Genetics and Genomics Commons^™

Population Genetics And Ecology Of Regional Malaria Vectors In Amazonian Brazil, Sascha Naomi Mckeon

Legacy Theses & Dissertations (2009 - 2024)

Species complexes are common among anopheline mosquitoes, but only some members of complexes are disease vectors. Research involving overall patterns of divergence, phylogenetic relationships and population structure is partly driven by the operational need to be able to reliably distinguish component taxa that may be involved in malaria transmission. Anopheles triannulatus, An. nuneztovari and An. albitarsis are broadly distributed species complexes that contain local and regionally important malaria vectors, whose genetic diversity has been largely overshadowed by studies involving An. darlingi, the principal vector of Central and South America. I have analyzed the ecological suitability of habitats and geographical ranges …

Image-Level And Group-Level Models For Drosophila Gene Expression Pattern Annotation, Quian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart Newfeld, Sudhir Kumar, Jieping Ye

Computer Science Faculty Publications

Background: Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment …

Investigation Of Bacterial Rna-Directed Dna Methylation Via Dcm And Hfq, Dandan Li

Wayne State University Theses

Bacterial small RNAs and the RNA chaperone Hfq play crucial roles in post-transcriptional gene regulation, often as parts of stress-response pathways, but little is known about their roles in regulation of gene transcription. A recent report showed that changes in methylation patterns caused by DNA cytosine methyltransferase (Dcm) were linked to gene regulation occurring during the transition to stationary phase. Here, we show that Dcm involves in the stress responses under nutrient starvation and cold stress. Dcm and Hfq together mediate gene expression under cold stress. Hfq promotes Dcm-catalyzed cytosine methylation at specific sites near the rpoS promoter, which is …

Genetic Diversity In Populations Of Epiphanes Chihuahuaensis (Rotifera: Monogononta) In The Northern Chihuahuan Desert, Diego E. Reyes

Open Access Theses & Dissertations

1. Cryptic speciation in zooplankton is a phenomenon that has been recently gaining much attention. This is due in part to advances in molecular techniques which help in the identification of morphologically indistinct species. Organisms that have been traditionally believed to have cosmopolitan distributions are being found to be composed of cryptic species complexes with high levels of genetic divergence among lineages.

2. Epiphanes chihuahuaensis is a member in the Epiphanes senta species complex. In a previous study by Schröder & Walsh (2007), genetic data, along with morphological and reproductive isolation data were employed to help delineate four species within …

Genetic Population Structure Of Us Atlantic Coastal Striped Bass (Morone Saxatilis), David T. Gauthier, Corinne A. Audemard, Jeanette E. L. Carlsson, Tanya L. Darden, Michael R. Denson, Kimberly S. Reece, Jens Carlsson

Biological Sciences Faculty Publications

Genetic population structure of anadromous striped bass along the US Atlantic coast was analyzed using 14 neutral nuclear DNA microsatellites. Young-of-the-year and adult striped bass (n = 1114) were sampled from Hudson River, Delaware River, Chesapeake Bay, North Carolina, and South Carolina. Analyses indicated clear population structure with significant genetic differentiation between all regions. Global multilocus F-ST was estimated at 0.028 (P < 0.001). Population structure followed an isolation-by-distance model and temporal sampling indicated a stable population structure more than 2 years at all locations. Significant structure was absent within Hudson River, whereas weak but significant genetic differences were observed between northern and southern samples in Chesapeake Bay. The largest and smallest effective striped bass population sizes were found in Chesapeake Bay and South Carolina, respectively. Coalescence analysis indicated that the highest historical gene flow has been between Chesapeake Bay and Hudson River populations, and that exchange has not been unidirectional. Bayesian analysis of contemporary migration indicated that Chesapeake Bay serves as a major source of migrants for Atlantic coastal regions from Albemarle Sound northward. In addition to examining population genetic structure, the data acquired during this project were capable of serving as a baseline for assigning fish with unknown origin to source region.

