keyword
MENU ▼
Read by QxMD icon Read
search

Artificial transcriptional factor

keyword
https://www.readbyqxmd.com/read/29235474/engineering-cell-signaling-using-tunable-crispr-cpf1-based-transcription-factors
#1
Yuchen Liu, Jinghong Han, Zhicong Chen, Hanwei Wu, Hongsong Dong, Guohui Nie
The catalytically dead Cpf1 endonuclease from Acidaminococcus sp. BV3L6 (dAsCpf1) has been used to construct effective transcriptional repressors in bacteria and plants. However, it is still unclear if dAsCpf1 can function in human cells as a transcriptional regulator or a signal conductor. Here, we repurpose the dAsCpf1 system in human cells for a variety of functions, including the activation or repression of gene transcription. Moreover, we construct programmable ligand-controlled dAsCpf1 systems either by coupling crRNAs with engineered riboswitches or by fusing dAsCpf1 proteins with G protein-coupled receptors...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29213259/characterization-of-a-suppressive-cis-acting-element-in-the-epstein-barr-virus-lmp1-promoter
#2
Masahiro Yoshida, Takayuki Murata, Keiji Ashio, Yohei Narita, Takahiro Watanabe, H M Abdullah Al Masud, Yoshitaka Sato, Fumi Goshima, Hiroshi Kimura
Latent membrane protein 1 (LMP1) is a major oncogene encoded by Epstein-Barr virus (EBV) and is essential for immortalization of B cells by the virus. Previous studies suggested that several transcription factors, such as PU.1, RBP-Jκ, NFκB, EBF1, AP-2 and STAT, are involved in LMP1 induction; however, the means by which the oncogene is negatively regulated remains unclear. Here, we introduced short mutations into the proximal LMP1 promoter that includes recognition sites for the E-box and Ikaros transcription factors in the context of EBV-bacterial artificial chromosome...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29188374/characterization-of-a-gene-regulatory-network-underlying-astringency-loss-in-persimmon-fruit
#3
Soichiro Nishiyama, Noriyuki Onoue, Atsushi Kono, Akihiko Sato, Keizo Yonemori, Ryutaro Tao
Transcriptome analysis of a persimmon population segregating for an astringency trait in fruit suggested central roles for a limited number of transcriptional regulators in the loss of proanthocyanidin accumulation. Persimmon (Diospyros kaki; 2n = 6x = 90) accumulates a large amount of proanthocyanidins (PAs) in its fruit, resulting in an astringent taste. Persimmon cultivars are classified into four types based on the nature of astringency loss and the amount of PAs at maturity. Pollination constant and non-astringent (PCNA)-type cultivars stop accumulating PAs in the early stages of fruit development and their fruit can be consumed when still firm without the need for artificial deastringency treatments...
November 29, 2017: Planta
https://www.readbyqxmd.com/read/29180668/regulation-of-human-and-mouse-telomerase-genes-by-genomic-contexts-and-transcription-factors-during-embryonic-stem-cell-differentiation
#4
De Cheng, Shuwen Wang, Wenwen Jia, Yuanjun Zhao, Fan Zhang, Jiuhong Kang, Jiyue Zhu
Differential regulation of telomerase reverse transcriptase (TERT) genes contribute to distinct aging and tumorigenic processes in humans and mice. To study TERT regulation, we generated mouse embryonic stem cell (ESC) lines containing single-copy bacterial artificial chromosome (BAC) reporters, covering hTERT and mTERT genes and their neighboring loci, via recombinase-mediated BAC targeting. ESC lines with chimeric BACs, in which two TERT promoters were swapped, were also generated. Using these chromatinized BACs, we showed that hTERT silencing during differentiation to embryoid bodies (EBs) and to fibroblast-like cells was driven by the human-specific genomic context and accompanied by increases of repressive epigenetic marks, H3K9me3 and H3K27me3, near its promoter...
November 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29173171/new-developments-in-crispr-cas-based-functional-genomics-and-their-implications-for-research-using-zebrafish
#5
Sergey V Prykhozhij, Lucia Caceres, Jason N Berman
Genome editing using CRISPR/Cas9 has advanced very rapidly in its scope, versatility and ease of use. Zebrafish (Danio rerio) has been one of the vertebrate model species where CRISPR/Cas9 has been applied very extensively for many different purposes and with great success. In particular, disease modeling in zebrafish is useful for testing specific gene variants for pathogenicity in a preclinical setting. Here we describe multiple advances in diverse species and systems that can improve genome editing in zebrafish...
