Genetics and Genomics Commons^™

Naturalized Offspring From An 85-Year-Old Chinese Chestnut (Castanea Mollissima) Planting: Stand Dynamics And Genetic Relationships, Amy Christel Miller

Open Access Theses

Chestnuts, members of the genus Castanea , family Fagaceae, are valuable worldwide, and all species have noteworthy ecological, economic, and cultural importance in their native ranges. Historically, American chestnut (Castanea dentata (Marshall) Borkh.) was an abundant tree species in eastern North America until its decimation in the early 20 th century by chestnut blight, caused by the fungus Cryphonectria parasitica . To regain the benefits of this prized species in North America, efforts are ongoing to produce and introduce blight-resistant hybrids of C. dentata and the blight-resistant Chinese chestnut ( C. mollissima Blume). It is important that the C. …

Redox Regulation Of Protein Translation In Eukaryotes, Maxim Gerashchenko

Department of Biochemistry: Dissertations, Theses, and Student Research

Gene expression may be controlled at multiple levels, e.g., through genomic architecture, transcription and translation. In the current work, we focused on regulation of protein synthesis. Historically, the investigation of the regulation of gene expression at the level of translation lagged behind the transcriptional control because of the lack of accessible high-throughput methods. Our research has begun with the finding of the use of alternative non-AUG start codon in thioredoxin-glutathione reductase (TGR), a selenoprotein involved in redox control during male reproduction. The use of this codon, CUG, relies on the Kozak consensus sequence and ribosomal scanning mechanism. However, the CUG …

Relating The Metatranscriptome And Metagenome Of The Human Gut, Eric A. Franzosa, Xochitl C. Morgan, Nicola Segata, Levi Waldron, Joshua Reyes, Ashlee M. Earl, Georgia Giannoukos, Matthew R. Boylan, Dawn Ciulla, Dirk Gevers, Jacques Izard, Wendy S. Garrett, Andrew T. Chan, Curtis Huttenhower

Department of Food Science and Technology: Faculty Publications

Although the composition of the human microbiome is now well-studied, the microbiota’s > 8 million genes and their regulation remain largely uncharacterized. This knowledge gap is in part because of the difficulty of acquiring large numbers of samples amenable to functional studies of the microbiota. We conducted what is, to our knowledge, one of the first human microbiome studies in a well-phenotyped prospective cohort incorporating taxonomic, metagenomic, and metatranscriptomic profiling at multiple body sites using self-collected samples. Stool and saliva were provided by eight healthy subjects, with the former preserved by three different methods (freezing, ethanol, and RNAlater) to validate self-collection. …

Stress Responses And Energy Storage In Drosophila Melanogaster Selected For Resistance To A Gram-Positive Bacillus Cereus Spores, Zhen Hu

School of Biological Sciences: Dissertations, Theses, and Student Research

A survival response study was carried out by using D. melanogaster and the opportunistic pathogen B. cereus as the agent of selection. The spores of B. cereus, a gram-positive bacteria that can cause the human pathogen disease, were applied in our artificial laboratory selection. Selected lines were treated with B. cereus spores. Wound control lines were punctured with a needle dipped into sterile H₂O. Control lines did not apply any treatment. Three different environmental treatments were used within each line type (autoclaved spores of B.cereus, sterile H₂O and no treatment). The autoclaved spores were …

Evaluating The Impact Of Genotype Errors On Rare Variant Tests Of Association, Kaitlyn Cook, Alejandra Benitez, Casey Fu, Nathan L. Tintle

Faculty Work Comprehensive List

The new class of rare variant tests has usually been evaluated assuming perfect genotype information. In reality, rare variant genotypes may be incorrect, and so rare variant tests should be robust to imperfect data. Errors and uncertainty in SNP genotyping are already known to dramatically impact statistical power for single marker tests on common variants and, in some cases, inflate the type I error rate. Recent results show that uncertainty in genotype calls derived from sequencing reads are dependent on several factors, including read depth, calling algorithm, number of alleles present in the sample, and the frequency at which an …

