A comprehensive overview of computational resources to aid in precision genome editing with engineered nucleases

2016 ◽  
pp. bbw052 ◽  
Author(s):  
Vinita Periwal
Keyword(s):  
Genome Editing ◽  
Comprehensive Overview ◽  
Engineered Nucleases ◽  
Computational Resources

Adenoviral vector DNA for accurate genome editing with engineered nucleases

2014 ◽  
Vol 11 (10) ◽  
pp. 1051-1057 ◽  
Author(s):  
Maarten Holkers ◽  
Ignazio Maggio ◽  
Sara F D Henriques ◽  
Josephine M Janssen ◽  
Toni Cathomen ◽  
...  
Keyword(s):  
Genome Editing ◽  
Adenoviral Vector ◽  
Engineered Nucleases ◽  
Vector Dna

Framing constructicography

2019 ◽  
Vol 35 (1) ◽  
pp. 41-85 ◽  
Author(s):  
Hans C. Boas ◽  
Benjamin Lyngfelt ◽  
Tiago Timponi Torrent
Keyword(s):  
Construction Grammar ◽  
Frame Semantics ◽  
Comprehensive Overview ◽  
Form And Function ◽  
And Function ◽  
Computational Resources

Abstract Constructicography can be defined as a blend between Construction Grammar and Practical Lexicography, which aims at developing constructicons: repositories of form and function pairings in a language. In this paper, we present a comprehensive overview of this emerging field by (i) tracking the origins of both Frame Semantics and Construction Grammar and the repercussions of their intertwined developments to Computational Lexicography and Constructicography; (ii) comparing the impacts of the different degrees of interconnection between constructicons and framenets and (iii) discussing the possible applications of these resources. Also, we argue that Constructicography, while obviously building on the accumulated knowledge compiled by numerous Construction Grammar approaches to language, also contributes to its mother theory, since the effort to build coherent formalized computational resources forces constructionist analysis to go beyond describing families of constructions into the enterprise of describing a coherent construction grammar of a language.

scholarly journals Genome Editing with Engineered Nucleases in Plants

2014 ◽  
Vol 56 (3) ◽  
pp. 389-400 ◽  
Author(s):  
Y. Osakabe ◽  
K. Osakabe
Keyword(s):  
Genome Editing ◽  
Engineered Nucleases

Therapeutic genome editing with engineered nucleases

2017 ◽  
Vol 37 (01) ◽  
pp. 45-52 ◽  
Author(s):  
Simone Haas ◽  
Viviane Dettmer ◽  
Toni Cathomen
Keyword(s):  
Gene Therapy ◽  
Genome Editing ◽  
Genetic Disorders ◽  
Zinc Finger Nucleases ◽  
New Era ◽  
Engineered Nucleases ◽  
Genetic Interventions ◽  
Type Gene ◽  
Programmable Nucleases ◽  
Cancer Immunotherapies

SummaryTargeted genome editing with designer nucleases, such as zinc finger nucleases, TALE nucleases, and CRISPR-Cas nucleases, has heralded a new era in gene therapy. Genetic disorders, which have not been amenable to conventional gene-addition-type gene therapy approaches, such as disorders with dominant inheritance or diseases caused by mutations in tightly regulated genes, can now be treated by precise genome surgery. Moreover, engineered nucleases enable novel genetic interventions to fight infectious diseases or to improve cancer immunotherapies. Here, we review the development of the different classes of programmable nucleases, discuss the challenges and improvements in translating gene editing into clinical use, and give an outlook on what applications can expect to enter the clinic in the near future.

scholarly journals Oligonucleotide-Mediated Genome Editing Provides Precision and Function to Engineered Nucleases and Antibiotics in Plants

2016 ◽  
Vol 170 (4) ◽  
pp. 1917-1928 ◽  
Author(s):  
Noel J. Sauer ◽  
Javier Narváez-Vásquez ◽  
Jerry Mozoruk ◽  
Ryan B. Miller ◽  
Zachary J. Warburg ◽  
...  
Keyword(s):  
Genome Editing ◽  
Engineered Nucleases ◽  
And Function

scholarly journals The ethics of genome editing in non-human animals: a systematic review of reasons reported in the academic literature

2019 ◽  
Vol 374 (1772) ◽  
pp. 20180106 ◽  
Author(s):  
Nienke de Graeff ◽  
Karin R. Jongsma ◽  
Josephine Johnston ◽  
Sarah Hartley ◽  
Annelien L. Bredenoord
Keyword(s):  
Systematic Review ◽  
Genome Editing ◽  
Public Involvement ◽  
Comprehensive Overview ◽  
The Public ◽  
Academic Literature ◽  
Ethical Implications ◽  
Public Acceptability ◽  
Adaptive Immune Systems ◽  
Academic Debate

