Download or read book Sequence Characterization of a Toll like Receptor TLR in Atlantic Salmon Salmo Salar from Expressed Sequence Tag EST Database written by Eszter Podor and published by . This book was released on 2003 with total page 62 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Identification and Annotation of Full length Genes in Atlantic Salmon Salmo Salar written by Jong S. Leong and published by . This book was released on 2010 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Large-scale expressed sequence tags (ESTs) in Atlantic salmon (Salmo salar) are examined to answer questions regarding salmonid transcriptomes. ESTs represent raw and incomplete gene sequences that need to be read, assembled and analyzed with computer software. The goal of this thesis was to develop an automatically curated and publicly accessible set of annotated full-length genes, representing a near-complete transcript set for Salmo salar. In turn, these genes provide the framework for studies in gene expression, conservation, and molecular evolution. The work presented here also touches on the results of a molecular evolution study, as an example of how full-length gene identification can be used to answer biological questions. Previous to this study, a limited number of Atlantic salmon cDNA libraries and ESTs were known. To further the goal of determining complete gene sequences, highly enriched full-length cDNA libraries and full-length libraries were created and sequenced, resulting in the ability to identify a large number of full-length reference genes. Together, all libraries represent a diverse pool of transcriptome sequences for Salmo salar. The goal of producing an accurate large-scale full-length gene set on a duplicated genome is not trivial. Complete systems for this objective do not readily exist. EST sequencing, EST assembly, and data storage, are just a few of the initial computational issues that are addressed. Once these issues are resolved, the multi-step workflow of full-length gene determination is described. The final challenge involving the development of a concise and universally accessible system for visualization is discussed. The resulting computational framework that has been developed is shown to be able to handle the intricacies and the size of a duplicated salmonid genome. It has been largely accepted that Atlantic salmon have undergone a recent genome duplication. Gene paralogs provide one source of evidence for this event. Analysis of paralogs revealed signatures of asymmetric evolution possibly due to relaxation of selective pressure. This thesis provides a complete Bioinformatics analysis pipeline to analyze and to visualize a set of full-length reference genes for Atlantic salmon. Using full-length genes as a framework, the topic of molecular evolution was addressed to show evidence of asymmetrical evolution among gene duplicates. The full-length reference genes, along with ESTs and all putative transcripts, have been made publicly available. These results serve as a valuable genomic resource for next-generation sequencing and for all other salmonid research endeavours.
Download or read book Isolation and Characterization of Atlantic Salmon Salmo Salar Olfactory Receptor Genes written by Jill Elizabeth Thorpe and published by . This book was released on 2000 with total page 94 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Cloning and Expression Analysis of Atlantic Salmon Salmo Salar CYP1A written by Christopher Benjamin Rees and published by . This book was released on 2001 with total page 134 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Identification and Annotation of Full length Genes in Atlantic Salmon Salmo Salar written by Jong S. Leong and published by . This book was released on 2010 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: Large-scale expressed sequence tags (ESTs) in Atlantic salmon (Salmo salar) are examined to answer questions regarding salmonid transcriptomes. ESTs represent raw and incomplete gene sequences that need to be read, assembled and analyzed with computer software. The goal of this thesis was to develop an automatically curated and publicly accessible set of annotated full-length genes, representing a near-complete transcript set for Salmo salar. In turn, these genes provide the framework for studies in gene expression, conservation, and molecular evolution. The work presented here also touches on the results of a molecular evolution study, as an example of how full-length gene identification can be used to answer biological questions. Previous to this study, a limited number of Atlantic salmon cDNA libraries and ESTs were known. To further the goal of determining complete gene sequences, highly enriched full-length cDNA libraries and full-length libraries were created and sequenced, resulting in the ability to identify a large number of full-length reference genes. Together, all libraries represent a diverse pool of transcriptome sequences for Salmo salar. The goal of producing an accurate large-scale full-length gene set on a duplicated genome is not trivial. Complete systems for this objective do not readily exist. EST sequencing, EST assembly, and data storage, are just a few of the initial computational issues that are addressed. Once these issues are resolved, the multi-step workflow of full-length gene determination is described. The final challenge involving the development of a concise and universally accessible system for visualization is discussed. The resulting computational framework that has been developed is shown to be able to handle the intricacies and the size of a duplicated salmonid genome. It has been largely accepted that Atlantic salmon have undergone a recent genome duplication. Gene paralogs provide one source of evidence for this event. Analysis of paralogs revealed signatures of asymmetric evolution possibly due to relaxation of selective pressure. This thesis provides a complete Bioinformatics analysis pipeline to analyze and to visualize a set of full-length reference genes for Atlantic salmon. Using full-length genes as a framework, the topic of molecular evolution was addressed to show evidence of asymmetrical evolution among gene duplicates. The full-length reference genes, along with ESTs and all putative transcripts, have been made publicly available. These results serve as a valuable genomic resource for next-generation sequencing and for all other salmonid research endeavours.
