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Efficient Genome Editing of an Extreme Thermophile, Thermus
www.nature.com/scientificreports OPEN Efcient genome editing of an extreme thermophile, Thermus thermophilus, using a thermostable Cas9 variant Bjorn Thor Adalsteinsson1*, Thordis Kristjansdottir1,2, William Merre3, Alexandra Helleux4, Julia Dusaucy5, Mathilde Tourigny4, Olafur Fridjonsson1 & Gudmundur Oli Hreggvidsson1,2 Thermophilic organisms are extensively studied in industrial biotechnology, for exploration of the limits of life, and in other contexts. Their optimal growth at high temperatures presents a challenge for the development of genetic tools for their genome editing, since genetic markers and selection substrates are often thermolabile. We sought to develop a thermostable CRISPR-Cas9 based system for genome editing of thermophiles. We identifed CaldoCas9 and designed an associated guide RNA and showed that the pair have targetable nuclease activity in vitro at temperatures up to 65 °C. We performed a detailed characterization of the protospacer adjacent motif specifcity of CaldoCas9, which revealed a preference for 5′-NNNNGNMA. We constructed a plasmid vector for the delivery and use of the CaldoCas9 based genome editing system in the extreme thermophile Thermus thermophilus at 65 °C. Using the vector, we generated gene knock-out mutants of T. thermophilus, targeting genes on the bacterial chromosome and megaplasmid. Mutants were obtained at a frequency of about 90%. We demonstrated that the vector can be cured from mutants for a subsequent round of genome editing. CRISPR-Cas9 based genome editing has not been reported previously in the extreme thermophile T. thermophilus. These results may facilitate development of genome editing tools for other extreme thermophiles and to that end, the vector has been made available via the plasmid repository Addgene. -
How Human H1 Histone Recognizes DNA
molecules Article How Human H1 Histone Recognizes DNA Olesya P. Luzhetskaya, Sergey E. Sedykh and Georgy A. Nevinsky * Institute of Chemical Biology and Fundamental Medicine, SD of Russian Academy of Sciences, 8 Lavrentiev Ave., 630090 Novosibirsk, Russia; [email protected] (O.P.L.); [email protected] (S.E.S.) * Correspondence: [email protected]; Tel.: +7-383-363-51-26; Fax: +7-383-363-51-53 Received: 11 August 2020; Accepted: 1 October 2020; Published: 5 October 2020 Abstract: Linker H1 histone is one of the five main histone proteins (H1, H2A, H2B, H3, and H4), which are components of chromatin in eukaryotic cells. Here we have analyzed the patterns of DNA recognition by free H1 histone using a stepwise increase of the ligand complexity method; the affinity of H1 histone for various single- and double-stranded oligonucleotides (d(pN)n; n = 1–20) was evaluated using their competition with 12-mer [32P]labeled oligonucleotide and protein–oligonucleotide complex delaying on nitrocellulose membrane filters. It was shown that minimal ligands of H1 histone (like other DNA-dependent proteins and enzymes) are different mononucleotides (dNMPs; Kd = (1.30 0.2) 2 ± 10 M). An increase in the length of single-stranded (ss) homo- and hetero-oligonucleotides (d(pA)n, × − d(pT)n, d(pC)n, and d(pN)n with different bases) by one nucleotide link regardless of their bases, leads to a monotonic increase in their affinity by a factor of f = 3.0 0.2. This factor f corresponds ± to the Kd value = 1/f characterizing the affinity of one nucleotide of different ss d(pN)n for H1 at n = 2–6 (which are covered by this protein globule) is approximately 0.33 0.02 M. -
Secretariat of the CBD Technical Series No. 82 Convention on Biological Diversity
