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Amber suppression

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https://www.readbyqxmd.com/read/27919800/increasing-the-fidelity-of-noncanonical-amino-acid-incorporation-in-cell-free-protein-synthesis
#1
Qinglei Gan, Chenguang Fan
BACKGROUND: Cell-free protein synthesis provides a robust platform for co-translational incorporation of noncanonical amino acid (ncAA) into proteins to facilitate biological studies and biotechnological applications. Recently, eliminating the activity of release factor 1 has been shown to increase ncAA incorporation in response to amber codons. However, this approach could promote mis-incorporation of canonical amino acids by near cognate suppression. METHODS: We performed a facile protocol to remove near cognate tRNA isoacceptors of the amber codon from total tRNAs, and used the phosphoserine (Sep) incorporation system as validation...
December 2, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27914361/development-of-cxcr4-modulators-by-virtual-hts-of-a-novel-amide-sulfamide-compound-library
#2
Renren Bai, Qi Shi, Zhongxing Liang, Younghyoun Yoon, Yiran Han, Amber Feng, Shuangping Liu, Yoonhyeun Oum, C Chris Yun, Hyunsuk Shim
CXCR4 plays a crucial role in recruitment of inflammatory cells to inflammation sites at the beginning of the disease process. Modulating CXCR4 functions presents a new avenue for anti-inflammatory strategies. However, using CXCR4 antagonists for a long term usage presents potential serious side effect due to their stem cell mobilizing property. We have been developing partial CXCR4 antagonists without such property. A new computer-aided drug design program, the FRESH workflow, was used for anti-CXCR4 lead compound discovery and optimization, which coupled both compound library building and CXCR4 docking screens in one campaign...
November 24, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27910233/a-genetically-encoded-allysine-for-the-synthesis-of-proteins-with-site-specific-lysine-dimethylation
#3
Zhipeng A Wang, Yu Zeng, Yadagiri Kurra, Xin Wang, Jeffery M Tharp, Erol C Vatansever, Willie W Hsu, Susie Dai, Xinqiang Fang, Wenshe R Liu
Using the amber suppression approach, N(ϵ) -(4-azidobenzoxycarbonyl)-δ,ϵ-dehydrolysine, an allysine precursor is genetically encoded in E. coli. Its genetic incorporation followed by two sequential biocompatible reactions allows convenient synthesis of proteins with site-specific lysine dimethylation. Using this approach, dimethyl-histone H3 and p53 proteins have been synthesized and used to probe functions of epigenetic enzymes including histone demethylase LSD1 and histone acetyltransferase Tip60. We confirmed that LSD1 is catalytically active toward H3K4me2 and H3K9me2 but inert toward H3K36me2, and methylation at p53 K372 directly activates Tip60 for its catalyzed acetylation at p53 K120...
December 2, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27903651/t-cells-encountering-myeloid-cells-programmed-for-amino-acid-dependent-immunosuppression-use-rictor-mtorc2-for-proliferative-checkpoint-decisions
#4
Lee-Ann Van de Velde, Chitra Subramanian, Amber M Smith, Luke Barron, Joseph E Qualls, Geoffrey Neale, Adolfo Alfonso-Pecchio, Suzanne Jackowski, Charles O Rock, Thomas A Wynn, Peter J Murray
Modulation of T cell proliferation and function by immunoregulatory myeloid cells is an essential means of preventing self-reactivity and restoring tissue homeostasis. Consumption of amino acids such as arginine and tryptophan by immunoregulatory macrophages is one pathway that suppresses local T cell proliferation. Using a reduced complexity in vitro macrophage: T cell co-culture system, we show that macrophage Arginase-1 (Arg1) is the only factor required by M2 macrophages to block T cells in G1, and this effect is mediated by L-arginine elimination rather than metabolite generation...
November 30, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27853654/tumor-necrosis-factor-links-chronic-obstructive-pulmonary-disease-and-k-ras-mutant-lung-cancer-through-induction-of-an-immunosuppressive-pro-tumor-microenvironment
#5
Lei Gong, Mauricio da Silva Caetano, Amber M Cumpian, Soudabeh Daliri, Alejandra Garza Flores, Seon Hee Chang, Cesar E Ochoa, Christopher M Evans, Zhentao Yu, Seyed Javad Moghaddam
Tumor necrosis factor (TNF) is known as an important regulator of tumor microenvironment and inflammation. TNF levels are markedly elevated in the bronchoalveolar lavage fluid (BALF) of patients with chronic obstructive pulmonary disease (COPD), which is an independent risk factor for lung cancer. We have previously shown that COPD-like airway inflammation promotes lung cancer in a K-ras mutant mouse model (CC-LR mouse). This was associated with a significant increase of neutrophils in BALF, accompanied by a marked increase in TNF level, suggesting a link between COPD, TNF, and lung cancer promotion...
