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Z B Chen, M M Pu, J Yao, X Cao, L Cheng
Objective: To screen the key microRNAs targeting Notch signaling pathway in inner ear and investigate its potential regulating function. Methods: The interaction network and the Core-Notch network, involved with key genes in Notch signal pathway and differential-expressed microRNAs in inner ear, were constructed by bioinformatics methods. The important microRNAs in regulating Notch signaling pathway were screened via topological and GO analysis, followed by in vivo and in vitro investigation. Results: MiRNA-384-5p was identified as a key regulator specifically expressed in mouse brain and inner ear, which could down-regulate Notch1 ...
November 7, 2018: Zhonghua Er Bi Yan Hou Tou Jing Wai Ke za Zhi, Chinese Journal of Otorhinolaryngology Head and Neck Surgery
Chenlei Zhu, Dong Cheng, Xubin Qiu, Ming Zhuang, Zhiwei Liu
BACKGROUND/AIMS: Long noncoding RNAs (lncRNAs) have been a research hotspot, as they play important roles in tumor development. However, their expression pattern and biological function in osteosarcoma have not yet been clarified. METHODS: Differentially expressed lncRNAs in osteosarcoma and paracarcinoma tissues were identified by screening an lncRNA microarray, and candidate lncRNAs were verified by quantitative real-time PCR (qRT-PCR). A series of bioinformatics and molecular biological methods were adopted to investigate the interaction among lncRNA, microRNA (miRNA), and miRNA target genes during the development and occurrence of osteosarcoma...
November 19, 2018: Cellular Physiology and Biochemistry
Chenxing Zhang, Chenyue Zhang, Jiamao Lin, Haiyong Wang
BACKGROUND/AIMS: An increasing number of studies have suggested that circular RNAs (circRNAs) have vital roles in carcinogenesis and tumor progression. However, the function of circRNAs in hepatocellular carcinoma (HCC) remains poorly characterized. METHODS: We investigated the levels of circRNAs in patients with HCC to identify potential diagnostic biomarkers. We examined circRNA expression profiles in liver tumors and paired non-cancerous liver tissues from three HCC patients with cancer thrombus using a circRNA microarray...
November 19, 2018: Cellular Physiology and Biochemistry
Sonia Gioffré, Veronica Ricci, Chiara Vavassori, Clarissa Ruggeri, Mattia Chiesa, Ivana Alfieri, Silvia Zorzan, Marta Buzzetti, Giuseppina Milano, Alessandro Scopece, Laura Castiglioni, Luigi Sironi, Giulio Pompilio, Gualtiero I Colombo, Yuri D'Alessandra
BACKGROUND: Doxorubicin (DOX) is a chemotherapeutic drug limited in its usefulness by an adverse side effect, cardiotoxicity. The mechanisms leading to this detrimental occurrence are not completely clear, and lately many authors focused their attention on the possible role of microRNAs (miRNAs), small regulators of cardiovascular functions, in this phenomenon. Notably, these molecules recently emerged also as potential circulating biomarkers of several cardiac diseases. Thus, the aim of this study was the simultaneous investigation of circulating and cardiac tissue miRNAs expression upon DOX treatment in vivo...
November 16, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Ara Jo, Hee-Eun Lee, Heui-Soo Kim
Horses (Equus caballus) have been domesticated and bred to enhance speed, strength, and agility. Members of the Equus caballus Endogenous Retrovirus (EqERV) family affect several of these abilities in horses. EqERV elements have been integrated in the horse genome during evolution and generate repeat elements such as long terminal repeats (LTRs). LTR sequences are involved in retrovirus replication and play an essential function in post-transcriptional control mechanisms, such as by providing binding sites for microRNAs (miRNAs) or generating miRNA precursors...
November 16, 2018: Gene
Haining Luo, Ying Han, Jiao Liu, Yunshan Zhang
This study aimed to determine the microRNA (miRNA) profiles in granulosa cells (GCs) from the follicular fluid (FF) of patients with varying levels of ovarian reserve function. We included 45 women undergoing in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) treatment. After collecting GCs from each patient, total RNA was extracted from 12 samples. Using Illumina/deep-sequencing technology, we analyzed the small RNAs in each group. Using the R package, we identified the differentially expressed (DE) miRNAs among patients with varying levels of ovarian reserve function...
