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https://www.readbyqxmd.com/read/28076792/the-mre11-nbs1-interface-is-essential-for-viability-and-tumor-suppression
#1
Jun Hyun Kim, Malgorzata Grosbart, Roopesh Anand, Claire Wyman, Petr Cejka, John H J Petrini
The Mre11 complex (Mre11, Rad50, and Nbs1) is integral to both DNA repair and ataxia telangiectasia mutated (ATM)-dependent DNA damage signaling. All three Mre11 complex components are essential for viability at the cellular and organismal levels. To delineate essential and non-essential Mre11 complex functions that are mediated by Nbs1, we used TALEN-based genome editing to derive Nbs1 mutant mice (Nbs1(mid) mice), which harbor mutations in the Mre11 interaction domain of Nbs1. Nbs1(mid) alleles that abolished interaction were incompatible with viability...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28071925/gene-editing-and-genetic-engineering-approaches-for-advanced-probiotics-a-review
#2
Ruby Yadav, Vishal Kumar, Mehak Baweja, Pratyoosh Shukla
The applications of probiotics are significant and thus resulted in need of genome analysis of probiotic strains. Various omics methods and systems biology approaches enables us to understand and optimize the metabolic processes. These techniques have increased the researcher's attention towards gut microbiome and provided a new source for the revelation of uncharacterized biosynthetic pathways which enables novel metabolic engineering approaches. In recent years, the broad and quantitative analysis of modified strains relies on systems biology tools such as in silico design which are commonly used methods for improving strain performance...
January 10, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28065270/functional-study-of-the-vitamin-k-cycle-enzymes-in-live-cells
#3
J-K Tie, D W Stafford
Vitamin K-dependent carboxylation, an essential posttranslational modification catalyzed by gamma-glutamyl carboxylase, is required for the biological functions of proteins that control blood coagulation, vascular calcification, bone metabolism, and other important physiological processes. Concomitant with carboxylation, reduced vitamin K (KH2) is oxidized to vitamin K epoxide (KO). KO must be recycled back to KH2 by the enzymes vitamin K epoxide reductase and vitamin K reductase in a pathway known as the vitamin K cycle...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28062361/redox-signaling-in-the-gastrointestinal-tract
#4
REVIEW
Salvador Pérez, Raquel Taléns-Visconti, Sergio Rius-Pérez, Isabela Finamor, Juan Sastre
Redox signaling regulates physiological self-renewal, proliferation, migration and differentiation in gastrointestinal epithelium by modulating Wnt/β-catenin and Notch signaling pathways mainly through NADPH oxidases (NOXs). In the intestine, intracellular and extracellular thiol redox status modulates the proliferative potential of epithelial cells. Furthermore, commensal bacteria contribute to intestine epithelial homeostasis through NOX1- and dual oxidase 2-derived reactive oxygen species (ROS). The loss of redox homeostasis is involved in the pathogenesis and development of a wide diversity of gastrointestinal disorders, such as Barrett's esophagus, esophageal adenocarcinoma, peptic ulcer, gastric cancer, ischemic intestinal injury, celiac disease, inflammatory bowel disease and colorectal cancer...
January 3, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28053091/fumarylacetoacetate-hydrolase-knockout-rabbit-model-for-hereditary-tyrosinemia-type-1
#5
Li Li, Quanjun Zhang, Huaqiang Yang, Qingjian Zou, Chengdan Lai, Fei Jiang, Ping Zhao, Zhiwei Luo, Jiayin Yang, Qian Chen, Yan Wang, Philip N Newsome, Jon Frampton, Patrick H Maxwell, Wenjuan Li, Shuhan Chen, Dongye Wang, Tak-Shing Siu, Sidney Tam, Hung-Fat Tse, Baoming Qin, Xichen Bao, Miguel A Esteban, Liangxue Lai
Hereditary tyrosinemia type 1 (HT1) is a severe human autosomal recessive disorder caused by the deficiency of fumarylacetoacetate hydroxylase (FAH), an enzyme catalyzing the last step in the tyrosine degradation pathway. Lack of FAH causes accumulation of toxic metabolites (fumarylacetoacetate and succinylacetone) in blood and tissues, ultimately resulting in severe liver and kidney damage with onset that ranges from infancy to adolescence. This tissue damage is lethal but can be controlled by administration of 2-(2-nitro-4-trifluoromethylbenzoyl)-1,3-cyclohexanedion (NTBC), which inhibits tyrosine catabolism upstream of the generation of fumarylacetoacetate and succinylacetone...