November 21, 2017: Current Gene Therapy
https://www.readbyqxmd.com/read/29155979/epigenetic-editing-of-the-dlg4-psd95-gene-improves-cognition-in-aged-and-alzheimer-s-disease-mice
#6
Fernando J Bustos, Estibaliz Ampuero, Nur Jury, Rodrigo Aguilar, Fahimeh Falahi, Jorge Toledo, Juan Ahumada, Jaclyn Lata, Paula Cubillos, Berta Henríquez, Miguel V Guerra, Jimmy Stehberg, Rachael L Neve, Nibaldo C Inestrosa, Ursula Wyneken, Marco Fuenzalida, Steffen Härtel, Miguel Sena-Esteves, Lorena Varela-Nallar, Marianne G Rots, Martin Montecino, Brigitte van Zundert
The Dlg4 gene encodes for post-synaptic density protein 95 (PSD95), a major synaptic protein that clusters glutamate receptors and is critical for plasticity. PSD95 levels are diminished in ageing and neurodegenerative disorders, including Alzheimer's disease and Huntington's disease. The epigenetic mechanisms that (dys)regulate transcription of Dlg4/PSD95, or other plasticity genes, are largely unknown, limiting the development of targeted epigenome therapy. We analysed the Dlg4/PSD95 epigenetic landscape in hippocampal tissue and designed a Dlg4/PSD95 gene-targeting strategy: a Dlg4/PSD95 zinc finger DNA-binding domain was engineered and fused to effector domains to either repress (G9a, Suvdel76, SKD) or activate (VP64) transcription, generating artificial transcription factors or epigenetic editors (methylating H3K9)...
November 16, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29137648/lesr-is-a-novel-upstream-regulator-that-controls-downstream-clp-expression-to-modulate-antibiotic-hsaf-biosynthesis-and-cell-aggregation-in-lysobacter-enzymogenes-oh11
#7
Huiyong Xu, Ruping Wang, Yangyang Zhao, Zheng Qing Fu, Guoliang Qian, Fengquan Liu
BACKGROUND: Heat-stable antifungal factor (HSAF) is a polycyclic tetramate macrolactam secondary metabolite that exhibits broad-spectrum inhibitory activities against filamentous fungal pathogens. The native yield of this chemical is low. It is also a great challenge to synthesize HSAF artificially, due to its complex structure. Understanding the regulatory mechanism underlying HSAF biosynthesis could provide genetic basis for engineering high HSAF-producing strain. The transcription factor Clp is a global regulator that controls bacterial pathogenicity and the expression of one hundred related genes in the phytopathogenic bacterium Xanthomonas campestris pv...
November 14, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29137361/downregulation-of-mir-199a-5p-promotes-prostate-adeno-carcinoma-progression-through-loss-of-its-inhibition-of-hif-1%C3%AE
#8
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...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29117182/structural-and-functional-analysis-of-coral-hypoxia-inducible-factor
#9
Didier Zoccola, Jonas Morain, Gilles Pagès, Natacha Caminiti-Segonds, Sandy Giuliano, Sylvie Tambutté, Denis Allemand
Tissues of symbiotic Cnidarians are exposed to wide, rapid and daily variations of oxygen concentration. Indeed, during daytime, intracellular O2 concentration increases due to symbiont photosynthesis, while during night, respiration of both host cells and symbionts leads to intra-tissue hypoxia. The Hypoxia Inducible Factor 1 (HIF-1) is a heterodimeric transcription factor used for maintenance of oxygen homeostasis and adaptation to hypoxia. Here, we carried out a mechanistic study of the response to variations of O2 concentrations of the coral model Stylophora pistillata...
2017: PloS One
https://www.readbyqxmd.com/read/29098147/synthetic-promoters-and-transcription-factors-for-heterologous-protein-expression-in-saccharomyces-cerevisiae
#10
Fabian Machens, Salma Balazadeh, Bernd Mueller-Roeber, Katrin Messerschmidt
Orthogonal systems for heterologous protein expression as well as for the engineering of synthetic gene regulatory circuits in hosts like Saccharomyces cerevisiae depend on synthetic transcription factors (synTFs) and corresponding cis-regulatory binding sites. We have constructed and characterized a set of synTFs based on either transcription activator-like effectors or CRISPR/Cas9, and corresponding small synthetic promoters (synPs) with minimal sequence identity to the host's endogenous promoters. The resulting collection of functional synTF/synP pairs confers very low background expression under uninduced conditions, while expression output upon induction of the various synTFs covers a wide range and reaches induction factors of up to 400...
