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Journal articles on the topic 'RT-PCR - Arrays'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Hessner, Martin J., Bixia Xiang, Shuang Jia, et al. "Three-color cDNA microarrays with prehybridization quality control yield gene expression data comparable to that of commercial platforms." Physiological Genomics 25, no. 1 (2006): 166–78. http://dx.doi.org/10.1152/physiolgenomics.00243.2005.

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Despite their lower cost and high content flexibility, a limitation of in-house-prepared arrays has been their susceptibility to quality control (QC) issues and lack of QC standards across laboratories. Therefore, we developed a novel three-color array system that allows prehybridization QC as well as the Matarray software to facilitate acquisition of accurate gene expression data. In this study, we compared performance of our rat cDNA array to the Affymetrix RG-U34A and Agilent G4130A arrays using 2,824 UniGenes represented on all three arrays. Before data filtering, poor interplatform agreem

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Bergqvist, Cecilia, Petra Holmström, Gunnel Lindegren, Nina Lagerqvist, Mikael Leijon, and Kerstin I. Falk. "Multiplex Nucleic Acid Suspension Bead Arrays for Detection and Subtyping of Filoviruses." Journal of Clinical Microbiology 53, no. 4 (2015): 1368–70. http://dx.doi.org/10.1128/jcm.02787-14.

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Here we describe multiplex suspension bead array systems that allow fast and reliable detection of reverse transcriptase (RT) PCR amplified filovirus genomes and also enable subtyping of Ebola virus species and Marburg virus strains. These systems have an analytical sensitivity equivalent to that of RT-PCR.

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Osman, Fatima, Christian Leutenegger, Deborah Golino, and Adib Rowhani. "Comparison of low-density arrays, RT-PCR and real-time TaqMan® RT-PCR in detection of grapevine viruses." Journal of Virological Methods 149, no. 2 (2008): 292–99. http://dx.doi.org/10.1016/j.jviromet.2008.01.012.

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Arikawa, Emi, Min You, Jie Wang, Jing-yi Lo, Sean Yu, and Jingping Yang. "Real-time PCR array for simultaneous evaluation of multiple cytokine mRNA expression (B204)." Journal of Immunology 178, no. 1_Supplement (2007): LB42—LB43. http://dx.doi.org/10.4049/jimmunol.178.supp.b204.

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Abstract Cytokine quantification is an important element in studies of inflammation and immune responses. Quantitative RT-PCR, a rapid and sensitive assay, is the preferred method to quantify cytokine mRNA levels because they are often expressed at low levels. The RT2Profiler™ PCR Array combines the reliable performance of SYBR® Green based RT-qPCR with multi-gene profiling capabilities to simultaneously analyze the expression of a panel of genes from the same pathway. Using PCR Arrays, we have monitored the mRNA levels of 84 different cytokines in human peripheral blood mononuclear cells (PBM

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Ida, Hisashi, Sharon A. Boylan, Andrea L. Weigel, and Leonard M. Hjelmeland. "Age-related changes in the transcriptional profile of mouse RPE/choroid." Physiological Genomics 15, no. 3 (2003): 258–62. http://dx.doi.org/10.1152/physiolgenomics.00126.2003.

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To evaluate the age-related changes in gene expression occurring in the complex of retinal pigmented epithelium, Bruch’s membrane, and choroid (RPE/choroid), we examined the gene expression profiles of young adult (2 mo) and old (24 mo) male C57BL/6 mice. cDNA probe sets from individual animals were synthesized using total RNA isolated from the RPE/choroid of each animal. Probes were amplified using the Clontech SMART system, radioactively labeled, and hybridized to two different Clontech Atlas mouse cDNA arrays. From each age group, three independent triplicates were hybridized to the arrays.

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Yildirim, Fatih, M. Enes Aslan, Hüseyin daştan, et al. "Comparative Expression Analysis of Genes Encoding Neurotransmitter Receptors Between Entrepreneurs and Non-Entrepreneurs." Pakistan Journal of Medical and Health Sciences 15, no. 10 (2021): 2928–32. http://dx.doi.org/10.53350/pjmhs2115102928.

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Introduction and Purpose: Recent studies revealed that different behavioral and physiological processes are closely related to different receptor levels in humans. On the other hand, there weren’t any studies that investigated neurotransmitter activity and entrepreneurship relationships. Little is known about how genes expressed in the blood are associated with entrepreneurship. In this study, we measured the expression of 84 genes encoding neurotransmitter receptors between the entrepreneurs and non-entrepreneurs (n=25) using RT-PCR arrays to monitor differentially expressed genes for explori

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Yildirim, Fatih, M. Enes Aslan, Hüseyin Daştan, et al. "Comparative Expression Analysis of Genes Encoding Neurotransmitter Receptors Between Entrepreneurs and Non-Entrepreneurs." Pakistan Journal of Medical and Health Sciences 15, no. 9 (2021): 3058–62. http://dx.doi.org/10.53350/pjmhs211593058.

