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https://www.readbyqxmd.com/read/28527665/therapeutic-editing-of-hepatocyte-genome-in-vivo
#1
REVIEW
Marina Ruiz de Galarreta, Amaia Lujambio
The recent development of gene editing platforms enables making precise changes in the genome of eukaryotic cells. Programmable nucleases, such as meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)-associated nucleases, have revolutionized the way research is conducted as they facilitate the rapid production of mutant or knock-out cellular and animal models. These same genetic tools can potentially be applied to cure or alleviate a variety of diseases, including genetic diseases that lack an efficient therapy...
May 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28527117/non-viral-and-viral-delivery-systems-for-crispr-cas9-technology-in-the-biomedical-field
#2
REVIEW
Zhi-Yao He, Ke Men, Zhou Qin, Yang Yang, Ting Xu, Yu-Quan Wei
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system provides a novel genome editing technology that can precisely target a genomic site to disrupt or repair a specific gene. Some CRISPR-Cas9 systems from different bacteria or artificial variants have been discovered or constructed by biologists, and Cas9 nucleases and single guide RNAs (sgRNA) are the major components of the CRISPR-Cas9 system. These Cas9 systems have been extensively applied for identifying therapeutic targets, identifying gene functions, generating animal models, and developing gene therapies...
May 2, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28527116/genome-editing-in-drosophila-melanogaster-from-basic-genome-engineering-to-the-multipurpose-crispr-cas9-system
#3
REVIEW
Xingjie Ren, Kristof Holsteens, Haiyi Li, Jin Sun, Yifan Zhang, Lu-Ping Liu, Qingfei Liu, Jian-Quan Ni
Nowadays, genome editing tools are indispensable for studying gene function in order to increase our knowledge of biochemical processes and disease mechanisms. The extensive availability of mutagenesis and transgenesis tools make Drosophila melanogaster an excellent model organism for geneticists. Early mutagenesis tools relied on chemical or physical methods, ethyl methane sulfonate (EMS) and X-rays respectively, to randomly alter DNA at a nucleotide or chromosomal level. Since the discovery of transposable elements and the availability of the complete fly genome, specific genome editing tools, such as P-elements, zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), have undergone rapid development...
May 1, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28526928/exosomes-in-cardiovascular-medicine
#4
REVIEW
Iain M Dykes
Exosomes are small, extracellular membrane-bound particles that mediate intercellular transport of a cytosolic cargo. Exosomal transfer of micro-RNA can modify gene expression in targeted cells. Exosome-based endocrine/paracrine signaling has been shown to be involved in a wide range of physiological processes including those associated with cardiovascular injury and disease, but remains relatively poorly understood. Exosomes offer great potential to the clinical field, with applications in both diagnostics and therapeutics...
May 19, 2017: Cardiology and Therapy
https://www.readbyqxmd.com/read/28523919/editing-plants-for-virus-resistance-using-crispr-cas
#5
J C Green, J S Hu
This minireview summarizes recent advancements using the clustered regularly interspaced palindromic repeats-associated nuclease systems (CRISPR-Cas) derived from prokaryotes to breed plants resistant to DNA and RNA viruses. The CRISPR-Cas system represents a powerful tool able to edit and insert novel traits into plants precisely at chosen loci offering enormous advantages to classical breeding. Approaches to engineering plant virus resistance in both transgenic and non-transgenic plants are discussed. Iterations of the CRISPR-Cas system, FnCas9 and C2c2 capable of editing RNA in eukaryotic cells offer a particular advantage for providing resistance to RNA viruses which represent the great majority of known plant viruses...
2017: Acta Virologica
https://www.readbyqxmd.com/read/28522396/ultrafast-spectroscopy-on-dna-cleavage-by-endonuclease-in-molecular-crowding
#6
Priya Singh, Susobhan Choudhury, Shreyasi Dutta, Aniruddha Adhikari, Siddhartha Bhattacharya, Debasish Pal, Samir Kumar Pal
The jam-packed intracellular environments differ the activity of a biological macromolecule from that in laboratory environments (in vitro) through a number of mechanisms called molecular crowding related to structure, function and dynamics of the macromolecule. Here, we have explored the structure, function and dynamics of a model enzyme protein DNase I in molecular crowing of polyethylene glycol (PEG; MW 3350). We have used steady state and picosecond resolved dynamics of a well-known intercalator ethidium bromide (EB) in a 20-mer double-stranded DNA (dsDNA) to monitor the DNA-cleavage by the enzyme in absence and presence PEG...
May 15, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28522326/gene-editing-and-clonal-isolation-of-human-induced-pluripotent-stem-cells-using-crispr-cas9
#7
Saniye Yumlu, Jürgen Stumm, Sanum Bashir, Anne-Kathrin Dreyer, Pawel Lisowski, Eric Danner, Ralf Kühn
Human induced pluripotent stem cells (hiPSCs) represent an ideal in vitro platform to study human genetics and biology. The recent advent of programmable nucleases makes also the human genome amenable to experimental genetics through either the correction of mutations in patient-derived iPSC lines or the de novo introduction of mutations into otherwise healthy iPSCs. The production of specific and sometimes complex genotypes in multiple cell lines requires efficient and streamlined gene editing technologies...
