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Synthetic transcriptional factor

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https://www.readbyqxmd.com/read/29681756/repressed-expression-of-a-gene-for-a-basic-helix-loop-helix-protein-causes-a-white-flower-phenotype-in-carnation
#1
Akane Totsuka, Emi Okamoto, Taira Miyahara, Takanobu Kouno, Emilio A Cano, Nobuhiro Sasaki, Aiko Watanabe, Keisuke Tasaki, Masahiro Nishihara, Yoshihiro Ozeki
In a previous study, two genes responsible for white flower phenotypes in carnation were identified. These genes encoded enzymes involved in anthocyanin synthesis, namely, flavanone 3-hydroxylase (F3H) and dihydroflavonol 4-reductase (DFR), and showed reduced expression in the white flower phenotypes. Here, we identify another candidate gene for white phenotype in carnation flowers using an RNA-seq analysis followed by RT-PCR. This candidate gene encodes a transcriptional regulatory factor of the basic helix-loop-helix (bHLH) type...
January 2018: Breeding Science
https://www.readbyqxmd.com/read/29680377/computational-re-design-of-synthetic-genetic-oscillators-for-independent-amplitude-and-frequency-modulation
#2
Marios Tomazou, Mauricio Barahona, Karen M Polizzi, Guy-Bart Stan
To perform well in biotechnology applications, synthetic genetic oscillators must be engineered to allow independent modulation of amplitude and period. This need is currently unmet. Here, we demonstrate computationally how two classic genetic oscillators, the dual-feedback oscillator and the repressilator, can be re-designed to provide independent control of amplitude and period and improve tunability-that is, a broad dynamic range of periods and amplitudes accessible through the input "dials." Our approach decouples frequency and amplitude modulation by incorporating an orthogonal "sink module" where the key molecular species are channeled for enzymatic degradation...
April 10, 2018: Cell Systems
https://www.readbyqxmd.com/read/29676910/5-phosphorothiolate-dinucleotide-cap-analogs-reagents-for-mrna-modification-and-potent-small-molecular-inhibitors-of-decapping-enzymes
#3
Blazej Andrzej Wojtczak, Pawel J Sikorski, Kaja Fac-Dabrowska, Anna Nowicka, Marcin Warminski, Dorota Kubacka, Elzbieta Nowak, Marcin Nowotny, Joanna Kowalska, Jacek Jemielity
The 5' cap consists of 7-methylguanosine (m7G) linked by a 5'-5'-triphosphate bridge to mRNA and acts as the master regu-lator of mRNA turnover and translation initiation in eukaryotes. Cap analogs that influence mRNA translation and turnover (either as small molecules or as part of an RNA transcript) are valuable tools for studying gene expression, which is often also of therapeutic relevance. Here, we synthesized a series of 15 dinucleotide cap (m7GpppG) analogs containing a 5'-phosphorothiolate (5'-PSL) moiety (i...
April 20, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29672220/environmental-hypoxia-favors-myoblast-differentiation-and-fast-phenotype-but-blunts-activation-of-protein-synthesis-after-resistance-exercise-in-human-skeletal-muscle
#4
Olouyomi Gnimassou, Rodrigo Fernández-Verdejo, Matthew Brook, Damien Naslain, Estelle Balan, Mariwan Sayda, Jessica Cegielski, Henri Nielens, Anabelle Decottignies, Jean-Baptiste Demoulin, Kenneth Smith, Philip J Atherton, Marc Francaux, Louise Deldicque
We hypothesized that a single session of resistance exercise performed in moderate hypoxic (FiO2 : 14%) environmental conditions would potentiate the anabolic response during the recovery period spent in normoxia. Twenty subjects performed a 1-leg knee extension session in normoxic or hypoxic conditions. Muscle biopsies were taken 15 min and 4 h after exercise in the vastus lateralis of the exercised and the nonexercised legs. Blood and saliva samples were taken at regular intervals before, during, and after the exercise session...
April 19, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29666238/rapid-acquisition-and-model-based-analysis-of-cell-free-transcription-translation-reactions-from-nonmodel-bacteria
#5
Simon J Moore, James T MacDonald, Sarah Wienecke, Alka Ishwarbhai, Argyro Tsipa, Rochelle Aw, Nicolas Kylilis, David J Bell, David W McClymont, Kirsten Jensen, Karen M Polizzi, Rebekka Biedendieck, Paul S Freemont
Native cell-free transcription-translation systems offer a rapid route to characterize the regulatory elements (promoters, transcription factors) for gene expression from nonmodel microbial hosts, which can be difficult to assess through traditional in vivo approaches. One such host, Bacillus megaterium , is a giant Gram-positive bacterium with potential biotechnology applications, although many of its regulatory elements remain uncharacterized. Here, we have developed a rapid automated platform for measuring and modeling in vitro cell-free reactions and have applied this to B...
