Genetics and Genomics Commons^™

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 …

Transcriptomic Characterization Of A Synergistic Genetic Interaction During Carpel Margin Meristem Development In Arabidopsis Thaliana, April N. Wynn, Elizabeth E. Rueschhoff, Robert G. Franks

Biological Sciences Research

In flowering plants the gynoecium is the female reproductive structure. In Arabidopsis thalianaovules initiate within the developing gynoecium from meristematic tissue located along the margins of the floral carpels. When fertilized the ovules will develop into seeds. SEUSS (SEU) and AINTEGUMENTA (ANT) encode transcriptional regulators that are critical for the proper formation of ovules from the carpel margin meristem (CMM). The synergistic loss of ovule initiation observed in the seu ant double mutant suggests that SEU and ANT share overlapping functions during CMM development. However the molecular mechanism underlying this synergistic interaction is unknown. Using …

Cdc42 Regulates Extracellular Matrix Remodeling In Three Dimensions*, Nisha S. Sipes, Benjamin Feng, Fukun Guo, Hyung-Ok Lee, Fu-Sheng Chou, Jonathan Cheng, James Mulloy, Yi Zheng

Peer Reviewed Articles

Extracellular matrix (ECM) actively participates in normal cell regulation and in the process of tumor progression. The Rho GTPase Cdc42 has been shown to regulate cell-ECM interaction in conventional two-dimensional culture conditions by using dominant mutants of Cdc42 in immortalized cell lines that may introduce nonspecific effects. Here, we employ three-dimensional culture systems for conditional gene targeted primary mouse embryonic fibroblasts that better simulate the reciprocal and adaptive interactions between cells and surrounding matrix to define the role of Cdc42 signaling pathways in ECM organization. Cdc42 deficiency leads to a defect in global cell-matrix interactions reflected by a decrease in …

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 …

Comparison Of Four Chip-Seq Analytical Algorithms Using Rice Endosperm H3k27 Trimethylation Profiling Data., Brandon M. Malone, Feng Tan, Susan M. Bridges, Zhaohua Peng

BCoE Publications

Chromatin immunoprecipitation coupled with high throughput DNA Sequencing (ChIP-Seq) has emerged as a powerful tool for genome wide profiling of the binding sites of proteins associated with DNA such as histones and transcription factors. However, no peak calling program has gained consensus acceptance by the scientific community as the preferred tool for ChIP-Seq data analysis. Analyzing the large data sets generated by ChIP-Seq studies remains highly challenging for most molecular biology laboratories.Here we profile H3K27me3 enrichment sites in rice young endosperm using the ChIP-Seq approach and analyze the data using four peak calling algorithms (FindPeaks, PeakSeq, USeq, and MACS). Comparison …

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 …

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 …

Micrornas And Phylogenomics Resolve The Relationships Of Tardigrada And Suggest That Velvet Worms Are The Sister Group Of Arthropoda, Lahcen I. Campbell, Omar Rota-Stabelli, Gregory D. Edgecombe, Trevor Marchioro, Stuart J. Longhorn, Maximilian J. Telford, Hervé Philippe, Lorena Rebecchi, Kevin J. Peterson, Davide Pisani

Dartmouth Scholarship

Morphological data traditionally group Tardigrada (water bears), Onychophora (velvet worms), and Arthropoda (e.g., spiders, insects, and their allies) into a monophyletic group of invertebrates with walking appendages known as the Panarthropoda. However, molecular data generally do not support the inclusion of tardigrades within the Panarthropoda, but instead place them closer to Nematoda (roundworms). Here we present results from the analyses of two independent genomic datasets, expressed sequence tags (ESTs) and microRNAs (miRNAs), which congruently resolve the phylogenetic relationships of Tardigrada. Our EST analyses, based on 49,023 amino acid sites from 255 proteins, significantly support a monophyletic Panarthropoda including Tardigrada and …

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. …

Development Of Novel Microsatellite Markers For High-Resolution Genetic Analysis Of The Western Slimy Salamander (Plethodon Albagula), Nathan Thomas Stephens