Pronounced Genetic Structure In A Highly Mobile Coral Reef Fish, Caesio Cuning, In The Coral Triangle, Amanda S. Ackiss, Shinta Pardede, Eric D. Crandall, Ma Carmen A. Ablan-Lagman, Ambariyanto, November Romena, Paul H. Barber, Kent E. Carpenter

Biological Sciences Faculty Publications

The redbelly yellowtail fusilier Caesio cuning has a tropical Indo-West Pacific range that straddles the Coral Triangle, a region of dynamic geological history and the highest marine biodiversity on the planet. Previous genetic studies in the Coral Triangle indicate the presence of multiple limits to connectivity. However, these studies have focused almost exclusively on benthic, reef-dwelling species. Schooling, reef-associated fusiliers (Perciformes: Caesionidae) account for a sizable portion of the annual reef catch in the Coral Triangle, yet to date, there have been no indepth studies on the population structure of fusiliers or other mid-water, reef-associated planktivores across this region. We …

The Causes And Consequences Of Individual Variation In Parental Care Behavior, Daniel P. Wetzel

Theses and Dissertations--Biology

Behavioral traits can be remarkably flexible depending on the conditions in which they are expressed, yet, in spite of this flexibility, persistent differences between individuals appear to limit the potential expression of behaviors. For example, despite evidence that parents provide variable amounts of parental care in response to changing environmental conditions, they also differ in the overall level of care they provide. I used a behavioral reaction norm approach to study individual variation in parental care behavior in free-living house sparrows (Passer domesticus). I investigated the nature of this variation by studying the relationship between different forms of …

A Comprehensive Research Framework For Geographic Parthenogenesis In Whiptail Lizards (Genus Aspidoscelis), Adam Leland

UNLV Theses, Dissertations, Professional Papers, and Capstones

One of the most compelling topics in biology has been the ubiquity of sexual reproduction in living organisms. Because the ecological and evolutionary advantages of sex are well founded, those organisms that reproduce asexually remain enigmatic. Parthenogenesis, the clonal reproduction of an all-female species without the need for males, is a relatively common form of asexual reproduction in vertebrates, and has been subject of numerous academic investigations. Many parthenogenic organisms also share aspects of their geographic distributions, such as inhabiting higher latitudes, higher altitudes, islands or island-like habitats, xeric environments, and marginal, disturbed or ecotonal habitats relative to their sexual …

Genetic Diversity Of North American Captive-Born Gorillas (Gorilla Gorilla Gorilla), Noah D. Simmons, Ronald S. Wagner, Joseph G. Lorenz

All Faculty Scholarship for the College of the Sciences

Western lowland gorillas (Gorilla gorilla gorilla) are designated as critically endangered and wild populations are dramatically declining as a result of habitat destruction, fragmentation, diseases (e.g., Ebola) and the illegal bushmeat trade. As wild populations continue to decline, the genetic management of the North American captive western lowland gorilla population will be an important component of the long‐term conservation of the species. We genotyped 26 individuals from the North American captive gorilla collection at 11 autosomal microsatellite loci in order to compare levels of genetic diversity to wild populations, investigate genetic signatures of a population bottleneck and identify …

Genetic Analysis Of Putative Familial Relationships In A Captive Chimpanzee (Pan Troglodytes) Population, Renato Robledo, Joseph G. Lorenz, Jeanne Beck, James Else, Patrick Bender

Anthropology and Museum Studies Faculty Scholarship

Twelve autosomal dinucleotide repeat loci were analyzed in chimpanzees genomes by DNA amplification using primers designed for analysis of human loci. The markers span the entire length of human chromosomes 21 and 22. Nine markers were polymorphic in chimpanzee as well, with a somewhat comparable level of polymorphism and allele size range. Even in the presence of very limited information and in spite of missing samples, it was possible to reconstruct a complex pedigree and to provide molecular data that corroborate family relationships that were deduced from cage history and behavioral data. The conclusions were further supported by mitochondrial DNA …

Delivering Genetic Education And Genetic Counseling For Rare Diseases In Rural Brazil, A.X. Acosta, K Abe-Sandes, R Giugliani, Alan H. Bittles

Research outputs 2013

Brazil is the largest country in Latin America, with an ethnically diverse, Portuguese-speaking and predominantly Roman Catholic population of some 194 million. Universal health care is provided under the Federal Unified Health System (Sistema Único de Saúde) but, as in many other middle and low income countries, access to medical genetics services is limited in rural and remote regions of the country. Since there is no formally recognized Genetic Counseling profession, genetic counseling is provided by physicians, trained either in medical genetics or a related clinical discipline. A comprehensive medical genetics program has been established in Monte Santo, an inland …

Genetics Answers Questions And Raises More, Aldemaro Romero Jr.

Publications and Research

No abstract provided.

