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Zhijun Zeng, Xia Huo, Yu Zhang, Machteld N Hylkema, Yousheng Wu, Xijin Xu
This study explored the effects of maternal exposure to e-waste environmental heavy metals on neonatal DNA methylation patterns. Neonatal umbilical cord blood (UCB) samples were collected from participants that resided in an e-waste recycling area, Guiyu and a nearby non-e-waste area, Haojiang in China. The concentrations of UCB lead (Pb), cadmium (Cd), manganese (Mn) and chromium (Cr) were measured by graphite furnace atomic absorption spectrometry. Epigenome-wide DNA methylation at 473, 844 CpG sites (CpGs) were assessed by Illumina 450 K BeadChip...
January 6, 2019: Environmental Research
Dongjuan Yuan, Shiqi Luo, Lian Xu, Xingda Zeng, Zhongdao Wu
MicroRNA plays a vital role in the regulation of host-parasite interaction. In recent years, genomic and transcriptomic resources have become increasingly available for many helminths, but only a limited number of reports in this area are on the regulatory effects of host microRNAs on parasitic nematodes. In this work, we screened increased expression of host microRNAs after nematode infection from miRNA-seq data and predicted target genes by combined bioinformatics analysis and transcriptional profiling. We elucidated regulatory effects of one host miRNA on nematode infection using miRNA inhibitor and adeno-associated virus (AAV)-based TuD miRNA inhibitor...
February 11, 2019: Biochimica et biophysica acta. Gene regulatory mechanisms
Juliah Khayeli Akhwale, Manfred Rohde, Christine Rohde, Boyke Bunk, Cathrin Spröer, Hans-Peter Klenk, Hamadi Iddi Boga, Johannes Wittmann
We report complete genome sequences of eight bacteriophages isolated from Haloalkaline Lake Elmenteita found on the floor of Kenyan Rift Valley. The bacteriophages were sequenced, annotated and a comparative genomic analysis using various Bioinformatics tools carried out to determine relatedness of the bacteriophages to each other, and to those in public databases. Basic genome properties like genome size, percentage coding density, number of open reading frames, percentage GC content and gene organizations revealed the bacteriophages had no relationship to each other...
2019: PloS One
Saúl Jijón-Moreno, Beatriz Eugenia Baca, Diana Carolina Castro-Fernández, Alberto Ramírez-Mata
Azospirillum brasilense is one of the most studied species of diverse agronomic plants worldwide. The benefits conferred to plants inoculated with Azospirillum have been primarily attributed to its capacity to fix atmospheric nitrogen and synthesize phytohormones, especially indole-3-acetic acid (IAA). The principal pathway for IAA synthesis involves the intermediate metabolite indole pyruvic acid. Successful colonization of plants by Azospirillum species is fundamental to the ability of these bacteria to promote the beneficial effects observed in plants...
2019: PloS One
Ana Julia Velez Rueda, Guillermo I Benítez, Julia Marchetti, Marcia Anahí Hasenahuer, María Silvina Fornasari, Nicolas Palopoli, Gustavo Parisi
The dynamic nature of technological developments invites us to rethink the learning spaces. In this context, science education can be enriched by the contribution of new computational resources, making the educational process more up-to-date, challenging, and attractive. Bioinformatics is a key interdisciplinary field, contributing to the understanding of biological processes that is often underrated in secondary schools. As a useful resource in learning activities, bioinformatics could help in engaging students to integrate multiple fields of knowledge (logical-mathematical, biological, computational, etc...
February 2019: PLoS Computational Biology
Giulia Palermo
CRISPR-Cas9 is a bacterial immune system with exciting applications for genome editing. In spite of extensive experimental characterization, the active site chemistry of the RuvC domain - which performs DNA cleavages - has remained elusive. Its knowledge is key for structure-based engineering aimed at improving DNA cleavages. Here, we deliver an in-depth characterization by using quantum-classical (QM/MM) molecular dynamics (MD) simulations and a Gaussian accelerated MD method, coupled with bioinformatics analysis...
February 14, 2019: Journal of Chemical Information and Modeling
Chengmin Xuan, Yong Gao, Mingwei Jin, Shumei Xu, Lei Wang, Yuan Wang, Rui Han, Kunpeng Shi, Xincheng Chen, Qi An
The ubiquitin-proteasome system is the primary cellular pathway for protein degradation, mediating 80% of intracellular protein degradation. Because of the widespread presence of ubiquitin-modified protein substrates, ubiquitination can regulate a variety of cellular activities including cell proliferation, apoptosis, autophagy, endocytosis, DNA damage repair, and immune responses. With the continuous generation of genomics data in recent years it has become particularly important to analyze these data effectively and reasonably...
