Swabs to Genomes: a Comprehensive Workflow
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Genome Signature-Based Dissection of Human Gut Metagenomes to Extract Subliminal Viral Sequences
ARTICLE Received 16 Apr 2013 | Accepted 8 Aug 2013 | Published 16 Sep 2013 DOI: 10.1038/ncomms3420 OPEN Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences Lesley A. Ogilvie1, Lucas D. Bowler1, Jonathan Caplin2, Cinzia Dedi1, David Diston2,w, Elizabeth Cheek3, Huw Taylor2, James E. Ebdon2 & Brian V. Jones1 Bacterial viruses (bacteriophages) have a key role in shaping the development and functional outputs of host microbiomes. Although metagenomic approaches have greatly expanded our understanding of the prokaryotic virosphere, additional tools are required for the phage- oriented dissection of metagenomic data sets, and host-range affiliation of recovered sequences. Here we demonstrate the application of a genome signature-based approach to interrogate conventional whole-community metagenomes and access subliminal, phylogen- etically targeted, phage sequences present within. We describe a portion of the biological dark matter extant in the human gut virome, and bring to light a population of potentially gut- specific Bacteroidales-like phage, poorly represented in existing virus like particle-derived viral metagenomes. These predominantly temperate phage were shown to encode functions of direct relevance to human health in the form of antibiotic resistance genes, and provided evidence for the existence of putative ‘viral-enterotypes’ among this fraction of the human gut virome. 1 Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK. 2 School of Environment and Technology, University of Brighton, Brighton BN2 4GJ, UK. 3 School of Computing, Engineering and Mathematics, University of Brighton, Brighton BN2 4GJ, UK. w Present address: Mikrobiologische and Biotechnologische Risiken Bundesamt fu¨r Gesundheit BAG, 3003 Bern, Switzerland. -
The Contribution of Mitochondrial Metagenomics to Large-Scale Data
Molecular Phylogenetics and Evolution 128 (2018) 1–11 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera T ⁎ Benjamin Linarda,i,j, , Alex Crampton-Platta,b,k, Jerome Morinierec, Martijn J.T.N. Timmermansa,d, Carmelo Andújara,b,l, Paula Arribasa,b,l, Kirsten E. Millera,b,m, Julia Lipeckia,n, Emeline Favreaua,o, Amie Huntera, Carola Gómez-Rodrígueze, Christopher Bartona,p, Ruie Niea,f, Conrad P.D.T. Gilletta,q, Thijmen Breeschotena,g,r, Ladislav Bocakh, Alfried P. Voglera,b a Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom b Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot SL5 7PY, United Kingdom c Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstrasse 21, 81247 München, Germany d Department of Natural Sciences, Hendon Campus, Middlesex University, London NW4 4BT, United Kingdom e Departamento de Zoología, Facultad de Biología, Universidad de Santiago de Compostela, c/ Lope Gómez de Marzoa s/n, 15782 Santiago de Compostela, Spain f Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China g Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands h Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic i LIRMM, Univ. Montpellier, -
Genome 559 Intro to Statistical and Computational Genomics
Genome 559! Intro to Statistical and Computational Genomics! Lecture 16a: Computational Gene Prediction Larry Ruzzo Today: Finding protein-coding genes coding sequence statistics prokaryotes mammals More on classes More practice Codons & The Genetic Code Ala : Alanine Second Base Arg : Arginine U C A G Asn : Asparagine Phe Ser Tyr Cys U Asp : Aspartic acid Phe Ser Tyr Cys C Cys : Cysteine U Leu Ser Stop Stop A Gln : Glutamine Leu Ser Stop Trp G Glu : Glutamic acid Leu Pro His Arg U Gly : Glycine Leu Pro His Arg C His : Histidine C Leu Pro Gln Arg A Ile : Isoleucine Leu Pro Gln Arg G Leu : Leucine Ile Thr Asn Ser U Lys : Lysine Ile Thr Asn Ser C Met : Methionine First Base A Third Base Ile Thr Lys Arg A Phe : Phenylalanine Met/Start Thr Lys Arg G Pro : Proline Val Ala Asp Gly U Ser : Serine Val Ala Asp Gly C Thr : Threonine G Val Ala Glu Gly A Trp : Tryptophane Val Ala Glu Gly G Tyr : Tyrosine Val : Valine Idea #1: Find Long ORF’s Reading frame: which