Genetics Commons^™

High Connectivity In The Deepwater Snapper Pristipomoides Filamentosus (Lutjanidae) Across The Indo-Pacific With Isolation Of The Hawaiian Archipelago, Michelle R. Gaither, Shelley A. Jones, Christopher Kelley, Stephen J. Newman, Laurie Sorenson, Brian W. Bowen

Fisheries Research Articles

In the tropical Indo-Pacific, most phylogeographic studies have focused on the shallow-water taxa that inhabit reefs to approximately 30 m depth. Little is known about the large predatory fishes, primarily snappers (subfamily Etelinae) and groupers (subfamily Epinephelinae) that occur at 100–400 m. These long-lived, slow-growing species support fisheries across the Indo-Pacific, yet no comprehensive genetic surveys within this group have been conducted. Here we contribute the first range-wide survey of a deepwater Indo-Pacific snapper, Pristipomoides filamentosus, with special focus on Hawai'i. We applied mtDNA cytochrome b and 11 microsatellite loci to 26 samples (N = 1,222) collected across …

Characterization Of A Novel Gef Kiaa1362, Emily Roach

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

Afghan Genetic Mysteries, Bernard Dupaigne

Human Biology Open Access Pre-Prints

Letter To The Editor

The Y-Str Genetic Diversity Of An Idaho Basque Population, With Comparison To European Basques And Us Caucasians, Josu Zubizarreta, Michael C. Davis, Greg Hampikian

Human Biology Open Access Pre-Prints

Fifty unrelated Basque males from southwest Idaho were typed for the 17 Y-STR loci in the Yfiler multiplex kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1 and DYS385a/b). A total of 42 haplotypes were identified, with no more than two individuals sharing a single haplotype. The haplotype diversity (HD) was 0.9935, and gene diversity (D) over loci was 0.457 ± 0.137. The Idaho Basque population was compared to the source population from the Basque autonomous region of Northern Spain and Southern France, as well as a US Caucasian population. The haplotype diversity …

Efficacy Of Genetically Modified Bt Toxins Against Insects With Different Genetic Mechanisms Of Resistance, Bruce E. Tabashnik, Fangneng P. Huang, Mukti N. Ghimire, B. Rogers Leonard, Blair D. Siegfried, Murugesan Rangasamy, Yajun Yang, Yidong Wu, Linda J. Gahan, David G. Heckel, Alejandro Bravo, Mario Soberón

Department of Entomology: Faculty Publications

Transgenic crops that produce Bacillus thuringiensis (Bt) toxins are grown widely for pest control, but insect adaptation can reduce their efficacy. The genetically modified Bt toxins Cry1AbMod and Cry1AcMod were designed to counter insect resistance to native Bt toxins Cry1Ab and Cry1Ac. Previous results suggested that the modified toxins would be effective only if resistance was linked with mutations in genes encoding toxin-binding cadherin proteins. Here we report evidence from five major crop pests refuting this hypothesis. Relative to native toxins, the potency of modified toxins was > 350-fold higher against resistant strains of Plutella xylostella and Ostrinia nubilalis …

A Population-Genetic Perspective On The Similarities And Differences Among Worldwide Human Populations, Noah A. Rosenberg

Human Biology Open Access Pre-Prints

Recent studies have produced a variety of advances in the investigation of genetic similarities and differences among human populations. Here, I pose a series of questions about human population- genetic similarities and differences, and I then answer these questions by numerical computation with a single shared population-genetic dataset. The collection of answers obtained provides an introductory perspective for understanding key results on the features of worldwide human genetic variation.

