Genetics and Genomics Commons^™

The Effect Of Temperature On Seed Quality And Quantity In Crosses Between European (Populus Tremula) And Hybrid Aspens (P. Tremula X P. Tremuloides), L. Koviuranta, T. Latva-Karjanmaa, P. Pulkkinen

Aspen Bibliography

Hybrid aspen (Populus tremula L. Populus tremuloides Michx.) plantations are expanding in Fennoscandia and the Baltic countries; however, the possible effects of plantations on the native European aspen (P. tremula) and the level of gene flow between European and hybrid aspen have not been investigated. We studied seed quantity and quality in intraspecific and interspecific crosses of the European and hybrid aspens over a two year period. In order to study whether elevated temperatures due to climate change would benefit the species differently, we performed the crosses in different temperatures. In both years, interspecific crosses produced more seeds with higher …

Gene, Pathway And Network Frameworks To Identify Epistatic Interactions Of Single Nucleotide Polymorphisms Derived From Gwas Data, Yu Liu, Sean Maxwell, Tao Feng, Xiaofeng Zhu, Robert C. Elston, Mehmet Koyutürk, Mark R. Chance

Faculty Scholarship

Background: Interactions among genomic loci (also known as epistasis) have been suggested as one of the potential sources of missing heritability in single locus analysis of genome-wide association studies (GWAS). The computational burden of searching for interactions is compounded by the extremely low threshold for identifying significant p-values due to multiple hypothesis testing corrections. Utilizing prior biological knowledge to restrict the set of candidate SNP pairs to be tested can alleviate this problem, but systematic studies that investigate the relative merits of integrating different biological frameworks and GWAS data have not been conducted.Results: We developed four biologically based frameworks to …

How The Leopard Hides Its Spots: Asip Mutations And Melanism In Wild Cats, Alexsandra Schneider, Victor A. David, Warren E. Johnson, Stephen J. O'Brien, Gregory S. Barsh, Marilyn Menotti-Raymond, Eduardo Eizirik

Biology Faculty Articles

The occurrence of melanism (darkening of the background coloration) is documented in 13 felid species, in some cases reaching high frequencies at the population level. Recent analyses have indicated that it arose multiple times in the Felidae, with three different species exhibiting unique mutations associated with this trait. The causative mutations in the remaining species have so far not been identified, precluding a broader assessment of the evolutionary dynamics of melanism in the Felidae. Among these, the leopard (Panthera pardus) is a particularly important target for research, given the iconic status of the ‘black panther’ and the extremely …

The Role Of Gene Duplication And Unconstrained Selective Pressures In The Melanopsin Gene Family Evolution And Vertebrate Circadian Rhythm Regulation, Rui Borges, Warren E. Johnson, Stephen J. O'Brien, Vitor Vasconcelos, Agostinho Antunes

Biology Faculty Articles

Melanopsin is a photosensitive cell protein involved in regulating circadian rhythms and other non-visual responses to light. The melanopsin gene family is represented by two paralogs,OPN4x and OPN4m, which originated through gene duplication early in the emergence of vertebrates. Here we studied the melanopsin gene family using an integrated gene/protein evolutionary approach, which revealed that the rhabdomeric urbilaterian ancestor had the same amino acid patterns (DRY motif and the Y and E conterions) as extant vertebrate species, suggesting that the mechanism for light detection and regulation is similar to rhabdomeric rhodopsins. Both OPN4m and OPN4x paralogs are found …

Draft Genome Sequence For Pseudomonas Aeruginosa Strain Pao579, A Mucoid Derivative Of Pao381, T. Ryan Withers, Shannon L. Johnson, Hongwei D. Yu

Biochemistry and Microbiology

Pseudomonas aeruginosa is an opportunistic pathogen that establishes a chronic lung infection in individuals afflicted with cystic fibrosis. Here, we announce the draft genome of P. aeruginosa strain PAO579, an alginate-overproducing derivative of strain PAO381.

Chapter 11: Genome-Wide Association Studies, William S. Bush, Jason H. Moore

Dartmouth Scholarship

Genome-wide association studies (GWAS) have evolved over the last ten years into a powerful tool for investigating the genetic architecture of human disease. In this work, we review the key concepts underlying GWAS, including the architecture of common diseases, the structure of common human genetic variation, technologies for capturing genetic information, study designs, and the statistical methods used for data analysis. We also look forward to the future beyond GWAS.

Review Of "Fifty Animals That Changed The Course Of History" By E. Chaline, John B. Jenkins

Biology Faculty Works

No abstract provided.

