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https://www.readbyqxmd.com/read/29236256/integrated-analysis-of-mirna-and-mrna-expression-profiles-to-identify-mirna-targets
#1
Zhiming Li, Chi-Meng Tzeng
miRNAs are involved in various biological processes and different diseases through interacting with their target mRNAs. Therefore, deciphering miRNA targets is important for diagnostics and therapeutics. However, it is still complex and expensive to do large scale screening for miRNA alterations and identify their downstream miRNA targets. Recently, integrating analysis of miRNA expression profiles and mRNA expression levels has been used to successfully identify the most prominent interactions. Here, we present a protocol that combines both expression data and computational prediction to refine the microarray result for identifying the miRNA targets...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29235573/constitutively-elevated-levels-of-socs1-suppress-innate-responses-in-df-1-immortalised-chicken-fibroblast-cells
#2
E S Giotis, C S Ross, R C Robey, A Nohturfft, S Goodbourn, M A Skinner
The spontaneously immortalised DF-1 cell line is rapidly replacing its progenitor primary chicken embryo fibroblasts (CEFs) for studies on avian viruses such as avian influenza but no comprehensive study has as yet been reported comparing their innate immunity phenotypes. We conducted microarray analyses of DF-1 and CEFs, under both normal and stimulated conditions using chicken interferon-α (chIFN-α) and the attenuated infectious bursal disease virus vaccine strain PBG98. We found that DF-1 have an attenuated innate response compared to CEFs...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235571/the-hypoxia-marker-caix-is-prognostic-in-the-uk-phase-iii-vortex-biobank-cohort-an-important-resource-for-translational-research-in-soft-tissue-sarcoma
#3
Laura Forker, Piers Gaunt, Stefano Sioletic, Patrick Shenjere, Robert Potter, Darren Roberts, Joely Irlam, Helen Valentine, David Hughes, Ana Hughes, Lucinda Billingham, Rob Grimer, Beatrice Seddon, Ananya Choudhury, Martin Robinson, Catharine M L West
BACKGROUND: Despite high metastasis rates, adjuvant/neoadjuvant systemic therapy for localised soft tissue sarcoma (STS) is not used routinely. Progress requires tailoring therapy to features of tumour biology, which need exploration in well-documented cohorts. Hypoxia has been linked to metastasis in STS and is targetable. This study evaluated hypoxia prognostic markers in the phase III adjuvant radiotherapy VorteX trial. METHODS: Formalin-fixed paraffin-embedded tumour biopsies, fresh tumour/normal tissue and blood were collected before radiotherapy...
December 12, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/29235553/pro-inflammatory-gene-expression-profile-in-obese-adults-with-high-plasma-gip-levels
#4
J Góralska, U Raźny, A Polus, J Stancel-Możwiłło, M Chojnacka, A Gruca, A Zdzienicka, A Dembińska-Kieć, B Kieć-Wilk, B Solnica, M Malczewska-Malec
BACKGROUND: GIP provides a novel link between the immune system and the gut, although results from different experimental and observational studies are contradictory, ranging from anti-inflammatory, through neutral to pro-inflammatory action of GIP. Thus, the aim of this study was to analyze inflammatory pathways on the level of gene expression and circulating inflammatory markers in relation to plasma GIP level. SUBJECTS/METHODS: The study included 128 obese adults...
December 13, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29235037/expression-and-significance-of-cytokeratin-7-a-squamocolumnar-junction-marker-in-head-and-neck-squamous-cell-carcinoma
#5
Mitra Mehrad, William D Dupont, W Dale Plummer, James S Lewis
The favorable features of high-risk human papillomavirus (HPV) in the head and neck are limited to those harboring transcriptionally-active HPV, which occur predominantly in the oropharynx (OP). Factors rendering the OP susceptible to HPV oncogenesis are largely unexplored. The role of cytokeratin 7 (CK7) in predisposition to HPV and cancer in the cervix has been evaluated. However, its significance in the H&N is unknown. CK7 immunohistochemistry was performed on a tissue microarray cohort of OP and non-oropharyngeal (NOP) squamous cell carcinomas (SCC) with known clinical follow-up and HPV E6/7 mRNA status...