Electroporation-Mediated Gene Transfer Directly To The Swine Heart, Barbara Hargrave, Harre Downey, Cathryn Lundberg, Annelise Israel, Yeong-Jer Chen, Richard Heller

Bioelectrics Publications

In vivo gene transfer to the ischemic heart via electroporation holds promise as a potential therapeutic approach for the treatment of heart disease. In the current study, we investigated the use of in vivo electroporation for gene transfer using three different penetrating electrodes and one non-penetrating electrode. The hearts of adult male swine were exposed through a sternotomy. Eight electric pulses synchronized to the rising phase of the R wave of the electrocardiogram were administered at varying pulse widths and field strengths following an injection of either a plasmid encoding luciferase or one encoding green fluorescent protein. Four sites on …

Family Matters: An Analysis Of Genetic Relatedness Of Tetraclita Rubescens (The Pink Volcano Barnacle) Over Several Spatial Scales At Monterey And Bodega Bay, California, Kelly N. Chang

Scripps Senior Theses

Inbreeding involves the mating of closely related individuals at a higher frequency than at random; this can decrease the average fitness of populations and individuals by reducing the presence of heterozygotes and augmenting the expression of deleterious genes. Since marine invertebrates exhibit widespread dispersal, their potential for inbreeding is often disregarded. The adult sessile state of barnacles creates the potential for inbreeding as a result of necessary copulation between neighboring individuals. Depending on the degree of mixing that occurs during dispersal, closely related individuals or siblings may settle in close proximity, generating the possibility of kin aggregation and consequent inbreeding. …

Investigation Of X Chromosome Recognition: The Role Of Small Rna In Drosophila Dosage Compensation, Debashish Unnikrishnan Menon

Wayne State University Dissertations

In humans and flies, females have two X chromosomes but males have one X chromosome and one Y chromosome. This leads to a fatal imbalance in X-linked gene expression in one sex. In mammals and in the fruit fly Drosophila, modulation of X chromosome expression is critical for survival. This process is termed dosage compensation. Flies increase expression from the male X chromosome two-fold. This is achieved by the Male Specific Lethal (MSL) complex, which consists of two large, non-coding RNA on the X transcripts (roX1 and roX2) and five proteins. The roX RNAs have a critical …

Identification And Quantification Of Gene Targets Associated With Post-Traumatic Stress Disorder, Matthew Monaco

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Impulsiveness Mediates The Association Between Gabra2 Snps And Lifetime Alcohol Problems, S. Villafuerte, V. Strumba, S. F. Stoltenberg, R. A. Zucker, M. Burmeister

Department of Psychology: Faculty Publications

Genetic variants in GABRA2 have previously been shown to be associated with alcohol measures, electroencephalography (EEG) β waves and impulsiveness-related traits. Impulsiveness is a behavioral risk factor for alcohol and other substance abuse. Here, we tested association between 11 variants in GABRA2 with NEO-impulsiveness and problem drinking. Our sample of 295 unrelated adult subjects was from a community of families with at least one male with DSM-IV alcohol use diagnosis, and from a socioeconomically comparable control group. Ten GABRA2 SNPs (single-nucleotide polymorphisms) were associated with the NEO-impulsiveness (P < 0.03). The alleles associated with higher impulsiveness correspond to the minor alleles identified in previous alcohol dependence studies. All ten SNPs are in linkage disequilibrium (LD) with each other and represent one effect on impulsiveness. Four SNPs and the corresponding haplotype from intron 3 to intron 4 were also associated with Lifetime Alcohol Problems Score (LAPS, P < 0.03) (not corrected for multiple testing). Impulsiveness partially mediates (22.6% average) this relation between GABRA2 and LAPS. Our results suggest that GABRA2 variation in …

Biogeography And Phylogeny Of Aigarchaeota, A Novel Phylum Of Archaea, Gisele Braga Goertz, Brian P. Hedlund

McNair Poster Presentations

‘Aigarchaeota’ is a candidate phylum of Archaea known only by 16S rRNA gene fragments from cultiva­tion-independent microbial surveys and a single composite genome from Candidatus ‘Caldiarchaeum sub­terraneum’, an inhabitant of a subterranean gold mine in Japan. Gene sequences associated with ‘Aigarchaeo­ta’ have been found in a variety of geothermal habits, however a comprehensive analysis of the phylogeny and distribution of ‘Aigarchaeota’ has not yet been done. Public databases were mined for 16S rRNA gene sequences related to known ‘Aigarchaeota’ and a combination of approaches were used to rigorously define the phylogenetic boundaries of the phylum, investigate its distribution, and …

