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https://www.readbyqxmd.com/read/28225823/a-novel-approach-to-eliminate-detection-of-contaminating-staphylococcal-species-introduced-during-clinical-testing
#1
Wanyuan Ao, Adrianne Clifford, Maylene Corpuz, Robert Jenison
We describe here a strategy that can distinguish between Staphylococcus species truly present in a clinical sample from contaminating Staphylococcus species introduced during the testing process. Contaminating Staphylococcus species are present at low levels in PCR reagents and colonize lab personnel. To eliminate detection of contaminants, we describe an approach that utilizes addition of sufficient quantities of either non-target Staphylococcal cells (Staphylococcus succinus or Staphylococcus muscae) or synthetic oligonucleotide templates to helicase dependent isothermal amplification reactions to consume Staphylococcus-specific tuf and mecA gene primers such that contaminating Staphylococcus amplification is suppressed to below assay limits of detection...
2017: PloS One
https://www.readbyqxmd.com/read/28224496/computationally-tractable-multivariate-hmm-in-genome-wide-mapping-studies
#2
Hyungwon Choi, Debashis Ghosh, Zhaohui Qin
Hidden Markov model (HMM) is widely used for modeling spatially correlated genomic data (series data). In genomics, datasets of this kind are generated from genome-wide mapping studies through high-throughput methods such as chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq). When multiple regulatory protein binding sites or related epigenetic modifications are mapped simultaneously, the correlation between data series can be incorporated into the latent variable inference in a multivariate form of HMM, potentially increasing the statistical power of signal detection...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28224494/modelling-chip-seq-data-using-hmms
#3
Veronica Vinciotti
Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) experiments have now become routine in biology for the detection of protein binding sites. In this chapter, we show how hidden Markov models can be used for the analysis of data generated by ChIP-seq experiments. We show how a hidden Markov model can naturally account for spatial dependencies in the ChIP-seq data, how it can be used in the presence of data from multiple ChIP-seq experiments under the same biological condition, and how it naturally accounts for the different IP efficiencies of individual ChIP-seq experiments...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28223509/high-throughput-screening-of-rare-metabolically-active-tumor-cells-in-pleural-effusion-and-peripheral-blood-of-lung-cancer-patients
#4
Yin Tang, Zhuo Wang, Ziming Li, Jungwoo Kim, Yuliang Deng, Yan Li, James R Heath, Wei Wei, Shun Lu, Qihui Shi
Malignant pleural effusion (MPE), the presence of malignant cells in pleural fluid, is often the first sign of many cancers and occurs in patients with metastatic malignancies. Accurate detection of tumor cells in pleural fluid is crucial because the presence of MPE denotes an advanced stage of disease and directs a switch in clinical managements. Cytology, as a traditional diagnostic tool, has limited sensitivity especially when tumor cells are not abundant, and may be confounded by reactive mesothelial cells in the pleural fluid...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223367/coordination-of-myeloid-differentiation-with-reduced-cell-cycle-progression-by-pu-1-induction-of-micrornas-targeting-cell-cycle-regulators-and-lipid-anabolism
#5
Lauren A Solomon, Shreya Podder, Jessica He, Nicholas L Jackson Chornenki, Kristen Gibson, Rachel G Ziliotto, Jess Rhee, Rodney P DeKoter
During macrophage development, myeloid progenitor cells undergo terminal differentiation coordinated with reduced cell cycle progression. Differentiation of macrophages from myeloid progenitors is accompanied by increased expression of the E26-transformation specific transcription factor PU.1. Reduced PU.1 expression leads to increased proliferation and impaired differentiation of myeloid progenitor cells. It is not understood how PU.1 coordinates macrophage differentiation with reduced cell cycle progression...
February 21, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28219444/a-functional-snp-associated-with-atopic-dermatitis-controls-cell-type-specific-methylation-of-the-vstm1-gene-locus
#6
Dilip Kumar, Kia Joo Puan, Anand Kumar Andiappan, Bernett Lee, Geertje H A Westerlaken, Doreen Haase, Rossella Melchiotti, Zhuang Li, Nurhashikin Yusof, Josephine Lum, Geraldine Koh, Shihui Foo, Joe Yeong, Alexessander Couto Alves, Juha Pekkanen, Liang Dan Sun, Astrid Irwanto, Benjamin P Fairfax, Vivek Naranbhai, John E A Common, Mark Tang, Chin Keh Chuang, Marjo-Riitta Jarvelin, Julian C Knight, Xuejun Zhang, Fook Tim Chew, Shyam Prabhakar, Liu Jianjun, De Yun Wang, Francesca Zolezzi, Michael Poidinger, E Birgitte Lane, Linde Meyaard, Olaf Rötzschke
BACKGROUND: Expression quantitative trait loci (eQTL) databases represent a valuable resource to link disease-associated SNPs to specific candidate genes whose gene expression is significantly modulated by the SNP under investigation. We previously identified signal inhibitory receptor on leukocytes-1 (SIRL-1) as a powerful regulator of human innate immune cell function. While it is constitutively high expressed on neutrophils, on monocytes the SIRL-1 surface expression varies strongly between individuals...
