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https://www.readbyqxmd.com/read/28087399/advances-with-using-crispr-cas-mediated-gene-editing-to-treat-infections-with-hepatitis-b-virus-and-hepatitis-c-virus
#1
REVIEW
Buhle Moyo, Kristie Bloom, Tristan Scott, Abdullah Ely, Patrick Arbuthnot
Chronic infections with hepatitis B and hepatitis C viruses (HBV and HCV) account for the majority of cases of cirrhosis and hepatocellular carcinoma. Current therapies for the infections have limitations and improved efficacy is necessary to prevent complications in carriers of the viruses. In the case of HBV persistence, the replication intermediate comprising covalently closed circular DNA (cccDNA) is particularly problematic. Licensed therapies have little effect on cccDNA and HBV replication relapses following treatment withdrawal...
January 10, 2017: Virus Research
https://www.readbyqxmd.com/read/28081148/characterization-of-multi-drug-resistant-enterococcus-faecalis-isolated-from-cephalic-recording-chambers-in-research-macaques-macaca-spp
#2
Stephanie E Woods, Mia T Lieberman, Francois Lebreton, Elise Trowel, César de la Fuente-Núñez, Joanne Dzink-Fox, Michael S Gilmore, James G Fox
Nonhuman primates are commonly used for cognitive neuroscience research and often surgically implanted with cephalic recording chambers for electrophysiological recording. Aerobic bacterial cultures from 25 macaques identified 72 bacterial isolates, including 15 Enterococcus faecalis isolates. The E. faecalis isolates displayed multi-drug resistant phenotypes, with resistance to ciprofloxacin, enrofloxacin, trimethoprim-sulfamethoxazole, tetracycline, chloramphenicol, bacitracin, and erythromycin, as well as high-level aminoglycoside resistance...
2017: PloS One
https://www.readbyqxmd.com/read/28071925/gene-editing-and-genetic-engineering-approaches-for-advanced-probiotics-a-review
#3
Ruby Yadav, Vishal Kumar, Mehak Baweja, Pratyoosh Shukla
The applications of probiotics are significant and thus resulted in need of genome analysis of probiotic strains. Various omics methods and systems biology approaches enables us to understand and optimize the metabolic processes. These techniques have increased the researcher's attention towards gut microbiome and provided a new source for the revelation of uncharacterized biosynthetic pathways which enables novel metabolic engineering approaches. In recent years, the broad and quantitative analysis of modified strains relies on systems biology tools such as in silico design which are commonly used methods for improving strain performance...
January 10, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28070592/therapeutic-genome-editing-with-engineered-nucleases
#4
Simone A Haas, Viviane Dettmer, Toni Cathomen
Targeted genome editing with designer nucleases, such as zinc finger nucleases, TALE nucleases, and CRISPR-Cas nucleases, has heralded a new era in gene therapy. Genetic disorders, which have not been amenable to conventional gene-addition-type gene therapy approaches, such as disorders with dominant inheritance or diseases caused by mutations in tightly regulated genes, can now be treated by precise genome surgery. Moreover, engineered nucleases enable novel genetic interventions to fight infectious diseases or to improve cancer immunotherapies...
January 10, 2017: Hämostaseologie
https://www.readbyqxmd.com/read/28065598/cas13b-is-a-type-vi-b-crispr-associated-rna-guided-rnase-differentially-regulated-by-accessory-proteins-csx27-and-csx28
#5
Aaron A Smargon, David B T Cox, Neena K Pyzocha, Kaijie Zheng, Ian M Slaymaker, Jonathan S Gootenberg, Omar A Abudayyeh, Patrick Essletzbichler, Sergey Shmakov, Kira S Makarova, Eugene V Koonin, Feng Zhang
CRISPR-Cas adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. Using a computational sequence database mining approach, we identify two class 2 CRISPR-Cas systems (subtype VI-B) that lack Cas1 and Cas2 and encompass a single large effector protein, Cas13b, along with one of two previously uncharacterized associated proteins, Csx27 and Csx28. We establish that these CRISPR-Cas systems can achieve RNA interference when heterologously expressed. Through a combination of biochemical and genetic experiments, we show that Cas13b processes its own CRISPR array with short and long direct repeats, cleaves target RNA, and exhibits collateral RNase activity...
