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https://www.readbyqxmd.com/read/28923848/body-shape-and-coloration-of-silkworm-larvae-are-influenced-by-a-novel-cuticular-protein
#1
Gao Xiong, Xiaoling Tong, Tingting Gai, Chunlin Li, Liang Qiao, Antónia Monteiro, Hai Hu, Minjin Han, Xin Ding, Songyuan Wu, Zhonghuai Xiang, Cheng Lu, Fangyin Dai
The genetic basis of body shape and coloration patterns on caterpillars is often assumed to be regulated separately, but it is possible that common molecules affect both types of trait simultaneously. Here we examine the genetic basis of a spontaneous cuticle defect in silkworm, where larvae exhibit a bamboo-like body shape and also decreased pigmentation. We performed linkage mapping and mutation screening to determine the gene product that affects body shape and coloration simultaneously. In these mutant larvae we identified a null mutation in BmorCPH24, a gene encoding a cuticular protein with low complexity sequence...
September 18, 2017: Genetics
https://www.readbyqxmd.com/read/28918053/ush2a-gene-editing-using-the-crispr-system
#2
Carla Fuster-García, Gema García-García, Elisa González-Romero, Teresa Jaijo, María D Sequedo, Carmen Ayuso, Rafael P Vázquez-Manrique, José M Millán, Elena Aller
Usher syndrome (USH) is a rare autosomal recessive disease and the most common inherited form of combined visual and hearing impairment. Up to 13 genes are associated with this disorder, with USH2A being the most prevalent, due partially to the recurrence rate of the c.2299delG mutation. Excluding hearing aids or cochlear implants for hearing impairment, there are no medical solutions available to treat USH patients. The repair of specific mutations by gene editing is, therefore, an interesting strategy that can be explored using the CRISPR/Cas9 system...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28913801/targeted-mutagenesis-in-hexaploid-bread-wheat-using-the-talen-and-crispr-cas-systems
#3
Yanpeng Wang, Yuan Zong, Caixia Gao
The use of sequence-specific transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats-associated system (CRISPR/Cas9) have provided powerful reverse genetic approaches to the targeted modification of genomes in numerous organisms. Both systems have been employed to generate loss-of-function alleles in bread wheat, by targeting multiple and single copies of genes. Here we present protocols for modifying the wheat genome using the two systems. The protocols include the design of TALEN and CRISPR/Cas9 target sites and their construction, evaluation of their activities in protoplasts, transformation of plants, and mutation screening...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28912524/precise-insertion-and-guided-editing-of-higher-plant-genomes-using-cpf1-crispr-nucleases
#4
Matthew B Begemann, Benjamin N Gray, Emma January, Gina C Gordon, Yonghua He, Haijun Liu, Xingrong Wu, Thomas P Brutnell, Todd C Mockler, Mohammed Oufattole
Precise genome editing of plants has the potential to reshape global agriculture through the targeted engineering of endogenous pathways or the introduction of new traits. To develop a CRISPR nuclease-based platform that would enable higher efficiencies of precise gene insertion or replacement, we screened the Cpf1 nucleases from Francisella novicida and Lachnospiraceae bacterium ND2006 for their capability to induce targeted gene insertion via homology directed repair. Both nucleases, in the presence of a guide RNA and repairing DNA template flanked by homology DNA fragments to the target site, were demonstrated to generate precise gene insertions as well as indel mutations at the target site in the rice genome...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28912455/a-crispr-screen-identifies-genes-controlling-etv2-threshold-expression-in-murine-hemangiogenic-fate-commitment
#5
Haiyong Zhao, Kyunghee Choi
The ETS transcription factor Etv2 is necessary and sufficient for the generation of hematopoietic and endothelial cells. However, upstream regulators of Etv2 in hemangiogenesis, generation of hematopoietic and endothelial cells, have not been clearly addressed. Here we track the developmental route of hemangiogenic progenitors from mouse embryonic stem cells, perform genome-wide CRISPR screening, and transcriptome analysis of en route cell populations by utilizing Brachyury, Etv2, or Scl reporter embryonic stem cell lines to further understand the mechanisms that control hemangiogenesis...
