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https://www.readbyqxmd.com/read/28523919/editing-plants-for-virus-resistance-using-crispr-cas
#1
J C Green, J S Hu
This minireview summarizes recent advancements using the clustered regularly interspaced palindromic repeats-associated nuclease systems (CRISPR-Cas) derived from prokaryotes to breed plants resistant to DNA and RNA viruses. The CRISPR-Cas system represents a powerful tool able to edit and insert novel traits into plants precisely at chosen loci offering enormous advantages to classical breeding. Approaches to engineering plant virus resistance in both transgenic and non-transgenic plants are discussed. Iterations of the CRISPR-Cas system, FnCas9 and C2c2 capable of editing RNA in eukaryotic cells offer a particular advantage for providing resistance to RNA viruses which represent the great majority of known plant viruses...
2017: Acta Virologica
https://www.readbyqxmd.com/read/28523558/epigenome-editing-in-the-brain
#2
Pavel Bashtrykov, Albert Jeltsch
Epigenome editing aims for an introduction or removal of chromatin marks at a defined genomic region using artificial EpiEffectors resulting in a modulation of the activity of the targeted functional DNA elements. Rationally designed EpiEffectors consist of a targeting DNA-binding module (such as a zinc finger protein, TAL effector, or CRISPR/Cas complex) and usually, but not exclusively, a catalytic domain of a chromatin-modifying enzyme. Epigenome editing opens a completely new strategy for basic research of the central nervous system and causal treatment of psychiatric and neurological diseases, because rewriting of epigenetic information can lead to the direct and durable control of the expression of disease-associated genes...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28522157/antiviral-goes-viral-harnessing-crispr-cas9-to-combat-viruses-in-humans
#3
REVIEW
Jasper Adriaan Soppe, Robert Jan Lebbink
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems are RNA-guided sequence-specific prokaryotic antiviral immune systems. In prokaryotes, small RNA molecules guide Cas effector endonucleases to invading foreign genetic elements in a sequence-dependent manner, resulting in DNA cleavage by the endonuclease upon target binding. A rewired CRISPR/Cas9 system can be used for targeted and precise genome editing in eukaryotic cells. CRISPR/Cas has also been harnessed to target human pathogenic viruses as a potential new antiviral strategy...
May 15, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28508226/erratum-to-introducing-precise-genetic-modifications-into-human-3pn-embryos-by-crispr-cas-mediated-genome-editing
#4
Xiangjin Kang, Wenyin He, Yuling Huang, Qian Yu, Yaoyong Chen, Xingcheng Gao, Xiaofang Sun, Yong Fan
No abstract text is available yet for this article.
May 15, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28506212/guideseq-a-bioconductor-package-to-analyze-guide-seq-datasets-for-crispr-cas-nucleases
#5
Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Hervé Pagès, Alper Kucukural, Manuel Garber, Scot A Wolfe
BACKGROUND: Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treating a variety of genetic disorders. In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites...
May 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28505256/crispr-cas-system-for-yeast-genome-engineering-advances-and-applications
#6
Vratislav Stovicek, Carina Holkenbrink, Irina Borodina
The methods based on the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system have quickly gained popularity for genome editing and transcriptional regulation in many organisms, including yeast. This review aims to provide a comprehensive overview of CRISPR application for different yeast species: from basic principles and genetic design to applications.
May 15, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28489428/a-single-molecule-view-of-genome-editing-proteins-biophysical-mechanisms-for-tales-and-crispr-cas9
#7
Luke Cuculis, Charles M Schroeder
Exciting new advances in genome engineering have unlocked the potential to radically alter the treatment of human disease. In this review, we discuss the application of single-molecule techniques to uncover the mechanisms behind two premier classes of genome editing proteins: transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas). These technologies have facilitated a striking number of gene editing applications in a variety of organisms; however, we are only beginning to understand the molecular mechanisms governing the DNA editing properties of these systems...
May 10, 2017: Annual Review of Chemical and Biomolecular Engineering
https://www.readbyqxmd.com/read/28487566/the-invasive-neisseria-meningitidis-menc-cc103-from-brazil-is-characterized-by-an-accessory-gene-repertoire
#8
Michel Abanto Marin, Erica Fonseca, Fernando Encinas, Fernanda Freitas, Dhian Almeida Camargo, Roney Santos Coimbra, Ivano de Filippis, Ana Carolina Vicente
Neisseria meningitidis infections are a major issue for global health. The invasive MenC ST-103 clonal complex (CC103) has been the most prevalent in meningococcal outbreaks in Brazil, occurring also in several countries worldwide. Here we have analysed the population structure and accessory genome of MenC CC103 strains from a global perspective. An in-depth phylogenomic analysis revealed a lineage of N. meningitidis causing meningitis in Brazil and the United Kingdom. This lineage was also characterized as harbouring a particular accessory genome composed of CRISPR/Cas and restriction modification systems...