Contour Extraction Of Drosophila Embryos Using Active Contours In Scale Space, Soujanya Siddavaram Ananta

Masters Theses & Specialist Projects

Contour extraction of Drosophila embryos is an important step to build a computational system for pattern matching of embryonic images which aids in the discovery of genes. Automatic contour extraction of embryos is challenging due to several image variations such as size, shape, orientation and neigh- boring embryos such as touching and non-touching embryos. In this thesis, we introduce a framework for contour extraction based on the connected components in the gaussian scale space of an embryonic image. The active contour model is applied on the images to refine embryo contours. Data cleaning methods are applied to smooth the jaggy …

Effects Of Slash Pile Burning After Restoring Conifer- Encroached Aspen, Christa M. Dagley, John-Pascal Berrill, Stephanie Coppeto, Kyle Jacobson

Aspen Bibliography

Removal of conifers encroaching aspen stands has been advocated and is being practiced in the Lake Tahoe Basin (EIP Project #10080: Aspen Community Restoration Projects). In remote and roadless areas, thinning of conifers is generating large volumes of wood and pile burning is currently being implemented to handle this biomass on site. However, the effects of pile burning on aspen are unknown, and there is an urgent need for guidelines to support design of thinning treatment prescriptions; specifically burn pile size and safe distances from live aspen trees of any size to prevent injury.

Septin Phosphorylation And Coiled-Coil Domains Function In Cell And Septin Ring Morphology In The Filamentous Fungus Ashbya Gossypii, Rebecca A. Meseroll, Patricia Occhipinti, Amy S. Gladfelter

Dartmouth Scholarship

Septins are a class of GTP-binding proteins conserved throughout many eukaryotes. Individual septin subunits associate with one another and assemble into heteromeric complexes that form filaments and higher-order structures in vivo. The mechanisms underlying the assembly and maintenance of higher-order structures in cells remain poorly understood. Septins in several organisms have been shown to be phosphorylated, although precisely how septin phosphorylation may be contributing to the formation of high-order septin structures is unknown. Four of the five septins expressed in the filamentous fungus, Ashbya gossypii, are phosphorylated, and we demonstrate here the diverse roles of these phosphorylation sites …

The Principal Genetic Determinants For Nasopharyngeal Carcinoma In China Involve The Hla Class I Antigen Recognition Groove, Minzhong Tang, J. A. Lautenberger, Xiaojiang Gao, Efe Sezgin, Sher L. Hendrickson, Jennifer L. Troyer, Victor A. David, Li Guan, Carl Mcintosh, Xiuchan Guo, Yuming Zheng, Jian Liao, Hong Deng, Michael Malasky, Bailey Kessing, Cheryl Winkler, Mary Carrington, Guy De The, Yi Zeng, Stephen J. O'Brien

Biology Faculty Articles

Nasopharyngeal carcinoma (NPC) is an epithelial malignancy facilitated by Epstein-Barr Virus infection. Here we resolve the major genetic influences for NPC incidence using a genome-wide association study (GWAS), independent cohort replication, and high-resolution molecular HLA class I gene typing including 4,055 study participants from the Guangxi Zhuang Autonomous Region and Guangdong province of southern China. We detect and replicate strong association signals involving SNPs, HLA alleles, and amino acid (aa) variants across the major histocompatibility complex-HLA-A, HLA –B, and HLA -C class I genes (P_{HLA-A-aa-site-62}= 7.4×10⁻²⁹; P _{HLA-B-aa-site-116}= 6.5×10⁻¹⁹; P _{HLA-C-aa-site-156} = 6.8×10 …

Inla Promotes Dissemination Of Listeria Monocytogenes To The Mesenteric Lymph Nodes During Food Borne Infection Of Mice, Elsa N. Bou Ghanem, Grant S. Jones, Tanya Myers-Morales, Pooja D. Patil, Achmad N. Hidayatullah, Sarah E. F. D'Orazio

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Intestinal Listeria monocytogenes infection is not efficient in mice and this has been attributed to a low affinity interaction between the bacterial surface protein InlA and E-cadherin on murine intestinal epithelial cells. Previous studies using either transgenic mice expressing human E-cadherin or mouse-adapted L. monocytogenes expressing a modified InlA protein (InlA(m)) with high affinity for murine E-cadherin showed increased efficiency of intragastric infection. However, the large inocula used in these studies disseminated to the spleen and liver rapidly, resulting in a lethal systemic infection that made it difficult to define the natural course of intestinal infection. We describe here a …

Intsormil- Centa’S New Bmr Sorghum Varieties Create A Surge In Dairy Production, René Clará Valencia

INTSORMIL Scientific Publications

Scientists from the INTSORMIL-CENTA project based at the National Center for Agricultural Technology and Forestry (CENTA) of El Salvador have worked for five years to develop varieties of sorghum for grain and forage that are highly nutritious to cattle. Using the gene bmr-12, received from Dr. Gebisa Ejeta of Purdue University, they combined commercial varieties CENTA S-2, S-3 CENTA, CENTA RCV and VG 146 and were able to form new varieties containing this same gene. The first generation created 76 new varieties.