Integration Versus Apartheid In Post-Roman Britain: A Response To Thomas Et Al. (2008), John E. Pattison

Human Biology Open Access Pre-Prints

The genetic surveys of the population of Britain conducted by Weale et al. and Capelli et al. produced estimates of the Germani immigration into Britain during the early Anglo-Saxon period, c.430-c.730. These estimates are considerably higher than the estimates of archaeologists. A possible explanation suggested that an apartheid-like social system existed in the early Anglo-Saxon kingdoms resulting in the Germani breeding more quickly than the Britons. Thomas et al. attempted to model this suggestion and showed that it was a possible explanation if all Anglo-Saxon kingdoms had such a system for up to 400 yrs. I noted that their explanation …

Exploring The Effects Of Hypoxia On Sulfate Reducing Anaerobes, Annaliese K. Jones

Senior Honors Projects

Exploring the Effects of Hypoxia on Sulfate Reducing Anaerobes

Annaliese K. Jones

Sponsor: Bethany Jenkins, Cell and Molecular Biology

As a student about to graduate with a degree in Biological Sciences, I find myself faced with the need to find my own independent research interests and scientific voice. As a result of my interests in the fields of both microbiology and ecology, I am drawn to questions surrounding the role and behavior of microorganisms in the environment. With climate change being an issue capturing the attention of a large portion of the scientific community, I have chosen to focus my …

Protein Trap Lines Of Drosophila To Demonstrate Spatio-Temporal Localization Of Proteins In An Undergraduate Lab, Oorvashi Roy Puli, Amit Singh

Biology Faculty Publications

The objective of this teaching note is to generate a laboratory exercise, which allows students to get a hands-on experience of a cell biology technique. The short duration of the laboratory classes is the biggest challenge with the development of a cell biology lab for an undergraduate curriculum. Therefore, it is necessary to design a laboratory exercise that enables the students to carry out cell biological assays in the desired time. This laboratory exercise focuses on tracking protein expression levels along a spatial (space) and temporal (time) axis in developing Drosophila melanogaster organ primordium. Here we use the protein trap …

The Incidence Of Plexiform Lesion Formation In Lines Divergently Selected For Ascites, James Grant Mason

Graduate Theses and Dissertations

Complex Vascular Lesions, (CVL) are a common vascular change associated with idiopathicpulmonary arterial hypertension (IPAH). CVL have been characterized in studies using animal models involving, but not limited to, Sprague-Dawley rats and poultry (Abe et al., 2010; Wideman et al., 2011).IPAH has been documented in poultry although no connection has been made with CVLs. The current study characterizes CVL in the lungs from broilers derived from lines divergently selected for 15 generations for ascites susceptibility under conditions of simulated high altitude. The ascites RES and SUS lines were sampled for CVL incidence over time. Both lines were reared in a …

Quantitative Comparison Of Cis-Regulatory Element (Cre) Activities In Transgenic Drosophila Melanogaster, William A. Rogers, Thomas M. Williams

Biology Faculty Publications

Gene expression patterns are specified by cis-regulatory element (CRE) sequences, which are also called enhancers or cis-regulatory modules. A typical CRE possesses an arrangement of binding sites for several transcription factor proteins that confer a regulatory logic specifying when, where, and at what level the regulated gene(s) is expressed. The full set of CREs within an animal genome encodes the organism′s program for development¹, and empirical as well as theoretical studies indicate that mutations in CREs played a prominent role in morphological evolution^2-4. Moreover, human genome wide association studies indicate that genetic variation in CREs …

Msh1 Influence On Plant Mitochondrial Genome Recombination And Phenotype In Tobacco, Peibei Sun

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

Plant mitochondrial genomes are composed of unusually complex structures, due to active recombination at numerous repeated sequences in the genome. The maintenance of mitochondrial genome stability is under the control of identifiable nuclear genes. In plants, three nuclear genes (MSH1, RECA3 and OSB1) have been shown to participate in recombination surveillance and the suppression of illegitimate recombination in mitochondria. Disruption of these loci in Arabidopsis results in reproducible mitochondrial genome rearrangements. We demonstrated that repeat-mediated de novo recombination was also enhanced in both Arabidopsis and tobacco during passage through in vitro culture. Furthermore, in vitro conditions led …

