Genetics and Genomics Commons^™

Phenotypic And Genetic Analyses Of Adaptation To Geothermal Soils In Yellow Monkeyflowers Of Yellowstone National Park, Peter Breigenzer

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Microgeographic adaptation, which occurs on a spatial scale smaller than the dispersal distance of the evolving organisms, provides a fertile context for understanding the genetic processes that shape natural variation and contribute to biological diversity. In plants, mosaics of distinct soil conditions can select for microgeographic divergence in the face of gene flow, leading to major life history transitions and novel trait evolution. Mimulus (monkeyflowers) is an emerging model genus for ecological genomics, due to tremendous diversity, experimental tractability, and a wealth of genomic resources. In Yellowstone National Park, Mimulus guttatus occurs in both geothermal soils and nearby nonthermal bogs …

What’S In A Gene: Undergraduates’ Ideas And Misconceptions About Gene Function, Justin M. Levaughn

Theses and Dissertations--Science, Technology, Engineering, and Mathematics (STEM) Education

The purpose of this study was to field test a two-tiered instrument including multiple-choice and short answer tasks to assess college students’ ideas and level of understanding in genetics. The instrument was constructed from previously tested assessment tasks and findings from the current research literature. Ninety-seven freshmen enrolled in a biology lab course were surveyed. Test validity and reliability were measured using Chronbach coefficients. Multiple-choice and short answer responses were analyzed using descriptive statistics to identify frequencies of answer selections. Written responses were independently evaluated using a five-point scoring rubric by three researchers to identify common misconceptions revealed in students’ …

The Role Of Sox4 In Regulating Choroid Fissure Closure And Retinal Neurogenesis, Wen Wen

Theses and Dissertations--Biology

The development of the vertebrate eye is tightly controlled by precise genetic regulations. From a single ocular primordium to bilateral eyes with complex structures and cell types, it requires intensive proliferation and migration for cells in both the ectoderm and mesoderm to accomplish ocular morphogenesis, and during this process cell differentiation and interaction takes place to establish the complex composition of ocular cell types and cellular connections. Genetic defects can lead to severe abnormalities in eye morphogenesis and cell differentiation during ocular development. A tremendous amount of work has been done to identify both intrinsic and extrinsic factors that regulate …

Differential Gene Expression Of Minnesota (Mn) Hygienic Honeybees (Apis Mellifera) Performing Hygienic Behavior, Eric Northrup

All Graduate Theses, Dissertations, and Other Capstone Projects

Hygienic behavior is the ability to remove dead and diseased brood from the comb early as to limit the detrimental impact of the parasite or pathogen. Minnesota (MN) Hygienic bees are generalists of hygienic behavior with the ability to remove several brood infected with several pathogens including the Varroa mite. This study explored the mechanisms of MN Hygienic behavior by comparing the transcriptome of MN Hygienic bee brains to non-hygienic bee brains via cDNA microarray. The results suggest that the brains of MN Hygienic bees may have a greater number of dendritic connections or are more sensitive to neurotransmitters. Quantitative …

Cellmapper: Rapid And Accurate Inference Of Gene Expression In Difficult-To-Isolate Cell Types, Bradlee D. Nelms, Levi Waldron, Luis A. Barrera, Andrew W. Weflen, Jeremy A. Goettel, Guoji Guo, Robert K. Montgomery, Marian R. Neutra, David T. Breault, Scott B. Snapper, Stuart H. Orkin, Martha L. Bulyk, Curtis Huttenhower, Wayne I. Lencer

Publications and Research

We present a sensitive approach to predict genes expressed selectively in specific cell types, by searching publicly available expression data for genes with a similar expression profile to known cell-specific markers. Our method, CellMapper, strongly outperforms previous computational algorithms to predict cell type-specific expression, especially for rare and difficult-to-isolate cell types. Furthermore, CellMapper makes accurate predictions for human brain cell types that have never been isolated, and can be rapidly applied to diverse cell types from many tissues. We demonstrate a clinically relevant application to prioritize candidate genes in disease susceptibility loci identified by GWAS.

