Genetics and Genomics Commons^™

The Role Of Ess1 In Survival, Morphogenetic Switching And Transcription In The Fungal Pathogen Candida Albicans, Dhanushki Poornima Samaranayake

Legacy Theses & Dissertations (2009 - 2024)

Candida albicans is a fungal pathogen that causes serious infections among immune-compromised patients and premature infants. C. albicans can become drug resistant, therefore, identifying new antifungal drug targets is an important goal. Here, we study a peptidyl-prolyl cis/trans isomerase called Ess1 as a potential drug target. Ess1 is conserved among pathogenic fungi, and therefore, potential inhibitors of Ess1 should display a broad spectrum of activity. We confirm that Ess1 is essential for growth in Candida albicans, but unlike the previously published find, deleting one copy of the C. albicans ESS1 gene did not affect morphogenetic switching. However, further reducing activity …

Successful Genotyping Of Microsatellites In The Woolly Mammoth, Yasuko Ishida, Alfred L. Roca, Stephen Fratpietro, Alex D. Greenwood

Biological Sciences Faculty Publications

Genetic analyses using ancient DNA from Pleistocene and early Holocene fossils have largely relied on mitochondrial DNA (mtDNA) sequences. Among woolly mammoths, Mammuthus primigenius, mtDNA analyses have identified 2 distinct clades (I and II) that diverged 1-2 Ma. Here, we establish that microsatellite markers can be effective on Pleistocene samples, successfully genotyping woolly mammoth specimens at 2 loci. Although significant differentiation at the 2 microsatellite loci was not detected between 16 clade I and 4 clade II woolly mammoths, our results demonstrate that the nuclear population structure of Pleistocene species can be examined using fast-evolving nuclear microsatellite markers.

Genome-Wide Expression Analysis In Down Syndrome: Insight Into Immunodeficiency, Chong Li, Lei Jin, Yun Bai, Qimin Chen, Lijun Fu, Minjun Yang, Huasheng Xiao, Guoping Zhao, Shengyue Wang

PCOM Scholarly Papers

Down syndrome (DS) is caused by triplication of Human chromosome 21 (Hsa21) and associated with an array of deleterious phenotypes, including mental retardation, heart defects and immunodeficiency. Genome-wide expression patterns of uncultured peripheral blood cells are useful to understanding of DS-associated immune dysfunction. We used a Human Exon microarray to characterize gene expression in uncultured peripheral blood cells derived from DS individuals and age-matched controls from two age groups: neonate (N) and child (C). A total of 174 transcript clusters (gene-level) with eight located on Hsa21 in N group and 383 transcript clusters including 56 on Hsa21 in C group …

Higher Il-6 And Il6:Igf Ratio In Patients With Barth Syndrome, Lori D. Wilson, Sadeeka Al-Majid, Cyril Rakovski, Christina D. Schwindt

Mathematics, Physics, and Computer Science Faculty Articles and Research

Background: Barth Syndrome (BTHS) is a serious X-linked genetic disorder associated with mutations in the tafazzin gene (TAZ, also called G4.5). The multi-system disorder is primarily characterized by the following pathologies: cardiac and skeletal myopathies, neutropenia, growth delay, and exercise intolerance. Although growth anomalies have been widely reported in BTHS, there is a paucity of research on the role of inflammation and the potential link to alterations in growth factors levels in BTHS patients.

Methods: Plasma from 36 subjects, 22 patients with Barth Syndrome (0.5 - 24 yrs) and 14 healthy control males (8 - 21 yrs) was …

Functional Promiscuity Of The Cog0720 Family, Gabriela Phillips, Laura L. Grochowski, Shilah Bonnett, Huimin Xu, Marc Bailly, Crysten Haas-Blaby, Basma El Yacoubi, Dirk Iwata-Reuyl, Robert H. White, Valérie De Crécy-Lagard

Chemistry Faculty Publications and Presentations

The biosynthesis of GTP derived metabolites such as tetrahydrofolate (THF), biopterin (BH4), and the modified tRNA nucleosides queuosine (Q) and archaeosine (G⁺) relies on several enzymes of the Tunnel-fold superfamily. A subset of these proteins include the 6-pyruvoyl-tetrahydropterin (PTPS-II), PTPS-III, and PTPS-I homologs, all members of the COG0720 family, that have been previously shown to transform 7,8-dihydroneopterin triphosphate (H₂NTP) into different products. PTPS-II catalyzes the formation of 6-pyruvoyltetrahydropterin in the BH₄ pathway. PTPS-III catalyzes the formation of 6-hydroxylmethyl-7,8-dihydropterin in the THF pathway. PTPS-I catalyzes the formation of 6-carboxy-5,6,7,8-tetrahydropterin in the Q pathway. Genes of these …

Cryptic Distant Relatives Are Common In Both Isolated And Cosmopolitan Genetic Samples, Brenna M. Henn, Lawrence S. Hon, J. Michael Macpherson, Nicholas Eriksson, Serge Saxonov, Itsik Pe'er, Joanna Mountain

