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https://www.readbyqxmd.com/read/29793177/long-noncoding-rna-gas5-suppresses-triple-negative-breast-cancer-progression-through-inhibition-of-proliferation-and-invasion-by-competitively-binding-mir-196a-5p
#1
Shuqin Li, Jun Zhou, Zhaoxin Wang, Peishun Wang, Xitao Gao, Yan Wang
Triple-negative breast cancer (TNBC) is considered to be the most aggressive and lethal type of breast cancer. Many studies have suggested that the dysfunction of long noncoding RNAs (lncRNAs) is correlated with breast cancer metastasis and progression. Here, we show that levels of the lncRNA, growth arrest-specific transcript 5 (GAS5), are decreased in TNBC tissues, and this down-regulation of GAS5 is associated with an aggressive tumor phenotype in patients, affecting clinical stage, lymph node metastasis and overall survival...
May 21, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29792937/a-reliable-targeted-next-generation-sequencing-strategy-for-diagnosis-of-myopathies-and-muscular-dystrophies-especially-for-the-giant-titin-and-nebulin-genes
#2
Reda Zenagui, Delphine Lacourt, Henri Pegeot, Kevin Yauy, Raul Juntas Morales, Corine Theze, François Rivier, Claude Cances, Guilhem Sole, Dimitri Renard, Ulrike Walther-Louvier, Xavier Ferrer-Monasterio, Caroline Espil, Marie-Christine Arné-Bes, Pascal Cintas, Emmanuelle Uro-Coste, Marie-Laure Martin Negrier, Valérie Rigau, Eric Bieth, Cyril Goizet, Mireille Claustres, Michel Koenig, Mireille Cossée
Myopathies and muscular dystrophies (M-MDs) are genetically heterogeneous diseases, with more than 100 identified genes, including the giant and complex titin (TTN) and nebulin (NEB) genes. Next-generation sequencing technology revolutionized M-MD diagnosis and revealed high frequency of TTN and NEB variants. We developed a next-generation sequencing diagnostic strategy targeted on the coding sequences of 135 M-MD genes. Comparison of two targeted capture technologies (SeqCap EZ Choice library capture kit (Roche-Nimblegen) and Nextera Rapid Capture Custom Enrichment kit (Illumina)) and of two whole exome sequencing kits (SureSelect V5 (Agilent) and TruSeq RapidExome capture (Illumina)) revealed best coverage with the SeqCap EZ Choice protocol...
May 21, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29792880/molecular-alterations-during-larval-development-of-haemonchus-contortus-in-vitro-are-under-tight-post-transcriptional-control
#3
Guangxu Ma, Tao Wang, Pasi K Korhonen, Ching-Seng Ang, Nicholas A Williamson, Neil D Young, Andreas J Stroehlein, Ross S Hall, Anson V Koehler, Andreas Hofmann, Robin B Gasser
In this study, we explored the molecular alterations in the developmental switch from the L3 to the exsheathed L3 (×L3) and to the L4 stage of Haemonchus contortus in vitro using an integrated transcriptomic, proteomic and bioinformatic approach. Totals of 9,754 mRNAs, 88 microRNAs (miRNAs) and 1,591 proteins were identified, and 6,686 miRNA-mRNA pairs inferred in all larval stages studied. Approximately 16% of transcripts in the combined transcriptome (representing all three larval stages) were expressed as proteins, and there were positive correlations (r = 0...
May 22, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29792335/synthesis-of-novel-thymol-derivatives-against-mrsa-and-esbl-producing-pathogenic-bacteria
#4
Shasank S Swain, Sudhir K Paidesetty, Rabindra N Padhy
Twelve substituted aryl-azo-thymol derivatives (4a to 4 l) were synthesized and characterized by several spectral techniques such as, FTIR, UV-vis, proton NMR, Mass spectrometry and elemental analysis. Antimicrobial activities were evaluated by agar-well diffusion method against isolated MRSA, ESBL-producing pathogenic bacteria and antifungal resistant fungi, in vitro. In addition, drug likeness properties of derivatives were assessed through bioinformatic tools such as, PASS prediction, molecular docking and Lipinski rules of five, along with determination of toxic nature and LD50 values...