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Introduction and Purpose: Recent studies revealed that different behavioral and physiological processes are closely related to different receptor levels in humans. On the other hand, there weren’t any studies that investigated neurotransmitter activity and entrepreneurship relationships. Little is known about how genes expressed in the blood are associated with entrepreneurship. In this study, we measured the expression of 84 genes encoding neurotransmitter receptors between the entrepreneurs and non-entrepreneurs (n=25) using RT-PCR arrays to monitor differentially expressed genes for explori

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Brokx, Stephen J., Michael Ellison, Troy Locke, Drell Bottorff, Laura Frost, and Joel H. Weiner. "Genome-Wide Analysis of Lipoprotein Expression in Escherichia coli MG1655." Journal of Bacteriology 186, no. 10 (2004): 3254–58. http://dx.doi.org/10.1128/jb.186.10.3254-3258.2004.

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ABSTRACT To gain insight into the cell envelope of Escherichia coli grown under aerobic and anaerobic conditions, lipoproteins were examined by using functional genomics. The mRNA expression levels of each of these genes under three growth conditions—aerobic, anaerobic, and anaerobic with nitrate—were examined by using both Affymetrix GeneChip E. coli antisense genome arrays and real-time PCR (RT-PCR). Many genes showed significant changes in expression level. The RT-PCR results were in very good agreement with the microarray data. The results of this study represent the first insights into th

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Li, Chun-Hong, Yong-Qing Zhu, Yu-Ling Meng, et al. "Isolation of genes preferentially expressed in cotton fibers by cDNA filter arrays and RT-PCR." Plant Science 163, no. 6 (2002): 1113–20. http://dx.doi.org/10.1016/s0168-9452(02)00320-5.

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Schuchardt, Eleanor L., Shelley D. Miyamoto, Timothy Crombleholme, et al. "Amniotic Fluid microRNA in Severe Twin-Twin Transfusion Syndrome Cardiomyopathy—Identification of Differences and Predicting Demise." Journal of Cardiovascular Development and Disease 9, no. 2 (2022): 37. http://dx.doi.org/10.3390/jcdd9020037.

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Twin-twin transfusion syndrome (TTTS) is a rare but serious cause of fetal cardiomyopathy with poorly understood pathophysiology and challenging prognostication. This study sought a nonbiased, comprehensive assessment of amniotic fluid (AF) microRNAs from TTTS pregnancies and associations of these miRNAs with clinical characteristics. For the discovery cohort, AF from ten fetuses with severe TTTS cardiomyopathy were selected and compared to ten normal singleton AF. Array panels assessing 384 microRNAs were performed on the discovery cohort and controls. Using a stringent q < 0.0025, arrays

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Müller, Stefanie, Robert Geffers, and Stephan Günther. "Analysis of gene expression in Lassa virus-infected HuH-7 cells." Journal of General Virology 88, no. 5 (2007): 1568–75. http://dx.doi.org/10.1099/vir.0.82529-0.

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The pathogenesis of Lassa fever is poorly understood. As the liver is a major target organ of Lassa virus, gene expression in Lassa virus-infected HuH-7 cells, a differentiated human hepatoma cell line, was studied. Cellular mRNA levels were measured at the late phase of acute infection, when virtually all cells expressed large amounts of nucleoprotein, and virus RNA concentration had reached >108 copies (ml supernatant)−1. Two types of transcription array were used: cDNA-based macroarrays with a set of 3500 genes (Atlas Human 1.2 arrays; Clontech) and oligonucleotide-based microarrays cove

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Siddaiah, Roopa, Lucy Emery, Heather Stephens, et al. "Early Salivary miRNA Expression in Extreme Low Gestational Age Newborns." Life 12, no. 4 (2022): 506. http://dx.doi.org/10.3390/life12040506.

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Background: MicroRNAs (miRNA) are small non-coding RNAs that regulate gene expression playing a key role in organogenesis. MiRNAs are studied in tracheal aspirates (TA) of preterm infants. However; this is difficult to obtain in infants who are not intubated. This study examines early salivary miRNA expression as non-invasive early biomarkers in extremely low gestational age newborns (ELGANs). Methods: Saliva was collected using DNA-genotek swabs, miRNAs were analyzed using RNA seq and RT PCR arrays. Salivary miRNA expression was compared to TA using RNA seq at 3 days of age, and longitudinal

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Yamamoto, Miki L., Jeong-Ah Kang, Josh A. Arribere, Amittha Wickrema, and John G. Conboy. "Identification of Alternative Splicing Changes in Erythroid Differentiation Using Human Exon Arrays." Blood 110, no. 11 (2007): 1707. http://dx.doi.org/10.1182/blood.v110.11.1707.1707.

