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https://www.readbyqxmd.com/read/29473500/crispr-cas-system-as-a-genome-engineering-platform-applications-in-biomedicine-and-biotechnology
#1
Atieh Hashemi
Genome editing mediated by clustered regularly interspaced palindromic repeats (CRISPR) and its associated proteins (Cas) has recently been considered to be used as efficient, rapid and site-specific tools in the modification of endogenous genes in biomedically important cell types and whole organisms. It has become a predictable and precise method of choice for genome engineering by specifying a 20-nt targeting sequence within its guide RNA. First, this review aims to describe the biology of CRISPR system...
February 20, 2018: Current Gene Therapy
https://www.readbyqxmd.com/read/29473438/crispr-and-personalized-treg-therapy-new-insights-into-the-treatment-of-rheumatoid-arthritis
#2
Fatemeh Safari, Safar Farajnia, Maryam Arya, Habib Zarredar, Ava Nasrolahi
INTRODUCTION: Rheumatoid arthritis (RA), as one of the most disabling autoimmune diseases, is a common health problem that progressively reduces the life quality of patients. Although various biologics have been introduced for RA, attempts to establish an efficient long-term therapies failed due to the heterogeneity of this disease. METHODS: In the last decade, immunomodulatory approaches such as T cell adoptive therapy have been developed for controlling autoimmunity...
February 23, 2018: Immunopharmacology and Immunotoxicology
https://www.readbyqxmd.com/read/29467456/genome-wide-crispr-screen-reveals-sgol1-as-a-druggable-target-of-sorafenib-treated-hepatocellular-carcinoma
#3
Weijian Sun, Bin He, Beng Yang, Wendi Hu, Shaobing Cheng, Heng Xiao, Zhengjie Yang, Xiaoyu Wen, Lin Zhou, Haiyang Xie, Xian Shen, Jian Wu, Shusen Zheng
The genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screen is a powerful tool used to identify therapeutic targets that can be harnessed for cancer treatment. This study aimed to assess the efficacy of genome-wide CRISPR screening to identify druggable genes associated with sorafenib-treated hepatocellular carcinoma (HCC). A genome-scale CRISPR knockout (GeCKO v2) library containing 123,411 single guide RNAs (sgRNAs) was used to identify loss-of-function mutations conferring sorafenib resistance upon HCC cells...
February 21, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29463653/efficient-and-scalable-precision-genome-editing-in-staphylococcus-aureus-through-conditional-recombineering-and-crispr-cas9-mediated-counterselection
#4
Kelsi Penewit, Elizabeth A Holmes, Kathyrn McLean, Mingxin Ren, Adam Waalkes, Stephen J Salipante
Staphylococcus aureus is an important human pathogen, but studies of the organism have suffered from the lack of a robust tool set for its genetic and genomic manipulation. Here we report the development of a system for the facile and high-throughput genomic engineering of S. aureus using single-stranded DNA (ssDNA) oligonucleotide recombineering coupled with clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-mediated counterselection. We identify recombinase EF2132 , derived from Enterococcus faecalis , as being capable of integrating single-stranded DNA oligonucleotides into the S...
February 20, 2018: MBio
https://www.readbyqxmd.com/read/29463029/nanoluciferase-reporter-gene-system-directed-by-tandemly-repeated-pseudo-palindromic-nfat-response-elements-facilitates-analysis-of-biological-endpoint-effects-of-cellular-ca-2-mobilization
#5
Wei Zhang, Terunao Takahara, Takuya Achiha, Hideki Shibata, Masatoshi Maki
NFAT is a cytoplasm-localized hyper-phosphorylated transcription factor that is activated through dephosphorylation by calcineurin, a Ca2+ /calmodulin-dependent phosphatase. A non-palindromic NFAT-response element (RE) found in the IL2 promoter region has been commonly used for a Ca2+ -response reporter gene system, but requirement of concomitant activation of AP-1 (Fos/Jun) often complicates the interpretation of obtained results. A new nanoluciferase (NanoLuc) reporter gene containing nine-tandem repeats of a pseudo-palindromic NFAT-RE located upstream of the IL8 promoter was designed to monitor Ca2+ -induced transactivation activity of NFAT in human embryonic kidney (HEK) 293 cells by measuring luciferase activities of NanoLuc and co-expressed firefly luciferase for normalization...
