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https://www.readbyqxmd.com/read/27926776/synuclein-%C3%AE-in-uterine-serous-carcinoma-impacts-survival-an-nrg-oncology-gynecologic-oncology-group-study
#1
Abigail D Winder, Kruti P Maniar, Jian-Jun Wei, Dachao Liu, Denise M Scholtens, John R Lurain, Julian C Schink, Barbara M Buttin, Virginia L Filiaci, Heather A Lankes, Nilsa C Ramirez, Kay Park, Meenakshi Singh, Richard W Lieberman, Robert S Mannel, Matthew A Powell, Floor J Backes, Cara A Mathews, Michael L Pearl, Angeles Alvarez Secord, David J Peace, David G Mutch, William T Creasman, J Julie Kim
BACKGROUND: Synuclein-γ (SNCG) is highly expressed in advanced solid tumors, including uterine serous carcinoma (USC). The objective of the current study was to determine whether SNCG protein was associated with survival and clinical covariates using the largest existing collection of USCs from the Gynecologic Oncology Group (GOG-8023). METHODS: High-density tissue microarrays (TMAs) of tumor tissues from 313 patients with USC were stained by immunohistochemistry for SNCG, p53, p16, FOLR1, pERK, pAKT, ER, PR, and HER2/neu...
December 7, 2016: Cancer
https://www.readbyqxmd.com/read/27925796/a-severe-asthma-disease-signature-from-gene-expression-profiling-of-peripheral-blood-from-u-biopred-cohorts
#2
Jeannette Bigler, Michael Boedigheimer, James P R Schofield, Paul J Skipp, Julie Corfield, Anthony Rowe, Ana R Sousa, Martin Timour, Lori Twehues, Xuguang Hu, Graham Roberts, Andrew A Welcher, Wen Yu, Kian F Chung, Ian M Adcock, Peter J Sterk, Ratko Djukanović
RATIONALE: Stratification of asthma at the molecular level, especially using accessible biospecimens, could greatly enable patient selection for targeted therapy. OBJECTIVES: To determine the value of blood to identify transcriptional differences between clinically defined asthmatic and non-asthmatic groups, identify potential patient subgroups based on gene expression, and explore biological pathways associated with identified differences. METHODS: Transcriptomics profiles were generated by microarray analysis of blood from 610 asthmatic and control participants in U-BIOPRED...
December 7, 2016: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/27924986/a-nasba-on-microgel-tethered-molecular-beacon-microarray-for-real-time-microbial-molecular-diagnostics
#3
Y Ma, X Dai, T Hong, G B Munk, M Libera
Despite their many advantages and successes, molecular beacon (MB) hybridization probes have not been extensively used in microarray formats because of the complicating probe-substrate interactions that increase the background intensity. We have previously shown that tethering to surface-patterned microgels is an effective means for localizing MB probes to specific surface locations in a microarray format while simultaneously maintaining them in as water-like an environment as possible and minimizing probe-surface interactions...
December 7, 2016: Analyst
https://www.readbyqxmd.com/read/27924984/infrared-imaging-of-high-density-protein-arrays
#4
Joëlle De Meutter, Julie Vandenameele, André Matagne, Erik Goormaghtigh
We propose in this paper that protein microarrays could be analysed by infrared imaging in place of enzymatic or fluorescence labelling. This label-free method reports simultaneously a large series of data on the spotted sample (protein secondary structure, phosphorylation, glycosylation, presence of impurities, etc.). In the present work, 100 μm protein spots each containing about 100 pg protein were deposited to form high density regular arrays. Using arrays of infrared detectors, high resolution images could be obtained where each pixel of the image is in fact a full infrared spectrum...
December 7, 2016: Analyst
https://www.readbyqxmd.com/read/27924973/selection-of-aptamers-based-on-a-protein-microarray-integrated-with-a-microfluidic-chip
#5
Xiaohui Liu, Hui Li, Wenchao Jia, Zhu Chen, Danke Xu
We developed an efficient and fast method based on a protein microarray integrated with a microfluidic chip for the process of SELEX (systematic evolution of ligands by exponential enrichment). Lactoferrin from bovine milk was used as a target protein, while bovine serum albumin (BSA), α-lactalbumin, β-lactoglobulin and casein were used as negative proteins. They were separately dotted and immobilized to prepare the protein microarray and the resulting microarray was further integrated into a microfluidic chip for the SELEX (PMM-SELEX) process...
