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Artificial transcriptional factor

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https://www.readbyqxmd.com/read/28428791/genome-wide-association-study-for-pre-harvest-sprouting-resistance-in-a-large-germplasm-collection-of-chinese-wheat-landraces
#1
Yong Zhou, Hao Tang, Meng-Ping Cheng, Kwame O Dankwa, Zhong-Xu Chen, Zhan-Yi Li, Shang Gao, Ya-Xi Liu, Qian-Tao Jiang, Xiu-Jin Lan, Zhi-En Pu, Yu-Ming Wei, You-Liang Zheng, Lee T Hickey, Ji-Rui Wang
Pre-harvest sprouting (PHS) is mainly caused by the breaking of seed dormancy in high rainfall regions, which leads to huge economic losses in wheat. In this study, we evaluated 717 Chinese wheat landraces for PHS resistance and carried out genome-wide association studies (GWAS) using to 9,740 DArT-seq and 178,803 SNP markers. Landraces were grown across six environments in China and germination testing of harvest-ripe grain was used to calculate the germination rate (GR) for each accession at each site. GR was highly correlated across all environments...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28413047/a-homolog-of-teleostean-signal-transducer-and-activator-of-transcription-3-stat3-from-rock-bream-oplegnathus-fasciatus-structural-insights-transcriptional-modulation-and-subcellular-localization
#2
S D N K Bathige, William Shanthakumar Thulasitha, Navaneethaiyer Umasuthan, J D H E Jayasinghe, Qiang Wan, Bo-Hye Nam, Jehee Lee
Signal transducer and activator of transcription 3 (STAT3) is one of the crucial transcription factors in the Janus kinase (JAK)/STAT signaling pathway, and it was previously considered as acute phase response factor. A number of interleukins (ILs) such as IL-5, IL-6, IL-9, IL-10, IL-12, and IL-22 are known to be involved in activation of STAT3. In addition, various growth factors and pathogenic or oxidative stresses mediate the activation of a wide range of functions via STAT3. In this study, a STAT3 homolog was identified and functionally characterized from rock bream (RbSTAT3), Oplegnathus fasciatus...
April 2017: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/28411220/the-global-transcription-factor-lrp-is-both-essential-for-and-inhibitory-to-xenorhabdus-nematophila-insecticidal-activity
#3
Ángel M Casanova-Torres, Upasana Shokal, Neta Morag, Ioannis Eleftherianos, Heidi Goodrich-Blair
In the entomopathogenic bacterium Xenorhabdus nematophila, cell-to-cell variation in the abundance of the Lrp transcription factor leads to virulence modulation: low Lrp levels are associated with a virulent phenotype and suppression of antimicrobial peptides (AMPs) in Manduca sexta insects, while cells that lack lrp or express high Lrp levels are virulence attenuated and elicit AMP expression. To better understand the basis of these phenotypes we examined X. nematophila expressing fixed Lrp levels. Unlike the lrp null mutant, the high-lrp strain is fully virulent in Drosophila melanogaster suggesting that these two strains have distinct underlying causes of virulence attenuation in M...
April 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28377102/can-we-predict-gene-expression-by-understanding-proximal-promoter-architecture
#4
REVIEW
Łukasz Huminiecki, Jarosław Horbańczuk
We review computational predictions of expression from the promoter architecture - the set of transcription factors that can bind the proximal promoter. We focus on spatial expression patterns in animals with complex body plans and many distinct tissue types. This field is ripe for change as functional genomics datasets accumulate for both expression and protein-DNA interactions. While there has been some success in predicting the breadth of expression (i.e., the fraction of tissue types a gene is expressed in), predicting tissue specificity remains challenging...
April 1, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28373747/andrographolide-activates-keap1-nrf2-are-ho-1-pathway-in-ht22-cells-and-suppresses-microglial-activation-by-a%C3%AE-42-through-nrf2-related-inflammatory-response
#5
Ji Yeon Seo, Euisun Pyo, Jin-Pyo An, Jinwoong Kim, Sang Hyun Sung, Won Keun Oh
Therapeutic approach of Alzheimer's disease (AD) has been gradually diversified. We examined the therapeutic and preventive potential of andrographolide, which is a lactone diterpenoid from Andrographis paniculata, and focused on the Kelch-like ECH-associated protein 1 (Keap1)/nuclear factor (erythroid-derived 2)-like 2 (Nrf2)-mediated heme oxygenase (HO)-1-inducing effects and the inhibitory activity of amyloid beta (Aβ)42-induced microglial activation related to Nrf2 and nuclear factor κB (NF-κB)-mediated inflammatory responses...
