Genetics and Genomics Commons^™

Analysis Of Primary Resistance Mutations To Hiv-1 Entry Inhibitors In Therapy Naive Subtype C Hiv-1 Infected Mother– Infant Pairs From Zambia, Hongyan Guo, Chang Liu, Bin Liu, Charles Wood, Xiaohong Kong

Nebraska Center for Virology: Faculty Publications

Background—Small molecular CCR5 inhibitors represent a new class of drugs for treating HIV-1 infection. The evaluation of the primary resistance mutations associated with entry inhibitors during HIV-1 perinatal transmission is required because they may have a profound impact on the clinical management in MTCT.

Objectives—To evaluate the primary resistance mutations to maraviroc and vicriviroc during perinatal transmission and analyze the sensitivity of Env derived from mother–infant pairs to maraviroc.

Study design—Nine MIPs infected by subtype C HIV-1 were recruited to analyze the prevalence and transmission of primary resistance mutations to maraviroc and vicriviroc. Moreover, Env derived from six MIPs were …

Early Childhood Infection Of Kaposi’S Sarcoma-Associated Herpesvirus In Zambian Households: A Molecular Analysis, Landon Olp, Danielle M. Shea, Maxine K. White, Clement Gondwe, Chipepo Kankasa, Charles Wood

Nebraska Center for Virology: Faculty Publications

Sub-Saharan Africa is endemic for Kaposi’s sarcoma-associated herpesvirus (KSHV) and there is a high rate of early childhood infection; however, the transmission sources are not well characterized. We examined household members as potential KSHV transmission sources to young children in the KSHV-endemic country of Zambia. To this end, we enrolled and followed Zambian households with at least one KSHV-seropositive child and collected longitudinal buccal swab samples. KSHV burden was evaluated and K1 sequences from the children were determined and analyzed for differences to K1 sequences from household members. The K1 sequences were also analyzed for evolution over time. We generated …

Diversification Under Sexual Selection: The Relative Roles Of Mate Preference Strength And The Degree Of Divergence In Mate Preferences, Rafael L. Rodríguez, Janette W. Boughman, David A. Gray, Eileen A. Hebets, Gerlinde Höbel, Laurel B. Symes

Eileen Hebets Publications

The contribution of sexual selection to diversification remains poorly understood after decades of research. This may be in part because studies have focused predominantly on the strength of sexual selection, which offers an incomplete view of selection regimes. By contrast, students of natural selection focus on environmental differences that help compare selection regimes across populations. To ask how this disparity in focus may affect the conclusions of evolutionary research, we relate the amount of diversification in mating displays to quantitative descriptions of the strength and the amount of divergence in mate preferences across a diverse set of case studies of …

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 …

Dna-Binding Site Recognition By Bhlh And Mads-Domain Transcription Factors, Joshua R. Werkman

Theses and Dissertations--Plant and Soil Sciences

Herewithin, two transcription factor (TF) regulatory complexes were investigated. A bHLH–MYB–WDR (BMW) DNA-binding complex from maize was the first complex to be studied. R, a maize bHLH involved in the activation of genes in the anthocyanin pathway, had been characterized to indirectly bind DNA despite the presence of a functional DNA-binding domain. Findings presented here reveal that this is only partially correct. Direct DNA-binding by R was found to be dependent upon two distinct dimerization domains that function as a switch. This switch-like mechanism allows R to be repurposed for the activation of promoters of differing cis-element structure.

The …

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 …

Candida Albicans Induces Arginine Biosynthetic Genes In Response To Host-Derived Reactive Oxygen Species, Claudia Jimenez-Lopez, John R. Collette, Kimberly M. Brothers, Kelly M. Shepardson, Robert A. Kramer

Dartmouth Scholarship

The interaction of Candida albicans with phagocytes of the host's innate immune system is highly dynamic, and its outcome directly impacts the progression of infection. While the switch to hyphal growth within the macrophage is the most obvious physiological response, much of the genetic response reflects nutrient starvation: translational repression and induction of alternative carbon metabolism. Changes in amino acid metabolism are not seen, with the striking exception of arginine biosynthesis, which is upregulated in its entirety during coculture with macrophages. Using single-cell reporters, we showed here that arginine biosynthetic genes are induced specifically in phagocytosed cells. This induction is …

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 …

A Qualitative Study On How Prenatal Genetic Counselors Prioritize Cultural Issues When Counseling Patients, Darcy Katherine Berry

Theses and Dissertations

The genetic counseling community has long recognized that the successful outcome of a session with a patient whose cultural background differs from the genetic counselor's is best achieved through recognition of the cultural differences and implementation of specific skills to overcome cultural barriers. Although research has examined the need and effects of cultural competency in genetic counseling, no prior study has evaluated how genetic counselors perceive the importance of addressing cultural issues in a genetic counseling session. Prenatal genetic counselors were recruited by emailing all NSGC members. For this study, sixteen prenatal genetic counselors were interviewed and asked to prioritize …

