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clustered regularly interspaced short palindromic repeats

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https://www.readbyqxmd.com/read/29145843/development-of-a-crispr-cas9-genome-editing-toolbox-for-corynebacterium-glutamicum
#1
Jiao Liu, Yu Wang, Yujiao Lu, Ping Zheng, Jibin Sun, Yanhe Ma
BACKGROUND: Corynebacterium glutamicum is an important industrial workhorse and advanced genetic engineering tools are urgently demanded. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) have revolutionized the field of genome engineering. The CRISPR/Cas9 system that utilizes NGG as protospacer adjacent motif (PAM) and has good targeting specificity can be developed into a powerful tool for efficient and precise genome editing of C...
November 16, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29141705/phenotypic-and-molecular-genetic-characteristics-of-yersinia-pestis-at-an-emerging-natural-plague-focus-junggar-basin-china
#2
Yujiang Zhang, Tao Luo, Chao Yang, Xihong Yue, Rong Guo, Xinhui Wang, Mingde Buren, Yuqin Song, Ruifu Yang, Hanli Cao, Yujun Cui, Xiang Dai
The 15th natural plague focus in China, the Junggar Basin plague focus, is located near an important communication route connecting China and Central Asia and was discovered after 2005. To characterize the phenotypic and genetic diversity of the Yersinia pestis population in this newly established focus, we collected 25 Y. pestis strains from six counties across Junggar Basin in 2005-2006, and determined their biochemical features and genotypes based on multiple-locus variable number of tandem repeats analysis and clustered regularly interspaced short palindromic repeats analysis...
October 23, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29130159/the-future-of-crispr-applications-in-the-lab-the-clinic-and-society
#3
Soren H Hough, Ayokunmi Ajetunmobi
CRISPR (clustered regularly interspaced short palindromic repeats) has emerged as one of the premiere biological tools of the century. Even more so than older genome editing techniques such as TALENs and ZFNs, CRISPR provides speed and ease-of-use heretofore unheard of in agriculture, the environment and human health. The ability to map the function of virtually every component of the genome in a scalable, multiplexed manner is unprecedented. Once those regions have been explored, CRISPR also presents an opportunity to take advantage of endogenous cellular repair pathways to change and precisely edit the genome [1-3]...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29130158/crispr-in-the-retina-evaluation-of-future-potential
#4
Galaxy Y Cho, Sally Justus, Jesse D Sengillo, Stephen H Tsang
Clustered regularly interspaced short palindromic repeats (CRISPR) has been gaining widespread attention for its ability for targeted genome surgery. In treating inherited retinal degenerations, gene therapies have had varied results; the ones effective in restoring eye sight are limited by transiency in its effect. Genome surgery, however, is a solution that could potentially provide the eye with permanent healthy cells. As retinal degenerations are irreversible and the retina has little regenerative potential, permanent healthy cells are vital for vision...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29130156/crispr-from-prokaryotic-immune-systems-to-plant-genome-editing-tools
#5
Anindya Bandyopadhyay, Shamik Mazumdar, Xiaojia Yin, William Paul Quick
The clustered regularly interspaced short palindromic repeats (CRISPR) system is a prokaryotic adaptive immune system that has the ability to identify specific locations on the bacteriophage (phage) genome to create breaks in it, and internalize the phage genome fragments in its own genome as CRISPR arrays for memory-dependent resistance. Although CRISPR has been used in the dairy industry for a long time, it recently gained importance in the field of genome editing because of its ability to precisely target locations in a genome...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29130154/a-transgenic-core-facility-s-experience-in-genome-editing-revolution
#6
Celvie L Yuan, Yueh-Chiang Hu
The use of animal models, particularly rodents, has been immensely important to nearly all aspects of biomedical research, from basic science exploration to translational discoveries into clinical applications. The transgenic core facility that provides animal model production, preservation, and recovery services has been fundamental to the success of research efforts using animals. Recent advances in genome editing technologies, especially the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) enzyme system, have transformed the tedious animal model production into a simple and effective procedure...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29130076/crispr-correction-of-a-homozygous-low-density-lipoprotein-receptor-mutation-in-familial-hypercholesterolemia-induced-pluripotent-stem-cells
#7
Linda Omer, Elizabeth A Hudson, Shirong Zheng, James B Hoying, Yuan Shan, Nolan L Boyd
Familial hypercholesterolemia (FH) is a hereditary disease primarily due to mutations in the low-density lipoprotein receptor (LDLR) that lead to elevated cholesterol and premature development of cardiovascular disease. Homozygous FH patients (HoFH) with two dysfunctional LDLR alleles are not as successfully treated with standard hypercholesterol therapies, and more aggressive therapeutic approaches to control cholesterol levels must be considered. Liver transplant can resolve HoFH, and hepatocyte transplantation has shown promising results in animals and humans...