January 4, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28049346/genoproteomics-assisted-improvement-of-andrographis-paniculata-toward-a-promising-molecular-and-conventional-breeding-platform-for-autogamous-plants-affecting-the-pharmaceutical-industry
#6
Alireza Valdiani, Daryush Talei, Surrinder K Lattoo, Rodomiro Ortiz, Søren Kjærsgaard Rasmussen, Jacqueline Batley, Mohd Yusop Rafii, Mahmood Maziah, Kallevettankuzhy K Sabu, Rambod Abiri, Suchirat Sakuanrungsirikul, Soon Guan Tan
Andrographis paniculata (Burm. f.) Wall. ex Nees. (AP) is a hermaphroditic, self-compatible, and habitual inbreeding plant. Its main bioactive component is andrographolide, which is capable of inducing autophagic cell death in some human cancer cells and helps fight HIV/AIDS. Increasing the andrographolide content by investigating the genetic mechanisms controlling its biosynthesis in order to improve and develop high-yielding cultivars are the main breeding targets for AP. However, there might exist some limitations or barriers for crossability within AP accessions...
January 3, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28039489/trail-receptor-gene-editing-unveils-trail-r1-as-a-master-player-of-apoptosis-induced-by-trail-and-er-stress
#7
Florent Dufour, Thibault Rattier, Andrei Alexandru Constantinescu, Luciana Zischler, Aymeric Morlé, Hazem Ben Mabrouk, Etienne Humblin, Guillaume Jacquemin, Eva Szegezdi, Fabien Delacote, Naziha Marrakchi, Gilles Guichard, Catherine Pellat-Deceunynk, Pierre Vacher, Patrick Legembre, Carmen Garrido, Olivier Micheau
TRAIL induces selective tumor cell death through TRAIL-R1 and TRAIL-R2. Despite the fact that these receptors share high structural homologies, induction of apoptosis upon ER stress, cell autonomous motility and invasion have solely been described to occur through TRAIL-R2. Using the TALEN gene-editing approach, we show that TRAIL-R1 can also induce apoptosis during unresolved unfolded protein response (UPR). Likewise, TRAIL-R1 was found to co-immunoprecipitate with FADD and caspase-8 during ER stress. Its deficiency conferred resistance to apoptosis induced by thaspigargin, tunicamycin or brefeldin A...
27, 2016: Oncotarget
https://www.readbyqxmd.com/read/28034789/bibac-gw-based-vectors-for-generating-reporter-lines-for-site-specific-genome-editing-in-planta
#8
Damar Tri Anggoro, Mariliis Tark-Dame, Aimee Walmsley, Rurika Oka, Mara de Sain, Maike Stam
When generating transgenic plants, one of the objectives is to achieve stable expression of the transgene. Transgene silencing can be avoided by single copy integration of the transgene. Binary systems that predominantly result in single copy integrations, such as BIBAC vectors, are also single-copy in E. coli, the organism in which the T-DNA to be delivered to the plant is assembled. Although a low-copy number is important for stable maintenance of large DNA fragments in E. coli, it hampers cloning into the vector due to a low DNA yield...
December 26, 2016: Plasmid
https://www.readbyqxmd.com/read/28018102/apolipoprotein-b100-is-required-for-hepatitis-c-infectivity-and-mipomersen-inhibits-hepatitis-c
#9
Esperance A K Schaefer, James Meixiong, Christina Mark, Amy Deik, Daniel L Motola, Dahlene Fusco, Andrew Yang, Cynthia Brisac, Shadi Salloum, Wenyu Lin, Clary B Clish, Lee F Peng, Raymond T Chung
AIM: To characterize the role of apolipoprotein B100 (apoB100) in hepatitis C viral (HCV) infection. METHODS: In this study, we utilize a gene editing tool, transcription activator-like effector nucleases (TALENs), to generate human hepatoma cells with a stable genetic deletion of APOB to assess of apoB in HCV. Using infectious cell culture-competent HCV, viral pseudoparticles, replicon models, and lipidomic analysis we determined the contribution of apoB to each step of the viral lifecycle...