of the 3 possible sequences of triples does the ribosome read? Open Reading Frame: No stop codons In random DNA average ORF = 64/3 = 21 triplets 300bp ORF once per 36kbp per strand But average protein ~ 1000bp So, coding DNA is not random–stops are rare Scanning for ORFs 1 2 3 U U A A U G U G U C A U U G A U U A A G! A A U U A C A C A G U A A C U A A U A C! 4 5 6 Idea #2: Codon Frequency,… Even between stops, coding DNA is not random In random DNA, Leu : Ala : Tryp = 6 : 4 : 1 But in real protein, ratios ~ 6.9 : 6.5 : 1 Even more: synonym usage is biased (in a species dependant way) Examples known with 90% AT 3rd base Why? E.g. -
Ijphs Jan Feb 07.Pmd
www.ijpsonline.com Review Article Pharmacogenomics and Computational Genomics: An Appraisal P. K. TRIPATHI*, SHALINI TRIPATHI AND N. K. JAIN1 Rajarshi Rananjay Sinh College of Pharmacy, Amethi-227 405, 1Department of Pharmaceutical Sciences, Dr. H. S. Gour Vishwavidyalaya, Sagar-470 003, India. Pharmacogenomics deals with the interactions of individual genetic constitution with drug therapy. It is very likely that pharmacogenetic tests will make up a significant proportion of total molecular biology testing in future. Therefore, this article emphasizes the applications of pharmacogenomics, and computational genome analysis in drug therapy. Patients sometimes experience adverse drug reactions for both efficacy and safety of a given drug regimen and (ADR) leading to deterioration of their underlying this is the central topic of pharmacogenomics. Drug condition in clinical practice. Physiology of individual development and pretreatment genetic analysis of patients patient can vary, so the response of an individual to drug will be two major practical aspects in pharmacogenomics. therapy may also be highly variable. This is a major Highly specialized drug research laboratories will achieve clinical problem, since this inter-individual variability is the first goal, while the second goal has to be achieved until now only partly predictable. Besides these medical by clinical .com).laboratories 2,3. problems, cost-benefit calculations for a given pharmacological therapy will be affected significantly. Drug development: This is exemplified by a recent US study, which estimates There are two pharmacogenomic approaches. First, for that over 100,000 patients die every year from ADRs1. most therapies a correct diagnosis is mandatory for a satisfactory therapeutic result. This is more relevant There are many factors such as age, sex, nutritional.medknow because many diseases may be caused by different status, kidney and liver function, concomitant diseases and genetic defects or be significantly affected by the genetic medications, and the disease that affects drug responses. -
Genome-Contric Metagenomic Investigation of 134 Samples
GENOME-CONTRIC METAGENOMIC INVESTIGATION OF 134 SAMPLES COLLECTED FROM BIOGAS REACTORS REVEALED IMPORTANT FUNCTIONAL ROLES FOR MICROBIAL SPECIES BELONGING TO UNDEREXPLORED TAXA Campanaro, S.1, Luo, G.2, Treu, L.3 Kougias, P.G.4, Zhu X.3, Angelidaki, I.3 1 University of Padova, Department of Biology, Via U. Bassi, 58b, 35131 Padova (PD), Italy 2 Fudan University, Department of Environmental Science and Engineering, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), 200433, Shanghai, China 3 Technical University of Denmark, Department of Environmental Engineering, Kgs. Lyngby DK-2800, Denmark 4 Institute of Animal Science, Hellenic Agricultural Organization DEMETER, Paralimni, Greece e-mail of the corresponding author: [email protected] Keywords: anaerobic digestion; metagenomics; metagenome-assembled genomes; taxonomy. INTRODUCTION In the past four years many samples collected from full-scale biogas plants and lab-scale reactors have been investigated using Illumina shotgun sequencing approaches and deposited in NCBI Sequence Read Archive database. In all these reactors, the Anaerobic Digestion (AD) process is performed by a plethora of different microorganisms organized in a complex functional network where different species have distinct roles in degradation of organic matter. Difficulties associated to cultivation of many prokaryotes present in natural and engineered ecosystems strongly limits the possibility to expand our knowledge regarding their physiology, genetics and function (Tringe and Rubin, 2005). Thanks to the bioinformatics approaches recently developed, which allow the reconstruction of microbial genomes starting from shotgun DNA sequences obtained from mixed cultures (Campanaro et al., 2016), it is now becoming possible to reveal the functional roles of microbial species resisting cultivation in axenic cultures. -
