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https://www.readbyqxmd.com/read/29782530/histone-methylation-changes-are-required-for-life-cycle-progression-in-the-human-parasite-schistosoma-mansoni
#1
David Roquis, Aaron Taudt, Kathrin K Geyer, Gilda Padalino, Karl F Hoffmann, Nancy Holroyd, Matt Berriman, Benoît Aliaga, Cristian Chaparro, Christoph Grunau, Ronaldo de Carvalho Augusto
Epigenetic mechanisms and chromatin structure play an important role in development. Their impact is therefore expected to be strong in parasites with complex life cycles and multiple, strikingly different, developmental stages, i.e. developmental plasticity. Some studies have already described how the chromatin structure, through histone modifications, varies from a developmental stage to another in a few unicellular parasites. However, this, to our knowledge, has never been done before in multicellular metazoan parasites...
May 21, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29782485/evaluation-and-application-of-summary-statistic-imputation-to-discover-new-height-associated-loci
#2
Sina Rüeger, Aaron McDaid, Zoltán Kutalik
As most of the heritability of complex traits is attributed to common and low frequency genetic variants, imputing them by combining genotyping chips and large sequenced reference panels is the most cost-effective approach to discover the genetic basis of these traits. Association summary statistics from genome-wide meta-analyses are available for hundreds of traits. Updating these to ever-increasing reference panels is very cumbersome as it requires reimputation of the genetic data, rerunning the association scan, and meta-analysing the results...
May 21, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29777275/overexpression-of-abcb4-contributes-to-acquired-doxorubicin-resistance-in-breast-cancer-cells-in-vitro
#3
Jia-Feng Huang, Chun-Jie Wen, Guo-Zhi Zhao, Yi Dai, Ying Li, Lan-Xiang Wu, Hong-Hao Zhou
PURPOSE: Doxorubicin is one of the most active agents in the first-line therapy for metastatic breast cancer, but its utility is partially limited by the frequent emergence of doxorubicin resistance. In this study, we aimed to investigate the role of ATP-binding cassette sub-family B, member 4 (ABCB4) in acquired doxorubicin resistance in breast cancer cells, as well as its potential mechanism. METHODS: In doxorubicin-sensitive and -resistant breast cancer cell lines MCF-7 and MDA-MB-231, the expression levels of ABCB4 were detected using real-time quantitative PCR and Western blot analysis, the DNA methylation and histone acetylation status of ABCB4 gene were investigated by bisulfite-sequencing PCR (BSP) and chromatin immunoprecipitation (ChIP) assays, and the doxorubicin sensitivity and intracellular doxorubicin accumulation were observed using cell cytotoxicity assay and flow cytometry...
May 18, 2018: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/29776538/rapid-detection-of-calr-type-1-and-type-2-mutations-using-pna-lna-clamping-loop-mediated-isothermal-amplification-on-a-cd-like-microfluidic-chip
#4
Guojun Cao, Jilie Kong, Zhifang Xing, Yigui Tang, Xinju Zhang, Xiao Xu, Zhihua Kang, Xueen Fang, Ming Guan
Bleeding and thrombosis represent common complications in myeloproliferative neoplasms (MPN) and significantly contribute to morbidity and mortality. Molecular markers, including CALR mutations, were considered not only as diagnostic markers, but also as risk factors for bleeding and thrombosis associated with MPN, especially for patients in remote primary hospitals. We sought to develop an easy-to-use assay for the rapid detection of CALR type 1 (CALR-1) and type 2 (CALR-2) mutations in Philadelphia chromosome-negative MPN patients...
September 18, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29775464/biochemical-characterization-of-recbcd-enzyme-from-an-antarctic-pseudomonas-species-and-identification-of-its-cognate-chi-%C3%AF-sequence
#5
Theetha L Pavankumar, Anurag K Sinha, Malay K Ray
Pseudomonas syringae Lz4W RecBCD enzyme, RecBCDPs, is a trimeric protein complex comprised of RecC, RecB, and RecD subunits. RecBCD enzyme is essential for P. syringae growth at low temperature, and it protects cells from low temperature induced replication arrest. In this study, we show that the RecBCDPs enzyme displays distinct biochemical behaviors. Unlike E. coli RecBCD enzyme, the RecD subunit is indispensable for RecBCDPs function. The RecD motor activity is essential for the Chi-like fragments production in P...