Ethnic Disparity In 21-Hydroxylase Gene Mutations Identified In Pakistani Congenital Adrenal Hyperplasia Patient, Aysha Habib Khan, Muniba Aban, Jamal Raza, Naeem Ul Haq, Abdul Jabbar, Tariq Moatter

Department of Pathology and Laboratory Medicine

Background: Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders caused by defects in the steroid 21 hydroxylase gene (CYP21A2). We studied the spectrum of mutations in CYP21A2 gene in a multi-ethnic population in Pakistan to explore the genetics of CAH.

Methods: A cross sectional study was conducted for the identification of mutations CYP21A2 and their phenotypic associations in CAH using ARMS-PCR assay.

Results: Overall, 29 patients were analyzed for nine different mutations. The group consisted of two major forms of CAH including 17 salt wasters and 12 simple virilizers. There were 14 phenotypic males and 15 females …

Investigating The Roles Of Ndj1 And Tid1 In Crossover Assurance In Saccharomyces Cerevisiae, Rianna Knowles

Master's Theses

Meiosis is the specialized process of cell division utilized during gametogenesis in all sexually reproducing eukaryotes, which consists of one round of DNA replication followed by two rounds of chromosome segregation and results in four haploid cells. Crossovers between homologous chromosomes promote proper alignment and segregation of chromosomes during meiosis.

Crossover interference is a genetic phenomenon in which crossovers are non-randomly placed along chromosomes. Crossover assurance ensures that every homologous chromosome pair obtains at least one crossover during Prophase I. Crossovers physically connect homologous pairs, allowing spindle fibers to attach and separate homologs properly. However, some organisms have shown an …

Erect Wing Facilitates Context-Dependent Wnt/Wingless Signaling By Recruiting The Cell-Specific Armadillo-Tcf Adaptor Earthbound To Chromatin, Nan Xin, Hassina Benchabane, Ai Tian, Kerrie Nguyen, Lindsay Klofas, Yashi Ahmed

Dartmouth Scholarship

During metazoan development, the Wnt/Wingless signal transduction pathway is activated repetitively to direct cell proliferation, fate specification, differentiation and apoptosis. Distinct outcomes are elicited by Wnt stimulation in different cellular contexts; however, mechanisms that confer context specificity to Wnt signaling responses remain largely unknown. Starting with an unbiased forward genetic screen in Drosophila, we recently uncovered a novel mechanism by which the cell-specific co-factor Earthbound 1 (Ebd1), and its human homolog jerky, promote interaction between the Wnt pathway transcriptional co-activators B-catenin/Armadillo and TCF to facilitate context-dependent Wnt signaling responses. Here, through the same genetic screen, we find an unanticipated requirement …

Heritable Epigenetic Variation Among Maize Inbreds, Steve R. Eichten, Ruth A. Swanson, James C. Schnable, Amanda J. Waters, Peter J. Hermanson, Sanzhen Liu, Cheng-Ting Yeh, Yi Jia, Karla Gendler, Michael Freeling, Patrick S. Schnable, Matthew W. Vaughn, Nathan M. Springer

Department of Agronomy and Horticulture: Faculty Publications

Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences. Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. A genome-wide profiling of DNA methylation in two different genotypes of Zea mays (ssp. mays), an organism with a complex genome of interspersed genes and repetitive elements, allowed the identification and characterization of examples of natural epigenetic variation. The distribution of DNA methylation …

Estimation Of A Non-Parametric Variable Importance Measure Of A Continuous Exposure, Chambaz Antoine, Pierre Neuvial, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

We define a new measure of variable importance of an exposure on a continuous outcome, accounting for potential confounders. The exposure features a reference level x0 with positive mass and a continuum of other levels. For the purpose of estimating it, we fully develop the semi-parametric estimation methodology called targeted minimum loss estimation methodology (TMLE) [van der Laan & Rubin, 2006; van der Laan & Rose, 2011]. We cover the whole spectrum of its theoretical study (convergence of the iterative procedure which is at the core of the TMLE methodology; consistency and asymptotic normality of the estimator), practical implementation, simulation …