Download or read book Identification and Characterisation of Toll like Receptors TLRs and the TLR Accessory Molecule UNC93B1 in Atlantic Salmon Salmo Salar written by and published by . This book was released on 2015 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: The sub-cellular localization was also investigated in TLR-GFP expression plasmid transfected Salmon Head Kidney-1 (SHK-1) cells. Lastly, attempts were made to develop a Human Embryonic Kidney (HEK) 293T cell line based platform to study TLR signalling and ligand specificity (Chapter 4).
Download or read book Isolation Characterization and Genetic Analysis of Simple Sequence Length Polymorhism in Atlantic Salmon Salmo Salar written by Audun Slettan and published by . This book was released on 1995 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Genetic Mapping in Atlantic Salmon Salmo Salar and Brown Trout Salmo Trutta written by Colin McGowan and published by . This book was released on 1996 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Characterization of Repetitive DNA Elements in the Genome of Atlantic Salmon Salmo Salar written by John L. Goodier and published by . This book was released on 1994 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Identification Evolution and Expression of the Trace Amine Associated Receptor TAAR Gene Family in Atlantic Salmon Salmo Salar written by Jordan Anthony Tessarolo and published by . This book was released on 2014 with total page 95 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is widely hypothesized that Atlantic salmon are imprinted at a young age with olfactory cues, which they use as a guide in order to return to their natal streams to spawn. However, the molecular mechanism(s) behind this biological phenomenon remain unknown. Therefore, in order to better understand imprinting and homing in Atlantic salmon, it is important to characterize the repertoire of olfactory receptors in thisspecies. A search of the first assembly of the Atlantic salmon genome revealed 27 putatively functional trace amine-associated receptor (TAAR) genes and 25 putative TAAR pseudo-genes. Genetic mapping, phylogenetic analysis, binding-site prediction, and quantitative PCR were performed using the Atlantic salmon TAAR genes. The identification of this gene family in Atlantic salmon will facilitate additional studiesinvolving olfaction and homing such as determining the range of allelic variation in olfactory receptors genes of different salmon populations.
Download or read book Comparative Linkage Analysis of North American and European Atlantic Salmon Salmo Salar and Detection of Quantitative Trait Loci for Body Weight and Condition Factor written by Darrin P. Reid and published by . This book was released on 2003 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Fate of Duplicated Regions of the Atlantic Salmon Salmo Salar Genome microform written by Leslie Mitchell and published by Library and Archives Canada = Bibliothèque et Archives Canada. This book was released on 2004 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene and genome duplications have played a major role in vertebrate evolution. Salmonids provide a useful resource for studying the consequences of these events as their common ancestor underwent a genome duplication between 25 and 120 miliion years ago. To understand how a genome reorganizes itself to cope with duplicated chromosomes and the importance of gene duplications for evolution and adaptation, homeologous regions of the Atlantic salmon genome were identified and studied within a large insert, genomic BAC library; these BACs contain the metallothionen event. A BAC from each region was subsequently shotgun subcloned and sequenced. Sequence analysis revealed the presence of 10 genes, retaining their collinearity between the BAcs, although pseudogenization events have occurred in one of the duplicate loci in two instances. Comparative genomic analysis revealed the existence of extraordinary conservation of syntney over time.