May 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28479296/the-mammalian-malonyl-coa-synthetase-acsf3-is-required-for-mitochondrial-protein-malonylation-and-metabolic-efficiency
#9
Caitlyn E Bowman, Susana Rodriguez, Ebru S Selen Alpergin, Michelle G Acoba, Liang Zhao, Thomas Hartung, Steven M Claypool, Paul A Watkins, Michael J Wolfgang
Malonyl-coenzyme A (malonyl-CoA) is a central metabolite in mammalian fatty acid biochemistry generated and utilized in the cytoplasm; however, little is known about noncanonical organelle-specific malonyl-CoA metabolism. Intramitochondrial malonyl-CoA is generated by a malonyl-CoA synthetase, ACSF3, which produces malonyl-CoA from malonate, an endogenous competitive inhibitor of succinate dehydrogenase. To determine the metabolic requirement for mitochondrial malonyl-CoA, ACSF3 knockout (KO) cells were generated by CRISPR/Cas-mediated genome editing...
April 26, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28479163/cell-penetrating-peptides-cpps-from-delivery-of-nucleic-acids-and-antigens-to-transduction-of-engineered-nucleases-for-application-in-transgenesis
#10
REVIEW
Gandhi Rádis-Baptista, Iana S Campelo, Jean-Étienne R L Morlighem, Luciana M Melo, Vicente J F Freitas
Cell-penetrating peptides (CPPs) have been studied for their capacity to translocate across the lipid membrane of several cell types. In membrane translocation, these peptides can remarkably transport biologically active hydrophilic molecules, such as pharmaceuticals, nucleic acids (DNA and RNA) and even high-molecular-weight proteins, Fig. 3 into the cell cytoplasm and organelles. The development of CPPs as transduction agents includes the modification of gene and protein expression, the reprogramming and differentiation of induced pluripotent stem cells and the preparation of cellular vaccines...
May 4, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28475872/rna-targeting-by-functionally-orthogonal-type-vi-a-crispr-cas-enzymes
#11
Alexandra East-Seletsky, Mitchell R O'Connell, David Burstein, Gavin J Knott, Jennifer A Doudna
CRISPR adaptive immunity pathways protect prokaryotic cells against foreign nucleic acids using CRISPR RNA (crRNA)-guided nucleases. In type VI-A CRISPR-Cas systems, the signature protein Cas13a (formerly C2c2) contains two separate ribonuclease activities that catalyze crRNA maturation and ssRNA degradation. The Cas13a protein family occurs across different bacterial phyla and varies widely in both protein sequence and corresponding crRNA sequence conservation. Although grouped phylogenetically together, we show that the Cas13a enzyme family comprises two distinct functional groups that recognize orthogonal sets of crRNAs and possess different ssRNA cleavage specificities...
May 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28473398/complete-genome-sequence-of-dolosigranulum-pigrum-from-a-patient-with-interstitial-lung-disease-using-single-molecule-real-time-sequencing-technology
#12
Rituparna Mukhopadhyay, Joselita Joaquin, Robin Hogue, Susan Fitzgerald, Guillaume Jospin, Kristin Mars, Jonathan A Eisen, Vishnu Chaturvedi
The whole genome sequence of Dolosigranulum pigrum isolated from the blood of a patient with interstitial lung disease was sequenced with the Pacific Biosciences RS II platform. The genome size is 2.1 Mb with 2,127 annotated coding sequences; it contained two clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) systems.
May 4, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28472712/casposons-mobile-genetic-elements-that-gave-rise-to-the-crispr-cas-adaptation-machinery
#13
REVIEW
Mart Krupovic, Pierre Béguin, Eugene V Koonin
A casposon, a member of a distinct superfamily of archaeal and bacterial self-synthesizing transposons that employ a recombinase (casposase) homologous to the Cas1 endonuclease, appears to have given rise to the adaptation module of CRISPR-Cas systems as well as the CRISPR repeats themselves. Comparison of the mechanistic features of the reactions catalyzed by the casposase and the Cas1-Cas2 heterohexamer, the CRISPR integrase, reveals close similarity but also important differences that explain the requirement of Cas2 for integration of short DNA fragments, the CRISPR spacers...
May 1, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28469255/automated-multiplex-genome-scale-engineering-in-yeast
#14
Tong Si, Ran Chao, Yuhao Min, Yuying Wu, Wen Ren, Huimin Zhao
Genome-scale engineering is indispensable in understanding and engineering microorganisms, but the current tools are mainly limited to bacterial systems. Here we report an automated platform for multiplex genome-scale engineering in Saccharomyces cerevisiae, an important eukaryotic model and widely used microbial cell factory. Standardized genetic parts encoding overexpression and knockdown mutations of >90% yeast genes are created in a single step from a full-length cDNA library. With the aid of CRISPR-Cas, these genetic parts are iteratively integrated into the repetitive genomic sequences in a modular manner using robotic automation...