January 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28064188/upset-the-drosophila-homologue-of-set3-is-required-for-viability-and-the-proper-balance-of-active-and-repressive-chromatin-marks
#6
Kyle A McElroy, Youngsook Lucy Jung, Barry M Zee, Charlotte I Wang, Peter J Park, Mitzi I Kuroda
Chromatin plays a critical role in faithful implementation of gene expression programs. Different post-translational modifications of histone proteins reflect the underlying state of gene activity, and many chromatin proteins write, erase, bind, or are repelled by these histone marks. One such protein is UpSET, the Drosophila homolog of yeast Set3 and mammalian KMT2E (MLL5). Here we show that UpSET is necessary for the proper balance between active and repressed states. Using CRISPR/Cas-9 editing, we generated S2 cells which are mutant for upset We found that loss of UpSET is tolerated in S2 cells, but that heterochromatin is misregulated, as evidenced by a strong decrease in H3K9me2 levels assessed by bulk histone post-translational modification quantification...
January 6, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28062037/single-molecule-insight-into-target-recognition-by-crispr-cas-complexes
#7
M Rutkauskas, A Krivoy, M D Szczelkun, C Rouillon, R Seidel
Ribonucleoprotein (RNP) complexes from CRISPR-Cas systems have attracted enormous interest since they can be easily and flexibly reprogrammed to target any desired locus for genome engineering and gene regulation applications. Basis for the programmability is a short RNA (crRNA) inside these complexes that recognizes the target nucleic acid by base pairing. For CRISPR-Cas systems that target double-stranded DNA this results in local DNA unwinding and formation of a so-called R-loop structure. Here we provide an overview how this target recognition mechanism can be dissected in great detail at the level of a single molecule...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28057934/the-driving-force-of-prophages-and-crispr-cas-system-in-the-evolution-of-cronobacter-sakazakii
#8
Haiyan Zeng, Jumei Zhang, Chensi Li, Tengfei Xie, Na Ling, Qingping Wu, Yingwang Ye
Cronobacter sakazakii is an important foodborne pathogens causing rare but life-threatening diseases in neonates and infants. CRISPR-Cas system is a new prokaryotic defense system that provides adaptive immunity against phages, latter play an vital role on the evolution and pathogenicity of host bacteria. In this study, we found that genome sizes of C. sakazakii strains had a significant positive correlation with total genome sizes of prophages. Prophages contributed to 16.57% of the genetic diversity (pan genome) of C...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28052722/road-to-the-future-of-systems-biotechnology-crispr-cas-mediated-metabolic-engineering-for-recombinant-protein-production
#9
Amir Roointan, Mohammad Hossein Morowvat
The rising potential for CRISPR-Cas-mediated genome editing has revolutionized our strategies in basic and practical bioengineering research. It provides a predictable and precise method for genome modification in a robust and reproducible fashion. Emergence of systems biotechnology and synthetic biology approaches coupled with CRISPR-Cas technology could change the future of cell factories to possess some new features which have not been found naturally. We have discussed the possibility and versatile potentials of CRISPR-Cas technology for metabolic engineering of a recombinant host for heterologous protein production...
January 4, 2017: Biotechnology & Genetic Engineering Reviews
https://www.readbyqxmd.com/read/28045163/crispr-cas9-technology-applications-in-genome-engineering-development-of-sequence-specific-antimicrobials-and-future-prospects
#10
REVIEW
César de la Fuente-Núñez, Timothy K Lu
The development of CRISPR-Cas9 technology has revolutionized our ability to edit DNA and to modulate expression levels of genes of interest, thus providing powerful tools to accelerate the precise engineering of a wide range of organisms. In addition, the CRISPR-Cas system can be harnessed to design "precision" antimicrobials that target bacterial pathogens in a DNA sequence-specific manner. This capability will enable killing of drug-resistant microbes by selectively targeting genes involved in antibiotic resistance, biofilm formation and virulence...
