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clustered regularly interspaced short palindromic repeats

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https://www.readbyqxmd.com/read/29786424/tuning-gene-activity-by-inducible-and-targeted-regulation-of-gene-expression-in-minimal-bacterial-cells
#1
Ana M Mariscal, Shigeyuki Kakizawa, Jonathan Y Hsu, Kazuki Tanaka, Luis González-González, Alicia Broto, Enrique Querol, Maria Lluch-Senar, Carlos Piñero-Lambea, Lijie Sun, Philip D Weyman, Kim S Wise, Chuck Merryman, Gavin Tse, Adam J Moore, Clyde A Hutchison, Hamilton O Smith, Masaru Tomita, J Craig Venter, John I Glass, Jaume Piñol, Yo Suzuki
Functional genomics studies in minimal mycoplasma cells enable unobstructed access to some of the most fundamental processes in biology. Conventional transposon bombardment and gene knockout approaches often fail to reveal functions of genes that are essential for viability, where lethality precludes phenotypic characterization. Conditional inactivation of genes is effective for characterizing functions central to cell growth and division, but tools are limited for this purpose in mycoplasmas. Here we demonstrate systems for inducible repression of gene expression based on clustered regularly interspaced short palindromic repeats-mediated interference (CRISPRi) in Mycoplasma pneumoniae and synthetic Mycoplasma mycoides, two organisms with reduced genomes actively used in systems biology studies...
May 22, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29785946/-crispr-cas-systems-in-genome-engineering-of-bacteriophages
#2
Cai Jiao Liang, Fan Mei Meng, Yun Can Ai
Researches on CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) systems, that are adaptive immunity systems encoded by prokaryotes, have promoted the development of new genome-editing tools. Bacteriophages are not only the driving elements for the evolution of prokaryotes' CRISPR arrays, but also the targets of the CRISPR/Cas systems. Studies on functional genomics of bacteriophages have been lagging behind the discovery of new phage strains and the sequencing of their genomes...
May 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29783744/interplay-between-er-ca-2-binding-proteins-stim1-and-stim2-is-required-for-store-operated-ca-2-entry
#3
Heather A Nelson, Colin A Leech, Richard F Kopp, Michael W Roe
Store-operated calcium entry (SOCE), a fundamentally important homeostatic and Ca2+ signaling pathway in many types of cells, is activated by the direct interaction of stromal interaction molecule 1 (STIM1), an endoplasmic reticulum (ER) Ca2+ -binding protein, with Ca2+ -selective Orai1 channels localized in the plasma membrane. While much is known about the regulation of SOCE by STIM1, the role of stromal interaction molecule 2 (STIM2) in SOCE remains incompletely understood. Here, using clustered regularly interspaced short palindromic repeats -CRISPR associated protein 9 (CRISPR-Cas9) genomic editing and molecular imaging, we investigated the function of STIM2 in NIH 3T3 fibroblast and αT3 cell SOCE...
May 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29777358/generation-of-genetically-engineered-animals-using-engineered-endonucleases
#4
REVIEW
Jong Geol Lee, Young Hoon Sung, In-Jeoung Baek
The key to successful drug discovery and development is to find the most suitable animal model of human diseases for the preclinical studies. The recent emergence of engineered endonucleases is allowing for efficient and precise genome editing, which can be used to develop potentially useful animal models for human diseases. In particular, zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeat systems are revolutionizing the generation of diverse genetically-engineered experimental animals including mice, rats, rabbits, dogs, pigs, and even non-human primates that are commonly used for preclinical studies of the drug discovery...
May 17, 2018: Archives of Pharmacal Research
https://www.readbyqxmd.com/read/29776993/tumor-immune-evasion-arises-through-loss-of-tnf-sensitivity
#5
Conor J Kearney, Stephin J Vervoort, Simon J Hogg, Kelly M Ramsbottom, Andrew J Freeman, Najoua Lalaoui, Lizzy Pijpers, Jessica Michie, Kristin K Brown, Deborah A Knight, Vivien Sutton, Paul A Beavis, Ilia Voskoboinik, Phil K Darcy, John Silke, Joseph A Trapani, Ricky W Johnstone, Jane Oliaro
Immunotherapy has revolutionized outcomes for cancer patients, but the mechanisms of resistance remain poorly defined. We used a series of whole-genome clustered regularly interspaced short palindromic repeat (CRISPR)-based screens performed in vitro and in vivo to identify mechanisms of tumor immune evasion from cytotoxic lymphocytes [CD8+ T cells and natural killer (NK) cells]. Deletion of key genes within the tumor necrosis factor (TNF) signaling, interferon-γ (IFN-γ) signaling, and antigen presentation pathways provided protection of tumor cells from CD8+ T cell-mediated killing and blunted antitumor immune responses in vivo...