2016: Oncoimmunology
https://www.readbyqxmd.com/read/27826734/motivations-and-barriers-to-treatment-uptake-and-adherence-among-people-living-with-hiv-in-australia-a-mixed-methods-systematic-review
#6
REVIEW
Amary Mey, David Plummer, Shailendra Dukie, Gary D Rogers, Maree O'Sullivan, Amber Domberelli
In Australia, approximately 30% of people diagnosed with HIV are not accessing treatment and 8% of those receiving treatment fail to achieve viral suppression. Barriers limiting effective care warrant further examination. This mixed-methods systematic review accessed health and social sector research databases between November and December 2015 to identify studies that explored the perspective of people living with HIV in Australia. Articles were included for analysis if they described the experiences, knowledge, attitudes and beliefs, in relation to treatment uptake and adherence, published between January 2000 and December 2015...
November 8, 2016: AIDS and Behavior
https://www.readbyqxmd.com/read/27769055/progesterone-potentiates-the-growth-inhibitory-effects-of-calcitriol-in-endometrial-cancer-via-suppression-of-cyp24a1
#7
Amber A Bokhari, Laura R Lee, Dewayne Raboteau, Jane Turbov, Isabel V Rodriguez, J Wesley Pike, Chad A Hamilton, G Larry Maxwell, Gustavo C Rodriguez, Viqar Syed
Here, we evaluated the expression of CYP24A1, a protein that inactivates vitamin D in tissues. CYP24A1 expression was increased in advanced-stage endometrial tumors compared to normal tissues. Similarly, endometrial cancer cells expressed higher levels of CYP24A1 than immortalized endometrial epithelial cells. RT-PCR and Western blotting were used to examine CYP24A1 mRNA and protein levels in endometrial cancer cells after 8, 24, 72, and 120 h of exposure to progesterone, progestin derivatives and calcitriol, either alone or in combination...
October 18, 2016: Oncotarget
https://www.readbyqxmd.com/read/27760338/metabolic-reprogramming-mediated-by-the-mtorc2-irf4-signaling-axis-is-essential-for-macrophage-alternative-activation
#8
Stanley Ching-Cheng Huang, Amber M Smith, Bart Everts, Marco Colonna, Erika L Pearce, Joel D Schilling, Edward J Pearce
Macrophage activation status is intrinsically linked to metabolic remodeling. Macrophages stimulated by interleukin 4 (IL-4) to become alternatively (or, M2) activated increase fatty acid oxidation and oxidative phosphorylation; these metabolic changes are critical for M2 activation. Enhanced glucose utilization is also characteristic of the M2 metabolic signature. Here, we found that increased glucose utilization is essential for M2 activation. Increased glucose metabolism in IL-4-stimulated macrophages required the activation of the mTORC2 pathway, and loss of mTORC2 in macrophages suppressed tumor growth and decreased immunity to a parasitic nematode...
October 18, 2016: Immunity
https://www.readbyqxmd.com/read/27750015/enhancement-of-image-contrast-stability-and-saldi-ms-detection-sensitivity-for-latent-fingerprint-analysis-by-tuning-the-composition-of-silver-gold-nanoalloys
#9
Yu-Hong Cheng, Yue Zhang, Siu-Leung Chau, Samuel Kin-Man Lai, Ho-Wai Tang, Kwan-Ming Ng
Metal alloy nanoparticles (NPs) offer a new combination of unique physicochemical properties based on their pure counterparts, which can facilitate the development of novel analytical methods. Here, we demonstrated that Ag-Au alloy NPs could be utilized for optical and mass spectrometric imaging of latent fingerprints (LFPs) with improved image contrast, stability, and detection sensitivity. Upon deposition of Ag-Au alloy NPs (Ag:Au = 60:40% wt), ridge regions of the LFP became amber-coloured, while the groove regions appeared purple-blue...
October 17, 2016: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/27685000/multiscale-simulations-on-spectral-tuning-and-the-photoisomerization-mechanism-in-fluorescent-rna-spinach
#10
Xin Li, Lung Wa Chung, Guohui Li
Fluorescent RNA aptamer Spinach can bind and activate a green fluorescent protein (GFP)-like chromophore (an anionic DFHBDI chromophore) displaying green fluorescence. Spectroscopic properties, spectral tuning, and the photoisomerization mechanism in the Spinach-DFHBDI complex have been investigated by high-level QM and hybrid ONIOM(QM:AMBER) methods (QM method: (TD)DFT, SF-BHHLYP, SAC-CI, LT-DF-LCC2, CASSCF, or MS-CASPT2), as well as classical molecular dynamics (MD) simulations. First, our benchmark calculations have shown that TD-DFT and spin-flip (SF) TD-DFT (SF-BHHLYP) failed to give a satisfactory description of absorption and emission of the anionic DFHBDI chromophore...
