DOCSLIB.ORG

Proteogenomics & Metaproteomics Using The

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Proteogenomics & Metaproteomics Using The PROTEOGENOMICS & METAPROTEOMICS USING THE GALAXY PLATFORM PRATIK JAGTAP University of Minnesota St.Paul / Minneapolis Minnesota, USA MINNEAPOLIS TO HYDERABAD MINNEAPOLIS, MINNESOTA Center for Mass Spectrometry and Proteomics hp://cbs.umn.edu/cmsp/home • PROTEOMICS • PROTEOGENOMICS • CHALLENGES • BIOLOGICAL INSIGHTS • METAPROTEOMICS • GALAXYP • LINKS AND ACKNOWLEDGMENTS GENOMIC AND PROTEOMIC DATABASES Finished and Published Genomes • 3551 Bacterial Genomes. • 211 Archaeal Genomes. • 58 Eukaryal Genomes. • 3363 Viral Genomes http://www.genomesonline.org/index DEFINING PROTEOMICS : LOOKING WITHIN Mass spectrum Reference Protein Database PepEde Spectral Match from genomic annotation PROTEOMICS WORKFLOW Search Database Peaklist Generation Eng et al 2011 Mol Cell Proteomics. 10(11): R111.009522. Database Search Peptide Spectral Match : Statistical Validation Protein Inference PROTEOGENOMICS Nat Methods. 11(11): 1114–1125. DEFINING PROTEOGENOMICS: LOOKING WITHIN AND WITHOUT Mass spectrum Reference Protein Database from genomic annotation RNASeq data Genome six-frame cDNA translation three- frame translation PROTEOGENOMICS : BIOINFORMATIC CHALLENGES • Large database sizes (6-frame and 3-frame translaon and metagenomic databases). • False Discovery Rate (FDR) EsEmaEon strategies (for novel pepdes). • False-posiEve sources and their eliminaEon. • Validaon of the pepde idenficaon. (Search using BLAST-P) • PSM EvaluaEon / Targeted proteomics of idenEfied pepdes. • Genomic localizaon. • Validang biological interpretaon. • Disparate tools and numerous processing steps. PROTEOGENOMICS: STEPS INVOLVED ~ 2 million proteins ~ 10,000 proteins ~ 5,000 proteins ~ 1,000 pepEdes ~ 100 pepEdes ~ 50 pepEdes 3D FRACTIONATED SALIVARY SUPERNATANT 6 individuals Salivary supernatant Digested O/N with trypsin The dataset was searched Hexapepde library enrichment against FASTA database with (ProteoMiner ™) followed by SCX / IEF human proteins, contaminant and LC-MS (200 FracEons) proteins, 3-frame translated cDNA database from EnSEMBL Thermofinnigan Orbitrap and Human Oral Microbiome (Orbi MS, MS/MS LTQ) database (HOMD). 200 RAW Files INPUTS : PEAKLISTS and SEARCH db Bandhakavi et al (2009) J. Prot. Res PROTEOGENOMICS WORKFLOW Galaxy-P provides an integrated platform for every step of proteogenomic analysis. • Build target database – download and translate EST databases. • Numerous tools for identification and text manipulation. • Workflow utilizing BLAST to identify novel peptides. • Tool to assess peptide-spectrum matches and visualize spectra. • Visualize identified peptides on the genome. • 140 steps: Seamless, integrated proteogenomic workflow. Flexible and accessible workflows for improved proteogenomic analysis using Galaxy framework. J. Proteome Res. (2014) DOI: 10.1021/pr500812t Link: z.umn.edu/pgfirstlook NOVEL PROTEOFORMS : PRB1 and PRB2 region PROTEOGENOMICS WORKFLOW Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. J Proteome Res. (2014) 13(12):5898-908. doi: 10.1021/pr500812t HIBERNATION PROTEOGENOMICS Tracing of core body temperature (Tb, black line) from a single animal measured by a surgically implanted transmier, along with the controlled ambient temperature (blue line) over the course of the hibernaon season. * TOR (Torpor), J-IBA (January IBA), M-IBA (March IBA) HIBERNATION PROTEOGENOMICS • The datasets were run in triplicates and were searched against proteomic dataset from RNASeq data. • Differenally expressed genes from RNASeq data and differenally expressed proteins from iTRAQ data