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Abstract Terminal erythroid differentiation is accompanied by extensive structural remodeling as the cell enucleates and eventually assumes the biconcave disk morphology of the mature cell. Previous studies have documented many changes at the transcriptional level essential for erythroid differentiation. Changes in erythroid gene expression also occur at the level of pre-mRNA alternative splicing: the activation of 4.1R (EPB41) exon 16 splicing in late erythroblasts increases 4.1R affinity for spectrin-actin and mechanically strengthens the plasma membrane. We hypothesize that analogous change

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Pidgeon, G. P., K. Gately, J. Lysaght, et al. "12-Lipoxygenase is a potential therapeutic target in non-small cell lung cancer." Journal of Clinical Oncology 25, no. 18_suppl (2007): 18129. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.18129.

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18129 Background: Platelet-type 12-LOX is an arachidonic acid metabolising enzyme resulting in the formation of 12(S)-HETE, which stimulates tumour cell adhesion, invasion and metastasis. We examined the expression of 12-LOX in NSCLC and its role in cell survival. Methods: A549 (adenocarcinoma), SK-MES1 (squamous cell lung carcinoma), H460 and H647 (large cell lung carcinoma) were grown in serum depleted media (0.5%) and screened for 12-LOX expression by RT-PCR and western blot analysis. Cells were treated with baicalein (10uM), a selective inhibitor of 12-LOX, or 12(S)-HETE (100ng/ml) and cel

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Camos, Mireia, Jordi Esteve, Dolors Colomer, et al. "Gene Expression Signature of Acute Myeloid Leukemia (AML) with T(8;16)(P11;P13) and MYST3-CREBBP Rearrangement: A Microarray Study Validated by Multiple Real-Time PCR." Blood 106, no. 11 (2005): 3009. http://dx.doi.org/10.1182/blood.v106.11.3009.3009.

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Abstract AML with t(8;16)(p11;p13) is an infrequent leukemia subtype with characteristic clinical-biological features. The t(8;16)(p11;p13) translocation leads to the fusion of MYST3 and CREBBP genes, probably resulting in a disturbed transcriptional program of a myelo-monocytic precursor. In this study, the genetic signature of MYST3-CREBBP AML was compared with other well-defined AML subtypes. Genotypic analyses using oligonucleotide U133A arrays (Affymetrix) were performed on RNA of 23 AML patients, including three MYST3-CREBBP cases, PML-RARa (n=3), RUNX1-CBF2T1 (n=3), CBFβ-MYH11 (n=3), t(

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López-Vázquez, Carmen, Isabel Bandín, and Carlos P. Dopazo. "Design and Evaluation of a Macroarray for Detection, Identification, and Typing of Viral Hemorrhagic Septicemia Virus (VHSV)." Animals 11, no. 3 (2021): 841. http://dx.doi.org/10.3390/ani11030841.

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The viral hemorrhagic septicemia virus (VHSV) is the causative agent of an important disease in freshwater and marine fishes. Its diagnosis officially relies on the isolation of the virus in cell culture and its identification by serological or polymerase chain reaction (PCR) methodologies. Nowadays, reverse transcription real-time quantitative PCR (RT-qPCR) is the most widely employed technique for the detection of this virus and some studies have reported the validation of RT-qPCR procedures for the detection, typing, and quantification of VHSV isolates. However, although the efficacy of thi

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Hanna, George J., Victoria A. Johnson, Daniel R. Kuritzkes, et al. "Comparison of Sequencing by Hybridization and Cycle Sequencing for Genotyping of Human Immunodeficiency Virus Type 1 Reverse Transcriptase." Journal of Clinical Microbiology 38, no. 7 (2000): 2715–21. http://dx.doi.org/10.1128/jcm.38.7.2715-2721.2000.

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The performances of two methods of nucleotide sequencing were compared for the detection of drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase (RT) in viruses isolated from highly RT inhibitor-experienced individuals. Of 11,677 amino acids deduced from population PCR products by both cycle sequencing and sequencing by hybridization to high-density arrays of oligonucleotide probes, 97.4% were concordant by both methods, 0.8% were discordant, and 1.7% had an ambiguous determination by at least one method. A higher rate of discordance (3.9%) was observed among

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Li, Jiang, Maria L. Spletter, and Jeffrey A. Johnson. "Dissecting tBHQ induced ARE-driven gene expression through long and short oligonucleotide arrays." Physiological Genomics 21, no. 1 (2005): 43–58. http://dx.doi.org/10.1152/physiolgenomics.00214.2004.

