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Artificial transcriptional factor

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https://www.readbyqxmd.com/read/28637858/maternal-and-nourishment-factors-interact-to-influence-offspring-developmental-trajectories-in-social-wasps
#1
Jennifer M Jandt, Sainath Suryanarayanan, John C Hermanson, Robert L Jeanne, Amy L Toth
The social and nutritional environments during early development have the potential to affect offspring traits, but the mechanisms and molecular underpinnings of these effects remain elusive. We used Polistes fuscatus paper wasps to dissect how maternally controlled factors (vibrational signals and nourishment) interact to induce different caste developmental trajectories in female offspring, leading to worker or reproductive (gyne) traits. We established a set of caste phenotype biomarkers in P. fuscatus females, finding that gyne-destined individuals had high expression of three caste-related genes hypothesized to have roles in diapause and mitochondrial metabolism...
June 28, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28623587/generation-of-dtales-and-libraries-of-synthetic-tale-activated-promoters-for-engineering-of-gene-regulatory-networks-in-plants
#2
Tom Schreiber, Alain Tissier
Transcription factors with programmable DNA-binding specificity constitute valuable tools for the design of orthogonal gene regulatory networks for synthetic biology. Transcription activator-like effectors (TALEs), as natural transcription regulators, were used to design, build, and test libraries of synthetic TALE-activated promoters (STAPs) that show a broad range of expression levels in plants. In this chapter, we present protocols for the construction of artificial TALEs and corresponding STAPs.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28623586/multiplexed-transcriptional-activation-or-repression-in-plants-using-crispr-dcas9-based-systems
#3
Levi G Lowder, Joseph W Paul, Yiping Qi
Novel tools and methods for regulating in vivo plant gene expression are quickly gaining popularity and utility due to recent advances in CRISPR-dCas9 chimeric effector regulators, otherwise known as CRISPR artificial transcription factors (CRISPR-ATFs). These tools are especially useful for studying gene function and interaction within various regulatory networks. First generation CRISPR-ATFs are nuclease-deactivated (dCas9) CRISPR systems where dCas9 proteins are fused to known transcriptional activator domains (VP64) or repressor domains (SRDX)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28614057/dual-effects-of-constitutively-active-androgen-receptor-and-full-length-androgen-receptor-for-n-cadherin-regulation-in-prostate-cancer
#4
Félicie Cottard, Pauline Ould Madi-Berthélémy, Eva Erdmann, Frédérique Schaff-Wendling, Céline Keime, Tao Ye, Jean-Emmanuel Kurtz, Jocelyn Céraline
Constitutively active androgen receptor (AR) variants have been involved in the expression of mesenchymal markers such as N-cadherin in prostate cancer (PCa). However, the underlying molecular mechanisms remain elusive. It remains unclear, whether N-cadherin gene (CDH2) is a direct transcriptional target of AR variants or whether the observed upregulation is due to indirect effects through additional regulatory factors. Moreover, the specific contribution of full-length AR and AR variants in N-cadherin regulation in PCa has never been explored deeply...
May 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28607440/an-arabidopsis-mutant-with-high-operating-efficiency-of-photosystem-ii-and-low-chlorophyll-fluorescence
#5
Niels van Tol, Martijn Rolloos, Dieuwertje Augustijn, A Alia, Huub J de Groot, Paul J J Hooykaas, Bert J van der Zaal
The overall light energy to biomass conversion efficiency of plant photosynthesis is generally regarded as low. Forward genetic screens in Arabidopsis have yielded very few mutants with substantially enhanced photochemistry. Here, we report the isolation of a novel Arabidopsis mutant with a high operating efficiency of Photosystem II (φPSII) and low chlorophyll fluorescence from a library of lines harboring T-DNA constructs encoding artificial transcription factors. This mutant was named Low Chlorophyll Fluorescence 1 (LCF1)...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28607206/downregulation-of-mir-199a-5p-promotes-prostate-adeno-carcinoma-progression-through-loss-of-its-inhibition-of-hif-1%C3%AE
#6
Jinjing Zhong, Rui Huang, Zhengzheng Su, Mengni Zhang, Miao Xu, Jing Gong, Ni Chen, Hao Zeng, Xueqin Chen, Qiao Zhou
Hypoxia-inducible factor-1 alpha (HIF-1α) plays key roles in cell survival under both hypoxia and normoxia conditions. Regulation of HIF-1α is complex and involves numerous molecules and pathways, including post-transcriptional regulation by microRNAs (miRNAs). Although upregulation of HIF-1α has been shown to promote prostate adenocarcinoma (PCa) progression, the mechanism by which miRNAs modulate HIF-1α in prostate cancer has not been clarified. Here, we show that miR-199a-5p is underexpressed in prostate adenocarcinoma...