The Mitogenome Of The Bed Bug Cimex Lectularius (Hemiptera: Cimicidae), Sergios-Orestis Kolokotronis, Jonathan Foox, Jeffrey A. Rosenfeld, Mercer R. Brugler, Darryl Reeves, Joshua B. Benoit, Warren Booth, Grant Robison, Michael Steffen, Zoe Sakas, Subba R. Palli, Coby Schal, Stephen Richards, Apurva Narechania, Richard H. Baker, Louis N. Sorkin, George Amato, Christopher E. Mason, Mark E. Siddall, Rob Desalle

Publications and Research

We report the extraction of a bed bug mitogenome from high-throughput sequencing projects originally focused on the nuclear genome of Cimex lectularius. The assembled mitogenome has a similar AT nucleotide composition bias found in other insects. Phylogenetic analysis of all protein-coding genes indicates that C. lectularius is clearly a member of a paraphyletic Cimicomorpha clade within the Order Hemiptera.

Coordination Of Rna Polymerase Ii Pausing And 3' End Processing Factor Recruitment With Alternative Polyadenylation, Becky Fusby, Soojin Kim, Benjamin Erickson, Hyunmin Kim, Martha L. Peterson, David L Bentley

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Most mammalian genes produce transcripts whose 3' ends are processed at multiple alternative positions by cleavage/polyadenylation (CPA). Poly(A) site cleavage frequently occurs cotranscriptionally and is facilitated by CPA factor binding to the RNA polymerase II (Pol II) C-terminal domain (CTD) phosphorylated on Ser2 residues of its heptad repeats (YS₂PTSPS). The function of cotranscriptional events in the selection of alternative poly(A) sites is poorly understood. We investigated Pol II pausing, CTD Ser2 phosphorylation, and processing factor CstF recruitment at wild-type and mutant IgM transgenes that use alternative poly(A) sites to produce mRNAs encoding the secreted and membrane-bound forms of …

A Variance Component Method For Integrated Pathway Analysis Of Gene Expression Data, Ellen E. Quillen, John Blangero, Laura Almasy

Human Genetics Publications

Background: The application of pathway and gene-set based analyses to high-throughput data is increasingly common and represents an effort to understand underlying biology where single-gene or single-marker analyses have failed. Many such analyses rely on the a priori identification of genes associated with the trait of interest. In contrast, this variance-component-based approach creates a similarity matrix of individuals based on the expression of genes in each pathway.

Methods: We compared 16 methods of calculating similarity for positive control matrices based on probes for the genes used to model the simulated Genetic Analysis Workshop phenotypes. Results: A simple correlation matrix outperforms …

Independent Test Assessment Using The Extreme Value Distribution Theory, Marcio Almeida, Lucy Blondell, Juan M. Peralta, Jack W. Kent Jr., Goo Jun, Tanya M. Teslovich, Christian Fuchsberger, Andrew R. Wood, Alisa K. Manning, Thomas D. Dyer, Ravindranath Duggirala, John Blangero

School of Medicine Publications

The new generation of whole genome sequencing platforms offers great possibilities and challenges for dissecting the genetic basis of complex traits. With a very high number of sequence variants, a naïve multiple hypothesis threshold correction hinders the identification of reliable associations by the overreduction of statistical power. In this report, we examine 2 alternative approaches to improve the statistical power of a whole genome association study to detect reliable genetic associations. The approaches were tested using the Genetic Analysis Workshop 19 (GAW19) whole genome sequencing data. The first tested method estimates the real number of effective independent tests actually being …

Genetic Structure And Connectivity Of The Endangered Giant Kangaroo Rat (Dipodomys Ingens) In A Heterogeneous Environment, Nathan Alexander

