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https://www.readbyqxmd.com/read/28727490/comparison-of-the-release-of-micrornas-and-extracellular-vesicles-from-platelets-in-response-to-different-agonists
#1
Ashley R Ambrose, Mohammed A Alsahli, Sameer A Kurmani, Alison H Goodall
On activation platelets release microRNAs and extracellular vesicles (EV) into circulation. The release of EV from platelets has been shown to be dependent on the agonist; in this study, we investigated whether the microRNA profile or EV released from platelets was also agonist specific. Washed platelets from healthy subjects were maximally stimulated with agonists specific for the receptors for collagen (Glycoprotein VI (GPVI)), thrombin (PAR1/PAR4), or ADP (P2Y1/P2Y12) with/without inhibiting secondary mediators, using aspirin to block cyclooxygenase-1 and apyrase to remove ADP...
July 20, 2017: Platelets
https://www.readbyqxmd.com/read/28727243/filamin-a-expression-predicts-early-recurrence-of-hepatocellular-carcinoma-after-hepatectomy
#2
Matteo Donadon, Luca Di Tommaso, Cristiana Soldani, Barbara Franceschini, Alfonso Terrone, Antonio Mimmo, Eleonora Vitali, Massimo Roncalli, Andrea Lania, Guido Torzilli
BACKGROUND & AIMS: Recurrence of hepatocellular carcinoma (HCC) after hepatectomy is very high. A predictive marker of early recurrence (ER) capable of personalizing follow-up and developing a new target therapy would be beneficial. The overexpression of Filamin-A (FLNA), a cytoskeleton protein with scaffolding properties, has recently been associated with progression in tumors. The aim of this study was to test the expression of FLNA in a cohort of patients operated for HCC. METHODS: A retrospective cohort of patients who underwent hepatic resection at Humanitas Clinical and Research Center between January 2004 and December 2014 was analyzed...
July 20, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28726915/oleuropein-represses-the-radiation-resistance-of-ovarian-cancer-by-inhibiting-hypoxia-and-microrna-299-targetted-heparanase-expression
#3
Yubai Xing, Dawei Cui, Shun Wang, Pingping Wang, Xiaojing Xing, Hui Li
Radiotherapy in ovarian cancer frequently invokes resistance; this severely compromises its therapeutic effect and results in poor clinical prognosis. How to overcome the acquired resistance and re-sensitize tumors to radiation is the central question in this clinical setting. Cancer cell survival was evaluated using a clonogenic assay. The microRNA expression profile was analyzed using a microarray. Transcript expression was determined using real time PCR. The expression of protein was determined by immunoblotting...
July 20, 2017: Food & Function
https://www.readbyqxmd.com/read/28726847/mapping-genome-wide-transcription-factor-binding-sites-using-dap-seq
#4
Anna Bartlett, Ronan C O'Malley, Shao-Shan Carol Huang, Mary Galli, Joseph R Nery, Andrea Gallavotti, Joseph R Ecker
To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than chromatin immunoprecipitation sequencing (ChIP-seq). DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell- and tissue-specific chemical modifications that are known to affect TF binding (such as DNA methylation) and providing increased specificity as compared with in silico predictions based on motifs from methods such as protein-binding microarrays (PBMs) and systematic evolution of ligands by exponential enrichment (SELEX)...
August 2017: Nature Protocols
https://www.readbyqxmd.com/read/28726551/extracellular-matrix-and-integrin-expression-profiles-in-fuchs-endothelial-corneal-dystrophy-cells-and-tissue-model
#5
Benjamin Goyer, Mathieu Thériault, Sébastien P Gendron, Isabelle Brunette, Patrick J Rochette, Stéphanie Proulx
Primary corneal endothelial cell cultures and 3D engineered tissue models were used to study the aberrant deposition of extracellular matrix (ECM) in a vision impairing pathology known as Fuchs endothelial corneal dystrophy (FECD). Corneal endothelial cells (CEC) were isolated from excised Descemet membranes of patients with end-stage FECD. CEC isolated from healthy corneas served as controls. Microarray gene profiling was performed on post-confluent cultures of healthy and FECD cells. Protein expression analyses were conducted on tissue models that were engineered by seeding an endothelium on previously devitalized human stromal carriers...
