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https://www.readbyqxmd.com/read/27920729/transcriptional-network-architecture-of-breast-cancer-molecular-subtypes
#1
Guillermo de Anda-Jáuregui, Tadeo E Velázquez-Caldelas, Jesús Espinal-Enríquez, Enrique Hernández-Lemus
Breast cancer heterogeneity is evident at the clinical, histological and molecular level. High throughput technologies allowed the identification of intrinsic subtypes that capture transcriptional differences among tumors. A remaining question is whether said differences are associated to a particular transcriptional program which involves different connections between the same molecules. In other words, whether particular transcriptional network architectures can be linked to specific phenotypes. In this work we infer, construct and analyze transcriptional networks from whole-genome gene expression microarrays, by using an information theory approach...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27919068/capturing-pairwise-and-multi-way-chromosomal-conformations-using-chromosomal-walks
#2
Pedro Olivares-Chauvet, Zohar Mukamel, Aviezer Lifshitz, Omer Schwartzman, Noa Oded Elkayam, Yaniv Lubling, Gintaras Deikus, Robert P Sebra, Amos Tanay
Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information. Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs) are highly conserved between cell types and species. Whether pairwise loops synergize to form higher-order structures is still unclear. Here we develop a conformation capture assay to study higher-order organization using chromosomal walks (C-walks) that link multiple genomic loci together into proximity chains in human and mouse cells...
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27916908/epidermal-growth-factor-receptor-status-in-circulating-tumor-cells-as-a-predictive-biomarker-of-sensitivity-in-castration-resistant-prostate-cancer-patients-treated-with-docetaxel-chemotherapy
#3
Takatsugu Okegawa, Naoshi Itaya, Hidehiko Hara, Mitsuhiro Tambo, Kikuo Nutahara
OBJECTIVE: We examined whether epidermal growth factor receptor (EGFR) expression in circulating tumor cells (CTCs) can be used to predict survival in a population of bone-metastatic castration-resistant prostate cancer (mCRPC) patients treated with docetaxel chemotherapy. METHODS: All patients with mCRPC who had experienced treatment failure with androgen-deprivation therapy and had received docetaxel chemotherapy were eligible. CTCs and EGFR expression in CTCs were enumerated with the CellSearch System in whole blood...
November 30, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27901131/porous-silicon-based-biosensors-towards-real-time-optical-detection-of-target-bacteria-in-the-food-industry
#4
Naama Massad-Ivanir, Giorgi Shtenberg, Nitzan Raz, Christel Gazenbeek, Dries Budding, Martine P Bos, Ester Segal
Rapid detection of target bacteria is crucial to provide a safe food supply and to prevent foodborne diseases. Herein, we present an optical biosensor for identification and quantification of Escherichia coli (E. coli, used as a model indicator bacteria species) in complex food industry process water. The biosensor is based on a nanostructured, oxidized porous silicon (PSi) thin film which is functionalized with specific antibodies against E. coli. The biosensors were exposed to water samples collected directly from process lines of fresh-cut produce and their reflectivity spectra were collected in real time...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900429/highly-selective-sio2-nh2-tio2-hollow-microspheres-for-simultaneous-enrichment-of-phosphopeptides-and-glycopeptides
#5
Dongpo Xu, Guoquan Yan, Mingxia Gao, Chunhui Deng, Xiangmin Zhang
Glycosylation and phosphorylation as the commonest and most important posttranslational modifications of proteins play critical roles in biological processes. Specific and sensitive strategies have been developed to identify the glycosylation and phosphorylation of proteins by mass spectrometry but most of these methods have mainly focused on enriching glycopeptides or phosphopeptides separately, and few of them can enrich both of them. In this work, highly selective SiO2-NH2@TiO2 hollow microspheres were designed and synthesized for the simultaneous selective enrichment of both phosphopeptides and glycopeptides...