April 17, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29665411/iterative-genome-editing-of-escherichia-coli-for-3-hydroxypropionic-acid-production
#6
Rongming Liu, Liya Liang, Alaksh Choudhury, Marcelo C Bassalo, Andrew D Garst, Katia Tarasava, Ryan T Gill
Synthetic biology requires strategies for the targeted, efficient, and combinatorial engineering of biological sub-systems at the molecular level. Here, we report the use of the iterative CRISPR EnAbled Trackable genome Engineering (iCREATE) method for the rapid construction of combinatorially modified genomes. We coupled this genome engineering strategy with high-throughput phenotypic screening and selections to recursively engineer multiple traits in Escherichia coli for improved production of the platform chemical 3-hydroxypropionic acid (3HP)...
April 14, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29656318/a-novel-tetrasubstituted-imidazole-as-a-prototype-for-the-development-of-anti-inflammatory-drugs
#7
Marcus Vinicius P S Nascimento, Antonio C M Munhoz, Lais C Theindl, Eduarda Talita B Mohr, Najla Saleh, Eduardo B Parisotto, Thaís A Rossa, Ariane Zamoner, Tania B Creczynski-Pasa, Fabíola B Filippin-Monteiro, Marcus M Sá, Eduardo Monguilhott Dalmarco
Although inflammation is a biological phenomenon that exists to protect the host against infections and/or related problems, its unceasing activation results in the aggravation of several medical conditions. Imidazoles, whether natural or synthetic, are molecules related to a broad spectrum of biological effects, including anti-inflammatory properties. In this study, we screened eight novel small molecules of the imidazole class synthesized by our research group for their in vitro anti-inflammatory activity...
April 14, 2018: Inflammation
https://www.readbyqxmd.com/read/29653414/new-insights-on-the-modulatory-roles-of-metformin-or-alpha-lipoic-acid-versus-their-combination-in-dextran-sulfate-sodium-induced-chronic-colitis-in-rats
#8
Fatma S Samman, Samah M Elaidy, Soha S Essawy, Mohammad S Hassan
BACKGROUND: Dextran sulfate sodium (DSS)-induced colitis is the most widely used model that resembles ulcerative colitis (UC) in human with challenging chronic mechanistic oxidative stress-inflammatory/immunological cascades. In models of acute colitis, reduction of oxidative stress and inflammatory burdens beside manipulation of many transcriptional factors were achieved by metformin or alpha-lipoic acid (α-LA). Currently, in vivo DSS-induced chronic colitis was conducted and the possible therapeutic roles of metformin and/or α-LA were explored...
November 24, 2017: Pharmacological Reports: PR
https://www.readbyqxmd.com/read/29642431/the-recombinant-inhibitor-of-dna-binding-id2-forms-multimeric-structures-via-the-helix-loop-helix-domain-and-the-nuclear-export-signal
#9
Cornelia Roschger, Mario Schubert, Christof Regl, Ancuela Andosch, Augusto Marquez, Thomas Berger, Christian G Huber, Ursula Lütz-Meindl, Chiara Cabrele
The inhibitor of DNA binding and cell differentiation 2 (Id2) is a helix-loop-helix (HLH) protein that acts as negative dominant regulator of basic-HLH transcription factors during development and in cancer. The structural properties of Id2 have been investigated so far by using synthetic or recombinant fragments reproducing single domains (N-terminus, HLH, C-terminus): the HLH domain tends to dimerize into a four-helix bundle, whereas the flanking regions are flexible. In this work, the intact protein was expressed in E...
April 7, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29629858/pseudomonas-aeruginosa-puma-acts-on-an-endogenous-phenazine-to-promote-self-resistance
#10
Abigail J Sporer, Christopher Beierschmitt, Anastasia Bendebury, Katherine E Zink, Alexa Price-Whelan, Marisa C Buzzeo, Laura M Sanchez, Lars E P Dietrich
The activities of critical metabolic and regulatory proteins can be altered by exposure to natural or synthetic redox-cycling compounds. Many bacteria, therefore, possess mechanisms to transport or transform these small molecules. The opportunistic pathogen Pseudomonas aeruginosa PA14 synthesizes phenazines, redox-active antibiotics that are toxic to other organisms but have beneficial effects for their producer. Phenazines activate the redox-sensing transcription factor SoxR and thereby induce the transcription of a small regulon, including the operon mexGHI-opmD, which encodes an efflux pump that transports phenazines, and PA14_35160 (pumA), which encodes a putative monooxygenase...
