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Artificial transcriptional factor

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https://www.readbyqxmd.com/read/29054965/adenovirus-mediated-artificial-microrna-targeting-fibrinogen-like-protein-2-attenuates-the-severity-of-acute-pancreatitis-in-mice
#1
Xiaohua Ye, Jin Ding, Yanping Chen, Jiayue Dong
Severe acute pancreatitis (SAP) remains to be challenging for its unpredictable inflammatory progression from acute pancreatitis to SAP. Apoptosis is an important pathology of SAP. Fibrinogen-like protein 2 (FGL2) has been reported to be involved in apoptosis. The present study aimed to explore the therapeutic effect of an adenovirus-mediated artificial microRNA targeting FGL2 (Ad-FGL2-miRNA) in taurocholate-induced murine pancreatitis models. Sodium taurocholate was retrogradely injected into the biliopancreatic ducts of the C57/BL mice to induce SAP...
October 20, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/29044990/transcriptome-analysis-for-uvb-induced-phototoxicity-in-mouse-retina
#2
Mi-Jin An, Chul-Hong Kim, Gyu-You Nam, Dae-Hyun Kim, Sangmyung Rhee, Sung-Jin Cho, Jung-Woong Kim
Throughout life, the human eye is continuously exposed to sunlight and artificial lighting. Ambient light exposure can lead to visual impairment and transient or permanent blindness. To mimic benign light stress conditions, Mus musculus eyes were exposed to low-energy UVB radiation, ensuring no severe morphological changes in the retinal structure post-exposure. We performed RNA-seq analysis to reveal the early transcriptional changes and key molecular pathways involved before the activation of the canonical cell death pathway...
October 17, 2017: Environmental Toxicology
https://www.readbyqxmd.com/read/29043679/er-membrane-protein-interactions-using-the-split-ubiquitin-system-sus
#3
Lisa Yasmin Asseck, Niklas Wallmeroth, Christopher Grefen
Protein-protein interactions (PPIs) play fundamental roles in all cellular processes. Especially membrane proteins facilitate a range of important biological functions in stimuli perception, signaling, and transport. Here we describe a detailed protocol for the yeast mating-based Split-Ubiquitin System (mbSUS) to study PPIs of ER membrane proteins in vivo. In contrast to the prominent Yeast Two-Hybrid, mbSUS enables analysis of full-length membrane proteins in their native cellular context. The system is based on the ubiquitin proteasome pathway leading to the release of an artificial transcription factor followed by activation of reporter genes to visualize PPIs...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29034619/-induction-and-regulation-of-cellulase-expression-in-filamentous-fungi-a-review
#4
Fei Zhang, Fengwu Bai, Xinqing Zhao
Production of bioenergy and bio-based chemicals by using fermentable sugars released from low-cost renewable lignocellulosic biomass has received great attention. Efficient cellulolytic enzymes are crucial for lignocellulose bioconversion, but high cellulase production cost is limiting the bioconversion efficiency of cellulosic biomass and industrial applications of lignocellulose biorefinery. Studies on induction and regulation of cellulase in filamentous fungi will help to further develop superior fungal strains for efficient cellulase production and reduce cellulase production cost...
November 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29033328/the-cys-arg-n-end-rule-pathway-is-a-general-sensor-of-abiotic-stress-in-flowering-plants
#5
Jorge Vicente, Guillermina M Mendiondo, Mahsa Movahedi, Marta Peirats-Llobet, Yu-Ting Juan, Yu-Yen Shen, Charlene Dambire, Katherine Smart, Pedro L Rodriguez, Yee-Yung Charng, Julie E Gray, Michael J Holdsworth
Abiotic stresses impact negatively on plant growth, profoundly affecting yield and quality of crops. Although much is known about plant responses, very little is understood at the molecular level about the initial sensing of environmental stress. In plants, hypoxia (low oxygen, which occurs during flooding) is directly sensed by the Cys-Arg/N-end rule pathway of ubiquitin-mediated proteolysis, through oxygen-dependent degradation of group VII Ethylene Response Factor transcription factors (ERFVIIs) via amino-terminal (Nt-) cysteine [1, 2]...