November 29, 2016: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/27897233/changes-in-the-membrane-associated-proteins-of-exosomes-released-from-human-macrophages-after-mycobacterium-tuberculosis-infection
#6
Gustavo Diaz, Lisa M Wolfe, Nicole A Kruh-Garcia, Karen M Dobos
Tuberculosis (TB) is the deadliest infectious disease worldwide. One obstacle hindering the elimination of TB is our lack of understanding of host-pathogen interactions. Exosomes, naturally loaded with microbial molecules, are circulating markers of TB. Changes in the host protein composition of exosomes from Mycobacterium tuberculosis (Mtb)-infected cells have not been described, can contribute to our understanding of the disease process, and serve as a direct source of biomarkers or as capture targets to enrich for exosomes containing microbial molecules...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27896285/rare-variants-in-optic-disc-area-gene-card10-enriched-in-primary-open-angle-glaucoma
#7
Tiger Zhou, Emmanuelle Souzeau, Shiwani Sharma, Owen M Siggs, Ivan Goldberg, Paul R Healey, Stuart Graham, Alex W Hewitt, David A Mackey, Robert J Casson, John Landers, Richard Mills, Jonathan Ellis, Paul Leo, Matthew A Brown, Stuart MacGregor, Kathryn P Burdon, Jamie E Craig
BACKGROUND: Genome-wide association studies (GWAS) have identified association of common alleles with primary open-angle glaucoma (POAG) and its quantitative endophenotypes near numerous genes. This study aims to determine whether rare pathogenic variants in these disease-associated genes contribute to POAG. METHODS: Participants fulfilled strict inclusion criteria of advanced POAG at a young age of diagnosis. Myocilin mutation carriers were excluded using direct sequencing...
November 2016: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/27894806/genetic-divergence-in-the-transcriptional-engram-of-chronic-alcohol-abuse-a-laser-capture-rna-seq-study-of-the-mouse-mesocorticolimbic-system
#8
Megan K Mulligan, Khyobeni Mozhui, Ashutosh K Pandey, Maren L Smith, Suzhen Gong, Jesse Ingels, Michael F Miles, Marcelo F Lopez, Lu Lu, Robert W Williams
Genetic factors that influence the transition from initial drinking to dependence remain enigmatic. Recent studies have leveraged chronic intermittent ethanol (CIE) paradigms to measure changes in brain gene expression in a single strain at 0, 8, 72 h, and even 7 days following CIE. We extend these findings using LCM RNA-seq to profile expression in 11 brain regions in two inbred strains - C57BL/6J (B6) and DBA/2J (D2) - 72 h following multiple cycles of ethanol self-administration and CIE. Linear models identified differential expression based on treatment, region, strain, or interactions with treatment...
October 15, 2016: Alcohol
https://www.readbyqxmd.com/read/27880678/evidence-for-an-alternative-mechanism-of-toxin-production-in-the-box-jellyfish-alatina-alata
#9
Cheryl Lewis Ames, Jason Macrander
Cubozoans (box jellyfish) have a reputation as the most venomous animals on the planet. Herein, we provide a review of cubozoan prey capture and digestion informed by the scientific literature. Like all cnidarians, box jellyfish envenomation originates from structures secreted within nematocyte post-Golgi vesicles called nematocysts. When tentacles come in contact with prey or would-be predators, a cocktail of toxins is rapidly deployed from nematocysts via a long spiny tubule that serves to immobilize the target organism...
November 2016: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/27878199/sonochemical-synthesis-of-highly-branched-flower-like-fe3o4-sio2-ag-microcomposites-and-their-application-as-versatile-sers-substrates
#10
Chongwen Wang, Junfeng Wang, Ping Li, Zhen Rong, Xiaofei Jia, Qiuling Ma, Rui Xiao, Shengqi Wang
We report a novel strategy for the synthesis of magnetic-based flower-like silver composite microspheres (Fe3O4@SiO2@Ag microflowers) with a highly branched shell structure through a sonochemical-assisted method. The obtained Fe3O4@SiO2@Ag microflowers possess good dispersity, high magnetic responsiveness, and highly reproducible structures. The size and morphology of the silver petal shell of these microflowers can be easily controlled by varying the experimental parameters. The silver petal provides an effectively large surface area for forming sufficient plasmonic hot spots and capturing target molecules...