December 12, 2017: Head and Neck Pathology
https://www.readbyqxmd.com/read/29234590/an-integrative-analysis-of-dna-methylation-in-osteosarcoma
#6
Jie Xu, Deng Li, Zhiqing Cai, Yingbin Zhang, Yulin Huang, Baohua Su, Ruofan Ma
Background: The study aimed to analyze aberrantly methylated genes, relevant pathways and transcription factors (TFs) in osteosarcoma (OS) development. Methods: Based on the DNA methylation microarray data GSE36002 that were downloaded from GEO database, the differentially methylated genes in promoter regions were identified between OS and normal samples. Pathway and function enrichment analyses of differentially methylated genes was performed. Subsequently, protein-protein interaction (PPI) network was constructed, followed by identification of cancer-associated differentially methylated genes and significant differentially methylated TFs...
November 2017: Journal of Bone Oncology
https://www.readbyqxmd.com/read/29234579/strategy-to-discover-full-length-amyloid-beta-peptide-ligands-using-high-efficiency-microarray-technology
#7
Clelia Galati, Natalia Spinella, Lucio Renna, Danilo Milardi, Francesco Attanasio, Michele Francesco Maria Sciacca, Corrado Bongiorno
Although the formation of β-amyloid (Aβ) fibrils in neuronal tissues is a hallmark of Alzheimer disease (AD), small-sized Aβ oligomers rather than mature fibrils have been identified as the most neurotoxic species. Therefore, the design of new inhibitors, able to prevent the aggregation of Aβ, is believed to be a promising therapeutic approach to AD. Unfortunately, the short-lived intermediate structures that occur in a solution along the Aβ aggregation pathway escape conventional experimental investigations and there is urgent need of new tools aimed at the discovery of agents targeting monomeric Aβ and blocking the early steps of amyloid aggregation...
2017: Beilstein Journal of Nanotechnology
https://www.readbyqxmd.com/read/29234488/sirt6-histone-deacetylase-functions-as-a-potential-oncogene-in-human-melanoma
#8
Liz Mariely Garcia-Peterson, Mary Ann Ndiaye, Chandra K Singh, Gagan Chhabra, Wei Huang, Nihal Ahmad
Melanoma is an aggressive skin cancer that can rapidly metastasize to become fatal, if not diagnosed early. Despite recent therapeutic advances, management of melanoma remains difficult. Therefore, novel molecular targets and strategies are required to manage this neoplasm. This study was undertaken to determine the role of the sirtuin SIRT6 in melanoma. Employing a panel of human melanoma cells and normal human melanocytes, we found significant SIRT6 mRNA and protein upregulation in melanoma cells. Further, using a tissue microarray coupled with quantitative Vectra analysis, we demonstrated significant SIRT6 overexpression in human melanoma tissues...
September 2017: Genes & Cancer
https://www.readbyqxmd.com/read/29234306/body-mass-index-influences-the-prognostic-impact-of-combined-nuclear-insulin-receptor-and-estrogen-receptor-expression-in-primary-breast-cancer
#9
Sofie Björner, Ann H Rosendahl, Maria Simonsson, Andrea Markkula, Karin Jirström, Signe Borgquist, Carsten Rose, Christian Ingvar, Helena Jernström
The prognostic importance of tumor-specific nuclear insulin receptor (InsR) expression in breast cancer is unclear, while membrane and cytoplasmic localization of InsR is better characterized. The insulin signaling network is influenced by obesity and may interact with the estrogen receptor α (ERα) signaling. The purpose was to investigate the interplay between nuclear InsR, ER, body mass index (BMI), and prognosis. Tumor-specific expression of nuclear InsR was evaluated by immunohistochemistry in tissue microarrays from 900 patients with primary invasive breast cancer without preoperative treatment, included in a population-based cohort in Sweden (2002-2012) in relation to prognosis...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/29234285/a-microarray-study-of-carpet-shell-clam-ruditapes-decussatus-shows-common-and-organ-specific-growth-related-gene-expression-differences-in-gills-and-digestive-gland
#10
Carlos Saavedra, Massimo Milan, Ricardo B Leite, David Cordero, Tomaso Patarnello, M Leonor Cancela, Luca Bargelloni
Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29234088/tear-proteome-analysis-in-ocular-surface-diseases-using-label-free-lc-ms-ms-and-multiplexed-microarray-biomarker-validation
#11
Javier Soria, Arantxa Acera, Jesús Merayo-LLoves, Juan A Durán, Nerea González, Sandra Rodriguez, Nikitas Bistolas, Soeren Schumacher, Frank F Bier, Harald Peter, Walter Stöcklein, Tatiana Suárez
