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https://www.readbyqxmd.com/read/28812932/celebrating-wobble-decoding-half-a-century-and-still-much-is-new
#1
Paul F Agris, Emily R Eruysal, Amithi Narendran, Ville Y P Väre, Sweta Vangaveti, Srivathsan V Ranganathan
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons...
August 16, 2017: RNA Biology
https://www.readbyqxmd.com/read/28812276/arundic-acid-increases-expression-and-function-of-astrocytic-glutamate-transporter-eaat1-via-the-erk-akt-and-nf-%C3%AE%C2%BAb-pathways
#2
Pratap Karki, Peter Hong, James Johnson, Edward Pajarillo, Deok-Soo Son, Michael Aschner, Eunsook Y Lee
Glutamate is the major excitatory neurotransmitter in the brain, but excessive synaptic glutamate must be removed to prevent excitotoxic injury and death. Two astrocytic glutamate transporters, excitatory amino acid transporter (EAAT) 1 and 2, play a major role in eliminating excess glutamate from the synapse. Dysregulation of EAAT1 contributes to the pathogenesis of multiple neurological disorders, such as Alzheimer's disease (AD), ataxia, traumatic brain injuries, and glaucoma. In the present study, we investigated the effect of arundic acid on EAAT1 to determine its efficacy in enhancing the expression and function of EAAT1, and its possible mechanisms of action...
August 15, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28810331/-effect-of-tsc2-gene-expression-downregulation-by-lentivirus-induced-rna-interference-on-u937-cell-line-and-its-mechanism
#3
Z F Xu, H X Liu, Y H Tan, X H Chen, F G Ren, Y F Zhang, J M Chang, N Zhang, J J Hu, H W Wang
Objective: To investigate the effect of biology and mTOR pathway activity of down-regulated TSC2 gene expression on U937 leukemia cells. Methods: Gene expression was down-regulated by lentivirus induced RNA interference on TSC2 high expressed U937 cell line; the proliferation, apoptosis and differentiation were detected by CCK-8 assay, colony formation assay and flow cytometry; the gene expression level and protein kinase activity were detected by qRT-PCR and Western blot. Results: Down-regulated expression of TSC2 gene promoted U937 cell proliferation and colony formation ability (P<0...
July 14, 2017: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
https://www.readbyqxmd.com/read/28810146/swarm-intelligence-enhanced-detection-of-non-small-cell-lung-cancer-using-tumor-educated-platelets
#4
Myron G Best, Nik Sol, Sjors G J G In 't Veld, Adrienne Vancura, Mirte Muller, Anna-Larissa N Niemeijer, Aniko V Fejes, Lee-Ann Tjon Kon Fat, Anna E Huis In 't Veld, Cyra Leurs, Tessa Y Le Large, Laura L Meijer, Irsan E Kooi, François Rustenburg, Pepijn Schellen, Heleen Verschueren, Edward Post, Laurine E Wedekind, Jillian Bracht, Michelle Esenkbrink, Leon Wils, Francesca Favaro, Jilian D Schoonhoven, Jihane Tannous, Hanne Meijers-Heijboer, Geert Kazemier, Elisa Giovannetti, Jaap C Reijneveld, Sander Idema, Joep Killestein, Michal Heger, Saskia C de Jager, Rolf T Urbanus, Imo E Hoefer, Gerard Pasterkamp, Christine Mannhalter, Jose Gomez-Arroyo, Harm-Jan Bogaard, David P Noske, W Peter Vandertop, Daan van den Broek, Bauke Ylstra, R Jonas A Nilsson, Pieter Wesseling, Niki Karachaliou, Rafael Rosell, Elizabeth Lee-Lewandrowski, Kent B Lewandrowski, Bakhos A Tannous, Adrianus J de Langen, Egbert F Smit, Michel M van den Heuvel, Thomas Wurdinger
Blood-based liquid biopsies, including tumor-educated blood platelets (TEPs), have emerged as promising biomarker sources for non-invasive detection of cancer. Here we demonstrate that particle-swarm optimization (PSO)-enhanced algorithms enable efficient selection of RNA biomarker panels from platelet RNA-sequencing libraries (n = 779). This resulted in accurate TEP-based detection of early- and late-stage non-small-cell lung cancer (n = 518 late-stage validation cohort, accuracy, 88%; AUC, 0.94; 95% CI, 0...
