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Amber suppression

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https://www.readbyqxmd.com/read/29683855/a-week-48-randomized-phase-3-trial-of-darunavir-cobicistat-emtricitabine-tenofovir-alafenamide-in-treatment-na%C3%A3-ve-hiv-1-patients
#1
Joseph J Eron, Chloe Orkin, Joel Gallant, Jean-Michel Molina, Eugenia Negredo, Andrea Antinori, Anthony Mills, Jacques Reynes, Erika Van Landuyt, Erkki Lathouwers, Veerle Hufkens, John Jezorwski, Simon Vanveggel, Magda Opsomer
OBJECTIVES: To investigate efficacy and safety of a single-tablet regimen of darunavir/cobicistat/emtricitabine/tenofovir alafenamide (D/C/F/TAF) 800/150/200/10 mg vs. darunavir/cobicistat plus emtricitabine/tenofovir disoproxyl fumarate (TDF) (control) in antiretroviral-treatment-naïve, HIV-1-infected adults. DESIGN: Phase-3, randomized, active-controlled, double-blind, international, multicenter, noninferiority study (NCT02431247). METHODS: Seven hundred and twenty-five participants were randomized (1 : 1) to D/C/F/TAF (362) or control (363)...
April 19, 2018: AIDS
https://www.readbyqxmd.com/read/29683449/optimizing-the-genetic-incorporation-of-chemical-probes-into-gpcrs-for-photo-crosslinking-mapping-and-bioorthogonal-chemistry-in-live-mammalian-cells
#2
Robert Serfling, Lisa Seidel, Thore Böttke, Irene Coin
The genetic incorporation of non-canonical amino acids (ncAAs) via amber stop codon suppression is a powerful technique to install artificial probes and reactive moieties onto proteins directly in the live cell. Each ncAA is incorporated by a dedicated orthogonal suppressor-tRNA/amino-acyl-tRNA-synthetase (AARS) pair that is imported into the host organism. The incorporation efficiency of different ncAAs can greatly differ, and be unsatisfactory in some cases. Orthogonal pairs can be improved by manipulating either the AARS or the tRNA...
April 9, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29620688/effects-of-branched-chain-amino-acid-supplementation-on-spontaneous-seizures-and-neuronal-viability-in-a-model-of-mesial-temporal-lobe-epilepsy
#3
Shaun E Gruenbaum, Roni Dhaher, Amedeo Rapuano, Hitten P Zaveri, Amber Tang, Nihal de Lanerolle, Tore Eid
BACKGROUND: The essential branched-chain amino acids (BCAAs) leucine, isoleucine, and valine have recently emerged as a potential novel treatment for medically refractory epilepsy. Blood-derived BCAAs can readily enter the brain, where they contribute to glutamate biosynthesis and may either suppress or trigger acute seizures. However, the effects of BCAAs on chronic (ie, spontaneous recurrent) seizures and epilepsy-associated neuron loss are incompletely understood. MATERIALS AND METHODS: Sixteen rats with mesial temporal lobe epilepsy were randomized into 2 groups that could drink, ad libitum, either a 4% solution of BCAAs in water (n=8) or pure water (n=8)...
April 3, 2018: Journal of Neurosurgical Anesthesiology
https://www.readbyqxmd.com/read/29615516/mutant-and-wild-type-p53-form-complexes-with-p73-upon-phosphorylation-by-the-kinase-jnk
#4
Eric R Wolf, Ciarán P McAtarsney, Kristin E Bredhold, Amber M Kline, Lindsey D Mayo
The transcription factors p53 and p73 are critical to the induction of apoptotic cell death, particularly in response to cell stress that activates c-Jun N-terminal kinase (JNK). Mutations in the DNA-binding domain of p53, which are commonly seen in cancers, result in conformational changes that enable p53 to interact with and inhibit p73, thereby suppressing apoptosis. In contrast, wild-type p53 reportedly does not interact with p73. We found that JNK-mediated phosphorylation of Thr81 in the proline-rich domain (PRD) of p53 enabled wild-type p53, as well as mutant p53, to form a complex with p73...