February 20, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28219405/ttbk2-circular-rna-promotes-glioma-malignancy-by-regulating-mir-217-hnf1%C3%AE-derlin-1-pathway
#7
Jian Zheng, Xiaobai Liu, Yixue Xue, Wei Gong, Jun Ma, Zhuo Xi, Zhongyou Que, Yunhui Liu
BACKGROUND: Circular RNAs are a subgroup of non-coding RNAs and generated by a mammalian genome. Herein, the expression and function of circular RNA circ-TTBK2 were investigated in human glioma cells. METHODS: Fluorescence in situ hybridization and quantitative real-time PCR were conducted to profile the cell distribution and expression of circ-TTBK2 and microRNA-217 (miR-217) in glioma tissues and cells. Immunohistochemical and western blot were used to determine the expression of HNF1β and Derlin-1 in glioma tissues and cells...
February 20, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28215080/a-scalable-epitope-tagging-approach-for-high-throughput-chip-seq-analysis
#8
Xiong Xiong, Yanxiao Zhang, Jian Yan, Surbhi Jain, Sora Chee, Bing Ren, Huimin Zhao
Eukaryotic transcriptional factors (TFs) typically recognize short genomic sequences alone or together with other proteins to modulate gene expression. Mapping of TF-DNA interactions in the genome is crucial for understanding the gene regulatory programs in cells. While chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is commonly used for this purpose, its application is severely limited by the availability of suitable antibodies for TFs. To overcome this limitation, we developed an efficient and scalable strategy named cmChIP-Seq that combines the clustered regularly interspaced short palindromic repeats (CRISPRs) technology with microhomology mediated end joining (MMEJ) to genetically engineer a TF with an epitope tag...
February 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28214999/e6-associated-protein-dependent-estrogen-receptor-regulation-of-protein-kinase-a-regulatory-subunit-r2a-expression-in-neuroblastoma
#9
Jean-Pierre Obeid, Youssef H Zeidan, Nawal Zafar, Jimmy El Hokayem
E6ap is a known transcriptional coregulator for estrogen receptor alpha (Er, Erα) in the presence of estrogen. Protein kinase A (PKA) contains two regulatory subunits derived from four genes. Recent evidence demonstrates that PKA regulates E6ap activity. Data generated in our lab indicated estrogen dependent regulation of Pkar2a levels. Our project sets to investigate a possible feedback mechanism constituting of Erα and E6ap transcriptional regulation of Pkar2a expression. Western blot evaluated protein regulation correlations with E2 in mouse neuroblastoma lines...
February 18, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28213474/a-bayesian-approach-for-analysis-of-whole-genome-bisulphite-sequencing-data-identifies-disease-associated-changes-in-dna-methylation
#10
Owen J L Rackham, Sarah R Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K Srivastava, Jacques Behmoaras, Petros Dellaportas, Leonardo Bottolo, Enrico Petretto
DNA methylation is a key epigenetic modification involved in gene regulation whose contribution to disease susceptibility remains to be fully understood. Here, we present a novel Bayesian smoothing approach (called ABBA) to detect differentially methylated regions (DMRs) from whole-genome bisulphite sequencing (WGBS). We also show how this approach can be leveraged to identify disease-associated changes in DNA methylation, suggesting mechanisms through which these alterations might affect disease. From a data modeling perspective, ABBA has the distinctive feature of automatically adapting to different correlation structures in CpG methylation levels across the genome whilst taking into account the distance between CpG sites as a covariate...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28213272/rev-erb-regulation-of-cholesterologenesis
#11
Sadichha Sitaula, Jinsong Zhang, Fernanda Ruiz, Thomas P Burris
REV-ERBα and REV-ERBβ are heme regulated nuclear receptors that are known to regulate metabolic pathways. We previously demonstrated that treatment of mice with synthetic REV-ERB agonists suppressed plasma cholesterol levels and the hepatic levels of the rate limiting enzyme in cholesterol biosynthesis (3-hydroxy-3-Mmethylglutaryl-CoA reductase). Here, we characterize the role of REV-ERB on the cholesterol biosynthetic pathway in greater detail. The REV-ERB agonist SR9009 reduced plasma cholesterol levels in both wild type C57Bl/6 and low density lipoprotein receptor (LDLR) null mice as well as reducing the expression of an array of genes within the cholesterol biosynthetic pathway...