December 7, 2016: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28011075/detection-of-on-target-and-off-target-mutations-generated-by-crispr-cas9-and-other-sequence-specific-nucleases
#10
REVIEW
Julia Zischewski, Rainer Fischer, Luisa Bortesi
The development of customizable sequence-specific nucleases such as TALENs, ZFNs and the powerful CRISPR/Cas9 system has revolutionized the field of genome editing. The CRISPR/Cas9 system is particularly versatile and has been applied in numerous species representing all branches of life. Regardless of the target organism, all researchers using sequence-specific nucleases face similar challenges: confirmation of the desired on-target mutation and the detection of off-target events. Here, we evaluate the most widely-used methods for the detection of on-target and off-target mutations in terms of workflow, sensitivity, strengths and weaknesses...
December 21, 2016: Biotechnology Advances
https://www.readbyqxmd.com/read/28002927/human-lactoferrin-efficiently-targeted-into-caprine-beta-lactoglobulin-locus-with-talens
#11
Yu-Guo Yuan, Shao-Zheng Song, Meng-Ming Zhu, Zheng-Yi He, Rui Lu, Ting Zhang, Fei Mi, Jin-Yu Wang, Yong Cheng
Objective: To create genetically modified goat as a biopharming source of recombinant human lacotoferrin (hLF) with TALEN. Methods: TALENs and targeting vector were transferred into cultured fibroblasts to insert hLF cDNA in the goat beta-lactoglobulin (BLG) locus with homology-directed repair (HDR). The gene targeted efficiency was checked using sequencing and TE7I assay. The bi-allelic gene targeted colonies were isolated and conformed with PCR, and used as donor cells for somatic cell nuclear transfer (SCNT)...
December 17, 2016: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/27994169/subfunctionalization-of-paralogous-aryl-hydrocarbon-receptors-from-the-frog-xenopus-laevis-distinct-target-genes-and-differential-responses-to-specific-agonists-in-a-single-cell-type
#12
Scott H Freeburg, Eric Engelbrecht, Wade H Powell
Gene duplication confers genetic redundancy that can facilitate subfunctionalization, the partitioning of ancestral functions between paralogs. We capitalize on a recent genome duplication in Xenopus laevis (African clawed frog) to interrogate possible functional differentiation between alloalleles of the aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor that mediates toxicity of dioxin-like compounds and plays a role in the physiology and development of the cardiovascular, hepatic, and immune systems in vertebrates...
October 19, 2016: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/27990003/current-status-of-genome-editing-in-vector-mosquitoes-a-review
#13
Appadurai Daniel Reegan, Stanislaus Antony Ceasar, Michael Gabriel Paulraj, Savarimuthu Ignacimuthu, Naif Abdullah Al-Dhabi
Mosquitoes pose a major threat to human health as they spread many deadly diseases like malaria, dengue, chikungunya, filariasis, Japanese encephalitis and Zika. Identification and use of novel molecular tools are essential to combat the spread of vector borne diseases. Genome editing tools have been used for the precise alterations of the gene of interest for producing the desirable trait in mosquitoes. Deletion of functional genes or insertion of toxic genes in vector mosquitoes will produce either knock-out or knock-in mutants that will check the spread of vector-borne diseases...
December 18, 2016: Bioscience Trends
https://www.readbyqxmd.com/read/27987038/efficient-genome-editing-of-differentiated-renal-epithelial-cells
#14
Alexis Hofherr, Tilman Busch, Nora Huber, Andreas Nold, Albert Bohn, Amandine Viau, Frank Bienaimé, E Wolfgang Kuehn, Sebastian J Arnold, Michael Köttgen
Recent advances in genome editing technologies have enabled the rapid and precise manipulation of genomes, including the targeted introduction, alteration, and removal of genomic sequences. However, respective methods have been described mainly in non-differentiated or haploid cell types. Genome editing of well-differentiated renal epithelial cells has been hampered by a range of technological issues, including optimal design, efficient expression of multiple genome editing constructs, attainable mutation rates, and best screening strategies...