May 18, 2018: Science Immunology
https://www.readbyqxmd.com/read/29766738/the-role-of-gene-editing-in-neurodegenerative-diseases
#6
Hueng-Chuen Fan, Ching-Shiang Chi, Yih-Jing Lee, Jeng-Dau Tsai, Shinn-Zong Lin, Horng-Jyh Harn
Neurodegenerative diseases (NDs), at least including Alzheimer's, Huntington's, and Parkinson's diseases, have become the most dreaded maladies because there are no precise diagnostic tools or definite treatments for these debilitating diseases. The increased prevalence and a substantial impact on the social-economic and medical care of NDs propel governments to develop policies to counteract the impact. Although the etiologies of NDs are still unknown, growing evidence suggests that genetic, cellular, and circuit alternations may cause the generation of abnormal misfolded proteins, which uncontrolledly accumulate to damage and eventually overwhelm the protein-disposal mechanisms of these neurons, leading to a common pathological feature of NDs...
January 1, 2018: Cell Transplantation
https://www.readbyqxmd.com/read/29764585/-construction-of-ezh2-knockout-animal-model-by-crispr-cas9-technology
#7
Fanrong Meng, Dan Zhao, Qinghua Zhou, Zhe Liu
BACKGROUND: It has been proven that CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated 9) system was the modern gene-editing technology through the constitutive expression of nucleases Cas9 in the mammalian, which binds to the specific site in the genome mediated by single-guide RNA (sgRNA) at desired genomic loci. The aim of this study is that the animal model of EZH2 gene knockout was constructed using CRISPR/Cas9 technology. METHODS: In this study, we designed two single-guide RNAs targeting the Exon3 and Exon4 of EZH2 gene...
May 20, 2018: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
https://www.readbyqxmd.com/read/29761214/analysis-of-resistance-genes-of-clinical-pannonibacter-phragmitetus-strain-31801-by-complete-genome-sequencing
#8
De-Song Ming, Qing-Qing Chen, Xiao-Tin Chen
To clarify the resistance mechanisms of Pannonibacter phragmitetus 31801, isolated from the blood of a liver abscess patient, at the genomic level, we performed whole genomic sequencing using a PacBio RS II single-molecule real-time long-read sequencer. Bioinformatic analysis of the resulting sequence was then carried out to identify any possible resistance genes. Analyses included Basic Local Alignment Search Tool searches against the Antibiotic Resistance Genes Database, ResFinder analysis of the genome sequence, and Resistance Gene Identifier analysis within the Comprehensive Antibiotic Resistance Database...
May 14, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29759820/clustered-regularly-interspaced-short-palindromic-repeats-based-genome-surgery-for-the-treatment-of-autosomal-dominant-retinitis-pigmentosa
#9
Yi-Ting Tsai, Wen-Hsuan Wu, Ting-Ting Lee, Wei-Pu Wu, Christine L Xu, Karen S Park, Xuan Cui, Sally Justus, Chyuan-Sheng Lin, Ruben Jauregui, Pei-Yin Su, Stephen H Tsang
PURPOSE: To develop a universal gene therapy to overcome the genetic heterogeneity in retinitis pigmentosa (RP) resulting from mutations in rhodopsin (RHO). DESIGN: Experimental study for a combination gene therapy that uses both gene ablation and gene replacement. PARTICIPANTS: This study included 2 kinds of human RHO mutation knock-in mouse models: RhoP23H and RhoD190N . In total, 23 RhoP23H/P23H , 43 RhoP23H/+ , and 31 RhoD190N/+ mice were used for analysis...