Multifactorial Patterns Of Gene Expression In Colonic Epithelial Cells Predict Disease Phenotypes In Experimental Colitis, Aubrey Leigh Frantz, Maria E. C. Bruno, Eric William Rogier, Halide Tuna, Donald A. Cohen, Subbarao Bondada, Ralph Lakshman Chelvarajan, J. Anthony Brandon, C. Darrell Jennings, Charlotte S. Kaetzel

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Background— The pathogenesis of inflammatory bowel disease (IBD) is complex and the need to identify molecular biomarkers is critical. Epithelial cells play a central role in maintaining intestinal homeostasis. We previously identified five “signature” biomarkers in colonic epithelial cells (CEC) that are predictive of disease phenotype in Crohn's disease. Here we investigate the ability of CEC biomarkers to define the mechanism and severity of intestinal inflammation.

Methods— We analyzed the expression of RelA, A20, pIgR, tumor necrosis factor (TNF), and macrophage inflammatory protein (MIP)-2 in CEC of mice with dextran sodium sulfate (DSS) acute colitis or T-cell-mediated chronic colitis. …

Phylogeny And Evolutionary Patterns In The Dwarf Crayfish Subfamily (Decapoda: Cambarellinae), C. Pedraza-Lara, I. Doadrio, J. Breinholt, Keith A. Crandall

Computational Biology Institute

The Dwarf crayfish or Cambarellinae, is a morphologically singular subfamily of decapod crustaceans that contains only one genus, Cambarellus. Its intriguing distribution, along the river basins of the Gulf Coast of United States (Gulf Group) and into Central México (Mexican Group), has until now lacked of satisfactory explanation. This study provides a comprehensive sampling of most of the extant species of Cambarellus and sheds light on its evolutionary history, systematics and biogeography. We tested the impact of Gulf Group versus Mexican Group geography on rates of cladogenesis using a maximum likelihood framework, testing different models of birth/extinction of lineages. We …

Scribble Acts In The Drosophila Fat-Hippo Pathway To Regulate Warts Activity, Shilpi Verghese, Indrayani Waghmare, Hailey Kwon, Katelin Hanes, Madhuri Kango-Singh

Biology Faculty Publications

Epithelial cells are the major cell-type for all organs in multicellular organisms. In order to achieve correct organ size, epithelial tissues need mechanisms that limit their proliferation, and protect tissues from damage caused by defective epithelial cells. Recently, the Hippo signaling pathway has emerged as a major mechanism that orchestrates epithelial development. Hippo signaling is required for cells to stop proliferation as in the absence of Hippo signaling tissues continue to proliferate and produce overgrown organs or tumors. Studies in Drosophila have led the way in providing a framework for how Hippo alters the pattern of gene transcription in target …

Survey Of Endosymbionts In The Diaphorina Citri Metagenome And Assembly Of A Wolbachia Wdi Draft Genome, Surya Saha, Wayne B. Hunter, Justin Reese, J. Kent Morgan, Mizuri Marutani-Hert, Hong Huang, Magdalen Lindeberg

School of Information Faculty Publications

Diaphorina citri (Hemiptera: Psyllidae), the Asian citrus psyllid, is the insect vector of Ca. Liberibacter asiaticus, the causal agent of citrus greening disease. Sequencing of the D. citrimetagenome has been initiated to gain better understanding of the biology of this organism and the potential roles of its bacterial endosymbionts. To corroborate candidate endosymbionts previously identified by rDNA amplification, raw reads from the D. citri metagenome sequence were mapped to reference genome sequences. Results of the read mapping provided the most support for Wolbachia and an enteric bacterium most similar to Salmonella. Wolbachia-derived reads were extracted using …

Freq-Seq: A Rapid, Cost-Effective, Sequencing-Based Method To Determine Allele Frequencies Directly From Mixed Populations, Lon Chubiz, Ming-Chun Lee, Nigel Delaney, Christopher Marx

Biology Department Faculty Works

No abstract provided.