May 15, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28521375/a-genetic-marker-associated-with-shoulder-dislocation
#8
Stuart Kim, John P Kleimeyer, Marwa A Ahmed, Andy L Avins, Michael Fredericson, Jason L Dragoo, John P A Ioannidis
Shoulder dislocations are common shoulder injuries associated with athletic activity in contact sports, such as football, rugby, wrestling, and hockey. Identifying genetic loci associated with shoulder dislocation could shed light on underlying mechanisms for injury and identify predictive genetic markers. To identify DNA polymorphisms associated with shoulder dislocation, a genome-wide association screen was performed using publically available data from the Research Program in Genes, Environment and Health including 662 cases of shoulder dislocation and 82 602 controls from the European ancestry group...
May 18, 2017: International Journal of Sports Medicine
https://www.readbyqxmd.com/read/28512214/correction-for-mu%C3%A3-oz-galv%C3%A3-n-et-al-distinct-roles-of-mus81-yen1-slx1-slx4-and-rad1-nucleases-in-the-repair-of-replication-born-double-strand-breaks-by-sister-chromatid-exchange
#9
Sandra Muñoz-Galván, Cristina Tous, Miguel G Blanco, Erin K Schwartz, Kirk T Ehmsen, Stephen C West, Wolf-Dietrich Heyer, Andrés Aguilera
No abstract text is available yet for this article.
June 1, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28508407/structural-conservation-of-the-pin-domain-active-site-across-all-domains-of-life
#10
REVIEW
M Senissar, M C Manav, D E Brodersen
The PIN domain (Pil N-terminus) is a compact RNA-binding protein domain present in all domains of life. This 120-residue domain consists of a central and parallel β sheet surrounded by α helices, which together organise 4-5 acidic residues in an active site that binds one or more divalent metal ions and in many cases has endoribonuclease activity. In bacteria and archaea, the PIN domain is primarily associated with toxin-antitoxin loci, consisting of a toxin (the PIN domain nuclease) and an antitoxin that inhibits the function of the toxin under normal growth conditions...
May 15, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28506802/stealth-magnetic-nanocarriers-of-sirna-as-platform-for-breast-cancer-theranostics
#11
J Bruniaux, S Ben Djemaa, K Hervé-Aubert, H Marchais, I Chourpa, S David
The endogenous mechanism of RNA interference is more and more used in research to obtain specific down-regulation of gene expression in diseases such as breast cancer. Currently, despite the new fields of study open up by RNA interference, the rapid degradation of siRNA by nucleases and their negative charges prevent them from crossing cell membranes. To overcome these limitations, superparamagnetic iron oxide nanoparticles (SPIONs) represent a promising alternative for nucleic acid delivery. Previously, we reported the magnetic siRNA nanovectors (MSN) formulation using electrostatic assembly of (1) SPIONs, also able to act as contrast agents for magnetic resonance imaging (MRI), (2) siRNA and (3) chitosan aiming at their protection and enhancing their transfection efficacy...
May 12, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28506212/guideseq-a-bioconductor-package-to-analyze-guide-seq-datasets-for-crispr-cas-nucleases
#12
Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Hervé Pagès, Alper Kucukural, Manuel Garber, Scot A Wolfe
BACKGROUND: Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treating a variety of genetic disorders. In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites...
May 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28505149/distinct-dna-binding-surfaces-in-the-atpase-and-linker-domains-of-mutl%C3%AE-determine-its-substrate-specificities-and-exert-separable-functions-in-meiotic-recombination-and-mismatch-repair
#13
Corentin Claeys Bouuaert, Scott Keeney
Mlh1-Mlh3 (MutLγ) is a mismatch repair factor with a central role in formation of meiotic crossovers, presumably through resolution of double Holliday junctions. MutLγ has DNA binding, nuclease, and ATPase activities, but how these relate to one another and to in vivo functions are unclear. Here, we combine biochemical and genetic analyses to characterize Saccharomyces cerevisiae MutLγ. Limited proteolysis and atomic force microscopy showed that purified recombinant MutLγ undergoes ATP-driven conformational changes...