April 3, 2018: Science Signaling
https://www.readbyqxmd.com/read/29610342/transcriptional-mutagenesis-mediated-by-8-oxog-induces-translational-errors-in-mammalian-cells
#5
Da-Peng Dai, Wei Gan, Hiroshi Hayakawa, Jia-Lou Zhu, Xiu-Qing Zhang, Guo-Xin Hu, Tao Xu, Zhe-Li Jiang, Li-Qun Zhang, Xue-Da Hu, Ben Nie, Yue Zhou, Jin Li, Xiao-Yang Zhou, Jian Li, Tie-Mei Zhang, Qing He, Dong-Ge Liu, Hai-Bo Chen, Nan Yang, Ping-Ping Zuo, Zhi-Xin Zhang, Huan-Ming Yang, Yao Wang, Samuel H Wilson, Yi-Xin Zeng, Jian-Ye Wang, Mutsuo Sekiguchi, Jian-Ping Cai
Reactive oxygen species formed within the mammalian cell can produce 8-oxo-7,8-dihydroguanine (8-oxoG) in mRNA, which can cause base mispairing during gene expression. Here we found that administration of 8-oxoGTP in MTH1-knockdown cells results in increased 8-oxoG content in mRNA. Under this condition, an amber mutation of the reporter luciferase is suppressed. Using second-generation sequencing techniques, we found that U-to-G changes at preassigned sites of the luciferase transcript increased when 8-oxoGTP was supplied...
April 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29603062/peripheral-blood-cell-interactions-of-cancer-derived-exosomes-affect-immune-function
#6
Heather R Ferguson Bennit, Amber Gonda, James R W McMullen, Janviere Kabagwira, Nathan R Wall
Cancer-derived exosomes are constitutively produced and secreted into the blood and biofluids of their host patients providing a liquid biopsy for early detection and diagnosis. Given their ubiquitous nature, cancer exosomes influence biological mechanisms that are beneficial to the tumor cells where they are produced and the microenvironment in which these tumors exist. Accumulating evidence suggests that exosomes transport proteins, lipids, DNA, mRNA, miRNA and long non coding RNA (lncRNA) for the purpose of cell-cell and cell-extracellular communication...
March 30, 2018: Cancer Microenvironment: Official Journal of the International Cancer Microenvironment Society
https://www.readbyqxmd.com/read/29570993/a-neural-circuit-for-the-suppression-of-pain-by-a-competing-need-state
#7
Amber L Alhadeff, Zhenwei Su, Elen Hernandez, Michelle L Klima, Sophie Z Phillips, Ruby A Holland, Caiying Guo, Adam W Hantman, Bart C De Jonghe, J Nicholas Betley
Hunger and pain are two competing signals that individuals must resolve to ensure survival. However, the neural processes that prioritize conflicting survival needs are poorly understood. We discovered that hunger attenuates behavioral responses and affective properties of inflammatory pain without altering acute nociceptive responses. This effect is centrally controlled, as activity in hunger-sensitive agouti-related protein (AgRP)-expressing neurons abrogates inflammatory pain. Systematic analysis of AgRP projection subpopulations revealed that the neural processing of hunger and inflammatory pain converge in the hindbrain parabrachial nucleus (PBN)...
March 22, 2018: Cell
https://www.readbyqxmd.com/read/29565959/identifying-levorphanol-ingestion-using-urine-biomarkers-in-health-care-patients
#8
Amber R Watson, Ali Roberts
BACKGROUND: Levorphanol is a long-acting opioid analgesic that is an optical isomer of dextrorphan, a metabolite of the over-the-counter cough suppressant dextromethorphan. Providers prescribing levorphanol for pain management may need to assess compliance through urine drug testing, as this agent is subject to abuse. Therefore, it is important to differentiate between dextromethorphan and levorphanol ingestion. OBJECTIVES: This article is the first to report urine concentrations of levorphanol/dextrorphan and 3-hydroxymorphinan in human urine and assesses the need for an enantiomeric analysis to distinguish between dextromethorphan and levorphanol ingestion...
