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https://www.readbyqxmd.com/read/28749433/hbv-drug-resistance-substitutions-existed-before-the-clinical-approval-of-nucleos-t-ide-analogues-a-bioinformatic-analysis-by-genbank-data-mining
#1
Xizhan Xu, Kuanhui Xiang, Mingze Su, Yao Li, Wei Ji, Yutang Li, Hui Zhuang, Tong Li
Naturally occurring nucleos(t)ide analogue resistance (NUCr) substitution frequencies in the reverse transcriptase (RT) of the hepatitis B virus (HBV) were studied extensively after the clinical approval of nucleos(t)ide analogues (NUCs; year of approval 1998). We aimed to study NUCr substitutions in HBV RT sequences obtained before 1998 and better understand the evolution of RT sequences without NUC pressures. Our strategy was to retrieve HBV sequences from GenBank deposited before 1998. The initial search used the keywords "hepatitis B virus" or "HBV" and 1139 sequences were found...
July 27, 2017: Viruses
https://www.readbyqxmd.com/read/28749409/host-response-comparison-of-h1n1-and-h5n1-infected-mice-identifies-two-potential-death-mechanisms
#2
Olivier Leymarie, Léa Meyer, Pierre-Louis Hervé, Bruno Da Costa, Bernard Delmas, Christophe Chevalier, Ronan Le Goffic
Highly pathogenic influenza A viruses (IAV) infections represent a serious threat to humans due to their considerable morbidity and mortality capacities. A good understanding of the molecular mechanisms responsible for the acute lung injury observed during this kind of infection is essential to design adapted therapies. In the current study, using an unbiased transcriptomic approach, we compared the host-responses of mice infected with two different subtypes of IAV: H1N1 vs. H5N1. The host-response comparison demonstrated a clear difference between the transcriptomic profiles of H1N1- and H5N1-infected mice despite identical survival kinetics and similar viral replications...
July 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28748912/a-novel-allosteric-site-in-casein-kinase-2%C3%AE-discovered-using-combining-bioinformatics-and-biochemistry-methods
#3
Hai-Ming Jiang, Jiang-Kai Dong, Kun Song, Tong-Dan Wang, Wen-Kang Huang, Jing-Miao Zhang, Xiu-Yan Yang, Ying Shen, Jian Zhang
Casein kinase 2 (CK2) is a highly pleiotropic serine-threonine kinase, which catalyzed phosphorylation of more than 300 proteins that are implicated in regulation of many cellular functions, such as signal transduction, transcriptional control, apoptosis and the cell cycle. On the other hand, CK2 is abnormally elevated in a variety of tumors, and is considered as a promising therapeutic target. The currently available ATP-competitive CK2 inhibitors, however, lack selectivity, which has impeded their development in cancer therapy...
July 27, 2017: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/28748551/identification-of-a-dimeric-kdg-aldolase-from-agrobacterium-tumefaciens
#4
Tatiana P Soares da Costa, Madhvi Patel, Sebastien Desbois, Ruchi Gupta, Pierre Faou, Matthew A Perugini
Agrobacterium tumefaciens is a Gram-negative bacterium and causative agent of Crown Gall disease that infects a variety of economically-important plants. The annotated A. tumefaciens genome contains 10 putative dapA genes, which code for dihydrodipicolinate synthase (DHDPS). However, we have recently demonstrated that only one of these genes (dapA7) encodes a functional DHDPS. The function of the other nine putative dapA genes is yet to be determined. Here, we demonstrate using bioinformatics that the product of the dapA5 gene (DapA5) possesses all the catalytic residues canonical to 2-keto-3-deoxygluconate (KDG) aldolase, which is a class I aldolase involved in glucose metabolism...