February 14, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28213235/preparation-and-characterization-of-a-packed-bead-immobilized-trypsin-reactor-integrated-into-a-pdms-microfluidic-chip-for-rapid-protein-digestion
#12
Adam Kecskemeti, Attila Gaspar
This paper demonstrates the design, efficiency and applicability of a simple, inexpensive and high sample throughput microchip immobilized enzymatic reactor (IMER) for rapid protein digestion. The IMER contains conventional silica particles with covalently immobilized trypsin packed inside of a poly(dimethylsiloxane) (PDMS) microchip channel (10mm×1mm×35µm). The microchip consists of 9 different channels, enabling 9 simultaneous protein digestions. Trypsin was covalently immobilized using carbodiimide activation, the ideal trypsin/silica particle ratio (i...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28212627/genome-wide-identification-of-direct-hbx-genomic-targets
#13
Francesca Guerrieri, Laura Belloni, Daniel D'Andrea, Natalia Pediconi, Loredana Le Pera, Barbara Testoni, Cecilia Scisciani, Oceane Floriot, Fabien Zoulim, Anna Tramontano, Massimo Levrero
BACKGROUND: The Hepatitis B Virus (HBV) HBx regulatory protein is required for HBV replication and involved in HBV-related carcinogenesis. HBx interacts with chromatin modifying enzymes and transcription factors to modulate histone post-translational modifications and to regulate viral cccDNA transcription and cellular gene expression. Aiming to identify genes and non-coding RNAs (ncRNAs) directly targeted by HBx, we performed a chromatin immunoprecipitation sequencing (ChIP-Seq) to analyse HBV recruitment on host cell chromatin in cells replicating HBV...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28211892/high-throughput-in-situ-cell-electroporation-microsystem-for-parallel-delivery-of-single-guide-rnas-into-mammalian-cells
#14
Shengtai Bian, Yicen Zhou, Yawei Hu, Jing Cheng, Xiaofang Chen, Youchun Xu, Peng Liu
Arrayed genetic screens mediated by the CRISPR/Cas9 technology with single guide RNA (sgRNA) libraries demand a high-throughput platform capable of transfecting diverse cell types at a high efficiency in a genome-wide scale for detection and analysis of sophisticated cellular phenotypes. Here we developed a high-throughput in situ cell electroporation (HiCEP) microsystem which leveraged the superhydrophobic feature of the microwell array to achieve individually controlled conditions in each microwell and coupled an interdigital electrode array chip with the microwells in a modular-based scheme for highly efficient delivery of exogenous molecules into cells...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28203345/sweet-s-syndrome-associated-with-clonal-hematopoiesis-of-indeterminate-potential-responsive-to-5-azacitidine
#15
REVIEW
George Yaghmour, Eric Wiedower, Bassam Yaghmour, Sara Nunnery, Eric Duncavage, Mike G Martin
Sweet's syndrome (SS) is a rare condition characterized by the abrupt appearance of painful skin lesions due to neutrophilic dermal infiltration. Hematologic neoplasms, particularly acute myeloid leukemia (AML) and myelodysplastic syndromes (MDSs), have been commonly reported in association with SS. Clonal hematopoiesis of indeterminate potential (CHIP) is an emerging entity that is a precursor state to myeloid neoplasms. CHIP has not been previously associated with SS. We report the case of a 71-year-old man who presented with recurrent, painful edematous and erythematous papules and nodules for 18 months despite treatment with corticosteroids...