October 14, 2016: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/27648860/identification-and-characterization-of-a-novel-nanobody-against-human-placental-growth-factor-to-modulate-angiogenesis
#11
Roghaye Arezumand, Reza Mahdian, Sirous Zeinali, Gholamreza Hassanzadeh-Ghassabeh, Kamran Mansouri, Hossein Khanahmad, Nabiollah Namvar-Asl, Hamzeh Rahimi, Mahdi Behdani, Reza Ahangari Cohan, Mehdi Eavazalipour, Ali Ramazani, Serge Muyldermans
Placental growth factor (PlGF), a member of vascular endothelial growth factors (VEGF) family, is considered as an important antigen associated with pathological conditions such as cancer cell growth, and metastasis. PlGF-targeting via nanobody (Nb) therefore could be beneficial to modulate these pathologies. In this work, phage-display and computational approach was employed to develop a high affinity PlGF-specific Nb. An Nb library was constructed against human recombinant PlGF (rPlGF). After panning on immobilized rPlGF the periplasmic-extract (PE) of individual colonies were screened by ELISA (PE-ELISA)...
October 2016: Molecular Immunology
https://www.readbyqxmd.com/read/27643646/metformin-increases-e-cadherin-in-tumors-of-diabetic-patients-with-endometrial-cancer-and-suppresses-epithelial-mesenchymal-transition-in-endometrial-cancer-cell-lines
#12
Ido Laskov, Paul Abou-Nader, Oreekha Amin, Charles-Andre Philip, Marie-Claude Beauchamp, Amber Yasmeen, Walter H Gotlieb
PURPOSE: Epithelial-mesenchymal transition (EMT) is a critical process for cancer metastasis and recurrence. Metformin, an effective oral antidiabetic drug, has been associated with decreased cancer risk and mortality. In this pilot study, we started to evaluate the effect of metformin on EMT in vivo and in vitro in endometrial cancer (EC). METHODS: Endometrial cancer cell lines and freshly isolated EC tumor specimens were used to assess EMT after metformin treatment...
September 2016: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/27626172/nestin-suppression-attenuates-invasive-potential-of-endometrial-cancer-cells-by-downregulating-tgf-%C3%AE-signaling-pathway
#13
Amber A Bokhari, Tabari M Baker, Batsukh Dorjbal, Sana Waheed, Christopher M Zahn, Chad A Hamilton, G Larry Maxwell, Viqar Syed
Nestin, an intermediate filament protein and a stem cell marker is expressed in several tumors. Until recently, little was known about the expression levels and the role of Nestin in endometrial cancer. Compared to the immortalized endometrial epithelial cell line EM-E6/E7-TERT, endometrial cancer cell lines express high to moderate levels of Nestin. Furthermore, endometrial tumors and tumor cell lines have a cancer stem-like cell subpopulation expressing CD133. Among the cancer lines, AN3CA and KLE cells exhibited both a significantly higher number of CD133+ cells and expressed Nestin at higher levels than Ishikawa cells...
September 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/27611942/oncogenic-activation-of-fak-drives-apoptosis-suppression-in-a-3d-culture-model-of-breast-cancer-initiation
#14
Scott Walker, Fiona Foster, Amber Wood, Thomas Owens, Keith Brennan, Charles H Streuli, Andrew P Gilmore
A key hallmark of cancer cells is the loss of positional control over growth and survival. Focal adhesion kinase (FAK) is a tyrosine kinase localised at sites of integrin-mediated cell adhesion to the extracellular matrix. FAK controls a number of adhesion-dependent cellular functions, including migration, proliferation and survival. Although FAK is overexpressed and activated in metastatic tumours, where it promotes invasion, it can also be elevated in cancers that have yet to become invasive. The contribution of FAK to the early stages of tumourigenesis is not known...
