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Amber suppression

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https://www.readbyqxmd.com/read/28611040/%C3%AE-catenin-is-a-candidate-therapeutic-target-for-myeloid-neoplasms-with-del-5q
#1
Liping Li, Yue Sheng, Wenshu Li, Chao Hu, Nupur Mittal, Kaoru Tohyama, Amber Seba, Youyang 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 pre-leukemic stage of myeloid neoplasms with a -5/del(5q)...
June 13, 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
#2
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
#3
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 translational regulation have so far been neglected. Here we describe a toolbox, based on amber suppression in the presence of Nε-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 8, 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
#4
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
#5
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
https://www.readbyqxmd.com/read/28422494/genetically-encoded-2-aryl-5-carboxytetrazoles-for-site-selective-protein-photo-cross-linking
#6
Yulin Tian, Marco Paolo Jacinto, Yu Zeng, Zhipeng Yu, Jun Qu, Wenshe R Liu, Qing Lin
The genetically encoded photo-cross-linkers promise to offer a temporally controlled tool to map transient and dynamic protein-protein interaction complexes in living cells. Here we report the synthesis of a panel of 2-aryl-5-carboxytetrazole-lysine analogs (ACTKs) and their site-specific incorporation into proteins via amber codon suppression in Escherichia coli and mammalian cells. Among five ACTKs investigated, N-methylpyrroletetrazole-lysine (mPyTK) was found to give robust and site-selective photo-cross-linking reactivity in E...
May 3, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28410215/cardiac-glycosides-suppress-the-maintenance-of-stemness-and-malignancy-via-inhibiting-hif-1%C3%AE-in-human-glioma-stem-cells
#7
Dae-Hee Lee, Sang Cheul Oh, Amber J Giles, Jinkyu Jung, Mark R Gilbert, Deric M Park
Tissue hypoxia contributes to solid tumor pathogenesis by activating a series of adaptive programs. We previously showed that hypoxia promotes the preferential expansion and maintenance of CD133 positive human glioma stem cells (GSC) in a hypoxia inducible factor 1 alpha (HIF-1α)-dependent mechanism. Here, we examined the activity of digitoxin (DT), a cardiac glycoside and a putative inhibitor of HIF-1α, on human GSC in vitro and in vivo. During hypoxic conditions (1% O2), we observed the effect of DT on the intracellular level of HIF-1α and the extracellular level of vascular endothelial growth factor (VEGF) in human GSC...
June 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28410196/the-p38-signaling-pathway-mediates-quiescence-of-glioma-stem-cells-by-regulating-epidermal-growth-factor-receptor-trafficking
#8
Akio Soeda, Justin Lathia, Brian J Williams, Qiulian Wu, Joseph Gallagher, Andreas Androutsellis-Theotokis, Amber J Giles, Chunzhang Yang, Zhengping Zhuang, Mark R Gilbert, Jeremy N Rich, Deric M Park
EGFR pathway is upregulated in malignant gliomas, and its downstream signaling is important for self-renewal of glioma cancer stem-like cells (GSC). p38 mitogen-activated protein kinase (MAPK) signaling, a stress-activated signaling cascade with suppressive and permissive effects on tumorigenesis, can promote internalization and ubiquitin ligase mediated degradation of EGFR. In this study, we investigated the role of p38 MAPK signaling on the self-renewal of GSCs with the hypothesis that inhibition may lead to enhanced self-renewal capacity by retention of EGFR...
May 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28383180/two-tier-screening-platform-for-directed-evolution-of-aminoacyl-trna-synthetases-with-enhanced-stop-codon-suppression-efficiency
#9
Andrew E Owens, Katherine T Grasso, Christine A Ziegler, Rudi Fasan
Genetic code expansion through amber stop codon suppression provides a powerful tool for introducing non-proteinogenic functionalities into proteins for a broad range of applications. However, ribosomal incorporation of noncanonical amino acids (ncAAs) by means of engineered aminoacyl-tRNA synthetases (aaRSs) often proceeds with significantly reduced efficiency compared to sense codon translation. Here, we report the implementation of a versatile platform for the development of engineered aaRSs with enhanced efficiency in mediating ncAA incorporation by amber stop codon suppression...