August 14, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28809961/biochemical-characterization-of-recombinant-influenza-a-polymerase-heterotrimer-complex-endonuclease-activity-and-evaluation-of-inhibitors
#5
Weimei Xing, Ona Barauskas, Thorsten Kirschberg, Anita Niedziela-Majka, Michael Clarke, Gabriel Birkus, Perry Weissburg, Xiaohong Liu, Brian E Schultz, Roman Sakowicz, HyockJoo Kwon, Joy Y Feng
Influenza polymerase is a heterotrimer composed of polymerase acidic protein A (PA) and basic proteins 1 (PB1) and 2 (PB2). The endonuclease active site, located in the PA subunit, cleaves host mRNA to prime viral mRNA transcription, and is essential for viral replication. To date, the human influenza A endonuclease activity has only been studied on the truncated active-site containing N-terminal domain of PA (PAN) or full-length PA in the absence of PB1 or PB2. In this study, we characterized the endonuclease activity of recombinant proteins of influenza A/PR8 containing full length PA, PA/PB1 dimer, and PA/PB1/PB2 trimer, observing 8...
2017: PloS One
https://www.readbyqxmd.com/read/28809853/rna-seq-analysis-of-amygdala-tissue-reveals-characteristic-expression-profiles-in-schizophrenia
#6
X Chang, Y Liu, C-G Hahn, R E Gur, P M A Sleiman, H Hakonarson
The amygdala brain region has been implicated in the pathophysiology of schizophrenia through emotion processing. However, transcriptome messages in the amygdala of schizophrenia patients have not been well studied. We used RNA sequencing to investigate gene-expression profiling in the amygdala tissues, and identified 569 upregulated and 192 downregulated genes from 22 schizophrenia patients and 24 non-psychiatric controls. Gene functional enrichment analysis demonstrated that the downregulated genes were enriched in pathways such as 'synaptic transmission' and 'behavior', whereas the upregulated genes were significantly over-represented in gene ontology pathways such as 'immune response' and 'blood vessel development'...
August 15, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28809766/crispr-cas9-editing-of-nf1-gene-identifies-crmp2-as-a-therapeutic-target-in-neurofibromatosis-type-1-related-pain-that-is-reversed-by-s-lacosamide
#7
Aubin Moutal, Xiaofang Yang, Wennan Li, Kerry B Gilbraith, Shizhen Luo, Song Cai, Liberty François-Moutal, Lindsey A Chew, Seul Ki Yeon, Shreya S Bellampalli, Chaoling Qu, Jennifer Y Xie, Mohab M Ibrahim, May Khanna, Ki Duk Park, Frank Porreca, Rajesh Khanna
Neurofibromatosis type 1 (NF1) is a rare autosomal dominant disease linked to mutations of the Nf1 gene. Patients with NF1 commonly experience severe pain. Studies on mice with Nf1 haploinsufficiency have been instructive in identifying sensitization of ion channels as a possible cause underlying the heightened pain suffered by patients with NF1. However, behavioral assessments of Nf1 mice have led to uncertain conclusions about the potential causal role of Nf1 in pain. We used the clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 (CRISPR/Cas9) genome editing system to create and mechanistically characterize a novel rat model of NF1-related pain...
