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clustered regularly interspaced short palindromic repeats

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https://www.readbyqxmd.com/read/28211909/a-crispr-cpf1-system-for-efficient-genome-editing-and-transcriptional-repression-in-plants
#1
Xu Tang, Levi G Lowder, Tao Zhang, Aimee A Malzahn, Xuelian Zheng, Daniel F Voytas, Zhaohui Zhong, Yiyi Chen, Qiurong Ren, Qian Li, Elida R Kirkland, Yong Zhang, Yiping Qi
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cpf1 has emerged as an effective genome editing tool in animals. Here we compare the activity of Cpf1 from Acidaminococcus sp. BV3L6 (As) and Lachnospiraceae bacterium ND2006 (Lb) in plants, using a dual RNA polymerase II promoter expression system. LbCpf1 generated biallelic mutations at nearly 100% efficiency at four independent sites in rice T0 transgenic plants. Moreover, we repurposed AsCpf1 and LbCpf1 for efficient transcriptional repression in Arabidopsis, and demonstrated a more than tenfold reduction in miR159b transcription...
February 17, 2017: Nature Plants
https://www.readbyqxmd.com/read/28207509/relationship-between-drug-resistance-and-the-clustered-regularly-interspaced-short-palindromic-repeat-associated-protein-genes-cas1-and-cas2-in-shigella-from-giant-panda-dung
#2
Lu Ren, Lin-Hua Deng, Ri-Peng Zhang, Cheng-Dong Wang, De-Sheng Li, Li-Xin Xi, Zhen-Rong Chen, Rui Yang, Jie Huang, Yang-Ru Zeng, Hong-Lin Wu, San-Jie Cao, Rui Wu, Yong Huang, Qi-Gui Yan
BACKGROUND: To detect drug resistance in Shigella obtained from the dung of the giant panda, explore the factors leading to drug resistance in Shigella, understand the characteristics of clustered, regularly interspaced, short, palindromic repeats (CRISPR), and assess the relationship between CRISPR and drug resistance. METHODS: We collected fresh feces from 27 healthy giant pandas in the Giant Panda Conservation base (Wolong, China). We identified the strains of Shigella in the samples by using nucleotide sequence analysis...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28207002/detecting-natural-adaptation-of-the-streptococcus-thermophilus-crispr-cas-systems-in-research-and-classroom-settings
#3
Alexander P Hynes, Marie-Laurence Lemay, Luc Trudel, Hélène Deveau, Michel Frenette, Denise M Tremblay, Sylvain Moineau
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas systems have been adapted into a powerful genome-editing tool. The basis for the flexibility of the tool lies in the adaptive nature of CRISPR-Cas as a bacterial immune system. Here, we describe a protocol to experimentally demonstrate the adaptive nature of this bacterial immune system by challenging the model organism for the study of CRISPR adaptation, Streptococcus thermophilus, with phages in order to detect natural CRISPR immunization...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28207001/genome-editing-using-facs-enrichment-of-nuclease-expressing-cells-and-indel-detection-by-amplicon-analysis
#4
Lindsey A Lonowski, Yoshiki Narimatsu, Anjum Riaz, Catherine E Delay, Zhang Yang, Francesco Niola, Katarzyna Duda, Elke A Ober, Henrik Clausen, Hans H Wandall, Steen H Hansen, Eric P Bennett, Morten Frödin
This protocol describes methods for increasing and evaluating the efficiency of genome editing based on the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated 9) system, transcription activator-like effector nucleases (TALENs) or zinc-finger nucleases (ZFNs). First, Indel Detection by Amplicon Analysis (IDAA) determines the size and frequency of insertions and deletions elicited by nucleases in cells, tissues or embryos through analysis of fluorophore-labeled PCR amplicons covering the nuclease target site by capillary electrophoresis in a sequenator...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28202591/non-classical-phase-diagram-for-virus-bacterial-coevolution-mediated-by-clustered-regularly-interspaced-short-palindromic-repeats
#5
Pu Han, Michael W Deem
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape recognition by CRISPR...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28199145/characterization-and-virulence-potential-of-serogroup-o113-shiga-toxin-producing-escherichia-coli-strains-isolated-from-beef-and-cattle-in-the-united-states
#6
Peter Feng, Sabine Delannoy, David W Lacher, Joseph M Bosilevac, Patrick Fach
Shiga toxin-producing Escherichia coli (STEC) of serotype O113:H21 have caused severe diseases but are unusual in that they do not produce the intimin protein required for adherence to intestinal epithelial cells. Strains of serogroup O113 are one of the most common STEC found in ground beef and beef products in the United States, but their virulence potential is unknown. We used a microarray to characterize 65 O113 strains isolated in the United States from ground beef, beef trim, cattle feces, and fresh spinach...
