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https://www.readbyqxmd.com/read/28431355/genome-wide-identification-and-analysis-of-the-populus-trichocarpa-tify-gene-family
#1
Yue Wang, Feng Pan, Danmei Chen, Wenyuan Chu, Huanlong Liu, Yan Xiang
The plant-specific TIFY proteins are widely present in land plants and play the important roles in the regulation of plant stress-responses. In this study, we carried out a bioinformatics analysis of TIFY genes in Populus trichocarpa by determining the phylogenetic relationship, chromosomal location and gene structure and expression profiles analysis under stresses. The 24 TIFY genes were identified and classified into four subfamilies (ZML, JAZ, PPD and TIFY). The 24 TIFY genes were irregularly located on 13 of the 19 chromosomes; ten gene pairs were involved in large-scale interchromosomal segmental duplication events; we identified 17 collinear TIFY gene pairs in the Populus trichocarpa genome...
April 13, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28431272/specific-microrna-mrna-regulatory-network-of-colon-cancer-invasion-mediated-by-tissue-kallikrein-related-peptidase-6
#2
Earlphia Sells, Ritu Pandey, Hwudaurw Chen, Bethany A Skovan, Haiyan Cui, Natalia A Ignatenko
Metastatic colon cancer is a major cause of deaths among colorectal cancer (CRC) patients. Elevated expression of kallikrein 6 (KLK6), a member of a kallikrein subfamily of peptidase S1 family serine proteases, has been reported in CRC and is associated with low patient survival rates and poor disease prognosis. We knocked down KLK6 expression in HCT116 colon cancer cells to determine the significance of KLK6 expression for metastatic dissemination and to identify the KLK6-associated microRNAs (miRNAs) signaling networks in metastatic colon cancer...
April 18, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28431173/programmatic-access-to-bioinformatics-tools-from-embl-ebi-update-2017
#3
Szymon Chojnacki, Andrew Cowley, Joon Lee, Anna Foix, Rodrigo Lopez
Since 2009 the EMBL-EBI provides free and unrestricted access to several bioinformatics tools via the user's browser as well as programmatically via Web Services APIs. Programmatic access to these tools, which is fundamental to bioinformatics, is increasingly important as more high-throughput data is generated, e.g. from proteomics and metagenomic experiments. Access is available using both the SOAP and RESTful approaches and their usage is reviewed regularly in order to ensure that the best, supported tools are available to all users...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28431148/truncated-orf1-proteins-can-suppress-line-1-retrotransposition-in-trans
#4
Mark Sokolowski, May Chynces, Dawn deHaro, Claiborne M Christian, Victoria P Belancio
Long interspersed element 1 (L1) is an autonomous non-LTR retroelement that is active in mammalian genomes. Although retrotranspositionally incompetent and functional L1 loci are present in the same genomes, it remains unknown whether non-functional L1s have any trans effect on mobilization of active elements. Using bioinformatic analysis, we identified over a thousand of human L1 loci containing at least one stop codon in their ORF1 sequence. RNAseq analysis confirmed that many of these loci are expressed...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28431087/a-method-for-learning-a-sparse-classifier-in-the-presence-of-missing-data-for-high-dimensional-biological-datasets
#5
Kristen Severson, Brinda Monian, J Christopher Love, Richard D Braatz
Motivation: This work addresses two common issues in building classification models for biological or medical studies: learning a sparse model, where only a subset of a large number of possible predictors is used, and training in the presence of missing data. This work focuses on supervised generative binary classification models, specifically linear discriminant analysis (LDA). The parameters are determined using an expectation maximization algorithm to both address missing data and introduce priors to promote sparsity...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430977/deep-mining-heterogeneous-networks-of-biomedical-linked-data-to-predict-novel-drug-target-associations
#6
Nansu Zong, Hyeoneui Kim, Victoria Ngo, Olivier Harismendy
Motivation: A heterogeneous network topology possessing abundant interactions between biomedical entities has yet to be utilized in similarity-based methods for predicting drug-target associations based on the array of varying features of drugs and their targets. Deep learning reveals features of vertices of a large network that can be adapted in accommodating the similarity-based solutions to provide a flexible method of drug-target prediction. Results: We propose a similarity-based drug-target prediction method that enhances existing association discovery methods by using a topology-based similarity measure...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430949/capturing-non-local-interactions-by-long-short-term-memory-bidirectional-recurrent-neural-networks-for-improving-prediction-of-protein-secondary-structure-backbone-angles-contact-numbers-and-solvent-accessibility
#7
Rhys Heffernan, Yuedong Yang, Kuldip Paliwal, Yaoqi Zhou