Cal Poly Humboldt theses and projects

Movement ecology and dispersal are important aspects of species’ life histories that can inform conservation and management. Dispersal is often cryptic and difficult to detect, but recent advances genetic technology and applications have provided new approaches to identifying and describing dispersal patterns. Giant kangaroo rats (Dipodomys ingens) are an endangered heteromyid that appear to persist in small subpopulations in a heterogeneous environment of their northern range, the Ciervo-Panoche Natural Area, California. Previous work suggested high levels of genetic diversity between populations with genetic distances not being correlated to geographic distances. Here, I identified landscape population structure through clustering …

The Uyghur Population And Genetic Susceptibility To Type 2 Diabetes: Potential Role For Variants In Capn10, Apm1 And Fut6 Genes, Feifei Zhao, Dolikun Mamatyusupu, Youxin Wang, Honghong Fang, Hao Wang, Qing Gao, Hao Dong, Siqi Ge, Xinwei Yu, Jie Zhang, Lijuan Wu, Manshu Song, Wei Wang

Research outputs 2014 to 2021

Genome-wide association studies have successfully identified over 70 loci associated with the risk of type 2 diabetes mellitus (T2DM) in multiple populations of European ancestry. However, the risk attributable to an individual variant is modest and does not yet provide convincing evidence for clinical utility. Association between these established genetic variants and T2DM in general populations is hitherto understudied in the isolated populations, such as the Uyghurs, resident in Hetian, far southern Xinjiang Uyghur Autonomous Region, China. In this case–control study, we genotyped 13 single-nucleotide polymorphisms (SNPs) at 10 genes associated with diabetes in 130 cases with T2DM and 135 …

Association Between Igf2bp2 Polymorphisms And Type 2 Diabetes Mellitus: A Case-Control Study And Meta-Analysis, Ping Rao, Hao Wang, Honghong Fang, Qing Gao, Jie Zhang, Manshu Song, Yong Zhou, Youxin Wang, Wei Wang

Research outputs 2014 to 2021

Background:

Genome-wide association studies (GWAS) found that IGF2BP2 rs4402960 and rs1470579 polymorphisms were associated with type 2 diabetes mellitus (T2DM) risk. Many studies have replicated this association, but yielded inconsistent results.

Materials and Methods:

A case-control study consisting of 461 T2DM patients and 434 health controls was conducted to detect the genetic susceptibility of IGF2BP2 in a northern Han Chinese population. A meta-analysis was to evaluate the association more precisely in Asians.

Results:

In the case-control study, the carriers of TT genotype at rs4402960 had a higher T2DM risk than the G carriers (TG + GG) (adjusted …

Analysis Of Fy Promoter And Hepatocystis Load In South African Vervet Monkeys (Chlorocebus Aethiops), Benjamin J. Gombash

All Master's Theses

There are species of Hepatocystis and Plasmodium, related blood parasites, that enter the cell through a chemokine receptor, coded for by the Duffy antigen/receptor for chemokines in humans, and the FY*0 (FY Null) allele in the promoter of this gene results in the absence of this receptor on the exterior of the cell (Miller et al., 1977; Miller et al., 1975; Miller et al., 1976; Barnwell et al., 1989; Perkins and Schall, 2002; Martinsen et al., 2008; Tung et al., 2009). Humans without the receptor show resistance to multiple strains of Plasmodium (Tournamelle, et al., 1995; Zimmerman, et al. …

Resolving Gnetum Evolutionary History, Angela Mcfadden

All Master's Theses

Gnetum are non-flowering seed plants of the tropics, indigenous to South America, Africa, and Asia. This group of about 40 species is fascinating to botanists because it shares distinctive morphological characteristics with flowering plants, such as broad leaves, woody stems, and flower-like strobili. There are still questions surrounding the relationships within the genus of Gnetum. With that in mind, I focused my work on generating phylogenetic hypotheses, using two molecular data sets: a concatenation of over 60 different chloroplast genes (66,815 base pairs), and the whole chloroplast genome (128,772 base pairs). This allowed me to compare the two phylogenies …

High Diversity Of Trypanosoma Cruzi Discrete Typing Units Circulating In Triatoma In Western Mexico, Uyen T. Nguyen