May 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28503153/investigating-engineered-ribonucleoprotein-particles-to-improve-oral-rnai-delivery-in-crop-insect-pests
#14
François-Xavier Gillet, Rayssa A Garcia, Leonardo L P Macedo, Erika V S Albuquerque, Maria C M Silva, Maria F Grossi-de-Sa
Genetically modified (GM) crops producing double-stranded RNAs (dsRNAs) are being investigated largely as an RNA interference (RNAi)-based resistance strategy against crop insect pests. However, limitations of this strategy include the sensitivity of dsRNA to insect gut nucleases and its poor insect cell membrane penetration. Working with the insect pest cotton boll weevil (Anthonomus grandis), we showed that the chimeric protein PTD-DRBD (peptide transduction domain-dsRNA binding domain) combined with dsRNA forms a ribonucleoprotein particle (RNP) that improves the effectiveness of the RNAi mechanism in the insect...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28499832/versatile-and-precise-gene-targeting-strategies-for-functional-studies-in-mammalian-cell-lines
#15
REVIEW
M Wassef, A Luscan, A Battistella, S Le Corre, H Li, M R Wallace, M Vidaud, R Margueron
The advent of programmable nucleases such as ZFNs, TALENs and CRISPR/Cas9 has brought the power of genetic manipulation to widely used model systems. In mammalian cells, nuclease-mediated DNA double strand break is mainly repaired through the error-prone non-homologous end-joining (NHEJ) repair pathway, eventually leading to accumulation of small deletions or insertions (indels) that can inactivate gene function. However, due to the variable size of the indels and the polyploid status of many cell lines (e...
May 10, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28497787/locus-specific-histone-deacetylation-using-a-synthetic-crispr-cas9-based-hdac
#16
Deborah Y Kwon, Ying-Tao Zhao, Janine M Lamonica, Zhaolan Zhou
Efforts to manipulate locus-specific histone acetylation to assess their causal role in gene expression and cellular and behavioural phenotypes have been impeded by a lack of experimental tools. The Cas9 nuclease has been adapted to target epigenomic modifications, but a detailed description of the parameters of such synthetic epigenome remodellers is still lacking. Here we describe a Cas9-based histone deacetylase (HDAC) and the design principles required to achieve locus-specific histone deacetylation. We assess its range of activity and specificity, and analyse target gene expression in two different cell types to investigate cellular context-dependent effects...
May 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/28495970/high-throughput-biochemical-profiling-reveals-sequence-determinants-of-dcas9-off-target-binding-and-unbinding
#17
Evan A Boyle, Johan O L Andreasson, Lauren M Chircus, Samuel H Sternberg, Michelle J Wu, Chantal K Guegler, Jennifer A Doudna, William J Greenleaf
The bacterial adaptive immune system CRISPR-Cas9 has been appropriated as a versatile tool for editing genomes, controlling gene expression, and visualizing genetic loci. To analyze Cas9's ability to bind DNA rapidly and specifically, we generated multiple libraries of potential binding partners for measuring the kinetics of nuclease-dead Cas9 (dCas9) interactions. Using a massively parallel method to quantify protein-DNA interactions on a high-throughput sequencing flow cell, we comprehensively assess the effects of combinatorial mismatches between guide RNA (gRNA) and target nucleotides, both in the seed and in more distal nucleotides, plus disruption of the protospacer adjacent motif (PAM)...
May 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28494568/-the-research-advances-and-applications-of-genome-editing-in-hereditary-eye-diseases
#18
S W Cai, Y Zhang, M Z Hou, Y Liu, X R Li
Genome editing is a cutting-edge technology that generates DNA double strand breaks at the specific genomic DNA sequence through nuclease recognition and cleavage, and then achieves insertion, replacement, or deletion of the target gene via endogenous DNA repair mechanisms, such as non-homologous end joining, homology directed repair, and homologous recombination. So far, more than 600 human hereditary eye diseases and systemic hereditary diseases with ocular phenotypes have been found. However, most of these diseases are of incompletely elucidated pathogenesis and without effective therapies...
May 11, 2017: [Zhonghua Yan Ke za Zhi] Chinese Journal of Ophthalmology
https://www.readbyqxmd.com/read/28493968/the-dead-hardened-floral-bracts-of-dispersal-units-of-wild-wheat-function-as-storage-for-active-hydrolases-and-in-enhancing-seedling-vigor
#19
Buzi Raviv, Gila Granot, Vered Chalifa-Caspi, Gideon Grafi
It is commonly assumed that the dead, hardened floral bracts of the dispersal unit of grasses have been evolved to protect seeds from predation and / or assist in fruit/caryopsis dispersal. While these structures have important agronomical and economical implications, their adaptive value has not been fully explored. We investigated the hypothesis that the maternally derived hardened floral bracts have been evolved not just as a means for caryopsis protection and dispersal, but also as storage for substances that might affect seed germination and seedling vigor...
2017: PloS One
https://www.readbyqxmd.com/read/28492553/a-balance-of-mad-and-myc-expression-dictates-larval-cell-apoptosis-and-adult-stem-cell-development-during-xenopus-intestinal-metamorphosis
#20
Morihiro Okada, Thomas C Miller, Luan Wen, Yun-Bo Shi
The Myc/Mad/Max network has long been shown to be an important factor in regulating cell proliferation, death and differentiation in diverse cell types. In general, Myc-Max heterodimers activate target gene expression to promote cell proliferation, although excess of c-Myc can also induce apoptosis. In contrast, Mad competes against Myc to form Mad-Max heterodimers that bind to the same target genes to repress their expression and promote differentiation. The role of the Myc/Mad/Max network during vertebrate development, especially, the so-called postembryonic development, a period around birth in mammals, is unclear...
May 11, 2017: Cell Death & Disease
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