February 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29462894/modeling-the-role-of-wnt-signaling-in-human-and-drosophila-stem-cells
#6
Prameet Kaur, Helen Jingshu Jin, Jay B Lusk, Nicholas S Tolwinski
The discovery of induced pluripotent stem (iPS) cells, barely more than a decade ago, dramatically transformed the study of stem cells and introduced a completely new way to approach many human health concerns. Although advances have pushed the field forward, human application remains some years away, in part due to the need for an in-depth mechanistic understanding. The role of Wnts in stem cells predates the discovery of iPS cells with Wnts established as major pluripotency promoting factors. Most work to date has been done using mouse and tissue culture models and few attempts have been made in other model organisms, but the recent combination of clustered regularly interspaced short palindromic repeats (CRISPR) gene editing with iPS cell technology provides a perfect avenue for exploring iPS cells in model organisms...
February 16, 2018: Genes
https://www.readbyqxmd.com/read/29462720/engineering-introns-to-express-rna-guides-for-cas9-and-cpf1-mediated-multiplex-genome-editing
#7
Dan Ding, Kaiyuan Chen, Yuedan Chen, Hong Li, Kabin Xie
The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) system has emerged as the revolutionary platform for DNA targeting. This system uses a site-specific RNA guide to direct a CRISPR effector (e.g., Cas9 and Cpf1) to a DNA target. Here, we elaborate a general strategy to simultaneously express multiple guide RNAs (gRNA) and CRISPR RNAs (crRNA) from introns of Cas9 and Cpf1. This method utilizes the endogenous tRNA processing system or crRNA processing activity of Cpf1 to cleave the spliced intron which contains tRNA-gRNA polycistron or crRNA-crRNA array...
February 17, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29462648/bovine-viral-diarrhea-virus-type-1-current-taxonomy-according-to-palindromic-nucleotide-substitutions-method
#8
Massimo Giangaspero, Claudio Apicella
Pestivirus bovine viral diarrhea virus type 1 species is responsible for cosmopolitan diseases affecting cattle and other ruminants, presenting a wide range of clinical manifestations, with relevant impact on zootechnic production. Understanding genomic characteristic and virus taxonomy is fundamental in order to sustain control and prophylactic programs. Given the recent various studies reporting a relatively high number of new strains, in particular from Asian countries, in the present study, four hundred-eighty-two genomic sequences have been evaluated applying the palindromic nucleotide substitutions method for genotyping...
February 17, 2018: Journal of Virological Methods
https://www.readbyqxmd.com/read/29461656/identification-and-characterization-of-acetyltransferase-type-toxin-antitoxin-loci-in-klebsiella-pneumoniae
#9
Hongliang Qian, Qingqing Yao, Cui Tai, Zixin Deng, Jianhua Gan, Hong-Yu Ou
A type II toxin-antitoxin (TA) system, in which the toxin contains a Gcn5-related N-acetyltransferase (GNAT) domain, has been characterized recently. GNAT toxin acetylates aminoacyl-tRNA and blocks protein translation. It is abolished by the cognate antitoxin that contains the ribbon-helix-helix (RHH) domain. Here, we present an experimental demonstration of the interaction of the GNAT-RHH complex with TA promoter DNA. First, the GNAT-RHH TA locus kacAT was found in Klebsiella pneumoniae HS11286, a strain resistant to multiple antibiotics...