November 16, 2018: Gene
Jun Li, Alicia T Lamere
Motivation: In the analysis of RNA-Seq data, detecting differentially expressed (DE) genes has been a hot research area in recent years and many methods have been proposed. DE genes show different average expression levels in different sample groups, and thus can be important biological markers. While generally very successful, these methods need to be further tailored and improved for cancerous data, which often features quite diverse expression in the samples from the cancer group, and this diversity is much larger than that in the control group...
November 19, 2018: Bioinformatics
Eugenio Del Prete, Angelo Facchiano, Pietro Liò
Coeliac disease (CD) is a complex, multifactorial pathology caused by different factors, such as nutrition, immunological response and genetic factors. Many autoimmune diseases are comorbidities for CD, and a comprehensive and integrated analysis with bioinformatics approaches can help in evaluating the interconnections among all the selected pathologies. We first performed a detailed survey of gene expression data available in public repositories on CD and less commonly considered comorbidities. Then we developed an innovative pipeline that integrates gene expression, cell-type data and online resources (e...
November 16, 2018: Briefings in Bioinformatics
Carine Rey, Philippe Veber, Bastien Boussau, Marie Sémon
Motivation: RNA sequencing is a widely used approach to obtain transcript sequences in non-model organisms, notably for performing comparative analyses. However, current bioinformatic pipelines do not take full advantage of pre-existing reference data in related species for improving RNA-seq assembly, annotation, and gene family reconstruction. Results: We built an automated pipeline named CAARS to combine novel data from RNA-Seq experiments with existing multi-species gene family alignments...
November 19, 2018: Bioinformatics
Henrik Failmezger, Ezgi Dursun, Sebastian Dümcke, Max Endele, Don Poron, Timm Schroeder, Anne Krug, Achim Tresch
Motivation: Recent imaging technologies allow for high-throughput tracking of cells as they migrate, divide, express fluorescent markers, and change their morphology. The interpretation of these data requires unbiased, efficient statistical methods that model the dynamics of cell phenotypes. Results: We introduce treeHFM, a probabilistic model which generalizes the theory of hidden Markov models to tree structured data. While accounting for the entire genealogy of a cell, treeHFM categorizes cells according to their primary phenotypic features...
November 19, 2018: Bioinformatics
Ameen Eetemadi, Ilias Tagkopoulos
Motivation: Gene expression prediction is one of the grand challenges in computational biology. The availability of transcriptomics data combined with recent advances in artificial neural networks provide an unprecedented opportunity to create predictive models of gene expression with far reaching applications. Results: We present the Genetic Neural Network (GNN), an artificial neural network for predicting genome-wide gene expression given gene knockouts and master regulator perturbations...
November 19, 2018: Bioinformatics
Xiang Wang, Kai Bin Hu, You Qian Zhang, Chun Jian Yang, Han Hui Yao
Cholangiocarcinoma (CCA) is a highly malignant and poorly differentiated bile duct cancer with an extremely poor prognosis, but the pathogenesis of CCA remains not well-known. Attention has been increasingly focused on long noncoding RNAs, which plays an important role in tumorigenesis. However, the roles of cancer specific lncRNA and its related competitive endogenous RNAs (ceRNA) network in CCA remain elusive. In this study, we comprehensively integrated expression profiles, including data on mRNAs, lncRNAs and miRNAs obtained from 36 CCA tissues and 9 normal tissues in The Cancer Genome Atlas...
November 7, 2018: Cancer Biomarkers: Section A of Disease Markers
Qianfeng Zhuang, Jie Shen, Zhen Chen, Mingran Zhang, Min Fan, Dong Xue, Hao Lu, Renfang Xu, Xiaozhou He, Jianquan Hou
OBJECTIVE: Renal cancer accounts for about 3% of human cancer, and clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cancer. Recently, microRNAs (miRNAs) are found to be the biomarkers for cancer diagnosis, prognosis and the targets for tumor management. This study aimed to examine the expression of miR-337-3p in ccRCC and to elucidate the molecular mechanisms underlying miR-337-3p-mediated ccRCC progression. METHODS: The miRNA and mRNA expression levels in ccRCC cells and tissues were measured by qRT-PCR...
