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https://www.readbyqxmd.com/read/28454467/investigation-of-differentially-expressed-micrornas-and-genes-in-cervical-cancer-using-an-integrated-bioinformatics-analysis
#1
Zhanzhan Xu, Yu Zhou, Fang Shi, Yexuan Cao, Thi Lan Anh Dinh, Jing Wan, Min Zhao
Cervical cancer is one of the most common types of cancer among women worldwide. In order to identify the microRNAs (miRNAs/miRs) and mRNAs associated with the carcinogenesis of cervical cancer, and to investigate the molecular mechanisms of cervical cancer, an miRNA microarray, GSE30656, and 3 mRNA microarrays, GSE63514, GSE39001 and GSE9750, for cervical cancer were retrieved from Gene Expression Omnibus. These datasets were analyzed in order to obtain differentially-expressed genes (DEGs) and miRNAs using the GEO2R tool...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454465/microarray-based-analysis-of-gene-regulation-by-mesenchymal-stem-cells-in-breast-cancer
#2
Ming Zhang, Chang E Gao, Wen Hui Li, Yi Yang, Li Chang, Jian Dong, Yan Xin Ren, De Dian Chen
Breast cancer is one of the most common malignant tumors with a high case-fatality rate among women. The present study aimed to investigate the effects of mesenchymal stem cells (MSCs) on breast cancer by exploring the potential underlying molecular mechanisms. The expression profile of GSE43306, which refers to MDA-MB-231 cells with or without a 1:1 ratio of MSCs, was downloaded from Gene Expression Omnibus database for differentially expressed gene (DEG) screening. The Database for Annotation, Visualization and Integrated Discovery was used for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454442/identification-of-target-genes-of-cediranib-in-alveolar-soft-part-sarcoma-using-a-gene-microarray
#3
Wenhua Jiang, Pengfei Liu, Xiaodong Li, Ping Wang
The aim of the present study was to identify the target genes of cediranib and the associated signaling pathways in alveolar soft part sarcoma (ASPS). A microarray dataset (GSE32569) was obtained from the Gene Expression Omnibus database. The R software package was used for data normalization and screening of differentially expressed genes (DEGs). The Database for Annotation, Visualization and Integrated Discovery was used to perform Gene Ontology analysis. Gene Set Enrichment Analysis was performed to obtain the up- and downregulated pathways in ASPS...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28453502/identification-of-key-genes-affecting-results-of-hyperthermia-in-osteosarcoma-based-on-integrative-chip-seq-targetscan-analysis
#4
Yuxia Shi, Fan Yang, Shuqing Wei, Gang Xu
BACKGROUND The purpose of this study was to research the effects of hyperthermia on osteosarcoma (OS) by integrating the Chromatin Immunoprecipitation with the generation sequencing (ChIP-Seq) and TargetScan analysis of heat shock transcription factor 1 (HSF1). MATERIAL AND METHODS The HSF1 ChIP-seq dataset of GSE60984 was downloaded from the Gene Expressed Omnibus (GEO) database. The HSF1-binding sites were screened by MACS2 in OS cells after 10 and 20 min of hyperthermia, and they were annotated using the ChIPseeker package...
April 28, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28453300/psychiatry-sex-and-science-the-making-of-adolescent-motherhood-in-southern-brazil
#5
Dominique P Béhague
Research linking teen motherhood to psychoneurodevelopmental causes and pathologies has proliferated in the past two decades. In Brazil, a psychodevelopmental project of teen motherhood has gained traction despite many experts' long-standing commitment to psychodynamic psychiatry and social epidemiology, generating epistemic tension rather than substitution. Drawing on historical ethnography conducted in Southern Brazil, I explore how this project materialized through the co-production of epistemic struggles, remedial interventions, and ontological politics...