2018: PloS One
https://www.readbyqxmd.com/read/29773832/distinct-epigenetic-landscapes-underlie-the-pathobiology-of-pancreatic-cancer-subtypes
#6
Gwen Lomberk, Yuna Blum, Rémy Nicolle, Asha Nair, Krutika Satish Gaonkar, Laetitia Marisa, Angela Mathison, Zhifu Sun, Huihuang Yan, Nabila Elarouci, Lucile Armenoult, Mira Ayadi, Tamas Ordog, Jeong-Heon Lee, Gavin Oliver, Eric Klee, Vincent Moutardier, Odile Gayet, Benjamin Bian, Pauline Duconseil, Marine Gilabert, Martin Bigonnet, Stephane Garcia, Olivier Turrini, Jean-Robert Delpero, Marc Giovannini, Philippe Grandval, Mohamed Gasmi, Veronique Secq, Aurélien De Reyniès, Nelson Dusetti, Juan Iovanna, Raul Urrutia
Recent studies have offered ample insight into genome-wide expression patterns to define pancreatic ductal adenocarcinoma (PDAC) subtypes, although there remains a lack of knowledge regarding the underlying epigenomics of PDAC. Here we perform multi-parametric integrative analyses of chromatin immunoprecipitation-sequencing (ChIP-seq) on multiple histone modifications, RNA-sequencing (RNA-seq), and DNA methylation to define epigenomic landscapes for PDAC subtypes, which can predict their relative aggressiveness and survival...
May 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29773620/draft-genome-sequence-of-a-fungus-fusarium-tricinctum-cultured-from-a-monoisolate-native-to-the-himalayas
#7
Narendra Meena, M Vasundhara, M Sudhakara Reddy, Prashanth Suravajhala, U S Raghavender, Krishna Mohan Medicherla
Here, we report the draft de novo genome sequence assembly of Fusarium tricinctum (strain T6), using IonTorrent sequencing chemistry and an Ion 530 chip ExT kit for sequencing. The genome assembly resulted in 42,732,204 bp from a total 6.62 Gb, with a median read length of 386 bp.
May 17, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29772439/long-noncoding-rna-meg3-inhibits-proliferation-of-chronic-myeloid-leukemia-cells-by-sponging-microrna21
#8
Ziye Li, Lin Yang, Xiaojun Liu, Ziyuan Nie, Jianmin Luo
The long noncoding RNA (lnc) maternally expressed 3 (MEG3) is downregulated in many types of cancers. However, the relationship between lncRNA MEG3, microRNA-21 (miR-21) and chronic myeloid leukemia (CML) blast crisis is unknown. This study examined bone marrow samples from 40 CML patients and 10 healthy donors. Proliferation and apoptosis assays, real-time polymerase chain reaction (PCR), bisulfite sequencing PCR, Western blotting, luciferase assay, RNA pull-down, RNA immunoprecipitation (RIP), co-immunoprecipitation (CoIP) and Chromatin immunoprecipitation (ChIP) were performed...
May 14, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29769126/polymorphism-and-plasma-levels-of-apolipoprotein-e-and-the-risk-of-aneurysmal-subarachnoid-hemorrhage-in-a-chinese-population-a-case-control-study
#9
Xiaofeng Liu, Weiwu Zhan, Qiumei Wu, Fengqing Wang, Bin Yang, Qishui Ou
BACKGROUND: Aneurysmal subarachnoid hemorrhage (aSAH) is the most common types of subarachnoid hemorrhage, which is a critical clinical problem with high morbidity, mortality, and economic impact. Recent studies have shown that APOE was a genetic risk factor of aSAH, however, the studies lack consistent conclusions and the evidence from Chinese Han population is rare. OBJECTIVE: To determine the relationship between APOE polymorphism and the incidence of aSAH in Chinese Fujian Han population and explore the possible mechanism of ApoE in the pathogenesis of aSAH...