May 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/28600722/genetic-dissection-of-plant-growth-habit-in-chickpea
#7
Hari D Upadhyaya, Deepak Bajaj, Rishi Srivastava, Anurag Daware, Udita Basu, Shailesh Tripathi, Chellapilla Bharadwaj, Akhilesh K Tyagi, Swarup K Parida
A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs...
June 9, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28600522/direct-competition-between-dna-binding-factors-highlights-the-role-of-kr%C3%A3-ppel-like-factor-1-in-the-erythroid-megakaryocyte-switch
#8
Laura J Norton, Samantha Hallal, Elizabeth S Stout, Alister P W Funnell, Richard C M Pearson, Merlin Crossley, Kate G R Quinlan
The Krüppel-like factor (KLF) family of transcription factors play critical roles in haematopoiesis. KLF1, the founding member of the family, has been implicated in the control of both erythropoiesis and megakaryopoiesis. Here we describe a novel system using an artificial dominant negative isoform of KLF1 to investigate the role of KLF1 in the erythroid/megakaryocytic switch in vivo. We developed murine cell lines stably overexpressing a GST-KLF1 DNA binding domain fusion protein (GST-KLF1 DBD), as well as lines expressing GST only as a control...
June 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28594167/toward-an-expanded-genome-structural-and-computational-characterization-of-an-artificially-expanded-genetic-information-system
#9
Nigel G J Richards, Millie M Georgiadis
Although the fundamental properties of DNA as first proposed by Watson and Crick in 1953 provided a basic understanding of how duplex DNA was organized and might be replicated, it was not until the first crystal structures of DNA (Z-DNA in 1979, B-DNA in 1980, and A-DNA in 1982) that the true complexity of the molecule began to be appreciated. Many crystal structures of oligonucleotides have since shed light on the helical forms that "Watson-Crick" DNA can adopt, their associated groove widths, and the properties of the nucleobase pairs and their interactions in all three helical forms...
June 8, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28574606/sfp1-and-rtg3-reciprocally-modulate-carbon-source-conditional-stress-adaptation-in-the-pathogenic-yeast-candida-albicans
#10
Stavroula L Kastora, Carmen Herrero-de-Dios, Gabriela M Alvelar, Carol A Munro, Alistair J P Brown
The pathogenicity of the clinically important yeast, Candida albicans, is dependent on robust responses to host-imposed stresses. These stress responses have generally been dissected in vitro at 30°C on artificial growth media that do not mimic host niches. Yet host inputs, such as changes in carbon source or temperature, are known to affect C. albicans stress adaptation. Therefore, we performed screens to identify novel regulators that promote stress resistance during growth on a physiologically relevant carboxylic acid and at elevated temperatures...
June 2, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28557624/rna-guided-activation-of-pluripotency-genes-in-human-fibroblasts
#11
Kai Xiong, Yan Zhou, Kristian Aabo Blichfeld, Poul Hyttel, Lars Bolund, Kristine Karla Freude, Yonglun Luo
Specific activation of endogenous genes can be achieved by programmable artificial transcription factors (ATFs). In this study, we compared two artificial, programmable, clustered regularly interspaced short palindromic repeats (CRISPR)-based, ubiquitous transcription factors: deficient CRISPR-associated protein 9 (dCas9)-VP64 (CRISPRa) alone, or a combination of dCas9-VP64 and MS2-P65-HSF1 [synergistic activation mediator (SAM) system] mediated activation of five pluripotency genes: KLF4 (K), LIN28 (L), MYC (M), OCT4 (O), and SOX2 (S) in human cells (HEK293T, HeLa, HepG2, and primary fibroblasts)...