July 3, 2017: Pain
https://www.readbyqxmd.com/read/28809012/comparative-genomics-as-a-foundation-for-evo-devo-studies-in-birds
#8
Phil Grayson, Simon Y W Sin, Timothy B Sackton, Scott V Edwards
Developmental genomics is a rapidly growing field, and high-quality genomes are a useful foundation for comparative developmental studies. A high-quality genome forms an essential reference onto which the data from numerous assays and experiments, including ChIP-seq, ATAC-seq, and RNA-seq, can be mapped. A genome also streamlines and simplifies the development of primers used to amplify putative regulatory regions for enhancer screens, cDNA probes for in situ hybridization, microRNAs (miRNAs) or short hairpin RNAs (shRNA) for RNA interference (RNAi) knockdowns, mRNAs for misexpression studies, and even guide RNAs (gRNAs) for CRISPR knockouts...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808124/rapid-rnase-l-driven-arrest-of-protein-synthesis-in-the-dsrna-response-without-degradation-of-translation-machinery
#9
Jesse Donovan, Sneha Rath, David Kolet-Mandrikov, Alexei Korennykh
Mammalian cells respond to double-stranded RNA (dsRNA) by activating a translation-inhibiting endoribonuclease, RNase L. Consensus in the field indicates that RNase L arrests protein synthesis by degrading ribosomal RNAs (rRNAs) and messenger RNAs (mRNAs). However, here we provide evidence for a different and far more efficient mechanism. By sequencing abundant RNA fragments generated by RNase L in human cells, we identify site-specific cleavage of two groups of non-coding RNAs: Y-RNAs, whose function is poorly understood, and cytosolic tRNAs, which are essential for translation...
August 14, 2017: RNA
https://www.readbyqxmd.com/read/28807694/reviewing-evidence-for-systematic-transcriptional-deletions-nucleotide-exchanges-and-expanded-codons-and-peptide-clusters-in-human-mitochondria
#10
REVIEW
Hervé Seligmann
Polymerization sometimes transforms sequences by (a) systematic deletions of mono-, dinucleotides after trinucleotides, or (b) 23 systematic nucleotide exchanges (9 symmetric, X<>Y, e.g. G<>T, 14 asymmetric, X > Y > Z > X, e.g. A > G > T > A), producing del- and swinger RNAs. Some peptides correspond to del- and swinger RNA translations, also according to tetracodons, codons expanded by a silent nucleotide. Here new analyzes assume different proteolytic patterns, partially alleviating false negative peptide detection biases, expanding noncanonical mitoproteome profiles...
August 11, 2017: Bio Systems
https://www.readbyqxmd.com/read/28806394/smggds-is-a-transient-nucleolar-protein-that-protects-cells-from-nucleolar-stress-and-promotes-the-cell-cycle-by-regulating-dream-complex-gene-expression
#11
P Gonyo, C Bergom, A C Brandt, S-W Tsaih, Y Sun, T M Bigley, E L Lorimer, S S Terhune, H Rui, M J Flister, R M Long, C L Williams
The chaperone protein and guanine nucleotide exchange factor SmgGDS (RAP1GDS1) is a key promoter of cancer cell proliferation and tumorigenesis. SmgGDS undergoes nucleocytoplasmic shuttling, suggesting that it has both cytoplasmic and nuclear functions that promote cancer. Previous studies indicate that SmgGDS binds cytoplasmic small GTPases and promotes their trafficking to the plasma membrane. In contrast, little is known about the functions of SmgGDS in the nucleus, or how these nuclear functions might benefit cancer cells...
August 14, 2017: Oncogene
https://www.readbyqxmd.com/read/28800730/genotypes-of-hepatitis-a-virus-in-turkey-first-report-and-clinical-profile-of-children-infected-with-sub-genotypes-ia-and-iiia
#12
Huseyin Yilmaz, Asiye Karakullukcu, Nuri Turan, Utku Y Cizmecigil, Aysun Yilmaz, Ayse A Ozkul, Ozge Aydin, Alper Gunduz, Mahmut Mete, Fadile Y Zeyrek, Taner T Kirazoglu, Juergen A Richt, Bekir Kocazeybek
BACKGROUND: Hepatitis A virus (HAV) is a food and water-borne virus causing clinical (mainly hepatitis) and subclinical disease in humans. It is important to characterize circulating strains of HAV in order to prevent HAV infections using efficacious vaccines. The aim of this study was the detection and characterization of the circulating strains of HAV in Turkey by performing serology, RT-PCR, sequencing and phylogenetic analysis. METHODS: In this study, 355 HAV suspected cases were analysed by ELISA for the presence of antibodies to HAV...
