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Amber suppression

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https://www.readbyqxmd.com/read/29456806/women-with-hereditary-breast-cancer-predispositions-should-avoid-using-their-smartphones-tablets-and-laptops-at-night
#1
EDITORIAL
Seyed Ali Reza Mortazavi, Seyed Mohammad Javad Mortazavi
Breast cancer is the most common malignancy among women, both in the developed and developing countries. Women with mutations in the BRCA1 and BRCA2 genes have an increased risk of breast and ovarian cancers. Recent studies show that short-wavelength visible light disturb the secretion of melatonin and causes circadian rhythm disruption. We have previously studied the health effects of exposure to different levels of radiofrequency electromagnetic fields (RF-EMFs) such as mobile phones, mobile base stations, mobile phone jammers, laptop computers, and radars...
February 2018: Iranian Journal of Basic Medical Sciences
https://www.readbyqxmd.com/read/29452937/epigenetic-chromatin-modification-by-amber-suppression-technology
#2
REVIEW
Heinz Neumann, Petra Neumann-Staubitz, Anna Witte, Daniel Summerer
The genetic incorporation of unnatural amino acids (UAAs) into proteins by amber suppression technology provides unique avenues to study protein structure, function and interactions both in vitro and in living cells and organisms. This approach has been particularly useful for studying mechanisms of epigenetic chromatin regulation, since these extensively involve dynamic changes in structure, complex formation and posttranslational modifications that are difficult to access by traditional approaches. Here, we review recent achievements in this field, emphasizing UAAs that help to unravel protein-protein interactions in cells by photo-crosslinking or that allow the biosynthesis of proteins with defined posttranslational modifications for studying their function and turnover in vitro and in cells...
February 13, 2018: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29439566/incorporation-of-non-proteinogenic-amino-acids-in-class-i-and-ii-lanti-biotics
#3
Nidhi Kakkar, Jessica G Perez, Wenshe R Liu, Michael C Jewett, Wilfred A van der Donk
Lantibiotics are ribosomally synthesized and post-translationally modified peptide natural products that contain thioether crosslinks formed by lanthionine and methyllanthionine residues. They exert potent antimicrobial activity against Gram-positive bacteria. We herein report production of analogues of two lantibiotics, lacticin 481 and nisin that contain non-proteinogenic amino acids using two different strategies involving amber stop codon suppression technology. These methods complement recent alternative approaches to incorporate non-proteinogenic amino acids into lantibiotics...
February 13, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29405002/generation-of-stable-amber-suppression-cell-lines
#4
Simon J Elsässer
Noncanonical amino acid mutagenesis via amber suppression provides the means to tailor proteins inside living cells. A wide range of noncanonical amino acids have been incorporated using the Methanococcus pyrrolysyl-tRNA synthetase/tRNACUA (PylRS/PylT) in mammalian cell systems in proof of principle experiments, for (1) minimal genetically encoded fluorescence or affinity tagging, (2) photo-control of enzymes, (3) genetically encoded posttranslational protein modifications. We have developed a general and efficient method to genomically integrate the PylRS/PylT amber suppression machinery using PiggyBac-mediated transposition...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29404996/using-amber-and-ochre-nonsense-codons-to-code-two-different-noncanonical-amino-acids-in-one-protein-gene
#5
Jeffery M Tharp, Wenshe R Liu
In Escherichia coli, conventional amber and ochre stop codons can be separately targeted by engineered amber-suppressing Methanocaldococcus jannaschii tyrosyl-tRNA synthetase-tRNAPyl and ochre-suppressing Methanosarcina maezi pyrrolysyl-tRNA synthetase-tRNAPyl pairs for coding two different noncanonical amino acids in one protein gene. Here, we describe the application of this approach to produce a protein with two distinct chemical functionalites which can be selectively labeled with two fluorescent dyes.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29380422/microrna-31-is-required-for-astrocyte-specification
#6
Gordon P Meares, Rajani Rajbhandari, Magda Gerigk, Chih-Liang Tien, Chenbei Chang, Samuel C Fehling, Amber Rowse, Kayln C Mulhern, Sindhu Nair, G Kenneth Gray, Nicolas F Berbari, Markus Bredel, Etty N Benveniste, Susan E Nozell
Previously, we determined microRNA-31 (miR-31) is a noncoding tumor suppressive gene frequently deleted in glioblastoma (GBM); miR-31 suppresses tumor growth, in part, by limiting the activity of NF-κB. Herein, we expand our previous studies by characterizing the role of miR-31 during neural precursor cell (NPC) to astrocyte differentiation. We demonstrate that miR-31 expression and activity is suppressed in NPCs by stem cell factors such as Lin28, c-Myc, SOX2 and Oct4. However, during astrocytogenesis, miR-31 is induced by STAT3 and SMAD1/5/8, which mediate astrocyte differentiation...