Effects Of Il8 And Immune Cells On The Regulation Of Luteal Progesterone Secretion, Heather Talbott, Abigail Delaney, Pan Zhang, Yangsheng Yu, Robert Cushman, Andrea S. Cupp, John S. Davis

Department of Animal Science: Faculty Publications

Recent studies suggest that chemokines may mediate the luteolytic action of PGF2α (PGF). Our objective was to identify chemokines induced by PGF in vivo and to determine the effects of IL8 on specific luteal cell types in vitro. Midcycle cows were injected with saline or PGF, ovaries were removed after 0.5 - 4 h and chemokine expression was analyzed by qPCR. In vitro expression of IL8 was analyzed after PGF administration and with cell signaling inhibitors to determine the mechanism of PGF-induced chemokine expression. Purified neutrophils were analyzed for migration and activation in response to IL8 and PGF. Purified …

Molblocks: Decomposing Small Molecule Sets And Uncovering Enriched Fragments, Dario Ghersi, Mona Singh

Interdisciplinary Informatics Faculty Publications

The chemical structures of biomolecules, whether naturally occurring or synthetic, are composed of functionally important building blocks. Given a set of small molecules—for example, those known to bind a particular protein—computationally decomposing them into chemically meaningful fragments can help elucidate their functional properties, and may be useful for designing novel compounds with similar properties. Here we introduce molBLOCKS, a suite of programs for breaking down sets of small molecules into fragments according to a predefined set of chemical rules, clustering the resulting fragments, and uncovering statistically enriched fragments. Among other applications, our software should be a great aid in large-scale …

Development Of A Quantitative Real-Time Polymerase Chain Reaction (Rt-Pcr) Assay For Plant Species, Kayla Curtis, Heather Miller Coyle

Forensic Science Publications

In order to facilitate optimal plant DNA quantitation and identification, an assay has been developed that uses generic plant PCR primers that amplify a region in the chloroplast genome of plant samples. The assay uses the SYBR green detection dye to detect the PCR product with a universal PCR primer set to the large subunit of ribulose bisphosphate carboxylase, rbcL, but can be used with any of the universal barcode primers for land plants (rbcL, matK, trnH, psbA). Standard dilutions of control wheat DNA of varying concentrations were tested to create a standard curve. Several plant DNA extractions of different …

Heterogeneity, Not Randomness, Sets Challenges For Quantitative Genetics And Epidemiology: A Response To Davey Smith’S “Gloomy Prospect”, Peter J. Taylor

Working Papers on Science in a Changing World

Social epidemiologist Davey Smith (2011) argues that epidemiologists should accept a gloomy prospect: considerable randomness at the individual level means that they should keep their focus on modifiable causes of disease at the population level. The difficulty epidemiology has had in moving from significant population-level risk factors to improved prediction of cases at an individual level is analogous to the lack of success in the search for systematic aspects of the non-shared environmental influences that human quantitative genetics claims overshadow common environmental influences (e.g., the family’s socioeconomic status which siblings have in common). This article responds to the argument and …

Multilocus Coalescent Analyses Reveal The Demographic History Of Mouse Lemur Sister Species., Christopher Blair, Kellie L. Heckman, Amy L. Russell, Anne D. Yoder

Publications and Research

Debate continues as to whether allopatric speciation or peripatric speciation through a founder effect is the predominant force driving evolution in vertebrates. The mouse lemurs of Madagascar are a system in which evolution has generated a large number of species over a relatively recent time frame. Here, we examine speciation patterns in a pair of sister species of mouse lemur, Microcebus murinus and M. griseorufus. These two species have ranges that are disparately proportioned in size, with M. murinus showing a much more extensive range that marginally overlaps that of M. griseorufus. Given that these two species are …

