Genetics and Genomics Commons^™

Piscine Myocarditis Virus (Pmcv) In Wild Atlantic Salmon Salmo Salar, Torstein Tengs Dr.

Dr. Torstein Tengs

Cardiomyopathy syndrome (CMS) is a severe cardiac disease of sea-farmed Atlantic salmon Salmo salar L., but CMS-like lesions have also been found in wild Atlantic salmon. In 2010 a double-stranded RNA virus of the Totiviridae family, provisionally named piscine myocarditis virus (PMCV), was described as the causative agent of CMS. In the present paper we report the first detection of PMCV in wild Atlantic salmon. The study is based on screening of 797 wild Atlantic salmon by real-time RT-PCR. The samples were collected from 35 different rivers along the coast of Norway, and all individuals included in the study were …

An Integrated Genetic Linkage Map For Silkworms With Three Parental Combinations And Its Application To The Mapping Of Single Genes And Qtl, Shuai Zhan, Jianhua Huang, Qiuhong Guo, Yunpo Zhao, Weihua Li, Xuexia Miao, Marian R. Goldsmith, Muwang Li, Yongping Huang

Marian R Goldsmith

Background: Bombyx mori, the domesticated silkworm, is a well-studied model insect with great economic and scientific significance. Although more than 400 mutations have been described in silkworms, most have not been identified, especially those affecting economically-important traits. Simple sequence repeats (SSRs) are effective and economical tools for mapping traits and genetic improvement. The current SSR linkage map is of low density and contains few polymorphisms. The purpose of this work was to develop a dense and informative linkage map that would assist in the preliminary mapping and dissection of quantitative trait loci (QTL) in a variety of silkworm strains. Results: …

Construction And Sequence Sampling Of Deep-Coverage Large-Insect Bac Libraries For Three Model Lepidopteran Species, Chengcang Wu, Dina Proestou, Dorothy Carter, Erica Nicholson, Filippe Santos, Shaying Zhao, Hong-Bin Zhang, Marian R. Goldsmith

Marian R Goldsmith

Background: Manduca sexta, Heliothis virescens, and Heliconius erato represent three widely-used insect model species for genomic and fundamental studies in Lepidoptera. Large-insert BAC libraries of these insects are critical resources for many molecular studies, including physical mapping and genome sequencing, but not available to date. Results: We report the construction and characterization of six large-insert BAC libraries for the three species and sampling sequence analysis of the genomes. The six BAC libraries were constructed with two restriction enzymes, two libraries for each species, and each has an average clone insert size ranging from 152–175 kb. We estimated that the genome …

A Bac-Based Integrated Linkage Map Of The Silkworm Bombyx Mori, Kimiko Yamamoto, Junko Nohata, Keiko Kadono-Okuda, Junko Narukawa, Motoe Sasanuma, Shun-Ichi Sasanuma, Hiroshi Minami, Michihiko Shimomura, Yoshitaka Suetsugu, Yutaka Banno, Kazutoyo Osoegawa, Pieter J. De Jong, Marian R. Goldsmith, Kazuei Mita

Marian R Goldsmith

Background: In 2004, draft sequences of the model lepidopteran Bombyx mori were reported using whole-genome shotgun sequencing. Because of relatively shallow genome coverage, the silkworm genome remains fragmented, hampering annotation and comparative genome studies. For a more complete genome analysis, we developed extended scaffolds combining physical maps with improved genetic maps. Results: We mapped 1,755 single nucleotide polymorphism (SNP) markers from bacterial artificial chromosome (BAC) end sequences onto 28 linkage groups using a recombining male backcross population, yielding an average inter-SNP distance of 0.81 cM (about 270 kilobases). We constructed 6,221 contigs by fingerprinting clones from three BAC libraries digested …

Extensive Conserved Synteny Of Genes Between The Karyotypes Of Manduca Sexta And Bombyx Mori Revealed By Bac-Fish Mapping, Yuji Yasukochi, Makiko Tanaka-Okuyama, Fukashi Shibata, Atsuo Yoshido, Frantisek Marec, Chengcang Wu, Hongbin Zhang, Marian R. Goldsmith, Ken Sahara