Escherichia Coli Recg Functionally Suppresses Human Bloom Syndrome Phenotypes, Michael W. Killen, Dawn M. Stults, William A. Wilson, Andrew J. Pierce

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Defects in the human BLM gene cause Bloom syndrome, notable for early development of tumors in a broad variety of tissues. On the basis of sequence similarity, BLM has been identified as one of the five human homologs of RecQ from Escherichia coli. Nevertheless, biochemical characterization of the BLM protein indicates far greater functional similarity to the E. coli RecG protein and there is no known RecG homolog in human cells. To explore the possibility that the shared biochemistries of BLM and RecG may represent an example of convergent evolution of cellular function where in humans BLM has evolved to …

Gene Expression Analysis Of A Murine Model With Pulmonary Vascular Remodeling Compared To End-Stage Ipah Lungs, Kayoko Shimodaira, Yoichiro Okubo, Eri Ochiai, Haruo Nakayama, Harutaka Katano, Megumi Wakayama, Minoru Shinozaki, Takao Ishiwatari, Daisuke Sasai, Naobumi Tochigi, Tetsuo Nemoto, Tsutomu Saji, Katsuhiko Kamei, Kazutoshi Shibuya

Microbiology, Immunology, and Molecular Genetics Faculty Publications

BACKGROUND: Idiopathic pulmonary arterial hypertension (IPAH) continues to be one of the most serious intractable diseases that might start with activation of several triggers representing the genetic susceptibility of a patient. To elucidate what essentially contributes to the onset and progression of IPAH, we investigated factors playing an important role in IPAH by searching discrepant or controversial expression patterns between our murine model and those previously published for human IPAH. We employed the mouse model, which induced muscularization of pulmonary artery leading to hypertension by repeated intratracheal injection of Stachybotrys chartarum, a member of nonpathogenic and ubiquitous fungus in our …

Cross-Ontology Multi-Level Association Rule Mining In The Gene Ontology., Prashanti Manda, Seval Ozkan, Hui Wang, Fiona M. Mccarthy, Susan M. Bridges

Bagley College of Engineering Publications and Scholarship

The Gene Ontology (GO) has become the internationally accepted standard for representing function, process, and location aspects of gene products. The wealth of GO annotation data provides a valuable source of implicit knowledge of relationships among these aspects. We describe a new method for association rule mining to discover implicit co-occurrence relationships across the GO sub-ontologies at multiple levels of abstraction. Prior work on association rule mining in the GO has concentrated on mining knowledge at a single level of abstraction and/or between terms from the same sub-ontology. We have developed a bottom-up generalization procedure called Cross-Ontology Data Mining-Level by …

Cephalopod Genomics: A Plan Of Strategies And Organization, Caroline B. Albertin, Laure Bonnaud, C. Titus Brown, Wendy J. Crookes-Goodson, Rute R. Da Fonseca, Carlo Di Cristo, Brian P. Dilkes, Eric Edsinger-Gonzales, Robert M. Freeman Jr., Roger T. Hanlon, Kristen M. Koenig, Annie R. Lindgren, Mark Q. Martindale, Patrick Minx, Leonid L. Moroz, Marie-Therese Nödl, Spencer V. Nyholm, Atsushi Ogura, Judit R. Pungor, Joshua J. C. Rosenthal, Erich M. Schwarz, Shuichi Shigeno, Jan M. Strugnell, Tim Wollesen, Guojie Zhang, Clifton W. Ragsdale

Biology Faculty Publications and Presentations

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an …

Genetic Diversity Of Neotropical Myotis (Chiroptera: Vespertilionidae) With An Emphasis On South American Species, Roxanne J. Larsen, Michelle C. Knapp, Hugh H. Genoways, Faisal Ali Anwarali Khan, Peter A. Larsen, Don E. Wilson, Robert J. Baker

University of Nebraska State Museum: Mammalogy Papers

Background: Cryptic morphological variation in the Chiropteran genus Myotis limits the understanding of species boundaries and species richness within the genus. Several authors have suggested that it is likely there are unrecognized species-level lineages of Myotis in the Neotropics. This study provides an assessment of the diversity in New World Myotis by analyzing cytochrome-b gene variation from an expansive sample ranging throughout North, Central, and South America. We provide baseline genetic data for researchers investigating phylogeographic and phylogenetic patterns of Myotis in these regions, with an emphasis on South America.

Methodology and Principal Findings: Cytochrome-b sequences were generated and …

The Consequences Of Denoising Marker-Based Metagenomic Data, John M. Gaspar, W. K. Thomas

Molecular, Cellular & Biomedical Sciences

No abstract provided.