July 20, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28726241/investigating-the-role-of-the-igf-axis-as-a-predictor-of-biochemical-recurrence-in-prostate-cancer-patients-post-surgery
#6
Kieran J Breen, Amanda O'Neill, Lisa Murphy, Yue Fan, Susie Boyce, Noel Fitzgerald, Emma Dorris, Lauren Brady, Stephen P Finn, Brian D Hayes, Ann Treacy, Ciara Barrett, Mardiana Abdul Aziz, Elaine W Kay, John M Fitzpatrick, R William G Watson
BACKGROUND: Between 20% and 35% of prostate cancer (PCa) patients who undergo treatment with curative intent (ie, surgery or radiation therapy) for localized disease will experience biochemical recurrence (BCR). Alterations in the insulin-like growth factor (IGF) axis and PTEN expression have been implicated in the development and progression of several human tumors including PCa. We examined the expression of the insulin receptor (INSR), IGF-1 receptor (IGF-1R), PTEN, and AKT in radical prostatectomy tissue of patients who developed BCR post-surgery...
July 20, 2017: Prostate
https://www.readbyqxmd.com/read/28725232/transcriptome-wide-identification-of-differentially-expressed-genes-in-solanum-lycopersicon-l-in-response-to-an-alfalfa-protein-hydrolysate-using-microarrays
#7
Andrea Ertani, Michela Schiavon, Serenella Nardi
An alfalfa-based protein hydrolysate (EM) has been tested in tomato (Solanum lycopersicon L.) plants at two different concentrations (0.1 and 1 mL L(-1)) to get insight on its efficacy as biostimulant in this species and to unravel possible metabolic targets and molecular mechanisms that may shed light on its mode of action. EM was efficient in promoting the fresh biomass and content in chlorophyll and soluble sugars of tomato plants, especially when it was applied at the concentration of 1 mL L(-1). This effect on plant productivity was likely related to the EM-dependent up-regulation of genes identified via microarray and involved in primary carbon and nitrogen metabolism, photosynthesis, nutrient uptake and developmental processes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28724602/the-clinical-and-prognostic-value-of-polo-like-kinase-1-in-lung-squamous-cell-carcinoma-patients-immunohistochemical-analysis
#8
Hefei Li, Haibo Wang, Zhenqing Sun, Qiang Guo, Hongyun Shi, Youchao Jia
Polo-like kinase 1 (PLK1) has been suggested to serve as oncogene in most human cancers. The aim of our study is to present more evidence about the clinical and prognostic value of PLK1 in lung squamous cell carcinoma patients. The status of PLK1 was observed in lung adenocarcinoma, lung squamous cell carcinoma and normal lung tissues through analyzing microarray data set (GEO accession number: GSE1213 and GSE 3627). PLK1 mRNA and protein expressions were detected in lung squamous cell carcinoma and normal lung tissues by using qRT-PCR and immunohistochemistry...
July 19, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28724556/performance-assessment-of-a-trypanosoma-cruzi-chimeric-antigen-in-multiplex-liquid-microarray-assays
#9
Fred Luciano Neves Santos, Paola Alejandra Fiorani Celedon, Nilson Ivo Tonin Zanchin, Amanda Leitolis, Sandra Crestani, Leonardo Foti, Wayner Vieira de Souza, Yara de Miranda Gomes, Marco Aurélio Krieger
Diagnosing chronic Chagas disease (CD) requires antibody--antigen detection methods, traditionally based on enzymatic assay techniques whose performance depend on the type and quality of antigen used. Previously, 4 recombinant chimeric proteins from Instituto de Biologia Molecular do Paraná (IBMP-8.1 to -8.4) comprising immuno-dominant regions of diverse Trypanosoma cruzi antigens showed excellent diagnostic performance in enzyme-linked immunosorbent assays. Considering that next-generation platforms offer improved CD diagnostic accuracy with different T...
July 19, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28724429/the-noncoding-rna-hoxd-as1-is-a-critical-regulator-of-the-metastasis-and-apoptosis-phenotype-in-human-hepatocellular-carcinoma
#10
Shan Lu, Jiansheng Zhou, Yimin Sun, Nan Li, Mingyong Miao, Binghua Jiao, Huan Chen
BACKGROUND: Despite accumulating evidence that long noncoding RNAs (lncRNAs) are associated with cancer development in multiple types of cancer, the biological roles of many lncRNAs in human hepatocellular carcinoma (HCC) metastasis have not been well characterized. METHODS: A lncRNA+ mRNA human gene expression microarray analysis was used to identify differentially expressed lncRNAs in metastatic HCC tissues compared to non-metastatic tissue. RESULTS: We observed remarkable overexpression of HOXD-AS1 in metastatic cancer tissues...
