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Transcription activator-like effectors

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https://www.readbyqxmd.com/read/28103141/modification-of-the-genome-of-domestic-animals
#1
Samantha N Lotti, Kathryn M Polkoff, Marcello Rubessa, Matthew B Wheeler
In the past few years, new technologies have arisen that enable higher efficiency of gene editing. With the increase ease of using gene editing technologies, it is important to consider the best method for transferring new genetic material to livestock animals. Microinjection is a technique that has proven to be effective in mice but is less efficient in large livestock animals. Over the years, a variety of methods have been used for cloning as well as gene transfer including; nuclear transfer, sperm mediated gene transfer (SMGT), and liposome-mediated DNA transfer...
January 19, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/28103009/fully-automated-one-step-synthesis-of-single-transcript-talen-pairs-using-a-biological-foundry
#2
Ran Chao, Jing Liang, Ipek Tasan, Tong Si, Linyang Ju, Huimin Zhao
Transcription activator-like effector nuclease (TALEN) is a programmable genome editing tool with wide applications. Since TALENs perform cleavage of DNA as heterodimers, a pair of TALENs must be synthesized for each target genome locus. Conventionally, TALEN pairs are either expressed on separate vectors or synthesized separately and then subcloned to the same vector. Neither approach allows high-throughput construction of TALEN libraries for large-scale applications. Here we present an assembly scheme to synthesize and express a pair of TALENs in a single transcript format with the help of a P2A self-cleavage sequence...
January 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28101374/arginine-methylation-of-usp9x-promotes-its-interaction-with-tdrd3-and-its-anti-apoptotic-activities-in-breast-cancer-cells
#3
Nithya Narayanan, Zhihao Wang, Ling Li, Yanzhong Yang
The Tudor domain-containing proteins are characterized by their specific interactions with methylated protein motifs, including methyl-arginines and methyl-lysines. The Tudor domain-containing protein 3 (TDRD3) is one of the major methyl-arginine effector molecules that recognizes methylated arginine residues on histones and the C-terminal domain of RNA polymerase II, and activates transcription. However, majority of the cellular TDRD3 localizes to the cytoplasm and its functions there are still elusive. Here, we have identified ubiquitin-specific protease 9 X-linked (USP9X) as a TDRD3-interacting protein by GST (glutathione S-transferase) pull-down and co-immunoprecipitation...
2017: Cell Discovery
https://www.readbyqxmd.com/read/28100769/the-ubiquitin-like-with-phd-and-ring-finger-domains-1-uhrf1-dna-methyltransferase-1-dnmt1-axis-is-a-primary-regulator-of-cell-senescence
#4
Hyun-Jung Jung, Hae-Ok Byun, Byul A Jee, Seongki Min, Un-Woo Jeoun, Young-Kyoung Lee, Yonghak Seo, Hyun Goo Woo, Gyesoon Yoon
As senescence develops, cells sequentially acquire diverse senescent phenotypes, along with simultaneous multi-stage gene reprogramming. It remains unclear what acts as the key regulator of the collective changes in gene expression at initiation of senescent reprogramming. Here we analysed time-series gene expression profiles obtained in two different senescence models in human diploid fibroblasts (HDF): replicative senescence and H2O2-induced senescence. Our results demonstrated that suppression of DNA methyltransferase 1 (DNMT1)-mediated DNA methylation activity was an initial event prior to the display of senescent phenotypes...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28100513/loss-of-ranbp2-in-motor-neurons-causes-the-disruption-of-nucleocytoplasmic-and-chemokine-signaling-and-proteostasis-of-hnrnph3-and-mmp28-and-the-development-of-amyotrophic-lateral-sclerosis-als-like-syndromes
#5
Kyoung-In Cho, Dosuk Yoon, Sunny Qiu, Zachary Danziger, Warren M Grill, William C Wetsel, Paulo A Ferreira
The pathogenic drivers of sporadic and familial motor neuron disease (MND), such ALS, are unknown. MND impair the Ran GTPase cycle, which controls nucleocytoplasmic transport, ribostasis and proteostasis; however, cause-effect mechanisms of Ran GTPase modulators in motoneuron pathobiology are heretofore elusive. The cytosolic and peripheral nucleoporin, Ranbp2, is a critical regulator of the Ran GTPase cycle and proteostasis of neurological disease-prone substrates, but the roles of Ranbp2 in motoneuron biology and disease remain unknown...
January 18, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28100489/tale-induced-bhlh-transcription-factors-that-activate-a-pectate-lyase-contribute-to-water-soaking-in-bacterial-spot-of-tomato
#6
Allison R Schwartz, Robert Morbitzer, Thomas Lahaye, Brian J Staskawicz
AvrHah1 [avirulence (avr) gene homologous to avrBs3 and hax2, no. 1] is a transcription activator-like (TAL) effector (TALE) in Xanthomonas gardneri that induces water-soaked disease lesions on fruits and leaves during bacterial spot of tomato. We observe that water from outside the leaf is drawn into the apoplast in X. gardneri-infected, but not X. gardneriΔavrHah1 (XgΔavrHah1)-infected, plants, conferring a dark, water-soaked appearance. The pull of water can facilitate entry of additional bacterial cells into the apoplast...