January 3, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28041849/inhibition-of-crispr-cas9-with-bacteriophage-proteins
#11
Benjamin J Rauch, Melanie R Silvis, Judd F Hultquist, Christopher S Waters, Michael J McGregor, Nevan J Krogan, Joseph Bondy-Denomy
Bacterial CRISPR-Cas systems utilize sequence-specific RNA-guided nucleases to defend against bacteriophage infection. As a countermeasure, numerous phages are known that produce proteins to block the function of class 1 CRISPR-Cas systems. However, currently no proteins are known to inhibit the widely used class 2 CRISPR-Cas9 system. To find these inhibitors, we searched cas9-containing bacterial genomes for the co-existence of a CRISPR spacer and its target, a potential indicator for CRISPR inhibition. This analysis led to the discovery of four unique type II-A CRISPR-Cas9 inhibitor proteins encoded by Listeria monocytogenes prophages...
January 12, 2017: Cell
https://www.readbyqxmd.com/read/28034840/establishment-of-porcine-xist-knockout-model-using-crispr-cas9-system
#12
Li Guoling, Zhong Cuili, Ni Sheng, Liu Dewu, Cai Gengyuan, Li Zicong, Yang Huaqiang, Wu Zhenfang
Somatic cell nuclear transfer technique has great applications in livestock breeding, production of genetically modified animals, rescue of endangered species and treatment of human diseases. However, the currently low efficiency in animals cloning, an average of less than 5%, greatly hindered the rapid development of this technique. Among many factors which affect the efficiency of cloning pigs, X chromosome inactivation is an important one. Moreover, Xist gene is closely related to X chromosome inactivation, suggesting that it may directly or indirectly affects cloning efficiency...
December 20, 2016: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28027431/from-classical-mutagenesis-to-nuclease-based-breeding-directing-natural-dna-repair-for-a-natural-end-product
#13
Michael Pacher, Holger Puchta
The production of mutants of crop plants by the use of chemical or physical genotoxins has a long tradition. These factors induce the natural DNA repair machinery to repair damages in an error-prone way. In case of radiation, multiple double strand breaks (DSBs) are induced randomly in the genome, leading in very rare cases to a desirable phenotype. In recent years the use of synthetic, site directed nucleases (SDNs), also referred to as sequence specific nucleases (SSNs), like the CRISPR/Cas system, enabled scientists to use exactly the same naturally occurring DNA repair mechanisms for the controlled induction of genomic changes at predefined sites in plant genomes...
December 27, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28017588/mutations-in-cas9-enhance-the-rate-of-acquisition-of-viral-spacer-sequences-during-the-crispr-cas-immune-response
#14
Robert Heler, Addison V Wright, Marija Vucelja, David Bikard, Jennifer A Doudna, Luciano A Marraffini
CRISPR loci and their associated (Cas) proteins encode a prokaryotic immune system that protects against viruses and plasmids. Upon infection, a low fraction of cells acquire short DNA sequences from the invader. These sequences (spacers) are integrated in between the repeats of the CRISPR locus and immunize the host against the matching invader. Spacers specify the targets of the CRISPR immune response through transcription into short RNA guides that direct Cas nucleases to the invading DNA molecules. Here we performed random mutagenesis of the RNA-guided Cas9 nuclease to look for variants that provide enhanced immunity against viral infection...
January 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28008168/cornerstones-of-crispr-cas-in-drug-discovery-and-therapy
#15
Christof Fellmann, Benjamin G Gowen, Pei-Chun Lin, Jennifer A Doudna, Jacob E Corn
The recent development of CRISPR-Cas systems as easily accessible and programmable tools for genome editing and regulation is spurring a revolution in biology. Paired with the rapid expansion of reference and personalized genomic sequence information, technologies based on CRISPR-Cas are enabling nearly unlimited genetic manipulation, even in previously difficult contexts, including human cells. Although much attention has focused on the potential of CRISPR-Cas to cure Mendelian diseases, the technology also holds promise to transform the development of therapies to treat complex heritable and somatic disorders...