February 14, 2019: IUBMB Life
Gerardo A Vitiello, Timothy G Bowler, Mengyuan Liu, Benjamin D Medina, Jennifer Q Zhang, Nesteene J Param, Jennifer K Loo, Rachel L Goldfeder, Frederic Chibon, Ferdinand Rossi, Shan Zeng, Ronald P DeMatteo
Gastrointestinal stromal tumor (GIST) is the most common human sarcoma, frequently characterized by an oncogenic mutation in the KIT or platelet-derived growth factor receptor alpha (PDGFRA) genes. We performed RNA sequencing of 75 human GIST tumors from 75 patients, comprising the largest cohort of GISTs sequenced to date, in order to discover differences in the immune infiltrates of KIT and PDGFRA-mutant GIST. Through bioinformatics, immunohistochemistry, and flow cytometry, we found that PDGFRA-mutant GISTs harbored more immune cells with increased cytolytic activity when compared to KIT-mutant GISTs...
February 14, 2019: Journal of Clinical Investigation
Huan Liu, Li Liu, Hong Zhu
To screen for differentially expressed microRNAs (miRNAs) between recurrent and primary cervical cancer patient samples, and investigate the prognostic value of the identified miRNAs, based on The Cancer Genome Atlas (TCGA) database. Differentially expressed miRNAs between recurrent and primary cervical cancer, identified from TCGA database, were selected by edgeR package in the R software. Overlapping target genes predicted by TargetScan, miRTarBase, and miRDB online analysis tools were chosen for Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis...
February 14, 2019: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Karolina Mikulska-Ruminska, Indira H Shrivastava, James Krieger, She Zhang, Hongchun Li, Hulya Bayir, Sally E Wenzel, Andrew P VanDemark, Valerian E Kagan, Ivet Bahar
Accurate modeling of structural dynamics of proteins and their differentiation across different species can help us understand generic mechanisms of function shared by family members and the molecular basis of the specificity of individual members. We focused here on the family of lipoxygenases, enzymes that catalyze lipid oxidation, the mammalian and bacterial structures of which have been elucidated. We present a systematic method of approach for characterizing the sequence, structure, dynamics and allosteric signaling properties of these enzymes using a combination of structure-based models and methods, and bioinformatics tools applied to a dataset of 88 structures...
February 14, 2019: Journal of Chemical Information and Modeling
Wei Wu, Ke He, Qian Guo, Jingdi Chen, Mengjiao Zhang, Kai Huang, Dongmei Yang, Lu Wu, Yunchao Deng, Xu Luo, Honggang Yu, Qianshan Ding, Guoan Xiang
In this study, microarray data analysis, real-time quantitative PCR and immunohistochemistry were used to detect the expression levels of SSRP1 in colorectal cancer (CRC) tissue and in corresponding normal tissue. The association between structure-specific recognition protein 1 (SSRP1) expression and patient prognosis was examined by Kaplan-Meier analysis. SSRP1 was knocked down and overexpressed in CRC cell lines, and its effects on proliferation, cell cycling, migration, invasion, cellular energy metabolism, apoptosis, chemotherapeutic drug sensitivity and cell phenotype-related molecules were assessed...
February 14, 2019: Journal of Cellular and Molecular Medicine
Ulfuara Shefa, Junyang Jung
A Schwann cell has regenerative capabilities and is an important cell in the peripheral nervous system. This microarray study is part of a bioinformatics study that focuses mainly on Schwann cells. Microarray data provide information on differences between microarray-based and experiment-based gene expression analyses. According to microarray data, several genes exhibit increased expression (fold change) but they are weakly expressed in experimental studies (based on morphology, protein and mRNA levels). In contrast, some genes are weakly expressed in microarray data and highly expressed in experimental studies; such genes may represent future target genes in Schwann cell studies...
June 2019: Neural Regeneration Research
Boris Kovacic, Margit Rosner, Karin Schlangen, Nina Kramer, Markus Hengstschläger
Genetic and biochemical screening approaches often fail to identify functionally relevant pathway networks because many signaling proteins contribute to multiple gene ontology pathways. We developed a DRUGPATH-approach to predict pathway-interactomes from high-content drug screen data. DRUGPATH is based upon combining z-scores of effective inhibitors with their corresponding and validated targets. We test DRUGPATH by comparing homeostatic pathways in human embryonic stem cells (hESCs), human induced pluripotent stem cells (hiPSCs) and human amniotic fluid stem cells (hAFSCs)...