August 11, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28799568/association-of-long-non-coding-rna-h19-and-microrna-21-expression-with-the-biological-features-and-prognosis-of-non-small-cell-lung-cancer
#13
Y Zhou, B Sheng, Q Xia, X Guan, Y Zhang
In recent years, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been shown to play important roles in tumor biological function. The aim of this study was to investigate the diagnostic and prognostic value of lncRNA H19 and miR-21 expression in non-small-cell lung cancer (NSCLC). H19 and miR-21 expression was measured in tumor tissues and corresponding non-tumor lung tissues from 200 patients by quantitative reverse transcription polymerase chain reaction. Moreover, the in vitro and in vivo effects of H19 knock out in A549 cells were investigated...
August 11, 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28794655/p2y12-and-p2y13-receptors-involved-in-adp%C3%AE-s-induced-the-release-of-il-1%C3%AE-il-6-and-tnf-%C3%AE-from-cultured-dorsal-horn-microglia
#14
Pei-Wen Liu, Ming-Xia Yue, Rui Zhou, Juan Niu, Du-Juan Huang, Tao Xu, Pei Luo, Xiao-Hong Liu, Jun-Wei Zeng
OBJECTIVE: P2 receptors have been implicated in the release of neurotransmitter and pro-inflammatory cytokines due to their response to neuroexcitatory substances in the microglia. Dorsal horn P2Y12 and P2Y13 receptors are involved in the development of pain behavior induced by peripheral nerve injury. However, it is not known whether P2Y12 and P2Y13 receptors activation is associated with the expression and the release of interleukin-1B (IL-1β), interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α) in cultured dorsal spinal cord microglia...
2017: Journal of Pain Research
https://www.readbyqxmd.com/read/28794002/klf4-regulation-of-ch25h-and-lxr-mitigates-atherosclerosis-susceptibility
#15
Zhao Li, Marcy Martin, Jin Zhang, Hsi-Yuan Huang, Liang Bai, Jiao Zhang, Jian Kang, Ming He, Jie Li, Mano R Maurya, Shakti Gupta, Guangjin Zhou, Panjamaporn Sangwung, Yong-Jiang Xu, Ting Lei, Hsien-Da Huang, Mohit Jain, Mukesh K Jain, Shankar Subramaniam, John Y-J Shyy
Background -Atherosclerosis is a multifaceted inflammatory disease involving cells in the vascular wall [e.g., endothelial cells (ECs)] as well as circulating and resident immunogenic cells (e.g., monocytes/macrophages). Acting as a ligand for liver X receptor (LXR), but an inhibitor of sterol regulatory element binding protein 2 (SREBP2), 25-hydroxycholesterol (25-HC) and its catalyzing enzyme cholesterol-25-hydroxylase (Ch25h) are important in regulating cellular inflammatory status and cholesterol biosynthesis in both ECs and monocytes/macrophages...
August 9, 2017: Circulation
https://www.readbyqxmd.com/read/28792938/m-6-a-mrna-methylation-controls-t-cell-homeostasis-by-targeting-the-il-7-stat5-socs-pathways
#16
Hua-Bing Li, Jiyu Tong, Shu Zhu, Pedro J Batista, Erin E Duffy, Jun Zhao, Will Bailis, Guangchao Cao, Lina Kroehling, Yuanyuan Chen, Geng Wang, James P Broughton, Y Grace Chen, Yuval Kluger, Matthew D Simon, Howard Y Chang, Zhinan Yin, Richard A Flavell
N(6)-methyladenosine (m(6)A) is the most common and abundant messenger RNA modification, modulated by 'writers', 'erasers' and 'readers' of this mark. In vitro data have shown that m(6)A influences all fundamental aspects of mRNA metabolism, mainly mRNA stability, to determine stem cell fates. However, its in vivo physiological function in mammals and adult mammalian cells is still unknown. Here we show that the deletion of m(6)A 'writer' protein METTL3 in mouse T cells disrupts T cell homeostasis and differentiation...