All Master's Theses

Chagas disease is caused by the protozoan parasite Trypanosoma cruzi, which is transmitted to domestic and sylvatic mammals via the feces of hematophagous hemiptera of the subfamily Triatominae (Reduviidae). Trypanosoma cruzi is found only in the Americas and displays remarkable genetic diversity. Seven discrete typing units (DTUs) are currently recognized (TcI–TcVI and TcBat). In Jalisco, Mexico, where Chagas disease has a high prevalence rate, TcI has historically been the only DTU reported. This study focused on the molecular identification of T. cruzi DTUs circulating in Triatoma near the Estación de Biología Chamela, on the southwest coast of Jalisco, Mexico. …

The Impact Of Oxygen On Bacterial Enteric Pathogens, Nathan Wallace, Ashley N. Zani, Elizabeth A. Abrams, Yvonne Sun

Biology Faculty Publications

Bacterial enteric pathogens are responsible for a tremendous amount of foodborne illnesses every year through the consumption of contaminated food products. During their transit from contaminated food sources to the host gastrointestinal tract, these pathogens are exposed and must adapt to fluctuating oxygen levels to successfully colonize the host and cause diseases. However, the majority of enteric infection research has been conducted under aerobic conditions. To raise awareness of the importance in understanding the impact of oxygen, or lack of oxygen, on enteric pathogenesis, we describe in this review the metabolic and physiological responses of nine bacterial enteric pathogens exposed …

Toward The Elucidation Of Cytoplasmic Diversity In North American Grape Breeding Programs, Jonathan Fresnedo-Ramirez, Qi Sun, Chin-Feng Hwang, Craig A. Ledbetter, David W. Ramming, Anne Fennell, M. Andrew Walker, James J. Luby, Matthew D. Clark, Jason P. Londo, Lance Cadle-Davidson, Gan-Yuan Zhong

Agronomy, Horticulture and Plant Science Faculty Publications

Plants have an intriguing tripartite genetic system: Nuclear genome 9 Mitochondria 9 Plastids and their interactions may impact germplasm breeding. In grapevine, the study of cytoplasmic genomes has been limited, and their role with respect to grapevine germplasm diversity has yet to be elucidated. In the present study, the results of an analysis of the cytoplasmic diversity among 6073 individuals (comprising cultivars, interspecific hybrids and segregating progenies) are presented. Genotyping by sequencing (GBS) was used to elucidate plastid and mitochondrial DNA sequences, and results were analyzed using multivariate techniques. Single nucleotide polymorphism (SNP) effects were annotated in reference to plastid …

Investigation Into The Cell Wall And Cellulose Biosynthesis In Model Species And In The C4 Model Plant Setaria Viridis, Mizuki Tateno

Theses and Dissertations--Plant and Soil Sciences

A uniform feature of all plant cells is the presence of a cell wall. The cell wall functions in facilitating directional expansion and is therefore important for cell shape and morphogenesis. All plant cell walls contain cellulose microfibrils embedded in a network of polysaccharides, lignin and protein. Cellulose is evolutionarily conserved and is made by all plants as well as other members of various taxonomic kingdoms. From a human perspective, the field of renewable energy has had an ever increasing interest in using the cell wall for production of renewable platform chemicals and fuels. However, the biosynthesis of these components …

Conservation Genetics On The Frontline, Kenneth W. Rand

Graduate Student Theses, Dissertations, & Professional Papers

Conservation genetics stands out as an effective tool for discovering and monitoring rare, endangered or invasive populations of plants and animals. Particularly when compared to traditional search and capture methods, it provides more holistic studies to preserve the disappearing biodiversity of the American West and the world.