February 13, 2019: Scientific Reports
Delfina A Ré, Patricia L M Lang, Cristian Yones, Agustin L Arce, Georgina Stegmayer, Diego Milone, Pablo A Manavella
Plants use molecular mechanisms to sense temperatures, trigger quick adaptive responses, and thereby cope with environmental changes. MicroRNAs (miRNAs) are key regulators of plants' development under such conditions. The catalytic action of DICER LIKE 1 (DCL1), in conjunction with HYPONASTIC LEAVES 1 (HYL1) and SERRATE (SE), produces miRNAs from double-stranded RNAs. As plants lack a stable internal temperature to which enzymatic reactions could be optimized during evolution, reactions like miRNA processing, have to be adjusted to fluctuating environmental temperatures...
February 13, 2019: Development
Emanuela Brunetto, Lucia De Monte, Gianpaolo Balzano, Barbara Camisa, Vincenzo Laino, Michela Riba, Silvia Heltai, Marco Bianchi, Claudio Bordignon, Massimo Falconi, Attilio Bondanza, Claudio Doglioni, Maria Pia Protti
BACKGROUND: The thymic stromal lymphopoietin (TSLP), a key cytokine for development of Th2 immunity, is produced by cancer associated fibroblasts (CAFs) in pancreatic cancer where predominant tumor infiltrating Th2 over Th1 cells correlates with reduced patients' survival. Which cells and molecules are mostly relevant in driving TSLP secretion by CAFs in pancreatic cancer is not defined. METHODS: We performed in vitro, in vivo and ex-vivo analyses. For in vitro studies we used pancreatic cancer cell lines, primary CAFs cultures, and THP1 cells...
February 13, 2019: Journal for Immunotherapy of Cancer
Rongjun Zou, Dingwen Zhang, Lei Lv, Wanting Shi, Zijiao Song, Bin Yi, Bingjia Lai, Qian Chen, Songran Yang, Ping Hua
BACKGROUND: Atrial fibrillation (AF) is one of the most prevalent sustained arrhythmias, however, epidemiological data may understate its actual prevalence. Meanwhile, AF is considered to be a major cause of ischemic strokes due to irregular heart-rhythm, coexisting chronic vascular inflammation, and renal insufficiency, and blood stasis. We studied co-expressed genes to understand relationships between atrial fibrillation (AF) and stroke and reveal potential biomarkers and therapeutic targets of AF-related stroke...
February 13, 2019: Journal of Translational Medicine
Jingwei Li, Xiaofei Liu, Hongzhi Chen, Ziyuan Sun, Hanhan Chen, Lei Wang, Xiaohui Sun, Xiangqi Li
BACKGROUND: Development of safe and effective chemopreventive agents is a winning strategy in reducing the morbidity and mortality of breast cancer. The current study was to investigate the mechanism-based chemopreventive potential of a Chinese herb formula Yanghe Huayan (YHHY) Decoction on the classical 7,12-dimethylbenz(a)anthracene (DMBA) induced rat mammary carcinogenesis model. METHODS: Female Sprague-Dawley rats at 42 days of age were orally administered with a human equivalent dose of YHHY Decoction at 0...
February 13, 2019: BMC Complementary and Alternative Medicine
Na Shen, Ting Wang, Delei Li, Aiguo Liu, Yanjun Lu
BACKGROUND: Deafness, autosomal recessive 77 (DFNB77) is a rare non-syndromic hearing loss (NSHL) worldwide, which is caused by deleterious variants within lipoxygenase homology domains 1 (LOXHD1). Here we identified that a novel missense variant of LOXHD1 was associated with NSHL in a Chinese family under consanguineous marriage. CASE PRESENTATION: A 28-year-old woman suffered a bilateral profound NSHL. Impedance audiometry, temporal bone computerized tomography (TBCT) scans and magnetic resonance imaging-inner ear hydrography (MRI-IEH) did not find any obvious abnormality of middle or inner ear...
February 13, 2019: BMC Medical Genetics
Yongzhi Yang, Ying Li, Qiao Chen, Yongshuai Sun, Zhiqiang Lu
BACKGROUND: With the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software for detecting footprints of WGDs has been restricted to a well-assembled genome. However, the massive poor quality genomes and the more accessible transcriptomes have been largely ignored, and in theoretically they are also likely to contribute to detect WGD using dS based method...
February 13, 2019: BMC Bioinformatics
Dongliang Yu, Ying Wan, Hidetaka Ito, Xiaoxia Ma, Tian Xie, Tingzhang Wang, Chaogang Shao, Yijun Meng
BACKGROUND: MicroRNAs (miRNAs) constitute a well-known small RNA (sRNA) species with important regulatory roles. To date, several bioinformatics tools have been developed for large-scale prediction of miRNAs based on high-throughput sequencing data. However, some of these tools become invalid without reference genomes, while some tools cannot supply user-friendly outputs. Besides, most of the current tools focus on the importance of secondary structures and sRNA expression patterns for miRNA prediction, while they do not pay attention to miRNA processing for reliability check...
February 13, 2019: BMC Genomics
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