Axl2 Integrates Polarity Establishment, Maintenance, And Environmental Stress Response In The Filamentous Fungus Ashbya Gossypii, Jonathan F. Anker, Amy S. Gladfelter

Dartmouth Scholarship

In budding yeast, new sites of polarity are chosen with each cell cycle and polarization is transient. In filamentous fungi, sites of polarity persist for extended periods of growth and new polarity sites can be established while existing sites are maintained. How the polarity establishment machinery functions in these distinct growth forms found in fungi is still not well understood. We have examined the function of Axl2, a transmembrane bud site selection protein discovered in Saccharomyces cerevisiae, in the filamentous fungus Ashbya gossypii. A. gossypii does not divide by budding and instead exhibits persistent highly polarized growth, and multiple axes …

Afro-Derived Amazonian Populations: Inferring Continental Ancestry And Population Substructure, Luana Gomes Lopes Maciel, Elzemar Martins Ribeiro-Rodrigues, Ney Pereira Cameiro Dos Santos, Ândrea K. C. Ribeiro Dos Santos, João Farias Guerreiro, Sidney Emanuel Batista Dos Santos

Human Biology Open Access Pre-Prints

A panel of Ancestry Informative Markers (AIMs) was used to identify population substructure and estimate individual and overall interethnic admixture in 294 individuals from seven African-derived communities of the Brazilian Amazon. A panel of 48 biallelic markers, representing the insertion (IN) or the deletion (DEL) of small DNA fragments, was employed for this purpose. Overall interethnic admixture estimates showed high miscegenation with other ethnic groups in all populations (between 46% and 64%). The proportion of ancestral genes varied significantly among individuals of the sample: the contribution of African genes varied between 12% and 75%; of European genes between 10% and …

Historical Sketch Of Slovak Haban (Hutterite) Population Based On Autosomal Str Analysis, Matúš Soták, E. Petrejčíková, D. Siváková, Krzysztof Rębała, A. Bôžiková, J. Bernasovská, J. Čarnogurská, I. Boroňová, S. Mačeková, L. Homol'ová, A. Sovičová, D. Gabriková, L. Rusínová, I. Bernasovský

Human Biology Open Access Pre-Prints

According to the Hutterite chronicles, the Habans arrived from Austrian Tyrol, Switzerland and northernmost Italy and stayed in four regions of Slovakia (Sobotište, Vel'ké, Leváre, Moravský, Svätý, Ján, Trenčín). There are some communities in western Slovakia, which retained their Haban cultural identity and still identify themselves as descendents of the Hutterite population with their own specific customs. Slovak Habans are typical founder population with significant social isolation for which high degree of inbreeding is typical. Present study investigated STR polymorphisms as a powerful genetic tool for population genetic studies. The aim was to perform a comparative, population genetic study based …

Human Alu Insertion Polymorphisms In North African Populations, Lotfi Cherni, Sabeh Frigi, Hajer Ennafaa, Nabil Mtiraoui, Touhami Mahjoub, Amel Benammar-Elgaaied

Human Biology Open Access Pre-Prints

Several features make Alu insertions a powerful tool used in population genetic studies: the polymorphic nature of many Alu insertions, the stability of an Alu insertion event and, furthermore, the ancestral state of an Alu insertion is known to be the absence of the Alu element at a particular locus and the presence of an Alu insertion at the site that forward mutational change. This study analyses seven Alu insertion polymorphisms in a sample of 297 individuals from the autochthonous population of Tunisia (Thala, Smar, Zarzis and Bou Salem) and Libya with the aim of studying their genetic structure with …

