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clustered regularly interspaced short palindromic repeats

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https://www.readbyqxmd.com/read/28934361/restriction-modification-mediated-barriers-to-exogenous-dna-uptake-and-incorporation-employed-by-prevotella-intermedia
#1
Christopher D Johnston, Chelsey A Skeete, Alexey Fomenkov, Richard J Roberts, Susan R Rittling
Prevotella intermedia, a major periodontal pathogen, is increasingly implicated in human respiratory tract and cystic fibrosis lung infections. Nevertheless, the specific mechanisms employed by this pathogen remain only partially characterized and poorly understood, largely due to its total lack of genetic accessibility. Here, using Single Molecule, Real-Time (SMRT) genome and methylome sequencing, bisulfite sequencing, in addition to cloning and restriction analysis, we define the specific genetic barriers to exogenous DNA present in two of the most widespread laboratory strains, P...
2017: PloS One
https://www.readbyqxmd.com/read/28933359/a-prospective-treatment-option-for-lysosomal-storage-diseases-crispr-cas9-gene-editing-technology-for-mutation-correction-in-induced-pluripotent-stem-cells
#2
REVIEW
Chloe L Christensen, Francis Y M Choy
Ease of design, relatively low cost and a multitude of gene-altering capabilities have all led to the adoption of the sophisticated and yet simple gene editing system: clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9). The CRISPR/Cas9 system holds promise for the correction of deleterious mutations by taking advantage of the homology directed repair pathway and by supplying a correction template to the affected patient's cells. Currently, this technique is being applied in vitro in human-induced pluripotent stem cells (iPSCs) to correct a variety of severe genetic diseases, but has not as of yet been used in iPSCs derived from patients affected with a lysosomal storage disease (LSD)...
February 24, 2017: Diseases (Basel)
https://www.readbyqxmd.com/read/28932198/progress-and-prospects-of-crispr-cas-systems-in-insects-and-other-arthropods
#3
REVIEW
Dan Sun, Zhaojiang Guo, Yong Liu, Youjun Zhang
Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated gene Cas9 represent an invaluable system for the precise editing of genes in diverse species. The CRISPR/Cas9 system is an adaptive mechanism that enables bacteria and archaeal species to resist invading viruses and phages or plasmids. Compared with zinc finger nucleases and transcription activator-like effector nucleases, the CRISPR/Cas9 system has the advantage of requiring less time and effort. This efficient technology has been used in many species, including diverse arthropods that are relevant to agriculture, forestry, fisheries, and public health; however, there is no review that systematically summarizes its successful application in the editing of both insect and non-insect arthropod genomes...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28928211/the-crispr-spacer-space-is-dominated-by-sequences-from-species-specific-mobilomes
#4
Sergey A Shmakov, Vassilii Sitnik, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin
Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average)...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28928209/combining-comprehensive-analysis-of-off-site-lambda-phage-integration-with-a-crispr-based-means-of-characterizing-downstream-physiology
#5
Yu Tanouchi, Markus W Covert
During its lysogenic life cycle, the phage genome is integrated into the host chromosome by site-specific recombination. In this report, we analyze lambda phage integration into noncanonical sites using next-generation sequencing and show that it generates significant genetic diversity by targeting over 300 unique sites in the host Escherichia coli genome. Moreover, these integration events can have important phenotypic consequences for the host, including changes in cell motility and increased antibiotic resistance...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28919449/genome-editing-in-fishes-and-their-applications
#6
Bo Zhu, Wei Ge
There have been revolutionary progresses in genome engineering in the past few years. The newly-emerged genome editing technologies including zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats associated with Cas9 (CRISPR/Cas9) have enabled biological scientists to perform efficient and precise targeted genome editing in different species. Fish represent the largest group of vertebrates with many species having values for both scientific research and aquaculture industry...
September 14, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28918562/crispr-cas9-genome-editing-in-wheat
#7
Dongjin Kim, Burcu Alptekin, Hikmet Budak
Genome editing has been a long-term challenge for molecular biology research, particularly for plants possess complex genome. The recently discovered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a versatile tool for genome editing which enables editing of multiple genes based on the guidance of small RNAs. Even though the efficiency of CRISPR/Cas9 system has been shown with several studies from diploid plants, its application remains a challenge for plants with polyploid and complex genome...