December 1, 2016: Nanoscale
https://www.readbyqxmd.com/read/27863249/lineage-specific-genome-architecture-links-enhancers-and-non-coding-disease-variants-to-target-gene-promoters
#11
Biola M Javierre, Oliver S Burren, Steven P Wilder, Roman Kreuzhuber, Steven M Hill, Sven Sewitz, Jonathan Cairns, Steven W Wingett, Csilla Várnai, Michiel J Thiecke, Frances Burden, Samantha Farrow, Antony J Cutler, Karola Rehnström, Kate Downes, Luigi Grassi, Myrto Kostadima, Paula Freire-Pritchett, Fan Wang, Hendrik G Stunnenberg, John A Todd, Daniel R Zerbino, Oliver Stegle, Willem H Ouwehand, Mattia Frontini, Chris Wallace, Mikhail Spivakov, Peter Fraser
Long-range interactions between regulatory elements and gene promoters play key roles in transcriptional regulation. The vast majority of interactions are uncharted, constituting a major missing link in understanding genome control. Here, we use promoter capture Hi-C to identify interacting regions of 31,253 promoters in 17 human primary hematopoietic cell types. We show that promoter interactions are highly cell type specific and enriched for links between active promoters and epigenetically marked enhancers...
November 17, 2016: Cell
https://www.readbyqxmd.com/read/27863237/the-ties-that-bind-mapping-the-dynamic-enhancer-promoter-interactome
#12
REVIEW
Cailyn H Spurrell, Diane E Dickel, Axel Visel
Coupling chromosome conformation capture to molecular enrichment for promoter-containing DNA fragments enables the systematic mapping of interactions between individual distal regulatory sequences and their target genes. In this Minireview, we describe recent progress in the application of this technique and related complementary approaches to gain insight into the lineage- and cell-type-specific dynamics of interactions between regulators and gene promoters.
November 17, 2016: Cell
https://www.readbyqxmd.com/read/27862666/filling-the-void-enriching-the-feature-space-of-successful-stopping
#13
René J Huster, Signe Schneider, Christina F Lavallee, Stefanie Enriquez-Geppert, Christoph S Herrmann
The ability to inhibit behavior is crucial for adaptation in a fast changing environment and is commonly studied with the stop signal task. Current EEG research mainly focuses on the N200 and P300 ERPs and corresponding activity in the theta and delta frequency range, thereby leaving us with a limited understanding of the mechanisms of response inhibition. Here, 15 functional networks were estimated from time-frequency transformed EEG recorded during processing of a visual stop signal task. Cortical sources underlying these functional networks were reconstructed, and a total of 45 features, each representing spectrally and temporally coherent activity, were extracted to train a classifier to differentiate between go and stop trials...
November 11, 2016: Human Brain Mapping
https://www.readbyqxmd.com/read/27862636/a-novel-method-for-a-high-enrichment-of-human-corneal-epithelial-stem-cells-for-genomic-analysis
#14
Jhansi Rani Kasinathan, Venkatesh Prajna Namperumalsamy, Muthukkaruppan Veerappan, Gowri Priya Chidambaranathan
Understanding the molecular mechanisms that regulate the corneal epithelial stem cells (CESCs) in maintaining corneal homeostasis remains elusive largely due to the lack of a specific marker for their isolation. This study aims to enrich CESCs from human donor limbal epithelium and to evaluate the level of enrichment based on expression of ΔNp63α, a putative CESC marker. A two-stage enrichment of CESCs was carried out. (a) The limbal basal epithelial cells were isolated by differential enzymatic treatment and five-fold enrichment was achieved from 2% of CESCs present in the total limbal epithelium...
December 2016: Microscopy Research and Technique
https://www.readbyqxmd.com/read/27861577/identifying-causal-genes-at-the-multiple-sclerosis-associated-region-6q23-using-capture-hi-c
#15
Paul Martin, Amanda McGovern, Jonathan Massey, Stefan Schoenfelder, Kate Duffus, Annie Yarwood, Anne Barton, Jane Worthington, Peter Fraser, Stephen Eyre, Gisela Orozco
BACKGROUND: The chromosomal region 6q23 has been found to be associated with multiple sclerosis (MS) predisposition through genome wide association studies (GWAS). There are four independent single nucleotide polymorphisms (SNPs) associated with MS in this region, which spans around 2.5 Mb. Most GWAS variants associated with complex traits, including these four MS associated SNPs, are non-coding and their function is currently unknown. However, GWAS variants have been found to be enriched in enhancers and there is evidence that they may be involved in transcriptional regulation of their distant target genes through long range chromatin looping...
