Genetics and Genomics Commons^™

Probing The Effects Of Tbhk2 On Trypanosoma Brucei Growth, Social Growth, And Inhibitor Response, Amber Hackler, William Mcalpine, Yijian Qiu, James Morris

Graduate Research and Discovery Symposium (GRADS)

In sub-Saharan Africa the protozoan parasite, Trypanosoma brucei, continues to be of major concern for the health and economic development of the region. This parasite is known to cause human African trypanosomiasis (HAT or African sleeping sickness) and nagana in livestock such as cattle. Social behaviors, such as colonization and migration, are important in the study of T. brucei because of the way the parasite infects its mammalian host. During the fly bloodmeal, the parasite first passes into the gut but then eventually migrates to the fly salivary glands where it will continue to develop before transmission as a parasitic …

Development Of Liriodendron Est-Ssr Markers And Genetic Composition Of Two Liriodendron Tulipifera L. Orchards, Xinfu Zhang

All Theses

Liriodendron tulipifera L., commonly known as yellow-poplar, is a fast-growing hardwood tree species with great ecological and economic value and is native to eastern North America. Liriodendron occupies an important phylogenetic position as a basal angiosperm and has been used in studies of the evolution of flowering plants. Genomic resources, such as Expressed Sequence Taq (EST) databases and Bacterial Artificial Chromosome (BAC) libraries, have been developed for this species. However, no genetic map is available for Liriodendron, and very few molecular markers have been developed. In this study, a total of 119 informative genomic SSR markers suitable were identified for …

The Genome Sequence Of The Most Widely Cultivated Cacao Type And Its Use To Identify Candidate Genes Regulating Pod Color, Juan C. Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone Iii, Omar Cornejo, Seth Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski

Publications

Background

Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders.

Results

We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina

1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of …

Conserved Noncoding Sequences Regulate Steady-State Mrna Levels In Arabidopsis Thaliana, Jacob Spangler

All Dissertations

Arabidopsis thaliana has undergone three whole genome duplications within its ancestry, and these events have dramatically affected its gene complement. Of the most recent whole genome duplication events (&alpha event), there remain 11,452 conserved noncoding sequences (CNSs) that have been retained proximal to &alpha duplicate gene pairs. As functional DNA elements are expected to diverge in sequence at a slower rate than nonfunctional DNA elements, the retained CNSs likely encode gene regulatory function. Within this dissertation I provide evidence for the regulatory role of CNSs within Arabidopsis thaliana. Using a collection of over 5,000 microarray RNA expression profiling datasets, I …

Characterization Of Two Type Iv Collagens Involved In Autosomal Recessive Hereditary Nephropathy, Keri Tabb

All Dissertations

The glomerular basement membrane (GBM) of the kidney is highly specialized and required for filtration of waste products from the bloodstream. One of the major structural and functional units of the GBM is a network composed of type IV collagen heterotrimers, or protomers. Early in development of the human and dog, an isoform switch occurs, and the α1α1α2 (IV) network found in the nascent GBM is replaced with α3α4α5 (IV) protomers. Mutations in any of the genes encoding proteins found in the mature GBM network may prevent protomer formation and cause a progressive disorder leading to end stage renal failure …

Analysis Of Genotype, Phenotype, And Age Progression In Phelan-Mcdermid Syndrome, Sara Sarasua

All Dissertations

Phelan-McDermid syndrome is a developmental disability syndrome associated with deletions of the terminal end of one copy of chromosome 22q13. The observed chromosomal aberrations include simple terminal deletions, interstitial deletions, deletions and duplications, and duplications without deletions. All patients have some degree of developmental disability and many also have hypotonia, autism, minor dysmorphic features, and seizures. I performed an epidemiological and cytogenetic investigation to better understand the etiology of Phelan-McDermid syndrome and to provide information to patients and their families, clinicians, and researchers investigating developmental disabilities. Deletions vary widely in size, from 60 kb to more than 9 Mb, but …

