Life Sciences Commons^™

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 …

Fanconi Anemia Protein Fancd2 Inhibits Trf1 Polyadp-Ribosylation Through Tankyrase1-Dependent Manner, Alex Lyakhovich, Maria Ramirez, Andres Castella, Amanda Simons, Jeffrey Parvin, Jordi Suralles

Amanda Simons

Background: Fanconi anemia (FA) is a rare autosomal recessive syndrome characterized by developmental abnormalities, progressive bone marrow failure, and predisposition to cancer. The key FA protein FANCD2 crosstalks with members of DNA damage and repair pathways that also play a role at telomeres. Therefore, we investigated whether FANCD2 has a similar involvement at telomeres. Results: We reveal that FANCD2 may perform a novel function separate to the FANCD2/BRCA pathway. This function includes FANCD2 interaction with one of the telomere components, the PARP family member tankyrase-1. Moreover, FANCD2 inhibits tankyrase-1 activity in vitro. In turn, FANCD2 deficiency increases the polyADPribosylation of …

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 …

Identification Of Genetic Risk Associated With Prostate Cancer Using Ancestry Informative Markers, Bradford Wilson

Bradford Wilson

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

Amy L. Russell

Pre-Settlement History May Obscure The Effect Of Forest Fragmentation On Genetic Variation In Eastern Red-Backed Salamanders, Mark Jordan, Douglas Morris, Scott Gibson

Mark A. Jordan

No abstract provided.

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

Inhibition Of Herpes Simplex Virus Type 1 With The Modified Green Tea Polyphenol Pamitoyl-Epigallocatechin Gallate., Aline De Oliveira, Sandra Adams, Lee Lee, Sean Murray, Stephen Hsu, Jeffrey Hammond, Douglas Dickinson, Ping Chen, Tin-Chun Chu

Tin-Chun Chu, Ph.D.

No abstract provided.

Epigallocatechin-3-Gallate Modulates Oxidative Stress In Exocrine Glands Of A Primary Sjogren’S Syndrome Mouse Model Prior To Disease Onset, Seiji Ohno, Hongfang Yu, Douglas Dickinson, Tin-Chun Chu, Kalu Ogbureke, Scott Derossi, Tetsuya Yamamoto, Stephen Hsu

Tin-Chun Chu, Ph.D.

No abstract provided.

The Molecular Basis Of Drug Resistance Against Hepatitis C Virus Ns3/4a Protease Inhibitors, Keith Romano, Akbar Ali, Cihan Aydin, Djade Soumana, Aysegul Ozen, Laura Deveau, Casey Silver, Hong Cao, Alicia Newton, Christos Petropoulos, Wei Huang, Celia Schiffer

Celia A. Schiffer

Hepatitis C virus (HCV) infects over 170 million people worldwide and is the leading cause of chronic liver diseases, including cirrhosis, liver failure, and liver cancer. Available antiviral therapies cause severe side effects and are effective only for a subset of patients, though treatment outcomes have recently been improved by the combination therapy now including boceprevir and telaprevir, which inhibit the viral NS3/4A protease. Despite extensive efforts to develop more potent next-generation protease inhibitors, however, the long-term efficacy of this drug class is challenged by the rapid emergence of resistance. Single-site mutations at protease residues R155, A156 and D168 confer …

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 …

Microbial Sunscreens: Opportunities And Obstacles, Tanya Soule

Tanya Soule

No abstract provided.

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.

Long-Term Correction Of Very Long-Chain Acyl-Coa Dehydrogenase Deficiency In Mice Using Aav9 Gene Therapy, Allison Keeler, Thomas Conlon, Glenn Walter, Huadong Zeng, Scott Shaffer, Fu Dungtao, Kirsten Erger, Travis Cossette, Qiushi Tang, Christian Mueller, Terence Flotte

Christian Mueller

Very long-chain acyl-coA dehydrogenase (VLCAD) is the rate-limiting step in mitochondrial fatty acid oxidation. VLCAD-deficient mice and patients clinical symptoms stem from not only an energy deficiency but also long-chain metabolite accumulations. VLCAD-deficient mice were treated systemically with 1 x 10(12) vector genomes of recombinant adeno-associated virus 9 (rAAV9)-VLCAD. Biochemical correction was observed in vector-treated mice beginning 2 weeks postinjection, as characterized by a significant drop in long-chain fatty acyl accumulates in whole blood after an overnight fast. Changes persisted through the termination point around 20 weeks postinjection. Magnetic resonance spectroscopy (MRS) and tandem mass spectrometry (MS/MS) revealed normalization of …