October 11, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29024972/effect-of-metabolic-status-on-conceptus-maternal-interactions-on-day-19-in-dairy-cattle-ii-effects-on-the-endometrial-transcriptome
#6
S Bauersachs, C A Simintiras, R G Sturmey, S Krebs, J Bick, H Blum, E Wolf, P Lonergan, N Forde
The aim of this study was to test the hypothesis that the metabolic stresses associated with lactation alter the ability of the endometrium to respond appropriately to the conceptus by examining endometrial gene expression on Day 19 of pregnancy. Immediately after calving, primiparous Holstein cows with similar production and fertility estimated breeding values (EBVs) were randomly divided into two groups and either dried off (i.e. never milked) immediately or milked twice daily. Approximately 65-75 days postpartum, grade 1 blastocysts recovered from superovulated Holstein heifer donors (n = 5) were transferred (1 per recipient) into lactating (n = 11) and non-lactating (n = 11) recipients...
August 31, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28986912/plant-gene-regulation-using-multiplex-crispr-dcas9-artificial-transcription-factors
#7
Levi G Lowder, Aimee Malzahn, Yiping Qi
Besides genome editing, the CRISPR-Cas9-based platform provides a new way of engineering artificial transcription factors (ATFs). Multiplex of guide RNA (gRNA) expression cassettes holds a great promise for many useful applications of CRISPR-Cas9. In this chapter, we provide a detailed protocol for building advanced multiplexed CRISPR-dCas9-Activator/repressor T-DNA vectors for carrying out transcriptional activation or repression experiments in plants. We specifically describe the assembly of multiplex T-DNA vectors that can express multiple gRNAs to activate a silenced gene, or to repress two independent miRNA genes simultaneously in Arabidopsis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28979287/an-optimized-transient-dual-luciferase-assay-for-quantifying-microrna-directed-repression-of-targeted-sequences
#8
Richard L Moyle, Lilia C Carvalhais, Lara-Simone Pretorius, Ekaterina Nowak, Gayathery Subramaniam, Jessica Dalton-Morgan, Peer M Schenk
Studies investigating the action of small RNAs on computationally predicted target genes require some form of experimental validation. Classical molecular methods of validating microRNA action on target genes are laborious, while approaches that tag predicted target sequences to qualitative reporter genes encounter technical limitations. The aim of this study was to address the challenge of experimentally validating large numbers of computationally predicted microRNA-target transcript interactions using an optimized, quantitative, cost-effective, and scalable approach...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28977475/functional-impacts-of-5-hydroxymethylcytosine-5-formylcytosine-and-5-carboxycytosine-at-a-single-hemi-modified-cpg-dinucleotide-in-a-gene-promoter
#9
Nataliya Kitsera, Julia Allgayer, Edris Parsa, Nadine Geier, Martin Rossa, Thomas Carell, Andriy Khobta
Enzymatic oxidation of 5-methylcytosine (5-mC) in the CpG dinucleotides to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxycytosine (5-caC) has central role in the process of active DNA demethylation and epigenetic reprogramming in mammals. However, it is not known whether the 5-mC oxidation products have autonomous epigenetic or regulatory functions in the genome. We used an artificial upstream promoter constituted of one cAMP response element (CRE) to measure the impact of 5-mC in a hemi-methylated CpG on the promoter activity and further explored the consequences of 5-hmC, 5-fC, and 5-caC in the same system...
August 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28968739/snpdelscore-combining-multiple-methods-to-score-deleterious-effects-of-noncoding-mutations-in-the-human-genome
#10
Roberto Vera Alvarez, Shan Li, David Landsman, Ivan Ovcharenko
Abstract: Addressing deleterious effects of noncoding mutations is an essential step towards the identification of disease-causal mutations of gene regulatory elements. Several methods for quantifying the deleteriousness of noncoding mutations using artificial intelligence, deep learning, and other approaches have been recently proposed. Although the majority of the proposed methods have demonstrated excellent accuracy on different test sets, there is rarely a consensus. In addition, advanced statistical and artificial learning approaches used by these methods make it difficult porting these methods outside of the labs that have developed them...
