Dissociation of mitochondrial and ribosomal biogenesis during thallium administration in rat kidney. by Sho Sugahara, Kana Unuma, Shuheng Wen, Takeshi Funakoshi, Toshihiko Aki, Koichi Uemura

“…To obtain insight into Tl toxicity in the kidney, rats were intraperitoneally administered Tl2SO4 (30 mg/kg), and the kidneys were removed 2 or 5 days later to examine the effects of Tl. Transcriptome analysis using DNA microarray of the rat kidney 2 and 5 days after Tl administration showed that cytoplasmic ribosomal proteins are the most upregulated category; many of the genes involved in ribosome biosynthesis were upregulated by Tl administration. …”
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Impacts of Macronutrients on Gene Expression: Recent Evidence to Understand Productive and Reproductive Performance of Livestock by Md. Mahmodul Hasan Sohel, Yusuf Konca, Mehmet Ulas Cinar

“…In order to identify the effects of nutrients on gene expression and to assess the interactions between genes and nutrition by means of various cutting-edge technologies, the interdisciplinary branch ‘Nutrigenomics’ was created. …”
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Non-replicating Mycobacterium tuberculosis elicits a reduced infectivity profile with corresponding modifications to the cell wall and extracellular matrix. by Joanna Bacon, Luke J Alderwick, Jon A Allnutt, Evelina Gabasova, Robert Watson, Kim A Hatch, Simon O Clark, Rose E Jeeves, Alice Marriott, Emma Rayner, Howard Tolley, Geoff Pearson, Graham Hall, Gurdyal S Besra, Lorenz Wernisch, Ann Williams, Philip D Marsh

“…Therefore, the focus of this study was to emulate environmental conditions encountered by M. tuberculosis in the granuloma, and determine the effect of such conditions on the physiology and infectivity of the organism. …”
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Neighbourhood continuity is not required for correct testis gene expression in Drosophila. by Lisa A Meadows, Yuk Sang Chan, John Roote, Steven Russell

“…We compare gene expression in individuals carrying inverted chromosomes with their non-inverted but otherwise identical progenitors using whole-transcriptome microarray analysis, validating these data with specific quantitative real-time PCR assays. …”
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Naloxonazine, an Amastigote-Specific Compound, Affects Leishmania Parasites through Modulation of Host-Encoded Functions. by Géraldine De Muylder, Benoit Vanhollebeke, Guy Caljon, Alan R Wolfe, James McKerrow, Jean-Claude Dujardin

“…We evaluated here whether this compound could present a host cell-dependent mechanism of action. Microarray profiling of THP-1 macrophages treated with naloxonazine showed upregulation of vATPases, which was further linked to an increased volume of intracellular acidic vacuoles. …”
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Multiple colonization with S. pneumoniae before and after introduction of the seven-valent conjugated pneumococcal polysaccharide vaccine. by Silvio D Brugger, Pascal Frey, Suzanne Aebi, Jason Hinds, Kathrin Mühlemann

“…Serotypes were identified by agglutination, multiplex PCR and microarray.<h4>Principal findings</h4>Rate of multiple colonization remained stable up to three years after PCV7 introduction. …”
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Herpes simplex virus type-1 infection and spread in a novel porcine corneal explant model is restricted to the epithelium. by Sana Arshad, Hafsa Rana, Naomi R Truong, Ushasree Pattamatta, Kirstie M Bertram, Andrew White, Holly R Chinnery, Nicole A Carnt, Anthony L Cunningham

“…We infected these corneas topically via high-density microarray patches (HD-MAPs) dipped in GFP-labelled HSV-1. …”
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Sensitive and precise quantification of insulin-like mRNA expression in Caenorhabditis elegans. by L Ryan Baugh, Nicole Kurhanewicz, Paul W Sternberg

“…We validated the platform using 53 RNA samples previously characterized by high density oligonucleotide microarray analysis. For this set of genes and the standard nCounter protocol, sensitivity and precision were comparable between the two platforms. …”
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CHD1 contributes to intestinal resistance against infection by P. aeruginosa in Drosophila melanogaster. by Johanna Sebald, Stefano Morettini, Valerie Podhraski, Cornelia Lass-Flörl, Alexandra Lusser

“…Evidence for a role as transcriptional regulator comes from its colocalization with elongating RNA polymerase II as well as from studies of fly Hsp70 transcription. Here we used microarray analysis to identify target genes of CHD1. …”
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Xirp proteins mark injured skeletal muscle in zebrafish. by Cécile Otten, Peter F van der Ven, Ilka Lewrenz, Sandeep Paul, Almut Steinhagen, Elisabeth Busch-Nentwich, Jenny Eichhorst, Burkhard Wiesner, Derek Stemple, Uwe Strähle, Dieter O Fürst, Salim Abdelilah-Seyfried