November 4, 2018: Cancer Biomarkers: Section A of Disease Markers
Xiaohui Huang, Rui Zhong, Xiukui He, Qingshan Deng, Xiuhong Peng, Jieming Li, Xiping Luo
Progesterone is often used to protect the endometrium and prevent endometrial cancer. An intensive study on its molecular mechanism in endometrial cancer would contribute to the development of more promising therapies. Relevant lncRNAs and mRNAs expression data in endometrial cancer cell line Ishikawa pretreated and post-treated with progesterone were derived from Gene Expression Omnibus (accession no. GSE29435), and then we analyzed long noncoding RNAs and mRNAs with differential expressions in two different conditions...
November 19, 2018: IUBMB Life
Daniele Raimondi, Gabriele Orlando, Francesco Tabaro, Tom Lenaerts, Marianne Rooman, Yves Moreau, Wim F Vranken
Next generation sequencing technologies are providing increasing amounts of sequencing data, paving the way for improvements in clinical genetics and precision medicine. The interpretation of the observed genomic variants in the light of their phenotypic effects is thus emerging as a crucial task to solve in order to advance our understanding of how exomic variants affect proteins and how the proteins' functional changes affect human health. Since the experimental evaluation of the effects of every observed variant is unfeasible, Bioinformatics methods are being developed to address this challenge in-silico, by predicting the impact of millions of variants, thus providing insight into the deleteriousness landscape of entire proteomes...
November 19, 2018: Scientific Reports
Meng Wang, Dong Han, Ziming Yuan, Hanqing Hu, Zhixun Zhao, Runkun Yang, Yinghu Jin, Chaoxia Zou, Yinggang Chen, Guiyu Wang, Xu Gao, Xishan Wang
Chemotherapy failure is the major cause of recurrence and poor prognosis in colorectal cancer (CRC) patients. The role of the differentially expressed lncRNAs in 5-Fluorouracil chemoresistance has not fully explained. Here, we observed lncRNA H19 was associated with the 5-Fu resistance in CRC. Quantitative analysis indicated that H19 was significantly increased in recurrent CRC patient samples. Kaplan-Meier survival analysis indicated that high H19 expression in CRC tissues was significantly associated with poor recurrent free survival...
November 19, 2018: Cell Death & Disease
Georges Dagher, Maria Luisa Lavitrano, Paul Hofman
Human biological samples are key resources in unravelling physiopathological factors underlying diseases and influencing their outcome. By making use of these resources, genomics, proteomics and molecular imaging techniques have achieved unprecedented progress in the past decade. The development of genomics platforms, molecular imaging as well as bioinformatics allowed a significant development of the biomarkers field thus realizing significant advances towards personalized medicine. The exponential increase of data, their complexity, the necessity of their integration for analysis require the development of appropriate infrastructures...
October 2018: Médecine Sciences: M/S
Yarden Golan, Adrian Lehvy, Guy Horev, Yehuda G Assaraf
Loss of function (LoF) mutations in the zinc transporter SLC30A2/ZnT2 result in impaired zinc secretion into breast milk consequently causing transient neonatal zinc deficiency (TNZD) in exclusively breastfed infants. However, the frequency of TNZD causing alleles in the general population is yet unknown. Herein, we investigated 115 missense SLC30A2/ZnT2 mutations from the ExAC database, equally distributed in the entire coding region, harboured in 668 alleles in 60 706 healthy individuals of diverse ethnicity...
November 18, 2018: Journal of Cellular and Molecular Medicine
Fanqiang Meng, Xiaoyu Zhu, Ting Nie, Fengxia Lu, Xiaomei Bie, Yingjian Lu, Frances Trouth, Zhaoxin Lu
Pullulanase plays an important role as a starch hydrolysis enzyme in the production of bio-fuels and animal feed, and in the food industry. Compared to the methods currently used for pullulanase production, synthesis by Bacillus subtilis would be safer and easier. However, the current yield of pullulanase from B. subtilis is low to meet industrial requirements. Therefore, it is necessary to improve the yield of pullulanase by B. subtilis . In this study, we mined 10 highly active promoters from B. subtilis based on transcriptome and bioinformatic data...
2018: Frontiers in Microbiology
Belinda Hernández, Adrian E Raftery, Stephen R Pennington, Andrew C Parnell
Bayesian Additive Regression Trees (BART) is a statistical sum of trees model. It can be considered a Bayesian version of machine learning tree ensemble methods where the individual trees are the base learners. However for datasets where the number of variables p is large the algorithm can become inefficient and computationally expensive. Another method which is popular for high dimensional data is random forests, a machine learning algorithm which grows trees using a greedy search for the best split points...
July 2018: Statistics and Computing
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