December 7, 2016: Lab on a Chip
https://www.readbyqxmd.com/read/27924729/conjugated-linoleic-acid-isomers-exert-differential-effects-on-an-adipocyte-model-of-hiv-associated-lipodystrophy
#6
Cathríona R Loonam, Sandra D O Dell, Anne Mullen
BACKGROUND: HIV-associated lipodystrophy is associated with decreased expression of PPAR-γ in adipose tissue. Conjugated linoleic acid (CLA) isomers (cis9, trans11 and trans10, cis12) are putative PPAR-γ agonists, but have not previously been investigated in the context of HIV-associated lipodystrophy. METHODS: 3T3-L1 pre-adipocytes were differentiated in the presence of ritonavir (20 μM as per previous experimental models) and 100 μM cis9,trans11, trans10,cis12 or vehicle control, DMSO...
December 7, 2016: Current HIV Research
https://www.readbyqxmd.com/read/27924609/constructing-tissue-microarrays-protocols-and-methods-considering-potential-advantages-and-disadvantages-for-downstream-use
#7
Lynne Bingle, Felipe P Fonseca, Paula M Farthing
Tissue microarrays were first constructed in the 1980s but were used by only a limited number of researchers for a considerable period of time. In the last 10 years there has been a dramatic increase in the number of publications describing the successful use of tissue microarrays in studies aimed at discovering and validating biomarkers. This, along with the increased availability of both manual and automated microarray builders on the market, has encouraged even greater use of this novel and powerful tool...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924603/differential-expression-and-functional-analysis-of-high-throughput-omics-data-using-open-source-tools
#8
Moritz Kebschull, Melanie Julia Fittler, Ryan T Demmer, Panos N Papapanou
Today, -omics analyses, including the systematic cataloging of messenger RNA and microRNA sequences or DNA methylation patterns in a cell population, organ, or tissue sample, allow for an unbiased, comprehensive genome-level analysis of complex diseases, offering a large advantage over earlier "candidate" gene or pathway analyses. A primary goal in the analysis of these high-throughput assays is the detection of those features among several thousand that differ between different groups of samples. In the context of oral biology, our group has successfully utilized -omics technology to identify key molecules and pathways in different diagnostic entities of periodontal disease...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924602/genome-wide-analysis-of-periodontal-and-peri-implant-cells-and-tissues
#9
Moritz Kebschull, Claudia Hülsmann, Per Hoffmann, Panos N Papapanou
Omics analyses, including the systematic cataloging of messenger RNA and microRNA sequences or DNA methylation patterns in a cell population, organ or tissue sample, are powerful means of generating comprehensive genome-level data sets on complex diseases. We have systematically assessed the transcriptome, miRNome and methylome of gingival tissues from subjects with different diagnostic entities of periodontal disease, and studied the transcriptome of primary cells ex vivo, or in vitro after infection with periodontal pathogens...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924550/detection-of-transcriptionally-active-mycotoxin-gene-clusters-dna-microarray
#10
Tamás Emri, Anna Zalka, István Pócsi
Various bioanalytical tools including DNA microarrays are frequently used to map global transcriptional changes in mycotoxin producer filamentous fungi. This effective hybridization-based transcriptomics technology helps researchers to identify genes of secondary metabolite gene clusters and record concomitant gene expression changes in these clusters initiated by versatile environmental conditions and/or gene deletions. Such transcriptional data are of great value when future mycotoxin control technologies are considered and elaborated...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924512/computational-analysis-reveals-microrna-mrna-regulatory-network-in-esophageal-squamous-cell-carcinoma
#11
Jie Zhao, Bi-Cheng Zhang, Li-Fang Yu, Wei-Xing Wang, Yong Zhao, Zhi-Guo Rao
MicroRNAs (miRNAs) are known to regulate post-transcriptional gene expression. They are involved in carcinogenesis and tumor progression. The aim of this study was to explore the microRNA-mRNA regulatory network in esophageal squamous cell carcinoma (ESCC) using comprehensive computational approaches. In this study we have selected a total of 11 miRNAs from one previously reported study in ESCC. The mRNA targets of these miRNAs were predicted using various algorithms. The expression profiles of these mRNA targets were identified on DNA microarray experiment dataset across ESCC tissue samples...