December 16, 2016: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/27984622/-applications-of-zfn-talen-and-crispr-cas9-techniques-in-disease-modeling-and-gene-therapy
#15
Guohua Zhao, Jiali Pu, Beisha Tang
Precise and effective modification of complex genomes at the predicted loci has long been an important goal for scientists. However, conventional techniques for manipulating genomes in diverse organisms and cells have lagged behind the rapid advance in genomic studies. Such genome engineering tools have featured low efficiency and off-targeting. The newly developed custom-designed nucleases, zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system have conferred genome modification with ease of customization, flexibility and high efficiency, which may impact biological research and studies on pathogenesis of human diseases...
December 10, 2016: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/27982048/efficient-generation-of-b2m-null-pigs-via-injection-of-zygote-with-talens
#16
Yong Wang, Yinan Du, Xiaoyang Zhou, Lulu Wang, Jian Li, Fengchao Wang, Zhengen Huang, Xingxu Huang, Hong Wei
Donor major histocompatibility complex class I (MHC I) molecules are the main targets of the host immune response after organ allotransplantation. Whether and how MHC I-deficiency of pig donor tissues affects rejection after xenotransplantation has not been assessed. Beta2-microglobulin (B2M) is indispensable for the assembly of MHC I receptors and therefore provides an effective target to disrupt cell surface MHC I expression. Here, we report the one-step generation of mutant pigs with targeted disruptions in B2m by injection of porcine zygotes with B2m exon 2-specific TALENs...
December 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27975310/a-t7-endonuclease-i-assay-to-detect-talen-mediated-targeted-mutation-of-hbv-cccdna
#17
Kristie Bloom, Abdullah Ely, Patrick Arbuthnot
Gene editing using designer nucleases is now widely used in many fields of molecular biology. The technology is being developed for the treatment of viral infections such as persistant hepatitis B virus (HBV). The replication intermediate of HBV comprising covalently closed circular DNA (cccDNA) is stable and resistant to available licensed antiviral agents. Advancing gene editing as a means of introducing targeted mutations into cccDNA thus potentially offers the means to cure infection by the virus. Essentially, targeted mutations are initiated by intracellular DNA cleavage, then error-prone nonhomologous end joining results in insertions and deletions (indels) at intended sites...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27943242/knockout-of-a-difficult-to-remove-cho-host-cell-protein-lipoprotein-lipase-for-improved-polysorbate-stability-in-monoclonal-antibody-formulations
#18
Josephine Chiu, Kristin N Valente, Nicholas E Levy, Lie Min, Abraham M Lenhoff, Kelvin H Lee
While the majority of host cell protein (HCP) impurities are effectively removed in typical downstream purification processes, a small population of HCPs are particularly challenging. Previous studies have identified HCPs that are challenging for a variety of reasons. Lipoprotein lipase (LPL)-a Chinese hamster ovary (CHO) HCP that functions to hydrolyze esters in triglycerides-was one of ten HCPs identified in previous studies as being susceptible to retention in downstream processing. LPL may degrade polysorbate 80 (PS-80) and polysorbate 20 (PS-20) in final product formulations due to the structural similarity between polysorbates and triglycerides...
December 12, 2016: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/27930742/analysis-of-domain-architecture-and-phylogenetics-of-family-2-glycoside-hydrolases-gh2
#19
David Talens-Perales, Anna Górska, Daniel H Huson, Julio Polaina, Julia Marín-Navarro
In this work we report a detailed analysis of the topology and phylogenetics of family 2 glycoside hydrolases (GH2). We distinguish five topologies or domain architectures based on the presence and distribution of protein domains defined in Pfam and Interpro databases. All of them share a central TIM barrel (catalytic module) with two β-sandwich domains (non-catalytic) at the N-terminal end, but differ in the occurrence and nature of additional non-catalytic modules at the C-terminal region. Phylogenetic analysis was based on the sequence of the Pfam Glyco_hydro_2_C catalytic module present in most GH2 proteins...
2016: PloS One
https://www.readbyqxmd.com/read/27908936/genome-editing-technologies-principles-and-applications
#20
REVIEW
Thomas Gaj, Shannon J Sirk, Sai-Lan Shui, Jia Liu
Targeted nucleases have provided researchers with the ability to manipulate virtually any genomic sequence, enabling the facile creation of isogenic cell lines and animal models for the study of human disease, and promoting exciting new possibilities for human gene therapy. Here we review three foundational technologies-clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9), transcription activator-like effector nucleases (TALENs), and zinc-finger nucleases (ZFNs)...
December 1, 2016: Cold Spring Harbor Perspectives in Biology
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