August 9, 2017: Nature
https://www.readbyqxmd.com/read/28790305/single-cardiomyocyte-nuclear-transcriptomes-reveal-a-lincrna-regulated-de-differentiation-and-cell-cycle-stress-response-in-vivo
#17
Kelvin See, Wilson L W Tan, Eng How Lim, Zenia Tiang, Li Ting Lee, Peter Y Q Li, Tuan D A Luu, Matthew Ackers-Johnson, Roger S Foo
Cardiac regeneration may revolutionize treatment for heart failure but endogenous progenitor-derived cardiomyocytes in the adult mammalian heart are few and pre-existing adult cardiomyocytes divide only at very low rates. Although candidate genes that control cardiomyocyte cell cycle re-entry have been implicated, expression heterogeneity in the cardiomyocyte stress-response has never been explored. Here, we show by single nuclear RNA-sequencing of cardiomyocytes from both mouse and human failing, and non-failing adult hearts that sub-populations of cardiomyocytes upregulate cell cycle activators and inhibitors consequent to the stress-response in vivo...
August 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28783176/short-stretches-of-rare-codons-regulate-translation-of-the-transcription-factor-zeb2-in-cancer-cells
#18
W R Wan Makhtar, G Browne, A Karountzos, C Stevens, Y Alghamdi, A R Bottrill, S Mistry, E Smith, M Bushel, J H Pringle, A E Sayan, E Tulchinsky
Two proteins comprising the ZEB family of zinc finger transcription factors, ZEB1 and ZEB2, execute EMT programs in embryonic development and cancer. By studying regulation of their expression, we describe a novel mechanism that limits ZEB2 protein synthesis. A protein motif located at the border of the SMAD-binding domain of ZEB2 protein induces ribosomal pausing and compromises protein synthesis. The function of this protein motif is dependent on stretches of rare codons, Leu(UUA)-Gly(GGU)-Val(GUA). Incorporation of these triplets in the homologous region of ZEB1 does not affect protein translation...
August 7, 2017: Oncogene
https://www.readbyqxmd.com/read/28780826/-influence-of-extremely-low-frequency-magnetic-field-on-circadian-rhythm-of-cryptochrome-in-mouse-embryonic-fibroblasts
#19
Z Y Sun, D Y Geng, C F Chen, P P Wang, T Song
Objective: To investigate the influence of extremely low-frequency magnetic field on periodical expression of cryptochrome (Cry) gene in mouse embryonic fibroblast NIH3T3 cells. Methods: The NIH3T3 cells were divided into magnetic field group and sham-exposure group. The NIH3T3 cells in the magnetic field group were stimulated by horse serum and then exposed to an extremely low-frequency magnetic field (50 Hz and 0.3 mT) for 48 hours, and those in the sham-exposure group were also stimulated by horse serum and then exposed to a coil for 48 hours...
June 20, 2017: Chinese Journal of Industrial Hygiene and Occupational Diseases
https://www.readbyqxmd.com/read/28780112/transcript-analysis-at-dgat1-reveals-different-mrna-profiles-in-river-buffaloes-with-extreme-phenotypes-for-milk-fat
#20
M Gu, G Cosenza, I Nicolae, A Bota, Y Guo, L Di Stasio, A Pauciullo
Buffalo DGAT1 (diacylglycerol O-acyltransferase 1) was mainly investigated for the characterization of the gene itself and for the identification of the K232A polymorphism, similar to what has been accomplished in cattle, although no information has been reported so far at the mRNA level. The importance of DGAT1 for lipid metabolism led us to investigate the transcript profiles of lactating buffaloes characterized as high (9.13 ± 0.23) and low (7.94 ± 0.29) for milk fat percentage, and to explore the genetic diversity at the RNA and DNA level...
August 2, 2017: Journal of Dairy Science
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