A Zebrafish Reporter Line Reveals Immune and Neuronal Expression of Endogenous Retrovirus
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Fosmid Library End Sequencing Reveals a Rarely Known Genome Structure of Marine Shrimp Penaeus Monodon
eScholarship Title Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon Permalink https://escholarship.org/uc/item/126680ch Journal BMC Genomics, 12(1) ISSN 1471-2164 Authors Huang, Shiao-Wei Lin, You-Yu You, En-Min et al. Publication Date 2011-05-17 DOI http://dx.doi.org/10.1186/1471-2164-12-242 Supplemental Material https://escholarship.org/uc/item/126680ch#supplemental Peer reviewed eScholarship.org Powered by the California Digital Library University of California Huang et al. BMC Genomics 2011, 12:242 http://www.biomedcentral.com/1471-2164/12/242 RESEARCHARTICLE Open Access Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon Shiao-Wei Huang1, You-Yu Lin1, En-Min You1, Tze-Tze Liu2, Hung-Yu Shu2, Keh-Ming Wu3, Shih-Feng Tsai3, Chu-Fang Lo1, Guang-Hsiung Kou1, Gwo-Chin Ma4, Ming Chen1,4,5, Dongying Wu6,7, Takashi Aoki8, Ikuo Hirono8 and Hon-Tsen Yu1* Abstract Background: The black tiger shrimp (Penaeus monodon) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses. -
Numerous Uncharacterized and Highly Divergent Microbes Which Colonize Humans Are Revealed by Circulating Cell-Free DNA
Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA Mark Kowarskya, Joan Camunas-Solerb, Michael Kerteszb,1, Iwijn De Vlaminckb, Winston Kohb, Wenying Panb, Lance Martinb, Norma F. Neffb,c, Jennifer Okamotob,c, Ronald J. Wongd, Sandhya Kharbandae, Yasser El-Sayedf, Yair Blumenfeldf, David K. Stevensond, Gary M. Shawd, Nathan D. Wolfeg,h, and Stephen R. Quakeb,c,i,2 aDepartment of Physics, Stanford University, Stanford, CA 94305; bDepartment of Bioengineering, Stanford University, Stanford, CA 94305; cChan Zuckerberg Biohub, San Francisco, CA 94158; dDepartment of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305; ePediatric Stem Cell Transplantation, Lucille Packard Children’s Hospital, Stanford University, Stanford, CA 94305; fDivision of Maternal–Fetal Medicine, Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305; gMetabiota, San Francisco, CA 94104; hGlobal Viral, San Francisco, CA 94104; and iDepartment of Applied Physics, Stanford University, Stanford, CA 94305 Contributed by Stephen R. Quake, July 12, 2017 (sent for review April 28, 2017; reviewed by Søren Brunak and Eran Segal) Blood circulates throughout the human body and contains mole- the body (18, 19); combining this observation with the average cules drawn from virtually every tissue, including the microbes and genome sizes of a human, bacterium, and virus (Gb, Mb, and viruses which colonize the body. Through massive shotgun sequenc- kb, respectively) suggests that approximately 1% of DNA by ing of circulating cell-free DNA from the blood, we identified mass in a human is derived from nonhost origins. Previous hundreds of new bacteria and viruses which represent previously studies by us and others have shown that indeed approximately unidentified members of the human microbiome. -
A Field Guide to Eukaryotic Transposable Elements
GE54CH23_Feschotte ARjats.cls September 12, 2020 7:34 Annual Review of Genetics A Field Guide to Eukaryotic Transposable Elements Jonathan N. Wells and Cédric Feschotte Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850; email: [email protected], [email protected] Annu. Rev. Genet. 2020. 54:23.1–23.23 Keywords The Annual Review of Genetics is online at transposons, retrotransposons, transposition mechanisms, transposable genet.annualreviews.org element origins, genome evolution https://doi.org/10.1146/annurev-genet-040620- 022145 Abstract Annu. Rev. Genet. 2020.54. Downloaded from www.annualreviews.org Access provided by Cornell University on 09/26/20. For personal use only. Copyright © 2020 by Annual Reviews. Transposable elements (TEs) are mobile DNA sequences that propagate All rights reserved within genomes. Through diverse invasion strategies, TEs have come to oc- cupy a substantial fraction of nearly all eukaryotic genomes, and they rep- resent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic be- havior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species. 23.1 Review in Advance first posted on , September 21, 2020. -
A Multiscale Tool to Explore Genomic Conservation