2017: Frontiers in Bioengineering and Biotechnology
https://www.readbyqxmd.com/read/29092905/estrogen-induces-egr1-to-fine-tune-its-actions-on-uterine-epithelium-by-controlling-pr-signaling-for-successful-embryo-implantation
#11
Hye-Ryun Kim, Yeon Sun Kim, Jung Ah Yoon, Seung Chel Yang, Mira Park, Dong-Won Seol, Sang Woo Lyu, Jin Hyun Jun, Hyunjung Jade Lim, Dong Ryul Lee, Haengseok Song
The harmonized actions of ovarian E2 and progesterone (P4) regulate the proliferation and differentiation of uterine cells in a spatiotemporal manner. Imbalances between these hormones often lead to infertility and gynecologic diseases. Whereas numerous factors that are involved in P4 signaling have been identified, few local factors that mediate E2 actions in the uterus have been revealed. Here, we demonstrate that estrogen induces the transcription factor, early growth response 1 (Egr1), to fine-tune its actions in uterine epithelial cells (ECs) that are responsible for uterine receptivity for embryo implantation...
November 1, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29084280/maximum-entropy-methods-for-extracting-the-learned-features-of-deep-neural-networks
#12
Alex Finnegan, Jun S Song
New architectures of multilayer artificial neural networks and new methods for training them are rapidly revolutionizing the application of machine learning in diverse fields, including business, social science, physical sciences, and biology. Interpreting deep neural networks, however, currently remains elusive, and a critical challenge lies in understanding which meaningful features a network is actually learning. We present a general method for interpreting deep neural networks and extracting network-learned features from input data...
October 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29080374/the-unfolded-protein-response-mediated-by-perk-is-casually-related-to-the-pathogenesis-of-intervertebral-disc-degeneration
#13
Takeshi Fujii, Nobuyuki Fujita, Satoshi Suzuki, Takashi Tsuji, Takashi Takaki, Kazuo Umezawa, Kota Watanabe, Takeshi Miyamoto, Keisuke Horiuchi, Morio Matsumoto, Masaya Nakamura
Although the number of patients with intervertebral disc (IVD) degeneration is increasing in aging societies, its etiology and pathogenesis remain elusive and there is currently no effective treatment to prevent this undesirable condition. The unfolded protein response (UPR) is a cellular machinery that plays critical roles in handling endoplasmic reticulum (ER) stress, a condition caused by the accumulation of unfolded proteins in the ER lumen. This study aimed to elucidate the potential role of the UPR mediated by pancreatic endoplasmic reticulum kinase (PERK), one of the major ER stress sensors in mammalian cells, in the development of IVD degeneration...
October 28, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/29069764/dual-effects-of-constitutively-active-androgen-receptor-and-full-length-androgen-receptor-for-n-cadherin-regulation-in-prostate-cancer
#14
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...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29061583/bioengineered-nrf2-sirna-is-effective-to-interfere-with-nrf2-pathways-and-improve-chemosensitivity-of-human-cancer-cells
#15
Peng-Cheng Li, Mei-Juan Tu, Pui Yan Ho, Joseph L Jilek, Zhijiang Duan, Qian-Yu Zhang, Ai-Xi Yu, Ai-Ming Yu
The nuclear factor (erythroid-derived 2)-like 2 (NRF2) is a transcription factor in the regulation of many oxidative enzymes and efflux transporters critical for oxidative stress and cellular defense against xenobiotics. NRF2 is dysregulated in patient osteosarcoma (OS) tissues and correlates with therapeutic outcomes. Nevertheless, research on the NRF2 regulatory pathways and its potential as a therapeutic target is limited to the use of synthetic small interfering RNA (siRNA) carrying extensive artificial modifications...
October 23, 2017: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/29054965/adenovirus-mediated-artificial-microrna-targeting-fibrinogen-like-protein-2-attenuates-the-severity-of-acute-pancreatitis-in-mice
#16
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
#17
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
#18
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
#19
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
#20
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 23, 2017: Current Biology: CB
keyword
keyword
95722
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"