May 5, 2018: Ophthalmology
https://www.readbyqxmd.com/read/29755603/bacterial-crispr-regions-general-features-and-their-potential-for-epidemiological-molecular-typing-studies
#10
REVIEW
Zahra Karimi, Ali Ahmadi, Ali Najafi, Reza Ranjbar
Introduction: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci as novel and applicable regions in prokaryotic genomes have gained great attraction in the post genomics era. Methods: These unique regions are diverse in number and sequence composition in different pathogenic bacteria and thereby can be a suitable candidate for molecular epidemiology and genotyping studies. Results:Furthermore, the arrayed structure of CRISPR loci (several unique repeats spaced with the variable sequence) and associated cas genes act as an active prokaryotic immune system against viral replication and conjugative elements...
2018: Open Microbiology Journal
https://www.readbyqxmd.com/read/29755309/targeted-delivery-of-crispr-cas9-mediated-cancer-gene-therapy-via-liposome-templated-hydrogel-nanoparticles
#11
Zeming Chen, Fuyao Liu, Yanke Chen, Jun Liu, Xiaoying Wang, Ann T Chen, Gang Deng, Hongyi Zhang, Jie Liu, Zhangyong Hong, Jiangbing Zhou
Due to its simplicity, versatility, and high efficiency, the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technology has emerged as one of the most promising approaches for treatment of a variety of genetic diseases, including human cancers. However, further translation of CRISPR/Cas9 for cancer gene therapy requires development of safe approaches for efficient, highly specific delivery of both Cas9 and single guide RNA to tumors. Here, novel core-shell nanostructure, liposome-templated hydrogel nanoparticles (LHNPs) that are optimized for efficient codelivery of Cas9 protein and nucleic acids is reported...
December 8, 2017: Advanced Functional Materials
https://www.readbyqxmd.com/read/29754773/genome-editing-in-plants-advancing-crop-transformation-and-overview-of-tools
#12
Tariq Shah, Tayyaba Andleeb, Sadia Lateef, Mehmood Ali Noor
Genome manipulation technology is one of emerging field which brings real revolution in genetic engineering and biotechnology. Targeted editing of genomes pave path to address a wide range of goals not only to improve quality and productivity of crops but also permit to investigate the fundamental roots of biological systems. These goals includes creation of plants with valued compositional properties and with characters that confer resistance to numerous biotic and abiotic stresses. Numerous novel genome editing systems have been introduced during the past few years; these comprise zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9)...
May 7, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29753601/crispr-cas9-mediated-genome-editing-of-the-fatty-acid-desaturase-2-gene-in-brassica-napus
#13
Ayako Okuzaki, Takumi Ogawa, Chie Koizuka, Kanako Kaneko, Mizue Inaba, Jun Imamura, Nobuya Koizuka
The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9-mediated genome editing system has been widely applied as a powerful tool for modifying preferable endogenous genes. This system is highly expected to be further applied for the breeding of various agronomically important plant species. Here we report the modification of a fatty acid desaturase 2 gene (FAD2), which encodes an enzyme that catalyzes the desaturation of oleic acid, in Brassica napus cv. Westar using the CRISPR/Cas9 system...
April 26, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29746416/crispr-genome-surgery-in-the-retina-in-light-of-off-targeting
#14
Galaxy Y Cho, Kellie A Schaefer, Alexander G Bassuk, Stephen H Tsang, Vinit B Mahajan
PURPOSE: Recent concerns regarding the clinical utilization of clustered regularly interspaced short palindromic repeats (CRISPR) involve uncertainties about the potential detrimental effects that many arise due to unintended genetic changes, as in off-target mutagenesis, during CRISPR genome surgery. This review gives an overview of off-targeting detection methods and CRISPR's place in the clinical setting, specifically in the field of ophthalmology. RESULTS: As CRISPR utilization in the laboratory setting has increased, knowledge regarding CRISPR mechanisms including its off-target effects has also increased...
May 7, 2018: Retina
https://www.readbyqxmd.com/read/29741584/translating-gwas-in-rheumatic-disease-approaches-to-establishing-mechanism-and-function-for-genetic-associations-with-ankylosing-spondylitis
#15
Julie A Osgood, Julian C Knight
Ankylosing spondylitis (AS) is a highly heritable chronic inflammatory arthritis characterized by osteoproliferation, fusion of affected joints and systemic manifestations. Many disease associations for AS have been reported through genome-wide association studies; however, identifying modulated genes and functional mechanism remains challenging. This review summarizes current genetic associations involving AS and describes strategic approaches for functional follow-up of disease-associated variants. Fine mapping using methods leveraging Bayesian approaches are outlined...
