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Amber suppression

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https://www.readbyqxmd.com/read/29155146/hdac-inhibitor-suppresses-proliferation-and-invasion-of-breast-cancer-cells-through-regulation-of-mir-200c-targeting-crkl
#1
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
#2
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
#3
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
#4
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)...
October 21, 2017: 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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28817804/structural-mechanism-for-modulation-of-synaptic-neuroligin-neurexin-signaling-by-mdga-proteins
#13
Jonathan Elegheert, Vedrana Cvetkovska, Amber J Clayton, Christina Heroven, Kristel M Vennekens, Samuel N Smukowski, Michael C Regan, Wanyi Jia, Alexandra C Smith, Hiro Furukawa, Jeffrey N Savas, Joris de Wit, Jo Begbie, Ann Marie Craig, A Radu Aricescu
Neuroligin-neurexin (NL-NRX) complexes are fundamental synaptic organizers in the central nervous system. An accurate spatial and temporal control of NL-NRX signaling is crucial to balance excitatory and inhibitory neurotransmission, and perturbations are linked with neurodevelopmental and psychiatric disorders. MDGA proteins bind NLs and control their function and interaction with NRXs via unknown mechanisms. Here, we report crystal structures of MDGA1, the NL1-MDGA1 complex, and a spliced NL1 isoform. Two large, multi-domain MDGA molecules fold into rigid triangular structures, cradling a dimeric NL to prevent NRX binding...
August 16, 2017: Neuron
https://www.readbyqxmd.com/read/28758366/pyrrolysine-amber-stop-codon-suppression-development-and-applications
#14
REVIEW
Robin Brabham, Martin A Fascione
The pyrrolysine tRNA synthetase-tRNA pair is probably one of the most promiscuous tRNA-synthetase pairs found in nature, capable of genetically encoding a plethora of noncanonical amino acids through stop codon reassignment. Proteins containing reactive handles, post-translational modification mimics or both can be produced in practical quantities, allowing inter alia the probing of biological pathways, generating antibody-drug conjugates and enhancing protein function. This Minireview summarises the development of pyrrolysine amber stop-codon suppression, presents some of the considerations required to utilise this technique to its greatest potential, and showcases the creative ways in which this technique has led to a better understanding of biological systems...
October 18, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28714866/ibrutinib-treatment-improves-t-cell-number-and-function-in-cll-patients
#15
MULTICENTER STUDY
Meixiao Long, Kyle Beckwith, Priscilla Do, Bethany L Mundy, Amber Gordon, Amy M Lehman, Kami J Maddocks, Carolyn Cheney, Jeffrey A Jones, Joseph M Flynn, Leslie A Andritsos, Farrukh Awan, Joseph A Fraietta, Carl H June, Marcela V Maus, Jennifer A Woyach, Michael A Caligiuri, Amy J Johnson, Natarajan Muthusamy, John C Byrd
BACKGROUND: Ibrutinib has been shown to have immunomodulatory effects by inhibiting Bruton's tyrosine kinase (BTK) and IL-2-inducible T cell kinase (ITK). The relative importance of inhibiting these 2 kinases has not been examined despite its relevance to immune-based therapies. METHODS: Peripheral blood mononuclear cells from chronic lymphocytic leukemia (CLL) patients on clinical trials of ibrutinib (BTK/ITK inhibitor; n = 19) or acalabrutinib (selective BTK inhibitor; n = 13) were collected serially...
August 1, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28611040/%C3%AE-catenin-is-a-candidate-therapeutic-target-for-myeloid-neoplasms-with-del-5q
#16
Liping Li, Yue Sheng, Wenshu Li, Chao Hu, Nupur Mittal, Kaoru Tohyama, Amber Seba, You-Yang Zhao, Howard Ozer, Tongyu Zhu, Zhijian Qian
Deletion of the chromosome 5q [del(5q)] is one of the most common cytogenetic abnormalities observed in patients with de novo myelodysplastic syndromes (MDS) and therapy-related MDS or acute myeloid leukemia (t-MDS/tAML). Emerging evidence indicates that activation of the Wnt/β-catenin pathway contributes to the development of myeloid neoplasms with del(5q). Whether β-catenin is a potential therapeutic target for myeloid neoplasms with del(5q) has yet to be evaluated. Here, we report that genetic deletion of a single allele of β-catenin rescues ineffective hematopoiesis in an Apc haploinsufficient mouse model, which recapitulates several characteristic features of the preleukemic stage of myeloid neoplasms with a -5/del(5q)...