November 2017: Hepatol Commun
https://www.readbyqxmd.com/read/29128367/nemo-links-nuclear-factor-%C3%AE%C2%BAb-to-human-diseases
#8
REVIEW
Gunter Maubach, Michael Naumann
The nuclear factor (NF)-κB essential modulator (NEMO) is a key regulator in NF-κB-mediated signaling. By transmitting extracellular or intracellular signals, NEMO can control NF-κB-regulated genes. NEMO dysfunction is associated with inherited diseases such as incontinentia pigmenti (IP), ectodermal dysplasia, anhidrotic, with immunodeficiency (EDA-ID), and some cancers. We focus on molecular studies, human case reports, and mouse models emphasizing the significance of NEMO molecular interactions and modifications in health and diseases...
November 8, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/29126790/translational-research-exploring-and-creating-genetic-diversity
#9
REVIEW
Pierre Jacob, Adi Avni, Abdelhafid Bendahmane
The crop selection process has created a genetic bottleneck ultimately restricting breeding output. Wild relatives of major crops as well as the so-called 'neglected plant' species represent a reservoir of genetic diversity that remains underutilized. These species could be used as a tool to discover new alleles of agronomic interest or could be the target of breeding programs. Targeted induced local lesions in the genome (TILLING) can be used to translate in neglected crops what has been discovered in major crops and reciprocally...
November 7, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/29123506/challenges-and-advances-for-genetic-engineering-of-non-model-bacteria-and-uses-in-consolidated-bioprocessing
#10
REVIEW
Qiang Yan, Stephen S Fong
Metabolic diversity in microorganisms can provide the basis for creating novel biochemical products. However, most metabolic engineering projects utilize a handful of established model organisms and thus, a challenge for harnessing the potential of novel microbial functions is the ability to either heterologously express novel genes or directly utilize non-model organisms. Genetic manipulation of non-model microorganisms is still challenging due to organism-specific nuances that hinder universal molecular genetic tools and translatable knowledge of intracellular biochemical pathways and regulatory mechanisms...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29115982/phage-typing-or-crispr-typing-for-epidemiological-surveillance-of-salmonella-typhimurium
#11
Manal Mohammed
OBJECTIVE: Salmonella Typhimurium is the most dominant Salmonella serovar around the world. It is associated with foodborne gastroenteritis outbreaks but has recently been associated with invasive illness and deaths. Characterization of S. Typhimurium is therefore very crucial for epidemiological surveillance. Phage typing has been used for decades for subtyping of S. Typhimurium to determine the epidemiological relation among isolates. Recent studies however have suggested that high throughput clustered regular interspaced short palindromic repeats (CRISPR) typing has the potential to replace phage typing...
November 7, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29114997/in-vitro-modeling-of-hiv-proviral-activity-in-microglia
#12
Lee A Campbell, Christopher T Richie, Yajun Zhang, Emily J Heathward, Lamarque M Coke, Emily Y Park, Brandon K Harvey
Microglia, the resident macrophages of the brain, play a key role in the pathogenesis of HIV-associated neurocognitive disorders (HAND) due to their productive infection by HIV. This results in the release of neurotoxic viral proteins and pro-inflammatory compounds which negatively affect the functionality of surrounding neurons. Because models of HIV infection within the brain are limited, we aimed to create a novel microglia cell line with an integrated HIV provirus capable of recreating several hallmarks of HIV infection...
November 8, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29114029/rapid-selection-free-high-efficiency-genome-editing-in-protozoan-parasites-using-crispr-cas9-ribonucleoproteins
#13
Lia Carolina Soares Medeiros, Lilith South, Duo Peng, Juan M Bustamante, Wei Wang, Molly Bunkofske, Natasha Perumal, Fernando Sanchez-Valdez, Rick L Tarleton
Trypanosomatids (order Kinetoplastida), including the human pathogens Trypanosoma cruzi (agent of Chagas disease), Trypanosoma brucei, (African sleeping sickness), and Leishmania (leishmaniasis), affect millions of people and animals globally. T. cruzi is considered one of the least studied and most poorly understood tropical disease-causing parasites, in part because of the relative lack of facile genetic engineering tools. This situation has improved recently through the application of clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9) technology, but a number of limitations remain, including the toxicity of continuous Cas9 expression and the long drug marker selection times...
November 7, 2017: MBio
https://www.readbyqxmd.com/read/29114020/identification-of-novel-alleles-conferring-superior-production-of-rose-flavor-phenylethyl-acetate-using-polygenic-analysis-in-yeast
#14
Bruna Trindade de Carvalho, Sylvester Holt, Ben Souffriau, Rogelio Lopes Brandão, Maria R Foulquié-Moreno, Johan M Thevelein
Flavor compound metabolism is one of the last areas in metabolism where multiple genes encoding biosynthetic enzymes are still unknown. A major challenge is the involvement of side activities of enzymes having their main function in other areas of metabolism. We have applied pooled-segregant whole-genome sequence analysis to identify novel Saccharomyces cerevisiae genes affecting production of phenylethyl acetate (2-PEAc). This is a desirable flavor compound of major importance in alcoholic beverages imparting rose- and honey-like aromas, with production of high 2-PEAc levels considered a superior trait...