2017: Mediators of Inflammation
https://www.readbyqxmd.com/read/28369316/annotatr-genomic-regions-in-context
#6
Raymond G Cavalcante, Maureen A Sartor
Motivation: Analysis of next-generation sequencing data often results in a list of genomic regions. These may include differentially methylated CpGs/regions, transcription factor binding sites, interacting chromatin regions, or GWAS-associated SNPs, among others. A common analysis step is to annotate such genomic regions to genomic annotations (promoters, exons, enhancers, etc.). Existing tools are limited by a lack of annotation sources and flexible options, the time it takes to annotate regions, an artificial one-to-one region-to-annotation mapping, a lack of visualization options to easily summarize data, or some combination thereof...
March 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28358915/enhancement-of-arabidopsis-growth-characteristics-using-genome-interrogation-with-artificial-transcription-factors
#7
Niels van Tol, Martijn Rolloos, Johan E Pinas, Christiaan V Henkel, Dieuwertje Augustijn, Paul J J Hooykaas, Bert J van der Zaal
The rapidly growing world population has a greatly increasing demand for plant biomass, thus creating a great interest in the development of methods to enhance the growth and biomass accumulation of crop species. In this study, we used zinc finger artificial transcription factor (ZF-ATF)-mediated genome interrogation to manipulate the growth characteristics and biomass of Arabidopsis plants. We describe the construction of two collections of Arabidopsis lines expressing fusions of three zinc fingers (3F) to the transcriptional repressor motif EAR (3F-EAR) or the transcriptional activator VP16 (3F-VP16), and the characterization of their growth characteristics...
2017: PloS One
https://www.readbyqxmd.com/read/28348568/a-bacterial-artificial-chromosome-reporter-system-for-expression-of-the-human-foxp3-gene-in-mouse-regulatory-t-cells
#8
Masato Tsuda, Yukiko Tone, Chihiro Ogawa, Yoshiko Nagaoka, Makoto Katsumata, Andra Necula, Duncan Howie, Esteban Masuda, Herman Waldmann, Masahide Tone
The transcription factor FOXP3 plays key roles in the development and function of regulatory T cells (Treg) capable of preventing and correcting immunopathology. There has been much interest in exploiting Treg as adoptive cell therapy in man, but issues of lack of nominal antigen-specificity and stability of FoxP3 expression in the face of pro-inflammatory cytokines have been a concern. In order to enable fundamental studies of human FOXP3 (hFOXP3) gene regulation and to provide preclinical tools to guide the selection of drugs that might modulate hFOXP3 expression for therapeutic purposes, we generated hFOXP3/AmCyan bacterial artificial chromosome (BAC) transgenic mice and transfectants, wherein hFOXP3 expression was read out as AmCyan expression...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28336944/kaposi-s-sarcoma-associated-herpesvirus-orf34-is-essential-for-late-gene-expression-and-virus-production
#9
Mayu Nishimura, Tadashi Watanabe, Syota Yagi, Takahiro Yamanaka, Masahiro Fujimuro
Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. KSHV establishes a life-long infection in its host and alternates between a latent and lytic infection state. During lytic infection, lytic-related genes are expressed in a temporal manner and categorized as immediate early, early, and late gene transcripts. ORF34 is an early-late gene that interacts with several viral transcription-associated factors, however its physiological importance remains poorly understood...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28335496/quantitative-analysis-of-the-kshv-transcriptome-following-primary-infection-of-blood-and-lymphatic-endothelial-cells
#10
A Gregory Bruce, Serge Barcy, Terri DiMaio, Emilia Gan, H Jacques Garrigues, Michael Lagunoff, Timothy M Rose
The transcriptome of the Kaposi's sarcoma-associated herpesvirus (KSHV/HHV8) after primary latent infection of human blood (BEC), lymphatic (LEC) and immortalized (TIME) endothelial cells was analyzed using RNAseq, and compared to long-term latency in BCBL-1 lymphoma cells. Naturally expressed transcripts were obtained without artificial induction, and a comprehensive annotation of the KSHV genome was determined. A set of unique coding sequence (UCDS) features and a process to resolve overlapping transcripts were developed to accurately quantitate transcript levels from specific promoters...