May 24, 2018: Natural Product Research
https://www.readbyqxmd.com/read/29792177/investigation-of-the-thermophilic-mechanism-in-the-genus-porphyrobacter-by-comparative-genomic-analysis
#5
Lin Xu, Yue-Hong Wu, Peng Zhou, Hong Cheng, Qian Liu, Xue-Wei Xu
BACKGROUND: Type strains of the genus Porphyrobacter belonging to the family Erythrobacteraceae and the class Alphaproteobacteria have been isolated from various environments, such as swimming pools, lake water and hot springs. P. cryptus DSM 12079T and P. tepidarius DSM 10594T out of all Erythrobacteraceae type strains, are two type strains that have been isolated from geothermal environments. Next-generation sequencing (NGS) technology offers a convenient approach for detecting situational types based on protein sequence differences between thermophiles and mesophiles; amino acid substitutions can lead to protein structural changes, improving the thermal stabilities of proteins...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29791965/searching-for-non-transposable-targets-of-planarian-nuclear-piwi-in-pluripotent-stem-cells-and-differentiated-cells
#6
Makoto Kashima, Kiyokazu Agata, Norito Shibata
Nuclear PIWIs together with their guide RNAs (piRNAs) epigenetically silence various genes including transposons in many organisms. In planarians, the nuclear piwi family gene, DjpiwiB is specifically transcribed in adult pluripotent stem cells (adult PSC, neoblast), but not in differentiated cells. However, the protein accumulates in the nuclei of both neoblasts and their descendant differentiated cells. Interestingly, PIWI(DjPiwiB)-piRNA complexes are indispensable for the repression of transposable genes at the onset of differentiation from neoblasts...
May 23, 2018: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/29791858/a-multi-layered-quantitative-in-vivo-expression-atlas-of-the-podocyte-unravels-kidney-disease-candidate-genes
#7
Markus M Rinschen, Markus Gödel, Florian Grahammer, Stefan Zschiedrich, Martin Helmstädter, Oliver Kretz, Mostafa Zarei, Daniela A Braun, Sebastian Dittrich, Caroline Pahmeyer, Patricia Schroder, Carolin Teetzen, HeonYung Gee, Ghaleb Daouk, Martin Pohl, Elisa Kuhn, Bernhard Schermer, Victoria Küttner, Melanie Boerries, Hauke Busch, Mario Schiffer, Carsten Bergmann, Marcus Krüger, Friedhelm Hildebrandt, Joern Dengjel, Thomas Benzing, Tobias B Huber
Damage to and loss of glomerular podocytes has been identified as the culprit lesion in progressive kidney diseases. Here, we combine mass spectrometry-based proteomics with mRNA sequencing, bioinformatics, and hypothesis-driven studies to provide a comprehensive and quantitative map of mammalian podocytes that identifies unanticipated signaling pathways. Comparison of the in vivo datasets with proteomics data from podocyte cell cultures showed a limited value of available cell culture models. Moreover, in vivo stable isotope labeling by amino acids uncovered surprisingly rapid synthesis of mitochondrial proteins under steady-state conditions that was perturbed under autophagy-deficient, disease-susceptible conditions...
May 22, 2018: Cell Reports
https://www.readbyqxmd.com/read/29791771/minimal-information-about-an-immuno-peptidomics-experiment-miaipe
#8
Jennie R Lill, Peter A van Veelen, Stefan Tenzer, Arie Admon, Etienne Caron, Josh Elias, Albert J R Heck, Miguel Marcilla, Fabio Marino, Markus Müller, Bjoern Peters, Anthony Purcell, Alessandro Sette, Theo Sturm, Nicola Ternette, Juan Antonio Vizcaíno, Michal Bassani-Sternberg
Minimal Information about an Immuno-Peptidomics Experiment (MIAIPE) is an initiative of the members of the Human Immuno-Peptidome Project (HIPP), an international program organized by the Human Proteome Organization (HUPO). The aim of the MIAIPE guidelines is to deliver technical guidelines representing the minimal information required to sufficiently support the evaluation and interpretation of immunopeptidomics experiments. The MIAIPE document has been designed to report essential information about sample preparation, mass spectrometric measurement and associated mass spectrometry (MS)-related bioinformatics aspects that are unique to immunopeptidomics and may not be covered by the general proteomics MIAPE (Minimal Information About a Proteomics Experiment) guidelines...