April 28, 2017: Medical Anthropology
https://www.readbyqxmd.com/read/28449114/neuro-symbolic-representation-learning-on-biological-knowledge-graphs
#6
Mona Alshahrani, Mohammed Asif Khan, Omar Maddouri, Akira R Kinjo, Núria Queralt-Rosinach, Robert Hoehndorf
Motivation: Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge. Results: We develop a novel method for feature learning on biological knowledge graphs...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28448670/molecular-mechanisms-underlying-the-filtration-bleb-maintaining-effects-of-suberoylanilide-hydroxamic-acid-saha
#7
Akiko Futakuchi, Toshihiro Inoue, Tomokazu Fujimoto, Utako Kuroda, Miyuki Inoue-Mochita, Eri Takahashi, Saori Ohira, Hidenobu Tanihara
Purpose: Suberoylanilide hydroxamic acid (SAHA) has been shown to support the maintenance of experimental filtration blebs in animal models. This study was performed to investigate the molecular mechanisms underlying the bleb-maintaining effects of SAHA in modulating wound healing activities of conjunctival fibroblasts. Methods: Human conjunctival fibroblasts (HConFs) were pretreated with SAHA before treatment with TGF-β2. Microarray-based screening was used to investigate the gene expression profiles...
April 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28448529/a-genome-wide-analysis-of-the-rna-guided-silencing-pathway-in-coffee-reveals-insights-into-its-regulatory-mechanisms
#8
Christiane Noronha Fernandes-Brum, Pâmela Marinho Rezende, Thales Henrique Cherubino Ribeiro, Raphael Ricon de Oliveira, Thaís Cunha de Sousa Cardoso, Laurence Rodrigues do Amaral, Matheus de Souza Gomes, Antonio Chalfun-Junior
microRNAs (miRNAs) are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs) are derived from double-stranded RNA (dsRNA) or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL) in processing the smallRNAs (sRNAs) and ARGONAUTE (AGO) as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR), Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover...
2017: PloS One
https://www.readbyqxmd.com/read/28448031/transcriptomic-analysis-of-c-elegans-rna-sequencing-data-through-the-tuxedo-suite-on-the-galaxy-project
#9
Francis R G Amrit, Arjumand Ghazi
Next generation sequencing (NGS) technologies have revolutionized the nature of biological investigation. Of these, RNA Sequencing (RNA-Seq) has emerged as a powerful tool for gene-expression analysis and transcriptome mapping. However, handling RNA-Seq datasets requires sophisticated computational expertise and poses inherent challenges for biology researchers. This bottleneck has been mitigated by the open access Galaxy project that allows users without bioinformatics skills to analyze RNA-Seq data, and the Database for Annotation, Visualization, and Integrated Discovery (DAVID), a Gene Ontology (GO) term analysis suite that helps derive biological meaning from large data sets...
April 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28446759/transcriptomic-response-of-durum-wheat-to-nitrogen-starvation
#10
Pasquale L Curci, Riccardo Aiese Cigliano, Diana L Zuluaga, Michela Janni, Walter Sanseverino, Gabriella Sonnante
Nitrogen (N) is a key macronutrient representing a limiting factor for plant growth and development and affects productivity in wheat. In this study, durum wheat response to N chronic starvation during grain filling was investigated through a transcriptomic approach in roots, leaves/stems, flag leaf and spikes of cv. Svevo. Nitrogen stress negatively influenced plant height, tillering, flag leaf area, spike and seed traits, and total N content. RNA-seq data revealed 4,626 differentially expressed genes (DEGs)...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446749/dynamics-of-chromatin-accessibility-during-tgf-%C3%AE-induced-emt-of-ras-transformed-mammary-gland-epithelial-cells
