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Crispr-Cas

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https://www.readbyqxmd.com/read/28731201/a-technological-and-regulatory-outlook-on-crispr-crop-editing
#1
Rea Globus, Udi Qimron
Generating plants with increased yields while maintaining low production and maintenance costs is highly important since plants are the major food source for humans and animals, as well as important producers of chemicals, pharmaceuticals, and fuels. Gene editing approaches, particularly the CRISPR-Cas system, are the preferred methods for improving crops, enabling quick, robust, and accurate gene manipulation. Nevertheless, new breeds of genetically-modified crops have initiated substantial debates concerning their biosafety, commercial use, and regulation...
July 21, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28730450/crispr-cas-rna-scaffolds-for-transcriptional-programming-in-yeast
#2
Jesse G Zalatan
CRISPR scaffold RNAs (scRNAs) provide a modular system for locus-specific transcriptional programming. scRNAs are generated by extending CRISPR guide RNA sequences with domains that recruit RNA-binding proteins, thus physically linking DNA binding and protein recruitment activities. A single scRNA molecule encodes information about the target locus and instructions about what regulatory function to execute at that locus. Sets of scRNA constructs can be used to generate synthetic multigene transcriptional programs in which some genes are activated and others are repressed...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729350/structures-of-the-crispr-genome-integration-complex
#3
Addison V Wright, Jun-Jie Liu, Gavin J Knott, Kevin W Doxzen, Eva Nogales, Jennifer A Doudna
CRISPR-Cas systems depend on the Cas1-Cas2 integrase to capture and integrate short foreign DNA fragments into the CRISPR locus, enabling adaptation to new viruses. We present crystal structures of Cas1-Cas2 bound to both donor and target DNA in intermediate and product integration complexes, as well as a cryo-electron microscopy structure of the full CRISPR locus integration complex including the accessory protein Integration Host Factor (IHF). The structures show unexpectedly that indirect sequence recognition dictates integration site selection by favoring deformation of the repeat and the flanking sequences...
July 20, 2017: Science
https://www.readbyqxmd.com/read/28725230/genetics-and-genomics-of-cotton-leaf-curl-disease-its-viral-causal-agents-and-whitefly-vector-a-way-forward-to-sustain-cotton-fiber-security
#4
REVIEW
Mehboob-Ur- Rahman, Ali Q Khan, Zainab Rahmat, Muhammad A Iqbal, Yusuf Zafar
Cotton leaf curl disease (CLCuD) after its first epidemic in 1912 in Nigeria, has spread to different cotton growing countries including United States, Pakistan, India, and China. The disease is of viral origin-transmitted by the whitefly Bemisia tabaci, which is difficult to control because of the prevalence of multiple virulent viral strains or related species. The problem is further complicated as the CLCuD causing virus complex has a higher recombination rate. The availability of alternate host crops like tomato, okra, etc...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28724535/priming-in-a-permissive-type-i-c-crispr-cas-system-reveals-distinct-dynamics-of-spacer-acquisition-and-loss
#5
Chitong Rao, Denny Chin, Alexander Wilson Ensminger
CRISPR-Cas is a bacterial and archaeal adaptive immune system that uses short, invader-derived sequences termed spacers to target invasive nucleic acids. Upon recognition of previously encountered invaders, the system can stimulate secondary spacer acquisitions, a process known as primed adaptation. Previous studies of primed adaptation have been complicated by intrinsically high interference efficiency of most systems against bona fide targets. As such, most primed adaptation to date has been studied within the context of imperfect sequence complementarity between spacers and targets...
July 19, 2017: RNA
https://www.readbyqxmd.com/read/28722012/type-iii-crispr-cas-systems-produce-cyclic-oligoadenylate-second-messengers
#6
Ole Niewoehner, Carmela Garcia-Doval, Jakob T Rostøl, Christian Berk, Frank Schwede, Laurent Bigler, Jonathan Hall, Luciano A Marraffini, Martin Jinek
In many prokaryotes, type III CRISPR-Cas systems detect and degrade invasive genetic elements by an RNA-guided, RNA-targeting multisubunit interference complex. The CRISPR-associated protein Csm6 additionally contributes to interference by functioning as a standalone ribonuclease that degrades invader RNA transcripts, but the mechanism linking invader sensing to Csm6 activity is not understood. Here we show that Csm6 proteins are activated through a second messenger generated by the type III interference complex...