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This paper compares the gene expression profiles identified by short (Affymetrix U95AV2) or long (Agilent Hu1A) oligonucleotide arrays on a model for upregulation of a cluster of antioxidant responsive element-driven genes by treatment with tert-butylhydroquinone. MAS 5.0, dCHIP, and RMA were applied to normalize the Affymetrix data, and Lowess regression was considered for Agilent data. SAM was used to identify the differential gene expression. A set of biological markers and housekeeping genes were chosen to evaluate the performance of multiple normalization approaches. Both arrays illustrat

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Williams, Nicole, Vinay Varadan, Aditi Vadodkar, et al. "TGFb signature at 2 weeks to predict response to preoperative therapy (PT) with bevacizumab (B) and chemotherapy (CT) in early breast cancer (EBC)." Journal of Clinical Oncology 31, no. 15_suppl (2013): 1046. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.1046.

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1046 Background: Gene expression profiles from core biopsies taken during PT for EBC may identify markers associated with benefit. B was recently shown to improve pathologic complete response (pCR) to CT in two randomized trials, but is associated with increased toxicity. Predictive signatures are critical to optimizing benefit. We have shown that changes in TGF-β pathway activity after one dose of B are associated with pCR. To confirm these results and understand the mechanism of alteration of the TGFb pathway, we evaluated the 61-gene TGFb signature by RT-PCR, measured markers of TGFb pathwa

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Hsieh, H. Ben, Robert A. Lersch, Daniel E. Callahan, et al. "Monitoring Signal Transduction in Cancer." Journal of Histochemistry & Cytochemistry 49, no. 8 (2001): 1057–58. http://dx.doi.org/10.1177/002215540104900814.

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This study targeted the development of a novel microarray tool to allow rapid determination of the expression levels of 58 different tyrosine kinase (tk) genes in small tumor samples. The goals were to define a reference probe for multi-sample comparison and to investigate the variability and reproducibility of the image acquisition and RT-PCR procedures. The small number of tk genes on our arrays enabled us to define a reference probe by artificially mixing all genes on the arrays. Such a probe provided contrast reference for comparative hybridization of control and sample DNA and enabled cro

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Salaverria, Itziar, Reiner Siebert, and Krzysztof Mrózek. "Appraisal of current technologies for the study of genetic alterations in hematologic malignancies with a focus on chromosome analysis and structural variants." Medizinische Genetik 36, no. 1 (2024): 13–20. http://dx.doi.org/10.1515/medgen-2024-2001.

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Abstract During the last five decades, chromosome analysis identified recurring translocations and inversions in leukemias and lymphomas, which led to cloning of genes at the breakpoints that contribute to oncogenesis. Such molecular cytogenetic methods as fluorescence in situ hybridization (FISH), copy number (CN) arrays or optical genome mapping (OGM) have augmented standard chromosome analysis. The use of both cytogenetic and molecular methods, such as reverse transcription-polymerase chain reaction (RT-PCR) and next generation sequencing (NGS), including whole-genome sequencing (WGS), disc

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Gomes, Evan, Virginia Urquidi, Yunpeng Cai, Yijun Sun, Charles Joel Rosser, and Steve Goodison. "Discovery of molecular biomarker signatures for the detection of bladder cancer." Journal of Clinical Oncology 31, no. 6_suppl (2013): 302. http://dx.doi.org/10.1200/jco.2013.31.6_suppl.302.

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302 Background: Bladder cancer (BCa) is among the five most common malignancies world-wide, and due to high rates of recurrence, one of the most prevalent. Improvements in non-invasive urine-based assays to detect BCa would benefit both patients and healthcare systems. In this study, the goal was to identify urothelial cell transcriptomic signatures associated with BCa. Methods: Gene expression profiling (Affymetrix U133 Plus 2.0 arrays) was applied to exfoliated urothelia obtained from a cohort of 92 subjects with known bladder disease status. Computational analyses identified candidate bioma

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Kao, Chi H. J., Karen S. Bishop, Dug Yeo Han, et al. "A comparison of the gene expression profiles and pathway network analyses after treatment of Prostate cancer cell lines with different Ganoderma lucidum based extracts." Functional Foods in Health and Disease 4, no. 5 (2014): 182. http://dx.doi.org/10.31989/ffhd.v4i5.12.