January 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095489/transgenic-expression-of-the-anti-parasitic-factor-tep1-in-the-malaria-mosquito-anopheles-gambiae
#7
Gloria Volohonsky, Ann-Katrin Hopp, Mélanie Saenger, Julien Soichot, Heidi Scholze, Jens Boch, Stéphanie A Blandin, Eric Marois
Mosquitoes genetically engineered to be resistant to Plasmodium parasites represent a promising novel approach in the fight against malaria. The insect immune system itself is a source of anti-parasitic genes potentially exploitable for transgenic designs. The Anopheles gambiae thioester containing protein 1 (TEP1) is a potent anti-parasitic protein. TEP1 is secreted and circulates in the mosquito hemolymph, where its activated cleaved form binds and eliminates malaria parasites. Here we investigated whether TEP1 can be used to create malaria resistant mosquitoes...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28095454/non-homologous-end-joining-and-homology-directed-dna-repair-frequency-of-double-stranded-breaks-introduced-by-genome-editing-reagents
#8
Michail Zaboikin, Tatiana Zaboikina, Carl Freter, Narasimhachar Srinivasakumar
Genome editing using transcription-activator like effector nucleases or RNA guided nucleases allows one to precisely engineer desired changes within a given target sequence. The genome editing reagents introduce double stranded breaks (DSBs) at the target site which can then undergo DNA repair by non-homologous end joining (NHEJ) or homology directed recombination (HDR) when a template DNA molecule is available. NHEJ repair results in indel mutations at the target site. As PCR amplified products from mutant target regions are likely to exhibit different melting profiles than PCR products amplified from wild type target region, we designed a high resolution melting analysis (HRMA) for rapid identification of efficient genome editing reagents...
2017: PloS One
https://www.readbyqxmd.com/read/28093273/identification-of-fhit-as-a-post-transcriptional-effector-of-thymidine-kinase-1-expression
#9
Daniel L Kiss, Catherine E Waters, Iman M Ouda, Joshua C Saldivar, Jenna R Karras, Zaynab A Amin, Seham Mahrous, Teresa Druck, Ralf A Bundschuh, Daniel R Schoenberg, Kay Huebner
FHIT is a genome caretaker gene that is silenced in >50% of cancers. Loss of Fhit protein expression promotes accumulation of DNA damage, affects apoptosis and epithelial-mesenchymal transition, though molecular mechanisms underlying these alterations have not been fully elucidated. Initiation of genome instability directly follows Fhit loss and the associated reduced Thymidine Kinase 1 (TK1) protein expression. The effects on TK1 of Fhit knockdown and Fhit induction in the current study confirmed the role of Fhit in regulating TK1 expression...
January 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28087948/regulation-of-immunity-to-tuberculosis
#10
Susanna Brighenti, Diane J Ordway
Immunity against Mycobacterium tuberculosis requires a balance between adaptive immune responses to constrain bacterial replication and the prevention of potentially damaging immune activation. Regulatory T (Treg) cells express the transcription factor Foxp3+ and constitute an essential counterbalance of inflammatory Th1 responses and are required to maintain immune homeostasis. The first reports describing the presence of Foxp3-expressing CD4+ Treg cells in tuberculosis (TB) emerged in 2006. Different Treg cell subsets, most likely specialized for different tissues and microenvironments, have been shown to expand in both human TB and animal models of TB...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28074901/live-visualization-of-genomic-loci-with-bifc-tale
#11
Huan Hu, Hongmin Zhang, Sheng Wang, Miao Ding, Hui An, Yingping Hou, Xiaojing Yang, Wensheng Wei, Yujie Sun, Chao Tang
Tracking the dynamics of genomic loci is important for understanding the mechanisms of fundamental intracellular processes. However, fluorescent labeling and imaging of such loci in live cells have been challenging. One of the major reasons is the low signal-to-background ratio (SBR) of images mainly caused by the background fluorescence from diffuse full-length fluorescent proteins (FPs) in the living nucleus, hampering the application of live cell genomic labeling methods. Here, combining bimolecular fluorescence complementation (BiFC) and transcription activator-like effector (TALE) technologies, we developed a novel method for labeling genomic loci (BiFC-TALE), which largely reduces the background fluorescence level...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28070697/development-of-a-dsred-expressing-heparg-cell-line-for-real-time-monitoring-of-hepatocyte-like-cell-differentiation-by-fluorescence-imaging-with-application-in-screening-of-novel-geometric-microstructured-cell-growth-substrates
#12
Mihaela Uta, Livia E Sima, Patrik Hoffmann, Valentina Dinca, Norica Branza-Nichita
The bipotent nature of the HepaRG cell line is a unique property among human hepatoma-derived cells. Cell treatment with specific differentiation inducers results in a mixture of hepatocyte- and biliary-like cells, accompanied by upregulation of liver-specific proteins, drug metabolizing enzymes, transcription regulators, membrane receptors or innate immune response effectors. These features make the HepaRG cells a suitable and handy replacement for primary hepatocytes, to study hepatic functions in vitro. However, cell differentiation is a long, variable process, requiring special culture conditions, while the resulting mixed cell populations is usually a major drawback...