#11
Mayu Arase, Yusuke Tamura, Natsumi Kawasaki, Kazunobu Isogaya, Ryo Nakaki, Anna Mizutani, Shuichi Tsutsumi, Hiroyuki Aburatani, Kohei Miyazono, Daizo Koinuma
Epithelial-mesenchymal transition (EMT) is induced by transforming growth factor (TGF)-β and facilitates tumor progression. We here performed global mapping of accessible chromatin in the mouse mammary gland epithelial EpH4 cell line and its Ras-transformed derivative (EpRas) using formaldehyde-assisted isolation of regulatory element (FAIRE)-sequencing. TGF-β and Ras altered chromatin accessibility either cooperatively or independently, and AP1, ETS, and RUNX binding motifs were enriched in the accessible chromatin regions of EpH4 and EpRas cells...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446635/a-motif-and-amino-acid-bias-bioinformatics-pipeline-to-identify-hydroxyproline-rich-glycoproteins
#12
Kim L Johnson, Andrew M Cassin, Andrew Lonsdale, Antony Bacic, Monika Susanne Doblin, Carolyn J Schultz
Intrinsically disordered proteins (IDPs) are functional proteins that lack a well-defined three dimensional structure. The study of IDPs is a rapidly growing area as the crucial biological functions of more of these proteins are uncovered. In plants, IDPs are implicated in plant stress responses, signalling and regulatory processes. A superfamily of cell wall proteins, the hydroxyproline-rich glycoproteins (HRGPs), have characteristic features of IDPs. Their protein backbones are rich in the disordering amino acid proline, they contain repeated sequence motifs and extensive post-translational modifications (glycosylation) and have been implicated in many biological functions...
April 26, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28446531/mining-exosomal-genes-for-pancreatic-cancer-targets
#13
Amy Makler, Ramaswamy Narayanan
BACKGROUND: Exosomes, cell-derived vesicles encompassing lipids, DNA, proteins coding genes and noncoding RNAs (ncRNAs) are present in diverse body fluids. They offer novel biomarker and drug therapy potential for diverse diseases, including cancer. MATERIALS AND METHODS: Using gene ontology, exosomal genes database and GeneCards metadata analysis tools, a database of cancer-associated protein coding genes and ncRNAs (n=2,777) was established. Variant analysis, expression profiling and pathway mapping were used to identify putative pancreatic cancer exosomal gene candidates...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28446150/signatures-of-co-evolutionary-host-pathogen-interactions-in-the-genome-of-the-entomopathogenic-nematode-steinernema-carpocapsae
#14
Mitzi Flores-Ponce, Miguel Vallebueno-Estrada, Eduardo González-Orozco, Hilda E Ramos-Aboites, J Noé García-Chávez, Nelson Simões, Rafael Montiel
BACKGROUND: The entomopathogenic nematode Steinernema carpocapsae has been used worldwide as a biocontrol agent for insect pests, making it an interesting model for understanding parasite-host interactions. Two models propose that these interactions are co-evolutionary processes in such a way that equilibrium is never reached. In one model, known as "arms race", new alleles in relevant genes are fixed in both host and pathogens by directional positive selection, producing recurrent and alternating selective sweeps...