were compared. - OCT shows the highest correla1on between protein and transcript expression. • FuncEonal analysis of differenEally expressed proteins revealed that: - Protein expression in APRIL rela1ve to AUGUST shows increased mitochondrial funcon and regula1on of muscle contracon. - Protein expression in OCTOBER rela1ve to AUGUST reveals increased hypoxia tolerance and hypertrophy at a 1me of decreased metabolism. - Protein expression in hiberna1on rela1ve to AUGUST highlights faGy acid and ketone metabolism and altered calcium handling and contracle funcon in the heart. • 162 novel pepde sequences were idenfied in all three replicates. METAPROTEOMICS / COMMUNITY PROTEOMICS / MICROBIOMES “The large-scale characterizaNon of the enNre protein complement of environmental microbiota at a given point in me” Bond and Wiilmes (2004) Environ. Microbiol. 6, 911–920. “Through the applicaNon of metaproteomics to different microbial consorNa over the past decade, we have learnt much about key funcNonal traits in the various environmental seVngs where they occur.” Wilmes P, Heintz-Buschart A, Bond PL. (2015) Proteomics. doi: 10.1002/pmic.201500183. DEFINING METAPROTEOMICS : LOOKING WITHIN AND WITHOUT Mass spectrum Reference Protein Database from genomic annotation RNASeq data Genome six-frame cDNA translation three- frame translation Metagenomic sequences DEFINING METAPROTEOMICS Mass spectrum Metagenomic sequences MATCHED PAIR OF CONTROL VERSUS LESION Oral premalignant lesion (OPML) versus control The dataset was searched Digested O/N with trypsin against FASTA database with human proteins, contaminant proteins, 3- SCX FracEonaEon and and LC-MS frame translated cDNA (7 FracEons) database from EnSEMBL and Human Oral Thermofinnigan Orbitrap Microbiome database (Orbi MS, MS/MS LTQ) (HOMD). 7 RAW Files each INPUTS : PEAKLISTS and SEARCH db Kooren et al (2010) Clin. Prot TAXONOMIC AND FUNCTIONAL ANALYSIS DEFINING METAPROTEOMICS: STEPS INVOLVED Metaproteomic analysis using the Galaxy framework. Proteomics. (2015) doi: 10.1002/pmic.201500074. METAPROTEOMICS : BIOLOGICAL INSIGHTS METAPROTEOMICS OF CHILDHOOD CARIES Sucrose No Sucrose • In vitro investigation of sucrose-induced changes in the metaproteomes of children with caries. Prof. Joel Rudney • Major shifts in taxonomy and function in paired microcosm oral biofilms grown without and with sucrose respectively. Twelve replicates have been analyzed. • SEED analysis of Oral microcosm biofilms showed characteristic NS and WS patterns of protein expression that were highly conserved across taxonomically diverse communities. Moreover, many of the proteins that differed between each pH phenotype had functions that would act to promote maintenance of neutral pH under NS conditions, or acid production and tolerance under WS conditions. • Targeted proteomic approaches then can be used to determine whether those proteins are also expressed when plaque is exposed to sucrose in the mouth. In that case, it may be possible to define a set of dysbiosis biomarkers that could be used to detect at-risk tooth surfaces before the development of overt carious lesions. GALAXY PLATFORM Goecks J et al Genome Biol. 2010;11(8):R86. Benefits of Galaxy • A web-based bioinformatics data analysis platform. • Software accessibility and usability. • Share-ability of tools, workflows and histories. • Reproducibility and ability to test and compare results after using multiple parameters. • Software tools can be used in a sequential manner to generate analytical workflows that can be reused, shared and creatively modified for multiple studies. GALAXY-P : IMPLEMENTATION OF PROTEOMICS TOOLS WITHIN GALAXY ENVIRONMENT. OUTPUT