Genetics and Genomics Commons^™

Intracellular Listeria Monocytogenes Comprises A Minimal But Vital Fraction Of The Intestinal Burden Following Foodborne Infection, Grant S. Jones, Kate M. Bussell, Tanya Myers-Morales, Abigail M. Fieldhouse, Elsa N. Bou Ghanem, Sarah E. F. D'Orazio

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Listeria monocytogenes is a highly adaptive bacterium that replicates as a free-living saprophyte in the environment as well as a facultative intracellular pathogen that causes invasive foodborne infections. The intracellular life cycle of L. monocytogenes is considered to be its primary virulence determinant during mammalian infection; however, the proportion of L. monocytogenes that is intracellular in vivo has not been studied extensively. In this report, we demonstrate that the majority of wild-type (strain EGDe) and mouse-adapted (InlA^m-expressing) L. monocytogenes recovered from the mesenteric lymph nodes (MLN) was extracellular within the first few days after foodborne infection. In addition, …

A Search For Parent-Of-Origin Effects On Honey Bee Gene Expression, Sarah D. Kocher, Jennifer M. Tsuruda, Joshua D. Gibson, Christine M. Emore, Miguel E. Arechavaleta-Velasco, David C. Queller, Joan E. Strassmann, Christina M. Grozinger, Michael R. Gribskov, Phillip San Miguel, Rick Westerman, Greg J. Hunt

Biology Faculty Research

Parent-specific gene expression (PSGE) is little known outside of mammals and plants. PSGE occurs when the expression level of a gene depends on whether an allele was inherited from the mother or the father. Kin selection theory predicts that there should be extensive PSGE in social insects because social insect parents can gain inclusive fitness benefits by silencing parental alleles in female offspring. We searched for evidence of PSGE in honey bees using transcriptomes from reciprocal crosses between European and Africanized strains. We found 46 transcripts with significant parent-of-origin effects on gene expression, many of which overexpressed the maternal allele. …

Distinct Physiological Roles For The Two Isoforms Of The Er Chaperone Grp170 In Caenorhabditis Elegans, Yuanyuan Li

Biology Theses

GRP170 is a large molecular chaperone found in the ER of all eukaryotes. The nematode Caenorhabditis elegans has two loci encoding GRP170: T24H7.2 (grp170a) and T14G8.3 (grp170b). The phenotypes of nematodes genetically deficient for either grp170a or grp170b were compared to a standard laboratory strain with functional grp170 loci. Worms that were deficient for grp170a developed 32% slower than the control strain. The loss of grp170a had a significant but modest reduction on the life span compared to the control strain. Worms deficient for grp170a also displayed significantly increased embryonic lethality and resulted in 6.9% arrested embryos. The loss of …

Differential Regulation Of The Two Grp170 Paralogues Of Caenorhabditis Elegans, Antonio L. Rockwell

Biology Theses

Abstract of a Thesis

Differential Regulation of the Two grp170 Paralogues of Caenorhabditis elegans

Caenorhabditis elegans has two loci encoding the large eukaryotic molecular chaperone Grp170, grp170a (T24H7.2) and grp170b (T14G8.3). To investigate expression of the two C. elegans grp170 loci during ER stress, the Unfolded Protein Response (UPR) was induced with the glycosylation inhibitor tunicamycin. Levels of grp170a mRNA did not significantly change in response to tunicamycin treatment while the levels of grp170b mRNA increased 6-fold. ER stress induction of grp170b was unaffected in worms defective for the ATF6 and PERK-1 UPR signal transduction pathways. However, worms defective …

Beyond Bivariate Correlations: Three-Block Partial Least Squares Illustrated With Vegetation, Soil, And Topography, Daehyun Kim, Thomas J. Dewitt, César S. B. Costa, John A. Kupfer, Ryan W. Mcewan, J. Anthony Stallins

Biology Faculty Publications

Ecologists, particularly those engaged in biogeomorphic studies, often seek to connect data from three or more domains. Using three-block partial least squares regression, we present a procedure to quantify and define bi-variance and tri-variance of data blocks related to plant communities, their soil parameters, and topography. Bi-variance indicates the total amount of covariation between these three domains taken in pairs, whereas tri-variance refers to the common variance shared by all domains. We characterized relationships among three domains (plant communities, soil properties, topography) for a salt marsh, four coastal dunes, and two temperate forests spanning several regions in the world. We …