Molecular Genetics Of Nodule Number Regulation: Cloning, Characterization And Functional Studies Of The Root Determined Nodulator1 (Rdn1) Gene In Medicago Truncatula, Tessema Kassaw

All Dissertations

Nitrogen is critical to life. However, the majority of nitrogen on earth (in the atmosphere) is inert and unavailable to nearly all organisms. Metabolically diverse prokaryotes are the only organisms capable of fixing atmospheric nitrogen; rhizobia set up a symbiosis with legume plants allowing the plants to benefit from this ability. Since nodulation and the subsequent nitrogen fixation processes are energy intensive, the host plant must balance hosting of the rhizobia by limiting the number of nodules it forms through a mechanism called Autoregulation of Nodulation (AON). My study of mutants in the model legume Medicago truncatula defective in AON …

Family Cancer History And Pedigrees As A Public Health Intervention For Promoting Health And Preventing Prostate Cancer In African American Men, Holisa Wharton

All Dissertations

ABSTRACT
Prostate cancer is the most common cancer diagnosed in men and the second leading cause of cancer death among men in the United States. African-American men have substantially higher prostate cancer incidence and mortality than European-American men. It is unclear whether this incidence is due to acquired DNA changes (sporadic cancer) or if germline Mendelian genetics/genomics (inherited cancer) is the source of this health disparity. To explore this cause, the focus of this dissertation paper is family health history and hereditary prostate cancer. A family history tool is the most commonly used predictive instrument for hereditary prostate cancer. The …

Cytogenetic Biodiversity In The Simulium Johannseni Group (Diptera: Simuliidae), Katherine Gleason

All Theses

Cryptic biodiversity, the presence of suborganismal variation in isomorphic populations of organisms, can have implications for management and conservation. Ecological variation in habitat and host species of populations of the black fly Simulium johannseni suggested the potential for cryptic biodiversity. Polytene chromosomes of larvae belonging to the S. johannseni group of black flies were characterized to discover fixed and polymorphic rearrangements. Larvae of S. johannseni from Wisconsin, South Carolina, and Alabama and of the closely related S. parmatum from South Carolina and Florida were analyzed. Simulium johannseni can be divided into two cytoforms corresponding to geographic location. Cytoform A, found …

Mapping Quantitative Trait Loci Associated With Resistance To Bacterial Spot (Xanthomonas Arboricola Pv. Pruni) In Peach, Nannan Yang

All Dissertations

Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is a serious disease that can affect peach fruit quality and production worldwide. This disease causes severe defoliation and blemishing of fruit, particularly in areas with high rainfall, strong winds, high humidity and sandy soil. The molecular basis of its tolerance and susceptibility in peach is yet to be understood. To study the genetics of the peach response to Xap, an F2 segregating population between two peach cultivars, `Clayton', a resistant phenotype, and `O'Henry', which is very susceptible to Xap, was created. Phenotypic data for leaf and fruit response to Xap …

Genetic Engineering Of Turfgrass For Enhanced Performance Under Environmental Stress, Man Zhou

All Dissertations

Turfgrass species are agriculturally and economically important perennial crops that are susceptible to biotic stress (e.g. fungal pathogens) and abiotic stress (e.g. salinity and drought). Every year, environmental stress significantly influences turfgrass quality and production causing economic loss globally. My research explores the feasibility of using two novel transgenes - Penaeidin4-1 (Pen4-1) from the shrimp, Litopenaeus setiferus, and microRNA319a (miR319a) from the rice, Oryza sativa, to genetically engineer turfgrass for enhanced tolerance to environmental stress.
The antimicrobial peptide - Pen4-1 has been reported to possess in vitro antifungal and antibacterial activities against various economically important pathogens. In this study, two …

Choline Supplementation And Dna Methylation In The Hippocampus And Prefrontal Cortex Of Rats Exposed To Alcohol During Development, Nicha K H Otero, Jennifer D. Thomas, Christopher Saski, Xiaoxia Xia, Sandra Kelly

Publications

BACKGROUND:

Some of the most frequent deficits seen in children with fetal alcohol spectrum disorders (FASD) and in animal models of FASD are spatial memory impairments and impaired executive functioning, which are likely related to alcohol-induced alterations of the hippocampus and prefrontal cortex (PFC), respectively. Choline, a nutrient supplement, has been shown in a rat model to ameliorate some of alcohol's teratogenic effects, and this effect may be mediated through choline's effects on DNA methylation.