March 19, 2017: Pathogens
https://www.readbyqxmd.com/read/28332603/the-arabidopsis-mir396-mediates-pathogen-associated-molecular-pattern-triggered-immune-responses-against-fungal-pathogens
#11
Mauricio Soto-Suárez, Patricia Baldrich, Detlef Weigel, Ignacio Rubio-Somoza, Blanca San Segundo
MicroRNAs (miRNAs) play a pivotal role in regulating gene expression during plant development. Although a substantial fraction of plant miRNAs has proven responsive to pathogen infection, their role in disease resistance remains largely unknown, especially during fungal infections. In this study, we screened Arabidopsis thaliana lines in which miRNA activity has been reduced using artificial miRNA target mimics (MIM lines) for their response to fungal pathogens. Reduced activity of miR396 (MIM396 plants) was found to confer broad resistance to necrotrophic and hemibiotrophic fungal pathogens...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28320314/quorum-sensing-of-streptococcus-mutans-is-activated-by-aggregatibacter-actinomycetemcomitans-and-by-the-periodontal-microbiome
#12
Szymon P Szafrański, Zhi-Luo Deng, Jürgen Tomasch, Michael Jarek, Sabin Bhuju, Manfred Rohde, Helena Sztajer, Irene Wagner-Döbler
BACKGROUND: The oral cavity is inhabited by complex microbial communities forming biofilms that can cause caries and periodontitis. Cell-cell communication might play an important role in modulating the physiologies of individual species, but evidence so far is limited. RESULTS: Here we demonstrate that a pathogen of the oral cavity, Aggregatibacter actinomycetemcomitans (A. act.), triggers expression of the quorum sensing (QS) regulon of Streptococcus mutans, a well-studied model organism for cariogenic streptococci, in dual-species biofilms grown on artificial saliva...
March 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28250238/a-study-on-regional-differences-in-decidualization-of-the-mouse-uterus
#13
Miao Zhao, Wen-Qian Zhang, Ji-Long Liu
Although regional differences in mouse decidualization have been recognized for decades, the molecular mechanisms remain under-studied. In the present study, by using RNA-seq, we compared transcriptomic differences between the anti-mesometrial (AM) region and the mesometrial (M) region of mouse uterus on day 8 of pregnancy. A total of 1423 differentially expressed genes were identified, of which 811 genes were up-regulated and 612 genes were down-regulated in the AM region compared to the M region. Gene ontology analysis showed that up-regulated genes were generally involved in cell metabolism and differentiation, whereas down-regulated genes were associated with lymphocyte themes and immune response...
March 1, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28249010/tfap2-paralogs-regulate-melanocyte-differentiation-in-parallel-with-mitf
#14
Hannah E Seberg, Eric Van Otterloo, Stacie K Loftus, Huan Liu, Greg Bonde, Ramakrishna Sompallae, Derek E Gildea, Juan F Santana, J Robert Manak, William J Pavan, Trevor Williams, Robert A Cornell
Mutations in the gene encoding transcription factor TFAP2A result in pigmentation anomalies in model organisms and premature hair graying in humans. However, the pleiotropic functions of TFAP2A and its redundantly-acting paralogs have made the precise contribution of TFAP2-type activity to melanocyte differentiation unclear. Defining this contribution may help to explain why TFAP2A expression is reduced in advanced-stage melanoma compared to benign nevi. To identify genes with TFAP2A-dependent expression in melanocytes, we profile zebrafish tissue and mouse melanocytes deficient in Tfap2a, and find that expression of a small subset of genes underlying pigmentation phenotypes is TFAP2A-dependent, including Dct, Mc1r, Mlph, and Pmel...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28244246/cobalt-ii-chloride-modifies-the-phenotype-of-macrophage-activation
#15
Mona Kumanto, Erja-Leena Paukkeri, Riina Nieminen, Eeva Moilanen
Cobalt (Co) is vital for cells in trace amounts, but excessive exposure to Co is possible due to surgical devices such as artificial metal-on-metal joints. Cobalt(II) chloride (CoCl2 ) has also been shown to imitate hypoxic conditions in cells by stabilizing the transcription factor hypoxia-inducible factor-1α (HIF-1α). The purpose of the present study was to investigate the possible immunomodulatory action of CoCl2 by investigating its effects on the expression of inflammatory genes in macrophages. The following factors were assessed: inducible nitric oxidase synthase (iNOS), NADPH oxidase 2 (NOX2), interleukin 6 (IL-6), arginase-1 and HIF-1α...