May 23, 2018: Proteomics
https://www.readbyqxmd.com/read/29791443/traceability-reproducibility-and-wiki-exploration-for-%C3%A3-la-carte-reconstructions-of-genome-scale-metabolic-models
#9
Méziane Aite, Marie Chevallier, Clémence Frioux, Camille Trottier, Jeanne Got, María Paz Cortés, Sebastián N Mendoza, Grégory Carrier, Olivier Dameron, Nicolas Guillaudeux, Mauricio Latorre, Nicolás Loira, Gabriel V Markov, Alejandro Maass, Anne Siegel
Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by the development of some major platforms and databases, and an explosion of individual bioinformatics methods. Consequently, many recent models result from "à la carte" pipelines, combining the use of platforms, individual tools and biological expertise to enhance the quality of the reconstruction...
May 23, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29790941/asaim-a-galaxy-based-framework-to-analyze-microbiota-data
#10
Bérénice Batut, Kévin Gravouil, Clémence Defois, Saskia Hiltemann, Jean-François Brugère, Eric Peyretaillade, Pierre Peyret
Background: New generations of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. Findings: We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses...
May 22, 2018: GigaScience
https://www.readbyqxmd.com/read/29790940/pycotools-a-python-toolbox-for-copasi
#11
Ciaran M Welsh, Nicola Fullard, Carole J Proctor, Alvaro Martinez-Guimera, Robert J Isfort, Charles C Bascom, Ryan Tasseff, Stefan A Przyborski, Daryl P Shanley
Motivation: COPASI is an open source software package for constructing, simulating and analysing dynamic models of biochemical networks. COPASI is primarily intended to be used with a graphical user interface but often it is desirable to be able to access COPASI features programmatically, with a high level interface. Results: PyCoTools is a Python package aimed at providing a high level interface to COPASI tasks with an emphasis on model calibration. PyCoTools enables the construction of COPASI models and the execution of a subset of COPASI tasks including time courses, parameter scans and parameter estimations...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790939/nextstrain-real-time-tracking-of-pathogen-evolution
#12
James Hadfield, Colin Megill, Sidney M Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A Neher
Summary: Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790936/simextargid-a-comprehensive-package-for-real-time-lc-ms-data-acquisition-and-analysis
#13
William M B Edmands, Josie Hayes, Stephen M Rappaport
Summary: Liquid chromatography mass spectrometry (LC-MS) is the favored method for untargeted metabolomic analysis of small molecules in biofluids. Here we present SimExTargId, an open-source R package for autonomous analysis of metabolomic data and real-time observation of experimental runs. This simultaneous, fully automated and multi-threaded (optional) package is a wrapper for vendor-independent format conversion (ProteoWizard), xcms- and CAMERA- based peak-picking, MetMSLine-based pre-processing and covariate-based statistical analysis...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790928/using-meshes-for-mesh-term-enrichment-and-semantic-analyses
#14
Guangchuang Yu
Summary: Medical Subject Headings (MeSH) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH provides unique and comprehensive annotations for life science. The meshes package implements measurement of the semantic similarity of MeSH terms and gene products to help using MeSH vocabulary in knowledge mining. Enrichment analysis to extract the biological meanings from gene list, expression profile and genomic regions is also provided using MeSH annotation...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790921/mascot-parameter-and-state-inference-under-the-marginal-structured-coalescent-approximation
#15
Nicola F Müller, David Rasmussen, Tanja Stadler
Motivation: The structured coalescent is widely applied to study demography within and migration between sub-populations from genetic sequence data. Current methods are either exact but too computationally inefficient to analyse large datasets with many sub-populations, or make strong approximations leading to severe biases in inference. We recently introduced an approximation based on weaker assumptions to the structured coalescent enabling the analysis of larger datasets with many different states...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790920/elucidating-the-role-of-the-maternal-embryonic-leucine-zipper-kinase-melk-in-adrenocortical-carcinoma
#16
Katja Kiseljak-Vassiliades, Yu Zhang, Adwitiya Kar, Raud Razzaghi, Mei Xu, Katherine Gowan, Christopher D Raeburn, Maria Albuja-Cruz, Kenneth L Jones, Hilary Somerset, Lauren Fishbein, Stephen Leong, Margaret E Wierman
Adrenocortical carcinoma (ACC) is an aggressive cancer with a five-year survival less than 35%. Mortality remains high due to lack of targeted therapies. Using bioinformatic analyses, we identified Maternal Embryonic Leucine Zipper Kinase (MELK) as 4.1-fold overexpressed in ACC compared to normal adrenal samples. High MELK expression in human tumors correlated with shorter survival and with increased expression of genes involved in cell division and growth. We investigated the functional effects of MELK inhibition using newly developed ACC cell lines with variable MELK expression, CU-ACC1 and CU-ACC2, compared with H295R cells...