Computational Genomics and Genetics of Developmental Disorders
Computational genomics and genetics of developmental disorders Hongjian Qi Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2018 © 2018 Hongjian Qi All Rights Reserved ABSTRACT Computational genomics and genetics of developmental disorders Hongjian Qi Computational genomics is at the intersection of computational applied physics, math, statistics, computer science and biology. With the advances in sequencing technology, large amounts of comprehensive genomic data are generated every year. However, the nature of genomic data is messy, complex and unstructured; it becomes extremely challenging to explore, analyze and understand the data based on traditional methods. The needs to develop new quantitative methods to analyze large-scale genomics datasets are urgent. By collecting, processing and organizing clean genomics datasets and using these datasets to extract insights and relevant information, we are able to develop novel methods and strategies to address specific genetics questions using the tools of applied mathematics, statistics, and human genetics. This thesis describes genetic and bioinformatics studies focused on utilizing and developing state-of-the-art computational methods and strategies in order to identify and interpret de novo mutations that are likely causing developmental disorders. We performed whole exome sequencing as well as whole genome sequencing on congenital diaphragmatic hernia parents-child trios and identified a new candidate risk gene MYRF. Additionally, we found male and female patients carry a different burden of likely-gene-disrupting mutations, and isolated and complex patients carry different gene expression levels in early development of diaphragm tissues for likely-gene-disrupting mutations. -
Bioinformatics Approach to Probe Protein-Protein Interactions
Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2013 Bioinformatics Approach to Probe Protein-Protein Interactions: Understanding the Role of Interfacial Solvent in the Binding Sites of Protein-Protein Complexes;Network Based Predictions and Analysis of Human Proteins that Play Critical Roles in HIV Pathogenesis. Mesay Habtemariam Virginia Commonwealth University Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Bioinformatics Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/2997 This Thesis is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. ©Mesay A. Habtemariam 2013 All Rights Reserved Bioinformatics Approach to Probe Protein-Protein Interactions: Understanding the Role of Interfacial Solvent in the Binding Sites of Protein-Protein Complexes; Network Based Predictions and Analysis of Human Proteins that Play Critical Roles in HIV Pathogenesis. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University. By Mesay Habtemariam B.Sc. Arbaminch University, Arbaminch, Ethiopia 2005 Advisors: Glen Eugene Kellogg, Ph.D. Associate Professor, Department of Medicinal Chemistry & Institute For Structural Biology And Drug Discovery Danail Bonchev, Ph.D., D.SC. Professor, Department of Mathematics and Applied Mathematics, Director of Research in Bioinformatics, Networks and Pathways at the School of Life Sciences Center for the Study of Biological Complexity. Virginia Commonwealth University Richmond, Virginia May 2013 ኃይልን በሚሰጠኝ በክርስቶስ ሁሉን እችላለሁ:: ፊልጵስዩስ 4:13 I can do all this through God who gives me strength. -
Molecular Complexity of Successive Bacterial Epidemics Deconvoluted by Comparative Pathogenomics
Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics Stephen B. Beresa,b, Ronan K. Carrolla,b, Patrick R. Sheaa,b, Izabela Sitkiewicza,b, Juan Carlos Martinez-Gutierreza,b, Donald E. Lowc, Allison McGeerd, Barbara M. Willeyd, Karen Greend, Gregory J. Tyrrelld, Thomas D. Goldmanf, Michael Feldgardeng, Bruce W. Birreng, Yuriy Fofanovh, John Boosi, William D. Wheatoni, Christiane Honischf, and James M. Mussera,b,1 aCenter for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and bDepartment of Pathology, The Methodist Hospital, Houston, TX 77030; cOntario Agency for Health Protection and Promotion, and University of Toronto, Toronto, ON M5G 1X5, Canada; dDepartment of Microbiology, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; eDepartment of Laboratory medicine and Pathology, University of Alberta, Edmonton, AB T6G 2J2, Canada; fSequenom, Inc., San Diego, CA 92121; gBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142; hDepartment of Computer Science and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204; and iRTI International, Research Triangle Park, NC 27709 Edited* by Charles R. Cantor, Sequenom Inc., San Diego, CA, and approved December 14, 2009 (received for review September 30, 2009) Understanding the fine-structure molecular architecture of bacterial century that GAS has the capacity to cause epidemics charac- epidemics has been a long-sought goal of infectious disease research. terized by rapid increase in disease frequency and severity. For We used short-read-length DNA sequencing coupled with mass example, Weech (6) described an epidemic of septic scarlet fever spectroscopy analysis of SNPs to study the molecular pathogenomics in Yunnanfu, China, that killed 50,000 people, fully 25% of the of three successive epidemics of invasive infections involving 344 population of the province. -
View: Latest Perspectives on Antiinflammatory Actions of Glucocorticoids
Fleuren et al. BioData Mining 2013, 6:2 http://www.biodatamining.org/content/6/1/2 BioData Mining RESEARCH Open Access Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining Wilco WM Fleuren1,2, Erik JM Toonen3, Stefan Verhoeven4, Raoul Frijters1,6, Tim Hulsen1,7, Ton Rullmann5, René van Schaik4, Jacob de Vlieg1,4 and Wynand Alkema1,8* * Correspondence: [email protected] Abstract 1Computational Drug Discovery (CDD), CMBI, NCMLS, Radboud Background: Glucocorticoids are potent anti-inflammatory agents used for the University Nijmegen Medical Centre, treatment of diseases such as rheumatoid arthritis, asthma, inflammatory bowel P.O. Box 91016500 HB, Nijmegen, disease and psoriasis. Unfortunately, usage is limited because of metabolic side- The Netherlands 8Present address: NIZO Food effects, e.g. insulin resistance, glucose intolerance and diabetes. To gain more insight Research BV, Ede, The Netherlands into the mechanisms behind glucocorticoid induced insulin resistance, it is important Full list of author information is to understand which genes play a role in the development of insulin resistance and available at the end of the article which genes are affected by glucocorticoids. Medline abstracts contain many studies about insulin resistance and the molecular effects of glucocorticoids and thus are a good resource to study these effects. Results: We developed CoPubGene a method to automatically identify gene-disease associations in Medline abstracts. We used this method to create a literature network of genes related to insulin resistance and to evaluate the importance of the genes in this network for glucocorticoid induced metabolic side effects and anti-inflammatory processes. -
Computational Genomics
Computational Genomics MSCBIO 2070 microRNAs: deux ou trois choses que je sais d'elle Takis Benos Department of Computational & Systems Biology February 29, 2016 Reading: handouts & papers miRNA genes: a couple of things we know about them l Size • 60-80bp pre-miRNA • 20-24 nucleotides mature miRNA l Role: translation regulation, cancer diagnosis l Location: intergenic or intronic l Regulation: pol II (mostly) l They were discovered as part of RNAi gene silencing studies © 2013-2016 Benos - Univ Pittsburgh 2 microRNA mechanisms of action l Translational inhibition in l Cap-40S initiation l 60S Ribosomal unit joining l Protein elongation l Premature ribosome drop off l Co-translational protein degradation • mRNA and protein degradation l mRNA cleavage and decay l Protein degradation l Sequestration