Late Developing Mammary Tumors And Hyperplasia Induced By A Low-Oncogenic Variant Of Mouse Mammary Tumor Virus (Mmtv) Express Genes Identical To Those Induced By Canonical Mmtv, Robert D. Bruno

School of Medical Diagnostics & Translational Sciences Publications

Background: The canonical milk-transmitted mouse mammary tumor virus (MMTV) of C3H mice (C3H-MMTV) rapidly induces tumors in 90% of infected animals by 8 months of age. Pro-viral insertions of C3H-MMTV into genomic DNA results in the overexpression of common core insertion site (CIS) genes, including Wnt1/10b, Rspo2, and Fgf3. Conversely, infection by either the endogenous Mtv-1 virus (in C3Hf) or the exogenous nodule-inducing virus (NIV) (in Balb/c NIV) induces premalignant mammary lesions and tumors with reduced incidence and longer latency than C3H-MMTV. Here, we asked whether Mtv-1/NIV affected the expression of core CIS genes.

Findings: We confirmed the presence of …

Functional And Mutational Analysis Of Human Recq-Like Dna Helicases In Saccharomyces Cerevisiae, Hamed Mirzaei-Souderjani

USF Tampa Graduate Theses and Dissertations

RecQ-like proteins are a family of DNA helicases that are evolutionary conserved from prokaryotes to eukaryotes. A large amount of experimental evidence suggests these proteins have a major role in the maintenance of genome stability. In humans five RecQ like helicase have been identified (RecQL1, BLM, WRN, RecQL4, and RecQL5), three of which are associated with rare genetic disorders with sever chromosomal and developmental abnormalities, and an elevated predisposition to cancer. Among the disease associated RecQ-like helicases, BLM and WRN have been subject to extensive research, while our collective knowledge about the function of RecQL4 is still very limited. Similarly, …

Sirt1 Regulation Of The Heat Shock Response In An Hsf1-Dependent Manner And The Impact Of Caloric Restriction, Rachel Rene Raynes

USF Tampa Graduate Theses and Dissertations

The heat shock response (HSR) is the cell's molecular reaction to protein damaging stress and is critical in the management of denatured proteins. Activation of HSF1, the master transcriptional regulator of the HSR, results in the induction of molecular chaperones called heat shock proteins (HSPs). Transcription of hsp genes is promoted by the hyperphosphorylation of HSF1, while the attenuation of the HSR is regulated by a dual mechanism involving negative feedback inhibition from HSPs and acetylation at a critical lysine residue within the DNA binding domain of HSF1, which results in a loss of affinity for DNA. SIRT1 is a …

Malnutrition In Sickle Cell Anemia: Implications For Infection, Growth And Maturation, Hyacinth I. Hyacinth, Oluwatoyosi A. Adekeye, Christopher S. Yilgwan

Journal of Social, Behavioral, and Health Sciences

Sickle cell anemia (SCA) is a genetic disease that affects mostly individuals of African and/or Hispanic descent, with the majority of cases in sub-Saharan Africa. Individuals with this disease show slowed growth, delayed sexual maturity, and poor immunologic function. These complications could partly be explained by the state of undernutrition associated with the disease. Proposed mechanism of undernutrition include protein hypermetabolism, decreased dietary intake possibly from interleukin-6-related appetite suppression, increased cardiac energy demand/expenditure, and increased red cell turnover. All the above mechanisms manifest as increased resting energy expenditure. Nutritional intervention utilizing single or multiple nutrient supplementation has led to improved …

Contour Extraction Of Drosophila Embryos Using Active Contours In Scale Space, Soujanya Siddavaram Ananta

Masters Theses & Specialist Projects

Contour extraction of Drosophila embryos is an important step to build a computational system for pattern matching of embryonic images which aids in the discovery of genes. Automatic contour extraction of embryos is challenging due to several image variations such as size, shape, orientation and neigh- boring embryos such as touching and non-touching embryos. In this thesis, we introduce a framework for contour extraction based on the connected components in the gaussian scale space of an embryonic image. The active contour model is applied on the images to refine embryo contours. Data cleaning methods are applied to smooth the jaggy …

Review Of "Fifty Animals That Changed The Course Of History" By E. Chaline, John B. Jenkins

Biology Faculty Works

No abstract provided.