Download or read book DNA Sequencing and Analysis of an Olfactory specific Gene Cloned from the Olfactory System of Atlantic Salmon Salmo Salar written by Joan M. Lloyd and published by . This book was released on 2001 with total page 422 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Identification Evolution and Expression of Three Olfactory Gene Families in Atlantic Salmon Salmo Salar written by Kimberley Anne Johnstone and published by . This book was released on 2011 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: It has been hypothesized that salmonids use olfactory cues to return to their natal rivers and streams. However, the key components of the molecular pathway involved in imprinting and homing are still unknown. If odorants are involved in salmon homing migration then olfactory receptors should play a critical role in the dissipation of information from the environment to the fish. To understand the molecular basis for imprinting and homing in Atlantic salmon (Salmo salar), it is important to identify and characterize the olfactory receptors in the Atlantic salmon genome. Aquatic chemical cues are received through the salmon nares and into the nasal cavity that contains a single olfactory organ, olfactory rosette. The olfactory rosette contains sensory neurons, which are thought to express only one olfactory receptor. In this study, three major superfamilies of fish olfactory receptors (MOR, ora and OlfC) were examined. To identify the olfactory genes in Atlantic salmon several genomic and bioinformatic techniques were used. First, an Atlantic salmon bacterial artificial chromosome (BAC) library was screened with probes designed from previously identified fish olfactory receptor sequences. Then a selected number of hybridization positive BACs containing olfactory receptors were shotgun cloned and sequenced. From these BAC sequences, two ora genes and 55 OlfC genes were identified in Atlantic salmon. The second technique used to identify olfactory receptors in Atlantic salmon was a bioinformatic approach that involved screening a 3-fold Atlantic salmon genome sequence for olfactory receptors. Using this approach, 24 MOR and the remaining five ora genes were identified, as well as another 24 partial genes or pseudogenes. As a first step to understand how olfactory receptors are involved in imprinting and homing, a suite of olfactory receptors were selected to examine the expression profiles of these genes across different life stages and life histories of wild Atlantic salmon from Newfoundland, Canada. Seven differentially expressed OlfC genes were identified in juvenile anadromous salmon compared to returning adult salmon. From this research, I hypothesize that OlfC genes may play an important role in the imprinting of home stream water olfactory cues in anadromous Atlantic salmon.
Download or read book Identification and Characterization of Toll like Receptor TLR 2 and 4 Mutations in Colorectal written by Homa Davoodi and published by . This book was released on 2009 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Toll-like receptor (TLRs) are the most important receptors in innate immunity that have been identified as a major class of pattern-recognition receptors. The TLR family comprises at least eleven members, these TLRs recognize a limited but highly conserved set of molecular structures, so called pathogen-associated molecular patterns (PAMPs). For example, TLR4 recognizes LPS, which is unique to gram-negative bacteria. Increasing evidence suggest that the ability of certain individuals to respond properly to TLR ligands may be impaired by single nucleotide polymorphisms (SNPs) within TLR genes. The role of TLRs signaling and effect of SNPs mutations on cancer outcome and survival is not exactly determined yet. The objectives of this study were firstly to detect the two most common TLR2 (Arg677Trp, Arg753Gln) and TLR4 SNPs (Asp299Gly, Thr3991lle) in colorectal cancer (CRC) secondly to evaluate the TLR2 and 4 expressions in colorectal cancer cell lines and the effect of polymorphisms on the TLR4 expression. The cytokine profiles secreted by colorectal cancer cells with mutany and non-mutant TLR4 and the expression of some signal transduction molecules involved in TLR4 signalling were also determined. Lastly, the impact of these SNPs on the cytotoxicity and apoptosis induction of the 5-Fluorouracil (5-FU) was also evaluated. PCR-RFLP was carried out on fifty normal blood samples and sixty human colorectal cancer paraffin-embedded blocks to determine the incidence of TLR2 and TLR4 mutations. The results showed two individuals were heterozygous for the Asp299Gly (D299G) and Thr399IIe (T3991) polymorphisms in the TLR4 gene. However, all samples in control group were the wild-type form. Since we could not find any TLR2 mutations in our samples, our study focused on the TLR4 gene. In Vitro studies were performed on HCT116 cell line transfected with mutant and wild-type TLR4 genotype. A series of experiments were conducted to examine the effect of TLR4 variations on the expression of TLR4 , LPS responsiveness and the response of the cells to the 5-FU as a chemotherapeutic agent. FACS analysis of TLR4 expression on transfected HCT116 cells showed that the expression of wild-type was higher than mutant TLR4. LPS induced TLR4 expression on transfected cells and the response of wild-type genotype to the LPS was more significant compared to the mutants. Western blot analysis and Dual Luciferase assay showed that the activity of pNF-kB was higher in cells transfected with plasmid for TLR4 D299G compared to the other cells. However, the activity of pAKT, pERK1 and pIRAK was higher in wild-type. The results of cytokine measurements showed that IL-8 levels were increased in wild-type and basal VEGF was high in un-transfected cells. Secreted VEGF levels was decreased by LPS in wild-type cells but increased in un-transfected cells. IL-17 was secreted by transfected cells at a low level and was not significantly affected by LPS. The results of MTT assay showed that the cytotoxicity effect of 5-Fu an tranfected cells expressing D299G TLR4 mutant was lower compared to the other cells. 