Use Of Social Media As A Support Network In Families With A Child Diagnosed With Trisomy 13, 18, Or 21, Ginger Elizabeth Edwardsen

Theses and Dissertations

Social media is a web based technology that allows individuals to communicate with other individuals, organizations, and communities about common interests and experiences. Recently, social media use has expanded into the healthcare field and many individuals are using social media to connect with others in similar situations and find support. Family members of children or pregnancies with trisomy 13, 18, or 21 were invited to participate in an online survey that explored the use of social media as a support network including their purposes for using social media as a support network, how often the use social media, and what …

Examining The Differences In Rapport Between Male And Female Cancer Genetic Counselors And Female Clients, John Abernethy

Theses and Dissertations

Genetic counseling is a field in which client-counselor rapport plays a critical role in client satisfaction with the genetic counseling process. One factor that may impact this rapport is gender of the genetic counselor. Previous studies in the field of psychological counseling suggest that gender is not a significant moderator of this rapport. To the best of our knowledge, no study has been published in the field of genetic counseling examining the impact that the gender of the genetic counselor has on client-counselor rapport. To study this effect, an amended version of Horvath & Greenberg's (1989) Working Alliance Inventory tool …

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 …

Working With Patients At Risk For Hereditary Degenerative Brain Disorders, Stephen John White

Theses and Dissertations

Hereditary degenerative brain disorders (HDBDs) are a unique class of genetic conditions that result in progressive loss of function within the nervous system, many of which present during adulthood. Given this, the diagnosis of a HDBD can be daunting for both the patient and the genetic counselor assisting in medical care. The purpose of this study was to find themes among genetic counselors who see this patient population and help provide a framework to counselors entering this field by recognizing verified methods of HDBD counseling. Sixteen genetic counselors who routinely see patients at-risk for HDBDs were interviewed concerning how they …

The Utility Of Phosphoglucose Isomerase (Pgic) Intron Sequences In The Phylogenetics Of Physaria (Brassicaceae), Troy Joseph Mensen

Honors Program Theses

The main goal of this research was to determine if the PgiC gene region is useable for phylogenetic analyses. Phylogenetic analysis is done by creating phylogenetic trees based off certain gene regions and comparing it to previously created trees from other gene sequences. The DNA region could then be used in further experiments and research. In particular, this research will be beneficial for Dr. Steve O'Kane and others continuing explorations with the Physaria genus. Future researchers and Dr. O'Kane would be able to use the successful PgiC gene to have a more accurate idea of Physaria phylogeny. In the end, …

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 …

The Tick Genus Amblyomma In Africa: Phylogeny And Mutilocus Dna Barcoding, Omobolanle Kushimo

College of Graduate Studies: Theses & Dissertations

The tick genus Amblyomma includes approximately 130 species, 28 of which are found on the African continent and/ or in Madagascar. In order to understand the evolutionary phylogeography of the genus, it is necessary to gain a better understanding of the relationships between African taxa. Therefore, the main goals of this work were to, (1) reconstruct the phylogenetic relationships of the African Amblyomma available to us and (2) test markers for their usefulness as barcoding tools to link unknown immature specimens to their corresponding adults. The mitochondrial gene markers used in this study (12SrDNA and COI) did not resolve the …

Innovative Applications Of Genetic Algorithms To Problems In Accelerator Physics, Alicia Hofler, Balša Terzić, Matthew Kramer, Anton Zvezdin, Vasiliy Morozov, Yves Roblin, Fanglei Lin, Colin Jarvis

Physics Faculty Publications

The genetic algorithm (GA) is a powerful technique that implements the principles nature uses in biological evolution to optimize a multidimensional nonlinear problem. The GA works especially well for problems with a large number of local extrema, where traditional methods (such as conjugate gradient, steepest descent, and others) fail or, at best, underperform. The field of accelerator physics, among others, abounds with problems which lend themselves to optimization via GAs. In this paper, we report on the successful application of GAs in several problems related to the existing Continuous Electron Beam Accelerator Facility nuclear physics machine, the proposed Medium-energy Electron-Ion …

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 …

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 Use Of Metagenomic Approaches To Analyze Changes In Microbial Communities, Girish Neelakanta, Hameeda Sultana

Biological Sciences Faculty Publications

Microbes are the most abundant biological entities found in the biosphere. Identification and measurement of microorganisms (including viruses, bacteria, archaea, fungi, and protists) in the biosphere cannot be readily achieved due to limitations in culturing methods. A non-culture based approach, called “metagenomics”, was developed that enabled researchers to comprehensively analyse microbial communities in different ecosystems. In this study, we highlight recent advances in the field of metagenomics for analyzing microbial communities in different ecosystems ranging from oceans to the human microbiome. Developments in several bioinformatics approaches are also discussed in context of microbial metagenomics that include taxonomic systems, sequence databases, …

Phylogeography Of The Christmas Tree Worm Spirobranchus Corniculatus (Annelida, Serpulidae) From The Coral Triangle, Australia, And Fiji, Abril Iñiguez, Craig J. Starger, Elena Kupriyanova, Demian Willette, Tristan Varman, Joshua A. Drew, Abdul Hamid Toha, Benedict Maralit, Kent E. Carpenter, Paul H. Barber

