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Experimental Validation of in Silico Modelpredicted Isocitrate
Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Islam, M. Ahsanul, Anatoli Tchigvintsev, Veronica Yim, Alexei Savchenko, Alexander F. Yakunin, Radhakrishnan Mahadevan, and Elizabeth A. Edwards. “Experimental Validation of in Silico Model-Predicted Isocitrate Dehydrogenase and Phosphomannose Isomerase from Dehalococcoides Mccartyi.” Microbial Biotechnology (September 16, 2015): n/a–n/a. As Published http://dx.doi.org/10.1111/1751-7915.12315 Publisher Wiley Blackwell Version Final published version Citable link http://hdl.handle.net/1721.1/99704 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/4.0/ bs_bs_banner Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi M. Ahsanul Islam,† Anatoli Tchigvintsev, Veronica and confirmed experimentally. Further bioinformatics Yim, Alexei Savchenko, Alexander F. Yakunin, analyses of these two protein sequences suggest Radhakrishnan Mahadevan and Elizabeth A. their affiliation to potentially novel enzyme families Edwards* within their respective larger enzyme super families. Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Introduction Canada As one of the smallest free-living organisms, Dehalococcoides mccartyi are important for their ability to Summary detoxify ubiquitous and stable groundwater pollutants Gene sequences annotated as proteins of unknown such as chlorinated ethenes and benzenes into benign or or non-specific function and hypothetical proteins less toxic compounds (Maymó-Gatell et al., 1997; Adrian account for a large fraction of most genomes. In et al., 2000; 2007a; He et al., 2003; Löffler et al., 2012). -
(12) Patent Application Publication (10) Pub. No.: US 2009/0176967 A1 Stennicke (43) Pub
US 20090176967A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2009/0176967 A1 Stennicke (43) Pub. Date: Jul. 9, 2009 (54) CONJUGATION OF FVII (30) Foreign Application Priority Data (75) Inventor: Henning Ralf Stennicke, Kokkedal Aug. 2, 2004 (DK) ........................... PA 2004 O1175 (DK) Publication Classification Correspondence Address: (51) Int. Cl. INTELLECTUALNOVO NORDISK, PROPERTYINC. DEPARTMENT C. f :08: 1OO COLLEGE ROADWEST C07K 5/10 (2006.015 PRINCETON, NJ 08540 (US) C07K 7/06 (2006.01) (73) Assignee: Novo Nordisk HealthCare A/G, CI2N 15/12 (2006.01) Zurich (CH) CI2N 5/8 (2006.01) CI2N I/19 (2006.01) (21) Appl. No.: 11/659,153 (52) U.S. Cl. ....... 530/330; 435/68. 1530/381: 536/23.5; 435/320.1; 435/254.2 (22) PCT Filed: Aug. 2, 2005 (57) ABSTRACT (86). PCT No.: PCT/EP2005/053756 New FVII polypeptides and FVIIa derivatives, uses of such S371371 (c)(1),(c)(1 peptides, and methods of producing these polypeptides and (2), (4) Date: Oct. 23, 2008 derivatives, are provided. (SEQID NO, 1) FVII Polypeptide variant A (Sortase A) 5 Ala-Asn-Ala-Phe-Leu-GLA-GLA-Leu-Arg-Pro-Gly-Ser-Leu-GLA-Arg-GLA-Cys-Lys 5 1O 15 GLA-GLA-Gln-Cys-Ser-Phe-GLA-GLA-Ala-Arg-GLA-Ile-Phe-Lys-Asp-Ala-GLA-Arg 2O 25 30 35 10 Thr-Lys-Leu-Phe-Trp-Ile-Ser-Tyr-Ser-Asp-Gly-Asp-Gln-Cys-Ala-Ser-Ser-Pro 40 45 5 O Cys-Gln-Asn-Gly-Gly-Ser-Cys-Lys-Asp-Gln-Leu-Gln-Ser-Tyr-Ile-Cys-Phe-Cys 15 55 8O 65 70 Leu-Pro-Ala-Phe-Glu-Gly-Arg-Asn-Cys-Glu-Thr-His-Lys-Asp-Asp-Gln-Leu-Ile 75 80 85 90 20 Cys-Val-Asn-Glu-Asn-Gly-Gly-Cys-Glu-Gln-Tyr-Cys-Ser-Asp-His-Thr-Gly-Thr 35 1OO 105 Lys-Arg-Ser-Cys-Arg-Cys-His-Glu-Gly-Tyr-Ser-Leu-Leu-Ala-Asp-Gly-Val-Ser 11 O 115 120 125 25 Cys-Thr-Pro-Thr-Val-Glu-Tyr-Pro-Cys-Gly-Lys-Ile-Pro-Ile-Leu-Glu-Lys-Arg 130 135 14 O Asn-Ala-Ser-Leu-Pro-Gln-Thr-Gly-Ile-Val-Gly-Gly-Lys-Val-Cys-Pro-Lys-Gly 3O 145 150 155 18O Glu-Cys-Pro-Trp-Gln-Wal-Leu-Leu-Leu-Val-Asn-Gly-Ala-Gln-Leu-Cys-Gly-Gly 165 170 175 18O 35 Thr-Leu-Ile-Asn-Thr-Ile-Trp-Val-Val-Ser-Ala-Ala-His-Cys-Phe-Asp-Tys-Ile 185 190 195 US 2009/0176967 A1 Jul. -
Microbial Community and Geochemical Analyses of Trans-Trench Sediments for Understanding the Roles of Hadal Environments
The ISME Journal (2020) 14:740–756 https://doi.org/10.1038/s41396-019-0564-z ARTICLE Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments 1 2 3,4,9 2 2,10 2 Satoshi Hiraoka ● Miho Hirai ● Yohei Matsui ● Akiko Makabe ● Hiroaki Minegishi ● Miwako Tsuda ● 3 5 5,6 7 8 2 Juliarni ● Eugenio Rastelli ● Roberto Danovaro ● Cinzia Corinaldesi ● Tomo Kitahashi ● Eiji Tasumi ● 2 2 2 1 Manabu Nishizawa ● Ken Takai ● Hidetaka Nomaki ● Takuro Nunoura Received: 9 August 2019 / Revised: 20 November 2019 / Accepted: 28 November 2019 / Published online: 11 December 2019 © The Author(s) 2019. This article is published with open access Abstract Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and fi 1234567890();,: 1234567890();,: Mariana Trenches. Tag-sequencing analyses showed speci c distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. -