February 2017: Therapeutic Advances in Hematology
https://www.readbyqxmd.com/read/28202838/role-of-ad4-binding-protein-steroidogenic-factor-1-in-regulating-nadph-production-in-adrenocortical-y-1-cells
#16
Bing Li, Takashi Baba, Kanako Miyabayashi, Tetsuya Sato, Yuichi Shima, Tomomi Ichinose, Daisuke Miura, Yasuyuki Ohkawa, Mikita Suyama, Ken-Ichirou Morohashi
Ad4-binding protein/steroidogenic factor 1 (Ad4BP/SF-1), a member of the nuclear receptor superfamily, is expressed in steroidogenic cells and regulates all steroidogenic gene expression. We recently employed mRNA and chromatin immunoprecipitation sequence (ChIP-seq) to demonstrate that Ad4BP/SF-1 directly regulates the expression of nearly all glycolytic genes. The pentose phosphate pathway (PPP) contributes to the production of nicotinamide adenine dinucleotide phosphate (NADPH). Although the expression of PPP genes and intracellular NADPH were decreased by Ad4BP/SF-1 knockdown, these genes were not the direct targets of Ad4BP/SF-1...
February 14, 2017: Endocrine Journal
https://www.readbyqxmd.com/read/28196473/2-7-million-samples-genotyped-for-hla-by-next-generation-sequencing-lessons-learned
#17
Gerhard Schöfl, Kathrin Lang, Philipp Quenzel, Irina Böhme, Jürgen Sauter, Jan A Hofmann, Julia Pingel, Alexander H Schmidt, Vinzenz Lange
BACKGROUND: At the DKMS Life Science Lab, Next Generation Sequencing (NGS) has been used for ultra-high-volume high-resolution genotyping of HLA loci for the last three and a half years. Here, we report on our experiences in genotyping the HLA, CCR5, ABO, RHD and KIR genes using a direct amplicon sequencing approach on Illumina MiSeq and HiSeq 2500 instruments. RESULTS: Between January 2013 and June 2016, 2,714,110 samples largely from German, Polish and UK-based potential stem cell donors have been processed...
February 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28193273/stub1-chip-mutations-cause-gordon-holmes-syndrome-as-part-of-a-widespread-multisystemic-neurodegeneration-evidence-from-four-novel-mutations
#18
Stefanie Nicole Hayer, Tine Deconinck, Benjamin Bender, Katrien Smets, Stephan Züchner, Selina Reich, Ludger Schöls, Rebecca Schüle, Peter De Jonghe, Jonathan Baets, Matthis Synofzik
BACKGROUND: CHIP, the protein encoded by STUB1, is a central component of cellular protein homeostasis and interacts with several key proteins involved in the pathogenesis of manifold neurodegenerative diseases. This gives rise to the hypothesis that mutations in STUB1 might cause a far more multisystemic neurodegenerative phenotype than the previously reported cerebellar ataxia syndrome. METHODS: Whole exome sequencing data-sets from n = 87 index subjects of two ataxia cohorts were screened for individuals with STUB1 mutations...
February 13, 2017: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/28193175/genome-wide-association-mapping-for-milk-fat-composition-and-fine-mapping-of-a-qtl-for-de-novo-synthesis-of-milk-fatty-acids-on-bovine-chromosome-13
#19
Hanne Gro Olsen, Tim Martin Knutsen, Achim Kohler, Morten Svendsen, Lars Gidskehaug, Harald Grove, Torfinn Nome, Marte Sodeland, Kristil Kindem Sundsaasen, Matthew Peter Kent, Harald Martens, Sigbjørn Lien
BACKGROUND: Bovine milk is widely regarded as a nutritious food source for humans, although the effects of individual fatty acids on human health is a subject of debate. Based on the assumption that genomic selection offers potential to improve milk fat composition, there is strong interest to understand more about the genetic factors that influence the biosynthesis of bovine milk and the molecular mechanisms that regulate milk fat synthesis and secretion. For this reason, the work reported here aimed at identifying genetic variants that affect milk fatty acid composition in Norwegian Red cattle...
February 13, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28190836/specificity-of-microrna-detection-on-a-power-free-microfluidic-chip-with-laminar-flow-assisted-dendritic-amplification
#20
Kazuki Hasegawa, Rina Negishi, Mutsuyoshi Matsumoto, Masafumi Yohda, Kazuo Hosokawa, Mizuo Maeda
MicroRNAs (miRNAs) are attracting considerable attention as potential biomarkers for the early diagnosis of cancer. We have been developing a detection method for miRNAs on a microfluidic chip with external-power-free fluid pumping and enzyme-free amplification. The assay is completed within 20 min. Here, we describe the specificity of this miRNA detection method. First, the specificity against mismatched sequences was investigated. The nonspecific detection of a 2-nucleotide mismatched sequence was negligible, while that of a 1-nucleotide mismatched sequence was observed to a reasonable extent...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
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