April 9, 2018: Microbiology
https://www.readbyqxmd.com/read/29628981/troglitazone-inhibits-matrix-metalloproteinase-9-expression-and-invasion-of-breast-cancer-cell-through-a-peroxisome-proliferator-activated-receptor-%C3%AE-dependent-mechanism
#11
On-Yu Hong, Hyun Jo Youn, Hye-Yeon Jang, Sung Hoo Jung, Eun-Mi Noh, Hee Suk Chae, Young-Ju Jeong, Won Kim, Cheorl-Ho Kim, Jong-Suk Kim
Purpose: Peroxisome proliferator-activated receptor γ (PPARγ) is involved in the pathology of numerous diseases including atherosclerosis, diabetes, obesity, and cancer. Matrix metalloproteinases (MMPs) play a significant role in tissue remodeling related to various processes such as morphogenesis, angiogenesis, tissue repair, invasion, and metastasis. We investigated the effects of PPARγ on MMP expression and invasion in breast cancer cells. Methods: MCF-7 cells were cultured and then cell viability was monitored in an MTT assay...
March 2018: Journal of Breast Cancer
https://www.readbyqxmd.com/read/29625007/synthetic-gene-network-with-positive-feedback-loop-amplifies-cellulase-gene-expression-in-neurospora-crassa
#12
Toru Matsu-Ura, Andrey A Dovzhenok, Samuel T Coradetti, Krithika R Subramanian, Daniel R Meyer, Jaesang J Kwon, Caleb Kim, Nathan Salomonis, N Louise Glass, Sookkyung Lim, Christian I Hong
Second-generation or lignocellulosic biofuels are a tangible source of renewable energy, which is critical to combat climate change by reducing the carbon footprint. Filamentous fungi secrete cellulose-degrading enzymes called cellulases, which are used for production of lignocellulosic biofuels. However, inefficient production of cellulases is a major obstacle for industrial-scale production of second-generation biofuels. We used computational simulations to design and implement synthetic positive feedback loops to increase gene expression of a key transcription factor, CLR-2, that activates a large number of cellulases in a filamentous fungus, Neurospora crassa...
April 6, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29620234/crocin-prevents-platelet%C3%A2-derived-growth-factor-bb%C3%A2-induced-vascular-smooth-muscle-cells-proliferation-and-phenotypic-switch
#13
Lijian Tong, Guoxian Qi
The phenotypic switch of vascular smooth muscle cells (VSMCs) is a major initiating factor for atherosclerotic cardiovascular diseases. Platelet‑derived growth factor‑BB (PDGF‑BB) initiates a number of biological processes that contribute to VSMC proliferation and phenotypic switch. Crocin, a component of saffron, has been reported to inhibit atheromatous plaque formation. However, the effects of crocin on PDGF‑BB‑induced VSMC proliferation and phenotypic switch remain unclear. The aim of the present study was to investigate the role of crocin on PDGF‑BB‑induced VSMCs proliferation and phenotypic switch and its underlying mechanisms...
April 5, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29617696/vr-10-thrombospondin-1-synthetic-polypeptide-s-impact-on-rhesus-choroid-retinal-endothelial-cells
#14
Run Tian, Fang Han, Jun Yang, Hai-Yan Zhao, Yan Mei, Ai-Ping Deng, Lin Fang, Xi-Rui Zhang
BACKGROUND/AIMS: This study aimed to investigate the effects of the VR-10 TSP-1 synthetic polypeptide on cytokines and the proliferation and migration of endothelial cells, as well as exploring a new method for anti-ocular neoangiogenesis. METHODS: We measured the proliferation of RF/6A cells by an MTT assay and investigated the migration of RF/6A cells by a Transwell chamber assay. We examined the mRNA transcript levels of TGF-β2, VEGF, PEDF, Bcl-2 and FasL in RF/6A cells by RT-PCR and evaluated the expression of Fas and caspase-3 proteins in RF/6A cells by western blot analysis...