METHODS:

Alcohol was given by intragastric intubation to rat pups during the neonatal period (postnatal days 2 to 10) (ET group), which is equivalent to …

Enhancing Genome Investigations In The Mosquito Culex Quinquefasciatus Via Bac Library Construction And Characterization, Paul V. Hickner, Becky Debruyn, Diane D. Lovin, Akio Mori, Christopher Saski, David W. Severson

Publications

Background

Culex quinquefasciatus (Say) is a major species in the Culex pipiens complex and an important vector for several human pathogens including West Nile virus and parasitic filarial nematodes causing lymphatic filariasis. It is common throughout tropical and subtropical regions and is among the most geographically widespread mosquito species. Although the complete genome sequence is now available, additional genomic tools are needed to improve the sequence assembly.

Findings

We constructed a bacterial artificial chromosome (BAC) library using the pIndigoBAC536 vector and HindIII partially digested DNA isolated from Cx. quinquefasciatus pupae, Johannesburg strain (NDJ). Insert size was estimated by Not …

A Genetically Anchored Physical Framework For Theobroma Cacao Cv. Matina 1-6, Christopher Saski, Frank Feltus, Margaret Staton, Barbara Blackmon, Stephen Ficklin, David Kuhn, Raymond Schnell, Howard Shapiro, Juan Carlos Motamayor

Publications

The fermented dried seeds of Theobroma cacao (cacao tree) are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robust T. cacao cultivars. However, problems inherent with assembly and resolution of …

Analysis Of Dna Methylation Differerences Between High And Low Chill Peach (Prunus Persica [L. Batsch]), Sherri Hughes-Murphree

All Theses

Chilling requirement is a critically important phenological trait that controls the timing of vegetative bud break and floral bloom, and impacts the climatic distribution of temperate tree species. However, the molecular basis of the chilling requirement trait is not well understood. Analysis of chilling requirement QTL from peach and apricot has detected numerous genes known to modulate DNA and histone methylation pathways. Evidence from other plant systems suggests these types of epigenetic mechanisms may play a role in temperature-modulated plant developmental responses.
For this study, DNA from vegetative buds of overwintering peach trees was examined for changes in methylation status …

C.Elegans Host Cell Factor (Cehcf) Associates With Sir-2.1 To Mediate Target Specificity Of Daf-16 And Lifespan, Yao Yao

All Theses

The programmed aging process, controlled by a complex gene network, exists in all living organisms. In past decades, studies on the model organism, the nematode worm Caenorhabditis elegans (C. elegans), have revealed some highly conserved molecular pathways involved in lifespan regulation. After entering nucleus, DAF-16 cooperates with corresponding cofactors to achieve its specificity and triggers the transcription of certain subsets of its targets. Here we report that a novel DAF-16 co-factor CeHCF (C.elegans Host Cell Factor) mediate lifespan by regulating NAD+-dependent protein deacetylase, SIR-2.1.
Lifespan assay using Cehcf RNAi revealed that the lifespan extension caused by loss of Cehcf could …

Population Genetics And Species Interactions: From Theory To Agro-Ecosystems, Cynthia Climer