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Background: Ganoderma lucidum is a type of fungus commonly consumed in Asia for the promotion of health and longevity. The observed biological activity of G. lucidum includes anti-cancer and anti-inflammatory effects which may be useful in the treatment and prevention of cancer and other chronic diseases. G. lucidum grows under conditions which range from tropical to temperate and has a different physiology depending on the geographical region in which it is grown. For this reason, the health benefits may vary depending on the form of G. lucidum and the environmental conditions to which it was

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Nagel, Stefan, Cristof Burek, Letizia Venturini, et al. "Comprehensive Analysis of Homeobox Genes in Hodgkin Lymphoma Cell Lines Identified Dysregulated Expression of HOXB9 Mediated by Constitutive Active ERK5 Signalling Pathway and BMI1." Blood 108, no. 11 (2006): 471. http://dx.doi.org/10.1182/blood.v108.11.471.471.

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Abstract Within the human genome nearly 200 homeobox genes have been identified. These are functionally involved in distinct developmental processes during embryogenesis and in the adult. Many have been implicated in cancer mostly following ectopic expression. In this study, we analyzed homeobox gene expression in Hodgkin lymphoma (HL) cell lines using degenerate primers for RT-PCR and Affymetrix U133A expression arrays followed by extended RT-PCR analysis of candidate homeobox genes in additional hematopoietic cell lines. We identified upregulated HOXB9 expression in HL, as well as in anaplas

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Tam, Stanley, Alfonso Clavijo, Eric K. Engelhard, and Mark C. Thurmond. "Fluorescence-based multiplex real-time RT-PCR arrays for the detection and serotype determination of foot-and-mouth disease virus." Journal of Virological Methods 161, no. 2 (2009): 183–91. http://dx.doi.org/10.1016/j.jviromet.2009.04.033.

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Chen, Jingrui, Jing wei, John Orgah, et al. "Cardioprotective Effect of Danhong Injection against Myocardial Infarction in Rats Is Critically Contributed by MicroRNAs." Evidence-Based Complementary and Alternative Medicine 2019 (August 26, 2019): 1–14. http://dx.doi.org/10.1155/2019/4538985.

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Background. Danhong injection (DHI) has been mainly used for the treatment of myocardial infarction, atherosclerosis, and coronary heart disease in clinical practice. Our previous studies have shown that DHI improves ventricular remodeling and preserves cardiac function in rats with myocardial infarction (MI). In this study, we focused on the potential mechanism of DHI in protecting cardiac function in MI rats. Methods. Sprague-Dawley rats were subjected to ligation of the left anterior descending coronary artery (LAD) to prepare a myocardial infarction (MI) model. After 14 day DHI interventio

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Puigdecanet, Eulalia, Blanca Espinet, Juan Jose Lozano, et al. "Gene Expression Profiling Distinguishes Essential Thrombocythemia from Polycythemia Vera Patients and Identifies a Common Expressed Set of Genes in Relation to JAK2V617F Status." Blood 112, no. 11 (2008): 2788. http://dx.doi.org/10.1182/blood.v112.11.2788.2788.

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Abstract Introduction. The existence of the JAK2V617F mutation in a high proportion of Myeloproliferative Disorders (MPD) BCR-ABL-negative has provided important insight into the pathogenesis of these diseases. However, much of the molecular abnormalities associated to BCR-ABL-negative MPD remain unknown, specially in those which do not display JAK2V617F. In a previous study, we performed gene expression analysis by using the microarray technique in 20 essential thrombocythemia (ET) patients (44K whole human genome oligo microarrays, Agilent Technologies) and the results were confirmed in 40 E

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Shanmugasundaram, Muthian, Annamalai Senthilvelan, and Anilkumar R. Kore. "C-5 Substituted Pyrimidine Nucleotides/Nucleosides: Recent Progress in Synthesis, Functionalization, and Applications." Current Organic Chemistry 23, no. 13 (2019): 1439–68. http://dx.doi.org/10.2174/1385272823666190809124310.

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The chemistry of C5 substituted pyrimidine nucleotide serves as a versatile molecular biology probe for the incorporation of DNA/RNA that has been involved in various molecular biology applications such as gene expression, chromosome, and mRNA fluorescence in situ hybridization (FISH) experiment, mutation detection on arrays and microarrays, in situ RT-PCR, and PCR. In addition to C5 substituted pyrimidine nucleotide, C5 substituted pyrimidine nucleoside displays a broad spectrum of biological applications such as antibacterial, antiviral and anticancer activities. This review focusses on the

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Henry, Travis J., and Rafael Fonseca. "MicroRNA 15a and 16-1 Target Identification in Deletion 13 Multiple Myeloma." Blood 112, no. 11 (2008): 631. http://dx.doi.org/10.1182/blood.v112.11.631.631.

