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Transcription activator-like effectors

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https://www.readbyqxmd.com/read/28207001/genome-editing-using-facs-enrichment-of-nuclease-expressing-cells-and-indel-detection-by-amplicon-analysis
#1
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/28201981/identification-of-effector-like-proteins-in-trichoderma-spp-and-role-of-a-hydrophobin-in-the-plant-fungus-interaction-and-mycoparasitism
#2
Paulina Guzmán-Guzmán, Mario Iván Alemán-Duarte, Luis Delaye, Alfredo Herrera-Estrella, Vianey Olmedo-Monfil
BACKGROUND: Trichoderma spp. can establish beneficial interactions with plants by promoting plant growth and defense systems, as well as, antagonizing fungal phytopathogens in mycoparasitic interactions. Such interactions depend on signal exchange between both participants and can be mediated by effector proteins that alter the host cell structure and function, allowing the establishment of the relationship. The main purpose of this work was to identify, using computational methods, candidates of effector proteins from T...
February 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28186692/targeted-genome-engineering-to-control-vegf-expression-in-human-umbilical-cord-blood-derived-mesenchymal-stem-cells-potential-implications-for-the-treatment-of-myocardial-infarction
#3
Hyun-Min Cho, Pyung-Hwan Kim, Hyun-Kyung Chang, Yi-Ming Shen, Kwaku Bonsra, Byung-Jae Kang, Soo-Young Yum, Joo-Hyun Kim, So-Yeong Lee, Min-Cheol Choi, Hyongbum Henry Kim, Goo Jang, Je-Yoel Cho
Human umbilical cord blood-derived mesenchymal stem cells (hUCB-MSCs) exhibit potency for the regeneration of infarcted hearts. Vascular endothelial growth factor (VEGF) is capable of inducing angiogenesis and can boost stem cell-based therapeutic effects. However, high levels of VEGF can cause abnormal blood vessel growth and hemangiomas. Thus, a controllable system to induce therapeutic levels of VEGF is required for cell therapy. We generated an inducible VEGF-secreting stem cell (VEGF/hUCB-MSC) that controls the expression of VEGF and tested the therapeutic efficacy in rat myocardial infarction (MI) model to apply functional stem cells to MI...
January 3, 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28185836/differential-gene-expression-profiling-of-human-adipose-stem-cells-differentiating-into-smooth-muscle-like-cells-by-tgf%C3%AE-1-bmp4
#4
Ayşe Eser Elçin, Mahmut Parmaksiz, Arin Dogan, Sukran Seker, Serap Durkut, Klara Dalva, Yaşar Murat Elçin
Regenerative repair of the vascular system is challenging from the perspectives of translational medicine and tissue engineering. There are fundamental hurdles in front of creating bioartificial arteries, which involve recaputilation of the three-layered structure under laboratory settings. Obtaining and maintaining smooth muscle characteristics is an important limitation, as the transdifferentiated cells fail to display mature phenotype. This study aims to shed light on the smooth muscle differentiation of human adipose stem cells (hASCs)...
February 6, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28182397/comeback-of-the-rat-in-biomedical-research
#5
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
#6
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/28168961/the-amyloid-precursor-protein-intracellular-domain-is-an-effector-molecule-of-metaplasticity
#7
Emilie Trillaud-Doppia, Jannic Boehm
BACKGROUND: Human studies and mouse models of Alzheimer's disease suggest that the amyloid precursor protein (APP) can cause changes in synaptic plasticity and is contributing to the memory deficits seen in Alzheimer's disease. While most of these studies attribute these changes to the APP cleavage product Aβ, in recent years it became apparent that the APP intracellular domain (APP-ICD) might play a role in regulating synaptic plasticity. METHODS: To separate the effects of APP-ICD on synaptic plasticity from Aβ-dependent effects, we created a chimeric APP in which the Aβ domain is exchanged for its homologous domain from the amyloid precursor-like protein 2...
December 22, 2016: Biological Psychiatry
https://www.readbyqxmd.com/read/28167953/biofortification-in-millets-a-sustainable-approach-for-nutritional-security
#8
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
#9
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
https://www.readbyqxmd.com/read/28165358/extending-immunological-profiling-in-the-gilthead-sea-bream-sparus-aurata-by-enriched-cdna-library-analysis-microarray-design-and-initial-studies-upon-the-inflammatory-response-to-pamps
#10
Sebastian Boltaña, Barbara Castellana, Giles Goetz, Lluis Tort, Mariana Teles, Victor Mulero, Beatriz Novoa, Antonio Figueras, Frederick W Goetz, Cristian Gallardo-Escarate, Josep V Planas, Simon Mackenzie
This study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ) to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a large collection of expressed sequence tags (EST) from two extensive targeted cDNA libraries characterizing mRNA transcripts regulated by both bacterial and viral challenge...