December 23, 2016: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/28005056/new-crispr-cas-systems-from-uncultivated-microbes
#16
David Burstein, Lucas B Harrington, Steven C Strutt, Alexander J Probst, Karthik Anantharaman, Brian C Thomas, Jennifer A Doudna, Jillian F Banfield
CRISPR-Cas systems provide microbes with adaptive immunity by employing short sequences, termed spacers, that guide Cas proteins to cleave foreign DNA(1,2). Class 2 CRISPR-Cas systems are streamlined versions in which a single Cas protein bound to RNA recognizes and cleaves targeted sequences(3,4). The programmable nature of these minimal systems has enabled their repurposing as a versatile technology that is broadly revolutionizing biological and clinical research(5). However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving untapped the vast majority of enzymes from organisms that have not been cultured...
December 22, 2016: Nature
https://www.readbyqxmd.com/read/27997045/dynamics-of-escherichia-coli-type-i-e-crispr-spacers-over-42-000-years
#17
Ekaterina Savitskaya, Anna Lopatina, Sofia Medvedeva, Mikhail Kapustin, Sergey Shmakov, Alexey Tikhonov, Irena I Artamonova, Maria Logacheva, Konstantin Severinov
CRISPR-Cas are nucleic acids-based prokaryotic immune systems. CRISPR arrays accumulate spacers from foreign DNA and provide resistance to mobile genetic elements containing identical or similar sequences. Thus, the set of spacers present in a given bacterium can be regarded as a record of encounters of its ancestors with genetic invaders. Such records should be specific for different lineages and change with time, as earlier acquired spacers get obsolete and are lost. Here, we studied Type I-E CRISPR spacers of Escherichia coli from extinct pachyderm...
December 20, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27996021/tcrispri-tunable-and-reversible-one-step-control-of-gene-expression
#18
Xin-Tian Li, Yonggun Jun, Michael J Erickstad, Steven D Brown, Adam Parks, Donald L Court, Suckjoon Jun
The ability to control the level of gene expression is a major quest in biology. A widely used approach employs deletion of a nonessential gene of interest (knockout), or multi-step recombineering to move a gene of interest under a repressible promoter (knockdown). However, these genetic methods are laborious, and limited for quantitative study. Here, we report a tunable CRISPR-cas system, "tCRISPRi", for precise and continuous titration of gene expression by more than 30-fold. Our tCRISPRi system employs various previous advancements into a single strain: (1) We constructed a new strain containing a tunable arabinose operon promoter PBAD to quantitatively control the expression of CRISPR-(d)Cas protein over two orders of magnitude in a plasmid-free system...
December 20, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27995873/the-crispr-cas-system-presents-multiple-transcriptional-units-including-antisense-rnas-that-are-expressed-in-minimal-medium-and-up-regulated-by-ph-in-salmonella-enterica-serovar-typhi
#19
Liliana Medina-Aparicio, Javier Esteban Rebollar-Flores, América Abigail Beltrán-Luviano, Alejandra Vázquez Ramos, Rosa María Gutíerrez-Ríos, Leticia Olvera, Edmundo Calva, Ismael Hernández Lucas
The CRISPR-Cas system is involved in bacterial immunity, virulence, gene regulation, biofilm formation and sporulation. In Salmonella enterica serovar Typhi this system consists of five transcriptional units including antisense RNAs. It was determined that these genetic elements are expressed in minimal medium and are up-regulated by pH. In addition, a transcriptional characterization of cas3 and ascse2-1 is included herein.
December 20, 2016: Microbiology
https://www.readbyqxmd.com/read/27994579/intraclonal-genome-stability-of-the-metallo-%C3%AE-lactamase-spm-1-producing-pseudomonas-aeruginosa-st277-an-endemic-clone-disseminated-in-brazilian-hospitals
#20
Ana P B Nascimento, Mauro F Ortiz, Willames M B S Martins, Guilherme L Morais, Lorena C C Fehlberg, Luiz G P Almeida, Luciane P Ciapina, Ana C Gales, Ana T R Vasconcelos
Carbapenems represent the mainstay therapy for the treatment of serious P. aeruginosa infections. However, the emergence of carbapenem resistance has jeopardized the clinical use of this important class of compounds. The production of SPM-1 metallo-β-lactamase has been the most common mechanism of carbapenem resistance identified in P. aeruginosa isolated from Brazilian medical centers. Interestingly, a single SPM-1-producing P. aeruginosa clone belonging to the ST277 has been widely spread within the Brazilian territory...
2016: Frontiers in Microbiology
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