July 19, 2017: Nature
https://www.readbyqxmd.com/read/28712502/gene-editing-with-talen-and-crispr-cas-in-rice
#7
Honghao Bi, Bing Yang
Engineered, site-specific nucleases induce genomic double-strand DNA breaks and break repair processes enable genome editing in a plethora of eukaryotic genomes. TALENs (transcription activator-like effector nucleases) and CRISPR/Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) are potent biotechnological tools used for genome editing. In rice, species-tailored editing tools have proven to be efficient and easy to use. Both tools are capable of generating DNA double-strand breaks (DSBs) in vivo and such breaks can be repaired either by error-prone NHEJ (nonhomologous end joining) that leads to nucleotide insertions or deletions or by HDR (homology-directed repair) if an appropriate exogenous DNA template is provided...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/28712499/use-of-crispr-cas9-for-crop-improvement-in-maize-and-soybean
#8
Doane Chilcoat, Zhan-Bin Liu, Jeffry Sander
CRISPR/Cas enables precise improvement of commercially relevant crop species by transgenic and nontransgenic methodologies. We have used CRISPR/Cas with or without DNA repair template in both corn and soybean for a range of applications including enhancing drought tolerance, improving seed oil composition, and endowing herbicide tolerance. Importantly, by pairing CRISPR/Cas technology with recent advances in plant tissue culture, these changes can be introduced directly into commercially relevant genotypes...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/28712497/use-of-crispr-cas9-for-symbiotic-nitrogen-fixation-research-in-legumes
#9
Longlong Wang, Longxiang Wang, Yu Zhou, Deqiang Duanmu
Nitrogen-fixing rhizobia have established a symbiotic relationship with the legume family through more than 60 million years of evolution. Hundreds of legume host genes are involved in the SNF (symbiotic nitrogen fixation) process, such as recognition of the bacterial partners, nodulation signaling and nodule development, maintenance of highly efficient nitrogen fixation within nodules, regulation of nodule numbers, and nodule senescence. However, investigations of SNF-related gene functions and dissecting molecular mechanisms of the complicated signaling crosstalk on a genomic scale were significantly restricted by insufficient mutant resources of several representative model legumes...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/28711373/comparative-genomic-and-phylogenetic-analysis-of-a-toxigenic-clinical-isolate-of-corynebacterium-diphtheriae-strain-b-d-16-78-from-malaysia
#10
Kar-Wai Hong, A W Asmah Hani, C A Nurul Aina Murni, R R Pusparani, Chee Kheong Chong, Khebir Verasahib, Wan Noraini W Yusoff, Noorliza M Noordin, Kok Keng Tee, Wai-Fong Yin, Choo Yee Yu, Geik Yong Ang, Kok-Gan Chan
In this study, we report the comparative genomics and phylogenetic analysis of Corynebacterium diphtheriae strain B-D-16-78 that was isolated from a clinical specimen in 2016. The complete genome of C. diphtheriae strain B-D-16-78 was sequenced using PacBio Single Molecule, Real-Time sequencing technology and consists of a 2,474,151-bp circular chromosome with an average GC content of 53.56%. The core genome of C. diphtheriae was also deduced from a total of 74 strains with complete or draft genome sequences and the core genome-based phylogenetic analysis revealed close genetic relationship among strains that shared the same MLST allelic profile...
July 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28710851/generation-of-apoptosis-resistant-hek293-cells-with-crispr-cas-mediated-quadruple-gene-knockout-for-improved-protein-and-virus-production
#11
Weifeng Zhang, Dan Xiao, Linlin Shan, Junli Zhao, Qinwen Mao, Haibin Xia
Apoptosis has important functions during pathophysiologic processes. However, from a biopharmaceutical point of view, active apoptosis of host cells is undesirable during viral packaging or protein expression, because it decreases the efficiency of viral or protein production. Here we used the CRISPR/Cas technique to knock out four pro-apoptotic genes, Caspase3, Caspase6, Caspase7 and AIF1, in HEK293 cells, and successfully produced an apoptosis-resistant cell line. Furthermore, this cell line showed higher expression levels of pro-apoptotic proteins and higher packaging efficiency for the virus carrying these proteins than control HEK293 cells...
July 15, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28700573/crispr-cas-encoding-of-a-digital-movie-into-the-genomes-of-a-population-of-living-bacteria
#12
Seth L Shipman, Jeff Nivala, Jeffrey D Macklis, George M Church
DNA is an excellent medium for archiving data. Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro. A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time. Using the Cas1-Cas2 integrase, the CRISPR-Cas microbial immune system stores the nucleotide content of invading viruses to confer adaptive immunity. When harnessed, this system has the potential to write arbitrary information into the genome...
July 12, 2017: Nature
https://www.readbyqxmd.com/read/28699694/the-epigenomics-of-schizophrenia-in-the-mouse
#13
REVIEW
Behnam Javidfar, Royce Park, Bibi S Kassim, Lucy K Bicks, Schahram Akbarian
Large-scale consortia including the Psychiatric Genomics Consortium, the Common Minds Consortium, BrainSeq and PsychENCODE, and many other studies taken together provide increasingly detailed insights into the genetic and epigenetic risk architectures of schizophrenia (SCZ) and offer vast amounts of molecular information, but with largely unexplored therapeutic potential. Here we discuss how epigenomic studies in human brain could guide animal work to test the impact of disease-associated alterations in chromatin structure and function on cognition and behavior...
July 12, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28698278/on-the-origin-of-reverse-transcriptase-using-crispr-cas-systems-and-their-hyperdiverse-enigmatic-spacer-repertoires
#14
Sukrit Silas, Kira S Makarova, Sergey Shmakov, David Páez-Espino, Georg Mohr, Yi Liu, Michelle Davison, Simon Roux, Siddharth R Krishnamurthy, Becky Xu Hua Fu, Loren L Hansen, David Wang, Matthew B Sullivan, Andrew Millard, Martha R Clokie, Devaki Bhaya, Alan M Lambowitz, Nikos C Kyrpides, Eugene V Koonin, Andrew Z Fire
Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains...