Motivation: The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some "short to intermediate" non-local interactions...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430873/bioinformatics-in-germany-toward-a-national-level-infrastructure
#8
Andreas Tauch, Arwa Al-Dilaimi
The German Network for Bioinformatics Infrastructure (de.NBI) is a national initiative funded by the German Federal Ministry of Education and Research (BMBF). The mission of de.NBI is (i) to provide high-quality bioinformatics services to users in basic and applied life sciences research from academia, industry and biomedicine; (ii) to offer bioinformatics training to users in Germany and Europe through a wide range of workshops and courses; and (iii) to foster the cooperation of the German bioinformatics community with international network structures such as the European life-sciences Infrastructure for biological Information (ELIXIR)...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28430871/cluspro-peptidock-efficient-global-docking-of-peptide-recognition-motifs-using-fft
#9
Kathryn A Porter, Bing Xia, Dmitri Beglov, Tanggis Bohnuud, Nawsad Alam, Ora Schueler-Furman, Dima Kozakov
Summary: We present an approach for the efficient docking of peptide motifs to their free receptor structures. Using a motif based search, we can retrieve structural fragments from the Protein Data Bank (PDB) that are very similar to the peptide's final, bound conformation. We use a Fast Fourier Transform (FFT) based docking method to quickly perform global rigid body docking of these fragments to the receptor. According to CAPRI peptide docking criteria, an acceptable conformation can often be found among the top-ranking predictions...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430868/most-visualization-software-for-producing-automated-textbook-style-maps-of-genome-scale-metabolic-networks
#10
James J Kelley, Shay Maor, Min Kyung Kim, Anatoliy Lane, Desmond S Lun
Summary: Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: 1. automation, since GEMs can be quite large; 2. production of understandable maps that provide ease in identification of pathways, reactions, and metabolites; and 3. visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (1), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (2) and comes close to satisfying (3)...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430858/mapping-genes-for-calcium-signaling-and-their-associated-human-genetic-disorders
#11
Matthias Hörtenhuber, Enrique M Toledo, Erik Smedler, Ernest Arenas, Seth Malmersjö, Lauri Louhivuori, Per Uhlén
Motivation: Signal transduction via calcium ions (Ca 2+ ) represents a fundamental signaling pathway in all eukaryotic cells. A large portion of the human genome encodes proteins used to assemble signaling systems that can transduce signals with diverse spatial and temporal dynamics. Results: Here, we provide a map of all of the genes involved in Ca 2+ signaling and link these genes to human genetic disorders. Using Gene Ontology terms and genome databases, 1,805 genes were identified as regulators or targets of intracellular Ca 2+ signals...
April 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430780/the-importance-of-standardization-for-biodiversity-comparisons-a-case-study-using-autonomous-reef-monitoring-structures-arms-and-metabarcoding-to-measure-cryptic-diversity-on-mo-orea-coral-reefs-french-polynesia
#12
Emma Ransome, Jonathan B Geller, Molly Timmers, Matthieu Leray, Angka Mahardini, Andrianus Sembiring, Allen G Collins, Christopher P Meyer
The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data...
2017: PloS One
https://www.readbyqxmd.com/read/28430743/microrna-148a-promotes-apoptosis-and-suppresses-growth-of-breast-cancer-cells-by-targeting-b-cell-lymphoma-2
#13
Qunying Li, Pingping Ren, Pengfei Shi, Yihan Chen, Feixiang Xiang, Li Zhang, Jing Wang, Qing Lv, Mingxing Xie
MicroRNAs (miRNAs) contribute toward tumorigenesis through the modulation of tumor-related genes. MiR-148a has been characterized as a tumor-suppressing miRNA and its downregulation has been reported in tumors of a variety of cancers. However, the functional role of miR-148a in breast cancer is not yet fully understood. Using both in-vitro and in-vivo models, we confirmed that miR-148a acts to inhibit the proliferation of breast cancer cells. Through the use of bioinformatic approaches in miRNA target prediction, we determined that B-cell lymphoma 2 (BCL-2) is a likely target of miR-148a...
April 20, 2017: Anti-cancer Drugs
https://www.readbyqxmd.com/read/28430657/microrna-signatures-predict-prognosis-of-patients-with-glioblastoma-multiforme-through-the-cancer-genome-atlas
#14
Ying Yuan, Hua Zhang, Xuexia Liu, Zhongming Lu, Guojun Li, Meixia Lu, Xiaofeng Tao
MicroRNAs (miRNAs) play major roles in various biological processes and have been implicated in the pathogenesis and malignant progression of glioblastoma multiforme (GBM). The aim of this study was to assess the predictive values of miRNAs for overall survival (OS) of patients with GBM. MiRNA expression profiles and clinical information of 563 GBM patients were obtained from the Cancer Genome Atlas. The most significantly altered miRNAs were identified and miRNA expression profiles were performed, through principal component analysis, the least absolute shrinkage and selection operator method...