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 …

Use Of Highly Polymorphic Dna Probes For Genotypic Analysis Following Bone Marrow Transplantation, Robert Knowlton, Valerie Brown, Jeffrey Braman, David Barker, James Schumm, Christine Murray, Tak Takvorian, Jerome Ritz, Helen Donis-Keller

Helen Donis-Keller

The use of DNA markers known as restriction fragment length polymorphisms is a sensitive and informative method of distinguishing patient and allogeneic donor cells after bone marrow transplantation. To apply the test, it is necessary in each case to find DNA probes that display patient-specific and donor-specific bands in Southern transfer hybridization. We have isolated a set of 12 cloned DNAs from highly polymorphic loci by which siblings can usually be distinguished. With just four of these probes, we can expect to distinguish the genotypes of the recipient and a sibling donor in more than 99% of cases (except between …

Mutations In The Ret Proto-Oncogene Are Associated With Men 2a And Fmtc, Helen Donis-Keller, Shenshen Dou, David Chi, Katrin Carlson, Koi Toshima, Terry Lairmore, James Howe, Jeffrey Moley, Paul Goodfellow, Samuel Wells

Helen Donis-Keller

Multiple endocrine neoplasia type 2A (MEN 2A) and familial medullary thyroid carcinoma (FMTC) are dominantly inherited conditions which predispose to the development of endocrine neoplasia. Evidence is presented that sequence changes within the coding region of the RET proto-oncogene, a putative transmembrane tyrosine kinase, may be responsible for the development of neoplasia in these inherited disorders. Single strand conformational variants (SSCVs) in exons 7 and 8 of the RET proto-oncogene were identified in eight MEN 2A and four FMTC families. The variants were observed only in the DNA of individuals who were either affected or who had inherited the MEN2A …

Single Missense Mutation In The Tyrosine Kinase Catalytic Domain Of The Ret Protooncogene Is Associated With Multiple Endocrine Neoplasia Type 2b., Katrin Carlson, Shenshen Dou, David Chi, N. Scavarda, Koi Toshima, C. Jackson, Samuel Wells, Paul Goodfellow, Helen Donis-Keller

Helen Donis-Keller

Multiple endocrine neoplasia type 2B (MEN 2B) is a human cancer syndrome characterized by medullary thyroid carcinoma (MTC), pheochromocytomas, mucosal neuromas, ganglioneuromas of the intestinal tract, and skeletal and ophthalmic abnormalities. It appears both as an inherited disorder and as de novo disease. Sequence analysis of germ-line DNA from MEN 2B patients revealed the existence of the same point mutation in the RET protooncogene in 34 unrelated individuals. This sequence difference was not observed in 93 unaffected individuals, including the normal parents of 14 de novo MEN 2B patients. The mutation (ATG-->ACG) results in the replacement of methionine with …

A Genetic Linkage Map Of The Human Genome, Helen Donis-Keller, Philip Green, Cynthia Helmes, Samuel Cartinhour, Barbara Weiffenbach, Karen Stephens, Tim Keith, Donald Bowden, Douglas Smith, Eric Lander, David Botstein, Gita Akots, Kenneth Rediker, Thomas Gravius, Valerie Brown, Marcia Rising, Carol Parker, Jody Powers, Diane Watt, Erick Kauffman, Angela Bricker, Pamela Phipps, Hans Muller-Kahle, Thomas Fulton, Siu Ng, James Schumm, Jeffrey Braman, Robert Knowlton, David Barker, Steven Crooks, Steven Lincoln, Mark Daly, Jeff Abrahamson

Helen Donis-Keller

We report the construction of a linkage map of the human genome, based on the pattern of inheritance of 403 polymorphic loci, including 393 RFLPs, in a panel of DNAs from 21 three-generation families. By a combination of mathematical linkage analysis and physical localization of selected clones, it was possible to arrange these loci into linkage groups representing 23 human chromosomes. We estimate that the linkage map is detectably linked to at least 95% of the DNA in the human genome.