Secretariat of the CBD Technical Series No. 82 Convention on Biological Diversity 82 SYNTHETIC BIOLOGY FOREWORD To be added by SCBD at a later stage. 1 BACKGROUND 2 In decision X/13, the Conference of the Parties invited Parties, other Governments and relevant 3 organizations to submit information on, inter alia, synthetic biology for consideration by the Subsidiary 4 Body on Scientific, Technical and Technological Advice (SBSTTA), in accordance with the procedures 5 outlined in decision IX/29, while applying the precautionary approach to the field release of synthetic 6 life, cell or genome into the environment. 7 Following the consideration of information on synthetic biology during the sixteenth meeting of the 8 SBSTTA, the Conference of the Parties, in decision XI/11, noting the need to consider the potential 9 positive and negative impacts of components, organisms and products resulting from synthetic biology 10 techniques on the conservation and sustainable use of biodiversity, requested the Executive Secretary 11 to invite the submission of additional relevant information on this matter in a compiled and synthesised 12 manner. The Secretariat was also requested to consider possible gaps and overlaps with the applicable 13 provisions of the Convention, its Protocols and other relevant agreements. A synthesis of this 14 information was thus prepared, peer-reviewed and subsequently considered by the eighteenth meeting 15 of the SBSTTA. The documents were then further revised on the basis of comments from the SBSTTA 16 and peer review process, and submitted for consideration by the twelfth meeting of the Conference of 17 the Parties to the Convention on Biological Diversity. -
Combatting Monsanto
Picture: Grassroots International Combatting Monsanto Grassroots resistance to the corporate power of agribusiness in the era of the ‘green economy’ and a changing climate La Via Campesina, Friends of the Earth International, Combat Monsanto Technical data name: “Combatting Monsanto Grassroots resistance to the corporate power of agribusiness in the era of the ‘green economy’ and a changing climate” author: Joseph Zacune ([email protected]) with contributions from activists around the world editing: Ronnie Hall ([email protected]) design and layout: Nicolás Medina – REDES-FoE Uruguay March 2012 Combatting Monsanto Grassroots resistance to the corporate power of agribusiness in the era of the ‘green economy’ and a changing climate INDEX Executive summary / 2 Company profile - Monsanto / 3 Opposition to Monsanto in Europe / 5 A decade of French resistance to GMOs / 6 Spanish movements against GM crops / 9 German farmers’ movement for GM-free regions / 10 Organising a movement for food sovereignty in Europe / 10 Monsanto, Quit India! / 11 Bt brinjal and biopiracy / 11 Bt cotton dominates cotton sector / 12 Spiralling debt still triggering suicides / 12 Stopping Monsanto’s new public-private partnerships / 13 Resistance to Monsanto in Latin America / 14 Brazilian peasant farmers’ movement against agribusiness / 14 Ten-year moratorium on GM in Peru / 15 Landmark ruling on toxic soy in Argentina / 15 Haitians oppose seed aid / 16 Guatemalan networks warn of new biosafety proposals / 17 Battle-lines drawn in the United States / 17 Stopping the -
Re-Coding the ‘Corrupt’ Code: CRISPR-Cas9 Interventions in Human Germ Line Editing
Re-coding the ‘corrupt’ code: CRISPR-Cas9 interventions in human germ line editing CRISPR-Cas9, Germline Intervention, Human Cognition, Human Rights, International Regulation Master Thesis Tilburg University- Law and Technology 2018-19 Tilburg Institute for Law, Technology, and Society (TILT) October 2019 Student: Srishti Tripathy Supervisors: Prof. Dr. Robin Pierce SRN: 2012391 Dr. Emre Bayamlioglu ANR: 659785 Re-coding the ‘corrupt’ code CRISPR-Cas9, Germline Intervention, Human Cognition, Human Rights, International Regulation This page is intentionally left blank 2 Re-coding the ‘corrupt’ code CRISPR-Cas9, Germline Intervention, Human Cognition, Human Rights, International Regulation 3 Re-coding the ‘corrupt’ code CRISPR-Cas9, Germline Intervention, Human Cognition, Human Rights, International Regulation Table of Contents CHAPTER 1: Introduction .............................................................................................................. 6 1.1 Introduction and Review - “I think I’m crazy enough to do it” ......................................................................... 6 1.2 Research Question and Sub Questions .......................................................................................................................... 9 1.4 Methodology ............................................................................................................................................................................. 9 1.4 Thesis structure: ................................................................................................................................................................. -