March 2017: Biomedical Microdevices
https://www.readbyqxmd.com/read/28053348/glucocorticoid-receptor-control-of-transcription-precision-and-plasticity-via-allostery
#13
Emily R Weikum, Matthew T Knuesel, Eric A Ortlund, Keith R Yamamoto
The glucocorticoid receptor (GR) is a constitutively expressed transcriptional regulatory factor (TRF) that controls many distinct gene networks, each uniquely determined by particular cellular and physiological contexts. The precision of GR-mediated responses seems to depend on combinatorial, context-specific assembly of GR-nucleated transcription regulatory complexes at genomic response elements. In turn, evidence suggests that context-driven plasticity is conferred by the integration of multiple signals, each serving as an allosteric effector of GR conformation, a key determinant of regulatory complex composition and activity...
January 5, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28053091/fumarylacetoacetate-hydrolase-knockout-rabbit-model-for-hereditary-tyrosinemia-type-1
#14
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/28053040/disruption-of-glucagon-like-peptide-1-signaling-in-sim1-neurons-reduces-physiological-and-behavioral-reactivity-to-acute-and-chronic-stress
#15
Sriparna Ghosal, Amy E B Packard, Parinaz Mahbod, Jessica M McKlveen, Randy J Seeley, Brent Myers, Yvonne Ulrich-Lai, Eric P Smith, David A D'Alessio, James P Herman
: Organismal stress initiates a tightly orchestrated set of responses involving complex physiological and neurocognitive systems. Here, we present evidence for glucagon-like peptide 1 (GLP-1)-mediated paraventricular hypothalamic circuit coordinating the global stress response. The GLP-1 receptor (Glp1r) in mice was knocked down in neurons expressing single-minded 1, a transcription factor abundantly expressed in the paraventricular nucleus (PVN) of the hypothalamus. Mice with single-minded 1-mediated Glp1r knockdown had reduced hypothalamic-pituitary-adrenal axis responses to both acute and chronic stress and were protected against weight loss associated with chronic stress...
January 4, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
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
#16
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/28034913/il-10-distinguishes-a-unique-population-of-activated-effector-like-cd8-t-cells-in-murine-acute-liver-inflammation
#17
Julia E Rood, Scott W Canna, Lehn K Weaver, John W Tobias, Edward M Behrens
Immune-mediated liver injury is a central feature of hyperinflammatory diseases, such as hemophagocytic syndromes, yet the immunologic mechanisms underlying those processes are incompletely understood. In this study, we used the toll-like receptor 9 (TLR9)-mediated model of a hemophagocytic syndrome known as macrophage activation syndrome (MAS) to dissect the predominant immune cell populations infiltrating the liver during inflammation. We identified CD8(+) T cells that unexpectedly produce interleukin-10 (IL-10) in addition to interferon-γ (IFN-γ) as a major hepatic population induced by TLR9 stimulation...
December 29, 2016: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/28028617/calcium-gated-k-channels-of-the-kca1-1-and-kca3-1-type-couple-intracellular-ca-2-signals-to-membrane-hyperpolarization-in-mesenchymal-stromal-cells-from-the-human-adipose-tissue
#18
Michail V Tarasov, Marina F Bystrova, Polina D Kotova, Olga A Rogachevskaja, Veronika Y Sysoeva, Stanislav S Kolesnikov
Electrogenesis in mesenchymal stromal cells (MSCs) remains poorly understood. Little is known about ion channels active in resting MSCs and activated upon MSC stimulation, particularly, by agonists mobilizing Ca(2+) in the MSC cytoplasm. A variety of Ca(2+)-gated ion channels may couple Ca(2+) signals to polarization of the plasma membrane. Here, we studied MSCs from the human adipose tissue and found that in cells responsive to ATP and adenosine with Ca(2+) transients or exhibiting spontaneous Ca(2+) oscillations, Ca(2+) bursts were associated with hyperpolarization mediated by Ca(2+)-gated K(+) channels...
December 27, 2016: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/28018102/apolipoprotein-b100-is-required-for-hepatitis-c-infectivity-and-mipomersen-inhibits-hepatitis-c
#19
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/28011634/structure-of-the-branched-chain-amino-acid-and-gtp-sensing-global-regulator-cody-from-bacillus-subtilis
#20
Vladimir M Levdikov, Elena V Blagova, Vicki L Young, Boris R Belitsky, Andrey Lebedev, Abraham L Sonenshein, Anthony J Wilkinson
CodY is a branched-chain amino acid (BCAA) and GTP sensor, and a global regulator of transcription in low G + C Gram-positive bacteria. It controls the expression of over 100 genes and operons, principally by repressing during growth genes whose products are required for adaptations to nutrient limitation. CodY consists of a GAF domain that binds BCAAs and a winged helix-turn-helix (wHTH) domain that binds to DNA, but the way in which these domains interact and the structural basis of the BCAA-dependence of this interaction are unknown...
December 23, 2016: Journal of Biological Chemistry
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