April 6, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28320938/effectiveness-of-unaids-targets-and-hiv-vaccination-across-127-countries
#10
Jan Medlock, Abhishek Pandey, Alyssa S Parpia, Amber Tang, Laura A Skrip, Alison P Galvani
The HIV pandemic continues to impose enormous morbidity, mortality, and economic burdens across the globe. Simultaneously, innovations in antiretroviral therapy, diagnostic approaches, and vaccine development are providing novel tools for treatment-as-prevention and prophylaxis. We developed a mathematical model to evaluate the added benefit of an HIV vaccine in the context of goals to increase rates of diagnosis, treatment, and viral suppression in 127 countries. Under status quo interventions, we predict a median of 49 million [first and third quartiles 44M, 58M] incident cases globally from 2015 to 2035...
April 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28288813/a-genomically-modified-escherichia-coli-strain-carrying-an-orthogonal-e-coli-histidyl-trna-synthetase%C3%A2-trna-his-pair
#11
Markus Englert, Oscar Vargas-Rodriguez, Noah M Reynolds, Yane-Shih Wang, Dieter Söll, Takuya Umehara
BACKGROUND: Development of new aminoacyl-tRNA synthetase (aaRS)•tRNA pairs is central for incorporation of novel non-canonical amino acids (ncAAs) into proteins via genetic code expansion (GCE). The Escherichia coli and Caulobacter crescentus histidyl-tRNA synthetases (HisRS) evolved divergent mechanisms of tRNA(His) recognition that prevent their cross-reactivity. Although the E. coli HisRS•tRNA(His) pair is a good candidate for GCE, its use in C. crescentus is limited by the lack of established genetic selection methods and by the low transformation efficiency of C...
March 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28212794/an-efficient-system-for-incorporation-of-unnatural-amino-acids-in-response-to-the-four-base-codon-agga-in-escherichia-coli
#12
Byeong Sung Lee, Suyeon Kim, Byoung Joon Ko, Tae Hyeon Yoo
BACKGROUND: Adding new amino acids to the set of building blocks for protein synthesis expands the scope of protein engineering, and orthogonal pairs of tRNA and aminoacyl-tRNA synthetase have been developed for incorporating unnatural amino acids (UAAs) into proteins. While diverse systems have been developed to incorporate UAAs in response to the amber codon, less research has been focused on four-base codons despites their advantages. In this study, we report an efficient method to incorporate UAA in response to an AGGA codon in Escherichia coli...
February 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28196426/development-of-a-functional-observational-battery-in-the-minipig-for-regulatory-neurotoxicity-assessments
#13
Miao Zhong, Catherine Shoemake, Amber Fuller, David White, Chris Hanks, Derek Brocksmith, Jason Liu, Shayne Gad, Guy Bouchard, Alain Stricker-Krongrad
A functional observational battery (FOB) is recommended as the first-tier neurotoxicity screening in the preclinical safety pharmacology testing guidelines. Minipigs have increasingly been used in regulatory toxicology studies; however, no current FOB protocol is available for neurotoxicity testing in these species. Hence, a minipig FOB instrument was developed. A complete crossover study with Sinclair minipigs was performed to evaluate physiologic, neurologic, and behavioral effects of amphetamine, ketamine, and diazepam...
January 1, 2017: International Journal of Toxicology
https://www.readbyqxmd.com/read/28165290/improved-fat-suppression-homogeneity-with-mdixon-turbo-spin-echo-tse-in-pediatric-spine-imaging-at-3-0%C3%A2-t
#14
Amber L Pokorney, Jonathan M Chia, Cory M Pfeifer, Jeffrey H Miller, Houchun H Hu
Background Robust fat suppression remains essential in clinical MRI to improve tissue signal contrast, minimize fat-related artifacts, and enhance image quality. Purpose To compare fat suppression between mDIXON turbo spin echo (TSE) and conventional frequency-selective and inversion-recovery methods in pediatric spine MRI. Material and Methods Images from T1-weighted (T1W) and T2-weighted (T2W) TSE sequences coupled with conventional methods and the mDIXON technique were compared in 36 patients (5.8 ± 5...