SynVisio: A Multiscale Tool to Explore Genomic Conservation A Thesis Submitted to the College of Graduate and Postdoctoral Studies in Partial Fulfillment of the Requirements for the degree of Master of Science in the Department of Computer Science University of Saskatchewan Saskatoon By Venkat Kiran Bandi ©Venkat Kiran Bandi, May/2020. All rights reserved. Permission to Use In presenting this thesis in partial fulfilment of the requirements for a Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis. Requests for permission to copy or to make other use of material in this thesis in whole or part should be addressed to: Head of the Department of Computer Science 176 Thorvaldson Building 110 Science Place University of Saskatchewan Saskatoon, Saskatchewan Canada S7N 5C9 Or Dean College of Graduate and Postdoctoral Studies University of Saskatchewan 116 Thorvaldson Building, 110 Science Place Saskatoon, Saskatchewan S7N 5C9 Canada i Abstract Comparative analysis of genomes is an important area in biological research that can shed light on an organism's internal functions and evolutionary history. -
Evolution and Function of Drososphila Melanogaster Cis-Regulatory Sequences
Evolution and Function of Drososphila melanogaster cis-regulatory Sequences By Aaron Hardin A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Molecular and Cell Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Michael Eisen, Chair Professor Doris Bachtrog Professor Gary Karpen Professor Lior Pachter Fall 2013 Evolution and Function of Drososphila melanogaster cis-regulatory Sequences This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License 2013 by Aaron Hardin 1 Abstract Evolution and Function of Drososphila melanogaster cis-regulatory Sequences by Aaron Hardin Doctor of Philosophy in Molecular and Cell Biology University of California, Berkeley Professor Michael Eisen, Chair In this work, I describe my doctoral work studying the regulation of transcription with both computational and experimental methods on the natural genetic variation in a population. This works integrates an investigation of the consequences of polymorphisms at three stages of gene regulation in the developing fly embryo: the diversity at cis-regulatory modules, the integration of transcription factor binding into changes in chromatin state and the effects of these inputs on the final phenotype of embryonic gene expression. i I dedicate this dissertation to Mela Hardin who has been here for me at all times, even when we were apart. ii Contents List of Figures iv List of Tables vi Acknowledgments vii 1 Introduction1 2 Within Species Diversity in cis-Regulatory Modules6 2.1 Introduction....................................6 2.2 Results.......................................8 2.2.1 Genome wide diversity in transcription factor binding sites......8 2.2.2 Genome wide purifying selection on cis-regulatory modules......9 2.3 Discussion.....................................9 2.4 Methods for finding polymorphisms...................... -
A Burst of Protein Sequence Evolution and a Prolonged Period of Asymmetric Evolution Follow Gene Duplication in Yeast
Downloaded from genome.cshlp.org on October 3, 2021 - Published by Cold Spring Harbor Laboratory Press Letter A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast Devin R. Scannell1,2 and Kenneth H. Wolfe Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland It is widely accepted that newly arisen duplicate gene pairs experience an altered selective regime that is often manifested as an increase in the rate of protein sequence evolution. Many details about the nature of the rate acceleration remain unknown, however, including its typical magnitude and duration, and whether it applies to both gene copies or just one. We provide initial answers to these questions by comparing the rate of protein sequence evolution among eight yeast species, between a large set of duplicate gene pairs that were created by a whole-genome duplication (WGD) and a set of genes that were returned to single-copy after this event. Importantly, we use a new method that takes into account the tendency for slowly evolving genes to be retained preferentially in duplicate. We show that, on average, proteins encoded by duplicate gene pairs evolved at least three times faster immediately after the WGD than single-copy genes to which they behave identically in non-WGD lineages. Although the high rate in duplicated genes subsequently declined rapidly, it has not yet returned to the typical rate for single-copy genes. In addition, we show that although duplicate gene pairs often have highly asymmetric rates of evolution, even the slower members of pairs show evidence of a burst of protein sequence evolution immediately after duplication. -
A Phd Position Is Available in the Research Group of Aoife Mclysaght