July 27, 2017: Proteins
https://www.readbyqxmd.com/read/28748468/nmr-and-ms-methods-for-metabolomics
#5
Alexander Amberg, Björn Riefke, Götz Schlotterbeck, Alfred Ross, Hans Senn, Frank Dieterle, Matthias Keck
Metabolomics, also often referred as "metabolic profiling," is the systematic profiling of metabolites in biofluids or tissues of organisms and their temporal changes. In the last decade, metabolomics has become more and more popular in drug development, molecular medicine, and other biotechnology fields, since it profiles directly the phenotype and changes thereof in contrast to other "-omics" technologies. The increasing popularity of metabolomics has been possible only due to the enormous development in the technology and bioinformatics fields...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28748209/metagenomic-data-of-free-cyanide-and-thiocyanate-degrading-bacterial-communities
#6
Lukhanyo Mekuto, Seteno K O Ntwampe, John B N Mudumbi, Enoch A Akinpelu, Maxwell Mewa-Ngongang
The data presented in this article contains the bacterial community structure of the free cyanide (CN(-)) and thiocyanate (SCN(-)) degrading organisms that were isolated from electroplating wastewater and synthetic SCN(-) containing wastewater. PCR amplification of the 16S rRNA V1-V3 regions was undertaken using the 27F and 518R oligonucleotide primers following the metacommunity DNA extraction procedure. The PCR amplicons were processed using the illumina® reaction kits as per manufacturer׳s instruction and sequenced using the illumina® MiSeq-2000, using the MiSeq V3 kit...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28747224/regions-of-common-inter-individual-dna-methylation-differences-in-human-monocytes-genetic-basis-and-potential-function
#7
Christopher Schröder, Elsa Leitão, Stefan Wallner, Gerd Schmitz, Ludger Klein-Hitpass, Anupam Sinha, Karl-Heinz Jöckel, Stefanie Heilmann-Heimbach, Per Hoffmann, Markus M Nöthen, Michael Steffens, Peter Ebert, Sven Rahmann, Bernhard Horsthemke
BACKGROUND: There is increasing evidence for inter-individual methylation differences at CpG dinucleotides in the human genome, but the regional extent and function of these differences have not yet been studied in detail. For identifying regions of common methylation differences, we used whole genome bisulfite sequencing data of monocytes from five donors and a novel bioinformatic strategy. RESULTS: We identified 157 differentially methylated regions (DMRs) with four or more CpGs, almost none of which has been described before...
July 26, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28747184/meg2-is-regulated-by-mir-181a-5p-and-functions-as-a-tumour-suppressor-gene-to-suppress-the-proliferation-and-migration-of-gastric-cancer-cells
#8
Zhijian Liu, Feng Sun, Yeting Hong, Yanqing Liu, Min Fen, Kai Yin, Xiaolong Ge, Feng Wang, Xi Chen, Wenxian Guan
BACKGROUND: Protein-tyrosine phosphatase MEG2 (MEG2) is a classic tyrosine-specific protein tyrosine phosphatase (PTP). It has been reported that MEG2 participates in the carcinogenesis of the breast and liver. However, functions of MEG2 in gastric cancer remain poorly understood. METHODS: We examined the expression of MEG2 protein by western blotting and that of miR-181a-5p by qRT-PCR. We used bioinformatic analyses to search for miRNAs that potentially target MEG2...
July 26, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28747151/comparative-analysis-of-targeted-long-read-sequencing-approaches-for-characterization-of-a-plant-s-immune-receptor-repertoire
#9
Michael Giolai, Pirita Paajanen, Walter Verweij, Kamil Witek, Jonathan D G Jones, Matthew D Clark
BACKGROUND: The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified...
July 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28744787/on-the-possibility-of-an-early-evolutionary-origin-for-the-spliced-leader-trans-splicing
#10
Zuzana Krchňáková, Juraj Krajčovič, Matej Vesteg
Trans-splicing is a process by which 5'- and 3'-ends of two pre-RNA molecules transcribed from different sites of the genome can be joined together to form a single RNA molecule. The spliced leader (SL) trans-splicing is mediated by the spliceosome and it allows the replacement of 5'-end of pre-mRNA by 5'(SL)-end of SL-RNA. This form of splicing has been observed in many phylogenetically unrelated eukaryotes. Either the SL trans-splicing (SLTS) originated in the last eukaryotic common ancestor (LECA) (or even earlier) and it was lost in most eukaryotic lineages, or this mechanism of RNA processing evolved several times independently in various unrelated eukaryotic taxa...