in P-bodies l Transcriptional inhibition l (through chromatin reorganization) © 2013-2016 Benos - Univ Pittsburgh 3 What is RNA interference (RNAi) ? l RNAi is a cellular process by which the expression of genes is regulated at the mRNA level l RNAi appeared under different names, until people realized it was the same process: l Co-supression l Post-transcriptional gene silencing (PTGS) l Quelling © 2013-2016 Benos - Univ Pittsburgh 4 Timeline for RNAi Dicsoveries © 2013-2016 Benos - Univ Pittsburgh 5 Nature Biotechnology 21, 1441 - 1446 (2003) From petunias to worms l In the early 90’s scientists tried to darken petunia’s color by overexpressing the chalcone synthetase gene. l The result: Suppressed action of chalcone synthetase l In 1995, Guo and Kemphues used anti-sense RNA to C. elegans par-1 gene to show they have cloned the correct gene. -
Computational Genomics Spring 2020 Syllabus
BIOSC 1542 (2204) – Computational Genomics Spring 2020 Syllabus INSTRUCTOR Dr. Miler T. Lee Office: A518 Langley Hall E-mail: [email protected] Phone: (412) 624-9186 Office Hour: TBD CLASS TIME MW 3:15-4:30 pm, A214 Langley Hall COURSE BIOSC 1542 will explore the use of computer-aided methods to generate and test OBJECTIVE biological hypotheses at whole-genome scales. Students will gain both a theoretical and practical understanding of working with genomic data, with a focus on high-throughput sequencing technologies. Students will read primary literature highlighting modern computational techniques and apply what they learn to a real-world research project. COURSE LOAD BIOSC 1542 is a 3 credit course, which is defined as 2.5 hours of classroom time and an average of 5 hours of outside study per week. PREREQUISITES Students are expected to have passed both BIOSC 1540 Computational Biology and CS 0011 Introduction to Computing for Scientists with a C or better grade. Familiarity with or willingness to learn fundamental molecular biology, mathematical, statistical, and computer science concepts will also be assumed. If in doubt, please consult with the instructor after referring to the prerequisite topic list distributed in class on the first day. COURSE We will be using CourseWeb, courseweb.pitt.edu/, to access course materials and to WEBSITE provide a Discussion Board to facilitate communication with your peers. If you need help with CourseWeb, contact the computer help desk at (412) 624-HELP. COURSE There is no required textbook for this course. The pace of computational biology MATERIALS research tends to rapidly render textbooks obsolete. -
Ubin – a Manual Refining Tool for Metagenomic Bins Designed for Educational 2 Purposes 3 4 Till L.V
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.15.204776; this version posted July 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 uBin – a manual refining tool for metagenomic bins designed for educational 2 purposes 3 4 Till L.V. Bornemann1, Sarah P. Esser1, Tom L. Stach1, Tim Burg2, and Alexander J. Probst1 5 6 1: Institute for Environmental Microbiology and Biotechnology, Department of Chemistry, 7 University Duisburg-Essen, Germany 8 2: Tim Burg, Im Acker 59, 56072 Koblenz, Germany 9 10 To whom the correspondence should be addressed: 11 [email protected] 12 13 Abstract 14 15 Resolving bacterial and archaeal genomes from metagenomes has revolutionized our 16 understanding of Earth’s biomes, yet producing high quality genomes from assembled 17 fragments has been an ever-standing problem. While automated binning software and their 18 combination produce prokaryotic bins in high-throughput, their manual refinement has been 19 slow and sometimes difficult. Here, we present uBin, a GUI-based, standalone bin refiner that 20 runs on all major operating platforms and was specifically designed for educational purposes. 21 When applied to the public CAMI dataset, refinement of bins was able to improve 78.9% of 22 bins by decreasing their contamination. We also applied the bin refiner as a standalone binner 23 to public metagenomes from the International Space Station and demonstrate the recovery of 24 near-complete genomes, whose replication indices indicate active proliferation of microbes in 25 Earth’s lower orbit.