We analyzed the tear film proteome of patients with dry eye (DE), meibomian gland dysfunction (MGD), and normal volunteers (CT). Tear samples were collected from 70 individuals. Of these, 37 samples were analyzed using spectral-counting-based LC-MS/MS label-free quantitation, and 33 samples were evaluated in the validation of candidate biomarkers employing customized antibody microarray assays. Comparative analysis of tear protein profiles revealed differences in the expression levels of 26 proteins, including protein S100A6, annexin A1, cystatin-S, thioredoxin, phospholipase A2, antileukoproteinase, and lactoperoxidase...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29234032/heat-failure-phenotypes-induced-by-knockdown-of-dapit-in-zebrafish-a-new-insight-into-mechanism-of-dilated-cardiomyopathy
#12
Yoji Nagata, Masakazu Yamagishi, Tetsuo Konno, Chiaki Nakanishi, Yoshihiro Asano, Shin Ito, Yuri Nakajima, Osamu Seguchi, Noboru Fujino, Masa-Aki Kawashiri, Seiji Takashima, Masafumi Kitakaze, Kenshi Hayashi
The pathogenesis of heart failure associated with dilated cardiomyopathy (DCM) may result in part from adenosine triphosphate (ATP) dysregulation in the myocardium. Under these conditions, diabetes-associated protein in insulin-sensitive tissue (DAPIT), which is encoded by the upregulated during skeletal muscle growth 5 (USMG5) gene, plays a crucial role in energy production by mitochondrial ATP synthase. To determine whether USMG5 is related to the development of heart failure, we performed clinical and experimental studies...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29233624/first-and-second-trimester-screening-for-fetal-structural-anomalies
#13
REVIEW
Lindsay Edwards, Lisa Hui
Fetal structural anomalies are found in up to 3% of all pregnancies and ultrasound-based screening has been an integral part of routine prenatal care for decades. The prenatal detection of fetal anomalies allows for optimal perinatal management, providing expectant parents with opportunities for additional imaging, genetic testing, and the provision of information regarding prognosis and management options. Approximately one-half of all major structural anomalies can now be detected in the first trimester, including acrania/anencephaly, abdominal wall defects, holoprosencephaly and cystic hygromata...
December 9, 2017: Seminars in Fetal & Neonatal Medicine
https://www.readbyqxmd.com/read/29232894/significant-down-regulation-of-biological-adhesion-genes-in-porcine-oocytes-after-ivm
#14
Joanna Budna, Piotr Celichowski, Artur Bryja, Marta Dyszkiewicz-Konwińska, Michal Jeseta, Dorota Bukowska, Paweł Antosik, Klaus Peter Brüssow, Małgorzata Bruska, Michał Nowicki, Maciej Zabel, Bartosz Kempisty
Proper maturation of the mammalian oocyte is a compound processes determining successful monospermic fertilization, however the number of fully mature porcine oocytes is still unsatisfactory. Since oocytes' maturation and fertilization involve cellular adhesion and membranous contact, the aim was to investigate cell adhesion ontology group in porcine oocytes. The oocytes were collected from ovaries of 45 pubertal crossbred Landrace gilts and subjected to two BCB tests. After the first test, only granulosa cell-free BCB⁺ oocytes were directly exposed to microarray assays and RT-qPCR ("before IVM" group), or first in vitro matured and then if classified as BCB⁺ passed to molecular analyses ("after IVM" group)...
December 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29232835/expression-profile-of-genes-regulating-steroid-biosynthesis-and-metabolism-in-human-ovarian-granulosa-cells-a-primary-culture-approach
#15
Wiesława Kranc, Maciej Brązert, Katarzyna Ożegowska, Mariusz J Nawrocki, Joanna Budna, Piotr Celichowski, Marta Dyszkiewicz-Konwińska, Maurycy Jankowski, Michal Jeseta, Leszek Pawelczyk, Małgorzata Bruska, Michał Nowicki, Maciej Zabel, Bartosz Kempisty
Because of the deep involvement of granulosa cells in the processes surrounding the cycles of menstruation and reproduction, there is a great need for a deeper understanding of the ways in which they function during the various stages of those cycles. One of the main ways in which the granulosa cells influence the numerous sex associated processes is hormonal interaction. Expression of steroid sex hormones influences a range of both primary and secondary sexual characteristics, as well as regulate the processes of oogenesis, folliculogenesis, ovulation, and pregnancy...