March 2018: Pain Physician
https://www.readbyqxmd.com/read/29529500/anti-inflammatory-hybrids-of-secondary-amines-and-amide-sulfamide-derivatives
#9
Renren Bai, Jian Sun, Zhongxing Liang, Younghyoun Yoon, Eric Salgado, Amber Feng, Yoonhyeun Oum, Yuanyuan Xie, Hyunsuk Shim
The CXCR4/CXCL12 chemokine axis can chemotactically accumulate inflammatory cells to local tissues and regulate the release of inflammatory factors. Developing novel CXCR4 modulators may provide a desirable strategy to control the development of inflammation. A series of novel hybrids were designed by integrating the key pharmacophores of three CXCR4 modulators. The majority of compounds displayed potent CXCR4 binding affinity. Compound 7a exhibited 1000-fold greater affinity than AMD3100 and significantly inhibited invasion of CXCR4-positive tumor cells...
March 2, 2018: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29528852/fixed-dose-darunavir-boosted-with-cobicistat-combined-with-emtricitabine-and-tenofovir-alafenamide-fumarate
#10
Muge Cevik, Chloe Orkin
PURPOSE OF REVIEW: In an era when virological efficacy approaches 100%, novel antiretroviral (ARV) therapies must deliver better tolerability, safety, and convenient coformulated regimens. We review the phase II and III clinical data on the fixed dose combination (FDC) darunavir (DRV) 800mg / cobicistat (COBI/C) 150 mg / emtricitabine (F/FTC) 200 mg / tenofovir alafenamide fumarate (TAF) 10mg (D/C/F/TAF) for the treatment of HIV-1 infection. RECENT FINDINGS: In an exploratory phase II study, D/C/F/TAF FDC demonstrated similar virological efficacy to darunavir/cobicistat FDC + F /tenofovir disoproxil fumarate (TDF) FDC in treatment-naive HIV-1-infected individuals with favorable bone and renal outcomes...
March 9, 2018: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/29517978/trap-seq-identifies-cystine-glutamate-antiporter-as-a-driver-of-recovery-from-liver-injury
#11
Amber W Wang, Kirk J Wangensteen, Yue J Wang, Adam M Zahm, Nicholas G Moss, Noam Erez, Klaus H Kaestner
Understanding the molecular basis of the regenerative response following hepatic injury holds promise for improved treatments of liver diseases. Here, we report an innovative method to profile gene expression specifically in the hepatocytes that regenerate the liver following toxic injury. We utilize the Fah-/- mouse, a model of hereditary tyrosinemia, which conditionally undergoes severe liver injury unless fumarylacetoacetate hydrolase (FAH) expression is reconstituted ectopically. We employ translating ribosome affinity purification followed by high-throughput RNA sequencing (TRAP-seq) to isolate mRNAs specific to repopulating hepatocytes...
March 8, 2018: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29501556/assessing-the-aversive-nature-of-pain-with-an-operant-approach-avoidance-paradigm
#12
Celina A Salcido, Amber L Harris Bozer, Christopher T McNabb, Perry N Fuchs
Preclinical pain assessments can be criticized for failing to adequately characterize the human clinical pain experience. Although recent assessments have improved upon this shortcoming, there are still significant limitations. One concern is that current procedures fail to examine underlying motivational drives related to pain. Therefore, we used a novel approach-avoidance paradigm that allowed a rat to either satisfy hunger or avoid noxious stimulation to reveal prioritizing of motivational drives. The operant paradigm utilized a single lever that the animal pressed for appetitive reward (approach)...
February 28, 2018: Physiology & Behavior
https://www.readbyqxmd.com/read/29456806/women-with-hereditary-breast-cancer-predispositions-should-avoid-using-their-smartphones-tablets-and-laptops-at-night
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
Jennifer M Binning, Amber M Smith, Judd F Hultquist, Charles S Craik, Nathalie Caretta Cartozo, 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 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29233219/a-molecular-engineering-toolbox-for-the-structural-biologist
#20
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
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