February 20, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29459880/molecular-phylogeny-and-dating-of-forsythieae-oleaceae-provide-insight-into-the-miocene-history-of-eurasian-temperate-shrubs
#10
Young-Ho Ha, Changkyun Kim, Kyung Choi, Joo-Hwan Kim
Tribe Forsythieae (Oleaceae), containing two genera ( Abeliophyllum and Forsythia ) and 13 species, is economically important plants used as ornamentals and in traditional medicine. This tribe species occur primarily in mountainous regions of Eurasia with the highest species diversity in East Asia. Here, we examine 11 complete chloroplast genome and nuclear cycloidea2 ( cyc2 ) DNA sequences of 10 Forsythia species and Abeliophyllum distichum using Illumina platform to provide the phylogeny and biogeographic history of the tribe...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29458716/selection-is-required-for-efficient-cas9-mediated-genome-editing-in-fusarium-graminearum
#11
Donald M Gardiner, Kemal Kazan
Genome engineering using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated nucleases, such as Cas9 (CRISPR-associated protein 9), are revolutionising molecular biology. In this study, we established a Cas9-based genome editing system in Fusarium graminearum, a highly destructive fungal pathogen of cereal crops. Although the molecular toolkit of F. graminearum is well developed compared to other fungi, Cas9-mediated engineering offers a number of potential benefits, such as the ability to create marker free mutants in this species...
February 2018: Fungal Biology
https://www.readbyqxmd.com/read/29458530/sumoylation-of-ie2p86-is-required-for-efficient-autorepression-of-the-human-cytomegalovirus-major-immediate-early-promoter
#12
Nina Reuter, Anna Reichel, Anne-Charlotte Stilp, Myriam Scherer, Thomas Stamminger
The human cytomegalovirus (HCMV) IE2p86 protein is pivotal for coordinated regulation of viral gene expression. Besides functioning as a promiscuous transactivator, IE2p86 is also known to negatively regulate its own transcription. This occurs via direct binding of IE2p86 to a 14-bp palindromic DNA element located between the TATA box and the transcription start site of the major immediate-early promoter (MIEP), which is referred to as the cis repression signal (CRS). However, the exact mechanism of IE2p86-based autorepression is still unclear...
February 8, 2018: Journal of General Virology
https://www.readbyqxmd.com/read/29457136/unexpected-evolutionary-benefit-to-phages-imparted-by-bacterial-crispr-cas9
#13
Pan Tao, Xiaorong Wu, Venigalla Rao
Bacteria and bacteriophages arm themselves with various defensive and counterdefensive mechanisms to protect their own genome and degrade the other's. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated) is an adaptive bacterial defense mechanism that recognizes short stretches of invading phage genome and destroys it by nuclease attack. Unexpectedly, we discovered that the CRISPR-Cas system might also accelerate phage evolution. When Escherichia coli bacteria containing CRISPR-Cas9 were infected with phage T4, its cytosine hydroxymethylated and glucosylated genome was cleaved poorly by Cas9 nuclease, but the continuing CRISPR-Cas9 pressure led to rapid evolution of mutants that accumulated even by the time a single plaque was formed...
February 2018: Science Advances
https://www.readbyqxmd.com/read/29456867/heterologous-and-endogenous-u6-snrna-promoters-enable-crispr-cas9-mediated-genome-editing-in-aspergillus-niger
#14
Xiaomei Zheng, Ping Zheng, Jibin Sun, Zhang Kun, Yanhe Ma
Background: U6 promoters have been used for single guide RNA (sgRNA) transcription in the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas9) genome editing system. However, no available U6 promoters have been identified in Aspergillus niger, which is an important industrial platform for organic acid and protein production. Two CRISPR/Cas9 systems established in A. niger have recourse to the RNA polymerase II promoter or in vitro transcription for sgRNA synthesis, but these approaches generally increase cloning efforts and genetic manipulation...
2018: Fungal Biology and Biotechnology
https://www.readbyqxmd.com/read/29454353/genetics-of-the-human-y-chromosome-and-its-association-with-male-infertility
#15
REVIEW
Stacy Colaco, Deepak Modi
The human Y chromosome harbors genes that are responsible for testis development and also for initiation and maintenance of spermatogenesis in adulthood. The long arm of the Y chromosome (Yq) contains many ampliconic and palindromic sequences making it predisposed to self-recombination during spermatogenesis and hence susceptible to intra-chromosomal deletions. Such deletions lead to copy number variation in genes of the Y chromosome resulting in male infertility. Three common Yq deletions that recur in infertile males are termed as AZF (Azoospermia Factor) microdeletions viz...