May 16, 2018: Lipids in Health and Disease
https://www.readbyqxmd.com/read/29767371/analysis-of-chip-seq-and-rna-seq-data-with-biowardrobe
#10
Sushmitha Vallabh, Andrey V Kartashov, Artem Barski
The massive amount of information produced by ChIP-Seq, RNA-Seq, and other next-generation sequencing-based methods requires computational data analysis. However, biologists performing these experiments often lack training in bioinformatics. BioWardrobe aims to bridge this gap by providing a convenient user interface and by automating routine data-processing steps. This protocol details the use of BioWardrobe for identifying and visualizing ChIP-Seq peaks, calculating RPKMs, performing differential binding or gene expression analysis, and creating plots and heat maps...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29767366/expression-profiling-of-differentially-regulated-genes-in-fanconi-anemia
#11
Binita Zipporah E, Kavitha Govarthanan, Pavithra Shyamsunder, Rama S Verma
Gene expression analysis mainly helps to study gene quantification methods by using various downstream detection approaches like imaging, amplification, probe hybridization, or sequencing. With respect to DNA, which is less static, mRNA levels vary over time, between cell types under divergent conditions. Gene expression analysis is principally focused on determination of mRNA levels transcribed from DNA. DNA microarrays are one of the robust and powerful tools to detect changes in multiple transcripts in larger cohorts in parallel...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29767364/single-cell-mrna-seq-using-the-fluidigm-c1-system-and-integrated-fluidics-circuits
#12
Haibiao Gong, Devin Do, Ramesh Ramakrishnan
Single-cell mRNA-seq is a valuable tool to dissect expression profiles and to understand the regulatory network of genes. Microfluidics is well suited for single-cell analysis owing both to the small volume of the reaction chambers and easiness of automation. Here we describe the workflow of single-cell mRNA-seq using C1 IFC, which can isolate and process up to 96 cells. Both on-chip procedure (lysis, reverse transcription, and preamplification PCR) and off-chip sequencing library preparation protocols are described...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29760208/rpon-dependent-direct-regulation-of-quorum-sensing-and-the-type-vi-secretion-system-in-pseudomonas-aeruginosa-pao1
#13
Xiaolong Shao, Xiaoning Zhang, Yingchao Zhang, Miao Zhu, Pan Yang, Jian Yuan, Yingpeng Xie, Tianhong Zhou, Wei Wang, Sheng Chen, Haihua Liang, Xin Deng
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen of humans, particularly those with cystic fibrosis. As a global regulator, RpoN controls a group of virulence-related factors and quorum sensing (QS) genes in P. aeruginosa To further gain insights into the direct targets of RpoN in vivo , the present study focused on identifying the direct targets of RpoN regulation in QS and the type VI secretion system (T6SS). We performed a chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-seq) assay that identified 1,068 binding sites of RpoN, mostly including metabolic genes, a group of genes in QS ( lasI , rhlI and pqsR ) and the T6SS ( hcpA and hcpB )...
May 14, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29760157/methyl-cpg-binding-protein-2-mediates-antifibrotic-effects-in-scleroderma-fibroblasts
#14
Ye He, Pei-Suen Tsou, Dinesh Khanna, Amr H Sawalha
OBJECTIVE: Emerging evidence supports a role for epigenetic regulation in the pathogenesis of scleroderma (SSc). We aimed to assess the role of methyl-CpG-binding protein 2 (MeCP2), a key epigenetic regulator, in fibroblast activation and fibrosis in SSc. METHODS: Dermal fibroblasts were isolated from patients with diffuse cutaneous SSc (dcSSc) and from healthy controls. MeCP2 expression was measured by qPCR and western blot. Myofibroblast differentiation was evaluated by gel contraction assay in vitro...
May 14, 2018: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/29757984/integrative-bioinformatics-and-functional-analyses-of-geo-encode-and-tcga-reveal-fadd-as-a-direct-target-of-the-tumor-suppressor-brca1
#15
Dinh-Duc Nguyen, Dong Gyu Lee, Sinae Kim, Keunsoo Kang, Je-Keun Rhee, Suhwan Chang
BRCA1 is a multifunctional tumor suppressor involved in several essential cellular processes. Although many of these functions are driven by or related to its transcriptional/epigenetic regulator activity, there has been no genome-wide study to reveal the transcriptional/epigenetic targets of BRCA1. Therefore, we conducted a comprehensive analysis of genomics/transcriptomics data to identify novel BRCA1 target genes. We first analyzed ENCODE data with BRCA1 chromatin immunoprecipitation (ChIP)-sequencing results and identified a set of genes with a promoter occupied by BRCA1...
May 14, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29757349/base-pair-resolution-detection-of-transcription-factor-binding-site-by-deep-deconvolutional-network
#16
Sirajul Salekin, Jianqiu Michelle Zhang, Yufei Huang
Motivation: Transcription factor (TF) binds to the promoter region of a gene to control gene expression. Identifying precise transcription factor binding sites (TFBS) is essential for understanding the detailed mechanisms of TF mediated gene regulation. However, there is a shortage of computational approach that can deliver single base pair (bp) resolution prediction of TFBS. Results: In this paper, we propose DeepSNR, a Deep Learning algorithm for predicting transcription factor binding location at Single Nucleotide Resolution de novo from DNA sequence...