November 7, 2017: MBio
https://www.readbyqxmd.com/read/29113998/rhoc-regulates-actin-remodeling-to-form-phagosomes-during-fc%C3%AE-r-mediated-phagocytosis
#15
Youhei Egami, Katsuhisa Kawai, Nobukazu Araki
Phagosome formation is a complicated process that requires spatiotemporally regulated actin reorganization. We found that RhoC GTPase is a critical regulator of FcγR-mediated phagocytosis in macrophages. Our live-cell imaging revealed that RhoC, but not RhoA, is recruited to phagocytic cups engulfing IgG-opsonized erythrocytes (IgG-Es). RhoC silencing by RNAi, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated RhoC knockout and the expression of dominant-negative or dominant-active RhoC mutants suppressed the phagocytosis of IgG-Es...
November 7, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/29103811/crispr-cas9-based-plant-genome-editing-significance-opportunities-and-recent-advances
#16
Neelam Soda, Lokesh Verma, Jitender Giri
Precise genome editing is a quantum leap in the field of plant sciences. Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated Cas9 protein have emerged as a powerful tool for precise genome editing. CRISPR-Cas9 system introduces small heritable mutations (indels) in the genome of an organism. This system also enables precise gene characterization in plants with complex genomes. Besides, it offers new opportunities of trait stacking, where addition of desirable traits or removal of undesirable traits can be achieved simultaneously in a single event...
October 27, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29100516/crispr-interference-guided-multiplex-repression-of-endogenous-competing-pathway-genes-for-redirecting-metabolic-flux-in-escherichia-coli
#17
Seong Keun Kim, Wonjae Seong, Gui Hwan Han, Dae-Hee Lee, Seung-Goo Lee
BACKGROUND: Multiplex control of metabolic pathway genes is essential for maximizing product titers and conversion yields of fuels, chemicals, and pharmaceuticals in metabolic engineering. To achieve this goal, artificial transcriptional regulators, such as clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi), have been developed to specifically repress genes of interest. RESULTS: In this study, we deployed a tunable CRISPRi system for multiplex repression of competing pathway genes and, thus, directed carbon flux toward production of molecules of interest in Escherichia coli...
November 3, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29099045/gene-editing-in-human-lymphoid-cells-role-for-donor-dna-type-of-genomic-nuclease-and-cell-selection-method
#18
Anastasia Zotova, Elena Lopatukhina, Alexander Filatov, Musa Khaitov, Dmitriy Mazurov
Programmable endonucleases introduce DNA breaks at specific sites, which are repaired by non-homologous end joining (NHEJ) or homology recombination (HDR). Genome editing in human lymphoid cells is challenging as these difficult-to-transfect cells may also inefficiently repair DNA by HDR. Here, we estimated efficiencies and dynamics of knockout (KO) and knockin (KI) generation in human T and B cell lines depending on repair template, target loci and types of genomic endonucleases. Using zinc finger nuclease (ZFN), we have engineered Jurkat and CEM cells with the 8...
November 2, 2017: Viruses
https://www.readbyqxmd.com/read/29098080/methylation-of-transcription-factor-yy2-regulates-its-transcriptional-activity-and-cell-proliferation
#19
Xiao-Nan Wu, Tao-Tao Shi, Yao-Hui He, Fei-Fei Wang, Rui Sang, Jian-Cheng Ding, Wen-Juan Zhang, Xing-Yi Shu, Hai-Feng Shen, Jia Yi, Xiang Gao, Wen Liu
Yin Yang 1 (YY1) is a multifunctional DNA-binding transcription factor shown to be critical in a variety of biological processes, and its activity and function have been shown to be regulated by multitude of mechanisms, which include but are not limited to post-translational modifications (PTMs), its associated proteins and cellular localization. YY2, the paralog of YY1 in mouse and human, has been proposed to function redundantly or oppositely in a context-specific manner compared with YY1. Despite its functional importance, how YY2's DNA-binding activity and function are regulated, particularly by PTMs, remains completely unknown...
2017: Cell Discovery
https://www.readbyqxmd.com/read/29097994/benefits-of-genomic-insights-and-crispr-cas-signatures-to-monitor-potential-pathogens-across-drinking-water-production-and-distribution-systems
#20
Ya Zhang, Masaaki Kitajima, Andrew J Whittle, Wen-Tso Liu
The occurrence of pathogenic bacteria in drinking water distribution systems (DWDSs) is a major health concern, and our current understanding is mostly related to pathogenic species such as Legionella pneumophila and Mycobacterium avium but not to bacterial species closely related to them. In this study, genomic-based approaches were used to characterize pathogen-related species in relation to their abundance, diversity, potential pathogenicity, genetic exchange, and distribution across an urban drinking water system...
2017: Frontiers in Microbiology
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