September 6, 2016: Oncotarget
https://www.readbyqxmd.com/read/27600875/evolving-orthogonal-suppressor-trnas-to-incorporate-modified-amino-acids
#15
Andre Maranhao, Andrew D Ellington
There have been considerable advancements in the incorporation of non-canonical amino acids (ncAA) into proteins over the last two decades. The most widely used method for site-specific incorporation of non-canonical amino acids, amber stop codon suppression, typically employs an orthogonal translation system (OTS) consisting of a heterologous aminoacyl-tRNA synthetase:tRNA pair that can potentially expand an organism's genetic code. However, the orthogonal machinery sometimes imposes fitness costs on an organism, in part due to mischarging and a lack of specificity...
September 7, 2016: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27545569/a-critical-test-of-the-electrostatic-contribution-to-catalysis-with-noncanonical-amino-acids-in-ketosteroid-isomerase
#16
Yufan Wu, Steven G Boxer
The vibrational Stark effect (VSE) has been used to measure the electric field in the active site of ketosteroid isomerase (KSI). These measured fields correlate with ΔG(⧧) in a series of conventional mutants, yielding an estimate for the electrostatic contribution to catalysis (Fried et al. Science 2014, 346, 1510-1513). In this work we test this result with much more conservative variants in which individual Tyr residues in the active site are replaced by 3-chlorotyrosine via amber suppression. The electric fields sensed at the position of the carbonyl bond involved in charge displacement during catalysis were characterized using the VSE, where the field sensitivity has been calibrated by vibrational Stark spectroscopy, solvatochromism, and MD simulations...
September 14, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27535706/melatonin-represses-metastasis-in-her2-postive-human-breast-cancer-cells-by-suppressing-rsk2-expression
#17
Lulu Mao, Whitney Summers, Shulin Xiang, Lin Yuan, Robert T Dauchy, Amberly Reynolds, Melissa A Wren-Dail, David Pointer, Tripp Frasch, David E Blask, Steven M Hill
: The importance of the circadian/melatonin signal in suppressing the metastatic progression of breast and other cancers has been reported by numerous laboratories including our own. Currently, the mechanisms underlying the antimetastatic actions of melatonin have not been well established. In the present study, the antimetastatic actions of melatonin were evaluated and compared on the ERα-negative, Her2-positive SKBR-3 breast tumor cell line and ERα-positive MCF-7 cells overexpressing a constitutively active HER2...
November 2016: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/27472361/the-effect-of-casein-protein-prior-to-sleep-on-fat-metabolism-in-obese-men
#18
Amber W Kinsey, Stacy R Cappadona, Lynn B Panton, Brittany R Allman, Robert J Contreras, Robert C Hickner, Michael J Ormsbee
We have previously shown that ingesting protein at night before sleep is either beneficial or non-detrimental to metabolism, health, and body composition in obese women. However, the overnight protein-induced lipolytic actions and mechanism for improved metabolism and body composition have not been fully established. Therefore, in a crossover design, twelve obese men (age, 27.0 ± 2.2 years) were randomly assigned to ingest (within 30 min of sleep) casein protein (CAS, 120 kcal) or a non-nutritive placebo (PLA) before going to sleep...
July 27, 2016: Nutrients
https://www.readbyqxmd.com/read/27456041/high-yield-cell-free-synthesis-of-human-egfr-by-ires-mediated-protein-translation-in-a-continuous-exchange-cell-free-reaction-format
#19
Robert B Quast, Andrei Sonnabend, Marlitt Stech, Doreen A Wüstenhagen, Stefan Kubick
Cell-free protein synthesis systems derived from eukaryotic sources often provide comparatively low amounts of several μg per ml of de novo synthesized membrane protein. In order to overcome this, we herein demonstrate the high-yield cell-free synthesis of the human EGFR in a microsome-containing system derived from cultured Sf21 cells. Yields were increased more than 100-fold to more than 285 μg/ml by combination of IRES-mediated protein translation with a continuous exchange cell-free reaction format that allowed for prolonged reaction lifetimes exceeding 24 hours...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27445154/diverse-functions-of-retinoic-acid-in-brain-vascular-development
#20
Stephanie Bonney, Susan Harrison-Uy, Swati Mishra, Amber M MacPherson, Youngshik Choe, Dan Li, Shou-Ching Jaminet, Marcus Fruttiger, Samuel J Pleasure, Julie A Siegenthaler
UNLABELLED: As neural structures grow in size and increase metabolic demand, the CNS vasculature undergoes extensive growth, remodeling, and maturation. Signals from neural tissue act on endothelial cells to stimulate blood vessel ingression, vessel patterning, and acquisition of mature brain vascular traits, most notably the blood-brain barrier. Using mouse genetic and in vitro approaches, we identified retinoic acid (RA) as an important regulator of brain vascular development via non-cell-autonomous and cell-autonomous regulation of endothelial WNT signaling...
July 20, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
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