September 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28911203/mutations-of-conserved-non-coding-elements-of-pitx2-in-patients-with-ocular-dysgenesis-and-developmental-glaucoma
#6
Meredith E Protas, Eric Weh, Tim Footz, Jay Kasberger, Scott C Baraban, Alex V Levin, L Jay Katz, Robert Ritch, Michael A Walter, Elena V Semina, Douglas B Gould
Mutations in FOXC1 and PITX2 constitute the most common causes of ocular anterior segment dysgenesis (ASD), and confer a high risk for secondary glaucoma. The genetic causes underlying ASD in approximately half of patients remain unknown, despite many of them being screened by whole exome sequencing. Here, we performed whole genome sequencing on DNA from two affected individuals from a family with dominantly inherited ASD and glaucoma to identify a 748-kb deletion in a gene desert that contains conserved putative PITX2 regulatory elements...
September 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28903573/crispr-in-research-and-treatment-of-multiple-myeloma
#7
M M Simicek, K Growkova, R Hájek
In the recent years, there was a remarkable advance in research and clinical implementation of the genome editing technologies. The most remarkable was a discovery of the bacterial adaptive immune system called CRISPR and its rapid transformation into a robust and broadly applicable technology that completely revolutionized both basic and applied biomedical research. Implementation of CRISPR makes genome modification easier, faster and significantly cheaper compare to any other currently available technology...
2017: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
https://www.readbyqxmd.com/read/28900740/crispr-cas9-mediated-multiple-single-guide-rnas-potently-abrogate-pseudorabies-virus-replication
#8
Yan-Dong Tang, Ji-Ting Liu, Tong-Yun Wang, Ming-Xia Sun, Zhi-Jun Tian, Xue-Hui Cai
Pseudorabies virus (PRV) is a swine herpesvirus that causes significant morbidity and mortality in swine populations and has caused huge economic losses in the worldwide swine industry. Currently, there is no effective antiviral drug in clinical use for PRV infection; it is also difficult to eliminate PRV from infected swine. In our study, we set out to combat these swine herpesvirus infections by exploiting the CRISPR/Cas9 system. We designed 75 single guide RNAs (sgRNA) by targeting both essential and non-essential genes across the genome of PRV...
September 12, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28894007/rabif-mss4-is-a-rab-stabilizing-holdase-chaperone-required-for-glut4-exocytosis
#9
Daniel R Gulbranson, Eric M Davis, Brittany A Demmitt, Yan Ouyang, Yihong Ye, Haijia Yu, Jingshi Shen
Rab GTPases are switched from their GDP-bound inactive conformation to a GTP-bound active state by guanine nucleotide exchange factors (GEFs). The first putative GEFs isolated for Rabs are RABIF (Rab-interacting factor)/MSS4 (mammalian suppressor of Sec4) and its yeast homolog DSS4 (dominant suppressor of Sec4). However, the biological function and molecular mechanism of these molecules remained unclear. In a genome-wide CRISPR genetic screen, we isolated RABIF as a positive regulator of exocytosis. Knockout of RABIF severely impaired insulin-stimulated GLUT4 exocytosis in adipocytes...
September 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28893845/highly-efficient-rapid-and-co-crispr-independent-genome-editing-in-caenorhabditis-elegans
#10
Harriet Prior, Ali K Jawad, Lauren MacConnachie, Asim A Beg
We describe a rapid and highly efficient method to generate point mutations in C. elegans using direct injection of CRISPR-Cas9 ribonucleoproteins. This versatile method does not require sensitized genetic backgrounds or co-CRISPR selection-based methods, and represents a single strategy that can used for creating genomic point mutations, regardless of location. As proof-of-principle, we show that knock-in mutants more faithfully report variant-associated phenotypes compared to transgenic overexpression. Data for nine knock-in mutants across five genes are presented that demonstrate high editing efficiencies (60%), a reduced screening workload (24 F1 progeny), and a rapid timescale (4-5 days)...