July 25, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28743673/genomic-landscape-of-copy-number-variation-and-copy-neutral-loss-of-heterozygosity-events-in-equine-sarcoids-reveals-increased-instability-of-the-sarcoid-genome
#11
Klaudia Pawlina, Artur Gurgul, Tomasz Szmatoła, Katarzyna Ropka-Molik, Ewelina Semik, Jolanta Klukowska-Rötzler, Christoph Koch, Kathrin Mählmann, Monika Bugno-Poniewierska
Although they are the most common neoplasms in equids, sarcoids are not fully characterized at the molecular level. Therefore, the objective of this study was to characterize the landscape of structural rearrangements, such as copy number variation (CNV) and copy neutral loss of heterozygosity (cnLOH), in the genomes of sarcoid tumor cells. This information will not only broaden our understanding of the characteristics of this genome but will also improve the general knowledge of this tumor and the mechanisms involved in its generation...
July 22, 2017: Biochimie
https://www.readbyqxmd.com/read/28743644/species-trees-from-consensus-single-nucleotide-polymorphism-snp-data-testing-phylogenetic-approaches-with-simulated-and-empirical-data
#12
Alexander N Schmidt-Lebuhn, Nicola C Aitken, Aaron Chuah
Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or population trees from SNP data is currently the BEAST template SNAPP which uses a Bayesian coalescent analysis. However, it is computationally extremely demanding and tolerates only small amounts of missing data. We used simulated and empirical SNPs from plants (Australian Craspedia, Asteraceae, and Pelargonium, Geraniaceae) to compare species trees produced (1) by SNAPP, (2) using SVD quartets, and (3) using Bayesian and parsimony analysis with several different approaches to summarising data from multiple samples into one set of traits per species...
July 22, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28743112/microrna-302b-3p-suppresses-cell-proliferation-through-akt-pathway-by-targeting-igf-1r-in-human-gastric-cancer
#13
Bo Guo, Zhenghao Zhao, Zhen Wang, Qian Li, Xiaofei Wang, Wenjing Wang, Tusheng Song, Che Huang
BACKGROUND/AIMS: MiR-302b is a major microRNA found in human embryonic stem cells and induced pluripotent stem cells. However, its function in gastric cancer progression remains unclear. METHODS: Quantitative reverse transcription-PCR was performed to detect the expression levels of miR-302b-3p in gastric cancer tissues. MTT, colony formation, and flow cytometer analyses were conducted to explore the function of miR-302b-3p in MKN-45/SGC-7901 cells. A dual-luciferase reporter was used to validate the bioinformatics-predicted target gene of miR-302b-3p...
July 25, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28742391/preface-selected-papers-from-the-workshop-bioinformatics-and-artificial-intelligence-joined-with-the-international-joint-conference-on-artificial-intelligence
#14
Abdoulaye Baniré Diallo, Engelbert Mephu Nguifo, Mohammed J Zaki
No abstract text is available yet for this article.
August 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28742206/bioinformatics-analysis-of-rna-seq-data-revealed-critical-genes-in-colon-adenocarcinoma
#15
W-D Xi, Y-J Liu, X-B Sun, J Shan, L Yi, T-T Zhang
OBJECTIVE: RNA-seq data of colon adenocarcinoma (COAD) were analyzed with bioinformatics tools to discover critical genes in the disease. Relevant small molecule drugs, transcription factors (TFs) and microRNAs (miRNAs) were also investigated. MATERIALS AND METHODS: RNA-seq data of COAD were downloaded from The Cancer Genome Atlas (TCGA). Differential analysis was performed with package edgeR. False positive discovery (FDR) < 0.05 and |log2 (fold change)|>1 were set as the cut-offs to screen out differentially expressed genes (DEGs)...