Three stories highlight the work done to preserve biodiversity through the use of conservation genetics:

1. Trout Rescue: A new hope for westslope cutthroat in Montana How to save a disappearing westslope cutthroat trout through genetic rescue by adding genetic diversity to ensuring future survival in increasingly warming waters more harm than good. …

Phylogenetic Analyses Of Andean And Amazonian Tree Communities In Ecuador, Samantha J. Worthy

Theses and Dissertations

The forests of Ecuador are known for their high levels of diversity and endemism, classifying the country as a biodiversity hotspot. Both the western Amazon and Andean montane forests are richly populated with tropical tree species that have been little studied in a community phylogenetic context. The implementation of elevational transects and trait based analyses having proven useful in gaining a better understanding of how environmental factors are affecting the tree community structure in these habitats. The goal of this research was to evaluate the magnitude ofDNA barcode diversity among Amazonian and Andean tree species. Specifically, the objectives were to …

Fgprp4 Kinase Is Important For Spliceosome B-Complex Activation And Splicing Efficiency In Fusarium Graminearum, Xuli Gao, Qiaojun Jin, Cong Jiang, Yang Li, Chaohui Li, Huiquan Liu, Zhensheng Kang, Jin-Rong Xu

Department of Botany and Plant Pathology Faculty Publications

PRP4 encodes the only kinase among the spliceosome components. Although it is an essential gene in the fission yeast and other eukaryotic organisms, the Fgprp4 mutant was viable in the wheat scab fungus Fusarium graminearum. Deletion of FgPRP4 did not block intron splicing but affected intron splicing efficiency in over 60% of the F. graminearum genes. The Fgprp4 mutant had severe growth defects and produced spontaneous suppressors that were recovered in growth rate. Suppressor mutations were identified in the PRP6, PRP31, BRR2, and PRP8 orthologs in nine suppressor strains by sequencing analysis with candidate tri-snRNP …

Chloroplast Rna-Binding Protein Rbd1 Promotes Chilling Tolerance Through 23s Rrna Processing In Arabidopsis, Shuai Wang, Ge Bai, Shu Wang, Leiyun Yang, Fen Yang, Yi Wang, Jiankang Zhu, Jian Hua

Department of Horticulture & Landscape Architecture Faculty Publications

Plants have varying abilities to tolerate chilling (low but not freezing temperatures), and it is largely unknown how plants such as Arabidopsis thaliana achieve chilling tolerance. Here, we describe a genome-wide screen for genes important for chilling tolerance by their putative knockout mutants in Arabidopsis thaliana. Out of 11,000 T-DNA insertion mutant lines representing half of the genome, 54 lines associated with disruption of 49 genes had a drastic chilling sensitive phenotype. Sixteen of these genes encode proteins with chloroplast localization, suggesting a critical role of chloroplast function in chilling tolerance. Study of one of these proteins RBD1 with an …

Fuzzy Unheritance: A Novel Form Of Somatic Cell Inheritance That Regulates Cell Population Heterogeneity, Batoul Abdallah

Wayne State University Dissertations

Multi-level heterogeneity is a characteristic feature of cancer cell populations. However, how a cell population regulates and maintains its cell population heterogeneity is not well understood. Based on conventional theories of genetic inheritance, cell division is precise, where a daughter cell inherits an identical karyotype from its mother cell. Therefore, errors that are generated during cell division occur at low frequencies that take prolonged time periods to accumulate. However, the overwhelming heterogeneity found in unstable cancers is largely inconsistent with current models of genetic inheritance. In order to determine the mechanism of how heterogeneity is regulated, the pattern of inherited …

Effective Drug Treatment Induces Drug Resistance Through Rapid Genome Alteration-Mediated Cancer Evolution, Steven Horne

Wayne State University Dissertations

The central paradox associated with current cancer therapeutic strategies is initially effective treatment, which eliminates a high tumor cell count, consistently results in successful drug resistance. Mathematical and evolutionary modeling have previously suggested that therapeutic intervention could provide selective pressure for the expansion of resistant variants. Drug-related stress has been associated with genome chaos, a common phenomenon in cancer characterized as rapid, stochastic genomic fragmentation and reorganization. Since cancer represents an evolutionary process, analysis within the context of genome-mediated cancer evolution can shed light on this key problem of therapeutics. We propose that genomic change is a general response to …

A Novel Role For Repetitive Sequences In Recognition Of The Drosophila Melanogaster X Chromosome, Sonal Suresh Joshi