Arxiv:2105.11503V2 [Physics.Bio-Ph] 26 May 2021 3.1 Geometry and Swimming Speeds of the Cells
The Bank Of Swimming Organisms at the Micron Scale (BOSO-Micro) Marcos F. Velho Rodrigues1, Maciej Lisicki2, Eric Lauga1,* 1 Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, United Kingdom. 2 Faculty of Physics, University of Warsaw, Warsaw, Poland. *Email: [email protected] Abstract Unicellular microscopic organisms living in aqueous environments outnumber all other creatures on Earth. A large proportion of them are able to self-propel in fluids with a vast diversity of swimming gaits and motility patterns. In this paper we present a biophysical survey of the available experimental data produced to date on the characteristics of motile behaviour in unicellular microswimmers. We assemble from the available literature empirical data on the motility of four broad categories of organisms: bacteria (and archaea), flagellated eukaryotes, spermatozoa and ciliates. Whenever possible, we gather the following biological, morphological, kinematic and dynamical parameters: species, geometry and size of the organisms, swimming speeds, actuation frequencies, actuation amplitudes, number of flagella and properties of the surrounding fluid. We then organise the data using the established fluid mechanics principles for propulsion at low Reynolds number. Specifically, we use theoretical biophysical models for the locomotion of cells within the same taxonomic groups of organisms as a means of rationalising the raw material we have assembled, while demonstrating the variability for organisms of different species within the same group. The material gathered in our work is an attempt to summarise the available experimental data in the field, providing a convenient and practical reference point for future studies. Contents 1 Introduction 2 2 Methods 4 2.1 Propulsion at low Reynolds number . -
Serine Proteases with Altered Sensitivity to Activity-Modulating
(19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants. -
Evolution of the 3-Hydroxypropionate Bicycle and Recent Transfer of Anoxygenic Photosynthesis Into the Chloroflexi
Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi Patrick M. Shiha,b,1, Lewis M. Wardc, and Woodward W. Fischerc,1 aFeedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608; bEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and cDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125 Edited by Bob B. Buchanan, University of California, Berkeley, CA, and approved August 21, 2017 (received for review June 14, 2017) Various lines of evidence from both comparative biology and the provide a hard geological constraint on these analyses, the timing geologic record make it clear that the biochemical machinery for of these evolutionary events remains relative, thus highlighting anoxygenic photosynthesis was present on early Earth and provided the uncertainty in our understanding of when and how anoxy- the evolutionary stock from which oxygenic photosynthesis evolved genic photosynthesis may have originated. ca. 2.3 billion years ago. However, the taxonomic identity of these A less recognized alternative is that anoxygenic photosynthesis early anoxygenic phototrophs is uncertain, including whether or not might have been acquired in modern bacterial clades relatively they remain extant. Several phototrophic bacterial clades are thought recently. This possibility is supported by the observation that to have evolved before oxygenic photosynthesis emerged, including anoxygenic photosynthesis often sits within a derived position in the Chloroflexi, a phylum common across a wide range of modern the phyla in which it is found (3). Moreover, it is increasingly environments. Although Chloroflexi have traditionally been thought being recognized that horizontal gene transfer (HGT) has likely to be an ancient phototrophic lineage, genomics has revealed a much played a major role in the distribution of phototrophy (8–10). -
Directed Sortase Evolution for Site-Specific Protein Engineering and Surface Functionalization
Directed sortase evolution for site-specific protein engineering and surface functionalization Von der Fakultät für Mathematik, Informatik und Naturwissenschaften der RWTH Aachen University zur Erlangung des akademischen Grades einer Doktorin der Naturwissenschaften genehmigte Dissertation vorgelegt von Zhi Zou Master of Biochemistry and Molecular Biology aus Huanggang, Hubei, P.R. China Berichter: Univ.-Prof. Dr. rer. nat. Ulrich Schwaneberg Univ.-Prof. Dr. rer. nat. Andrij Pich Tag der mündlichen Prüfung: 26.02.2019 Diese Dissertation ist auf den Internetseiten der Universitätsbibliothek verfügbar. Table of Contents Table of Contents Acknowledgements ....................................................................................................................................... 