March 28, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29617125/quantitative-characterization-of-translational-riboregulators-using-an-in-vitro-transcription-translation-system
#15
Anis Senoussi, Jonathan Lee Tin Wah, Yoshihiro Shimizu, Jérôme Robert, Alfonso Jaramillo, Sven Findeiss, Ilka M Axmann, André Estevez-Torres
Riboregulators are short RNA sequences that, upon binding to a ligand, change their secondary structure and influence the expression rate of a downstream gene. They constitute an attractive alternative to transcription factors for building synthetic gene regulatory networks because they can be engineered de novo. However, riboregulators are generally designed in silico and tested in vivo, which provides little quantitative information about their performances, thus hindering the improvement of design algorithms...
April 4, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29614034/novel-1-e-3-e-5-e-1-6-bis-substituted-phenyl-hexa-1-3-5-triene-analogs-inhibit-melanogenesis-in-b16f10-cells-and-zebrafish
#16
Jisun Oh, Jungeun Kim, Jin Ho Jang, Sangwoo Lee, Chul Min Park, Woo-Keun Kim, Jong-Sang Kim
The present study aimed to evaluate the anti-melanogenic activity of 1,6-diphenyl-1,3,5-hexatriene and its derivatives in B16F10 murine melanoma cells and zebrafish embryos. Twenty five (1 E ,3 E ,5 E )-1,6- bis (substituted phenyl)hexa-1,3,5-triene analogs were synthesized and their non-cytotoxic effects were predictively analyzed using three-dimensional quantitative structure-activity relationship approach. Inhibitory activities of these synthetic compounds against melanin synthesis were determined by evaluating melanin content and melanogenic regulatory enzyme expression in B16F10 cells...
April 3, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29613773/an-orthogonal-and-ph-tunable-sensor-selector-for-muconic-acid-biosynthesis-in-yeast
#17
Tim Snoek, David Romero-Suarez, Jie Zhang, Francesca Ambri, Mette L Skjoedt, Suresh Sudarsan, Michael K Jensen, Jay D Keasling
Microbes offer enormous potential for production of industrially relevant chemicals and therapeutics, yet the rapid identification of high-producing microbes from large genetic libraries is a major bottleneck in modern cell factory development. Here, we develop and apply a synthetic selection system in Saccharomyces cerevisiae that couples the concentration of muconic acid, a plastic precursor, to cell fitness by using the prokaryotic transcriptional regulator BenM driving an antibiotic resistance gene. We show that the sensor-selector does not affect production nor fitness, and find that tuning pH of the cultivation medium limits the rise of nonproducing cheaters...
April 5, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29609044/design-development-and-application-of-whole-cell-based-antibiotic-specific-biosensor
#18
Yuriy Rebets, Stefan Schmelz, Oleksandr Gromyko, Stepan Tistechok, Lutz Petzke, Andrea Scrima, Andriy Luzhetskyy
Synthetic biology techniques hold great promise for optimising the production of natural products by microorganisms. However, evaluating the phenotype of a modified bacterium represents a major bottleneck to the engineering cycle - particularly for antibiotic-producing actinobacteria strains, which grow slowly and are challenging to genetically manipulate. Here, we report the generation and application of antibiotic-specific whole-cell biosensor derived from TetR transcriptional repressor for use in identifying and optimising antibiotic producers...
March 30, 2018: Metabolic Engineering
https://www.readbyqxmd.com/read/29596001/identification-of-candidate-genes-involved-in-the-salt-tolerance-of-date-palm-phoenix-dactylifera-l-based-on-a-yeast-functional-bioassay
#19
Himanshu V Patankar, Ibtisam Al-Harrasi, Rashid Al-Yahyai, Mahmoud W Yaish
Although date palm is a relatively salt-tolerant plant, the molecular basis of this tolerance is complex and poorly understood. Therefore, this study aimed to identify the genes involved in salinity tolerance using a basic yeast functional bioassay. To achieve this, a date palm cDNA library was overexpressed in Saccharomyces cerevisiae cells. The expression levels of selected genes that make yeast cells tolerant to salt were subsequently validated in the leaf and root tissues of date palm seedlings using a quantitative PCR method...
March 29, 2018: DNA and Cell Biology
https://www.readbyqxmd.com/read/29580240/exploring-native-genetic-elements-as-plug-in-tools-for-synthetic-biology-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#20
Deng Liu, Himadri B Pakrasi
BACKGROUND: The unicellular cyanobacterium Synechocystis sp. PCC 6803 has been widely used as a photoautotrophic host for synthetic biology studies. However, as a green chassis to capture CO2 for biotechnological applications, the genetic toolbox for Synechocystis 6803 is still a limited factor. RESULTS: We systematically characterized endogenous genetic elements of Synechocystis 6803, including promoters, ribosome binding sites, transcription terminators, and plasmids...
March 26, 2018: Microbial Cell Factories
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