Use Of Natural Variation Reveals Core Genes In The Transcriptome Of Iron-Deficient Arabidopsis Thaliana Roots, Ricardo J. Stein, Brian M. Waters

Department of Agronomy and Horticulture: Faculty Publications

Iron (Fe) is an essential mineral micronutrient for plants and animals. Plants respond to Fe deficiency by increasing root uptake capacity. Identification of gene networks for Fe uptake and homeostasis could result in improved crop growth and nutritional value. Previous studies have used microarrays to identify a large number of genes regulated by Fe deficiency in roots of three Arabidopsis ecotypes. However, a large proportion of these genes may be involved in secondary or genotype-influenced responses rather than in a universal role in Fe uptake or homeostasis. Here we show that a small percentage of the Fe deficiency transcriptome of …

High Ethanol Titers From Cellulose By Using Metabolically Engineered Thermophilic, Anaerobic Microbes, D. Aaron Argyros, Shital A. Tripathi, Trisha F. Barrett, Stephen R. Rogers, Lawrence F. Feinberg, Daniel G. Olson, Justin M. Foden, Bethany B. Miller, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza

Dartmouth Scholarship

This work describes novel genetic tools for use in Clostridium thermocellum that allow creation of unmarked mutations while using a replicating plasmid. The strategy employed counter-selections developed from the native C. thermocellum hpt gene and the Thermoanaerobacterium saccharolyticum tdk gene and was used to delete the genes for both lactate dehydrogenase (Ldh) and phosphotransacetylase (Pta). The Δldh Δpta mutant was evolved for 2,000 h, resulting in a stable strain with 40:1 ethanol selectivity and a 4.2-fold increase in ethanol yield over the wild-type strain. Ethanol production from cellulose was investigated with an engineered coculture of organic acid-deficient engineered strains of …

Global Analysis Of Serine-Threonine Protein Kinase Genes In Neurospora Crassa, Gyungsoon Park, Jacqueline A. Servin, Gloria E. Turner, Lorena Altamirano

Dartmouth Scholarship

Serine/threonine (S/T) protein kinases are crucial components of diverse signaling pathways in eukaryotes, including the model filamentous fungus Neurospora crassa. In order to assess the importance of S/T kinases to Neurospora biology, we embarked on a global analysis of 86 S/T kinase genes in Neurospora. We were able to isolate viable mutants for 77 of the 86 kinase genes. Of these, 57% exhibited at least one growth or developmental phenotype, with a relatively large fraction (40%) possessing a defect in more than one trait. S/T kinase knockouts were subjected to chemical screening using a panel of eight chemical treatments, with …

Ecology And Genetic Structure Of A Northern Temperate Vibrio Cholerae Population Related To Toxigenic Isolates, Brian M. Schuster, Anna L. Tyzik, Rachel A. Donner, Megan J. Striplin, Salvador Almagro-Moreno

Dartmouth Scholarship

Although Vibrio cholerae is an important human pathogen, little is known about its populations in regions where the organism is endemic but where cholera disease is rare. A total of 31 independent isolates confirmed as V. cholerae were collected from water, sediment, and oysters in 2008 and 2009 from the Great Bay Estuary (GBE) in New Hampshire, a location where the organism has never been detected. Environmental analyses suggested that abundance correlates most strongly with rainfall events, as determined from data averaged over several days prior to collection. Phenotyping, genotyping, and multilocus sequence analysis (MLSA) revealed a highly diverse endemic …

Roles Of Ras1 Membrane Localization During Candida Albicans Hyphal Growth And Farnesol Response, Amy E. Piispanen, Ophelie Bonnefoi, Sarah Carden, Aurelie Deveau