Marian R Goldsmith

Background: Genome sequencing projects have been completed for several species representing four highly diverged holometabolous insect orders, Diptera, Hymenoptera, Coleoptera, and Lepidoptera. The striking evolutionary diversity of insects argues a need for efficient methods to apply genome information from such models to genetically uncharacterized species. Constructing conserved synteny maps plays a crucial role in this task. Here, we demonstrate the use of fluorescence in situ hybridization with bacterial artificial chromosome probes as a powerful tool for physical mapping of genes and comparative genome analysis in Lepidoptera, which have numerous and morphologically uniform holokinetic chromosomes. Methodology/Principal Findings: We isolated 214 clones …

Kaikobase: An Integrated Silkworm Genome Database And Data Mining Tool, Michihiko Shimomura, Hiroshi Minami, Yoshitaka Suetsugu, Hajime Ohyanagi, Chikatada Satoh, Baltazar Antonio, Yoshiaki Nagamura, Keiko Kadono-Okuda, Hideyuki Kajiwara, Hideki Sezutsu, Javaregowda Nagaraju, Marian R. Goldsmith, Qingyou Xia, Kimiko Yamamoto, Kazuei Mita

Marian R Goldsmith

Background: The silkworm, Bombyx mori, is one of the most economically important insects in many developing countries owing to its large-scale cultivation for silk production. With the development of genomic and biotechnological tools, B. mori has also become an important bioreactor for production of various recombinant proteins of biomedical interest. In 2004, two genome sequencing projects for B. mori were reported independently by Chinese and Japanese teams; however, the datasets were insufficient for building long genomic scaffolds which are essential for unambiguous annotation of the genome. Now, both the datasets have been merged and assembled through a joint collaboration between …

Evolution Of Repetitive Proteins: Spider Silks From Nephila Clavipes (Tetragnathidae) And Araneus Bicentenarius (Araneidae), Richard D. Beckwitt, Steven Arcidiacono, Robert Stote

Richard D Beckwitt

Spider silks are highly repetitive proteins, characterized by regions of polyalanine and glycine-rich repeating units. We have obtained two variants of the Spidroin 1 (NCF-1) silk gene sequence from Nephila clavipes. One sequence (1726 bp) was from a cloned cDNA, and the other (1951 bp) was from PCR of genomic DNA. When these sequences are compared with each other and the previously published Spidroin 1 sequence, there are differences due to sequence rearrangements, as well as single base substitutions. These variations are similar to those that have been reported from other highly repetitive genes, and probably represent the results …

أمراض الأطفال المزمنة, Suad Fahad Alferaih

Dr. Suad Fahad AlFuraih

No abstract provided.

Genetic Determinants Of Cerebral Edema In Severe Traumatic Brain Injury: A Pilot Study Of The Role Of Cacna1 And Aqp4 Gene Mutations, Raphael A. Carandang, Susanne Muehlschlegel, Wiley R. Hall, Cynthia Ouillette, Robert H. Brown Jr.

Dr Robert Brown

Cerebral edema is the one of the most significant predictors of poor outcome after traumatic brain injury. It is still unclear what the pathophysiological and cellular mechanisms and predictors of post-traumatic edema are. The exponential growth in genetic information has opened an avenue for investigation in traumatic brain injury and implicated specific genes in the pathophysiology of post-traumatic injury edema. Two examples are the Aquaporin-4 and CACNA1 genes, which respectively encode water and calcium channels. The Aquaporin-4 gene on chromosome 18q11.2-12.1 encodes the Aquaporin-4 protein (AQP4) water channel. AQP4 is one of the bidirectional high capacity water channels that is …

Molecular Surveillance Of Low Pathogenic Avianinfluenza Viruses In Wild Birds Across The United States:Inferences From The Hemagglutinin Gene, Antoinette J. Piaggio, Susan A. Shriner, Kaci Van Dalen, Alan B. Franklin, Theodore D. Anderson, Sergios-Orestis Kolokotronis

Alan B Franklin

A United States interagency avian influenza surveillance plan was initiated in 2006 for early detection of highly pathogenic avian influenza viruses (HPAIV) in wild birds. The plan included a variety of wild bird sampling strategies including the testing of fecal samples from aquatic areas throughout the United States from April 2006 through December 2007. Although HPAIV was not detected through this surveillance effort we were able to obtain 759 fecal samples that were positive for low pathogenic avian influenza virus (LPAIV). We used 136 DNA sequences obtained from these samples along with samples from a public influenza sequence database for …