May 5, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29732405/broad-and-diverse-mechanisms-used-by-deubiquitinase-family-members-in-regulating-the-type-i-interferon-signaling-pathway-during-antiviral-responses
#16
Qingxiang Liu, Yaoxing Wu, Yunfei Qin, Jiajia Hu, Weihong Xie, F Xiao-Feng Qin, Jun Cui
The innate immune response conferred by type I interferons is essential for host defense against viral infection but needs to be tightly controlled to avoid immunopathology. We performed a systematic functional screening by CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) knockout and overexpression to investigate the roles of the deubiquitinating enzyme (DUB) family in regulating antiviral immunity. We demonstrated that the expression of a large fraction of DUBs underwent complex temporal alteration, suggesting a dynamic program of feedback regulation...
May 2018: Science Advances
https://www.readbyqxmd.com/read/29731757/an-efficient-crispr-cas9-platform-for-rapidly-generating-simultaneous-mutagenesis-of-multiple-gene-homoeologs-in-allotetraploid-oilseed-rape
#17
Chao Li, Mengyu Hao, Wenxiang Wang, Hui Wang, Fan Chen, Wen Chu, Baohong Zhang, Desheng Mei, Hongtao Cheng, Qiong Hu
With the rapid development of sequence specific nucleases (SSNs) for genome targeting, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) is now considered the most promising method for functional genetic researches, as well as genetic improvement in crop plants. However, the gene redundancy feature within the allotetraploid rapeseed genome is one of the major obstacles for simultaneous modification of different homologs in the first generation. In addition, large scale screening to identify mutated transgenic plants is very time-and labor-consuming using the conventional restriction enzyme-based approaches...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29729377/toolboxes-for-cyanobacteria-recent-advances-and-future-direction
#18
REVIEW
Tao Sun, Shubin Li, Xinyu Song, Jinjin Diao, Lei Chen, Weiwen Zhang
Photosynthetic cyanobacteria are important primary producers and model organisms for studying photosynthesis and elements cycling on earth. Due to the ability to absorb sunlight and utilize carbon dioxide, cyanobacteria have also been proposed as renewable chassis for carbon-neutral "microbial cell factories". Recent progresses on cyanobacterial synthetic biology have led to the successful production of more than two dozen of fuels and fine chemicals directly from CO2 , demonstrating their potential for scale-up application in the future...
May 2, 2018: Biotechnology Advances
https://www.readbyqxmd.com/read/29729270/rbm14-is-indispensable-for-pluripotency-maintenance-and-mesoderm-development-of-mouse-embryonic-stem-cells
#19
Guilai Chen, Da Zhang, Linlin Zhang, Guihai Feng, Boya Zhang, Yihui Wu, Wei Li, Ying Zhang, Baoyang Hu
The pluripotency of embryonic stem cells (ESCs) is maintained by core pluripotency transcription factors, cofactors and several signaling pathways. RBM14 is a component of the para-speckle complex, which has been implicated in multiple important biological processes. The role of RBM14 in ESCs and lineage differentiation remains to be elucidated. In the present study, we provided evidence that RBM14 plays important roles in maintaining pluripotency and in the early differentiation of ESCs. RBM14 was demonstrated to be expressed in mouse embryonic stem cells (mESCs) and localized in the nucleus...
May 2, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29726937/design-principles-for-nuclease-deficient-crispr-based-transcriptional-regulators
#20
Michael K Jensen
The engineering of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated proteins continues to expand the toolkit available for genome editing, reprogramming gene regulation, genome visualisation and epigenetic studies of living organisms. In this review, the emerging design principles on the use of nuclease-deficient CRISPR-based reprogramming of gene expression will be presented. The review will focus on the designs implemented in yeast both at the level of CRISPR proteins and guide RNA (gRNA), but will lend due credits to the seminal studies performed in other species where relevant...
June 1, 2018: FEMS Yeast Research
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