A PhD position is available in the research group of Aoife McLysaght in Trinity College Dublin to work on comparative genomics of vertebrates with a focus on understanding dosage sensitive genes in terms of evolution and disease. The execution of the project will involve bioinformatics and computer programming as well as statistical analysis of data. For examples of the kinds of things we work on, look up our papers on PubMed: https://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=mclysaght+a[au]&dispmax=50 Applicants should be in the final year of, or hold, a bachelor's degree in molecular biology with an interest and aptitude for programming and bioinformatics; or vice versa (computer science bachelor's with an interest in molecular biology). Interest and enthusiasm for molecular evolution is essential. Students will be expected to be self-motivated and creative and to work closely with other members of the team. This is a four-year position and comes with a tax-free stipend of 18000euro and covers fees up to EU level (non-EU students may apply, but fees are only covered up to EU rates). TCD is Ireland’s top ranked University and a member of the League of European Research Universities (LERU). The McLysaght lab is funded by a European Research Council (ERC) Starting Grant. Lab: http://www.gen.tcd.ie/molevol/ Applications including a cover letter, CV, summary of scientific interests and reasons for being interested in our research group, and contact details for two referees should be made to [email protected]. -
Copycontrol™ Fosmid Autoinduction Solution
CopyControl™ Fosmid Autoinduction Solution Cat. No. AIS107F Available exclusively thru Lucigen. lucigen.com/epibio www.lucigen.com MA263E CopyControl™ Fosmid Autoinduction Solution • 12/2016 1 MA263E CopyControl™ Fosmid Autoinduction Solution 1. Introduction The CopyControl™ Fosmid Autoinduction Solution is designed to induce CopyControl Fosmid clones and clones retrofitted with the EZ-Tn5™ <oriV/KAN-2> Transposon, grown in TransforMax™ EPI300™ E. coli cells, from single-copy number to a higher-copy number of approximately 50 fosmids per cell. The Fosmid Autoinduction Solution induces expression of a mutant trfA gene contained in the TransforMax EPI300 cells. Expression of trfA gene results in initiation of replication from the oriV high copy origin of replication and subsequent amplification of the CopyControl clones to high copy number. The Fosmid Autoinduction protocol improves upon the existing induction protocol by including the autoinduction supplement in the media prior to culture inoculation, removing the need for time-consuming subculturing and the 2-hour incubation required in the standard induction protocol. The Fosmid Autoinduction Solution also contains cell growth enhancers which boost cell numbers and typically provides higher DNA yields than with the standard CopyControl induction protocol. The hands-off autoinduction protocol makes CopyControl Fosmid Autoinduction solution ideal for high-throughput purification protocols in 96-well format. The autoinduction solution is also compatible with larger scale DNA purifications and can be scaled according to the amount of media used. 2. Product Specifications Storage: Store only at –20°C in a freezer without a defrost cycle. Mix thoroughly after thawing. Size and Formulation: CopyControl Fosmid Autoinduction Solution is available in a 50-ml size concentrate of 500X in sterile water. -
Protocol for Epifos™ Fosmid Library Production
EpiFOS™ Fosmid Library Production Kit Cat. No. FOS0901 Connect with Epicentre on our blog (epicentral.blogspot.com), Facebook (facebook.com/EpicentreBio), and Twitter (@EpicentreBio). www.epicentre.com Lit. # 149 • 8/2012 1 EPILIT149 Rev. A EpiFOS™ Fosmid Library Production Kit 1. Overview of the EpiFOS Fosmid Library Production Process Fosmid vectors1-3 provide an improved method for cloning and the stable maintenance of cosmid-sized (35-45 kb) libraries in E. coli. The stability of such large constructs in vivo is facilitated by the pEpiFOS™-5 vector that maintains the clones at single copy in the cell. The EpiFOS Fosmid Library Production Kit will produce a complete and unbiased primary fosmid library. The kit utilizes a novel strategy of cloning randomly sheared, end-repaired DNA. Shearing the DNA leads to the generation of highly random DNA fragments in contrast to more biased libraries that result from fragmenting the DNA by partial restriction digests. The steps involved (protocols for steps 2-7 are included in this manual): 1. Purify DNA from the desired source (the kit does not supply materials for this step). 2. Shear the DNA to approximately 40-kb fragments. 3. End-repair the sheared DNA to blunt, 5′-phosphorylated ends. 4. Size-resolve the end-repaired DNA by Low Melting Point (LMP) agarose gel electrophoresis. 5. Purify the blunt-end DNA from the LMP agarose gel. 6. Ligate the blunt-end DNA to the Cloning-Ready pEpiFOS-5 vector. 7. Package the ligated DNA and plate on EPI100™-T1R Plating Strain. Grow clones overnight. pEpiFOS-5 is a 7518 bp. -
Identification of an Unusual Glycosyltransferase from a Non