An Analysis Of The Differential Methylation And Expression Of Imprinted Genes In M. M. Musculus, M. M. Domesticus, And Their Hybrids, Anna P. Rice

All NMU Master's Theses

Epigenetics has been found to have an effect on many aspects of biology. Epigenetics refers to modifications of the double-stranded DNA molecule, which do not change the nucleotide sequence but do affect gene expression. DNA methylation is a type of epigenetic modification. Genomic imprinting is a pattern of gene expression that is primarily achieved through DNA methylation, and it results in the expression of only one allele at a particular locus. In this study, I analyzed the methylation patterns of five imprinted genes in the hybrids of two different lab strains of the house mouse subspecies, M. m. musculus and …

Identification Of Familial Wilms Tumor Predisposition Genes Using Whole Genome Sequencing, Timothy B. Palculict

Dissertations and Theses (Open Access)

Wilms tumor, a childhood tumor arising from undifferentiated renal mesenchyme, is diagnosed in North America at a frequency of 1 in 10,000 live births and accounts for 5% of all pediatric cancers. The etiology of Wilms tumor is heterogeneous with multiple genes known to have an effect on Wilms tumor development; however, these genes are rarely associated with familial Wilms tumor. Gene mutations in WT1, WTX, CTNNB1 and TP53 are observed in a third of sporadic tumors, while the causative gene(s) responsible for familial Wilms tumor are largely unknown. Approximately 2% of Wilms tumor patients have a family …

In Vivo Significance Of The Mdm4 And P73 Interaction During Development And Tumorigenesis, Mehrnoosh Tashakori

Dissertations and Theses (Open Access)

The tumor suppressor protein p53 is negatively regulated by Mdm4 protein. The significance of such regulation was determined from mouse models. Mdm4-deficient mice are embryonic lethal at E7.5 in a p53-dependent manner. p73, a member of the p53-family, is a transcription factor with tumor suppressor activity. In vitro studies show that Mdm4 binds to p73 and, further, comprehensive biochemical studies revealed that Mdm4 has higher affinity for p73 than p53. However, little is known about the significance of the Mdm4 and p73 interaction in vivo. This study aimed to elucidate the biological consequences of this interaction during embryogenesis …

Germline Mutation Detection In Next Generation Sequencing Data And Tp53 Mutation Carrier Probability Estimation For Li-Fraumeni Syndrome, Gang Peng

Dissertations and Theses (Open Access)

Next generation sequencing technology has been widely used in genomic analysis, but its application has been compromised by the missing true variants, especially when these variants are rare. We proposed a family-based variant calling method, FamSeq, integrating Mendelian transmission information with de novo mutation and sequencing data to improve the variant calling accuracy. We investigated the factors impacting the improvement of family-based variant calling in simulation data and validated it in real sequencing data. In both simulation and real data, FamSeq works better than the single individual based method.

In FamSeq, we implemented four different methods for the Mendelian genetic …

Detection Of Genes Influencing Chronic And Mendelian Disease Via Loss-Of-Function Variation, Alexander H. Li

Dissertations and Theses (Open Access)

A typical human exome harbors dozens of loss-of-function (LOF) variants predicted to severely disrupt or abolish gene function. These variants are enriched at the extremely rare end of the allele frequency spectrum (< 0.1%), suggesting purifying selection against these sites. However, most previous population-based sequencing studies have not included analysis of genotype-phenotype relationships with LOF variants. Thus, the contribution of LOF variation to health and disease within the general population remains largely uncharacterized.