December 2016: Journal of Huazhong University of Science and Technology. Medical Sciences
https://www.readbyqxmd.com/read/27924451/mir-124-promotes-newborn-olfactory-bulb-neuron-dendritic-morphogenesis-and-spine-density
#12
Guifa Li, Shucai Ling
Using microarray analysis, we detected microRNA-124 (miR-124) to be abundantly expressed in the olfactory bulb (OB). miR-124 regulates adult neurogenesis in the subventricular zone (SVZ). However, much less is known about its role in newborn OB neurons. Here, using both gain-of-function and loss-of-function approaches, we demonstrate that brain-specific miR-124 affects dendritic morphogenesis and spine density in newborn OB neurons. Functional Annotation Clustering of miR-124 targets was enriched in "cell morphogenesis involved in neuron differentiation...
December 6, 2016: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/27924190/network-analysis-of-human-post-mortem-microarrays-reveals-novel-genes-micrornas-and-mechanistic-scenarios-of-potential-importance-in-fighting-huntington-s-disease
#13
Sreedevi Chandrasekaran, Danail Bonchev
Huntington's disease is a progressive neurodegenerative disorder characterized by motor disturbances, cognitive decline, and neuropsychiatric symptoms. In this study, we utilized network-based analysis in an attempt to explore and understand the underlying molecular mechanism and to identify critical molecular players of this disease condition. Using human post-mortem microarrays from three brain regions (cerebellum, frontal cortex and caudate nucleus) we selected in a four-step procedure a seed set of highly modulated genes...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27924046/new-data-and-features-for-advanced-data-mining-in-manteia
#14
Olivier Tassy
Manteia is an integrative database available online at http://manteia.igbmc.fr which provides a large array of OMICs data related to the development of the mouse, chicken, zebrafish and human. The system is designed to use different types of data together in order to perform advanced datamining, test hypotheses or provide candidate genes involved in biological processes or responsible for human diseases. In this new version of the database, Manteia has been enhanced with new expression data originating from microarray and next generation sequencing experiments...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924034/comprehensive-characterization-annotation-and-innovative-use-of-infinium-dna-methylation-beadchip-probes
#15
Wanding Zhou, Peter W Laird, Hui Shen
Illumina Infinium DNA Methylation BeadChips represent the most widely used genome-scale DNA methylation assays. Existing strategies for masking Infinium probes overlapping repeats or single nucleotide polymorphisms (SNPs) are based largely on ad hoc assumptions and subjective criteria. In addition, the recently introduced MethylationEPIC (EPIC) array expands on the utility of this platform, but has not yet been well characterized. We present in this paper an extensive characterization of probes on the EPIC and HM450 microarrays, including mappability to the latest genome build, genomic copy number of the 3' nested subsequence and influence of polymorphisms including a previously unrecognized color channel switch for Type I probes...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923830/a-myc-activity-signature-predicts-poor-clinical-outcomes-in-myc-associated-cancers
#16
MoonSun Jung, Amanda J Russell, Bing Liu, Joshy George, Pei Yan Liu, Tao Liu, Anna DeFazio, David D L Bowtell, Andre Oberthuer, Wendy B London, Jamie I Fletcher, Michelle Haber, Murray D Norris, Michelle J Henderson
Myc transcriptional activity is frequently deregulated in human cancers, but a Myc-driven gene signature with prognostic ability across multiple tumor types remains lacking. Here we selected 18 Myc-regulated genes from published studies of Myc family targets in epithelial ovarian cancer (EOC) and neuroblastoma. A Myc family activity score derived from the 18 genes was correlated to MYC/MYCN/MYCL1 expression in a panel of 35 cancer cell lines. The prognostic ability of this signature was evaluated in neuroblastoma, medulloblastoma, diffuse large B-cell lymphoma (DLBCL), and EOC microarray gene expression datasets using Kaplan-Meier and multivariate Cox-regression analyses, and was further validated in 42 primary neuroblastomas using qPCR...