July 19, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28724397/partial-uniparental-isodisomy-of-chromosome-16-unmasks-a-deleterious-biallelic-mutation-in-ift140-that-causes-mainzer-saldino-syndrome
#11
Benjamin M Helm, Jason R Willer, Azita Sadeghpour, Christelle Golzio, Eric Crouch, Samantha Schrier Vergano, Nicholas Katsanis, Erica E Davis
BACKGROUND: The ciliopathies represent an umbrella group of >50 clinical entities that share both clinical features and molecular etiology underscored by structural and functional defects of the primary cilium. Despite the advances in gene discovery, this group of entities continues to pose a diagnostic challenge, in part due to significant genetic and phenotypic heterogeneity and variability. We consulted a pediatric case from asymptomatic, non-consanguineous parents who presented as a suspected ciliopathy due to a constellation of retinal, renal, and skeletal findings...
July 19, 2017: Human Genomics
https://www.readbyqxmd.com/read/28723967/epitope-determination-of-immunogenic-proteins-of-neisseria-gonorrhoeae
#12
Daniel O Connor, Lena Danckert, Sebastian Hoppe, Frank F Bier, Markus von Nickisch-Rosenegk
Neisseria gonorrhoeae is the causative organism of gonorrhoea, a sexually transmitted disease that globally accounts for an estimated 80 to 100 million new infections per year. Increasing resistances to all common antibiotics used for N. gonorrhoeae treatment pose the risk of an untreatable disease. Further knowledge of ways of infection and host immune response are needed to understand the pathogen-host interaction and to discover new treatment alternatives against this disease. Therefore, detailed information about immunogenic proteins and their properties like epitope sites could advance further research in this area...
2017: PloS One
https://www.readbyqxmd.com/read/28723760/bioinformatics-analysis-to-identify-the-critical-genes-micrornas-and-long-noncoding-rnas-in-melanoma
#13
Qian Zhang, Yang Wang, Jiulong Liang, Yaguang Tian, Yu Zhang, Kai Tao
Melanoma, which is usually induced by ultraviolet light exposure and the following DNA damage, is the most dangerous skin cancer. The purpose of the present study was to screen key molecules involved in melanoma.Microarray data of E-MTAB-1862 were downloaded from the ArrayExpress database, which included 21 primary melanoma samples and 11 benign nevus samples. In addition, the RNASeq version 2 and microRNA (miRNA) sequencing data of cutaneous melanoma were downloaded from The Cancer Genome Atlas database. After identifying the differentially expressed genes (DEGs) using Limma package, enrichment analysis and protein-protein interaction (PPI) network analysis were performed separately for them using DAVID software and Cytoscape software...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28723211/improving-fore-a-new-inlet-design-for-filtering-samples-through-individual-microarray-spots
#14
Victoria de Lange, Marco Habegger, Marco Schmidt, János Vörös
In this publication we present an improvement to our previously introduced vertical flow microarray, the FoRe array, which capitalizes on the fusion of immunofiltration and densely packed micron test sites. Filtering samples through individual microarray spots allows us to rapidly analyze dilute samples with high-throughput and high signal-to-noise. Unlike other flowthrough microarrays, in the FoRe design samples are injected into micron channels and sequentially exposed to different targets. This arrangement makes it possible to increase the sensitivity of the microarray by simply increasing the sample volume or to rapidly reconcentrate samples after preprocessing steps dilute the analyte...
March 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28719624/sequence-specific-dna-binding-by-myc-max-to-low-affinity-non-e-box-motifs
#15
Michael Allevato, Eugene Bolotin, Mark Grossman, Daniel Mane-Padros, Frances M Sladek, Ernest Martinez
The MYC oncoprotein regulates transcription of a large fraction of the genome as an obligatory heterodimer with the transcription factor MAX. The MYC:MAX heterodimer and MAX:MAX homodimer (hereafter MYC/MAX) bind Enhancer box (E-box) DNA elements (CANNTG) and have the greatest affinity for the canonical MYC E-box (CME) CACGTG. However, MYC:MAX also recognizes E-box variants and was reported to bind DNA in a "non-specific" fashion in vitro and in vivo. Here, in order to identify potential additional non-canonical binding sites for MYC/MAX, we employed high throughput in vitro protein-binding microarrays, along with electrophoretic mobility-shift assays and bioinformatic analyses of MYC-bound genomic loci in vivo...