In recent years, new genome editing technologies have emerged that can edit the genome of non-human animals with progressively increasing efficiency. Despite ongoing academic debate about the ethical implications of these technologies, no comprehensive overview of this debate exists. To address this gap in the literature, we conducted a systematic review of the reasons reported in the academic literature for and against the development and use of genome editing technologies in animals. Most included articles were written by academics from the biomedical or animal sciences. The reported reasons related to seven themes: human health, efficiency, risks and uncertainty, animal welfare, animal dignity, environmental considerations and public acceptability. Our findings illuminate several key considerations about the academic debate, including a low disciplinary diversity in the contributing academics, a scarcity of systematic comparisons of potential consequences of using these technologies, an underrepresentation of animal interests, and a disjunction between the public and academic debate on this topic. As such, this article can be considered a call for a broad range of academics to get increasingly involved in the discussion about genome editing, to incorporate animal interests and systematic comparisons, and to further discuss the aims and methods of public involvement. This article is part of a discussion meeting issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.

Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae

2019 ◽  
Author(s):  
Beatriz T Magalhães ◽  
Anália Lourenço ◽  
Nuno F Azevedo
Keyword(s):  
Single Molecule ◽  
Structural Information ◽  
Computational Modelling ◽  
Main Process ◽  
Translation Process ◽  
Comprehensive Overview ◽  
Efficient Manner ◽  
Ribonucleic Acids ◽  
Scale Modelling ◽  
Computational Resources

Abstract This work provides a systematic and comprehensive overview of available resources for the molecular-scale modelling of the translation process through agent-based modelling. The case study is the translation in Saccharomyces cerevisiae, one of the most studied yeasts. The data curation workflow encompassed structural information about the yeast (i.e. the simulation environment), and the proteins, ribonucleic acids and other types of molecules involved in the process (i.e. the agents). Moreover, it covers the main process events, such as diffusion (i.e. motion of molecules in the environment) and collision efficiency (i.e. interaction between molecules). Data previously determined by wet-lab techniques were preferred, resorting to computational predictions/extrapolations only when strictly necessary. The computational modelling of the translation processes is of added industrial interest, since it may bring forward knowledge on how to control such phenomena and enhance the production of proteins of interest in a faster and more efficient manner.

scholarly journals Comparison of T7E1 and Surveyor Mismatch Cleavage Assays to Detect Mutations Triggered by Engineered Nucleases

2015 ◽  
Vol 5 (3) ◽  
pp. 407-415 ◽  
Author(s):  
Léna Vouillot ◽  
Aurore Thélie ◽  
Nicolas Pollet
Keyword(s):  
Genome Editing ◽  
Mutation Detection ◽  
Point Mutations ◽  
Targeted Mutagenesis ◽  
Single Nucleotide ◽  
Heteroduplex Dna ◽  
Hit Rate ◽  
Engineered Nucleases ◽  
Mismatch Cleavage ◽  
Surveyor Nuclease

Abstract Genome editing using engineered nucleases is used for targeted mutagenesis. But because genome editing does not target all loci with similar efficiencies, the mutation hit-rate at a given locus needs to be evaluated. The analysis of mutants obtained using engineered nucleases requires specific methods for mutation detection, and the enzyme mismatch cleavage method is used commonly for this purpose. This method uses enzymes that cleave heteroduplex DNA at mismatches and extrahelical loops formed by single or multiple nucleotides. Bacteriophage resolvases and single-stranded nucleases are used commonly in the assay but have not been compared side-by-side on mutations obtained by engineered nucleases. We present the first comparison of the sensitivity of T7E1 and Surveyor EMC assays on deletions and point mutations obtained by zinc finger nuclease targeting in frog embryos. We report the mutation detection limits and efficiencies of T7E1 and Surveyor. In addition, we find that T7E1 outperforms the Surveyor nuclease in terms of sensitivity with deletion substrates, whereas Surveyor is better for detecting single nucleotide changes. We conclude that T7E1 is the preferred enzyme to scan mutations triggered by engineered nucleases.

scholarly journals The position of the target site for engineered nucleases improves the aberrant mRNA clearance in in vivo genome editing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jae Hoon Lee ◽  
Sungsook Yu ◽  
Tae Wook Nam ◽  
Jae-il Roh ◽  
Young Jin ◽  
...  
Keyword(s):  
Genome Editing ◽  
Target Site ◽  
Engineered Nucleases
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