Using whole exome sequence from 8,554 participants in the Atherosclerosis Risk in Communities (ARIC) study, we explored the impact of LOF variation on a broad spectrum of human phenotypes. First, we selected 20 common chronic disease risk factor phenotypes and performed gene-based association tests. Analysis of this sample verified two relationships in well-studied genes (PCSK9 and APOC3) and identified eight new loci. Novel relationships included …

Functional Analysis Of Synthetic Gene Circuits Controlling A Protein Pump In Yeast, Junchen Diao

Dissertations and Theses (Open Access)

Synthetic biology aims to build biological devices to understand living systems and explore new applications. Synthetic gene circuits such as genetic switches, oscillators and logic gates are at the core of many synthetic biology applications. These gene circuits often include a sensor/regulator protein capable to detect small molecules and then transduce them into a regulatory signal to generate measurable output. Similar signal transduction networks are also abundant in nature. However, in many natural and engineered scenarios, the output also affects the regulator/sensor protein. How such interactions between the regulator/sensor and the output affect synthetic gene circuit function has not been …

N-Acetylglucosamine Regulates Virulence Properties In Microbial Pathogens, Shamoon Naseem, James B. Konopka

Department of Molecular Genetics and Microbiology Faculty Publications

There is growing evidence that the sugar N-acetylglucosamine (GlcNAc) plays diverse roles in cell signaling pathways that impact the virulence properties of microbes and host cells. GlcNAc is already well known as a ubiquitous structural component at the cell surface that forms part of bacterial cell wall peptidoglycan, cell wall chitin in fungi and parasites, and extracellular matrix glycosaminoglycans of animal cells. Chitin and peptidoglycan have been previously linked to cell signaling as they can stimulate responses in plant and animal host cells [1–3]. Recent studies now indicate that GlcNAc released from these polymers can also …

Polyq-Dependent Rna–Protein Assemblies Control Symmetry Breaking, Changhwan Lee, Patricia Occhipinti, Amy S. Gladfelter

Dartmouth Scholarship

Dendritic growth in fungi and neurons requires that multiple axes of polarity are established and maintained within the same cytoplasm. We have discovered that transcripts encoding key polarity factors including a formin, Bni1, and a polarisome scaffold, Spa2, are nonrandomly clustered in the cytosol to initiate and maintain sites of polarized growth in the fungus Ashbya gossypii. This asymmetric distribution requires the mRNAs to interact with a polyQ-containing protein, Whi3, and a Pumilio protein with a low-complexity sequence, Puf2. Cells lacking Whi3 or Puf2 had severe defects in establishing new sites of polarity and failed to localize Bni1 protein. Interaction …

Genome-Wide Meta-Analysis In Alopecia Areata Resolves Hla Associations And Reveals Two New Susceptibility Loci, Regina C. Betz, Lynn Petukhova, Stephan Ripke, Hailiang Huang, Androniki Menelaou, Silke Redeler, Tim Becker, Stefanie Heilmann, Tarek Yamany, Madeleine Duvic, Maria Hordinsky, David Norris, Vera H. Price, Julian Mackay-Wiggan, Annemieke De Jong, Gina M. Destefano, Susanne Moebus, Markus Böhm, Ulrike Blume-Peytavi, Hans Wolff, Gerhard Lutz, Roland Kruse, Li Bian, Christopher I. Amos

Dartmouth Scholarship

Alopecia areata (AA) is a prevalent autoimmune disease with ten known susceptibility loci. Here we perform the first meta-analysis in AA by combining data from two genome-wide association studies (GWAS), and replication with supplemented ImmunoChip data for a total of 3,253 cases and 7,543 controls. The strongest region of association is the MHC, where we fine-map 4 independent effects, all implicating HLA-DR as a key etiologic driver. Outside the MHC, we identify two novel loci that exceed statistical significance, containing ACOXL/BCL2L11(BIM) (2q13); GARP (LRRC32) (11q13.5), as well as a third nominally significant region SH2B3(LNK)/ ATXN2 (12q24.12). Candidate susceptibility gene expression …

Population Genetic Structure Of The Dwarf Seahorse (Hippocampus Zosterae) In Florida, Nathan Fedrizzi, Melanie L. J. Stiassny, J. T. Boehm, Eric R. Dougherty, George Amato, Martin Mendez