Genetic Analysis Of Eight Loci Tightly Linked To Neurofibromatosis 1, Karen Stephens, Philip Green, V. Riccardi, Siu Ng, Marcia Rising, David Barker, J. Darby, K. Falls, F. Collins, H. Willard, Helen Donis-Keller

Helen Donis-Keller

The genetic locus for neurofibromatosis 1 (NF1) has recently been mapped to the pericentromeric region of chromosome 17. We have genotyped eight previously identified RFLP probes on 50 NF1 families to determine the placement of the NF1 locus relative to the RFLP loci. Thirty-eight recombination events in the pericentromeric region were identified, eight involving crossovers between NF1 and loci on either chromosomal arm. Multipoint linkage analysis resulted in the unique placement of six loci at odds greater than 100:1 in the order of pter-A10-41-EW301-NF1-EW207-CRI-L581-CRI-L946 -qter. Owing to insufficient crossovers, three loci--D17Z1, EW206, and EW203--could not be uniquely localized. In this …

A Polymorphic Dna Marker Linked To Cystic Fibrosis Is Located On Chromosome 7, Robert Knowlton, Odile Cohen-Haguenauer, Nguyen Van Cong, Jean Frézal, Valerie Brown, David Barker, Jeffrey Braman, James Schumm, Lap-Chee Tsui, Manuel Buchwald, Helen Donis-Keller

Helen Donis-Keller

Although cystic fibrosis (CF) is among the most common inherited diseases in Caucasian populations, the basic biochemical defect is not yet known. CF is inherited as an autosomal recessive trait apparently due to mutations in a single gene, whence the efforts made to identify the genetic locus responsible by linkage studies. Two markers have recently been identified that are genetically linked to CF: one is a genetic variation in serum level of activity of the enzyme paraoxonase, and the other is a restriction fragment length polymorphism (RFLP) identified with a randomly isolated DNA probe. We report here that the genetic …

Chromosomal Bar Codes Produced By Multicolor Fluorescence In Situ Hybridization With Multiple Yac Clones And Whole Chromosome Painting Probes, Christoph Lengauer, Michael Speicher, Susanne Popp, Anna Jauch, Masafumi Taniwaki, Ramaiah Nagaraja, Harold Riethman, Helen Donis-Keller, Michele D'Urso, David Schelssinger, Thomas Cremer

Helen Donis-Keller

Colored chromosome staining patterns, termed chromosomal ‘bar codes’ (CBCs), were obtained on human chromosomes by fluorescence in situhybridization (FISH) with pools of Alu-PCR products from YAC dones containing human DNA inserts ranging from 100 kbp to 1 Mbp. In contrast to conventional G- or R-bands, the chromosomal position, extent, Individual color and relative signal intensity of each ‘bar’ could be modified depending on probe selection and labeling procedures. Alu-PCR amplification products were generated from 31 YAC clones which mapped to 37 different chromosome bands. For multiple color FISH, Alu-PCR amplification products from various clones were either biotinylated or labeled …

Predictive Dna Testing And Prophylactic Thyroidectomy In Patients At Risk For Multiple Endocrine Neoplasia Type 2a, Samuel Wells, David Chi, Koi Toshima, Louis Dehner, Cheryl Coffin, S. Dowton, Jennifer Ivanovich, Mary Debenedettl, William Dilley, Jeffrey Moley, Jeffrey Norton, Helen Donis-Keller

Helen Donis-Keller

Background: Missense germ-line mutations in the RET protooncogene are associated with multiple endocrine neoplasia type 2A (MEN 2A). Detection of these mutant alleles in kindred members predicts disease inheritance and provides the basis for preventative thyroidectomy. Methods: A polymerase chain reaction (PCR)-based genetic test for the 19 known RET mutations was designed to study 132 members of 7 kindreds with MEN 2A. Haplotypes also were constructed using genetic markers flanking the MEN 2A locus. Plasma calcitonin (CT) concentrations were determined before and after provocative testing. Results: Direct DNA testing and haplotype analysis showed that 21 of 58 kindred members at …