Deglaciation Explains Bat Extinction In The Caribbean, Liliana M. Davalos, Amy L. Russell

Amy L. Russell

Two Different High Throughput Sequencing Approaches Identify Thousands Of De Novo Genomic Markers For The Genetically Depleted Bornean Elephant., Reeta Sharma, Benoit Goossens, Benoit Goossens, Célia Kun-Rodrigues, Tatiana Teixeira, Nurzhafarina Othman, Nurzhafarina Othman, Jason Q. Boone, Nathaniel K. Jue, Craig Obergfell, Rachel J. O'Neill, Lounès Chikhi, Lounès Chikhi, Lounès Chikhi

Nathaniel Jue

Democracia E Biotecnologia: Argumentos Para A Construção De Um Discurso Pautado Na Agência Humana Como Vetor Transformador Da Realidade, Carolina Altoé Velasco

Carolina Altoé Velasco

O artigo objetiva demonstrar que os processos biotecnológico e democrático têm em comum a interferência da agência humana como vetor transformador de suas realidades. Utiliza-se como marco teórico-metodológico as obras de Guillermo O’Donnell e Adela Cortina. Guillermo O’Donnell reconhece o impacto motivado pela tecnologia e globalização na sociedade e a agência humana como fomentadora do processo democrático. Já Adela Cortina considera a pessoa (contemplada por sujeito autônomo e solidário) a medida da democracia e esta como forma de vida. A eleição de Cortina para travar um diálogo com o pensamento de O’Donnell se dá em razão da abordagem feita a …

Increased Microrna-155 Expression In The Serum And Peripheral Monocytes In Chronic Hcv Infection, Shashi Bala, Yaphet Tilahun, Odette Taha, Hawau Alao, Karen Kodys, Donna Catalano, Gyongyi Szabo

Gyongyi Szabo

BACKGROUND: Hepatitis C Virus (HCV), a single stranded RNA virus, affects millions of people worldwide and leads to chronic infection characterized by chronic inflammation in the liver and in peripheral immune cells. Chronic liver inflammation leads to progressive liver damage. MicroRNAs (miRNA) regulate inflammation (miR-155, -146a and -125b) as well as hepatocyte function (miR-122). METHODS: Here we hypothesized that microRNAs are dysregulated in chronic HCV infection. We examined miRNAs in the circulation and in peripheral monocytes of patients with chronic HCV infection to evaluate if specific miRNA expression correlated with HCV infection. RESULTS: We found that monocytes from chronic HCV …

Regulatory Elements Of Xenopus Col2a1 Drive Cartilaginous Gene Expression In Transgenic Frogs, Ryan R. Kerney, Brian K. Hall, James Hanken

Ryan Kerney

This study characterizes regulatory elements of collagen 2α1 (col2a1) in Xenopus that enable transgene expression in cartilage-forming chondrocytes. The reporters described in this study drive strong cartilage-specific gene expression, which will be a valuable tool for further investigations of Xenopus skeletal development. While endogenous col2a1 mRNA is expressed in many embryonic tissues, its expression becomes restricted to tadpole and adult chondrocytes. This chondrocyte-specific expression is recapitulated by col2a1 reporter constructs, which were tested through I-SceI meganuclease-mediated transgenesis. These constructs contain a portion of the Xenopus tropicalis col2a1 intron, which aligns to a cartilage-specific intronic enhancer that has been well characterized …

Cryptococcal Genotype Influences Immunologic Response And Human Clinical Outcome After Meningitis, Darin L. Wiesner, Oleksandr Moskalenko, Jennifer M. Corcoran, Tami Mcdonald, Melissa A. Rolfes, David B. Meya, Henry Kajumbula, Andrew Kambugu, Paul R. Bohjanen, Joseph F. Knight, David R. Boulware, Kirsten Nielsen

Tami McDonald

No abstract provided.