January 30, 2018: Glia
https://www.readbyqxmd.com/read/29304101/fab-based-inhibitors-reveal-ubiquitin-independent-functions-for-hiv-vif-neutralization-of-apobec3-restriction-factors
#7
Jennifer M Binning, Amber M Smith, Judd F Hultquist, Charles S Craik, Nathalie Caretta, Melody G Campbell, Lily Burton, Florencia La Greca, Michael J McGregor, Hai M Ta, Koen Bartholomeeusen, B Matija Peterlin, Nevan J Krogan, Natalia Sevillano, Yifan Cheng, John D Gross
The lentiviral protein Viral Infectivity Factor (Vif) counteracts the antiviral effects of host APOBEC3 (A3) proteins and contributes to persistent HIV infection. Vif targets A3 restriction factors for ubiquitination and proteasomal degradation by recruiting them to a multi-protein ubiquitin E3 ligase complex. Here, we describe a degradation-independent mechanism of Vif-mediated antagonism that was revealed through detailed structure-function studies of antibody antigen-binding fragments (Fabs) to the Vif complex...
January 5, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29233219/a-molecular-engineering-toolbox-for-the-structural-biologist
#8
Galia T Debelouchina, Tom W Muir
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29155146/hdac-inhibitor-suppresses-proliferation-and-invasion-of-breast-cancer-cells-through-regulation-of-mir-200c-targeting-crkl
#9
Xuehai Bian, Zhongxing Liang, Amber Feng, Eric Salgado, Hyunsuk Shim
Although histone deacetylase (HDAC) inhibitors have been shown to effectively induce the inhibition of proliferation and migration in breast cancer, the anticancer mechanism remains poorly understood. Our studies show that miR-200c was significantly downregulated in breast cancer cell lines compared to normal cell lines and inversely correlated with the levels of class IIa HDACs and CRKL. HDAC inhibitors and the ectopic expression of miR-200c as tumor suppressors inhibited the proliferation, invasion, and migration of breast cancer cells by downregulating CRKL...
November 15, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/29120463/compartmentalized-partnered-replication-for-the-directed-evolution-of-genetic-parts-and-circuits
#10
Zhanar Abil, Jared W Ellefson, Jimmy D Gollihar, Ella Watkins, Andrew D Ellington
Compartmentalized partnered replication (CPR) is an emulsion-based directed evolution method based on a robust and modular phenotype-genotype linkage. In contrast to other in vivo directed evolution approaches, CPR largely mitigates host fitness effects due to a relatively short expression time of the gene of interest. CPR is based on gene circuits in which the selection of a 'partner' function from a library leads to the production of a thermostable polymerase. After library preparation, bacteria produce partner proteins that can potentially lead to enhancement of transcription, translation, gene regulation, and other aspects of cellular metabolism that reinforce thermostable polymerase production...