The Deadlock in European GM Crop Authorisations As a Wicked Problem by Design
The Deadlock in European GM Crop Authorisations as a Wicked Problem by Design A need for Repoliticisation of the Decision-making Process Ruth Mampuys The Deadlock in European GM Crop Authorisations as a Wicked Problem by Design A need for Repoliticisation of the Decision-making Process Ruth Mampuys Colofon Sociology, Theory and Methodology | Erasmus School of Law | 2020 Author: Ruth Mampuys Thesis design & layout: Bart Erkamp Cover design: Matteo Bettoni The Deadlock in European GM Crop Authorisations as a Wicked Problem by Design A need for Repoliticisation of the Decision-making Process Thesis To obtain the degree of Doctor from the Erasmus University Rotterdam By command of the rector magnificus Prof.dr. F.A. van der Duijn Schouten and in accordance with the decision of the Doctorate Board. The public defence shall be held on Thursday 28 january 2021 at 15:30 hrs by Ruth Mampuys born in Enschede, the Netherlands Doctoral Committee Promotors: Prof. dr. W. van der Burg Prof. dr. F.W.A. Brom Other members: Prof. dr. A. Arcuri Prof. dr. K. Millar Prof. dr. J.E.J. Prins Copromotor: Dr. L.M. Poort CONTENTS PREFACE 1 LIST OF ABBREVIATIONS AND ACRONYMS 5 CHAPTER 1 Biotechnology governance: why, how and by whom? 9 1. Introduction 11 2. Varying definitions of biotechnology and GMOs 14 3. Recurring themes in discussions about biotechnology 17 3.1 Fundamental moral perspectives 18 3.2 Attitudes on risks/benefits 19 3.3 Broader issues 20 4. Regulatory framework for GMOs in Europe 21 4.1 Prerequisite: an environmental risk and food safety assessment 24 4.2 Regulatory decision-making: Comitology 25 4.3 Decision-making in practice 30 5. -
The 50Th Anniversary of the Discovery of Trisomy 21: the Past, Present, and Future of Research and Treatment of Down Syndrome
REVIEW The 50th anniversary of the discovery of trisomy 21: The past, present, and future of research and treatment of Down syndrome Andre´Me´garbane´, MD, PhD1,2, Aime´ Ravel, MD1, Clotilde Mircher, MD1, Franck Sturtz, MD, PhD1,3, Yann Grattau, MD1, Marie-Odile Rethore´, MD1, Jean-Maurice Delabar, PhD4, and William C. Mobley, MD, PhD5 Abstract: Trisomy 21 or Down syndrome is a chromosomal disorder HISTORICAL REVIEW resulting from the presence of all or part of an extra Chromosome 21. Clinical description It is a common birth defect, the most frequent and most recognizable By examining artifacts from the Tumaco-La Tolita culture, form of mental retardation, appearing in about 1 of every 700 newborns. which existed on the border between current Colombia and Although the syndrome had been described thousands of years before, Ecuador approximately 2500 years ago, Bernal and Briceno2 it was named after John Langdon Down who reported its clinical suspected that certain figurines depicted individuals with Tri- description in 1866. The suspected association of Down syndrome with somy 21, making these potteries the earliest evidence for the a chromosomal abnormality was confirmed by Lejeune et al. in 1959. existence of the syndrome. Martinez-Frias3 identified the syn- Fifty years after the discovery of the origin of Down syndrome, the term drome in a terra-cotta head from the Tolteca culture of Mexico “mongolism” is still inappropriately used; persons with Down syn- in 500 patients with AD in which the facial features of Trisomy drome are still institutionalized. Health problems associated with that 21 are clearly displayed. -
Comparative Genomics of the Restriction-Modification Systems in Helicobacter Pylori