2017: PloS One
https://www.readbyqxmd.com/read/28719601/clic-a-tool-for-expanding-biological-pathways-based-on-co-expression-across-thousands-of-datasets
#16
Yang Li, Alexis A Jourdain, Sarah E Calvo, Jun S Liu, Vamsi K Mootha
In recent years, there has been a huge rise in the number of publicly available transcriptional profiling datasets. These massive compendia comprise billions of measurements and provide a special opportunity to predict the function of unstudied genes based on co-expression to well-studied pathways. Such analyses can be very challenging, however, since biological pathways are modular and may exhibit co-expression only in specific contexts. To overcome these challenges we introduce CLIC, CLustering by Inferred Co-expression...
July 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28719380/comparison-of-different-antibody-clones-for-immunohistochemistry-detection-of-programmed-cell-death-ligand-1-pd-l1-on-non-small-cell-lung-carcinoma
#17
Edwin R Parra, Pamela Villalobos, Barbara Mino, Jaime Rodriguez-Canales
Programmed cell death ligand 1 (PD-L1) is a major immune checkpoint protein that mediates antitumor immune suppression and response. Preliminary data suggest that its detection using immunohistochemistry (IHC) in formalin-fixed and paraffin-embedded tissues may predict clinical response to PD-1/PD-L1 therapy. In diagnostic pathology, it is essential to count with a validated IHC that can reliably detect PD-L1-positive cases. The present study was conducted to compare and validate different PD-L1 commercial clones and identify which ones can be reliably used by surgical pathologist to detect PD-L1 expression in human cancer tissues...
July 17, 2017: Applied Immunohistochemistry & Molecular Morphology: AIMM
https://www.readbyqxmd.com/read/28718514/aldehyde-dehydrogenase-1-a1-regulates-energy-metabolism-in-adipocytes-from-different-species
#18
Kefeng Yang, Christopher Adin, Qiwen Shen, Ly James Lee, Lianbo Yu, Paolo Fadda, Arpad Samogyi, Kathleen Ham, Lu Xu, Chen Gilor, Ouliana Ziouzenkova
BACKGROUND: Survival and longevity of xenotransplants depend on immune function and ability to integrate energy metabolism between cells from different species. However, mechanisms for interspecies cross talk in energy metabolism are not well understood. White adipose tissue stores energy and is capable of mobilization and dissipation of energy as heat (thermogenesis) by adipocytes expressing uncoupling protein 1 (Ucp1). Both pathways are under the control of vitamin A metabolizing enzymes...
July 17, 2017: Xenotransplantation
https://www.readbyqxmd.com/read/28717852/elevated-s100a8-protein-expression-in-breast-cancer-cells-and-breast-tumor-stroma-is-prognostic-of-poor-disease-outcome
#19
P Miller, K M Kidwell, D Thomas, M Sabel, J M Rae, D F Hayes, B I Hudson, D El-Ashry, M E Lippman
PURPOSE: Elevated S100A8 expression has been observed in cancers of the bladder, esophagus, colon, ovary, and breast. S100A8 is expressed by breast cancer cells as well as by infiltrating immune and myeloid cells. Here we investigate the association of elevated S100A8 protein expression in breast cancer cells and in breast tumor stroma with survival outcomes in a cohort of breast cancer patients. PATIENTS AND METHODS: Tissue microarrays (TMA) were constructed from breast cancer specimens from 417 patients with stage I-III breast cancer treated at the University of Michigan Comprehensive Cancer Center between 2004 and 2006...
July 17, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28717590/construction-of-a-fur-null-mutant-and-rna-sequencing-provide-deeper-global-understanding-of-the-aliivibrio-salmonicida-fur-regulon
#20
Sunniva Katharina Thode, Cecilie Bækkedal, Jenny Johansson Söderberg, Erik Hjerde, Hilde Hansen, Peik Haugen
BACKGROUND: The ferric uptake regulator (Fur) is a transcription factor and the main regulator of iron acquisition in prokaryotes. When bound to ferric iron, Fur recognizes its DNA binding site and generally executes its function by repressing transcription of its target genes. Due to its importance in virulence, the Fur regulon is well studied for several model bacteria. In our previous work, we used computational predictions and microarray to gain insights into Fur-regulation in Aliivibrio salmonicida, and have identified a number of genes and operons that appear to be under direct control of Fur...
2017: PeerJ
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