July 11, 2017: MBio
https://www.readbyqxmd.com/read/28695850/assembly-of-francisella-novicida-cpf1-endonuclease-in-complex-with-guide-rna-and-target-dna
#15
Pablo Alcón, Guillermo Montoya, Stefano Stella
Bacteria and archaea use the CRISPR-Cas system as an adaptive response against infection by foreign nucleic acids. Owing to its remarkable flexibility, this mechanism has been harnessed and adopted as a powerful tool for genome editing. The CRISPR-Cas system includes two classes that are subdivided into six types and 19 subtypes according to conservation of the cas gene and loci organization. Recently, a new protein with endonuclease activity belonging to class 2 type V has been identified. This endonuclease, termed Cpf1, in complex with a single CRISPR RNA (crRNA) is able to recognize and cleave a target DNA preceded by a 5'-TTN-3' protospacer-adjacent motif (PAM) complementary to the RNA guide...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28695481/a-novel-rat-model-of-nonalcoholic-fatty-liver-disease-constructed-through-crispr-cas-based-hydrodynamic-injection
#16
Qin Yu, Rui-Zhi Tan, Quan Gan, Xia Zhong, You-Qiang Wang, Jing Zhou, Li Wang
CRISPR/Cas technology has been widely used in generating conventional and conditional gene knockout animals through germline mutation. A recent study has demonstrated that CRISPR/Cas system also worked on nongermline mutation in mice liver via hydrodynamic injection of vector plasmid to blood circulation. However, whether this is also applied to rat and what is the optimal concentration of vector plasmid still need to be studied. Here, we attempted to use pX330-Pten plasmid to knock down the expression of Pten in rat liver for generation of nonalcoholic fatty liver disease (NAFLD) rat model...
July 10, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/28685575/biodegradable-amino-ester-nanomaterials-for-cas9-mrna-delivery-in-vitro-and-in-vivo
#17
Xinfu Zhang, Bin Li, Xiao Luo, Weiyu Zhao, Justin Jiang, Chengxiang Zhang, Min Gao, Xiaofang Chen, Yizhou Dong
Efficient and safe delivery of the CRISPR/Cas system is one of the key challenges for genome-editing applications in humans. Herein, we designed and synthesized a series of biodegradable lipidlike compounds containing ester groups for the delivery of mRNA-encoding Cas9. Two lead materials, termed N-methyl-1,3-propanediamine (MPA)-A and MPA-Ab, showed a tunable rate of biodegradation. MPA-A with linear ester chains was degraded dramatically faster than MPA-Ab with branched ester chains in the presence of esterase or in wild-type mice...
July 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28684898/autophagy-regulates-the-stemness-of-cervical-cancer-stem-cells
#18
Yi Yang, Li Yu, Jin Li, Ya Hong Yuan, Xiao Li Wang, Shi Rong Yan, Dong Sheng Li, Yan Ding
Cancer stem cells (CSCs) are a rare population of multipotent cells with the capacity to self-renew. It has been reported that there are CSCs in cervical cancer cells. Pluripotency-associated (PA) transcription factors such as Oct4, Sox2, Nanog and CD44 have been used to isolate CSCs subpopulations. In this study, we showed that autophagy plays an important role in the biological behavior of cervical cancer cells. The expression of the autophagy protein Beclin 1 and LC3B was higher in tumorspheres established from human cervical cancers cell lines (and CaSki) than in the parental adherent cells...
2017: Biologics: Targets & Therapy
https://www.readbyqxmd.com/read/28684374/investigating-crispr-cas-systems-in-clostridium-botulinum-via-bioinformatics-tools
#19
Manica Negahdaripour, Navid Nezafat, Nasim Hajighahramani, Seyyed Soheil Rahmatabadi, Younes Ghasemi
The Clustered regularly interspaced short palindromic repeats (CRISPR) systems are a type of innate immunity found in some prokaryotes, which protect them against alien genetic elements by targeting foreign nucleic acids. Some other functions are also attributed to these systems. Clostridium botulinum bacteria produce botulinum neurotoxins (BoNT), one of the deadliest known toxins for humans and some animals. Food poisoning due to these bacteria is still a challenge in food industries. On the other hand, BoNT has been widely investigated for therapeutic applications including different muscle disorders...
July 3, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28674106/crispr-cas-adaptive-immunity-and-the-three-rs
#20
Tom Killelea, Edward L Bolt
In this summary we focus on fundamental biology of CRISPR-Cas adaptive immunity in bacteria. Emphasis is placed on emerging information about functional interplay between CRISPR associated (Cas) proteins and proteins that remodel DNA during homologous recombination, DNA replication or DNA repair. We highlight how replication forks may act as "trigger-points" for CRISPR adaptation events, and the potential for Cascade interference complexes to act as precise roadblocks to DNA replication by an invader mobile genetic element, without the need for DNA double strand breaks...
July 3, 2017: Bioscience Reports
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