Publications and Research

The dwarf seahorse (Hippocampus zosterae) is widely distributed throughout near-shore habitats of the Gulf of Mexico and is of commercial significance in Florida, where it is harvested for the aquarium and curio trades. Despite its regional importance, the genetic structure of dwarf seahorse populations remains largely unknown. As an aid to ongoing conservation efforts, we employed three commonly applied mtDNA markers (ND4, DLoop and CO1) to investigate the genetic structuring of H. zosterae in Florida using samples collected throughout its range in the state. A total of 1450 bp provided sufficient resolution to delineate four populations of dwarf seahorses, as …

Zbtb20 Is A Sequence-Specific Transcriptional Repressor Of Alpha-Fetoprotein Gene, Hai Zhang, Dongmei Cao, Luting Zhou, Ye Zhang, Xiaoqin Guo, Hui Li, Yuxia Chen, Brett T. Spear, Jia-Wei Wu, Zhifang Xie, Weiping J Zhang

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Alpha-fetoprotein (AFP) represents a classical model system to study developmental gene regulation in mammalian cells. We previously reported that liver ZBTB20 is developmentally regulated and plays a central role in AFP postnatal repression. Here we show that ZBTB20 is a sequence-specific transcriptional repressor of AFP. By ELISA-based DNA-protein binding assay and conventional gel shift assay, we successfully identified a ZBTB20-binding site at -104/-86 of mouse AFP gene, flanked by two HNF1 sites and two C/EBP sites in the proximal promoter. Importantly, mutation of the core sequence in this site fully abolished its binding to ZBTB20 in vitro, as well …

Topbp1 Governs Hematopoietic Stem/Progenitor Cells Survival In Zebrafish Definitive Hematopoiesis., Lei Gao, Dantong Li, Ke Ma, Wenjuan Zhang, Tao Xu, Wenge Zhu, +12 Additional Authors

Biochemistry and Molecular Medicine Faculty Publications

In vertebrate definitive hematopoiesis, nascent hematopoietic stem/progenitor cells (HSPCs) migrate to and reside in proliferative hematopoietic microenvironment for transitory expansion. In this process, well-established DNA damage response pathways are vital to resolve the replication stress, which is deleterious for genome stability and cell survival. However, the detailed mechanism on the response and repair of the replication stress-induced DNA damage during hematopoietic progenitor expansion remains elusive. Here we report that a novel zebrafish mutantcas003 with nonsense mutation in topbp1 gene encoding topoisomerase II β binding protein 1 (TopBP1) exhibits severe definitive hematopoiesis failure. Homozygous topbp1cas003 mutants manifest reduced number of HSPCs …

A Linkage Based Imputation Method For Missing Snp Markers In Association Mapping, Yi Xu, Yajun Wu, Michael G. Gonda, Jixiang Wu

Animal Science Faculty Publications

Association mapping has been widely used in detecting genetic markers associated with traits of importance in research areas such as plant breeding, human disease and animal breeding. In recent years, various useful statistical methods and computing tools have been developed for association mapping studies. One of the critical challenges in association mapping is missing markers.

The Utilization Of Polymerase Chain Reaction, Dna Barcoding And Bioinformatics In Identifying Plant Species, Lindee J. Triplett, Ryan Foo, Ronald W. Strohmeyer (Mentor)

Idaho Conference on Undergraduate Research

Bioinformatics and DNA barcoding is a process used to identify plants, animals, and fungi. DNA barcoding in plants utilizes a key variable region in the genome, the RuBisCo large subunit (RbcL) on Chloroplast DNA. Once the DNA is extracted, Polymerase Chain Reaction (PCR) amplifies that region and that sample is sent off for sequencing. Bioinformatics and DNA barcoding helps taxonomists determine the sequence of the RbcL gene as well as obtain a unique barcode that can be used to identify plants. Several plant species from our local campus were sequenced and identified using the previously described methods.