December 2017: Nature Protocols
https://www.readbyqxmd.com/read/29104064/a-chemical-proteomics-approach-to-reveal-direct-protein-protein-interactions-in-living-cells
#11
Ralph E Kleiner, Lisa E Hang, Kelly R Molloy, Brian T Chait, Tarun M Kapoor
Protein-protein interactions mediate essential cellular processes, however the detection of native interactions is challenging since they are often low affinity and context dependent. Here, we develop a chemical proteomics approach in vivo CLASPI [iCLASPI] (in vivo crosslinking-assisted and stable isotope labeling by amino acids in cell culture [SILAC]-based protein identification) relying upon photo-crosslinking, amber suppression, and SILAC-based quantitative proteomics to profile context-dependent protein-protein interactions in living cells...
October 25, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/29101797/blocking-nocturnal-blue-light-for-insomnia-a-randomized-controlled-trial
#12
Ari Shechter, Elijah Wookhyun Kim, Marie-Pierre St-Onge, Andrew J Westwood
The use of light-emitting electronic devices before bedtime may contribute to or exacerbate sleep problems. Exposure to blue-wavelength light in particular from these devices may affect sleep by suppressing melatonin and causing neurophysiologic arousal. We aimed to determine if wearing amber-tinted blue light-blocking lenses before bedtime improves sleep in individuals with insomnia. Fourteen individuals (n = 8 females; age ± SD 46.6 ± 11.5 y) with insomnia symptoms wore blue light-blocking amber lenses or clear placebo lenses in lightweight wraparound frames for 2 h immediately preceding bedtime for 7 consecutive nights in a randomized crossover trial (4-wk washout)...
January 2018: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/29096043/evolving-the-n-terminal-domain-of-pyrrolysyl-trna-synthetase-for-improved-incorporation-of-noncanonical-amino-acids
#13
Vangmayee Sharma, Yu Zeng, W Wesley Wang, Yuchen Qiao, Yadagiri Kurra, Wenshe Liu
By evolving the N-terminal domain of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) that directly interacts with tRNAPyl, a mutant clone that displays improved amber suppression efficiency for the genetic incorporation of N-(tert-butoxycarbonyl)-l-lysine three-fold more than the wild type was identified. The identified mutations are R19H/H29R/T122S. Direct transfer of these mutations to two other PylRS mutants that were previously evolved for the genetic incorporation of N-acetyl- l-lysine and N-(4-azidobenzoxycarbonyl)- l-δ,ε-dehydrolysine respectively also improved the incorporation efficiency of these two noncanonical amino acids...
November 2, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29037038/conformationally-dynamic-radical-transfer-within-ribonucleotide-reductase
#14
Brandon L Greene, Alexander T Taguchi, JoAnne Stubbe, Daniel G Nocera
Ribonucleotide reductases (RNR) catalyze the reduction of nucleotides to deoxynucleotides through a mechanism involving an essential cysteine based thiyl radical. In the E. coli class 1a RNR the thiyl radical (C439(•)) is a transient species generated by radical transfer (RT) from a stable diferric-tyrosyl radical cofactor located >35 Å away across the α2:β2 subunit interface. RT is facilitated by sequential proton-coupled electron transfer (PCET) steps along a pathway of redox active amino acids (Y122β ↔ [W48β?] ↔ Y356β ↔ Y731α ↔ Y730α ↔ C439α)...
November 9, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28984438/engineering-the-genetic-code-in-cells-and-animals-biological-considerations-and-impacts
#15
Lei Wang
Expansion of the genetic code allows unnatural amino acids (Uaas) to be site-specifically incorporated into proteins in live biological systems, thus enabling novel properties selectively introduced into target proteins in vivo for basic biological studies and for engineering of novel biological functions. Orthogonal components including tRNA and aminoacyl-tRNA synthetase (aaRS) are expressed in live cells to decode a unique codon (often the amber stop codon UAG) as the desired Uaa. Initially developed in E...