Identification of an unusual glycosyltransferase from a non-cultivated microorganism and the construction of an improved Escherichia coli strain harboring the rpoD gene from Clostridium cellulolyticum for metagenome searches Dissertation Zur Erlangung der Würde des Doktors der Naturwissenschaften des Fachbereichs Biologie, der Fakultät für Mathematik, Informatik und Naturwissenschaften, der Universität Hamburg vorgelegt von Julia Jürgensen aus Henstedt-Ulzburg Hamburg 2015 Table of contents I Table of contents 1 Introduction ...................................................................................................... 1 1.1 Flavonoids................................................................................................... 1 1.2 Glycosyltransferases ................................................................................... 3 1.3 Biotechnology ............................................................................................. 4 1.3.1 Biotechnological relevance of glycosyltranferases....................................... 5 1.4 Metagenomics ............................................................................................. 5 1.5 Transcription ............................................................................................... 7 1.6 Phyla ........................................................................................................... 8 1.6.1 Proteobacteria ............................................................................................. 8 1.6.2 Firmicutes .................................................................................................. -
Variation in Proviral Content Among Human Genomes Mediated by LTR Recombination Jainy Thomas1* , Hervé Perron2,3 and Cédric Feschotte4*
Thomas et al. Mobile DNA (2018) 9:36 https://doi.org/10.1186/s13100-018-0142-3 RESEARCH Open Access Variation in proviral content among human genomes mediated by LTR recombination Jainy Thomas1* , Hervé Perron2,3 and Cédric Feschotte4* Abstract Background: Human endogenous retroviruses (HERVs) occupy a substantial fraction of the genome and impact cellular function with both beneficial and deleterious consequences. The vast majority of HERV sequences descend from ancient retroviral families no longer capable of infection or genomic propagation. In fact, most are no longer represented by full-length proviruses but by solitary long terminal repeats (solo LTRs) that arose via non-allelic recombination events between the two LTRs of a proviral insertion. Because LTR-LTR recombination events may occur long after proviral insertion but are challenging to detect in resequencing data, we hypothesize that this mechanism is a source of genomic variation in the human population that remains vastly underestimated. Results: We developed a computational pipeline specifically designed to capture dimorphic proviral/solo HERV allelic variants from short-read genome sequencing data. When applied to 279 individuals sequenced as part of the Simons Genome Diversity Project, the pipeline retrieves most of the dimorphic loci previously reported for the HERV-K(HML2) subfamily as well as dozens of additional candidates, including members of the HERV-H and HERV-W families previously involved in human development and disease. We experimentally validate several of these newly discovered dimorphisms, including the first reported instance of an unfixed HERV-W provirus and an HERV-H locus driving a transcript (ESRG) implicated in the maintenance of embryonic stem cell pluripotency. -
3 Main Classification of Vectors (With Diagram)
4/20/2020 3 Main Classification of Vectors (With Diagram) Privacy Policy | Join our Community :- Upload Now 3 Main Classification of Vectors (With Diagram) Article shared by : The classifications are: 1. On the Basis of Our Aim with Gene of Interest 2. On the Basis of Host Cell Used 3. On the Basis of Cellular Nature of Host Cell. Vector Classification # 1. On the Basis of Our Aim with Gene of Interest: The point is what we are targeting from our gene of interest — its multiple copies or its protein product. Depending on these criteria vec tors are of following two types: 1. Cloning Vectors: We use a cloning vec tor when our aim is to just obtain numer ous copies (clones) of our gene of interest (hence the name cloning vectors). These are mostly used in construction of gene libraries. A number of organisms can be used as sources for cloning vectors. Some are created synthetically, as in the case of yeast artificial chromosomes and bacte rial artificial chromosomes, while others are taken from bacteria and bacteriopha ges. In all cases, the vector needs to be genetically modified in order to accommo date the foreign DNA by creating an in sertion site where the new DNA will fit ted. Example: PUC cloning vectors, pBR322 cloning vectors, etc. 2. Expression Vectors or Expression construct: www.biotechnologynotes.com/recombinant-dna-technology/3-main-classification-of-vectors-with-diagram/395 1/64 4/20/2020 3 Main Classification of Vectors (With Diagram) We use an expression vector when our aim is to obtain the protein prod uct of our gene of interest.