INPUT TOOLS CENTRAL PANE HISTORY TOOLS & WORKFLOWS • Software tools can be used in a sequential manner to generate analytical workflows that can be reused, shared and creatively modified for multiple studies. For example, Protein Database Downloader downloads UniProt protein FASTA databases of various organisms. GALAXY-P : IMPLEMENTATION OF PROTEOMICS TOOLS WITHIN GALAXY ENVIRONMENT. PROTEOGENOMICS: STEPS INVOLVED ~ 2 million proteins ~ 10,000 proteins ~ 5,000 proteins ~ 1,000 pepEdes ~ 100 pepEdes ~ 50 pepEdes RNASeq DERIVED PROTEOMIC DATABASES “Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.” Sheynkman G et al BMC Genomics. doi: 10.1186/1471-2164-15-703. Gloria Sheynkman James Johnson PROTEOGENOMICS WORKFLOW Galaxy-P provides an integrated platform for every step of proteogenomic analysis. • Build target database – download and translate EST databases or perform gene prediction with Augustus. • Numerous tools for identification and text manipulation. • Workflow utilizing BLAST to identify novel peptides. • Tool to assess peptide-spectrum matches and visualize spectra. • Visualize identified peptides on the genome. • 140 steps: Seamless, integrated proteogenomic workflow. Flexible and accessible workflows for improved proteogenomic analysis using Galaxy framework. J. Proteome Res. (2014) DOI: 10.1021/pr500812t Link: z.umn.edu/pgfirstlook PSM EVALUATION 6 GENOME VISUALIZATION USING IGV BROWSER 7 GALAXYP : ONGOING PROJECTS REPERTOIRE OF WORKFLOWS • Sharing of analytical workflows that can be reused, shared and creatively modified for multiple studies. • Multiple workflows for metaproteomics, quantitative proteomics, proteogenomics, RNASeq workflows, are being developed, shared and used. COMMUNITY BASED SOFTWARE DEVELOPMENT • Community-based software development model should prove effective for future implementation, testing and continued improvement of command-line driven software tools. • We plan to offer the many functionalities of MS-GF+ and PeptideShaker in Galaxy, along with opportunities for integration with other software tools via use of workflows. COMMUNITY-BASED SOFTWARE DEVELOPMENT Soware Developers SearchGUI / PepEdeShaker Galaxy Improvements Wrapper to the soZware USER FORUM / tool GITHUB Users test the tools and provide feedback Soware tool to
Load more

Recommended publications
  • Clinical Implications of Recent Advances in Proteogenomics
    Clinical implications of recent advances in proteogenomics Marie Locard-Paulet, Olivier Pible, Anne Gonzalez de Peredo, Béatrice Alpha-Bazin, Christine Almunia, Odile Burlet-Schiltz, J. Armengaud To cite this version: Marie Locard-Paulet, Olivier Pible, Anne Gonzalez de Peredo, Béatrice Alpha-Bazin, Christine Almu- nia, et al.. Clinical implications of recent advances in proteogenomics. Expert Review of Proteomics, Taylor & Francis, 2016, 13 (2), pp.185-199. 10.1586/14789450.2016.1132169. hal-03080146 HAL Id: hal-03080146 https://hal.archives-ouvertes.fr/hal-03080146 Submitted on 19 Mar 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Publisher: Taylor & Francis Journal: Expert Review of Proteomics DOI: 10.1586/14789450.2016.1132169 Review Clinical implications of recent advances in proteogenomics Marie Locard-Paulet1,2, Olivier Pible3, Anne Gonzalez de Peredo1,2, Béatrice Alpha-Bazin3, Christine Almunia3, Odile Burlet-Schiltz1,2, Jean Armengaud3* 1CNRS, IPBS (Institut de Pharmacologie et Biologie Structurale), 205 route de Narbonne, 31077 Toulouse, France. 2Université de Toulouse, UPS, IPBS, 31077 Toulouse, France. 3CEA-Marcoule, DSV/IBITEC-S/SPI/Li2D, Laboratory “Innovative technologies for Detection and Diagnostics”, BP 17171, F-30200 Bagnols-sur-Cèze, France.