Phylogenetics Links Monster Larva To Deep-Sea Shrimp., Heather D Bracken-Grissom, Darryl L Felder, Nicole L Vollmer, Joel W Martin, Keith A Crandall

Computational Biology Institute

Mid-water plankton collections commonly include bizarre and mysterious developmental stages that differ conspicuously from their adult counterparts in morphology and habitat. Unaware of the existence of planktonic larval stages, early zoologists often misidentified these unique morphologies as independent adult lineages. Many such mistakes have since been corrected by collecting larvae, raising them in the lab, and identifying the adult forms. However, challenges arise when the larva is remarkably rare in nature and relatively inaccessible due to its changing habitats over the course of ontogeny. The mid-water marine species Cerataspis monstrosa (Gray 1828) is an armored crustacean larva whose adult identity …

Gametes: A Fast, Direct Algorithm For Generating Pure, Strict, Epistatic Models With Random Architectures, Ryan J. Urbanowicz, Jeff Kiralis, Nicholas A. Sinnott-Armstrong, Tamra Heberling, Jonathan M. Fisher, Jason H. Moore

Dartmouth Scholarship

Background: Geneticists who look beyond single locus disease associations require additional strategies for the detection of complex multi-locus effects. Epistasis, a multi-locus masking effect, presents a particular challenge, and has been the target of bioinformatic development. Thorough evaluation of new algorithms calls for simulation studies in which known disease models are sought. To date, the best methods for generating simulated multi-locus epistatic models rely on genetic algorithms. However, such methods are computationally expensive, difficult to adapt to multiple objectives, and unlikely to yield models with a precise form of epistasis which we refer to as pure and strict. Purely and …

Serotonin System Gene Polymorphisms Are Associated With Impulsivity In A Context Dependent Manner, Scott F. Stoltenberg, Christa C. Christ, Krista B. Highland

Department of Psychology: Faculty Publications

Impulsivity is a risk factor for adverse outcomes and characterizes several psychiatric disorders and risk for suicide. There is strong evidence that genetic variation influences individual differences in impulsivity, but the details are not yet understood. There is growing interest in better understanding the context dependency of genetic effects that is reflected in studies examining gender specificity, gene × environment interaction and epistasis (gene-gene interaction). In a cross-sectional study we examined whether polymorphisms in six serotonin system candidate genes and the experience of early life trauma (age 0–12) were associated with individual differences in impulsivity in a nonclinical sample of …

Some Like It Hot, Some Like It Warm: Phenotyping To Explore Thermotolerance Diversity, C. H. Yeh, Nicholas J. Kaplinsky, C. Hu, Y. Y. Charng

Biology Faculty Works

Plants have evolved overlapping but distinct cellular responses to different aspects of high temperature stress. These responses include basal thermotolerance, short- and long-term acquired thermotolerance, and thermotolerance to moderately high temperatures. This ‘thermotolerance diversity’ means that multiple phenotypic assays are essential for fully describing the functions of genes involved in heat stress responses. A large number of genes with potential roles in heat stress responses have been identified using genetic screens and genome wide expression studies. We examine the range of phenotypic assays that have been used to characterize thermotolerance phenotypes in both Arabidopsis and crop plants. Three major variables …

Organellar Signaling Expands Plant Phenotypic Variation And Increases The Potential For Breeding The Epigenome, Roberto De La Rosa Santamaria

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

MUTS HOMOLOGUE 1 (MSH1) is a nuclear gene unique to plants that functions in mitochondria and plastids, where it confers genome stability. Phenotypic effects of MSH1 down- regulation were studied in sorghum inbreed line Tx430 and Arabidopsis ecotype Columbia-0, with the hypothesis that RNAi suppression of MSH1 triggers retrograde signaling from organelles to the nucleus, alters the epigenome, and derives heritable phenotypic variation suitable for artificial selection. An array of morphological traits and metabolic pathways was detected, including leaf variegation, male sterility and dwarfism, associated with altered gibberellic acid metabolism, higher levels of reactive oxygen species (ROS), and decreased synthesis …

Development And Characterization Of 11 Novel Microsatellite Loci For The Roundscale Spearfish Tetrapturus Georgii And Their Cross-Species Amplification Among Other Istiophorid Species, Andrea M. Bernard, Kevin A. Feldheim, Mahmood S. Shivji

Marine & Environmental Sciences Faculty Articles

Eleven novel polymorphic microsatellite loci were developed and characterized for the recently validated roundscale spearfish Tetrapturus georgii. Characterization of these markers, based on 35 roundscale spearfish from the western North Atlantic, revealed two to 21 alleles per locus with an average expected heterozygosity (HE) of 0·09–0·94, and all loci conformed to Hardy–Weinberg expectations. Cross-amplification of these 11 loci against all other eight known istiophorid species indicates promising prospects for the utility of these markers for istiophorids in general.