September 11, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28887438/-silencing-of-retrotransposons-by-setdb1-inhibits-the-interferon-response-in-acute-myeloid-leukemia
#11
Trinna L Cuellar, Anna-Maria Herzner, Xiaotian Zhang, Yogesh Goyal, Colin Watanabe, Brad A Friedman, Vasantharajan Janakiraman, Steffen Durinck, Jeremy Stinson, David Arnott, Tommy K Cheung, Subhra Chaudhuri, Zora Modrusan, Jonas Martin Doerr, Marie Classon, Benjamin Haley
A propensity for rewiring genetic and epigenetic regulatory networks, thus enabling sustained cell proliferation, suppression of apoptosis, and the ability to evade the immune system, is vital to cancer cell propagation. An increased understanding of how this is achieved is critical for identifying or improving therapeutic interventions. In this study, using acute myeloid leukemia (AML) human cell lines and a custom CRISPR/Cas9 screening platform, we identify the H3K9 methyltransferase SETDB1 as a novel, negative regulator of innate immunity...
September 8, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28882874/haploid-mammalian-genetic-screen-identifies-ubxd8-as-a-key-determinant-of-hmgcr-degradation-and-cholesterol-biosynthesis
#12
Anke Loregger, Matthijs Raaben, Josephine Tan, Saskia Scheij, Martina Moeton, Marlene van den Berg, Hila Gelberg-Etel, Elmer Stickel, Joseph Roitelman, Thijn Brummelkamp, Noam Zelcer
OBJECTIVE: The cellular demand for cholesterol requires control of its biosynthesis by the mevalonate pathway. Regulation of HMGCR (3-hydroxy-3-methylglutaryl coenzyme A reductase), a rate-limiting enzyme in this pathway and the target of statins, is a key control point herein. Accordingly, HMGCR is subject to negative and positive regulations. In particular, the ability of oxysterols and intermediates of the mevalonate pathway to stimulate its proteasomal degradation is an exquisite example of metabolically controlled feedback regulation...
September 7, 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28879857/improving-crispr-cas9-on-target-specificity
#13
Muhammad Jamal, Arif Ullah, Muhammad Ahsan, Rohit Tyagi, Zeshan Habib, Khaista Rehman
The CRISPR-Cas9 has revolutionized the field of molecular biology, medical genetics and medicine. The technology is robust, facile and simple to achieve genome targeting in cells and organisms. However, to propagate these nucleases for therapeutic application, the on-target specificity is of paramount importance. Although the binding and cleavage of off-target sites by Cas9 is issue of concern, however the specificity of CRISPR technology is greatly improved in current research employing the use of engineer nucleases, improved gRNA selection, novel Cas9 orhtologs and the advancement in methods to detect and screen off-target sites and its effects...
September 7, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28878801/crispr-cas9-a-practical-approach-in-date-palm-genome-editing
#14
REVIEW
Muhammad N Sattar, Zafar Iqbal, Muhammad N Tahir, Muhammad S Shahid, Muhammad Khurshid, Abdullatif A Al-Khateeb, Suliman A Al-Khateeb
The genetic modifications through breeding of crop plants have long been used to improve the yield and quality. However, precise genome editing (GE) could be a very useful supplementary tool for improvement of crop plants by targeted genome modifications. Various GE techniques including ZFNs (zinc finger nucleases), TALENs (transcription activator-like effector nucleases), and most recently clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 (CRISPR-associated protein 9)-based approaches have been successfully employed for various crop plants including fruit trees...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28877472/alpk1-and-tifa-dependent-innate-immune-response-triggered-by-the-helicobacter-pylori-type-iv-secretion-system
#15
Stephanie Zimmermann, Lennart Pfannkuch, Munir A Al-Zeer, Sina Bartfeld, Manuel Koch, Jianping Liu, Cindy Rechner, Meike Soerensen, Olga Sokolova, Alla Zamyatina, Paul Kosma, André P Mäurer, Frithjof Glowinski, Klaus-Peter Pleissner, Monika Schmid, Volker Brinkmann, Alexander Karlas, Michael Naumann, Marion Rother, Nikolaus Machuy, Thomas F Meyer
Activation of transcription factor NF-κB is a hallmark of infection with the gastric pathogen Helicobacter pylori, associated with inflammation and carcinogenesis. Genome-wide RNAi screening revealed numerous host factors involved in H. pylori-, but not IL-1β- and TNF-α-dependent NF-κB regulation. Pathway analysis including CRISPR/Cas9-knockout and recombinant protein technology, immunofluorescence microscopy, immunoblotting, mass spectrometry, and mutant H. pylori strains identified the H. pylori metabolite D-glycero-β-D-manno-heptose 1,7-bisphosphate (βHBP) as a cagPAI type IV secretion system (T4SS)-dependent effector of NF-κB activation in infected cells...