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Abstract Deletion 13 multiple myeloma (MM) is detected in nearly 50 % of patients diagnosed with MM and confers a shorter survival. A region of minimal deletion was identified for chromosome 13 using Agilent 500K aCGH arrays that included microRNAs 15a and 16- 1. MicroRNAs (miRs) are small RNAs that negatively regulate gene expression through degradation of mRNA transcripts or translational inhibition. In order to determine the contribution of deletion of miRs 15a and 16-1 to MM progression, miR precursors were transfected into KMS-11 and JJN3 adherent myeloma cell lines and total RNA hybridiz

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Kõks, Sulev, Rupert W. Overall, Marilin Ivask, et al. "Silencing of the WFS1 gene in HEK cells induces pathways related to neurodegeneration and mitochondrial damage." Physiological Genomics 45, no. 5 (2013): 182–90. http://dx.doi.org/10.1152/physiolgenomics.00122.2012.

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The gene WFS1 encodes a protein with unknown function although its functional deficiency causes different neuropsychiatric and neuroendocrine syndromes. In the present study, we aimed to find the functional networks influenced by the time-dependent silencing of WFS1 in HEK cells. We performed whole genome gene expression profiling (Human Gene 1.0 ST Arrays) in HEK cells 24, 48, 72, and 96 h after transfection with three different WFS1 siRNAs. To verify silencing we performed quantitative RT-PCR and Western blot analysis. Analysis was conducted in two ways. First we analyzed the overall effect

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Chenchik, Alex, Tianbing Liu, Mikhail Makhanov, et al. "Streamlined 96-well plate method for simultaneous single-cell TCR immune receptor repertoire analysis and immunophenotyping." Journal of Immunology 212, no. 1_Supplement (2024): 1529_5870. http://dx.doi.org/10.4049/jimmunol.212.supp.1529.5870.

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Abstract This study describes an efficient immune profiling method by FACS-sorting single cells in a 96-well plate to assess clonotype repertoire diversity, paired-chain information, and cell phenotypes in a single, multiplex RT-PCR-based assay without the use of any specialized equipment. It is a cost-effective alternative to conventional single-cell technologies such as microwell arrays or droplet microfluidics. The 96-well plate contains primers for either T-cell receptor (TCR) / or TCR / chains, together with primers for 30 key T-cell markers. T cells from PBMCs are sorted in a single-cell

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Abruzzo, Lynne V., Kathleen Y. Lee, Alexandra Fuller, et al. "Validation of oligonucleotide microarray data using microfluidic low-density arrays: a new statistical method to normalize real-time RT-PCR data." BioTechniques 38, no. 5 (2005): 785–92. http://dx.doi.org/10.2144/05385mt01.

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Rahman, H. Ur, X. Yue, Q. Yu, W. Zhang, Q. Zhang, and P. Li. "Current PCR-based methods for the detection of mycotoxigenic fungi in complex food and feed matrices." World Mycotoxin Journal 13, no. 2 (2020): 139–50. http://dx.doi.org/10.3920/wmj2019.2455.

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Mycotoxins are toxic secondary fungal metabolites produced by certain types of filamentous fungi, such as Aspergillus, Fusarium, and Penicillium spp. Mycotoxigenic fungi and their produced mycotoxins are considered to be an important issue in food and feed safety due to their toxic effects like carcinogenicity, immunosuppression, neurotoxicity, nephrotoxicity, and hepatotoxicity on humans and animals. To boost the safety level of food and feedstuff, detection and identification of toxins are essential at critical control points across food and feed chains. Zero-tolerance policies by the Europe

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Ekwemalor, Kingsley, Emmanuel Asiamah, Bertha Osei, Hamid Ismail, and Mulumebet Worku. "Evaluation of the Effect of Probiotic Administration on Gene Expression in Goat Blood." Journal of Molecular Biology Research 7, no. 1 (2017): 88. http://dx.doi.org/10.5539/jmbr.v7n1p88.

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The objective of this study was to assess the molecular impact of probiotic administration on genes involved in homeostasis and immunity in goat blood. Following initial screening for infection, one-week post weaning, female SpanishXBoer goats were drenched daily with the recommended doses of FASTtrak microbial pack (Conklin Company Inc., Shakopee, MN) in 10 mL sterile water over an 8-week period. The control group were given sterile water. Blood samples were collected weekly. Total RNA was isolated from blood collected at the beginning of the study (week 0) and at the end of the study (week 8

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Garcia, Leah A., Keisha K. King, Monica G. Ferrini, Keith C. Norris, and Jorge N. Artaza. "1,25(OH)2Vitamin D3 Stimulates Myogenic Differentiation by Inhibiting Cell Proliferation and Modulating the Expression of Promyogenic Growth Factors and Myostatin in C2C12 Skeletal Muscle Cells." Endocrinology 152, no. 8 (2011): 2976–86. http://dx.doi.org/10.1210/en.2011-0159.