April 26, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28445746/crosstalk-and-the-dynamical-modularity-of%C3%A2-feed-forward-loops-in-transcriptional-regulatory-networks
#15
Michael A Rowland, Ahmed Abdelzaher, Preetam Ghosh, Michael L Mayo
Network motifs, such as the feed-forward loop (FFL), introduce a range of complex behaviors to transcriptional regulatory networks, yet such properties are typically determined from their isolated study. We characterize the effects of crosstalk on FFL dynamics by modeling the cross regulation between two different FFLs and evaluate the extent to which these patterns occur in vivo. Analytical modeling suggests that crosstalk should overwhelmingly affect individual protein-expression dynamics. Counter to this expectation we find that entire FFLs are more likely than expected to resist the effects of crosstalk (≈20% for one crosstalk interaction) and remain dynamically modular...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445484/transcriptome-analysis-of-creeping-bentgrass-exposed-to-drought-stress-and-polyamine-treatment
#16
Yingmei Ma, Vijaya Shukla, Emily B Merewitz
Creeping bentgrass is an important cool-season turfgrass species sensitive to drought. Treatment with polyamines (PAs) has been shown to improve drought tolerance; however, the mechanism is not yet fully understood. Therefore, this study aimed to evaluate transcriptome changes of creeping bentgrass in response to drought and exogenous spermidine (Spd) application using RNA sequencing (RNA-Seq). The high-quality sequences were assembled and 18,682 out of 49,190 (38%) were detected as coding sequences. A total of 22% and 19% of genes were found to be either up- or down-regulated due to drought while 20% and 34% genes were either up- or down- regulated in response to Spd application under drought conditions, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28444334/antiquity-s-missive-to-transhumanism1
#17
Susan B Levin
To reassure those concerned about wholesale discontinuity between human existence and posthumanity, transhumanists assert shared ground with antiquity on vital challenges and aspirations. Because their claims reflect key misconceptions, there is no shared vision for transhumanists to invoke. Having exposed their misuses of Prometheus, Plato, and Aristotle, I show that not only do transhumanists and antiquity crucially diverge on our relation to ideals, contrast-dependent aspiration, and worthy endeavors but that illumining this divide exposes central weaknesses in transhumanist argumentation...
April 21, 2017: Journal of Medicine and Philosophy
https://www.readbyqxmd.com/read/28443052/gih-qi-beyond-affordance
#18
Yang Lee, Robert E Shaw, Zheng Jin
Ancient Eastern thought posited the ontological integration of the "mind-body world". The body-mind syncretism was a foundational precept in Eastern philosophy in which "Gih" ("Qi") was considered the basic entity of the universe and the human being. This study attempts to build a meta-theory and to demonstrate empirical designs for Gih, discussing the problems of the mind and body, or the subject and object, compared with the concept of "affordance" proposed by ecological approaches. The notion of Gih extends beyond that of affordance in that Gih activates a psychosomatic process between the physical condition and the mental state that facilitates the bi-directional interactions between subject and object...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28440471/time-dependent-differential-expression-of-long-non-coding-rnas-following-peripheral-nerve-injury
#19
Bin Pan, Heng-Xing Zhou, Yi Liu, Jia-Yin Yan, Yao Wang, Xue Yao, Yan-Qiu Deng, Shu-Yi Chen, Lu Lu, Zhi-Jian Wei, Xiao-Hong Kong, Shi-Qing Feng
Long non-coding RNAs (lncRNAs) are widely accepted as key players in various biological processes. However, the roles of lncRNA in peripheral nerve regeneration remain completely unknown. Thus, in this study, we performed microarray analysis to measure lncRNA expression in the distal segment of the sciatic nerve at 0, 3, 7 and 14 days following injury. We identified 5,354 lncRNAs that were differentially expressed: 3,788 lncRNAs were differentially expressed between days 0 and 3; 3,314 lncRNAs were differentially expressed between days 0 and 7; and 2,400 lncRNAs were differentially expressed between days 0 and 14...
April 21, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28440443/microrna-expression-in-esophageal-squamous-cell-carcinoma-novel-diagnostic-and-prognostic-biomarkers
#20
Yan Wang, Jinnan Zhang, Wei Zhao, Donglin Wang, Wenduan Ma, Shengtao Shang, Chao Feng, Haixin Yu
The aim of the present study was to identify more effective molecular diagnostic biomarkers for esophageal squamous cell carcinoma (ESCC). The non‑coding RNA profile GSE43732, generated from 238 paired frozen tissues from 119 patients, was analyzed. Raw data were preprocessed and the differentially expressed miRNAs were screened by limma package with log2 fold change >2. Prognosis‑associated miRNAs were identified using receiver operating characteristic (ROC) and Kaplan-Meier (KM) curve analysis. miRNAs with an area under the ROC curve of ≥0...
April 13, 2017: Molecular Medicine Reports
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