Five Fundamental Gaps In Nature-Nurture Science, Peter J. Taylor

Working Papers on Science in a Changing World

Difficulties identifying causally relevant genetic variants underlying patterns of human variation have been given competing interpretations. The debate is illuminated in this article by drawing attention to the issue of underlying heterogeneity—the possibility that genetic and environmental factors or entities underlying a trait are heterogeneous—as well as four other fundamental gaps in the methods and interpretation of classical quantitative genetics: "Genetic" and "environmental" fractions of variation in traits are distinct from measurable genetic and environmental factors underlying the traits’ development; Standard formulas for partitioning variation in human traits are unreliable; Methods for translation from fractions of variation to measurable …

How To Get The Most From Microarray Data: Advice From Reverse Genomics, Ivan P. Gorlov, Ji-Yeon Yang, Jinyoung Byun, Christopher Logothetis, Olga Y. Gorlova, Kim-Anh Do, Christopher Amos

Dartmouth Scholarship

Whole-genome profiling of gene expression is a powerful tool for identifying cancer-associated genes. Genes differentially expressed between normal and tumorous tissues are usually considered to be cancer associated. We recently demonstrated that the analysis of interindividual variation in gene expression can be useful for identifying cancer associated genes. The goal of this study was to identify the best microarray data–derived predictor of known cancer associated genes. We found that the traditional approach of identifying cancer genes—identifying differentially expressed genes—is not very efficient. The analysis of interindividual variation of gene expression in tumor samples identifies cancer-associated genes more effectively. The results …

Deletion Mutant Library For Investigation Of Functional Outputs Of Cyclic Diguanylate Metabolism In Pseudomonas Aeruginosa Pa14, Dae-Gon Ha, Megan E. Richman, George A. O'Toole

Dartmouth Scholarship

We constructed a library of in-frame deletion mutants targeting each gene in Pseudomonas aeruginosa PA14 predicted to participate in cyclic di-GMP (c-di-GMP) metabolism (biosynthesis or degradation) to provide a toolkit to assist investigators studying c-di-GMP-mediated regulation by this microbe. We present phenotypic assessments of each mutant, including biofilm formation, exopolysaccharide (EPS) production, swimming motility, swarming motility, and twitch motility, as a means to initially characterize these mutants and to demonstrate the potential utility of this library.

Draft Genome Sequence Of Xylella Fastidiosa Pear Leaf Scorch Strain In Taiwan, C.-C. Su, W.-L. Deng, F.-J. Jan, C.-J. Chang, Hong Huang, J. Chen

School of Information Faculty Publications

The draft genome sequence of Xylella fastidiosa pear leaf scorch strain PLS229, isolated from the pear cultivar Hengshan (Pyrus pyrifolia) in Taiwan, is reported here. The bacterium has a genome size of 2,733,013 bp, with a G+C content of 53.1%. The PLS229 genome was annotated and has 3,259 open reading frames and 50 RNA genes.

Proteins Associated With Sf3a60 In T. Brucei, Benson Nyambega, Claudia Helbig, Daniel K. Masiga, Christine Clayton, Mariano J. Levin

All Peer-Reviewed Publications

Trypanosoma brucei relies on Spliced leader trans splicing to generate functional messenger RNAs. Trans splicing joins the specialized SL exon from the SL RNA to pre-mRNAs and is mediated by the trans-spliceosome, which is made up of small nuclear ribonucleoprotein particles and non-snRNP factors. Although the trans spliceosome is essential for trypanosomatid gene expression, not all spliceosomal protein factors are known and of these, only a few are completely characterized. In this study, we have characterized the trypanosome Splicing Factor, SF3a60, the only currently annotated SF3a component. As expected, epitope-tagged SF3a60 localizes in the trypanosome nucleus. SF3a60 is essential for …

Investigating A Role For The Ccaat/Enhancer-Binding Protein Δ In The Developing Zebrafish, Alisha Jennifer Beirl