February 17, 2018: Reproductive Biology and Endocrinology: RB&E
https://www.readbyqxmd.com/read/29453634/comparison-of-serological-and-molecular-typing-methods-for-epidemiological-investigation-of-tenacibaculum-species-pathogenic-for-fish
#16
Clara Fernández-Álvarez, Yolanda Torres-Corral, Ysabel Santos
In the present study, the potential of serological methods, the repetitive extragenic palindromic PCR (REP-PCR) and the enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) for the typing of the species Tenacibaculum maritimum, Tenacibaculum soleae and Tenacibaculum discolor was evaluated. Moreover, molecular and proteomic techniques were used to assess variability among strains belonging to different serotypes, as well as isolated from different host species and geographical areas. Slide agglutination and dot-blot assays demonstrated the lack of immunological relationships among Tenacibaculum species analyzed...
February 16, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29452198/microbial-infection-pattern-pathogenic-features-and-resistance-mechanism-of-carbapenem-resistant-gram-negative-bacilli-during-long-term-hospitalization
#17
Shuxian Wen, Donghua Feng, Zerong Lu, Junyan Liu, Brian M Peters, Hailing Tang, Danhong Su, Yong-Ping Lin, Ling Yang, Zhenbo Xu, Mark E Shirtliff, Dingqiang Chen
BACKGROUND: Carbapenem-resistant Gram-negative bacilli (GNB) have become an important cause of nosocomial infections of hospitalized patients. METHODS: To investigate the microbial infection patterns and molecular epidemiology characteristics of the carbapenem-resistant GNB isolates from a long-term hospitalized patient, antimicrobial susceptibility testing, phenotypic screening test for carbapenemase production, PCR screening and DNA sequencing of carbapenemase genes, repetitive extragenic palindromic sequence-based PCR (REP-PCR), multilocus sequencing typing (MLST) and genetic environment analysis were performed...
February 13, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29449560/knockout-of-zebrafish-interleukin-7-receptor-il7r-by-the-crispr-cas9-system-delays-retinal-neurodevelopment
#18
Shijiao Cai, Yang Chen, Yue Shang, Jianlin Cui, Zongjin Li, Yuhao Li
Interleukin 7 receptor (il7r), a transmembrane receptor, belongs to the type I cytokine receptor family. Il7r is involved in the pathogenesis of neurodegenerative disorders, such as multiple sclerosis. Targeted knockdown of il7r leads to delayed myelination, highlighting the potential role of il7r in the development of the nervous system. Zebrafish is an ideal model for the study of neurogenesis; moreover, the il7r gene is highly conserved between zebrafish and human. The aim of the present study was to investigate the novel function of il7r in neurogenesis...
February 15, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29446996/recent-advances-in-therapeutic-genome-editing-in-china
#19
Yang Yang, Qingnan Wang, Qian Li, Ke Men, Zhiyao He, Hongxin Deng, Weizhi Ji, Yuquan Wei
Editing of the genome to correct disease-causing mutations is a promising approach for the treatment of human diseases. Recent advances in the development of programmable nuclease-based genome editing tools have substantially improved the ability to make precise changes in the human genome. Genome editing technologies are already being used to correct genetic mutations in affected tissues and cells to treat diseases that are refractory to traditional gene therapies. Chinese scientists have made remarkable breakthroughs in the field of therapeutic genome editing, particularly with the first clinical trial involving the clustered regularly interspaced short palindromic repeats-caspase 9 system that began in China...
February 2018: Human Gene Therapy
https://www.readbyqxmd.com/read/29446747/crispr-cas9-genome-editing-a-promising-tool-for-therapeutic-applications-of-induced-pluripotent-stem-cells
#20
Yanli Zhang, Danuta Sastre, Feng Wang
Induced pluripotent stem cells hold tremendous potential for biological and therapeutic applications. The development of efficient technologies for the targeted genome alteration of stem cells in disease models is a prerequisite for utilizing stem cells to their full potential. The revolutionary technology for genome editing known as the clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 (Cas9) system is recently recognized as a powerful tool for editing DNA at specific loci...
February 14, 2018: Current Stem Cell Research & Therapy
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