June 2017: Cellular Reprogramming
https://www.readbyqxmd.com/read/28553258/an-overview-of-monthly-rhythms-and-clocks
#12
REVIEW
Florian Raible, Hiroki Takekata, Kristin Tessmar-Raible
Organisms have evolved to cope with geophysical cycles of different period lengths. In this review, we focus on the adaptations of animals to the lunar cycle, specifically, on the occurrence of biological rhythms with monthly (circalunar) or semi-monthly (circasemilunar) period lengths. Systematic experimental investigation, starting in the early twentieth century, has allowed scientists to distinguish between mythological belief and scientific facts concerning the influence of the lunar cycle on animals. These studies revealed that marine animals of various taxa exhibit circalunar or circasemilunar reproductive rhythms...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28547869/the-zinc-finger-domain-of-ring-finger-protein-141-reveals-a-unique-ring-fold
#13
Kazuhide Miyamoto, Airi Uechi, Kazuki Saito
Human RING finger protein 141 (RFP141) is a germ cell-specific transcription factor during spermatogenesis. We synthesized a compact construct encoding the C-terminal zinc finger of RFP141 (RFP141C peptide). Herein we determined the solution structure of the RFP141C peptide by nuclear magnetic resonance (NMR). Moreover, NMR data and the chemical modification of cysteine residues demonstrated that the RFP141C peptide binds to two zinc atoms in a cross-brace arrangement. The Simple Modular Architecture Research Tool database predicted the structure of RFP141C as a RING finger...
May 25, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28533388/selective-lowering-of-synapsins-induced-by-oligomeric-%C3%AE-synuclein-exacerbates-memory-deficits
#14
Megan E Larson, Susan J Greimel, Fatou Amar, Michael LaCroix, Gabriel Boyle, Mathew A Sherman, Hallie Schley, Camille Miel, Julie A Schneider, Rakez Kayed, Fabio Benfenati, Michael K Lee, David A Bennett, Sylvain E Lesné
Mounting evidence indicates that soluble oligomeric forms of amyloid proteins linked to neurodegenerative disorders, such as amyloid-β (Aβ), tau, or α-synuclein (αSyn) might be the major deleterious species for neuronal function in these diseases. Here, we found an abnormal accumulation of oligomeric αSyn species in AD brains by custom ELISA, size-exclusion chromatography, and nondenaturing/denaturing immunoblotting techniques. Importantly, the abundance of αSyn oligomers in human brain tissue correlated with cognitive impairment and reductions in synapsin expression...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28503202/stabilization-of-foxp3-expression-by-crispr-dcas9-based-epigenome-editing-in-mouse-primary-t-cells
#15
Masahiro Okada, Mitsuhiro Kanamori, Kazue Someya, Hiroko Nakatsukasa, Akihiko Yoshimura
BACKGROUND: Epigenome editing is expected to manipulate transcription and cell fates and to elucidate the gene expression mechanisms in various cell types. For functional epigenome editing, assessing the chromatin context-dependent activity of artificial epigenetic modifier is required. RESULTS: In this study, we applied clustered regularly interspaced short palindromic repeats (CRISPR)-dCas9-based epigenome editing to mouse primary T cells, focusing on the Forkhead box P3 (Foxp3) gene locus, a master transcription factor of regulatory T cells (Tregs)...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28463102/high-intracellular-c-di-gmp-levels-antagonize-quorum-sensing-and-virulence-gene-expression-in-burkholderia-cenocepacia-h111
#16
Nadine Schmid, Angela Suppiger, Elisabeth Steiner, Gabriella Pessi, Volkhard Kaever, Mustafa Fazli, Tim Tolker-Nielsen, Urs Jenal, Leo Eberl
The opportunistic human pathogen Burkholderia cenocepacia H111 uses two chemically distinct signal molecules for controlling gene expression in a cell density-dependent manner: N-acyl-homoserine lactones (AHLs) and cis-2-dodecenoic acid (BDSF). Binding of BDSF to its cognate receptor RpfR lowers the intracellular c-di-GMP level, which in turn leads to differential expression of target genes. In this study we analysed the transcriptional profile of B. cenocepacia H111 upon artificially altering the cellular c-di-GMP level...
May 3, 2017: Microbiology
https://www.readbyqxmd.com/read/28428791/genome-wide-association-study-for-pre-harvest-sprouting-resistance-in-a-large-germplasm-collection-of-chinese-wheat-landraces
#17
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
#18
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
#19
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 strains expressing fixed Lrp levels...
June 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28377102/can-we-predict-gene-expression-by-understanding-proximal-promoter-architecture
#20
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...
June 2017: Trends in Biotechnology
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