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https://www.readbyqxmd.com/read/29145601/identification-and-functional-analysis-of-potential-prophage-derived-recombinases-for-genome-editing-in-lactobacillus-casei
#1
Yongping Xin, Tingting Guo, Yingli Mu, Jian Kong
Numerous LAB bacteriophage genomes have been sequenced, while the functional genes are yet to be exploited. In this study, a λ Red-like recombinase operon LCABL_13040-50-60 was identified from a prophage PLE3 in Lactobacillus casei BL23 genome, and its recombination function was confirmed by replacement of a 167 bp galK fragment with chloramphenicol-resistant gene (cat) in the L. casei BL23 genome. Further functional analysis showed that LCABL_13040 and LCABL_13060 were analogs to the host nuclease inhibitor (Redγ) and 5'-3' exonuclease (Redα/RecE), respectively...
November 14, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29145596/a-crispr-cas9-based-exploration-into-the-elusive-mechanism-for-lactate-export-in-saccharomyces-cerevisiae
#2
Robert Mans, Else-Jasmijn Hassing, Melanie Wijsman, Annabel Giezekamp, Jack T Pronk, Jean-Marc Daran, Antonius J A van Maris
CRISPR/Cas9-based genome editing allows rapid, simultaneous modification of multiple genetic loci in Saccharomyces cerevisiae. Here, this technique was used in a functional analysis study aimed at identifying the hitherto unknown mechanism of lactate export in this yeast. First, an S. cerevisiae strain was constructed with deletions in 25 genes encoding transport proteins, including the complete aqua(glycero)porin family and all known carboxylic-acid transporters. The 25-deletion strain was then transformed with an expression cassette for Lactobacillus casei lactate dehydrogenase (LcLDH)...
November 14, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/29141997/crispr-cas9-mediated-genome-editing-reveals-the-synergistic-effects-of-%C3%AE-defensin-family-members-on-sperm-maturation-in-rat-epididymis
#3
Chaobao Zhang, Yuchuan Zhou, Shengsong Xie, Qianqian Yin, Chunhua Tang, Zimei Ni, Jian Fei, Yonglian Zhang
The epididymis is a male reproductive organ involved in posttesticular sperm maturation and storage, but the mechanism underlying sperm maturation remains unclear. β-Defensins (Defbs) belong to a family of small, cysteine-rich, cationic peptides that are antimicrobial and modulate the immune response. A large number of Defb genes are expressed abundantly in the male reproductive tract, especially in the epididymis. We and other groups have shown the involvement of several Defb genes in regulation of sperm function...
November 15, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29141958/dna-methylation-defines-regional-identity-of-human-intestinal-epithelial-organoids-and-undergoes-dynamic-changes-during-development
#4
Judith Kraiczy, Komal M Nayak, Kate J Howell, Alexander Ross, Jessica Forbester, Camilla Salvestrini, Roxana Mustata, Sally Perkins, Amanda Andersson-Rolf, Esther Leenen, Anke Liebert, Ludovic Vallier, Philip C Rosenstiel, Oliver Stegle, Gordon Dougan, Robert Heuschkel, Bon-Kyoung Koo, Matthias Zilbauer
OBJECTIVE: Human intestinal epithelial organoids (IEOs) are increasingly being recognised as a highly promising translational research tool. However, our understanding of their epigenetic molecular characteristics and behaviour in culture remains limited. DESIGN: We performed genome-wide DNA methylation and transcriptomic profiling of human IEOs derived from paediatric/adult and fetal small and large bowel as well as matching purified human gut epithelium. Furthermore, organoids were subjected to in vitro differentiation and genome editing using CRISPR/Cas9 technology...