April 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430325/identification-of-a-disease-causing-mutation-in-a-chinese-patient-with-retinitis-pigmentosa-by-targeted-next-generation-sequencing
#15
Jianping Xiao, Xueqin Guo, Yong Wang, Mingkun Shao, Xiaoming Wei, Lique Du, Long Li, Yan Sun, Yun Yang
PURPOSE: To identify disease-causing mutations in a Chinese patient with retinitis pigmentosa (RP). METHODS: A detailed clinical examination was performed on the proband. Targeted next-generation sequencing (NGS) combined with bioinformatics analysis was performed on the proband to detect candidate disease-causing mutations. Sanger sequencing was performed on all subjects to confirm the candidate mutations and assess cosegregation within the family. RESULTS: Clinical examinations of the proband showed typical characteristics of RP...
April 14, 2017: European Journal of Ophthalmology
https://www.readbyqxmd.com/read/28429758/intracellular-lipid-binding-protein-family-diversity-from-oyster-crassostrea-gigas-genomic-and-structural-features-of-invertebrate-lipid-transporters
#16
Guilherme de Toledo-Silva, Guilherme Razzera, Flavia Lucena Zacchi, Nestor Cubas Wendt, Jacó Joaquim Mattos, Afonso Celso Dias Bainy
Intracellular lipid binding proteins (iLBPs) play a role in the transport and cellular uptake of fatty acids and gene expression regulation. The aim of this work was to characterize the iLBP gene family of the Pacific oyster Crassostrea gigas, one of the most cultivated marine bivalves in the world, using bioinformatics and molecular biology approaches. A total of 26 different iLBPs transcripts were identified in the Pacific oyster genome, including alternative splicing and gene duplication events. The oyster iLBP gene family seems to be more expanded than in other invertebrates...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429323/protein-targeting-to-the-plastid-of-euglena
#17
Dion G Durnford, Steven D Schwartzbach
The lateral transfer of photosynthesis between kingdoms through endosymbiosis is among the most spectacular examples of evolutionary innovation. Euglena, which acquired a chloroplast indirectly through an endosymbiosis with a green alga, represents such an example. As with other endosymbiont-derived plastids from eukaryotes, there are additional membranes that surround the organelle, of which Euglena has three. Thus, photosynthetic genes that were transferred from the endosymbiont to the host nucleus and whose proteins are required in the new plastid, are now faced with targeting and plastid import challenges...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28429075/toward-personalized-management-in-bladder-cancer-the-promise-of-novel-molecular-taxonomy
#18
REVIEW
Marie-Lisa Eich, Lars Dyrskjøt, George J Netto
Empowered by the recent advances in next generation sequencing and bioinformatics technology, an unprecedented wave of integrated transcriptomic and genomic studies have impacted the field of bladder cancer. These studies not only have confirmed previously charted genetic pathways in bladder cancer development but also have led to the discovery of numerous additional crucial driver genetic alterations. As a result, a novel genomic-based taxonomy is emerging that promises to better define clinically relevant intrinsic subtypes of bladder cancer...
April 21, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28428828/bioinformatics-analysis-of-key-genes-and-latent-pathway-interactions-based-on-the-anaplastic-thyroid-carcinoma-gene-expression-profile
#19
Yun Huang, Yiming Tao, Xinying Li, Shi Chang, Bo Jiang, Feng Li, Zhi-Ming Wang
Anaplastic thyroid carcinoma (ATC) is an aggressive malignant disease in older adults with a high mortality rate. The present study aimed to examine several key genes and pathways, which are associated with ATC. The GSE33630 gene expression profile was downloaded from the Gene Expression Omnibus database, which included 11 ATC and 45 normal thyroid samples. The differentially expressed genes (DEGs) in ATC were identified using the Limma package in R. The Gene Ontology functions and Kyoto Encyclopedia of Genes and Genomes pathways of the selected DEGs were enriched using the Database for Annotation, Visualization and Integrated Discovery...
January 2017: Oncology Letters
https://www.readbyqxmd.com/read/28428792/identification-of-candidate-genes-and-biosynthesis-pathways-related-to-fertility-conversion-by-wheat-ktm3315a-transcriptome-profiling
#20
Jiali Ye, Yang Duan, Gan Hu, Xingxia Geng, Gaoming Zhang, Pengjiao Yan, Zihan Liu, Lingli Zhang, Xiyue Song
The Aegilops kotschyi thermo-sensitive cytoplasmic male sterility (K-TCMS) system may facilitate hybrid wheat (Triticum aestivum L.) seed multiplication and production. The K-TCMS line is completely male sterile during the normal wheat-growing season, whereas its fertility can be restored in a high-temperature environment. To elucidate the molecular mechanisms responsible for male sterility/fertility conversion and candidate genes involved with pollen development in K-TCMS, we employed RNA-seq to sequence the transcriptomes of anthers from K-TCMS line KTM3315A during development under sterile and fertile conditions...
2017: Frontiers in Plant Science
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