May 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29755444/microfluidic-pcr-amplification-and-miseq-amplicon-sequencing-techniques-for-high-throughput-detection-and-genotyping-of-human-pathogenic-rna-viruses-in-human-feces-sewage-and-oysters
#17
Mamoru Oshiki, Takayuki Miura, Shinobu Kazama, Takahiro Segawa, Satoshi Ishii, Masashi Hatamoto, Takashi Yamaguchi, Kengo Kubota, Akinori Iguchi, Tadashi Tagawa, Tsutomu Okubo, Shigeki Uemura, Hideki Harada, Naohiro Kobayashi, Nobuo Araki, Daisuke Sano
Detection and genotyping of pathogenic RNA viruses in human and environmental samples are useful for monitoring the circulation and prevalence of these pathogens, whereas a conventional PCR assay followed by Sanger sequencing is time-consuming and laborious. The present study aimed to develop a high-throughput detection-and-genotyping tool for 11 human RNA viruses [Aichi virus; astrovirus; enterovirus; norovirus genogroup I (GI), GII, and GIV; hepatitis A virus; hepatitis E virus; rotavirus; sapovirus; and human parechovirus] using a microfluidic device and next-generation sequencer...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29753018/ets-transcription-factor-etsrp-etv2-is-required-for-lymphangiogenesis-and-directly-regulates-vegfr3-flt4-expression
#18
Jennifer A Davis, Andrew L Koenig, Allison Lubert, Brendan Chestnut, Fang Liu, Sharina Palencia Desai, Tamara Winkler, Karolina Pociute, Kyunghee Choi, Saulius Sumanas
The molecular mechanisms initiating the formation of the lymphatic system, lymphangiogenesis, are still poorly understood. Here we have identified a novel role in lymphangiogenesis for an ETS transcription factor, Etv2/Etsrp, a known regulator of embryonic vascular development. Through the use of fully validated photoactivatable morpholinos we show that inducible Etv2 inhibition in zebrafish embryos at 1day post-fertilization (dpf) results in significant inhibition of lymphangiogenesis, while development of blood vessels is unaffected...
May 9, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29752288/comparison-of-hepatic-nrf2-and-ahr-binding-in-2-3-7-8-tetrachlorodibenzo-p-dioxin-tcdd-treated-mice-demonstrates-nrf2-independent-pkm2-induction
#19
Rance Nault, Claire M Doskey, Kelly A Fader, Cheryl E Rockwell, Timothy R Zacharewski
2,3,7,8-Tetrachlorodibenzo- p -dioxin (TCDD) induces hepatic oxidative stress following activation of the aryl hydrocarbon receptor (AhR). Our recent studies showed TCDD induced pyruvate kinase muscle isoform 2 ( Pkm2 ) as a novel antioxidant response in normal differentiated hepatocytes. To investigate cooperative regulation between nuclear factor, erythroid derived 2, like 2 ( Nrf2 ) and the AhR in the induction of Pkm2 , hepatic ChIP-seq analyses were integrated with RNA-seq time course data from mice treated with TCDD for 2 - 168h...
May 11, 2018: Molecular Pharmacology
https://www.readbyqxmd.com/read/29748186/dicer-in-macrophages-prevents-atherosclerosis-by-promoting-mitochondrial-oxidative-metabolism
#20
Yuanyuan Wei, Judit Corbalán-Campos, Rashmi Gurung, Lucia Natarelli, Mengyu Zhu, Nicole Exner, Florian Erhard, Franziska Greulich, Claudia Geißler, N Henriette Uhlenhaut, Ralf Zimmer, Andreas Schober
Background -Alternative macrophage activation, which relies on mitochondrial oxidative metabolism, plays a central role in resolution of inflammation and prevents atherosclerosis. Moreover, macrophages handle large amounts of cholesterol and triglycerides derived from the engulfed modified lipoproteins during atherosclerosis. Although several microRNAs regulate macrophage polarization, the role of microRNA-generating enzyme Dicer in macrophage activation during atherosclerosis is unknown. Methods -To evaluate the role of Dicer in atherosclerosis, Apoe-/- mice with or without macrophage-specific Dicer deletion were fed a high-fat diet for 12 weeks...
May 10, 2018: Circulation
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