May 4, 2017: Nature Communications
https://www.readbyqxmd.com/read/28458663/h-ns-mutation-mediated-crispr-cas-activation-inhibits-phage-release-and-toxin-production-of-escherichia-coli-stx2-phage-lysogen
#15
Qiang Fu, Shiyu Li, Zhaofei Wang, Wenya Shan, Jingjiao Ma, Yuqiang Cheng, Hengan Wang, Yaxian Yan, Jianhe Sun
Shiga toxin-converting bacteriophages (Stx phages) carry the stx gene and convert nonpathogenic bacterial strains into Shiga toxin-producing bacteria. There is limited understanding of the effect that an Escherichia coli (E. coli) clustered regularly interspaced short palindromic repeats (CRISPR)-Cas adaptive immune system has on Stx phage lysogen. We investigated heat-stable nucleoid-structuring (H-NS) mutation-mediated CRISPR-Cas activation and its effect on E. coli Stx2 phage lysogen. The Δhns mutant (MG1655Δhns) of the E...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28448738/site-specific-recruitment-of-epigenetic-factors-with-a-modular-crispr-cas-system
#16
Tobias Anton, Sebastian Bultmann
Dissecting the complex network of epigenetic modifications requires tools that combine precise recognition of DNA sequences with the capability to modify epigenetic marks. The CRISPR/Cas system has been proven to be a valuable addition to existing methodologies that fulfill these tasks. So far, sequence-specific editing of epigenetic modifications such as DNA methylation and histone posttranslational modifications relied on direct fusions of enzymatically inactivated Cas9 (dCas9) with epigenetic effectors. Here, we report a novel, modular system that facilitates the recruitment of any GFP-tagged protein to desired genomic loci...
February 23, 2017: Nucleus
https://www.readbyqxmd.com/read/28448636/successful-vitrification-of-pronuclear-stage-pig-embryos-with-a-novel-cryoprotective-agent-carboxylated-%C3%AE%C2%B5-poly-l-lysine
#17
Maki Kamoshita, Tsubasa Kato, Katsuyoshi Fujiwara, Takafumi Namiki, Kazuaki Matsumura, Suong-Hyu Hyon, Junya Ito, Naomi Kashiwazaki
Vitrification is a powerful tool for the efficient production of offspring derived from cryopreserved oocytes or embryos in mammalian species including domestic animals. Genome editing technologies such as transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated (Cas)9 are now available even for domestic species, suggesting that the vitrification of embryos at the pronuclear stage (PN) will be more important because they could provide genomic host cells to be targeted by TALENs or CRISPR/Cas9...
2017: PloS One
https://www.readbyqxmd.com/read/28445233/preclinical-models-for-translational-sarcoma-research
#18
Rainer Hamacher, Sebastian Bauer
PURPOSE OF REVIEW: Sarcoma is a basket term for mesenchymal tumors for which more than 75 genetically and histologically distinct subtypes are recognized. Therapeutic progress has largely been achieved with classical chemotherapeutic drugs that were tested in empirical clinical trials. However, outcome in metastatic patients remains poor and with few exceptions numerous trials have failed or only provided limited improvement in recent years. RECENT FINDINGS: Given the genomic heterogeneity, preclinical model systems will be indispensable to identify new molecular targets and to prioritize drugs and drug combinations...
April 25, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/28444368/simultaneous-targeting-of-multiple-gene-homeologues-to-alter-seed-oil-production-in-camelina-sativa
#19
J A Aznar-Moreno, T P Durrett
The ability to easily transform Camelina sativa with biosynthetic enzymes derived from other plants has made this oil seed crop an ideal platform for the production of unusual lipids valuable for different applications. However, in addition to expressing transgenic enzymes, the suppression of endogenous enzyme activity to reduce competition for common substrates or cofactors is also required to enhance the production of target compounds. As camelina possesses a relatively undifferentiated hexaploid genome, up to three gene homeologues can encode for any particular enzymatic activity, complicating efforts to alter endogenous biosynthetic pathways...
April 21, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28443611/corrigendum-the-driving-force-of-prophages-and-crispr-cas-system-in-the-evolution-of-cronobacter-sakazakii
#20
Haiyan Zeng, Jumei Zhang, Chensi Li, Tengfei Xie, Na Ling, Qingping Wu, Yingwang Ye
No abstract text is available yet for this article.
April 26, 2017: Scientific Reports
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