All Dissertations

Population genetics is the study of allele frequency distributions and changes due to evolutionary processes such as selection, adaptation, genetic drift and gene flow to understand how these processes impact populations over space and time. Population genetics theory can be utilized to understand not only population level interactions, but also interactions among closely related species. In this dissertation I have utilized population genetics in three conceptually related projects. Utilizing genome-wide gene coding markers, I have tested the impact of population size changes on the genetic diversity of coding genes in a model system (Arabidopsis lyrata subsp. petraea). This study tests …

Sequencing Of A Qtl-Rich Region Of The Theobroma Cacao Genome Using Pooled Bacs And The Identification Of Trait Specific Candidate Genes, Frank A. Feltus, Christopher Saski, Keithanne Mockaitis, Niina Haiminen, Laxmi Parida, Zachary Smith, James Ford, Margaret E. Staton, Stephen P. Ficklin, Barbara P. Blackmon, Chun-Huai Cheng, Raymond J. Schnell, David N. Kuhn, Juan-Carlos Motamayor

Publications

BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library.

New Genomic Resources For Switchgrass: A Bac Library And Comparative Analysis Of Homoeologous Genomic Regions Harboring Bioenergy Traits, Christopher Saski, Zhigang Li, Frank A. Feltus, Hong Luo

Publications

Switchgrass, a C4 species and a warm-season grass native to the prairies of North America, has been targeted for development into an herbaceous biomass fuel crop. Genetic improvement of switchgrass feedstock traits through marker-assisted breeding and biotechnology approaches calls for genomic tools development. Establishment of integrated physical and genetic maps for switchgrass will accelerate mapping of value added traits useful to breeding programs and to isolate important target genes using map based cloning. The reported polyploidy series in switchgrass ranges from diploid (2X = 18) to duodecaploid (12X = 108). Like in other large, repeat-rich plant genomes, this genomic complexity …

Construction Of Papaya Male And Female Bac Libraries And Application In Physical Mapping Of The Sex Chromosomes, Andrea R. Gschwend, Qingyi Yu, Paul Moore, Christopher Saski, Cuixia Chen, Jianping Wang, Jong-Kuk Na, Ray Ming

Publications

Papaya is a major fruit crop in the tropics and has recently evolved sex chromosomes. Towards sequencing the papaya sex chromosomes, two bacterial artificial chromosome (BAC) libraries were constructed from papaya male and female genomic DNA. The female BAC library was constructed using restriction enzyme BstY I and consists of 36,864 clones with an average insert size of 104 kb, providing 10.3x genome equivalents. The male BAC library was constructed using restriction enzyme EcoR I and consists of 55,296 clones with an average insert size of 101 kb, providing 15.0x genome equivalents. The male BAC library was used in constructing …

Adventures In The Enormous: A 1.8 Million Clone Bac Library For The 21.7 Gb Genome Of Loblolly Pine, Zenaida Magbanua, Seval Ozkan, Benjamin Bartlett, Philippe Chouvarine, Christopher Saski, Aaron Siston, Richard Cronn, C Dana Nelson, Daniel Peterson

Publications

Loblolly pine (LP; Pinus taeda L.) is the most economically important tree in the U.S. and a cornerstone species in southeastern forests. However, genomics research on LP and other conifers has lagged behind studies on flowering plants due, in part, to the large size of conifer genomes. As a means to accelerate conifer genome research, we constructed a BAC library for the LP genotype 7-56. The LP BAC library consists of 1,824,768 individually-archived clones making it the largest single BAC library constructed to date, has a mean insert size of 96 kb, and affords 7.6X coverage of the 21.7 Gb …

The Genetics Of Metal Uptake In Caulobacter Crescentus: Characterization Of Regulators And Identification Of Receptors, Leah Howell

All Dissertations

Caulobacter crescentus is an oligotrophic, Gram negative bacterium with a dimorphic lifecycle. It is a model system for cell cycle regulation and cellular development. Since C. crescentus resides primarily in freshwater, this microorganism can also serve as a model system for nutrient uptake by oligotrophic freshwater species. This study focused on TonB-dependent receptors and metal-dependent regulators in C. crescentus.
To maintain appropriate levels of iron within the cell, bacteria have evolved mechanisms to control iron uptake, storage, and use. In microbes, there are two protein families possessing members that accomplish this: Fur and Rrf2. In the C. crescentus genome, there …