Wayne State University Dissertations

In humans and fruit flies, males have one X chromosome while females have two. This imbalance in gene dosage is potentially lethal, and the process of dosage compensation corrects it. The MSL (Male Specific Lethal) complex, which is composed of five proteins and one of two functionally redundant long non-coding roX (RNA on the X) RNAs, brings about dosage compensation in Drosophila melanogaster. In fruit fly dosage compensation, all the genes on the single male X chromosome are upregulated approximately twofold, via chromatin modifications, to equalize gene dosage with the two X chromosomes of females. This process calls for highly …

An Analysis Of The Interaction Between Sin3 And Methionine Metabolism In Drosophila, Mengying Liu

Wayne State University Dissertations

Chromatin modification and cellular metabolism are tightly connected. The mechanism for this cross-talk, however, remains incompletely understood. SIN3 controls histone acetylation through association with the histone deacetylase RPD3. In this study, my major goal is to explore the mechanism of how SIN3 regulates cellular metabolism.

Methionine metabolism generates the major methyl donor S-adenosylmethionine (SAM) for histone methylation. In collaboration with others, I report that reduced levels of some enzymes involved in methionine metabolism and histone demethylases lead to lethality, as well as wing development and cell proliferation defects in Drosophila melanogaster. Additionally, disruption of methionine metabolism can directly affect histone …

Modeling The Mechanism Underlying Environmental And Genetic Determinants Of Gene Expression And Complex Traits, Gregory Alan Moyerbrailean

Wayne State University Dissertations

Advances in next-generation sequencing technologies and functional genomics strategies have allowed researchers to identify both common and rare genetic variation, to deeply profile gene expression, and even to determine regions of active gene transcription.

While these technologies and strategies have contributed greatly to our understanding of complex traits and diseases, there are many biological questions and analytical issues to be addressed.

Genome-wide association studies (GWAS) have successfully identified large numbers of genetic variants associated with complex traits and diseases. However, in many cases the mechanistic link between the phenotype and associated variant remains unclear. This may be because most variants …

Payer Perspectives On Preemptive Pharmacogenetic Testing, Nicholas Keeling

Electronic Theses and Dissertations

Purpose: As preemptive pharmacogenetics expands in the academic healthcare setting, further study is needed to assess the views of additional stakeholders in the marketplace on this technology and the barriers and facilitators to their uptake. The purpose of this study is to investigate the perspectives and opinions about coverage policies for preemptive pharmacogenetic testing of third-party payers. Methods: A qualitative study utilizing a blended inductive and directed approach was conducted. A screener survey determined interview eligibility as well as demographic data. Semi-structured interviews were conducted with payers from organizations of varying structure and beneficiary populations. Meaning units and codes were …

System Genetic Analysis Of Mechanisms Underlying Excessive Alcohol Consumption, Maren L. Smith

Theses and Dissertations

Increased alcohol consumption over time is one of the characteristic symptoms of Alcohol Use Disorder (AUD). The molecular mechanisms underlying this escalation in intake is still the subject of study. However, the mesocortical and mesolimbic dopamine pathways, and the extended amygdala, because of their involvement in reward and reinforcement are believed to play key roles in these behavioral changes. Multiple gene expression studies have shown that alcohol affects the expression of thousands of genes in the brain. The studies discussed in this document use the systems biology technique of co-expression network analysis to attempt to find

patterns within genome-wide expression …

A Pipeline For Creation Of Genome-Scale Metabolic Reconstructions, Shaun W. Norris

Theses and Dissertations

The decreasing costs of next generation sequencing technologies and the increasing speeds at which they work have lead to an abundance of 'omic datasets. The need for tools and methods to analyze, annotate, and model these datasets to better understand biological systems is growing. Here we present a novel software pipeline to reconstruct the metabolic model of an organism in silico starting from its genome sequence and a novel compilation of biological databases to better serve the generation of metabolic models. We validate these methods using five Gardnerella vaginalis strains and compare the gene annotation results to NCBI and the …