    [Show full text]
  • Metaproteomics As a Tool for Studying the Protein Landscape of Human-Gut Bacterial Species
    bioRxiv preprint doi: https://doi.org/10.1101/2021.09.02.458484; this version posted September 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species Moses Stamboulian1, Jamie Canderan1, and Yuzhen Ye1 1Luddy School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN 47408. Email address: Moses Stamboulian, [email protected] Jamie Canderan, [email protected] Yuzhen Ye, [email protected] Corresponding author: Yuzhen Ye, [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.09.02.458484; this version posted September 3, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Host-microbiome interactions and the microbial community have broad impact in human health and diseases. Most microbiome based studies are performed at the genome level based on next-generation sequencing techniques, but metaproteomics is emerging as a pow- erful technique to study microbiome functional activity by characterizing the complex and dynamic composition of microbial proteins. We conducted a large-scale survey of human gut microbiome metaproteomic data to identify generalist species that are ubiquitously expressed across all samples and specialists that are highly expressed in a small subset of samples associ- ated with a certain phenotype.
    [Show full text]
  • A Decade of Metaproteomics: Where We Stand and What the Future Holds
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Open Repository and Bibliography - Luxembourg www.proteomics-journal.com Page 1 Proteomics Viewpoint A decade of metaproteomics: where we stand and what the future holds Paul Wilmes1, Anna Heintz-Buschart1 and Philip L. Bond2 1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg 2Advanced Water Management Centre, University of Queensland, Brisbane, Australia Correspondence: Paul Wilmes, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg; Philip L. Bond, Advanced Water Management Centre, University of Queensland, Queensland 4072, Australia E-mail: [email protected]; [email protected] Fax: (352) 466644 6188; (61) 07 33654726 Received: 15-May-2015; Revised: 06-Jul-2015; Accepted: 05-Aug-2015. This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/pmic.201500183. This article is protected by copyright. All rights reserved. www.proteomics-journal.com Page 2 Proteomics Abstract We are living through exciting times during which we are able to unravel the “microbial dark matter” in and around us through the application of high-resolution “meta-omics”. Metaproteomics offers the ability to resolve the major catalytic units of microbial populations and thereby allows the establishment of genotype-phenotype linkages from in situ samples. A decade has passed since the term “metaproteomics” was first coined and corresponding analyses were carried out on mixed microbial communities.
    [Show full text]
  • Personalized Single-Cell Proteogenomics to Distinguish Acute Myeloid Leukemia from Nonmalignant Clonal Hematopoiesis
    RESEARCH BRIEF Personalized Single-Cell Proteogenomics to Distinguish Acute Myeloid Leukemia from Nonmalignant Clonal Hematopoiesis Laura W. Dillon1, Jack Ghannam1, Chidera Nosiri1, Gege Gui1, Meghali Goswami1, Katherine R. Calvo2, Katherine E. Lindblad1, Karolyn A. Oetjen1, Matthew D. Wilkerson3,4,5, Anthony R. Soltis3,4, Gauthaman Sukumar4,6, Clifton L. Dalgard5,6, Julie Thompson1, Janet Valdez1, Christin B. DeStefano1, Catherine Lai1, Adam Sciambi7, Robert Durruthy-Durruthy7, Aaron Llanso7, Saurabh Gulati7, Shu Wang7, Aik Ooi7, Pradeep K. Dagur8, J. Philip McCoy8, Patrick Burr9, Yuesheng Li9, and Christopher S. Hourigan1 ABSTRACT Genetic mutations associated with acute myeloid leukemia (AML) also occur in age- related clonal hematopoiesis, often in the same individual. This makes confident assignment of detected variants to malignancy challenging. The issue is particularly crucial for AML posttreatment measurable residual disease monitoring, where results can be discordant between genetic sequencing and flow cytometry. We show here that it is possible to distinguish AML from clonal hematopoiesis and to resolve the immunophenotypic identity of clonal architecture. To achieve this, we first design patient-specific DNA probes based on patient’s whole-genome sequencing and then use them for patient-personalized single-cell DNA sequencing with simultaneous single-cell antibody– oligonucleotide sequencing. Examples illustrate AML arising from DNMT3A- and TET2-mutated clones as well as independently. The ability to personalize single-cell proteogenomic assessment for individual patients based on leukemia-specific genomic features has implications for ongoing AML precision medicine efforts. SIGNIFICANCE: This study offers a proof of principle of patient-personalized customized single-cell proteogenomics in AML including whole-genome sequencing–defined structural variants, currently unmeasurable by commercial “off-the-shelf” panels.