6 Abbreviations and acronyms ......................................................................................................................... 7 Abstract .......................................................................................................................................................... 9 1. Chapter I: Introduction ............................................................................................................................ 11 1.1. Sortases: sources, classes, and functions ......................................................................................... 11 1.1.1 Class A sortases: sortase A ........................................................................................................................ -
Proteome Characterization of Brachyspira Strains
ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Department of Cellular Biology, Physiology and Immunology Doctoral Program in Immunology Proteome characterization of Brachyspira strains. Identification of bacterial antigens. Doctoral Thesis Mª Vanessa Casas López Bellaterra, July 2017 Department of Cellular Biology, Physiology and Immunology Doctoral Program in Immunology Proteome characterization of Brachyspira strains. Identification of bacterial antigens. Doctoral thesis presented by Mª Vanessa Casas López To obtain the Ph.D. in Immunology This work has been carried out in the Proteomics Laboratory CSIC/UAB under the supervision of Dr. Joaquin Abián and Dra. Montserrat Carrascal. Ph.D. Candidate Ph.D. Supervisor Mª Vanessa Casas López Dr. Joaquin Abián Moñux CSIC Research Scientist Department Tutor Ph.D. Supervisor Dra. Dolores Jaraquemada Pérez de Dra. Montserrat Carrascal Pérez Guzmán CSIC Tenured Scientist UAB Immunology Professor Bellaterra, July 2017 “At My Most Beautiful” R.E.M. from the album “Up” (1998) “And after all, you’re my wonderwall” Oasis from the album “(What´s the Story?) Morning Glory” (1995) Agradecimientos A mis directores de tesis, por su tiempo, sus ideas y consejos. -
Evolution of the 3-Hydroxypropionate Bicycle and Recent Transfer of Anoxygenic Photosynthesis Into the Chloroflexi
Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi Patrick M. Shiha,b,1, Lewis M. Wardc, and Woodward W. Fischerc,1 aFeedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608; bEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and cDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125 Edited by Bob B. Buchanan, University of California, Berkeley, CA, and approved August 21, 2017 (received for review June 14, 2017) Various lines of evidence from both comparative biology and the provide a hard geological constraint on these analyses, the timing geologic record make it clear that the biochemical machinery for of these evolutionary events remains relative, thus highlighting anoxygenic photosynthesis was present on early Earth and provided the uncertainty in our understanding of when and how anoxy- the evolutionary stock from which oxygenic photosynthesis evolved genic photosynthesis may have originated. ca. 2.3 billion years ago. However, the taxonomic identity of these A less recognized alternative is that anoxygenic photosynthesis early anoxygenic phototrophs is uncertain, including whether or not might have been acquired in modern bacterial clades relatively they remain extant. Several phototrophic bacterial clades are thought recently. This possibility is supported by the observation that to have evolved before oxygenic photosynthesis emerged, including anoxygenic photosynthesis often sits within a derived position in the Chloroflexi, a phylum common across a wide range of modern the phyla in which it is found (3). Moreover, it is increasingly environments. Although Chloroflexi have traditionally been thought being recognized that horizontal gene transfer (HGT) has likely to be an ancient phototrophic lineage, genomics has revealed a much played a major role in the distribution of phototrophy (8–10). -
The Exposed Proteomes of Brachyspira Hyodysenteriae and B. Pilosicoli
ORIGINAL RESEARCH published: 21 July 2016 doi: 10.3389/fmicb.2016.01103 The Exposed Proteomes of Brachyspira hyodysenteriae and B. pilosicoli Vanessa Casas 1, Santiago Vadillo 2, Carlos San Juan 2, Montserrat Carrascal 1 and Joaquin Abian 1* 1 Consejo Superior de Investigaciones Científicas/UAB Proteomics Laboratory, Instituto de Investigaciones Biomedicas de Barcelona–Consejo Superior de Investigaciones Científicas, Institut d’investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain, 2 Departamento Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain Brachyspira hyodysenteriae and Brachyspira pilosicoli are well-known intestinal pathogens in pigs. B. hyodysenteriae is the causative agent of swine dysentery, a disease with an important