February 28, 2017: Basic & Clinical Pharmacology & Toxicology
https://www.readbyqxmd.com/read/28235878/botrytis-fragariae-a-new-species-causing-gray-mold-on-strawberries-shows-high-frequencies-of-specific-and-efflux-based-fungicide-resistance
#16
Sabrina Rupp, Cecilia Plesken, Sibylle Rumsey, Madeline Dowling, Guido Schnabel, Roland W S Weber, Matthias Hahn
Botrytis cinerea causes pre- and postharvest decay of many fruit and vegetable crops. A survey of German strawberry fields revealed Botrytis strains that differed from B. cinerea in diagnostic PCR markers and growth appearance. Phylogenetic analyses showed that these strains belong to an undescribed species in Botrytis clade 2, named Botrytisfragariae sp. nov. Isolates of Bfragariae were detected in strawberry fields throughout Germany, sometimes at frequencies similar to those of B. cinerea, and in the southeastern United States...
May 1, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28212751/stable-heritable-germline-silencing-directs-somatic-silencing-at-an-endogenous-locus
#17
Olga Minkina, Craig P Hunter
The importance of transgenerationally inherited epigenetic states to organismal fitness remains unknown as well-documented examples are often not amenable to mechanistic analysis or rely on artificial reporter loci. Here we describe an induced silenced state at an endogenous locus that persists, at 100% transmission without selection, for up to 13 generations. This unusually persistent silencing enables a detailed molecular genetic analysis of an inherited epigenetic state. We find that silencing is dependent on germline nuclear RNAi factors and post-transcriptional mechanisms...
February 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28199003/applications-of-induced-pluripotent-stem-cell-technologies-in-spinal-cord-injury
#18
REVIEW
Narihito Nagoshi, Hideyuki Okano
Numerous basic research studies have suggested the potential efficacy of neural precursor cell (NPC) transplantation in spinal cord injury (SCI). However, in most such studies the origin of the cells used was mainly fetal tissue or embryonic stem cells, both of which carry potential ethical concerns with respect to clinical use. The development of induced pluripotent stem cells (iPSCs) opened a new path toward regenerative medicine for SCI. iPSCs can be generated from somatic cells by induction of transcription factors, and induced to differentiate into NPCs with characteristics of cells of the central nervous system...
February 15, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28185461/-epithelial-mesenchymal-transition-in-tumor-tissue-and-its-role-for-metastatic-spread-of-cancer
#19
V M Matějka, J Fínek, M Králíčková
BACKGROUND: Metastasis, recurrence, and resistance to chemotherapy are leading causes of the majority of cancer-related mortality worldwide. The process of metastasis can be artificially divided into a series of sequential, highly organized, and organ-specific steps. The underlying mechanisms are still poorly understood, but are believed to be mediated by epithelial-mesenchymal transition (EMT). First described in embryogenesis, EMT is a cellular reprogramming process in which epithelial cells acquire a mesenchymal phenotype...
2017: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
https://www.readbyqxmd.com/read/28145403/regulation-of-ft-splicing-by-an-endogenous-cue-in-temperate-grasses
#20
Zhengrui Qin, Jiajie Wu, Shuaifeng Geng, Nan Feng, Fengjuan Chen, Xingchen Kong, Gaoyuan Song, Kai Chen, Aili Li, Long Mao, Liang Wu
Appropriate flowering timing is crucial for plant reproductive success. The florigen, FLOWERING LOCUS T (FT), interacts with 14-3-3 proteins and the bZIP transcription factor FD, functioning at core nodes in multiple flowering pathways. There are two FT homologues, FT1 and FT2, in Brachypodium distachyon. Here we show that FT2 undergoes age-dependent alternative splicing (AS), resulting in two splice variants (FT2α and FT2β). The FT2β-encoded protein cannot interact with FD or 14-3-3s but is able to form heterodimers with FT2α and FT1, thereby interfering with the florigen-mediated assembly of the flowering initiation complex...
February 1, 2017: Nature Communications
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