May 21, 2018: Endocrinology
https://www.readbyqxmd.com/read/29790911/panda-view-an-easy-to-use-tool-for-statistical-analysis-and-visualization-of-quantitative-proteomics-data
#17
Cheng Chang, Kaikun Xu, Chaoping Guo, Jinxia Wang, Qi Yan, Jian Zhang, Fuchu He, Yunping Zhu
Summary: Compared with the numerous software tools developed for identification and quantification of -omics data, there remains a lack of suitable tools for both downstream analysis and data visualization. To help researchers better understand the biological meanings in their -omics data, we present an easy-to-use tool, named PANDA-view, for both statistical analysis and visualization of quantitative proteomics data and other -omics data. PANDA-view contains various kinds of analysis methods such as normalization, missing value imputation, statistical tests, clustering and principal component analysis, as well as the most commonly-used data visualization methods including an interactive volcano plot...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790910/sos-notebook-an-interactive-multi-language-data-analysis-environment
#18
Bo Peng, Gao Wang, Jun Ma, Man Chong Leong, Chris Wakefield, James Melott, Yulun Chiu, Di Du, John N Weinstein
Motivation: Complex bioinformatic data analysis workflows involving multiple scripts in different languages can be difficult to consolidate, share, and reproduce. An environment that streamlines the entire processes of data collection, analysis, visualization and reporting of such multi-language analyses is currently lacking. Results: We developed Script of Scripts (SoS) Notebook, a web-based notebook environment that allows the use of multiple scripting language in a single notebook, with data flowing freely within and across languages...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790909/ebic-an-evolutionary-based-parallel-biclustering-algorithm-for-pattern-discovery
#19
Patryk Orzechowski, Moshe Sipper, Xiuzhen Huang, Jason H Moore
Motivation: Biclustering algorithms are commonly used for gene expression data analysis. However, accurate identification of meaningful structures is very challenging and state-of-the-art methods are incapable of discovering with high accuracy different patterns of high biological relevance. Results: In this paper a novel biclustering algorithm based on evolutionary computation, a subfield of artificial intelligence (AI), is introduced. The method called EBIC aims to detect order-preserving patterns in complex data...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790906/bcseq-an-r-package-for-fast-sequence-mapping-in-high-throughput-shrna-and-crispr-screens
#20
Jiaxing Lin, Jeremy Gresham, Tongrong Wang, So Young Kim, James Alvarez, Jeffrey S Damrauer, Scott Floyd, Joshua Granek, Andrew Allen, Cliburn Chan, Jichun Xie, Kouros Owzar
Summary: CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings among similar sequences in the barcode library in a statistically principled manner, and be computationally efficient. Herein we present bcSeq, an open source R package that implements a fast and parallelized algorithm for mapping high-throughput sequencing reads to a barcode library while tolerating sequencing error...
May 22, 2018: Bioinformatics
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