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Although a few hundred single nucleotide polymorphisms (SNPs) suffice to infer close familial relationships, high density genome-wide SNP data make possible the inference of more distant relationships such as 2nd to 9th cousinships. In order to characterize the relationship between genetic similarity and degree of kinship given a timeframe of 100–300 years, we analyzed the sharing of DNA inferred to be identical by descent (IBD) in a subset of individuals from the 23andMe customer database (n = 22,757) and from the Human Genome Diversity Panel (HGDP-CEPH, n = 952). With data from 121 populations, we show that the average amount …

Decision Memo: Pando Aspen Clone Restoration Project, Kurt Robins

Aspen Bibliography

The Pando Clone is located in Township 26 South, Range 1 East, Sections 24 and 25 about 1 mile southwest of the Lakeside Resort on State Highway 25 and about 1 mile due east of Mallard Bay at the southwest corner of Fish Lake (see map). The Pando Clone is the largest aspen clone in the world and the largest (most massive) single living organism in existence that has been discovered to date (Grant, 1993; DeWoody et al, 2008). It encompasses approximately 106 acres and is estimated to weigh in excess of 13 million pounds (Grant, 1993). This clone is …

Causes And Consequences Of Mitochondrial Variation In Caenorhabditid Nematodes, Kiley Ann Hicks

Dissertations and Theses

Mitochondria are dynamic organelles that harbor their own stream-lined genome and generate much of the ATP necessary to sustain eukaryotic life via an electron transport chain (ETC). Because of the central role for mitochondria in organismal physiology, mitochondrial genetic and phenotypic variation can alter organismal fitness and affect population genetic and evolutionary outcomes. Despite the far-reaching relevance of mitochondria to evolutionary processes and human health, we lack a basic understanding of the causes and consequences of mitochondrial genetic and phenotypic variation. In this thesis, I quantified mitochondrial reactive oxygen species (ROS), membrane potential (δΨM), and mitochondrial morphological traits within Caenorhabditis …

Population Genetics Of A Tolerant Fish In An Agriculturally Dominated Watershed, Mark Jordan, Deepal Patel, Matthew Richardville, Kathryn Sanders, Robert Gillespie

Mark A. Jordan

No abstract provided.

Recent Progress In Polymorphism-Based Population Genetic Inference., Jessica Crisci, Yu-Ping Poh, Angela Bean, Alfred Simkin, Jeffrey Jensen

Jessica L Crisci

The recent availability of whole-genome sequencing data affords tremendous power for statistical inference. With this, there has been great interest in the development of polymorphism-based approaches for the estimation of population genetic parameters. These approaches seek to estimate, for example, recently fixed or sweeping beneficial mutations, the rate of recurrent positive selection, the distribution of selection coefficients, and the demographic history of the population. Yet despite estimating similar parameters using similar data sets, results between methodologies are far from consistent. We here summarize the current state of the field, compare existing approaches, and attempt to reconcile emerging discrepancies. We also …

Economic Impact Of Stable Flies (Diptera: Muscidae) On Cattle Production., David Taylor, Roger Moon, Darrell Mark

David B. Taylor

Stable flies, Stomoxys calcitrans (L.), are among the most damaging arthropod pests of cattle worldwide. The last estimate of their economic impact on United States cattle production was published 20 yr ago and placed losses at $608 million. Subsequently, several studies of effects of stable flies on beef cattle weight gain and feed efficiency have been published, and stable flies have become increasingly recognized as pests of cattle on pasture and range. We analyzed published studies and developed yield-loss functions to relate stable fly infestation levels to cattle productivity, and then estimated the economic impact of stable flies on cattle …

Inheritance Of Humeral Spotting In The Croaking Gourami (Osphronemidae: Trichopsis Vittatus), Jack Frankel, Lisa Alder-Golden, Andre Porter

Jack Frankel

Efficacy Of Cyromazine To Control Immature Stable Flies (Diptera: Muscidae) Developing In Winter Hay Feeding Sites, David B. Taylor, Kristina Friesen, Jerry J. Zhu, Kai Sievert

David B. Taylor

Hay mixed with manure and urine residues at sites where hay has been provided as supplemental winter feed for cattle provide an excellent substrate for the development of immature stable flies, Stomoxys calcitrans (L.). Such sites are primary sources of early summer stable flies in the central United States and no effective measures are currently available to control fly development in them. A single application of granular cyromazine in May provided 97% reduction in the number of adult stable flies emerging from hay feeding sites. Stable fly control did not decline during the 12 wk season. A small decline in …

A Shared Gene Expression Signature In Mouse Models Of Ebv-Associated And Non-Ebv-Associated Burkitt Lymphoma, Kathryn T. Bieging, Kamonwan Fish, Subbarao Bondada, Richard Longnecker