Genomic Tools Development For Aquilegia: Construction Of A Bac-Based Physical Map, Guang-Chen Fang, Barbara P. Blackmon, David C. Henry, Margaret E. Staton, Christopher Saski, Scott A. Hodges, Jeff P. Tomkins, Hong Luo

Publications

The genus Aquilegia, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relatively unstudied clade in the angiosperm phylogenetic tree that bridges the gap between these two major plant groups. Aquilegia species are closely related and their distribution covers highly diverse habitats. These provide rich resources to better understand the genetic basis of adaptation to different pollinators and habitats that in turn leads to rapid speciation. To gain insights into the genome structure and facilitate gene identification, comparative genomics and whole-genome shotgun …

Complete Plastid Genome Sequences Of Three Rosids (Castanea, Prunus, Theobroma): Evidence For At Least Two Independent Transfers Of Rpl22 To The Nucleus, Robert K. Jansen, Christopher Saski, Seung-Bum Lee, Anne K. Hansen, Henry Daniell

Publications

Functional gene transfer from the plastid to the nucleus is rare among land plants despite evidence that DNA transfer to the nucleus is relatively frequent. During the course of sequencing plastid genomes from representative species from three rosid genera (Castanea, Prunus, Theobroma) and ongoing projects focusing on the Fagaceae and Passifloraceae, we identified putative losses of rpl22 in these two angiosperm families. We further characterized rpl22 from three species of Passiflora and one species of Quercus and identified sequences that likely represent pseudogenes. In Castanea and Quercus, both members of the Fagaceae, we identified a …

Candidate Gene Studies In Patients With Autism Spectrum Disorder, Pamela Jackson

All Dissertations

Autism Spectrum Disorder is a grouping of disorders that range from the diagnosis of Asperger Syndrome to Autistic Disorder (formally known as autism). Attention Deficit Disorders and Pervasive Developmental Disorder-Not Otherwise Specified are also a part of this spectrum of disorders. Autism Spectrum Disorder affects one out of every 110 children and has a male to female ratio of 4:1. This has led to the need to identify genes that may be causative for this disorder.
Several genome-wide scans have been conducted and have identified locations in the human genome that may contain causative genes for Autism Spectrum Disorder. One …

The Population Genetics Of The Endangered Scalloped Hammerhead Shark, Sphyrna Lewini, Across Its Eastern Pacific Range, Holly Nance

All Dissertations

I have characterized the population genetic structure, inferred the evolutionary processes shaping it, and estimated effective population size (Ne) using different contemporary and coalescent methods in the endangered scalloped hammerhead shark, Sphyrna lewini, throughout its Eastern Pacific (EP) range. I found significant genetic differentiation among seven coastal sites between Mexico and Ecuador using 15 microsatellite loci, and significant isolation by distance among samples of mtDNA control region haplotypes. While Bayesian statistical analyses and coalescent-based methods revealed low levels of ecological connectivity between most sampled sites (point estimates of Nm = 0.6 - 7.3), mismatch analyses showed that all populations experienced …

Mapping Quantitative Trait Loci Associated With Chilling Requirement And Bloom Date In Peach, Shenghua Fan

All Dissertations

Chilling requirement (CR), together with heat requirement (HR), determines bloom date (BD), which impacts climatic distribution of genotypes of temperate tree species. The molecular basis of floral bud CR is poorly understood despite its importance to fruit tree adaptation and production. A peach F2 populations developed from two genotypes with contrasting CR values was used for QTL mapping for CR, HR and BD. Using the Contender × Fla.92-2c population, 20 QTLs with additive effects were identified for three traits including one major QTL for CR and two major QTLs for BD. Particularly, one genomic region of 2cM pleiotropic for the …