Identifying Genetic Variants And Characterizing Their Role In Clubfoot, Katelyn S. Weymouth

Dissertations and Theses (Open Access)

Clubfoot is a common, complex birth defect affecting 4,000 newborns in the United States and 135,000 world-wide each year. The clubfoot deformity is characterized by inward and rigid downward displacement of one or both feet, along with persistent calf muscle hypoplasia. Despite strong evidence for a genetic liability, there is a limited understanding of the genetic and environmental factors contributing to the etiology of clubfoot. The studies described in this dissertation were performed to identify variants and/or genes associated with clubfoot. Genome-wide linkage scan performed on ten multiplex clubfoot families identified seven new chromosomal regions that provide new areas to …

Genetic Analysis Of The Hippo Pathway In Mouse Liver, Li Lu

Dissertations and Theses (Open Access)

Cancer therapy and tumor treatment remain unsolved puzzles. Genetic screening for tumor suppressor genes in Drosophila revealed the Hippo-signaling pathway as a kinase cascade consisting of five core components. Disrupting the pathway by deleting the main component genes breaks the balance of cell proliferation and apoptosis and results in epithelial tissue tumorigenesis. The pathway is therefore believed to be a tumor suppressor pathway. However, a corresponding role in mammals is yet to be determined. Our lab began to investigate the tumor suppression function of the potent mammalian Hippo pathway by putting floxed alleles into the mouse genome flanking the functional-domain-expressing …

The Role Of The Arched Helicases In Exosome-Mediated Function, A. Alejandra Klauer

Dissertations and Theses (Open Access)

RNA processing and degradation are two important functions that control gene expression and promote RNA fidelity in the cell. A major ribonuclease complex, called the exosome, is involved in both of these processes. The exosome is composed of ten essential proteins with only one catalytically active subunit, called Rrp44. While the same ten essential subunits make up both the nuclear and cytoplasmic exosome, there are nuclear and cytoplasmic exosome cofactors that promote specific exosome functions in each of the cell compartments. To date, it is unclear how the exosome distinguishes between RNA substrates. We hypothesize that compartment specific cofactors may …

Tet1: A Unique Dna Demethylase For Maintenance Of Dna Methylation Pattern, Chunlei Jin

Dissertations and Theses (Open Access)

DNA methylation at the C5 position of cytosine (5-methylcytosine, 5mC) is a crucial epigenetic modification of the genome and has been implicated in numerous cellular processes in mammals, including embryonic development, transcription, X chromosome inactivation, genomic imprinting and chromatin structure. Like histone modifications, DNA methylation is also dynamic and reversible. However, in contrast to well defined DNA methyltransferases, the enzymes responsible for erasing DNA methylation still remain to be studied. The ten-eleven translocation family proteins (TET1/2/3) were recently identified as Fe(II)/2-oxoglutarate (2OG)-dependent 5mC dioxygenases, which consecutively convert 5mC into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine and 5-carboxylcytosine both in vitro and in mammalian …

A Genetic, Transgenic, And Transcriptomic Analysis Of Larval Salivary Gland Physiology In Drosophila Melanogaster, Elana A. Paladino

UNLV Theses, Dissertations, Professional Papers, and Capstones

Cholesterol is the precursor to a unique class of lipophilic signaling molecules called steroid hormones that initiate the development of sexual characteristics, reactions to stress, and maintenance of metabolism, among many other functions. Although much progress has been made in understanding the function of these signaling hormones, we do not fully understand how a single steroid can cause many distinct, tissue-specific responses. Drosophila melanogaster is an effective model for understanding steroid hormone action because of its simplicity. The steroid molting hormone 20-hydroxyecdysone (hereafter, 20E) is the primary active steroid in Drosophila and mediates not only larval molts and the emergence …

Septin Phosphorylation And Coiled-Coil Domains Function In Cell And Septin Ring Morphology In The Filamentous Fungus Ashbya Gossypii, Rebecca A. Meseroll, Patricia Occhipinti, Amy S. Gladfelter

Dartmouth Scholarship

Septins are a class of GTP-binding proteins conserved throughout many eukaryotes. Individual septin subunits associate with one another and assemble into heteromeric complexes that form filaments and higher-order structures in vivo. The mechanisms underlying the assembly and maintenance of higher-order structures in cells remain poorly understood. Septins in several organisms have been shown to be phosphorylated, although precisely how septin phosphorylation may be contributing to the formation of high-order septin structures is unknown. Four of the five septins expressed in the filamentous fungus, Ashbya gossypii, are phosphorylated, and we demonstrate here the diverse roles of these phosphorylation sites …