February 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28161521/germ-cell-regeneration-mediated-enhanced-mutagenesis-in-the-ascidian-ciona-intestinalis-reveals-flexible-germ-cell-formation-from-different-somatic-cells
#11
Keita Yoshida, Akiko Hozumi, Nicholas Treen, Tetsushi Sakuma, Takashi Yamamoto, Maki Shirae-Kurabayashi, Yasunori Sasakura
The ascidian Ciona intestinalis has a high regeneration capacity that enables the regeneration of artificially removed primordial germ cells (PGCs) from somatic cells. We utilized PGC regeneration to establish efficient methods of germ line mutagenesis with transcription activator-like effector nucleases (TALENs). When PGCs were artificially removed from animals in which a TALEN pair was expressed, somatic cells harboring mutations in the target gene were converted into germ cells, this germ cell population exhibited higher mutation rates than animals not subjected to PGC removal...
February 1, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28152074/multiple-ubxn-family-members-inhibit-retrovirus-and-lentivirus-production-and-canonical-nf%C3%AE%C2%BA%C3%AE-signaling-by-stabilizing-i%C3%AE%C2%BAb%C3%AE
#12
Yani Hu, Kaitlin O'Boyle, Jim Auer, Sagar Raju, Fuping You, Penghua Wang, Erol Fikrig, Richard E Sutton
UBXN proteins likely participate in the global regulation of protein turnover, and we have shown that UBXN1 interferes with RIG-I-like receptor (RLR) signaling by interacting with MAVS and impeding its downstream effector functions. Here we demonstrate that over-expression of multiple UBXN family members decreased lentivirus and retrovirus production by several orders-of-magnitude in single cycle assays, at the level of long terminal repeat-driven transcription, and three family members, UBXN1, N9, and N11 blocked the canonical NFκB pathway by binding to Cullin1 (Cul1), inhibiting IκBα degradation...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28143781/phenformin-enhances-the-efficacy-of-erk-inhibition-in-nf1-mutant-melanoma
#13
Sebastian Trousil, Shuang Chen, Chan Mu, Fiona M Shaw, Zhan Yao, Yuping Ran, Tiwari Shakuntala, Taha Merghoub, Dieter Manstein, Neal Rosen, Lewis C Cantley, Jonathan H Zippin, Bin Zheng
Inactivation of the tumor suppressor neurofibromin 1 (NF1) presents a newly characterized melanoma subtype, for which currently no targeted therapies are clinically available. Pre-clinical studies suggest that ERK inhibitors are likely to provide benefit, albeit with limited efficacy as single agent; therefore, there is a need for rationally designed combination therapies. Here, we evaluate the combination of the ERK inhibitor SCH772984 and the biguanide phenformin. Combination of both compounds showed potent synergy in cell viability assays and cooperatively induced apoptosis...
January 28, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28143772/stearoyl-coa-desaturase-promotes-liver-fibrosis-and-tumor-development-in-mice-via-wnt-signaling-and-stabilization-of-low-density-lipoprotein-receptor-related-proteins-5-and-6
#14
Keane K Y Lai, Soo-Mi Kweon, Feng Chi, Edward Hwang, Yasuaki Kabe, Reiichi Higashiyama, Lan Qin, Rui Yan, Raymond P Wu, Naoaki Fujii, Samuel French, Jun Xu, Jian-Ying Wang, Ramanchadran Murali, Lopa Mishra, Ju-Seog Lee, James M Ntambi, Hidekazu Tsukamoto
BACKGROUND & AIMS: Stearoyl-CoA desaturase (SCD) synthesizes monounsaturated fatty acids (MUFAs) and has been associated with development of metabolic syndrome, tumorigenesis, and stem cell characteristics. We investigated whether and how SCD promotes liver fibrosis and tumor development in mice. METHODS: Rodent primary hepatic stellate cells (HSCs), mouse liver tumor-initiating stem cell-like cells (TICs), and human hepatocellular carcinoma (HCC) cell lines were exposed to Wnt signaling inhibitors and changes in gene expression patterns were analyzed...
January 28, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28139645/visualization-of-aging-associated-chromatin-alterations-with-an-engineered-tale-system
#15
Ruotong Ren, Liping Deng, Yanhong Xue, Keiichiro Suzuki, Weiqi Zhang, Yang Yu, Jun Wu, Liang Sun, Xiaojun Gong, Huiqin Luan, Fan Yang, Zhenyu Ju, Xiaoqing Ren, Si Wang, Hong Tang, Lingling Geng, Weizhou Zhang, Jian Li, Jie Qiao, Tao Xu, Jing Qu, Guang-Hui Liu
Visualization of specific genomic loci in live cells is a prerequisite for the investigation of dynamic changes in chromatin architecture during diverse biological processes, such as cellular aging. However, current precision genomic imaging methods are hampered by the lack of fluorescent probes with high specificity and signal-to-noise contrast. We find that conventional transcription activator-like effectors (TALEs) tend to form protein aggregates, thereby compromising their performance in imaging applications...
