, about 18.2 million adults age 20 and older have Coronary Artery Disease in the United States. Early diagnosis is therefore of crucial importance to help prevent debilitating consequences, and principally death for many patients. In this study we use data containing gene expression values from peripheral blood samples in 198 non-diabetic patients, with the goal of developing an age and sex gene expression model for diagnosis of Coronary Artery Disease. We employ machine learning methods to obtain a classification based on genetic information, age and sex. Our implementation uses feed forward …