September 5, 2017: Cell Reports
https://www.readbyqxmd.com/read/28873439/crispr-focus-a-web-server-for-designing-focused-crispr-screening-experiments
#16
Qingyi Cao, Jian Ma, Chen-Hao Chen, Han Xu, Zhi Chen, Wei Li, X Shirley Liu
The recently developed CRISPR screen technology, based on the CRISPR/Cas9 genome editing system, enables genome-wide interrogation of gene functions in an efficient and cost-effective manner. Although many computational algorithms and web servers have been developed to design single-guide RNAs (sgRNAs) with high specificity and efficiency, algorithms specifically designed for conducting CRISPR screens are still lacking. Here we present CRISPR-FOCUS, a web-based platform to search and prioritize sgRNAs for CRISPR screen experiments...
2017: PloS One
https://www.readbyqxmd.com/read/28871271/somatic-embryogenesis-in-coffee-the-evolution-of-biotechnology-and-the-integration-of-omics-technologies-offer-great-opportunities
#17
REVIEW
Nádia A Campos, Bart Panis, Sebastien C Carpentier
One of the most important crops cultivated around the world is coffee. There are two main cultivated species, Coffea arabica and C. canephora. Both species are difficult to improve through conventional breeding, taking at least 20 years to produce a new cultivar. Biotechnological tools such as genetic transformation, micropropagation and somatic embryogenesis (SE) have been extensively studied in order to provide practical results for coffee improvement. While genetic transformation got many attention in the past and is booming with the CRISPR technology, micropropagation and SE are still the major bottle neck and urgently need more attention...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28868328/creating-a-raw264-7-crispr-cas9-genome-wide-library
#18
Brooke A Napier, Denise M Monack
The bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 genome editing tools are used in mammalian cells to knock-out specific genes of interest to elucidate gene function. The CRISPR-Cas9 system requires that the mammalian cell expresses Cas9 endonuclease, guide RNA (gRNA) to lead the endonuclease to the gene of interest, and the PAM sequence that links the Cas9 to the gRNA. CRISPR-Cas9 genome wide libraries are used to screen the effect of each gene in the genome on the cellular phenotype of interest, in an unbiased high-throughput manner...
May 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28864683/a-crispr-cas9-based-screening-for-non-homologous-end-joining-inhibitors-reveals-ouabain-and-penfluridol-as-radiosensitizers
#19
Jie Du, Jun Shang, Fei Chen, Yushuo Zhang, Narui Yin, Ting Xie, Haowen Zhang, Jiahua Yu, Fenju Liu
Non-homologous end joining (NHEJ) is the major pathway responsible for the repair of ionizing radiation (IR)-induced DNA double-strand breaks (DSBs), and correspondingly regulates the cellular response to IR. Identification of NHEJ inhibitors could substantially enhance the tumor radiosensitivity and improve the therapeutic efficiency of radiotherapy. In present study, we demonstrated a screening for NHEJ inhibitors by using the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system and high-resolution melting (HRM) analysis...
September 1, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28861060/crispr-cas-systems-features-and-the-gene-reservoir-role-of-coagulase-negative-staphylococci
#20
Ciro C Rossi, Thaysa Souza-Silva, Amanda V Araújo-Alves, Marcia Giambiagi-deMarval
The claimed role of gene reservoir of coagulase-negative staphylococci (CoNS) could be contradicted by estimates that CRISPR/Cas systems are found in the genomes of 40-50% of bacteria, as these systems interfere with plasmid uptake in staphylococci. To further correlate this role with presence of CRISPR, we analyzed, by computational methods, 122 genomes from 15 species of CoNS. Only 15% of them harbored CRISPR/Cas systems, and this proportion was much lower for S. epidermidis and S. haemolyticus, the CoNS most frequently associated with opportunistic infections in humans...
2017: Frontiers in Microbiology
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