September 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28953977/an-acquired-mechanism-of-antifungal-drug-resistance-simultaneously-enables-candida-albicans-to-escape-from-intrinsic-host-defenses
#11
Irene A I Hampe, Justin Friedman, Mira Edgerton, Joachim Morschhäuser
The opportunistic fungal pathogen Candida albicans frequently produces genetically altered variants to adapt to environmental changes and new host niches in the course of its life-long association with the human host. Gain-of-function mutations in zinc cluster transcription factors, which result in the constitutive upregulation of their target genes, are a common cause of acquired resistance to the widely used antifungal drug fluconazole, especially during long-term therapy of oropharyngeal candidiasis. In this study, we investigated if C...
September 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28947819/a-dual-targeted-%C3%AE-defensin-and-exome-sequencing-approach-to-identify-validate-and-functionally-characterise-genes-associated-with-bull-fertility
#12
Ronan Whiston, Emma K Finlay, Matthew S McCabe, Paul Cormican, Paul Flynn, Andrew Cromie, Peter J Hansen, Alan Lyons, Sean Fair, Patrick Lonergan, Cliona O' Farrelly, Kieran G Meade
Bovine fertility remains a critical issue underpinning the sustainability of the agricultural sector. Phenotypic records collected on >7,000 bulls used in artificial insemination (AI) were used to identify 160 reliable and divergently fertile bulls for a dual strategy of targeted sequencing (TS) of fertility-related β-defensin genes and whole exome sequencing (WES). A haplotype spanning multiple β-defensin genes and containing 94 SNPs was significantly associated with fertility and functional analysis confirmed that sperm from bulls possessing the haplotype showed significantly enhanced binding to oviductal epithelium...
September 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28928947/puzzles-in-modern-biology-v-why-are-genomes-overwired
#13
Steven A Frank
Many factors affect eukaryotic gene expression. Transcription factors, histone codes, DNA folding, and noncoding RNA modulate expression. Those factors interact in large, broadly connected regulatory control networks. An engineer following classical principles of control theory would design a simpler regulatory network. Why are genomes overwired? Neutrality or enhanced robustness may lead to the accumulation of additional factors that complicate network architecture. Dynamics progresses like a ratchet. New factors get added...
2017: F1000Research
https://www.readbyqxmd.com/read/28918014/artificial-zinc-finger-transcription-factor-of-a20-suppresses-restenosis-in-sprague-dawley-rats-after-carotid-injury-via-the-ppar%C3%AE-pathway
#14
Zhaoyou Meng, Pan Gao, Lin Chen, Jing Peng, Jialu Huang, Min Wu, Kangning Chen, Zhenhua Zhou
The inhibition of inflammation and vascular smooth muscle cell (VSMC) proliferation is an ideal strategy to suppress intimal hyperplasia after percutaneous transluminal angioplasty (PTA). Evidence has indicated that overexpression of A20 suppresses neointima formation, but its low transfection efficiency limits its application. Hence, we upregulated A20 expression via transfection of rAd.ATF (recombinant adenovirus vector of artificial transcription factor) and rAd.A20 in rat carotid arteries after balloon dilatation (in vivo) and isolated VSMCs (in vitro)...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28910180/nrf2-mediated-ho-1-induction-and-antineuroinflammatory-activities-of-halleridone
#15
Ji Yeon Seo, Euisun Pyo, Junsoo Park, Jong-Sang Kim, Sang Hyun Sung, Won Keun Oh
Nuclear factor E2-related factor 2 (Nrf2) is the master regulator of antioxidant enzymes and is known to act on the nuclear factor kappa-light-chain-enhancer of activated B cell (NF-κB) signaling pathway. Few studies have examined the bioactivity of halleridone. Herein, we investigated whether halleridone, which was isolated from the stems of the plant Cornus walteri, could regulate Nrf2-mediated heme oxygenase (HO)-1 expression and prevent intramicroglial inflammation induced by amyloid beta (Aβ)1-42 overexpression...