November 15, 2017: Gut
https://www.readbyqxmd.com/read/29141633/genome-modification-of-cxcr4-by-staphylococcus-aureus-cas9-renders-cells-resistance-to-hiv-1-infection
#5
Qiankun Wang, Shuliang Chen, Qiaoqiao Xiao, Zhepeng Liu, Shuai Liu, Panpan Hou, Li Zhou, Wei Hou, Wenzhe Ho, Chunmei Li, Li Wu, Deyin Guo
BACKGROUND: The CRISPR/Cas9 system has been widely used for genome editing in mammalian cells. CXCR4 is a co-receptor for human immunodeficiency virus type 1 (HIV-1) entry, and loss of CXCR4 function can protect cells from CXCR4 (X4)-tropic HIV-1 infection, making CXCR4 an important target for HIV-1 gene therapy. However, the large size of the CRISPR/SpCas9 system presents an obstacle to its efficient delivery into primary CD4(+) T cells. Recently, a small Staphylococcus aureus Cas9 (SaCas9) has been developed as a genome editing tool can address this question...
November 15, 2017: Retrovirology
https://www.readbyqxmd.com/read/29141604/genome-wide-identification-of-mirnas-and-lncrnas-in-cajanus-cajan
#6
Chandran Nithin, Amal Thomas, Jolly Basak, Ranjit Prasad Bahadur
BACKGROUND: Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) are an abundant class of small ncRNAs (~22nt long) that negatively regulate gene expression at the levels of messenger RNAs stability and translation inhibition, on the other hand, long ncRNAs (lncRNAs) are a large and diverse class of transcribed non-protein coding RNA molecules (> 200nt) that play both up-regulatory as well as down-regulatory roles at the transcriptional level...
November 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29141166/designing-ethical-trials-of-germline-gene-editing
#7
Bryan Cwik
The recent announcement that researchers have successfully used the CRISPR (clustered regularly interspaced short palindromic repeats) gene-editing technique to correct a mutation that leads to hypertrophic cardiomyopathy in human embryos is the latest reminder of the urgency of the social and..
November 16, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/29141136/systemic-mrna-delivery-to-the-lungs-by-functional-polyester-based-carriers
#8
Yunfeng Yan, Hu Xiong, Xinyi Zhang, Qiang Cheng, Daniel John Siegwart
Messenger RNA (mRNA) has recently come into focus as an emerging therapeutic class with great potential for protein replacement therapy, cancer immunotherapy, regenerative medicine, vaccines, and gene editing. However, the lack of effective and safe delivery methods impedes the broad application of mRNA-based therapeutics. Here, we report a robust approach to develop efficient polymeric delivery carriers for mRNA. Lead polyesters were identified by in vitro screening of a 480-member combinatorially modified poly(trimethylolpropane allyl ether-co-suberoyl chloride) library for the delivery of luciferase encoding mRNA (Luc mRNA) to IGROV1 cells...
November 15, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/29140568/crispr-cas9-based-safe-harbor-gene-editing-in-rhesus-ipscs
#9
Ravi Chandra Yada, John W Ostrominski, Ilker Tunc, So Gun Hong, Jizhong Zou, Cynthia E Dunbar
NHP iPSCs provide a unique opportunity to test safety and efficacy of iPSC-derived therapies in clinically relevant NHP models. To monitor these cells in vivo, there is a need for safe and efficient labeling methods. Gene insertion into genomic safe harbors (GSHs) supports reliable transgene expression while minimizing the risk the modification poses to the host genome or target cell. Specifically, this protocol demonstrates targeting of the adeno-associated virus site 1 (AAVS1), one of the most widely used GSH loci in the human genome, with CRISPR/Cas9, allowing targeted marker or therapeutic gene insertion in rhesus macaque induced pluripotent stem cells (RhiPSCs)...
November 15, 2017: Current Protocols in Stem Cell Biology
https://www.readbyqxmd.com/read/29140512/a-novel-tetratricopeptide-repeat-protein-white-to-green1-is-required-for-early-chloroplast-development-and-affects-rna-editing-in-chloroplasts
#10
Fei Ma, Yingchun Hu, Yan Ju, Qianru Jiang, Zhijun Cheng, Quan Zhang, Sodmergen
The chloroplast is essential for plant photosynthesis and production, but the regulatory mechanism of chloroplast development is still elusive. Here, a novel gene, WHITE TO GREEN1 (WTG1), was identified to have a function in chloroplast development and plastid gene expression by screening Arabidopsis leaf coloration mutants. WTG1 encodes a chloroplast-localized tetratricopeptide repeat protein that is expressed widely in Arabidopsis cells. Disruption of WTG1 suppresses plant growth, retards leaf greening and chloroplast development, and represses photosynthetic gene expression, but complemented expression of WTG1 restored a normal phenotype...