Directional Selection Causes Decanalization In A Group I Ribozyme, Eric J. Hayden, Christian Weikert, Andreas Wagner

Eric J. Hayden

A canalized genotype is robust to environmental or genetic perturbations. Canalization is expected to result from stabilizing selection on a well-adapted phenotype. Decanalization, the loss of robustness, might follow periods of directional selection toward a new optimum. The evolutionary forces causing decanalization are still unknown, in part because it is difficult to determine the fitness effects of mutations in populations of organisms with complex genotypes and phenotypes. Here, we report direct experimental measurements of robustness in a system with a simple genotype and phenotype, the catalytic activity of an RNA enzyme. We find that the robustness of a population of …

Prevalence Of Tick Borne Encephalitis Virus In Tick Nymphs In Relation To Climatic Factors On The Southern Coast Of Norway, Torstein Tengs Dr.

Dr. Torstein Tengs

BACKGROUND

Tick-borne encephalitis (TBE) is among the most important vector borne diseases of humans in Europe and is currently identified as a major health problem in many countries. TBE endemic zones have expanded over the past two decades, as well as the number of reported cases within endemic areas. Multiple factors are ascribed for the increased incidence of TBE, including climatic change. The number of TBE cases has also increased in Norway over the past decade, and the human cases cluster along the southern coast of Norway. In Norway the distribution and prevalence of TBE virus (TBEV) in tick populations …

The Role Of Epigenetics In Evolution: The Extended Synthesis, Aaron W. Schrey, Christina L. Richards, Victoria Meller, Vincent Sollars, Douglas M. Ruden

Vincent E Sollars

Evolutionary biology is currently experiencing an emergence of several research topics that transcend the boundaries of the Modern Synthesis, which was the last major conceptual integration in evolutionary biology [1]. The Modern Synthesis used the concepts of population genetics to integrate Mendelian genetics with evolution by natural selection [2]. Pigliucci [3, and citations within] identified several major areas of innovation that transcend the Modern Synthesis: epigenetics, evolvability, phenotypic plasticity, evolution on adaptive landscapes, evolutionary developmental biology, and systems biology. Integrating these new ideas with the Modern Synthesis will form a new conceptual framework of evolution, which they termed the Extended …

Disparities In Allele Frequencies And Population Differentiation For 101 Disease-Associated Single Nucleotide Polymorphisms Between Puerto Ricans And Non-Hispanic Whites, Josiemer Mattei, Laurence D. Parnell, Chao-Qiang Lai, Bibiana Garcia-Bailo, Xian Adiconis, Jian Shen, Donna Arnett, Serkalem Demissie, Katherine L. Tucker, Jose M. Ordovas

Katherine L. Tucker

Background: Variations in gene allele frequencies can contribute to differences in the prevalence of some common complex diseases among populations. Natural selection modulates the balance in allele frequencies across populations. Population differentiation (FST) can evidence environmental selection pressures. Such genetic information is limited in Puerto Ricans, the second largest Hispanic ethnic group in the US, and a group with high prevalence of chronic disease. We determined allele frequencies and population differentiation for 101 single nucleotide polymorphisms (SNPs) in 30 genes involved in major metabolic and disease-relevant pathways in Puerto Ricans (n = 969, ages 45–75 years) and compared them to …

Serum Microrna-122 And Mir-155 As Biomarkers Of Liver Injury And Inflammation In Models Of Acute And Chronic Liver Disease, Shashi Bala, Jan Petrasek, Shiv Mundkur, Donna Catalano, Jeanine Ward, Ivan Levin, Hawau Alao, Karen Kodys, Gyongyi Szabo

Gyongyi Szabo

Background: MicroRNAs (miRs) are small non-coding molecules that regulate gene expression. MiRs expression levels change not only in diseased tissues but also in circulation. Further, miRs are stable in frozen samples that make them attractive for biomarker discovery. Recent reports suggest altered expression of circulating miRNAs in various diseases. MiR-122 is highly abundant in hepatocytes where it regulates different metabolic pathways while miR-155 is a central regulator of inflammation. The aim of this study was to evaluate circulating miRNAs as potential markers of hepatocyte damage and inflammation in liver diseases. Methods: Serum/plasma and liver samples were collected from C57/BL6 mice …

A Strain Of Piscine Myocarditis Virus (Pmcv) Infecting Argentina Silus (Ascanius), Torstein Tengs Dr.

Dr. Torstein Tengs

No abstract.