Comparative genomics of the restriction-modification systems in Helicobacter pylori Lee-Fong Lin, Janos Posfai, Richard J. Roberts, and Huimin Kong* New England Biolabs, Inc., 32 Tozer Road, Beverly, MA 01915 Communicated by Charles R. Cantor, Sequenom Industrial Genomics, Inc., San Diego, CA, December 22, 2000 (received for review October 31, 2000) Helicobacter pylori is a Gram-negative bacterial pathogen with a small are subject to loss or gain of a repeat unit, presumably through genome of 1.64–1.67 Mb. More than 20 putative DNA restriction- slipped-strand mispairing during replication. This results in frame- modification (R-M) systems, comprising more than 4% of the total shifting, which can alternatively activate or inactivate genes (10). genome, have been identified in the two completely sequenced H. Tetranucleotide repeats were found in a Type III DNA methylase pylori strains, 26695 and J99, based on sequence similarities. In this gene and the length of the repeat tract determined the phase study, we have investigated the biochemical activities of 14 Type II variation rate (11). In the case of the H. pylori 26695 genome, 27 R-M systems in H. pylori 26695. Less than 30% of the Type II R-M putative genes that contain simple sequence repeats and that may systems in 26695 are fully functional, similar to the results obtained be subject to phase variation have been identified. These putative from strain J99. Although nearly 90% of the R-M genes are shared by phase-variable elements can be divided into three groups: lipopoly- the two H. pylori strains, different sets of these R-M genes are saccharide (LPS) biosynthesis, cell-surface-associated proteins and functionally active in each strain. -
Numerical and Structural Chromosome Aberrations in Cauliflower (Brassica Oleracea Var
Numerical and structural chromosome aberrations in cauliflower (Brassica oleracea var. botrytis) and Arabidopsis thaliana Xianwen Ji Thesis committee Promotor Prof. Dr J.H.S.G.M. de Jong Personal chair at the Laboratory of Genetics Wageningen University Co-promotor Dr E. Wijnker Researcher at the University of Hamburg, Germany Other members Prof. Dr G.C. Angenent, Wageningen University Dr G.F. Sanchez Perez, Wageningen University Dr A.B. Bonnema, Wageningen University Dr K. van Dun, Rijk Zwaan Breeding Company, Fijnaart, the Netherlands This research was conducted under the auspices of the Graduate School of Experimental Plant Sciences Numerical and structural chromosome aberrations in cauliflower (Brassica oleracea var. botrytis) and Arabidopsis thaliana Xianwen Ji Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday 5 December 2014 at 1.30 p.m. in the Aula Xianwen Ji Numerical and structural chromosome aberrations in cauliflower Brassica( oleracea var. botrytis) and Arabidopsis thaliana 137 pages PhD thesis, Wageningen University, Wageningen, NL (2014) With references, with summaries in English, Dutch and Chinese ISBN 978-94-6257-160-0 Contents Chapter 1 General Introduction 7 Chapter 2 FISH painting with repetitive DNA sequences for chromosome identification in aneuploid cauliflower (Brassica oleracea L. var. botrytis) 29 Chapter 3 Cross-species chromosome painting with Arabidopsis BACs on cauliflower (Brassica oleracea L. var. botrytis for karyotype analysis and chromosome identification 47 Chapter 4 Meiotic aberrations leading to aneuploidy in Cauliflower (Brassica oleracea L. -
Biotech Gallery Gene-Ius Resources Brow Se Select Language ▼
6/14/2014 Madagascar student prank shows March Against Monsanto has heartless agenda | Genetic Literacy Project Subscribe to Our Daily or Weekly Newsletter Follow Like 2.3k Follow 1,759 follow ers 197 Enter Your Email Address → Search About Human Agriculture Biotech Gallery Gene-ius Resources Brow se Select Language ▼ Biotech Gallery March Against Monsanto Madagascar student prank shows March Against Monsanto has heartless agenda Dustin Eirdosh | June 10, 2014 | Genetic Literacy Project Like 513 Tw eet 89 Share 5 15 426 On May 30, the global group March Against Monsanto (see GLP Facts) held its third coordinated protest in hundreds of Name March Against Monsanto Founded 2013 cities around the world. Hundreds of thousands of people Type Advocacy Organization reportedly participated. But what does this group really Founder(s) Tami Canal Website http://w w w .march- stand for beyond their obvious disdain for one company, against-monsanto.com/ Monsanto, and biotechnology? One