November 11, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29138405/ca-2-signals-initiate-at-immobile-ip3-receptors-adjacent-to-er-plasma-membrane-junctions
#11
Nagendra Babu Thillaiappan, Alap P Chavda, Stephen C Tovey, David L Prole, Colin W Taylor
IP3 receptors (IP3Rs) release Ca(2+) from the ER when they bind IP3 and Ca(2+). The spatial organization of IP3Rs determines both the propagation of Ca(2+) signals between IP3Rs and the selective regulation of cellular responses. Here we use gene editing to fluorescently tag endogenous IP3Rs, and super-resolution microscopy to determine the geography of IP3Rs and Ca(2+) signals within living cells. We show that native IP3Rs cluster within ER membranes. Most IP3R clusters are mobile, moved by diffusion and microtubule motors...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29138316/germline-cas9-expression-yields-highly-efficient-genome-engineering-in-a-major-worldwide-disease-vector-aedes-aegypti
#12
Ming Li, Michelle Bui, Ting Yang, Christian S Bowman, Bradley J White, Omar S Akbari
The development of CRISPR/Cas9 technologies has dramatically increased the accessibility and efficiency of genome editing in many organisms. In general, in vivo germline expression of Cas9 results in substantially higher activity than embryonic injection. However, no transgenic lines expressing Cas9 have been developed for the major mosquito disease vector Aedes aegypti Here, we describe the generation of multiple stable, transgenic Ae. aegypti strains expressing Cas9 in the germline, resulting in dramatic improvements in both the consistency and efficiency of genome modifications using CRISPR...
November 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29137643/efficient-gene-editing-in-corynebacterium-glutamicum-using-the-crispr-cas9-system
#13
Feng Peng, Xinyue Wang, Yang Sun, Guibin Dong, Yankun Yang, Xiuxia Liu, Zhonghu Bai
BACKGROUND: Corynebacterium glutamicum (C. glutamicum) has traditionally been used as a microbial cell factory for the industrial production of many amino acids and other industrially important commodities. C. glutamicum has recently been established as a host for recombinant protein expression; however, some intrinsic disadvantages could be improved by genetic modification. Gene editing techniques, such as deletion, insertion, or replacement, are important tools for modifying chromosomes...
November 14, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29136157/depletion-of-recombination-specific-co-factors-by-the-c-terminal-mutant-of-the-activation-induced-cytidine-deaminase-causes-the-dominant-negative-effect-on-class-switch-recombination
#14
Azza Al Ismail, Afzal Husain, Maki Kobayashi, Tasuku Honjo, Nasim A Begum
Activation-induced cytidine deaminase (AID) is essential for class-switch recombination (CSR) and somatic hypermutation (SHM) of immunoglobulin (Ig) genes. Studies on in vitro mutagenized AID as well as its mutations in human patients with Hyper-IgM (HIGM)-syndrome type II revealed that C-terminal AID mutations were defective in CSR whereas their DNA cleavage and SHM activities remained intact. The C-terminal mutants of AID were speculated to exert the dominant negative effect on wild type WT AID whereas its mechanism remains unknown...