    [Show full text]
  • And Metaproteomics-Based Rapid Assay of Individual 2 Microbiome Responses to Drugs
    bioRxiv preprint doi: https://doi.org/10.1101/543256; this version posted June 7, 2019. 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 RapidAIM: A culture- and metaproteomics-based Rapid Assay of Individual 2 Microbiome responses to drugs 3 4 Authors: Leyuan Li1, Zhibin Ning1, Xu Zhang1, Janice Mayne1, Kai Cheng1, Alain Stintzi*1, 5 Daniel Figeys*1,2,3 6 Affiliations: 7 1 Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of 8 Medicine, University of Ottawa, Ottawa, Canada. 9 2 Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada. 10 3 Canadian Institute for Advanced Research, Toronto, Canada. 11 *To whom correspondence should be addressed: Emails: [email protected] (DF), and [email protected] (AS). 12 13 Abstract: 14 Background: Human-targeted drugs may exert off-target effects on the gut microbiota. 15 However, our understanding of such effects is limited due to a lack of rapid and scalable assay to 16 comprehensively assess microbiome responses to drugs. Drugs can drastically change the overall 17 microbiome abundance, microbial composition and functions of a gut microbiome. Although we 18 could comprehensively observe these microbiome responses using a series of tests, for the 19 purpose of a drug screening, it is important to decrease the number of analytical tools used. 20 Results: Here, we developed an approach to screen compounds against individual microbiomes 21 in vitro using metaproteomics adapted for both absolute bacterial abundances and functional 22 profiling of the microbiome.
    [Show full text]
  • In This Issue High-Throughput Single Protein Pulling Backpack Recorders for Zebra Finches a Deeper Look at Proteogenomics Genome
    NATURE METHODS | VOL.11 NO.11 | NOVEMBER 2014 IN THIS ISSUE software tool that bins genomic fragments that have Improving tools for synthetic first undergone limited preassembly into contigs. biology Their strategy uses a variational Bayesian approach combining sequence composition and correlated To rapidly and reliably engineer biological abundance across multiple samples to produce networks—one of the promises of synthetic sequence assignments. CONCOCT bins genomes with biology—a larger repertoire of regulatory high precision and recall in simulated and real data, elements and better characterization of their providing higher coverage than can typically be performance are needed. Two groups now deliver reached by single-cell sequencing. on each of these aspects. Smolke and colleagues Brief Communication p1144 present a model to predict the expression of a target gene that is regulated by a microRNA and then extend the model to anticipate the High-throughput single protein behavior of genetic circuits that use protein- responsive microRNA switches to detect the pulling concentration of a nuclear protein in mammalian One of the main technical challenges in making cells. Fussenegger and colleagues create a library single-molecule force spectroscopy measurements of protein-responsive ribozymes for translational control and then design a three-input AND gate has been the method’s low-throughput nature, which in mammalian cells that combines transcriptional has precluded the screening of large protein-variant and translational control. libraries. Nash and colleagues now describe a system Articles p1147, p1154, News and Views p1105 that readily enables thousands of protein pulling measurements. They begin with a microspotted DNA array and synthesize proteins in situ with the aid of A deeper look at proteogenomics microfluidics-based cell-free expression technology.