December 9, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29232382/charting-the-transcriptional-landscape-of-cells-of-renin-lineage-following-podocyte-depletion
#16
Aaron D McClelland, Julia Lichtnekert, Diana G Eng, Jeffrey W Pippin, Kenneth W Gross, Sina A Gharib, Stuart J Shankland
Renin producing cells of the juxtaglomerulus, herein called cells of renin lineage (CoRL), have garnered recent interest for their propensity to act as a progenitor source for various kidney cell types including podocytes. Despite recent advances, the process of transdifferentiation of CoRL to podocytes is poorly understood. In this study, we employed a transgenic reporter mouse line which permanently labels CoRL with ZsGreen fluorescent protein, allowing for isolation by fluorescence-activated cell sorting...
2017: PloS One
https://www.readbyqxmd.com/read/29232372/attenuated-expression-of-mtr-in-both-prenatally-androgenized-mice-and-women-with-the-hyperandrogenic-phenotype-of-pcos
#17
Lei Lei, Lijun Ding, Jing Su, Mengyuan Liu, Qingqing Shi, Jianjun Zhou, Haixiang Sun, Guijun Yan
Polycystic ovary syndrome (PCOS) is a common endocrine, metabolic and heterogeneous disorder in women of reproductive age, the exact etiology of which remains unknown. To unravel the molecular mechanisms underlying the hyperandrogenic phenotype of PCOS, prenatally androgenized (PNA) mice were used to mimic this phenotype in women with PCOS. Using microarray analysis, 1188 differentially expressed genes, including 671 upregulated and 517 downregulated genes, were identified in ovaries from PNA mice. Five differentially expressed genes (Aldh1a7, Bhmt, Mtr, Nrcam, Ptprg) were validated, and decreased MTR expression was shown in ovaries of PNA mice...
2017: PloS One
https://www.readbyqxmd.com/read/29231270/profiling-and-characterization-of-micrornas-responding-to-sodium-butyrate-treatment-in-a549-cells
#18
Xiaoqiang Xiao, Yingjie Cao, Haoyu Chen
Butyrate inhibits growth of lung cancer. However, the molecular mechanism is still unclear. Here we profiled miRNAs that responded to sodium butyrate(NaB) stimulation in A549 cells, a non-small cell lung cancer cell line, using microarray. We found 33 up-regulated microRNAs and 22 down-regulated microRNAs (log2≥1.5 folds, P-value<0.05). The expression of miR-3935, miR-574-3p and miR-494-3p was confirmed by realtime qPCR. Then,we explored their potential targets of miR-574-3p and miR-494-3p using long noncoding RNA(LncRNA) microarray...
December 12, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29231220/plug-and-actuate-on-demand-multimodal-individual-addressability-of-microarray-plates-using-modular-hybrid-acoustic-wave-technology
#19
Amgad R Rezk, Shwathy Ramesan, Leslie Y Yeo
The microarray titre plate remains a fundamental workhorse in genomic, proteomic and cellomic analyses that underpin the drug discovery process. Nevertheless, liquid handling technologies for sample dispensing, processing and transfer have not progressed significantly beyond conventional robotic micropipetting techniques, which are not only at their fundamental sample size limit, but are also prone to mechanical failure and contamination. This is because alternative technologies to date suffer from a number of constraints, mainly their limitation to carry out only a single liquid operation such as dispensing or mixing at a given time, and their inability to address individual wells, particularly at high throughput...
December 12, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/29230463/real-time-two-photon-lithography-in-controlled-flow-to-create-a-single-microparticle-array-and-particle-cluster-array-for-optofluidic-imaging
#20
Bing Xu, Yang Shi, Zhaoxin Lao, Jincheng Ni, Guoqiang Li, Yanlei Hu, Jiawen Li, Jiaru Chu, Dong Wu, Koji Sugioka
Microarray technology provides an excellent platform for biomedical and biochemical research including basic scientific studies, drug discovery, and diagnostics. Here, we develop a novel method referred to as real-time two-photon lithography in a controlled flow in which femtosecond laser two-photon lithography is performed in situ in the sequential mode stopping and flowing the flow of liquid resin containing microparticles to achieve 100% trapping on a one-bead-to-one-trap basis. Polydisperse particles can be all trapped to form a desired array by freely designing trap structures, resulting in an unprecedentedly high capture efficiency of ∼100%...
December 12, 2017: Lab on a Chip
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