February 15, 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28198371/method-for-dual-viral-vector-mediated-crispr-cas9-gene-disruption-in-primary-human-endothelial-cells
#7
Haixia Gong, Menglin Liu, Jeff Klomp, Bradley J Merrill, Jalees Rehman, Asrar B Malik
Human endothelial cells (ECs) are widely used to study mechanisms of angiogenesis, inflammation, and endothelial permeability. Targeted gene disruption induced by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-Associated Protein 9 (Cas9) nuclease gene editing is potentially an important tool for definitively establishing the functional roles of individual genes in ECs. We showed that co-delivery of adenovirus encoding EGFP-tagged Cas9 and lentivirus encoding a single guide RNA (sgRNA) in primary human lung microvascular ECs (HLMVECs) disrupted the expression of the Tie2 gene and protein...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28198142/therapeutic-genome-engineering-via-crispr-cas-systems
#8
REVIEW
Ana M Moreno, Prashant Mali
Differences in genomes underlie most organismal diversity, and aberrations in genomes underlie many disease states. With the growing knowledge of the genetic and pathogenic basis of human disease, development of safe and efficient platforms for genome and epigenome engineering will transform our ability to therapeutically target human diseases and also potentially engineer disease resistance. In this regard, the recent advent of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) RNA-guided nuclease systems have transformed our ability to target nucleic acids...
February 15, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28196955/identification-of-human-junctional-adhesion-molecule-1-as-a-functional-receptor-for-the-hom-1-calicivirus-on-human-cells
#9
Stanislav V Sosnovtsev, Carlos Sandoval-Jaime, Gabriel I Parra, Christine M Tin, Ronald W Jones, Jo Soden, Donna Barnes, Jim Freeth, Alvin W Smith, Kim Y Green
The Hom-1 vesivirus was reported in 1998 following the inadvertent transmission of the animal calicivirus San Miguel sea lion virus to a human host in a laboratory. We characterized the Hom-1 strain and investigated the mechanism by which human cells could be infected. An expression library of 3,559 human plasma membrane proteins was screened for reactivity with Hom-1 virus-like particles, and a single interacting protein, human junctional adhesion molecule 1 (hJAM1), was identified. Transient expression of hJAM1 conferred susceptibility to Hom-1 infection on nonpermissive Chinese hamster ovary (CHO) cells...
February 14, 2017: MBio
https://www.readbyqxmd.com/read/28196600/genome-editing-in-hpscs-reveals-gata6-haploinsufficiency-and-a-genetic-interaction-with-gata4-in-human-pancreatic-development
#10
Zhong-Dong Shi, Kihyun Lee, Dapeng Yang, Sadaf Amin, Nipun Verma, Qing V Li, Zengrong Zhu, Chew-Li Soh, Ritu Kumar, Todd Evans, Shuibing Chen, Danwei Huangfu
Human disease phenotypes associated with haploinsufficient gene requirements are often not recapitulated well in animal models. Here, we have investigated the association between human GATA6 haploinsufficiency and a wide range of clinical phenotypes that include neonatal and adult-onset diabetes using CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9-mediated genome editing coupled with human pluripotent stem cell (hPSC) directed differentiation. We found that loss of one GATA6 allele specifically affects the differentiation of human pancreatic progenitors from the early PDX1+ stage to the more mature PDX1+NKX6...
February 8, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28191783/concise-review-the-potential-use-of-intestinal-stem-cells-to-treat-patients-with-intestinal-failure
#11
Sung Noh Hong, James C Y Dunn, Matthias Stelzner, Martín G Martín
Intestinal failure is a rare life-threatening condition that results in the inability to maintain normal growth and hydration status by enteral nutrition alone. Although parenteral nutrition and whole organ allogeneic transplantation have improved the survival of these patients, current therapies are associated with a high risk for morbidity and mortality. Development of methods to propagate adult human intestinal stem cells (ISCs) and pluripotent stem cells raises the possibility of using stem cell-based therapy for patients with monogenic and polygenic forms of intestinal failure...
February 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28188222/characterization-of-genomic-deletion-efficiency-mediated-by-clustered-regularly-interspaced-short-palindromic-repeats-crispr-cas9-nuclease-system-in-mammalian-cells
#12
Matthew C Canver, Daniel E Bauer, Abhishek Dass, Yvette Y Yien, Jacky Chung, Takeshi Masuda, Takahiro Maeda, Barry H Paw, Stuart H Orkin
No abstract text is available yet for this article.
February 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28186905/hmmcas-a-web-tool-for-the-identification-and-domain-annotations-of-cas-proteins
#13
Guoshi Chai, Min Yu, Lixu Jiang, Yaocong Duan, Jian Huang
The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) adaptive immune systems are discovered in many bacteria and most archaea. These systems are encoded by cas (CRISPR-associated) operons that have an extremely diverse architecture. The most crucial step in the depiction of cas operons composition is the identification of cas genes or Cas proteins. With the continuous increase of the newly sequenced archaeal and bacterial genomes, the recognition of new Cas proteins is becoming possible, which not only provides candidates for novel genome editing tools but also helps to understand the prokaryotic immune system better...