January 1, 2017: Acta Radiologica
https://www.readbyqxmd.com/read/28131845/safer-topical-treatment-for-inflammation-using-5%C3%AE-tetrahydrocorticosterone-in-mouse-models
#15
Annalisa Gastaldello, Dawn E W Livingstone, Amber J Abernethie, Nicola Tsang, Brian R Walker, Patrick W F Hadoke, Ruth Andrew
Use of topical glucocorticoid for inflammatory skin conditions is limited by systemic and local side-effects. This investigation addressed the hypothesis that topical 5α-tetrahydrocorticosterone (5αTHB, a corticosterone metabolite) inhibits dermal inflammation without affecting processes responsible for skin thinning and impaired wound healing. The topical anti-inflammatory properties of 5αTHB were compared with those of corticosterone in C57Bl/6 male mice with irritant dermatitis induced by croton oil, whereas its effects on angiogenesis, inflammation, and collagen deposition were investigated by subcutaneous sponge implantation...
April 1, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28106981/controlling-multicycle-replication-of-live-attenuated-hiv-1-using-an-unnatural-genetic-switch
#16
Zhe Yuan, Nanxi Wang, Guobin Kang, Wei Niu, Qingsheng Li, Jiantao Guo
A safe and effective human immunodeficiency virus type 1 (HIV-1) vaccine is urgently needed, but remains elusive. While HIV-1 live-attenuated vaccine can provide potent protection as demonstrated in rhesus macaque-simian immunodeficiency virus model, the potential pathogenic consequences associated with the uncontrolled virus replication preclude such vaccine from clinical applications. We investigated a novel approach to address this problem by controlling live-attenuated HIV-1 replication through an unnatural genetic switch that was based on the amber suppression strategy...
April 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28050852/microbial-biomass-in-compost-during-colonization-of-agaricus-bisporus
#17
Aurin M Vos, Amber Heijboer, Henricus T S Boschker, Barbara Bonnet, Luis G Lugones, Han A B Wösten
Agaricus bisporus mushrooms are commercially produced on a microbe rich compost. Here, fungal and bacterial biomass was quantified in compost with and without colonization by A. bisporus. Chitin content, indicative of total fungal biomass, increased during a 26-day period from 576 to 779 nmol N-acetylglucosamine g(-1) compost in the absence of A. bisporus (negative control). A similar increase was found in the presence of this mushroom forming fungus. The fungal phospholipid-derived fatty acid (PLFA) marker C18:2ω6, indicative of the living fraction of the fungal biomass, decreased from 575 to 280 nmol g(-1) compost in the negative control...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28042700/a-versatile-approach-for-site-specific-lysine-acylation-in-proteins
#18
Zhipeng A Wang, Yadagiri Kurra, Xin Wang, Yu Zeng, Yan-Jiun Lee, Vangmayee Sharma, Hening Lin, Susie Y Dai, Wenshe R Liu
Using amber suppression in coordination with a mutant pyrrolysyl-tRNA synthetase-tRNA(Pyl) pair, azidonorleucine is genetically encoded in E. coli. Its genetic incorporation followed by traceless Staudinger ligation with a phosphinothioester allows the convenient synthesis of a protein with a site-specifically installed lysine acylation. By simply changing the phosphinothioester identity, any lysine acylation type could be introduced. Using this approach, we demonstrated that both lysine acetylation and lysine succinylation can be installed selectively in ubiquitin and synthesized histone H3 with succinylation at its K4 position (H3K4su)...
February 1, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/27966891/combining-sense-and-nonsense-codon-reassignment-for-site-selective-protein-modification-with-unnatural-amino-acids
#19
Zhenling Cui, Sergey Mureev, Mark E Polinkovsky, Zakir Tnimov, Zhong Guo, Thomas Durek, Alun Jones, Kirill Alexandrov
Incorporation of unnatural amino acids (uAAs) via codon reassignment is a powerful approach for introducing novel chemical and biological properties to synthesized polypeptides. However, the site-selective incorporation of multiple uAAs into polypeptides is hampered by the limited number of reassignable nonsense codons. This challenge is addressed in the current work by developing Escherichia coli in vitro translation system depleted of specific endogenous tRNAs. The translational activity in this system is dependent on the addition of synthetic tRNAs for the chosen sense codon...
December 30, 2016: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27919800/increasing-the-fidelity-of-noncanonical-amino-acid-incorporation-in-cell-free-protein-synthesis
#20
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
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