September 16, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28913801/targeted-mutagenesis-in-hexaploid-bread-wheat-using-the-talen-and-crispr-cas-systems
#8
Yanpeng Wang, Yuan Zong, Caixia Gao
The use of sequence-specific transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats-associated system (CRISPR/Cas9) have provided powerful reverse genetic approaches to the targeted modification of genomes in numerous organisms. Both systems have been employed to generate loss-of-function alleles in bread wheat, by targeting multiple and single copies of genes. Here we present protocols for modifying the wheat genome using the two systems. The protocols include the design of TALEN and CRISPR/Cas9 target sites and their construction, evaluation of their activities in protoplasts, transformation of plants, and mutation screening...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28910979/crispr-cas9-based-efficient-genome-editing-in-staphylococcus-aureus
#9
Qi Liu, Yu Jiang, Lei Shao, Ping Yang, Bingbing Sun, Sheng Yang, Daijie Chen
Staphylococcus aureus is an important pathogenic bacterium prevalent in nosocomial infections and associated with high morbidity and mortality rates, which arise from the significant pathogenicity and multi-drug resistance. However, the typical genetic manipulation tools used to explore the relevant molecular mechanisms of S. aureus have multiple limitations: leaving a scar in the genome, comparatively low gene-editing efficiency, and prolonged experimental period. Here, we present a single-plasmid based on the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system which allows rapid and efficient chromosomal manipulation in S...
September 1, 2017: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/28905515/crispr-cas9-mediated-efficient-targeted-mutagenesis-in-grape-in-the-first-generation
#10
Xianhang Wang, Mingxing Tu, Dejun Wang, Jianwei Liu, Yajuan Li, Zhi Li, Yuejin Wang, Xiping Wang
The clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) system is a powerful tool for editing plant genomes. Efficient genome editing of grape (Vitis vinifera) suspension cells using the type II CRISPR/Cas9 system has been demonstrated; however, it has not been established whether this system can be applied to get biallelic mutations in the first generation of grape. In this current study, we designed four guide RNAs for the VvWRKY52 transcription factor gene for using with the CRISPR/Cas9 system, and obtained transgenic plants via Agrobacterium-mediated transformation, using somatic embryos of the Thompson Seedless cultivar...
September 14, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28904745/genome-editing-of-the-hiv-co-receptors-ccr5-and-cxcr4-by-crispr-cas9-protects-cd4-t-cells-from-hiv-1-infection
#11
Zhepeng Liu, Shuliang Chen, Xu Jin, Qiankun Wang, Kongxiang Yang, Chenlin Li, Qiaoqiao Xiao, Panpan Hou, Shuai Liu, Shaoshuai Wu, Wei Hou, Yong Xiong, Chunyan Kong, Xixian Zhao, Li Wu, Chunmei Li, Guihong Sun, Deyin Guo
BACKGROUND: The main approach to treat HIV-1 infection is combination antiretroviral therapy (cART). Although cART is effective in reducing HIV-1 viral load and controlling disease progression, it has many side effects, and is expensive for HIV-1 infected patients who must remain on lifetime treatment. HIV-1 gene therapy has drawn much attention as studies of genome editing tools have progressed. For example, zinc finger nucleases (ZFN), transcription activator like effector nucleases (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 have been utilized to successfully disrupt the HIV-1 co-receptors CCR5 or CXCR4, thereby restricting HIV-1 infection...
2017: Cell & Bioscience
https://www.readbyqxmd.com/read/28901971/xenotransplantation-past-present-and-future
#12
Burcin Ekser, Ping Li, David K C Cooper
PURPOSE OF REVIEW: To review the progress in the field of xenotransplantation with special attention to most recent encouraging findings which will eventually bring xenotransplantation to the clinic in the near future. RECENT FINDINGS: Starting from early 2000, with the introduction of galactose-α1,3-galactose (Gal)-knockout pigs, prolonged survival especially in heart and kidney xenotransplantation was recorded. However, remaining antibody barriers to non-Gal antigens continue to be the hurdle to overcome...
September 8, 2017: Current Opinion in Organ Transplantation
https://www.readbyqxmd.com/read/28899753/precise-gene-editing-of-chicken-na-h-exchange-type-1-chnhe1-confers-resistance-to-avian-leukosis-virus-subgroup-j-alv-j
#13
Hong Jo Lee, Kyung Youn Lee, Kyung Min Jung, Kyung Je Park, Ko On Lee, Jeong-Yong Suh, Yongxiu Yao, Venugopal Nair, Jae Yong Han
Avian leukosis virus subgroup J (ALV-J), first isolated in the late 1980s, has caused economic losses to the poultry industry in many countries. As all chicken lines studied to date are susceptible to ALV infection, there is enormous interest in developing resistant chicken lines. The ALV-J receptor, chicken Na(+)/H(+) exchange 1 (chNHE1) and the critical amino acid sequences involved in viral attachment and entry have already been characterized. However, there are no reported attempts to induce resistance to the virus by targeted genome modification of the receptor sequences...
September 9, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28894651/metacrast-reference-guided-extraction-of-crispr-spacers-from-unassembled-metagenomes
#14
Abraham G Moller, Chun Liang
Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide valuable insights into microbial ecology by linking environmental viruses to their microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool-MetaCRAST) that constrains searches based on user-specified direct repeats (DRs)...