    [Show full text]
  • Minireview: Novel Micropeptide Discovery by Proteomics and Deep Sequencing Methods
    fgene-12-651485 May 6, 2021 Time: 11:28 # 1 MINI REVIEW published: 06 May 2021 doi: 10.3389/fgene.2021.651485 Minireview: Novel Micropeptide Discovery by Proteomics and Deep Sequencing Methods Ravi Tharakan1* and Akira Sawa2,3 1 National Institute on Aging, National Institutes of Health, Baltimore, MD, United States, 2 Departments of Psychiatry, Neuroscience, Biomedical Engineering, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States, 3 Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States A novel class of small proteins, called micropeptides, has recently been discovered in the genome. These proteins, which have been found to play important roles in many physiological and cellular systems, are shorter than 100 amino acids and were overlooked during previous genome annotations. Discovery and characterization of more micropeptides has been ongoing, often using -omics methods such as proteomics, RNA sequencing, and ribosome profiling. In this review, we survey the recent advances in the micropeptides field and describe the methodological and Edited by: conceptual challenges facing future micropeptide endeavors. Liangliang Sun, Keywords: micropeptides, miniproteins, proteogenomics, sORF, ribosome profiling, proteomics, genomics, RNA Michigan State University, sequencing United States Reviewed by: Yanbao Yu, INTRODUCTION J. Craig Venter Institute (Rockville), United States The sequencing and publication of complete genomic sequences of many organisms have aided Hongqiang Qin, the medical sciences greatly, allowing advances in both human genetics and the biology of human Dalian Institute of Chemical Physics, Chinese Academy of Sciences, China disease, as well as a greater understanding of the biology of human pathogens (Firth and Lipkin, 2013).
    [Show full text]
  • Pathophysiology and Proteogenomics of Post-Infectious and Post-Hemorrhagic Hydrocephalus in Infants
    University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2020-07-21 Pathophysiology and Proteogenomics of Post-infectious and Post-hemorrhagic Hydrocephalus in Infants Isaacs, Albert M. Isaacs, A. M. (2020). Pathophysiology and Proteogenomics of Post-infectious and Post-hemorrhagic Hydrocephalus in Infants (Unpublished doctoral thesis). University of Calgary, Calgary, AB. http://hdl.handle.net/1880/112344 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Pathophysiology and Proteogenomics of Post-infectious and Post-hemorrhagic Hydrocephalus in Infants by Albert M. Isaacs A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY GRADUATE PROGRAM IN NEUROSCIENCE CALGARY, ALBERTA JULY, 2020 © Albert M. Isaacs 2020 Abstract Post-infectious (PIH) and post-hemorrhagic (PHH) hydrocephalus occur as sequalae of neonatal sepsis or intraventricular hemorrhage (IVH) of prematurity, respectively. Together, PIH and PHH represent the most common form of infantile hydrocephalus, the most common indication for neurosurgery
    [Show full text]
  • Proteogenomics and Hi-C Reveal Transcriptional Dysregulation in High Hyperdiploid Childhood Acute Lymphoblastic Leukemia
    Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia. Yang, M., Vesterlund, M., Siavelis, I., Moura-Castro, LH., Castor, A., Fioretos, T., Jafari, R., Lilljebjörn, H., Odom, DT., Olsson, L., Ravi, N., Woodward, EL., Harewood, L., & Paulsson, K. (2019). Proteogenomics and Hi- C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia. Nature Communications, 10, [1519]. https://doi.org/10.1038/s41467-019-09469-3 Published in: Nature Communications Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2019 the authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected].