August 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/28596531/rf1-attenuation-enables-efficient-non-natural-amino-acid-incorporation-for-production-of-homogeneous-antibody-drug-conjugates
#17
Gang Yin, Heather T Stephenson, Junhao Yang, Xiaofan Li, Stephanie M Armstrong, Tyler H Heibeck, Cuong Tran, Mary Rose Masikat, Sihong Zhou, Ryan L Stafford, Alice Y Yam, John Lee, Alexander R Steiner, Avinash Gill, Kalyani Penta, Sonia Pollitt, Ramesh Baliga, Christopher J Murray, Christopher D Thanos, Leslie M McEvoy, Aaron K Sato, Trevor J Hallam
Amber codon suppression for the insertion of non-natural amino acids (nnAAs) is limited by competition with release factor 1 (RF1). Here we describe the genome engineering of a RF1 mutant strain that enhances suppression efficiency during cell-free protein synthesis, without significantly impacting cell growth during biomass production. Specifically, an out membrane protease (OmpT) cleavage site was engineered into the switch loop of RF1, which enables its conditional inactivation during cell lysis. This facilitates extract production without additional processing steps, resulting in a scaleable extract production process...
June 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28594177/a-versatile-toolbox-for-the-control-of-protein-levels-using-n-%C3%AE%C2%B5-acetyl-l-lysine-dependent-amber-suppression
#18
Wolfram Volkwein, Christopher Maier, Ralph Krafczyk, Kirsten Jung, Jürgen Lassak
The analysis of the function of essential genes in vivo depends on the ability to experimentally modulate levels of their protein products. Current methods to address this are based on transcriptional or post-transcriptional regulation of mRNAs, but approaches based on the exploitation of translation regulation have so far been neglected. Here we describe a toolbox, based on amber suppression in the presence of N(ε)-acetyl-l-lysine (AcK), for translational tuning of protein output. We chose the highly sensitive luminescence system LuxCDABE as a reporter and incorporated a UAG stop codon into the gene for the reductase subunit LuxC...
June 27, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28584229/circadian-tunable-perovskite-quantum-dot-based-down-converted-multi-package-white-led-with-a-color-fidelity-index-over-90
#19
Hee Chang Yoon, Ji Hye Oh, Soyoung Lee, Jae Byung Park, Young Rag Do
New metrics of the color and circadian performances of down-converted white light-emitting diodes (DC-WLEDs) are rapidly becoming popular in smart lighting systems. This is due to the increased desire for accurate analytical methods to measure the effects of newly developed quantum dot (QD)-based lighting on the vision, color, and circadian sensors of retina cells in the human eye. In this regard, a two-measure system known as technical memorandum TM-30-2015 (Illuminating Engineering Society of North America), encompassing the color fidelity index (CFI, R f ) and the color gamut index (CGI, R g ), has been developed as a new metrics of color to replace the currently utilized color rendering index (CRI, R a )...
June 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28468969/protein-kinase-ck2-controls-the-fate-between-th17-cell-and-regulatory-t-cell-differentiation
#20
Sara A Gibson, Wei Yang, Zhaoqi Yan, Yudong Liu, Amber L Rowse, Amy S Weinmann, Hongwei Qin, Etty N Benveniste
CK2 is a highly conserved and pleiotropic serine/threonine kinase that promotes many prosurvival and proinflammatory signaling pathways, including PI3K/Akt/mTOR and JAK/STAT. These pathways are essential for CD4(+) T cell activation and polarization, but little is known about how CK2 functions in T cells. In this article, we demonstrate that CK2 expression and kinase activity are induced upon CD4(+) T cell activation. Targeting the catalytic activity of CK2 using the next-generation small molecule inhibitor CX-4945 in vitro significantly and specifically inhibited mouse and human Th17 cell differentiation while promoting the generation of Foxp3(+) regulatory T cells (Tregs)...
June 1, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
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