November 10, 2017: International Immunology
https://www.readbyqxmd.com/read/29133827/blastocyst-formation-rate-and-transgene-expression-are-associated-with-gene-insertion-into-safe-and-non-safe-harbors-in-the-cattle-genome
#15
Milad Khorramian Ghahfarokhi, Kianoush Dormiani, Ali Mohammadi, Farnoosh Jafarpour, Mohammad Hossein Nasr-Esfahani
Integration target site is the most important factor in successful production of transgenic animals. However, stable expression of transgene without disturbing the function of the host genome depends on promoter methylation, transgene copy number and transcriptional activity in integration regions. Recently, new genome-editing tools have made much progress, however little attention has been paid to the identification of genomic safe harbors. The aim of the present study was to evaluate the effect of insertion site, promoter and copy number of transgene on the production of embryos from cattle fibroblast cells following somatic cell nuclear transfer (SCNT)...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133817/transgenic-cavendish-bananas-with-resistance-to-fusarium-wilt-tropical-race-4
#16
James Dale, Anthony James, Jean-Yves Paul, Harjeet Khanna, Mark Smith, Santy Peraza-Echeverria, Fernando Garcia-Bastidas, Gert Kema, Peter Waterhouse, Kerrie Mengersen, Robert Harding
Banana (Musa spp.) is a staple food for more than 400 million people. Over 40% of world production and virtually all the export trade is based on Cavendish banana. However, Cavendish banana is under threat from a virulent fungus, Fusarium oxysporum f. sp. cubense tropical race 4 (TR4) for which no acceptable resistant replacement has been identified. Here we report the identification of transgenic Cavendish with resistance to TR4. In our 3-year field trial, two lines of transgenic Cavendish, one transformed with RGA2, a gene isolated from a TR4-resistant diploid banana, and the other with a nematode-derived gene, Ced9, remain disease free...
November 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/29133816/disruption-of-diphthamide-synthesis-genes-and-resulting-toxin-resistance-as-a-robust-technology-for-quantifying-and-optimizing-crispr-cas9-mediated-gene-editing
#17
Tobias Killian, Steffen Dickopf, Alexander K Haas, Claudia Kirstenpfad, Klaus Mayer, Ulrich Brinkmann
We have devised an effective and robust method for the characterization of gene-editing events. The efficacy of editing-mediated mono- and bi-allelic gene inactivation and integration events is quantified based on colony counts. The combination of diphtheria toxin (DT) and puromycin (PM) selection enables analyses of 10,000-100,000 individual cells, assessing hundreds of clones with inactivated genes per experiment. Mono- and bi-allelic gene inactivation is differentiated by DT resistance, which occurs only upon bi-allelic inactivation...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133799/hit-and-run-epigenetic-editing-prevents-senescence-entry-in-primary-breast-cells-from-healthy-donors
#18
Emily A Saunderson, Peter Stepper, Jennifer J Gomm, Lily Hoa, Adrienne Morgan, Michael D Allen, J Louise Jones, John G Gribben, Tomasz P Jurkowski, Gabriella Ficz
Aberrant promoter DNA hypermethylation is a hallmark of cancer; however, whether this is sufficient to drive cellular transformation is not clear. To investigate this question, we use a CRISPR-dCas9 epigenetic editing tool, where an inactive form of Cas9 is fused to DNA methyltransferase effectors. Using this system, here we show simultaneous de novo DNA methylation of genes commonly methylated in cancer, CDKN2A, RASSF1, HIC1 and PTEN in primary breast cells isolated from healthy human breast tissue. We find that promoter methylation is maintained in this system, even in the absence of the fusion construct, and this prevents cells from engaging senescence arrest...
November 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29132724/emerging-entities-in-renal-cell-neoplasia-thyroid-like-follicular-renal-cell-carcinoma-and-multifocal-oncocytoma-like-tumours-associated-with-oncocytosis
#19
REVIEW
John N Eble, Brett Delahunt
The list of accepted entities of renal cell neoplasia has burgeoned since the turn of the century through recognition of rare tumour types and the discovery of genetic mutations driving renal neoplasia syndromes. This growth has not finished and in this report we present examples of each of these types which were not included in the 2016 World Health Organization classification of renal neoplasia, but are candidates for inclusion in the next edition of the classification. Thyroid-like follicular renal cell carcinoma is a rare tumour type with a distinctive microscopic appearance resembling follicles of the thyroid gland...
November 10, 2017: Pathology
https://www.readbyqxmd.com/read/29132310/rapid-evolutionary-divergence-of-diploid-and-allotetraploid-gossypium-mitochondrial-genomes
#20
Zhiwen Chen, Hushuai Nie, Yumei Wang, Haili Pei, Shuangshuang Li, Lida Zhang, Jinping Hua
BACKGROUND: Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes of G. hirsutum (AD1), G. barbadense (AD2), G. raimondii (D5) and G. arboreum (A2), together with data of six other mitochondrial genomes, to elucidate the evolution and diversity of mitochondrial genomes within Gossypium...
November 13, 2017: BMC Genomics
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