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Skeletal muscle wasting is an important public health problem associated with aging, chronic disease, cancer, kidney dialysis, and HIV/AIDS. 1,25-Dihydroxyvitamin D (1,25-D3), the active form of vitamin D, is widely recognized for its regulation of calcium and phosphate homeostasis in relation to bone development and maintenance and for its calcemic effects on target organs, such as intestine, kidney, and parathyroid glands. Emerging evidence has shown that vitamin D administration improves muscle performance and reduces falls in vitamin D-deficient older adults. However, little is known of th

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Wood, Richard J., Laurie Tchack, Giana Angelo, Richard E. Pratt, and Larry A. Sonna. "DNA microarray analysis of vitamin D-induced gene expression in a human colon carcinoma cell line." Physiological Genomics 17, no. 2 (2004): 122–29. http://dx.doi.org/10.1152/physiolgenomics.00002.2003.

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The full extent to which 1,25-dihydroxyvitamin D3 affects gene expression in human intestinal epithelial cells is unknown. We used oligonucleotide arrays to catalog vitamin D-induced changes in gene expression in Caco-2 cells, a human colon carcinoma cell line. Five paired sets of Caco-2 cell cultures were subjected to either control conditions or 1,25-dihydroxyvitamin D (10−7 mol/l × 24 h), and RNA was analyzed on an Affymetrix cDNA array containing 12,625 human sequences. Only 13 sequences representing 12 distinct genes exhibited statistically significant changes in expression of twofold or

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Chiaretti, Sabina, Simona Tavolaro, Emanuela Ghia, et al. "Detection of the NUP214-ABL Rearrangement in T-ALL by High-Density Oligonucleotide Arrays: Evidence of the Value of This Approach in the Identification of Gene Amplifications." Blood 106, no. 11 (2005): 1211. http://dx.doi.org/10.1182/blood.v106.11.1211.1211.

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Abstract The translocation t(9;22), hallmark of CML, is also detected in B-lineage acute lymphoblastic leukemia (ALL). This aberration leads to the BCR/ABL rearrangement that induces a constitutive activation of the tyrosine kinase ABL1. Although BCR/ABL rearrangements were previously considered a rare event in T-ALL, recent data showed the involvement of ABL1 also in this malignancy. Specifically, a new fusion gene involving ABL1 and NUP214, both located at the 9q34 region, has been reported. This abnormality was detected by FISH analysis and reconfirmed by array CGH and PCR analysis. We prev

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Peng, Ying, Han-Wen Zhang, Wei-Han Cao, Ying Mao, and Ruo-Chuan Cheng. "Exploration of the Potential Biomarkers of Papillary Thyroid Cancer (PTC) Based on RT² Profiler PCR Arrays and Bioinformatics Analysis." Cancer Management and Research Volume 12 (September 2020): 9235–46. http://dx.doi.org/10.2147/cmar.s266473.

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Sciortino, Maria-Teresa, Mikiko Suzuki, Brunella Taddeo, and Bernard Roizman. "RNAs Extracted from Herpes Simplex Virus 1 Virions: Apparent Selectivity of Viral but Not Cellular RNAs Packaged in Virions." Journal of Virology 75, no. 17 (2001): 8105–16. http://dx.doi.org/10.1128/jvi.75.17.8105-8116.2001.

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ABSTRACT Following the lead of recent studies on the presence of RNA in virions of human cytomegalovirus, we investigated the presence and identity of RNAs from purified virions of herpes simple virus 1. To facilitate these studies, we designed primers for all known open reading frames (ORFs) and also constructed cDNA arrays containing probes designed to detect all known transcripts. In the first series of experiments, labeled DNA made by reverse transcription of poly(A)+ RNA extracted from infected HEp-2 or rabbit skin cells hybridized to all but two of the probes in the cDNA array. A similar

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Bao, Fei, Mary L. Nordberg, Paula Polk, et al. "Characterization of Gene Expression Associated with Cyclophosphamide Resistance in Chronic Myeloid Leukemia (CML)." Blood 106, no. 11 (2005): 1532. http://dx.doi.org/10.1182/blood.v106.11.1532.1532.

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Abstract Cyclophosphamide (CP) is one of the alkylating agents collectively referred to as oxazaphosphorines that are used to treat many types of cancers including myeloid leukemia. Tumor cell drug resistance is an important factor for clinical treatment failure. The mechanisms of drug resistance are multifactorial and incompletely understood. KBM-7 human CML cell line was established from blast cells from a patient in the terminal phase of CML. In the CP resistance model, the B5-180 sub-line was isolated following exposure to the in vitro active CP analog 4HC. B5-180 cells were cross-resistan

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Evans, Jasmine A., Patricia Mendonca, and Karam F. A. Soliman. "Involvement of Nrf2 Activation and NF-kB Pathway Inhibition in the Antioxidant and Anti-Inflammatory Effects of Hesperetin in Activated BV-2 Microglial Cells." Brain Sciences 13, no. 8 (2023): 1144. http://dx.doi.org/10.3390/brainsci13081144.