2017: PeerJ
https://www.readbyqxmd.com/read/28894415/loss-of-fmrp-impaired-hippocampal-long-term-plasticity-and-spatial-learning-in-rats
#15
Yonglu Tian, Chaojuan Yang, Shujiang Shang, Yijun Cai, Xiaofei Deng, Jian Zhang, Feng Shao, Desheng Zhu, Yunbo Liu, Guiquan Chen, Jing Liang, Qiang Sun, Zilong Qiu, Chen Zhang
Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by mutations in the FMR1 gene that inactivate expression of the gene product, the fragile X mental retardation 1 protein (FMRP). In this study, we used clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) technology to generate Fmr1 knockout (KO) rats by disruption of the fourth exon of the Fmr1 gene. Western blotting analysis confirmed that the FMRP was absent from the brains of the Fmr1 KO rats (Fmr1(exon4-KO) )...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28893837/crrnas-in-porphyromonas-gingivalis-crispr-cas-i-c-system
#16
Michal Burmistrz, Jose Ignacio Rodriguez Martinez, Daniel Krochmal, Dominika Staniec, Krzysztof Pyrc
The CRISPR-Cas (clustered regularly interspaced short palindromic repeats - CRISPR associated) system is unique to prokaryotes and provides the majority of bacteria and archaea with immunity against nucleic acids of foreign origin. crRNAs are the key element of this system, since they are responsible for its selectivity and effectiveness. Typical crRNAs consist of a spacer sequence flanked with 5' and 3' handles originating from repeat sequences that are important for recognition of these small RNAs by the Cas machinery...
September 11, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28892093/rapid-generation-of-col7a1-mouse-model-of-recessive-dystrophic-epidermolysis-bullosa-and-partial-rescue-via-immunosuppressive-dermal-mesenchymal-stem-cells
#17
Beau R Webber, Kyle T O'Connor, Ron T McElmurry, Elise N Durgin, Cindy R Eide, Christopher J Lees, Megan J Riddle, Wendy E Mathews, Natasha Y Frank, Mark A Kluth, Christoph Ganss, Branden S Moriarity, Markus H Frank, Mark J Osborn, Jakub Tolar
Recessive dystrophic epidermolysis bullosa (RDEB) is a debilitating and ultimately lethal blistering disease caused by mutations to the Col7a1 gene. Development of novel cell therapies for the treatment of RDEB would be fostered by having immunodeficient mouse models able to accept human cell grafts; however, immunodeficient models of many genodermatoses such as RDEB are lacking. To overcome this limitation, we combined the clustered regularly interspaced short palindromic repeats and associated nuclease (CRISPR/Cas9) system with microinjection into NOD/SCID IL2rγc(null) (NSG) embryos to rapidly develop an immunodeficient Col7a1(-/-) mouse model of RDEB...
September 11, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28882870/crispr-cas9-mediated-gene-editing-in-human-ipsc-derived-macrophage-reveals-lysosomal-acid-lipase-function-in-human-macrophages
#18
Hanrui Zhang, Jianting Shi, Melanie A Hachet, Chenyi Xue, Robert C Bauer, Hongfeng Jiang, Wenjun Li, Junichiro Tohyama, John Millar, Jeffrey Billheimer, Michael C Phillips, Babak Razani, Daniel J Rader, Muredach P Reilly
OBJECTIVE: To gain mechanistic insights into the role of LIPA(lipase A), the gene encoding LAL (lysosomal acid lipase) protein, in human macrophages. APPROACH AND RESULTS: We used CRISPR (clustered regularly interspaced short palindromic repeats )/Cas9 (CRISPR-associated protein 9) technology to knock out LIPA in human induced pluripotent stem cells and then differentiate to macrophage (human-induced pluripotent stem cells-derived macrophage [IPSDM]) to explore the human macrophage LIPA loss-of-function phenotypes...
September 7, 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28879858/crispr-mediated-genome-engineering-and-its-application-in-industry
#19
Saeed Kaboli, Hasan Babazada
The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) method has been dramatically changing the field of genome engineering. It is a rapid, highly efficient and versatile tool for precise modification of genome that uses a guide RNA (gRNA) to target Cas9 to a specific sequence. This novel RNA-guided genome-editing technique has become a revolutionary tool in biomedical science and has many innovative applications in different fields. In this review, we briefly introduce the Cas9-mediated genome-editing tool, summarize the recent advances in CRISPR/Cas9 technology to engineer the genomes of a wide variety of organisms, and discuss their applications to treatment of fungal and viral disease...
September 7, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28879854/treating-genetic-disorders-using-state-of-the-art-technology
#20
Muhammad Jamal, Arif Ullah, Muhammad Ahsan, Rohit Tyagi, Zeshan Habib, Faheem Ahmad Khan, Khaista Rehman
CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR associated Protein 9), basically a bacterial immune system is now widely applicable to engineer genomes of a number of cells and organisms because of its simplicity and robustness. In research avenue the system has been optimized to regulate gene expression, modify epigenome and edit target locus. These applications make CRISPR/Cas9, a technology of choice to edit disease causing mutations as well as the epigenome more efficiently than ever before...
September 7, 2017: Current Issues in Molecular Biology
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