Dissertations and Theses

The CCAAT/enhancer-binding protein delta (C/EBPδ) is a highly conserved transcription factor capable of regulating numerous cell fate processes, such as cell growth, differentiation, proliferation and apoptosis. C/EBPδ is inducible during cellular stress responses, including inflammation and responses to growth factor deprivation or thermal stress. C/EBPδ is stress-inducible in a diversity of fishes, including the zebrafish Danio rerio; however, little is known about its role in fish development. Here I show that overexpression of C/EBPδ leads to severe developmental defects, including reduced body length, edema, liver malformation and retinal abnormalities. The proportion of individuals that display developmental abnormalities is significantly …

Integrated Assessment Of Predicted Mhc Binding And Cross-Conservation With Self Reveals Patterns Of Viral Camouflage, Lu He, Anne S. De Groot, Andres H. Gutierrez, William D. Martin, Lenny Moise, Chris Bailey-Kellogg

Dartmouth Scholarship

Immune recognition of foreign proteins by T cells hinges on the formation of a ternary complex sandwiching a constituent peptide of the protein between a major histocompatibility complex (MHC) molecule and a T cell receptor (TCR). Viruses have evolved means of "camouflaging" themselves, avoiding immune recognition by reducing the MHC and/or TCR binding of their constituent peptides. Computer-driven T cell epitope mapping tools have been used to evaluate the degree to which articular viruses have used this means of avoiding immune response, but most such analyses focus on MHC-facing ‘agretopes'. Here we set out a new means of evaluating the …

Interaction Between Allelic Variations In Vitamin D Receptor And Retinoid X Receptor Genes On Metabolic Traits, Karani S. Vimaleswaran, Alana Cavadino, Diane J. Berry, Massimo Mangino, Peter Andrews, Jason H. Moore

Dartmouth Scholarship

Low vitamin D status has been shown to be a risk factor for several metabolic traits such as obesity, diabetes and cardiovascular disease. The biological actions of 1, 25-dihydroxyvitamin D, are mediated through the vitamin D receptor (VDR), which heterodimerizes with retinoid X receptor, gamma (RXRG). Hence, we examined the potential interactions between the tagging polymorphisms in the VDR (22 tag SNPs) and RXRG (23 tag SNPs) genes on metabolic outcomes such as body mass index, waist circumference, waist-hip ratio (WHR), high- and low-density lipoprotein (LDL) cholesterols, serum triglycerides, systolic and diastolic blood pressures and glycated haemoglobin in the 1958 …

Is Sickle Cell Trait As Benign As Is Usually Assumed?, Carroll Nicole Flansburg

USF Tampa Graduate Theses and Dissertations

Abstract

Introduction Sickle cell trait carriers may experience sickling events, which can cause severe health problems. Some sickle cell haplotypes contain genetic modifiers that are associated with increased levels of fetal hemoglobin, which is resistant to sickling. The aim of this study is to determine if sickle cell trait individuals who do not carry these modifiers are more likely to experience sickling episodes than those who do carry the modifiers.

Methods: Participants were eligible for inclusion in this study if they were male, 18 years of age or older, a sickle cell trait carrier, and had previously played any level …

Cd46-Mediated Transduction Of A Species D Adenovirus Vaccine Improves Mucosal Vaccine Efficacy, Zenaido T. Camacho, Michael A. Barry, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

The high levels of preexisting immunity against Adenovirus type 5 (Ad5) have deemed Ad5 unusable for translation as a human vaccine vector. Low seroprevalent alternative viral vectors may be less impacted by preexisting immunity, but they may also have significantly different phenotypes from that of Ad5. In this study we compare species D Ads (26, 28, and 48) to the species C Ad5. In vitro transduction studies show striking differences between the species C and D viruses. Most notably, Ad26 transduced human dendritic cells much more effectively than Ad5. In vivo imaging studies showed strikingly different transgene expression profiles. The …