Biological Sciences Faculty Publications

Christmas Tree Woms is a common name given to a group of large and colourful serpulid polychaetes of the genus Spirobranchus that are obligate symbionts of hermatypic corals commonly found in tropical and subtropical regions world-wide. While current taxonomic species delimitations of these worms are based almost exclusively on the morphology of opercular structures, particularly the number and shape of calcareous opercular horns, high levels of intraspecific variation in this morphological feature have made species boundaries within the genus difficult to resolve. Molecular work to differentiate serpulid worms has long been hampered by the availability of informative markers. Recent work …

The Effect Of Temperature On Seed Quality And Quantity In Crosses Between European (Populus Tremula) And Hybrid Aspens (P. Tremula X P. Tremuloides), L. Koviuranta, T. Latva-Karjanmaa, P. Pulkkinen

Aspen Bibliography

Hybrid aspen (Populus tremula L. Populus tremuloides Michx.) plantations are expanding in Fennoscandia and the Baltic countries; however, the possible effects of plantations on the native European aspen (P. tremula) and the level of gene flow between European and hybrid aspen have not been investigated. We studied seed quantity and quality in intraspecific and interspecific crosses of the European and hybrid aspens over a two year period. In order to study whether elevated temperatures due to climate change would benefit the species differently, we performed the crosses in different temperatures. In both years, interspecific crosses produced more seeds with higher …

Gene, Pathway And Network Frameworks To Identify Epistatic Interactions Of Single Nucleotide Polymorphisms Derived From Gwas Data, Yu Liu, Sean Maxwell, Tao Feng, Xiaofeng Zhu, Robert C. Elston, Mehmet Koyutürk, Mark R. Chance

Faculty Scholarship

Background: Interactions among genomic loci (also known as epistasis) have been suggested as one of the potential sources of missing heritability in single locus analysis of genome-wide association studies (GWAS). The computational burden of searching for interactions is compounded by the extremely low threshold for identifying significant p-values due to multiple hypothesis testing corrections. Utilizing prior biological knowledge to restrict the set of candidate SNP pairs to be tested can alleviate this problem, but systematic studies that investigate the relative merits of integrating different biological frameworks and GWAS data have not been conducted.Results: We developed four biologically based frameworks to …

Detection Of Genomic Inversion From Single End Read, Pankaj Ghimire

Master's Theses

Structural Variations (SVs) are genomic rearrangements that include both copy-number variants,such as insertion,deletions, duplications and balanced variants like inversion and translocations. These SVs are getting more attentions for research and investigation because of their role on human phenotype, genetic diseases and genomic rearrangements. Evolution of Next-generation Sequencing has provided golden opportunities to investigate these variants and make their wider and clear spectrum in human genome. This investigation includes identification of type of SVs and their breakpoints at base pair level. For their effective identification and breakpoint resolution, many techniques are devised mainly based on paired end read. With relatively low …

Localization And Mutational Analysis Of The Nuclear And Aggregation-Prone Ime4 Protein In Saccharomyces Cerevisiae, Patricia M. Dehon

LSU New Orleans Theses and Dissertations

In Saccharomyces cerevisiae, Ime4 is a protein that is induced during meiosis and has a primary role in regulating sporulation in starving diploids. One function of Ime4 is methylation of adenosine residues within mRNA transcripts. Recent studies have shown Ime4 to be induced in haploids during the mating response, although its role in mating has not been determined. In this report, I identify the subcellular localization of Ime4 during the mating response through treatment with alpha factor. A plasmid containing IME4-GFP under the control of the medium strength promoter CYC1 was created in order to express the protein in a …

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 …

Draft Genome Sequence For Pseudomonas Aeruginosa Strain Pao579, A Mucoid Derivative Of Pao381, T. Ryan Withers, Shannon L. Johnson, Hongwei D. Yu

Biochemistry and Microbiology

Pseudomonas aeruginosa is an opportunistic pathogen that establishes a chronic lung infection in individuals afflicted with cystic fibrosis. Here, we announce the draft genome of P. aeruginosa strain PAO579, an alginate-overproducing derivative of strain PAO381.

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

Biology Faculty Works

No abstract provided.

Effects Of Slash Pile Burning After Restoring Conifer- Encroached Aspen, Christa M. Dagley, John-Pascal Berrill, Stephanie Coppeto, Kyle Jacobson

Aspen Bibliography

Removal of conifers encroaching aspen stands has been advocated and is being practiced in the Lake Tahoe Basin (EIP Project #10080: Aspen Community Restoration Projects). In remote and roadless areas, thinning of conifers is generating large volumes of wood and pile burning is currently being implemented to handle this biomass on site. However, the effects of pile burning on aspen are unknown, and there is an urgent need for guidelines to support design of thinning treatment prescriptions; specifically burn pile size and safe distances from live aspen trees of any size to prevent injury.