December 6, 2016: Cancer Research
https://www.readbyqxmd.com/read/27923825/rational-selection-of-syngeneic-preclinical-tumor-models-for-immunotherapeutic-drug-discovery
#17
Suzanne I S Mosely, John E Prime, Richard C A Sainson, Jens-Oliver Koopmann, Dennis Y Q Wang, Danielle M Greenawalt, Miika J Ahdesmaki, Rebecca Leyland, Stefanie Mullins, Luciano Pacelli, Danielle Marcus, Judith Anderton, Amanda Watkins, Jane Coates Ulrichsen, Philip Brohawn, Brandon W Higgs, Matthew McCourt, Hazel Jones, James A Harper, Michelle Morrow, Viia Valge-Archer, Ross Stewart, Simon J Dovedi, Robert W Wilkinson
Murine syngeneic tumor models are critical to novel immuno-based therapy development but the molecular and immunological features of these models are still not clearly defined. The translational relevance of differences between the models is not fully understood, impeding appropriate preclinical model selection for target validation, and ultimately hindering drug development. Across a panel of commonly-used murine syngeneic tumor models, we showed variable responsiveness to immunotherapies. We employed array comparative genomic hybridization, whole-exome sequencing, exon microarray analysis, and flow cytometry to extensively characterize these models, which revealed striking differences that may underlie these contrasting response profiles...
December 6, 2016: Cancer Immunology Research
https://www.readbyqxmd.com/read/27922691/microarray-expression-profiles-of-genes-in-lung-tissues-of-rats-subjected-to-focal-cerebral-ischemia-induced-lung-injury-following-bone-marrow-derived-mesenchymal-stem-cell-transplantation
#18
Yue Hu, Liu-Lin Xiong, Piao Zhang, Ting-Hua Wang
Ischemia-induced stroke is the most common disease of the nervous system and is associated with a high mortality rate worldwide. Cerebral ischemia may lead to remote organ dysfunction, particular in the lungs, resulting in lung injury. Nowadays, bone marrow-derived mesenchymal stem cells (BMSCs) are widely studied in clinical trials as they may provide an effective solution to the treatment of neurological and cardiac diseases; however, the underlying molecular mechanisms remain unknown. In this study, a model of permanent focal cerebral ischemia-induced lung injury was successfully established and confirmed by neurological evaluation and lung injury scores...
December 6, 2016: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/27922623/molecular-mechanisms-underlying-the-positive-role-of-treadmill-training-in-locomotor-recovery-after-spinal-cord-injury
#19
Q Liu, B Zhang, C Liu, D Zhao
OBJECTIVES: This study aimed to investigate the molecular mechanisms underlying the positive role of treadmill training (TMT) in locomotor recovery. METHODS: GSE52763 microarray data were downloaded from GEO database, which was collected from the lumbar spinal cord samples of three groups of mice: mice subjected to contusive injury and killed 1 week after injury (I1), mice subjected to injury and killed 3 weeks after injury (I3), and mice subjected to injury and TMT beginning at week 1 and lasting until week 3 (T3)...
December 6, 2016: Spinal Cord
https://www.readbyqxmd.com/read/27922124/convex-analysis-of-mixtures-for-separating-non-negative-well-grounded-sources
#20
Yitan Zhu, Niya Wang, David J Miller, Yue Wang
Blind Source Separation (BSS) is a powerful tool for analyzing composite data patterns in many areas, such as computational biology. We introduce a novel BSS method, Convex Analysis of Mixtures (CAM), for separating non-negative well-grounded sources, which learns the mixing matrix by identifying the lateral edges of the convex data scatter plot. We propose and prove a sufficient and necessary condition for identifying the mixing matrix through edge detection in the noise-free case, which enables CAM to identify the mixing matrix not only in the exact-determined and over-determined scenarios, but also in the under-determined scenario...
December 6, 2016: Scientific Reports
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