Microbiology, Immunology, and Molecular Genetics Faculty Publications

The link between EBV infection and Burkitt lymphoma (BL) is strong, but the mechanism underlying that link has been elusive. We have developed a mouse model for EBV-associated BL in which LMP2A, an EBV latency protein, and MYC are expressed in B cells. Our model has demonstrated the ability of LMP2A to accelerate tumor onset, increase spleen size, and bypass p53 inactivation. Here we describe the results of total gene expression analysis of tumor and pretumor B cells from our transgenic mouse model. Although we see many phenotypic differences and changes in gene expression in pretumor B cells, the transcriptional …

Reverse Protection Assay: A Tool To Analyze Transcriptional Rates From Individual Promoters, Yan O. Zubo, Victor V. Kusnetsov, Thomas Börner, Karsten Liere

Dartmouth Scholarship

Transcriptional activity of entire genes in chloroplasts is usually assayed by run-on analyses. To determine not only the overall intensity of transcription of a gene, but also the rate of transcription from a particular promoter, we created the Reverse RNase Protection Assay (RePro): in-organello run-on transcription coupled to RNase protection to define distinct transcript ends during transcription. We demonstrate successful application of RePro in plastid promoter analysis and transcript 3' end processing.

The Murine Caecal Microrna Signature Depends On The Presence Of The Endogenous Microbiota, Natasha Singh, Elize A. Shirdel, Levi Waldron, Regan-Heng Zhang, Igor Jurisica, Elena M. Comelli

Publications and Research

The intestinal messenger RNA expression signature is affected by the presence and compo-sition of the endogenous microbiota, with effects on host physiology. The intestine is also characterized by a distinctive micronome. However, it is not known if microbes also impact intestinal gene expression epigenetically. We investigated if the murine caecal microRNA expression signature depends on the presence of the microbiota, and the potential implica-tions of this interaction on intestinal barrier function. Three hundred and thirty four mi-croRNAs were detectable in the caecum of germ-free and conventional male mice and 16 were differentially expressed, with samples from the two groups clustering …

Fine Roots Of Aspen Clones In High Salt And Petroleum Hydrocarbon Pollution, Kim Yrjälä, Ivika Ostonen, Shinjini Mukherjee, Timo Sipila, Lu-Min Vaario, Pertti Pulkkinen

Aspen Bibliography

The quality of polluted soil can much be improved and the environmental risks reduced by use of phytoremediation. Harmful hydrocarbon compounds can be degraded through the activity of plant and its associated microbes. We previously showed that PAHs increase aromatic ring-cleavage gene diversity in rhizosphere of birch (Sipilä et al. 2008, Yrjälä et al. 2010a) and the rhizosphere of aspen harbors Burkholderia bacteria able to degrade aromatics (Yrjälä et al. 2010b). The results are promising for successful remediation of polluted soils with woody plants. The aim of our studies is to elucidate the response of the plant and the associated …

Modeling Protein Expression And Protein Signaling Pathways, Donatello Telesca, Peter Muller, Steven Kornblau, Marc Suchard, Yuan Ji

COBRA Preprint Series

High-throughput functional proteomic technologies provide a way to quantify the expression of proteins of interest. Statistical inference centers on identifying the activation state of proteins and their patterns of molecular interaction formalized as dependence structure. Inference on dependence structure is particularly important when proteins are selected because they are part of a common molecular pathway. In that case inference on dependence structure reveals properties of the underlying pathway. We propose a probability model that represents molecular interactions at the level of hidden binary latent variables that can be interpreted as indicators for active versus inactive states of the proteins. The …

Natural Disease Resistance In Threatened Staghorn Corals, Steven V. Vollmer, David I. Kline

Steve Vollmer

Disease epidemics have caused extensive damage to tropical coral reefs and to the reef-building corals themselves, yet nothing is known about the abilities of the coral host to resist disease infection. Understanding the potential for natural disease resistance in corals is critically important, especially in the Caribbean where the two ecologically dominant shallow-water corals, Acropora cervicornis and A. palmata, have suffered an unprecedented mass die-off due to White Band Disease (WBD), and are now listed as threatened under the US Threatened Species Act and as critically endangered under the IUCN Red List criteria. Here we examine the potential for natural …

Genetic Diversity And Connectivity In The Threatened Staghorn Coral (Acropora Cervicornis) In Florida, Elizabeth M. Hemond, Steven V. Vollmer

Steve Vollmer

Over the past three decades, populations of the dominant shallow water Caribbean corals, Acropora cervicornis and A. palmata, have been devastated by white-band disease (WBD), resulting in the listing of both species as threatened under the U.S. Endangered Species Act. A key to conserving these threatened corals is understanding how their populations are genetically interconnected throughout the greater Caribbean. Genetic research has demonstrated that gene flow is regionally restricted across the Caribbean in both species. Yet, despite being an important site of coral reef research, little genetic data has been available for the Florida Acropora, especially for the staghorn coral, …