November 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28983143/synthetic-biology-approach-for-the-development-of-conditionally-replicating-hiv-1-vaccine
#16
Nanxi Wang, Zhe Yuan, Wei Niu, Qingsheng Li, Jiantao Guo
While the combined antiretroviral therapy has resulted in a significant decrease in HIV-1 related morbidity and mortality, the HIV-1 pandemic has not been substantially averted. To curtail the 2.4 million new infections each year, a prophylactic HIV-1 vaccine is urgently needed. This review first summarizes four major completed clinical efficacy trials of prophylactic HIV-1 vaccine and their outcomes. Next, it discusses several other approaches that have not yet advanced to clinical efficacy trials, but provided valuable insights into vaccine design...
March 2017: Journal of Chemical Technology and Biotechnology
https://www.readbyqxmd.com/read/28978417/detection-and-treatment-of-fiebig-stage-i-hiv-1-infection-in-young-at-risk-women-in-south-africa-a-prospective-cohort-study
#17
Krista L Dong, Amber Moodley, Douglas S Kwon, Musie S Ghebremichael, Mary Dong, Nasreen Ismail, Zaza M Ndhlovu, Jenniffer M Mabuka, Daniel M Muema, Karyn Pretorius, Nina Lin, Bruce D Walker, Thumbi Ndung'u
BACKGROUND: HIV incidence among young women in sub-Saharan Africa remains high and their inclusion in vaccine and cure efforts is crucial. We aimed to establish a cohort of young women detected during Fiebig stage I acute HIV infection in whom treatment was initiated immediately after diagnosis to advance research in this high-risk group. METHODS: 945 women aged 18-23 years in KwaZulu-Natal, South Africa, who were HIV uninfected and sexually active consented to HIV-1 RNA testing twice a week and biological sampling and risk assessment every 3 months during participation in a 48-96 week life-skills and job-readiness programme...
September 29, 2017: Lancet HIV
https://www.readbyqxmd.com/read/28913971/chemical-functionalization-strategies-and-intracellular-applications-of-nanobodies
#18
Dominik Schumacher, Jonas Helma, Anselm F L Schneider, Heinrich Leonhardt, Christian Hackenberger
Nanobodies can be considered as next-generation life science tools for the recognition and modulation of antigens that are inaccessible to conventional antibodies. Due to their compact structure and high stability, nanobodies see frequent usage in basic research. Their chemical functionalization facilitates powerful diagnostic tools and opens the way towards promising therapeutic applications. In this review, central aspects of nanobody functionalization are given together with selected applications in molecular cell biology...
September 15, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28910072/mapping-the-binding-site-for-escitalopram-and-paroxetine-in-the-human-serotonin-transporter-using-genetically-encoded-photo-cross-linkers
#19
Hafsteinn Rannversson, Jacob Andersen, Benny Bang-Andersen, Kristian Strømgaard
In spite of the important role of the human serotonin transporter (hSERT) in depression treatment, the molecular details of how antidepressant drugs bind are still not completely understood, in particular those related to potential high- and low-affinity binding sites in hSERT. Here, we utilize amber codon suppression in hSERT to encode the photo-cross-linking unnatural amino acid p-azido-l-phenylalanine into the suggested high- and low-affinity binding sites. We then employ UV-induced cross-linking with azF to map the binding site of escitalopram and paroxetine, two prototypical selective serotonin reuptake inhibitors (SSRIs)...
September 26, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28866886/efficient-expression-of-glutathione-peroxidase-with-chimeric-trna-in-amber-less-escherichia-coli
#20
Zhenlin Fan, Jian Song, Tuchen Guan, Xiuxiu Lv, Jingyan Wei
The active center of selenium-containing glutathione peroxidase (GPx) is selenocysteine (Sec), which is is biosynthesized on its tRNA in organisms. The decoding of Sec depends on a specific elongation factor and a Sec Insertion Sequence (SECIS) to suppress the UGA codon. The expression of mammalian GPx is extremely difficult with traditional recombinant DNA technology. Recently, a chimeric tRNA (tRNA(UTu)) that is compatible with elongation factor Tu (EF-Tu) has made selenoprotein expression easier. In this study, human glutathione peroxidase (hGPx) was expressed in amber-less Escherichia coli C321...
September 12, 2017: ACS Synthetic Biology
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