Is Trust Always Better Than Distrust? The Potential Value Of Distrust In Newer Virtual Teams Engaged In Short-Term Decision-Making, Paul Benjamin Lowry, Ryan M. Schuetzler, Justin Scott Giboney, Thomas A. Gregory

Information Systems and Quantitative Analysis Faculty Publications

The debate on the benefits of trust or distrust in groups has generated a substantial amount of research that points to the positive aspects of trust in groups, and generally characterizes distrust as a negative group phenomenon. Therefore, many researchers and practitioners assume that trust is inherently good and distrust is inherently bad. However, recent counterintuitive evidence obtained from face-to-face (FtF) groups indicates that the opposite might be true; trust can prove detrimental, and distrust instrumental, to decision-making in groups. By extending this argument to virtual teams (VTs), we examined the value of distrust for VTs completing routine and non-routine …

Genetic Variation And Species Distribution Of Subterranean Termites In The Southeastern U.S. Focusing On Family Structure And The Invasive Formosan Subterranean Termite, Mark Allan Janowiecki

Graduate Theses and Dissertations

This work applies molecular genetic tools to distinguish the identity and understand the biology of termites, particularly Reticulitermes Holmgren and Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae) in the southeastern U.S. Termites are important economic pests costing billions of dollars annually to Americans but also are important wood decomposers in natural settings. Molecular tools are essential for species identification because of the morphological ambiguities among species. The cryptic nest structure of subterranean termites which prevents adequate sampling makes molecular genetic tools essential to examine an entire colony.

A molecular diagnostic technique was created to differentiate Coptotermes formosanus, an invasive species in the …

Population Structure Of Central Stoneroller (Campostoma Anomalum) On The Ozark Plateau In Arkansas And Missouri, Mallory Jane Jeffers

Graduate Theses and Dissertations

Stream fishes on the Ozark Plateau have been influenced both by historic events (i.e. vicariance versus dispersal) and ecological forces (i.e. flow regime). To examine the role of these processes, genetic structure of Central Stoneroller (Campostoma anomalum), an ecologically important omnivorous minnow with a broad distribution and elevated abundance, was evaluated across populations in the White River drainage of the Ozark Plateau in Arkansas and Missouri. Fin clips of five to eight individuals were taken at each of 20 sites (N=138 individuals; average=6.9), selected so as to represent two different flow regimes: intermittently flashy (N=10 sites; N=73 individuals; average=7.3/ site) …

Gene Expression During The First 28 Days Of Axolotl Limb Regeneration I: Experimental Design And Global Analysis Of Gene Expression, S. Randal Voss, Alex Palumbo, Radha Nagarajan, David M. Gardiner, Ken Muneoka, Arnold J. Stromberg, Antony T. Athippozhy

Biology Faculty Publications

While it is appreciated that global gene expression analyses can provide novel insights about complex biological processes, experiments are generally insufficiently powered to achieve this goal. Here we report the results of a robust microarray experiment of axolotl forelimb regeneration. At each of 20 post-amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1 mm of heterogeneous tissue collected from the distal limb tip. We show that the limb transcription program diverges progressively with time from the non-injured state, and divergence among time adjacent samples is mostly gradual. However, punctuated episodes of transcription …

Transcriptome Sequencing And Annotation Of The Polychaete Hermodice Carunculata (Annelida, Amphinomidae), Shaadi Mehr, Aida Verdes, Rob Desalle, John S. Sparks, Vincent A. Pieribone, David F. Gruber

Publications and Research

Background: The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for coral disease. While amphinomids are a key group for determining the root of the Annelida, their phylogenetic position has been difficult to resolve, and their publically available genomic data was scarce.

Results: We performed deep transcriptome sequencing (Illumina HiSeq) and profiling on Hermodice carunculata collected in the Western Atlantic Ocean. We focused this study on 58,454 predicted Open Reading Frames (ORFs) of genes longer than 200 amino acids …

Role Of Metabolic Shifts In Protection From Mutation Damage: Characterizing Mitochondrial Membrane Potential In C. Elegans Gas-1 Mutants, Lauren S. Muñoz-Tremblay

PSU McNair Scholars Online Journal

Many terminal human diseases are caused by mutations affecting mitochondrial functioning. Mitochondria are essential organelles responsible for producing cellular energy, adenosine triphosphate (ATP) via oxidative phosphorylation (OXPHOS) at mitochondrial electron transport chains (ETC). Proper ETC functioning relies on maintenance of the electrochemical gradient essential for energy production, known as mitochondrial membrane potential (ΔψM). The inner mitochondrial membrane is the site of the ETC and is most closely in contact with the enzymatic processes occurring within the mitochondrial matrix. Mutations affecting protein components of the ETC are especially troublesome for organelle health. ETC mutants commonly express altered ΔψM, as well as …