student in Madagascar VIEW GLP FACTS embarked on a mission to find out by setting up a fake “Madagascar Against Monsanto” group and posting outrageous pictures and statements, to see if activists would VIEW BIOTECH GALLERY ARCHIVE embrace or reject his bizarre extremism. What happened? *********** Related Articles: Madagascar student prank show s “Sir, I am afraid for my future, afraid because March Against Monsanto has threatened me and my community,” March Against Monsanto has heartless agenda Navid Rakotofala told me amidst a fury of reactions to his unconventional expose prank to explore just how outrageously far “mainstream” anti-GMO activists would go to to spread their message. -
Evolution on the X Chromosome: Unusual Patterns and Processes
REVIEWS Evolution on the X chromosome: unusual patterns and processes Beatriz Vicoso and Brian Charlesworth Abstract | Although the X chromosome is usually similar to the autosomes in size and cytogenetic appearance, theoretical models predict that its hemizygosity in males may cause unusual patterns of evolution. The sequencing of several genomes has indeed revealed differences between the X chromosome and the autosomes in the rates of gene divergence, patterns of gene expression and rates of gene movement between chromosomes. A better understanding of these patterns should provide valuable information on the evolution of genes located on the X chromosome. It could also suggest solutions to more general problems in molecular evolution, such as detecting selection and estimating mutational effects on fitness. Haldane’s rule Sex-chromosome systems have evolved independently the predictions of theoretical models of X-chromosome The disproportionate loss of many times, and have attracted much attention from evolution will shed light on the assumptions on which fitness to the heterogametic evolutionary geneticists. This work has mainly focused the models are based, such as the degree of dominance of sex in F1 hybrids between on the steps leading to the initial evolution of sex chro- mutations and the existence of opposing forces species. mosomes, and the genetic degeneration of Y and W of selection on males and females, leading to a better 1 Clade chromosomes . Here, we discuss the evolution of the understanding of the forces that shape the evolution of A group of species which share X chromosome in long-established sex-chromosome eukaryotic genomes. a common ancestor. -
Continuous Variation in Y-Chromosome Structure of Rumex Acetosa
Heredity 57 (1986) 247-254 The Genetical Society of Great Britain Received 16 December 1985 Continuous variation in Y-chromosome structure of Rumex acetosa A. S. Wilby and School of Biological Sciences, J. S. Parker Queen Mary College, Mile End Road, London El 4NS. The dioecious angiosperm Rumex acetosa has an XXIXY1Y2sex-chromosomesystem. Each V-chromosome is heterochromatic except for a minute terminal euchromatic pairing segment. The Vs are constant in size but have a variable centromere position. The centromeres can be located anywhere within the central 40 per cent of the chromosome but are excluded from the two distal 30 per cent regions. In a sample of 270 males from 18 different populations 68 distinct variants have been identified on the basis of V-morphology. All populations are highly polymorphic with a minimum of four variants in a sample of ten males. The origin and significance of this massive variability is considered in this paper. Increased mutation rate of the Ys may be implicated in maintenance of this variation. I NTRO DUCTI ON these "inert" Ys has been described (Vana, 1972) variation in their structure has been overlooked. Sex-determinationin animals is usually genic and Extensive heterochroinatic content is a charac- frequently associated with visibly-differentiated teristic of many Y- and W-chromosomes. Indeed, sex-chromosomes. Sex expression in plants, some have argued that the process of hetero- however, is usually more plastic, and is subject to chromatinisation itself was implicated in the initial environmental influences such as temperature and phase of sex-chromosome differentiation (Jones, photoperiod (Heslop-Harrison, 1957).