January 31, 2017: Cell Research
https://www.readbyqxmd.com/read/28137869/akt-signaling-is-critical-for-memory-cd8-t-cell-development-and-tumor-immune-surveillance
#16
Anne Rogel, Jane E Willoughby, Sarah L Buchan, Henry J Leonard, Stephen M Thirdborough, Aymen Al-Shamkhani
Memory CD8(+) T cells confer long-term immunity against tumors, and anticancer vaccines therefore should maximize their generation. Multiple memory CD8(+) T-cell subsets with distinct functional and homing characteristics exist, but the signaling pathways that regulate their development are ill defined. Here we examined the role of the serine/threonine kinase Akt in the generation of protective immunity by CD8(+) T cells. Akt is known to be activated by the T-cell antigen receptor and the cytokine IL-2, but its role in T-cell immunity in vivo has not been explored...
January 30, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28136159/crispr-cas-type-ii-based-synthetic-biology-applications-in-eukaryotic-cells
#17
Mario Andrea Marchisio, Zhiwei Huang
The CRISPR-Cas system has rapidly reached a huge popularity as a new, powerful method for precise DNA editing and genome reengineering. In Synthetic Biology, the CRISPR-Cas type II system has inspired the construction of a novel class of RNA-based transcription factors. In their simplest form, they are made of a CRISPR RNA molecule, which targets a promoter sequence, and a deficient Cas9 (i.e. deprived of any nuclease activity) that has been fused to an activation or a repression domain. Up- and down-regulation of single genes in mammalian and yeast cells have been achieved with satisfactory results...
January 31, 2017: RNA Biology
https://www.readbyqxmd.com/read/28132804/avrxa27-binding-influences-unwinding-of-the-double-stranded-dna-in-the-upt-box
#18
Jing Zhao, Bo Zhang, Junpeng Jiang, Nanv Liu, Qi Wei, Xuguang Xi, Jing Fu
Transcription-Activator Like (TAL) effectors, delivered by Xanthomonas pathogens bind specifically to UP-regulated by TAL effectors (UPT) box of the host gene promoter to arouse disease or trigger defense response. This type of protein-DNA interaction model has been applied in site-directed genome editing. However, the off-target effects of TAL have severely hindered the development of this promising technology. To better exploit the specific interaction and to deeper understand the TAL-induced host transcription rewiring, the binding between the central repeat region (CRR) of the TAL effector AvrXa27 and its UPT box variants was studied by kinetics analysis and TAL-blocked helicase unwinding assay...
January 26, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28131063/constitutive-heterologous-overexpression-of-a-tir-nb-arc-lrr-gene-encoding-a-putative-disease-resistance-protein-from-wild-chinese-vitis-pseudoreticulata-in-arabidopsis-and-tobacco-enhances-resistance-to-phytopathogenic-fungi-and-bacteria
#19
Zhifeng Wen, Liping Yao, Stacy D Singer, Hanif Muhammad, Zhi Li, Xiping Wang
Plants use resistance (R) proteins to detect pathogen effector proteins and activate their innate immune response against the pathogen. The majority of these proteins contain an NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) domain along with a leucine-rich repeat (LRR), and some also bear a toll interleukin 1 receptor (TIR) domain. In this study, we characterized a gene encoding a TIR-NB-ARC-LRR R protein (VpTNL1) (GenBank accession number KX649890) from wild Chinese grapevine Vitis pseudoreticulata accession "Baihe-35-1", which was identified previously from a transcriptomic analysis of leaves inoculated with powdery mildew (PM; Erysiphe necator (Schw...
January 17, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28123068/molecular-remission-of-infant-b-all-after-infusion-of-universal-talen-gene-edited-car-t-cells
#20
Waseem Qasim, Hong Zhan, Sujith Samarasinghe, Stuart Adams, Persis Amrolia, Sian Stafford, Katie Butler, Christine Rivat, Gary Wright, Kathy Somana, Sara Ghorashian, Danielle Pinner, Gul Ahsan, Kimberly Gilmour, Giovanna Lucchini, Sarah Inglott, William Mifsud, Robert Chiesa, Karl S Peggs, Lucas Chan, Farzin Farzeneh, Adrian J Thrasher, Ajay Vora, Martin Pule, Paul Veys
Autologous T cells engineered to express chimeric antigen receptor against the B cell antigen CD19 (CAR19) are achieving marked leukemic remissions in early-phase trials but can be difficult to manufacture, especially in infants or heavily treated patients. We generated universal CAR19 (UCART19) T cells by lentiviral transduction of non-human leukocyte antigen-matched donor cells and simultaneous transcription activator-like effector nuclease (TALEN)-mediated gene editing of T cell receptor α chain and CD52 gene loci...
January 25, 2017: Science Translational Medicine
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