5-Fu increased TLR4 expression on transfected cells and LPS has a synergistic effect with 5-FU. LPS increased the apoptosis induced by 5-FU and suggesting that it may be useful as an adjuvant in chemotherapy. HMGBI, an endogenous ligand for TLR4, was secreted by 5-FU-treated cells and also detected in cell lysate. TLR4 is functionally active on transfected HT116 cell line. The increased activity of pNF-kB in cells transfected with plasmid expressing TLR4 D299G may lead to decreased-cytotoxicity effect of 5-FU in this variant. Therefore, it is possible that the CRC patients who harbor this polymorphism tend to be more resistant to drug compared to the wild-type. High level of pNF-kB can also explain the association of this polymorphism with Inflammatory Bowel Disease (IBD) susceptibility to infectious disease and even cancer.
Download or read book Toll Like Receptors written by Claire E. McCoy and published by Humana Press. This book was released on 2011-01-26 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In addition to their invaluable role in the fight against infection, Toll-Like Receptors (TLRs) in an under- or over-active state can lead to the pathogenesis of disease, making these receptors a key focal point for many research laboratories. In Toll-Like Receptors: Methods and Protocols, experts in the field contribute techniques currently used to study TLRs, their downstream signalling pathways, and their role in the pathogenesis of disease, with sections examining TLR expression and the application of genetic techniques and microarray analysis to TLR research. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include brief introductions to the topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and Notes sections highlighting tips on troubleshooting and avoiding known pitfalls. Versatile and cutting-edge, Toll-Like Receptors: Methods and Protocols provides an ideal manual for a wide range of biologists and medical researchers studying these vital components of the immune system.
Download or read book Repetitive Landscape of the Atlantic Salmon Genome written by Siemon Hian Siem Ng and published by . This book was released on 2006 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The duplication of genes and genomes is considered a major force in evolution. Ohno, in 1970, theorized that with two copies of the genome, one copy would be under normal evolutionary constraints while the other copy could serve as raw material for evolution. Salmonids are a classical example of species containing duplicated genomes, and they offer an opportunity to investigate how such genomes undergo reorganization as they attain a stable diploid state. Repetitive elements play an important role in genome reorganization. Therefore, I investigated the repeat structure and organization of the Atlantic salmon genome. An analysis of the fingerprinted CHORI-214 BACs classified the singletons, or those that contained few restriction sites, into three categories of repetitive structures. The first group contains histone genes in a tandemly repeating cluster of H4 - H2B - H1 - H2A - H3. A second group contains the ribosomal DNA (rDNA) cistron. Intriguingly, fluorescent in situ hybridization (FISH) analysis indicated that one of each of the duplicated histone and rDNA clusters was lost or rearranged in the genome. The remaining group of BACs contains novel repetitive sequences and tRNA clusters. The Atlantic salmon EST libraries and BAC-end sequences were data-mined for simple sequence repeats (SSRs) and 2,497 SSRs were recovered. 154 SSR loci gave clean PCR amplicons and 94 produced polymorphic banding patterns with eleven of the EST-SSRs indicating duplicated loci. These loci were mapped on the Atlantic salmon linkage map. Novel repetitive elements were detected in the sequences of Atlantic salmon BACs and ESTs. Using computational tools for data-mining, repetitive elements were identified and classified based on sequence similarity to other known repetitive elements such as SINES, LINEs and retrotransposons. A repeat database that can be used to mask repetitive elements, is now available for the Atlantic salmon genome. A website was developed to host the Atlantic salmon linkage and physical maps, correlating them based on marker hybridization. A BAC annotation pipeline analyzes the BAC sequences for ORFs, transcript similarity and repetitive elements. Information generated from sequence annotation, microsatellite development and repetitive element identification provides essential resources for investigating salmonid genomes.