Dartmouth Scholarship

Many Ras GTPases localize to membranes via C-terminal farnesylation and palmitoylation, and localization regulates function. In Candida albicans, a fungal pathogen of humans, Ras1 links environmental cues to morphogenesis. Here, we report the localization and membrane dynamics of Ras1, and we characterize the roles of conserved C-terminal cysteine residues, C287 and C288, which are predicted sites of palmitoylation and farnesylation, respectively. GFP-Ras1 is localized uniformly to plasma membranes in both yeast and hyphae, yet Ras1 plasma membrane mobility was reduced in hyphae compared to that in yeast. Ras1-C288S was mislocalized to the cytoplasm and could not support hyphal development. …

Activation Of Jnk Signaling Mediates Amyloid-Ss- Dependent Cell Death, Meghana Tare, Rohan Modi, Jaison Nainaparampil, Oorvashi Roy Puli, Shimpi Bedi, Pedro Fernandez-Funez, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Background: Alzheimer's disease (AD) is an age related progressive neurodegenerative disorder. One of the reasons for Alzheimer's neuropathology is the generation of large aggregates of Aß42 that are toxic in nature and induce oxidative stress, aberrant signaling and many other cellular alterations that trigger neuronal cell death. However, the exact mechanisms leading to cell death are not clearly understood.

Methodology/Principal Findings: We employed a Drosophila eye model of AD to study how Aß42 causes cell death. Misexpression of higher levels of Aß42 in the differentiating photoreceptors of fly retina rapidly induced aberrant cellular phenotypes and cell death. We found that …

First Transcriptome Of The Testis-Vas Deferens-Male Accessory Gland And Proteome Of The Spermatophore From Dermacentor Variabilis (Acari: Ixodidae), Daniel E. Sonenshine, Brooke W. Bissinger, Noble Egekwu, Kevin V. Donohue, Sayed M. Khalil, R. Michael Roe

Biological Sciences Faculty Publications

Ticks are important vectors of numerous human diseases and animal diseases. Feeding stimulates spermatogenesis, mating and insemination of male factors that trigger female reproduction. The physiology of male reproduction and its regulation of female development are essentially a black box. Several transcriptomes have catalogued expression of tick genes in the salivary glands, synganglion and midgut but no comprehensive investigation has addressed male reproduction and mating. Consequently, a new global approach using transcriptomics, proteomics, and quantitative gene expression is needed to understand male reproduction and stimulation of female reproduction.This first transcriptome to the reproductive biology of fed male ticks, Dermacentor variabilis …

Type Ii Toxoplasma Gondii Ku80 Knockout Strains Enable Functional Analysis Of Genes Required For Cyst Development And Latent Infection, Barbara A. Fox, Alejandra Falla, Leah M. Rommereim, Tadakimi Tomita

Dartmouth Scholarship

Type II Toxoplasma gondii KU80 knockouts (Δku80) deficient in nonhomologous end joining were developed to delete the dominant pathway mediating random integration of targeting episomes. Gene targeting frequency in the type II Δku80 Δhxgprt strain measured at the orotate (OPRT) and the uracil (UPRT) phosphoribosyltransferase loci was highly efficient. To assess the potential of the type II Δku80 Δhxgprt strain to examine gene function affecting cyst biology and latent stages of infection, we targeted the deletion of four parasite antigen genes (GRA4, GRA6, ROP7, and tgd057 …

Dna Secondary Structures And Their Contribution To Mutagenesis In B. Subtilis Stationary Phase Cells, Carmen Vallin, Holly Martin, Christian Ross, Ronald Yasbin, Eduardo Robleto

Undergraduate Research Opportunities Program (UROP)

It is widely known and accepted that the cause of many mutations in cells are generated during the replication process of actively dividing cells, however more recent research has shown that mutations also arise in non growing conditions, a phenomenon known as stationary phase mutagenesis. Much of what is known come from studies in eukaryotic and bacterial models. It has been proposed that in non~growing cells, the process of transcription plays an important role in mutagenesis. We test the hypothesis that DNA secondary structures, formed during transcription, promote mutagenesis. The transcription-generated structures are speculated to be prone to mutations by …