July 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28742197/mir-24-alleviates-cardiomyocyte-apoptosis-after-myocardial-infarction-via-targeting-bim
#16
L-J Pan, X Wang, Y Ling, H Gong
OBJECTIVE: Ischemia hypoxia induces cardiomyocyte (CM) apoptosis in the process of acute myocardial infarction (AMI). It was showed that pro-apoptosis factor BIM participates in regulating tumor cell apoptosis under ischemia or hypoxia condition, while its role in CM apoptosis after AMI is still unclear. It was revealed that miR-24 expression was significantly reduced in myocardial tissue after AMI. Bioinformatics analysis exhibits that miR-24 is targeted to the 3'-UTR of BIM. This study aims to investigate the role of miR-24 in mediating BIM expression and CM apoptosis...
July 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28742110/evaluation-of-exome-variants-using-the-ion-proton-platform-to-sequence-error-prone-regions
#17
Heewon Seo, Yoomi Park, Byung Joo Min, Myung Eui Seo, Ju Han Kim
The Ion Proton sequencer from Thermo Fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. However, misleading variant-calling errors can occur. We performed a systematic evaluation and manual curation of read-level alignments for the 675 ultrarare variants reported by the Ion Proton sequencer from 27 whole-exome sequencing data but that are not present in either the 1000 Genomes Project and the Exome Aggregation Consortium. We classified positive variant calls into 393 highly likely false positives, 126 likely false positives, and 156 likely true positives, which comprised 58...
2017: PloS One
https://www.readbyqxmd.com/read/28742099/variants-of-acan-are-associated-with-severity-of-lumbar-disc-herniation-in-patients-with-chronic-low-back-pain
#18
Romain Shanil Perera, Poruwalage Harsha Dissanayake, Upul Senarath, Lalith Sirimevan Wijayaratne, Aranjan Lional Karunanayake, Vajira Harshadeva Weerabaddana Dissanayake
INTRODUCTION: Disc herniation is a complex spinal disorder associated with disability and high healthcare cost. Lumbar disc herniation is strongly associated with disc degeneration. Candidate genes of the aggrecan metabolic pathway may associate with the severity of lumbar disc herniation. OBJECTIVES: This study evaluated the association of single nucleotide variants (SNVs) of the candidate genes of the aggrecan metabolic pathway with the severity of lumbar disc herniation in patients with chronic mechanical low back pain...
2017: PloS One
https://www.readbyqxmd.com/read/28741388/comparative-proteomic-analysis-of-the-effect-of-the-four-herb-chinese-medicine-anbp-on-promoting-mouse-skin-wound-healing
#19
Li Chen, Qian Hou, Zhong-Zhi Zhou, Mei-Rong Li, Ling-Zhi Zhong, Xiang-Dong Deng, Zi-Ying Zhu, Zhong-Yi Cheng, Jun Zhu, Cong-Lian Xiang, Wen-Jun He, Xiao-Bing Fu
Traditional Chinese medicine has great potential to improve wound healing. ANBP, the mixture of 4 Chinese herbs- Agrimoniapilosa, Nelumbonucifera, Boswelliacarteri, and Pollen typhae-is effective in trauma treatment while its mechanism is still elusive. In this study, quantitative proteomics and bioinformatics analyses were performed to decipher the possible roles of ANBP in accelerated wound healing of mouse skin. Among all 3171 identified proteins, 90, 71, 80, and 140 proteins were found to be differently expressed in 6 hours, 3 days, 7 days, and 14 days ANBP-treated tissues compared with corresponding control tissues, respectively...
July 1, 2017: International Journal of Lower Extremity Wounds
https://www.readbyqxmd.com/read/28741359/evaluation-of-parameters-for-confident-phosphorylation-site-localization-using-an-orbitrap-fusion-tribrid-mass-spectrometer
#20
Samantha Ferries, Simon Perkins, Philip J Brownridge, Amy Campbell, Patrick A Eyers, Andrew R Jones, Claire E Eyers
Confident identification of sites of protein phosphorylation by mass spectrometry (MS) is essential to advance understanding of phosphorylation-mediated signaling events. However, development of novel instrumentation requires that methods for MS data acquisition and its interrogation be evaluated and optimized for high throughput phosphoproteomics. Here, we compare and contrast eight MS acquisition methods on the novel tribrid Orbitrap Fusion MS platform, using both a synthetic phosphopeptide library and a complex phosphopeptide-enriched cell lysate...
July 25, 2017: Journal of Proteome Research
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