    [Show full text]
  • A Community Proposal to Integrate Proteomics Activities In
    F1000Research 2017, 6:875 Last updated: 05 OCT 2021 OPINION ARTICLE A community proposal to integrate proteomics activities in ELIXIR [version 1; peer review: 2 approved] Juan Antonio Vizcaíno 1, Mathias Walzer 1, Rafael C. Jiménez 2, Wout Bittremieux3, David Bouyssié4, Christine Carapito4, Fernando Corrales5, Myriam Ferro4, Albert J.R. Heck6,7, Peter Horvatovich 8, Martin Hubalek9, Lydie Lane10,11, Kris Laukens3, Fredrik Levander12, Frederique Lisacek13,14, Petr Novak15, Magnus Palmblad 16, Damiano Piovesan17, Alfred Pühler18, Veit Schwämmle 19, Dirk Valkenborg20-22, Merlijn van Rijswijk 23,24, Jiri Vondrasek9, Martin Eisenacher25, Lennart Martens26,27, Oliver Kohlbacher 28-31 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK 2ELIXIR Hub, Cambridge, CB10 1SD, UK 3Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium 4French Proteomics Infrastructure ProFI, Grenoble, (EDyP U1038, CEA/Inserm/ Grenoble Alpes University) Toulouse (IPBS, Université de Toulouse, CNRS, UPS), Strasbourg (LSMBO, IPHC UMR7178, CNRS-Université de Strasbourg), France 5ProteoRed, Proteomics Unit, Centro Nacional de Biotecnología (CSIC), Madrid, 28049, Spain 6Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3548 CH, The Netherlands 7Netherlands Proteomics Center, Utretcht, 3584 CH, The Netherlands 8Analytical Biochemistry, Department of Pharmacy,
    [Show full text]
  • Gut Microbiome’ on 7Th & 8Th June 2018 in Brussels
    THE ESSENTIAL ROLES OF CARBOHYDRATES IN PROMOTING GUT MICROBIOTA FUNCTION THROUGH ALL STAGES OF LIFE This paper was co-authored by Nathalie Juge†, Sabine Flitsch‡, Rodney Townsend§ and Claire Doherty‡ using input from group discussions that took place at the CarboMet workshop ‘The Role of Carbohydrates in the Gut Microbiome’ on 7th & 8th June 2018 in Brussels. CarboMet (Metrology of Carbohydrates for European Bioindustries) is a four-year Coordination and Support Action (CSA) funded by Horizon 2020 FET-OPEN (Grant agreement no. 737395). https://carbomet.eu/) The primary aim of the CSA is to mobilise the European academic and industrial community to identify generic measurement, data management and metrological challenges that must be met in order to advance and exploit carbohydrate knowledge and applications. The potential for exploitation of carbohydrates lies in their diversity and structural complexity – subtle changes in the three-dimensional structure of a carbohydrate profoundly affects (for example) its ability to protect against or fight infectious disease. However, these subtle structural differences present a challenge for their analysis. Sophisticated measurement and metrological capabilities for analysing carbohydrates are available but are nowhere near as advanced or as routinely used in other areas such as gene sequencing. Therefore as a first stage CarboMet has organised some open, Europe-wide workshops to identify key topics where our understanding needs to be advanced urgently, and where current limitations in our measurement, data management and metrological capabilities are hindering progress. The Workshops were also asked to recommend appropriate Work Programmes that should be supported by Horizon 2020 and its successor, Horizon Europe.
    [Show full text]
  • ANNUAL REPORT Marine Science Institute UC SANTA BARBARA Table of Contents
    2018–2019 ANNUAL REPORT Marine Science Institute UC SANTA BARBARA Table of Contents 3 Mission Statement 4 From the Director Overview 5 Executive Summary 7 10 Organizational Charts Administrative Staff 11 Centers and Units 12 13 MSI Advisory Committee, Administrative & Technical Staff 16 Statistical Summary Research Support Summary 17 Statistical Summary 2018–2019 19 Five-Year Research Support 21 Summary Funding Agencies 22 24 Principal Investigators 30 Postdoctoral Researchers, Graduate and Undergraduate Students 33 Space 39 Other Projects & Activities Coastal Research Center 40 Marine Biotechnology Center 42 Ocean & Coastal Policy Center 52 Analytical Laboratory 54 Education and Outreach 55 56 Awards Administered Awards 57 Research Summaries 66 2 Mission Statement The Marine Science Institute at the University of California, Santa Barbara, is committed to fostering innovative and significant research, to promoting effective stewardship, and to sharing exciting discoveries of the world’s oceans. 3 From the Director 4 Overview The Marine Science Institute (MSI) provides an intellectual and physical environment at UCSB that fosters world-renowned marine research. The institute brings together marine researchers from across the UCSB campus and supports multi-investigator collaborative projects and individual research efforts. The scientific membership at MSI consists of both ladder faculty and professional researchers. In 2018-2019 MSI membership included 25 ladder faculty and 32 professional researchers with 228 additional participants distributed across postdoctoral scholars, graduate students and undergraduates. Beyond research, MSI’s Research Experience and Education Facility (REEF) educates UCSB students and the general public about MSI science. MSI is housed in the marine science research building (MSRB) on the UCSB campus.
    [Show full text]