“…Through the use of Xirp1 and Xirp2a as markers, myocellular injury can now be detected, even though functional studies indicate that these proteins are not essential in this process. …”
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The apoptotic and genomic studies on A549 cell line induced by silver nitrate by Ayse Kaplan, Gulsen Akalin Ciftci, Hatice Mehtap Kutlu

“…The influences of silver nitrate were studied via MTT assay, flow cytometry, immunocytochemical, confocal and transmission electron microscopy, and microarray assays. Silver nitrate showed inhibitory effects against A549 cells in a dose- and time-dependent manner for 24, 48, and 72 h and induced apoptosis. …”
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Pain-stimulated ultrasound vocalizations and their impact on pain response in mice. by Satoka Kasai, Saki Ukai, Junpei Kuroda, Tsugumi Yamauchi, Daisuke Yamada, Akiyoshi Saitoh, Satoshi Iriyama, Masashi Suzuki, Kazuki Arita, Yoshio Nakano, Satoru Miyazaki, Kazumi Yoshizawa

“…We also examined the effects of psychological stress caused by the ultrasound on an inflammatory pain model of mice. …”
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NF1 expression profiling in IDH-wildtype glioblastoma: genomic associations and survival outcomes by Michael Chang, Mohamed Sherief, Maria Ioannou, Viveka Chinnasamy, Lucy Chen, Michael Frost, Michelle Mattson-Hoss, Herb Sarnoff, David O. Kamson, Matthias Holdhoff, Debraj Mukherjee, Chetan Bettegowda, Jordina Rincon-Torroella, Victoria Croog, Peng Huang, Fausto J. Rodriguez, Calixto-Hope G. Lucas, Karisa C. Schreck

“…Methods We assembled a single-institution, retrospective cohort of 542 IDH-wildtype GBM with somatic next generation sequencing to investigate the frequency and nature of detected NF1 alterations. We selected 69 GBMs from which to build a tissue microarray (TMA) of 44 NF1-wildtype and 25 NF1-mutant cases. …”
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Differential and directional estrogenic signaling pathways induced by enterolignans and their precursors. by Yun Zhu, Kayoko Kawaguchi, Ryoiti Kiyama

“…All the enterolignans/precursors examined showed activation of the Erk1/2 and PI3K/Akt pathways, indicating the involvement of rapid signaling through the non-genomic estrogen signaling pathway. However, when their effects on specific cell functions, cell cycle progression and chemokine (MCP-1) secretion were examined, positive effects were observed only for enterolactone, suggesting that signals are given in certain directions at a position closer to cell functions. …”
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Analysis of Gene Expression in Human Dermal Fibroblasts Treated with Senescence-Modulating COX Inhibitors by Jeong A. Han, Jong-Il Kim

“…To figure out causal factors for the senescence-modulating effect of the inhibitors, we here performed cDNA microarray experiment and subsequent Gene Set Enrichment Analysis. …”
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Genes that act downstream of sensory neurons to influence longevity, dauer formation, and pathogen responses in Caenorhabditis elegans. by Marta M Gaglia, Dae-Eun Jeong, Eun-A Ryu, Dongyeop Lee, Cynthia Kenyon, Seung-Jae Lee

“…However, the mechanisms underlying these effects are incompletely understood. Using whole-genome microarray analysis, we identified transcripts whose levels are altered by mutations in the intraflagellar transport protein daf-10, which result in impaired development and function of many sensory neurons in C. elegans. …”
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Constitutional Chromothripsis on Chromosome 2: A Rare Case with Severe Presentation by Afia Hasnain, Laura L. Thompson, Nicole L. Hoppman, Karine Hovanes, Jing Liu, Bita Hashemi

“…We concluded that the complexity of the genomic rearrangement and the combined dosage/structural effect of these copy number variants are likely explanations for the severe presentation in our patient.…”
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RRHGE: A Novel Approach to Classify the Estrogen Receptor Based Breast Cancer Subtypes by Ashish Saini, Jingyu Hou, Wanlei Zhou

“…We propose a novel method to measure and extract the reliable (biologically true or valid) interactions from gene interaction networks and incorporate the extracted reliable gene interactions into our proposed RRHGE algorithm to identify significant gene signatures from microarray gene expression data for classifying ER+ and ER− breast cancer samples. …”
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Integrated multiomics analysis identifies potential biomarkers and therapeutic targets for autophagy associated AKI to CKD transition by Yaojun Wang, Qiang Li

“…We performed weighted correlation network analysis (WGCNA) using two microarray datasets (GSE139061 and GSE66494) in the GEO database and identified autophagy signatures by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and GSEA enrichment analysis. …”
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Theory on the coupled stochastic dynamics of transcription and splice-site recognition. by Rajamanickam Murugan, Gabriel Kreiman

“…We evaluate these theoretical predictions by considering human and mouse exon microarray data as well as RNAseq data from multiple different tissues. …”
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