September 14, 2017: Journal of Medicinal Food
https://www.readbyqxmd.com/read/28841424/mechanical-induction-of-dentin-like-differentiation-by-adult-mouse-bone-marrow-stromal-cells-using-compressive-scaffolds
#16
Basma Hashmi, Tadanori Mammoto, James Weaver, Thomas Ferrante, Amanda Jiang, Elisabeth Jiang, Juani Feliz, Donald E Ingber
Tooth formation during embryogenesis is controlled through a complex interplay between mechanical and chemical cues. We have previously shown that physical cell compaction of dental mesenchyme cells during mesenchymal condensation is responsible for triggering odontogenic differentiation during embryogenesis, and that expression of Collagen VI stabilizes this induction. In addition, we have shown that synthetic polymer scaffolds that artificially induce cell compaction can induce embryonic mandible mesenchymal cells to initiate tooth differentiation both in vitro and in vivo...
August 17, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28827804/recruitment-of-armitage-and-yb-to-a-transcript-triggers-its-phased-processing-into-primary-pirnas-in-drosophila-ovaries
#17
Radha Raman Pandey, David Homolka, Kuan-Ming Chen, Ravi Sachidanandam, Marie-Odile Fauvarque, Ramesh S Pillai
Small RNAs called PIWI -interacting RNAs (piRNAs) are essential for transposon control and fertility in animals. Primary processing is the small RNA biogenesis pathway that uses long single-stranded RNA precursors to generate millions of individual piRNAs, but the molecular mechanisms that identify a transcript as a precursor are poorly understood. Here we demonstrate that artificial tethering of the piRNA biogenesis factor, Armi, to a transcript is sufficient to direct it into primary processing in Drosophila ovaries and in an ovarian cell culture model...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28804119/artificial-intelligence-dna-mimicry-and-human-health
#18
George B Stefano, Richard M Kream
The molecular evolution of genomic DNA across diverse plant and animal phyla involved dynamic registrations of sequence modifications to maintain existential homeostasis to increasingly complex patterns of environmental stressors. As an essential corollary, driver effects of positive evolutionary pressure are hypothesized to effect concerted modifications of genomic DNA sequences to meet expanded platforms of regulatory controls for successful implementation of advanced physiological requirements. It is also clearly apparent that preservation of updated registries of advantageous modifications of genomic DNA sequences requires coordinate expansion of convergent cellular proofreading/error correction mechanisms that are encoded by reciprocally modified genomic DNA...
August 14, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28803237/atf3-dependent-regulation-of-egr1-in-vitro-and-in-vivo
#19
Ilona Schoen, Sabine Koitzsch
BACKGROUND/AIMS: Activating transcription factor 3 (ATF3) and early growth response protein 1 (EGR1) are reported to interact, but their use as prognostic factors in cancer is discussed controversially. METHODS: We measured ATF3 and EGR1 gene expression changes in human mini-organ cultures (MOCs) of healthy nasal epithelia, UM-SCC-22B, and FADUDD cells after acid reflux exposure. Next, ATF3 and EGR1 gene expression was analysed in tumour tissues and related to the median expression of autologous reference tissue samples...
August 12, 2017: ORL; Journal for Oto-rhino-laryngology and its related Specialties
https://www.readbyqxmd.com/read/28801913/design-of-synthetic-promoters-for-gene-circuits-in-mammalian-cells
#20
Pratik Saxena, Daniel Bojar, Martin Fussenegger
Synthetic biology, the synthesis of engineering and biology, has rapidly matured and has dramatically increased the complexity of artificial gene circuits in recent years. The deployment of intricate synthetic gene circuits in mammalian cells requires the establishment of very precise and orthogonal control of transgene expression. In this chapter, we describe methods of modulating the expression of transgenes at the transcriptional level. Using cAMP-response element-binding protein (CREB)-dependent promoters as examples, a tool for the precise tuning of gene expression by using different core promoters and by varying the binding affinity of transcription factor operator sites is described...
2017: Methods in Molecular Biology
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