Cell Wall Mutants In Arabidopsis Thaliana, Christy Jane Moore

Theses and Dissertations

Plant cell walls are versatile structures, playing important roles in communication, defense, organization and support. The importance of each of these functions varies by cell type, with specialized cells often utilizing one or two functions more than others. Trichomes, or leaf hairs, and hypocotyl cells for instance, exhibit distinct cell wall characteristics. Trichomes have developed very thick cell walls with several raised structures, known as papillae, on their surfaces. It is believed that these cells function in defense against predators, making it difficult to crawl on the leaf surface, and in protection against ultra violet radiation, through refraction of light …

Evolution And Otitis Media: A Review, And A Model To Explain High Prevalence In Indigenous Populations, Mahmood F. Bhutta

Human Biology Open Access Pre-Prints

Inflammation of the middle ear (otitis media) comprises a group of disorders that are highly prevalent in childhood, and indeed are amongst the most common disorders of childhood. Otitis media is also heritable, and has effects on fecundity. This means that otitis media is subject to evolution, yet the evolutionary selection forces that may determine susceptibility to otitis media have never been adequately explored.

Here I undertake a critical analysis of evolutionary forces that may determine susceptibility to middle ear inflammation. These forces include those determining function of the middle ear, those affecting host immunity, and those affecting colonization by, …

Mutations That Separate The Functions Of The Proofreading Subunit Of The Escherichia Coli Replicase, Zakiya Whatley, Kenneth N. Kreuzer

Biology Faculty Publications

The dnaQ gene of Escherichia coli encodes the Ɛ subunit of DNA polymerase III, which provides the 3' - 5' exonuclease proofreading activity of the replicative polymerase. Prior studies have shown that loss of Ɛ leads to high mutation frequency, partially constitutive SOS, and poor growth. In addition, a previous study from our laboratory identified dnaQ knockout mutants in a screen for mutants specifically defective in the SOS response after quinolone (nalidixic acid) treatment. To explain these results, we propose a model whereby, in addition to proofreading, Ɛ plays a distinct role in replisome disassembly and/or processing of stalled replication …

Activity Of The Porcine Gonadotropin-Releasing Hormone Receptor Gene Promoter Is Partially Conferred By A Distal Gonadotrope Specific Element (Gse) Within An Upstream Enhancing Region, Two Proximal Gses And A Retinoid X Receptor Binding Site, Rebecca Cederberg, Jacqueline Smith, Emily A. Mcdonald, Chanho Lee, Amy R. Perkins, Brett R. White

Department of Animal Science: Faculty Publications

Background: Regulation of gonadotropin-releasing hormone (GnRH) receptor (GnRHR) numbers on gonadotropes within the anterior pituitary gland represents a critical point for control of reproductive function. Binding of GnRH to its receptor regulates follicle stimulating hormone (FSH) and luteinizing hormone (LH) release and levels of this G-protein coupled receptor on the surface of gonadotropes determines their sensitivity to GnRH pulses. While transcriptional regulation of this gene has been studied in mice, rats, humans and sheep, little is known about its regulation in the pig, an important agricultural species and human research model.

Methods: We isolated 5118 bp of 5′ flanking …

The Role Of Fire In Aspen Ecology And Restoration, Douglas J. Shinneman, Kevin D. Krasnow, Susan K. Mcilroy

Aspen Bibliography

Quaking aspen is generally considered to be a fire-adapted species because it regenerates prolifically after fire, and it can be replaced by more shade-tolerant tree species in the absence of fire. As early-successional aspen stands transition to greater conifer-dominance, they become increasingly fire prone, until fire returns, and aspen again temporarily dominate. While this disturbance-succession cycle is critical to the persistence of aspen on many landscapes, some aspen stands persist on the landscape without fire. The complex role of fire is an important consideration for developing conservation and restoration strategies intended to sustain aspen.