February 7, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28182397/comeback-of-the-rat-in-biomedical-research
#14
Judith R Homberg, Markus Wöhr, Natalia Alenina
Rats were the first mammalian species domesticated for scientific purposes, and they soon became the most widely used animal model in biomedical sciences, including cardiovascular research and behavioral neuroscience. Yet, after the development of technologies to manipulate genes, researchers largely shifted to the use of mice. However, as we lay out with examples from drug addiction, social behavior, and cardiovascular research, rats have experimental advantages over mice. With the introduction of zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN) methodologies, and, specifically, the clustered regularly interspaced short palindromic repeats (CRISPR) associated system, gene targeting is no longer limited to mice...
February 9, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28178187/may-i-cut-in-gene-editing-approaches-in-human-induced-pluripotent-stem-cells
#15
REVIEW
Nicholas Brookhouser, Sreedevi Raman, Christopher Potts, David A Brafman
In the decade since Yamanaka and colleagues described methods to reprogram somatic cells into a pluripotent state, human induced pluripotent stem cells (hiPSCs) have demonstrated tremendous promise in numerous disease modeling, drug discovery, and regenerative medicine applications. More recently, the development and refinement of advanced gene transduction and editing technologies have further accelerated the potential of hiPSCs. In this review, we discuss the various gene editing technologies that are being implemented with hiPSCs...
February 6, 2017: Cells
https://www.readbyqxmd.com/read/28177825/enhancement-of-single-guide-rna-transcription-for-efficient-crispr-cas-based-genomic-engineering
#16
Kumiko Ui-Tei, Shohei Maruyama, Yuko Nakano
Genomic engineering using clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) protein is a promising approach for targeting the genomic DNA of virtually any organism in a sequence-specific manner. Recent remarkable advances in CRISPR/Cas technology have made it a feasible system for use in therapeutic applications and biotechnology. In the CRISPR/Cas system, a guide RNA (gRNA), interacting with the Cas protein, recognizes a genomic region with sequence complementarity, and the double-stranded DNA at the target site is cleaved by the Cas protein...
January 26, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28174230/crispr-cas9-coupled-affinity-purification-mass-spectrometry-analysis-revealed-a-novel-role-of-neurofibromin-in-mtor-signaling
#17
Xu Li, Min Gao, Jong Min Choi, Beom-Jun Kim, Mao-Tian Zhou, Zhen Chen, Antrix N Jain, Sung Yun Jung, Jingsong Yuan, Wenqi Wang, Yi Wang, Junjie Chen
Neurofibromin (NF1) is a well-known tumor suppressor that is commonly mutated in cancer patients. It physically interacts with RAS and negatively regulates RAS GTPase activity. Despite the importance of NF1 in cancer, a high-quality endogenous NF1 interactome has yet to be established. In this study, we combined clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated gene knockout technology with affinity purification using antibodies against endogenous proteins, followed by mass spectrometry analysis, to sensitively and accurately detect NF1 protein-protein interactions in unaltered in vivo settings...
February 7, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28168222/tgprelid-a-mitochondrial-protein-linked-to-multidrug-resistance-in-the-parasite-toxoplasma-gondii
#18
Victoria Jeffers, Edwin T Kamau, Ananth R Srinivasan, Jonathan Harper, Preethi Sankaran, Sarah E Post, Joseph M Varberg, William J Sullivan, Jon P Boyle
New drugs to control infection with the protozoan parasite Toxoplasma gondii are needed as current treatments exert toxic side effects on patients. Approaches to develop novel compounds for drug development include screening of compound libraries and targeted inhibition of essential cellular pathways. We identified two distinct compounds that display inhibitory activity against the parasite's replicative stage: F3215-0002, which we previously identified during a compound library screen, and I-BET151, an inhibitor of bromodomains, the "reader" module of acetylated lysines...
January 2017: MSphere
https://www.readbyqxmd.com/read/28167953/biofortification-in-millets-a-sustainable-approach-for-nutritional-security
#19
REVIEW
A Vinoth, R Ravindhran
Nutritional insecurity is a major threat to the world's population that is highly dependent on cereals-based diet, deficient in micronutrients. Next to cereals, millets are the primary sources of energy in the semi-arid tropics and drought-prone regions of Asia and Africa. Millets are nutritionally superior as their grains contain high amount of proteins, essential amino acids, minerals, and vitamins. Biofortification of staple crops is proved to be an economically feasible approach to combat micronutrient malnutrition...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28167937/antiviral-defenses-in-plants-through-genome-editing
#20
REVIEW
Gustavo Romay, Claude Bragard
Plant-virus interactions based-studies have contributed to increase our understanding on plant resistance mechanisms, providing new tools for crop improvement. In the last two decades, RNA interference, a post-transcriptional gene silencing approach, has been used to induce antiviral defenses in plants with the help of genetic engineering technologies. More recently, the new genome editing systems (GES) are revolutionizing the scope of tools available to confer virus resistance in plants. The most explored GES are zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats/Cas9 endonuclease...
2017: Frontiers in Microbiology
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