Student Theses and Dissertations

Polymorphic microsatellite DNA markers were developed and characterized for the western slimy salamander (Plethodon albagula). Salamanders from the Spillway Mine in Garland County, Arkansas were sampled for DNA and a microsatellite-enriched library was created for this species. The library yielded 1654 sequences from which 142 candidate loci containing simple tandem repeats were identified; 28 polymerase chain reaction primer pairs representing 28 candidate loci were tested in this study and eight were selected for development based on robust amplification and polymorphism in PCR-based analysis of P. albagula population samples. Of these eight loci, six were determined to be unlinked in a …

Enhancing Genome Investigations In The Mosquito Culex Quinquefasciatus Via Bac Library Construction And Characterization, Paul V. Hickner, Becky Debruyn, Diane D. Lovin, Akio Mori, Christopher Saski, David W. Severson

Publications

Background

Culex quinquefasciatus (Say) is a major species in the Culex pipiens complex and an important vector for several human pathogens including West Nile virus and parasitic filarial nematodes causing lymphatic filariasis. It is common throughout tropical and subtropical regions and is among the most geographically widespread mosquito species. Although the complete genome sequence is now available, additional genomic tools are needed to improve the sequence assembly.

Findings

We constructed a bacterial artificial chromosome (BAC) library using the pIndigoBAC536 vector and HindIII partially digested DNA isolated from Cx. quinquefasciatus pupae, Johannesburg strain (NDJ). Insert size was estimated by Not …

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 …

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 …

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 …

Gc-Content Normalization For Rna-Seq Data, Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit

U.C. Berkeley Division of Biostatistics Working Paper Series

Background: Transcriptome sequencing (RNA-Seq) has become the assay of choice for high-throughput studies of gene expression. However, as is the case with microarrays, major technology-related artifacts and biases affect the resulting expression measures. Normalization is therefore essential to ensure accurate inference of expression levels and subsequent analyses thereof.

Results: We focus on biases related to GC-content and demonstrate the existence of strong sample-specific GC-content effects on RNA-Seq read counts, which can substantially bias differential expression analysis. We propose three simple within-lane gene-level GC-content normalization approaches and assess their performance on two different RNA-Seq datasets, involving different species and experimental designs. …

Mutant Alcohol Dehydrogenase Leads To Improved Ethanol Tolerance In Clostridium Thermocellum, Steven D. Brown, Adam M. Guss, Tatiana V. Karpinets, Jerry M. Parks

Dartmouth Scholarship

Clostridium thermocellum is a thermophilic, obligately anaerobic, Gram-positive bacterium that is a candidate microorganism for converting cellulosic biomass into ethanol through consolidated bioprocessing. Ethanol intolerance is an important metric in terms of process economics, and tolerance has often been described as a complex and likely multigenic trait for which complex gene interactions come into play. Here, we resequence the genome of an ethanol-tolerant mutant, show that the tolerant phenotype is primarily due to a mutated bifunctional acetaldehyde-CoA/alcohol dehydrogenase gene (adhE), hypothesize based on structural analysis that cofactor specificity may be affected, and confirm this hypothesis using enzyme assays. …

Comparative Genomics Of The Pathogenic Ciliate Ichthyophthirius Multifiliis, Its Free-Living Relatives And A Host Species Provide Insights Into Adoption Of A Parasitic Lifestyle And Prospects For Disease Control, Robert S. Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B. Hostetler, Daniel Brami, Vinita S. Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H. Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W. Mather, Akhil B. Vaidya, David E. Wilkes, Vidyalakshmi Rajagopalan, David J. Asai, Chad G. Pearson, Robert C. Findly, Harry W. Dickerson, Martin Wu, Cindy Martens, Yves Van De Peer, David S. Roos, Donna M. Cassidy-Hanley, Theodore G. Clark

Publications and Research

Background

Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental studies challenging. Unlike most well-studied protozoan parasites, Ich belongs to a phylum composed primarily of free-living members. Indeed, it is closely related to the model organism Tetrahymena thermophila. Genomic studies represent a promising strategy to reduce the impact of this disease and to understand the evolutionary transition to parasitism.

Results

We report the sequencing, assembly and annotation …