"Genetics In Geographically Structured Populations: Defining, Estimating And Interpreting Fst.", Kent E. Holsinger, Bruce S. Weir

Kent E Holsinger

Wright's F-statistics, and especially F(ST), provide important insights into the evolutionary processes that influence the structure of genetic variation within and among populations, and they are among the most widely used descriptive statistics in population and evolutionary genetics. Estimates of F(ST) can identify regions of the genome that have been the target of selection, and comparisons of F(ST) from different parts of the genome can provide insights into the demographic history of populations. For these reasons and others, F(ST) has a central role in population and evolutionary genetics and has wide applications in fields that range from disease association mapping …

Codon Optimization For Alpha 1-Antitrypsin Disease, Timothy Menz, Qiushi Tang, Lina Song, Christian Mueller, Terence R. Flotte

Christian Mueller

Alpha 1-antitrypsin deficiency is a genetic disorder caused by defective production of alpha 1-antitrypsin (AAT). Gene therapy approaches have been conducted in patients with AAT deficiency with successful AAT expression, but not to the therapeutic levels required to reduce the risk of emphysema. Codon optimization, a somewhat new and evolving technique, is used by many scientists to maximize protein expression in living organisms by altering translational and transcriptional efficiency as well as protein refolding. The purpose of this study was to develop single stranded and double stranded AAT gene constructs, test their protein expression in vitro, and compare with those …

A Reference-Free Algorithm For Computational Normalization Of Shotgun Sequencing Data, C. Titus Brown, Adina Howe, Qingpeng Zhang, Alexis B. Pyrkosz, Timothy H. Brom

Adina Howe

Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and high sequencing error rates of modern sequencers present many new computational challenges in data interpretation. These challenges have led to the development of new classes of mapping tools and {\em de novo} assemblers. These algorithms are challenged by the continued improvement in sequencing throughput. We here describe digital normalization, a single-pass computational algorithm that systematizes coverage in shotgun sequencing data sets, thereby decreasing sampling variation, discarding redundant data, …

Quantification Of Piscine Reovirus (Prv) At Different Stages Of Atlantic Salmon Salmo Salar Production, Torstein Tengs Dr.

Dr. Torstein Tengs

The newly described piscine reovirus (PRV) appears to be associated with the development of heart and skeletal muscle inflammation (HSMI) in farmed Atlantic salmon Salmo salar L. PRV seems to be ubiquitous among fish in Norwegian salmon farms, but high viral loads and tissue distribution support a causal relationship between virus and disease. In order to improve understanding of the distribution of PRV in the salmon production line, we quantified PRV by using real-time PCR on heart samples collected at different points in the life cycle from pre-smolts to fish ready for slaughter. PRV positive pre-smolts were found in about …

Regression Approaches For Microarray Data Analysis, Mark R. Segal, Kam D. Dahlquist, Bruce R. Conklin

Mark R Segal

A variety of new procedures have been devised to handle the two sample comparison (e.g., tumor versus normal tissue) of gene expression values as measured with microarrays. Such new methods are required in part because of some defining characteristics of microarray-based studies: (i) the very large number of genes contributing expression measures which far exceeds the number of samples (observations) available, and (ii) the fact that by virtue of pathway/network relationships, the gene expression measures tend to be highly correlated. These concerns are exacerbated in the regression setting, where the objective is to relate gene expression, simultaneously for multiple genes, …

A Novel Topology For Representing Protein Folds, Mark R. Segal

Mark R Segal

Various topologies for representing three dimensional protein structures have been advanced for purposes ranging from prediction of folding rates to ab initio structure prediction. Examples include relative contact order, Delaunay tessellations, and backbone torsion angle distributions. Here we introduce a new topology based on a novel means for operationalizing three dimensional proximities with respect to the underlying chain. The measure involves first interpreting a rank-based representation of the nearest neighbors of each residue as a permutation, then determining how perturbed this permutation is relative to an unfolded chain. We show that the resultant topology provides improved association with folding and …

Phylogenetics Of Morus (Moraceae) Inferred From Its And Trnl-Trnf Sequence Data., Madhav Nepal

Madhav Nepal

Flatbed Scanner Report - Optical Density Dynamic Range, George Mcnamara

George McNamara

George McNamara (now at University of Miami) report for Hua Yu and Richard Jove, City of Hope National Medical Center, on optical density dynamic range of several flatbed scanners.