2016: PloS One
https://www.readbyqxmd.com/read/27857205/principles-of-proteome-allocation-are-revealed-using-proteomic-data-and-genome-scale-models
#16
Laurence Yang, James T Yurkovich, Colton J Lloyd, Ali Ebrahim, Michael A Saunders, Bernhard O Palsson
Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the "generalist" (wild-type) E. coli proteome and phenotype across diverse growth environments...
November 18, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27852218/rna-seq-based-transcriptomic-map-reveals-new-insights-into-mouse-salivary-gland-development-and-maturation
#17
Christian Gluck, Sangwon Min, Akinsola Oyelakin, Kirsten Smalley, Satrajit Sinha, Rose-Anne Romano
BACKGROUND: Mouse models have served a valuable role in deciphering various facets of Salivary Gland (SG) biology, from normal developmental programs to diseased states. To facilitate such studies, gene expression profiling maps have been generated for various stages of SG organogenesis. However these prior studies fall short of capturing the transcriptional complexity due to the limited scope of gene-centric microarray-based technology. Compared to microarray, RNA-sequencing (RNA-seq) offers unbiased detection of novel transcripts, broader dynamic range and high specificity and sensitivity for detection of genes, transcripts, and differential gene expression...
November 16, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27851967/a-compendium-of-chromatin-contact-maps-reveals-spatially-active-regions-in-the-human-genome
#18
Anthony D Schmitt, Ming Hu, Inkyung Jung, Zheng Xu, Yunjiang Qiu, Catherine L Tan, Yun Li, Shin Lin, Yiing Lin, Cathy L Barr, Bing Ren
The three-dimensional configuration of DNA is integral to all nuclear processes in eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide chromosome conformation capture studies have uncovered features of chromatin organization in cultured cells, but genome architecture in human tissues has yet to be explored. Here, we report the most comprehensive survey to date of chromatin organization in human tissues. Through integrative analysis of chromatin contact maps in 21 primary human tissues and cell types, we find topologically associating domains highly conserved in different tissues...
November 15, 2016: Cell Reports
https://www.readbyqxmd.com/read/27851806/5-hydroxymethylcytosine-precedes-loss-of-cpg-methylation-in-enhancers-and-genes-undergoing-activation-in-cardiomyocyte-maturation
#19
David K Kranzhöfer, Ralf Gilsbach, Björn A Grüning, Rolf Backofen, Thomas G Nührenberg, Lutz Hein
BACKGROUND: Cardiomyocytes undergo major changes in DNA methylation during maturation and transition to a non-proliferative state after birth. 5'-hydroxylation of methylated cytosines (5hmC) is not only involved in DNA loss of CpG methylation but is also thought to be an epigenetic mark with unique distribution and functions. Here, we sought to get insight into the dynamics of 5'-hydroxymethylcytosine in newborn and adult cardiomyocytes. METHODS: Cardiomyocyte nuclei from newborn and adult C57BL/6 mice were purified by flow cytometric sorting...
2016: PloS One
https://www.readbyqxmd.com/read/27825131/outlyzer-software-for-extracting-low-allele-frequency-tumor-mutations-from-sequencing-background-noise-in-clinical-practice
#20
Etienne Muller, Nicolas Goardon, Baptiste Brault, Antoine Rousselin, Germain Paimparay, Angelina Legros, Robin Fouillet, Olivia Bruet, Aurore Tranchant, Florian Domin, Chankannira San, Céline Quesnelle, Thierry Frebourg, Agathe Ricou, Sophie Krieger, Dominique Vaur, Laurent Castera
Highlighting tumoral mutations is a key step in oncology for personalizing care. Considering the genetic heterogeneity in a tumor, software used for detecting mutations should clearly distinguish real tumor events of interest that could be predictive markers for personalized medicine from false positives. OutLyzer is a new variant-caller designed for the specific and sensitive detection of mutations for research and diagnostic purposes. It is based on statistic and local evaluation of sequencing background noise to highlight potential true positive variants...
November 4, 2016: Oncotarget
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