impact on pig production while B. pilosicoli is responsible of a milder diarrheal disease in these animals, porcine intestinal spirochetosis. Recent sequencing projects have provided information for the genome of these species facilitating the search of vaccine candidates using reverse vaccinology approaches. However, practically no experimental evidence exists of the actual gene products being expressed and of those proteins exposed on the cell surface or released to the cell media. Using a Edited by: cell-shaving strategy and a shotgun proteomic approach we carried out a large-scale Alexandre Morrot, Federal University of Rio de Janeiro, characterization of the exposed proteins on the bacterial surface in these species as well Brazil as of peptides and proteins in the extracellular medium. The study included three strains Reviewed by: of B. hyodysenteriae and two strains of B. pilosicoli and involved 148 LC-MS/MS runs on Ana Varela Coelho, Instituto de Tecnologia Química e a high resolution Orbitrap instrument. -
Research Project Summary
Division of Science, Research and Environmental Health Research Project Summary August 2016 Applying Innovative Diagnostic Tools at New Jersey Publicly Funded Sites Authors Donna E. Fennell, Ph.D.1 and Max Häggblom, Ph.D.2 Prepared By Robert Mueller, M.S. (Project Manager) 3 Abstract This project demonstrated the use of Environmental Molecular Diagnostic Tools (EMDs) for detecting microbial biodegradation of contaminants and identifying bacteria responsible for contaminant biodegradation or biotransformation at three contaminated sites in New Jersey. These sites were unique based on the contamination present, and EMDs were selected to address a particular issue at each site. EMDs is a collective term that describes a group of advanced and emerging techniques used to analyze biological and chemical characteristics of soils, sediments, groundwater, and surface water. Many of these tools were originally developed for applications in medicine, defense, and industry. Over the last decade, great advances have been made in adapting and applying EMDs for site characterization, remediation, monitoring, and closure. EMDs are important and valuable because they can provide key information not available using traditional analytical methods (e.g., groundwater analysis for volatile organic compounds). While they are intended to complement these traditional methods, EMDs can bring a new perspective to all stages in the environmental management decision-making process. As a result of this work, a bio-augmentation/bio-stimulation design was developed for an organic solvent plume at one site. At a second site, Stable Isotope Probing (SIP) was used to confirm the presence of dehalogenating organisms and bio-stimulation demonstrated rapid reductive dechlorination. Finally, aniline degrading organisms were studied using SIP. -
Modulation of Listeria Monocytogenes Biofilm Formation Using Small Molecules and Enzymes
MODULATION OF LISTERIA MONOCYTOGENES BIOFILM FORMATION USING SMALL MOLECULES AND ENZYMES MODULATION OF LISTERIA MONOCYTOGENES BIOFILM FORMATION USING SMALL MOLECULES AND ENZYMES By UYEN THI TO NGUYEN, B.Sc. A Thesis Submitted to the School of Graduate Studies in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy McMaster University © Copyright by Uyen T.T. Nguyen, July 2014 Ph.D. – U.T.T. Nguyen; McMaster University – Biochemistry and Biomedical Sciences McMaster University DOCTOR OF PHILOSOPHY (2014) Hamilton, Ontario (Biochemistry and Biomedical Sciences) TITLE: Modulation of Listeria monocytogenes biofilm formation using small molecules and enzymes AUTHOR: Uyen Thi To Nguyen, B.Sc. (McMaster University) SUPERVISOR: Dr. Lori L. Burrows NUMBER OF PAGES: xvii, 217 ii Ph.D. – U.T.T. Nguyen; McMaster University – Biochemistry and Biomedical Sciences ABSTRACT Inadequately disinfected food contact surfaces colonized by Listeria monocytogenes can come into contact with ready-to-eat food products causing cross-contamination and food-borne outbreaks. L. monocytogenes is tolerant of high salt, low temperatures and low pH, in part due to its ability to form biofilms, defined as communities of microorganisms that are surrounded by a self-produced extracellular polymeric substance that can adhere to surfaces. Biofilm formation is a complex process involving a series of poorly defined physiological changes that together lead to tolerance of disinfectants and antibiotics. To better understand the process of L. monocytogenes biofilm development, and to investigate ways in which colonization of surfaces might be prevented, we developed a microtiter biofilm assay suitable for high throughput screening. The assay was used to identify small molecules (protein kinase inhibitors and previously FDA-approved bioactive drugs) that modulate L.