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Alzheimer’s disease is a progressive neurodegenerative disorder leading to cognitive decline and memory loss. The incidence of this disease continues to increase due to the limited number of novel therapeutics that prevent or slow down its progression. Flavonoids have been investigated for their potential effects on cellular damage triggered by excessive reactive oxygen species (ROS) and neuroinflammatory conditions. This study investigated the effect of the flavonoid hesperetin on LPS-activated murine BV-2 microglial cells. Results show that hesperetin reduced nitric oxide levels and increase

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Jean, Séverine, Chantal Bideau, Laurence Bellon, et al. "The expression of genes induced in melanocytes by exposure to 365-nm UVA: study by cDNA arrays and real-time quantitative RT-PCR." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1522, no. 2 (2001): 89–96. http://dx.doi.org/10.1016/s0167-4781(01)00326-8.

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Peluso, Anna Lucia, Antonio Ieni, Chiara Mignogna, and Pio Zeppa. "Lymph Node Fine-Needle Cytology: Beyond Flow Cytometry." Acta Cytologica 60, no. 4 (2016): 372–84. http://dx.doi.org/10.1159/000447734.

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Lymph node (LN) fine-needle cytology (FNC) coupled with flow cytometry immunophenotyping provides relevant information for the diagnosis of non-Hodgkin lymphoma (NHL). Numerous studies have shown FNC samples to be suitable for different molecular procedures; in this review, some of the molecular procedures most commonly employed for NHL are briefly described and evaluated in this perspective. Fluorescence in situ hybridization and chromogenic in situ hybridization are briefly described. Polymerase chain reaction (PCR)-based assays are used to identify and quantify mutations and translocations,

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Dickinson, Kristin, Adam J. Case, Kevin Kupzyk, and Leorey Saligan. "Exploring Biologic Correlates of Cancer-Related Fatigue in Men With Prostate Cancer: Cell Damage Pathways and Oxidative Stress." Biological Research For Nursing 22, no. 4 (2020): 514–19. http://dx.doi.org/10.1177/1099800420933347.

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The pathobiology of cancer-related fatigue (CRF) remains elusive, hindering the development of targeted treatments. Radiation therapy (RT), a common treatment for men with prostate cancer, induces cell damage through the generation of free radicals and oxidative stress. We hypothesized that disruption in cellular responses to this surge of nonphysiological oxidative stress might contribute to CRF in men with prostate cancer treated with RT. We evaluated the potential role of three cell damage pathways (apoptosis, autophagy, necrosis) and oxidative stress in CRF in men with prostate cancer rece

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Khoral, Priya, Robert J. Guo, Jahangir Abdi, and Hong Chang. "Prima-1Met Combined with Bortezomib Has Synergistic Anti-Myeloma Activity By Modulation of Apoptosis and Cell Cycle Regulating Genes." Blood 126, no. 23 (2015): 4213. http://dx.doi.org/10.1182/blood.v126.23.4213.4213.

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Abstract INTRODUCTION Multiple Myeloma (MM) is a plasma-cell malignancy characterized by dismal prognosis and a high level of relapse, thus novel therapeutic approaches are needed. PRIMA-1Met is a novel small molecule showing anti-tumour activity and currently in clinical phase I-II trials. We recently demonstrated that PRIMA-1Met has potent anti-MM activity in vitro and in vivo. Bortezomib (BTZ) is a proteasome inhibitor that has been successfully used for treating some cases of relapsed MM. The aim of the current study is to determine whether PRIMA-1Met could be used in combination with BTZ

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Kurt, Robert A., Chiquita Palha De Sousa, Christopher Blum, and Erica Sgroe. "Murine mammary carcinoma cells and CD11c+ dendritic cells elicit distinct responses to lipopolysaccharide and exhibit differential expression of genes required for TLR4 signaling (40.4)." Journal of Immunology 182, no. 1_Supplement (2009): 40.4. http://dx.doi.org/10.4049/jimmunol.182.supp.40.4.

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Abstract Particular attention has been given to Toll-like receptors (TLR) on dendritic cells (DC) because of their ability to bridge innate and adaptive defenses. Since TLR are also expressed by epithelial cells, and because the majority of cancers are carcinomas, and thus of epithelial origin, we were interested in comparing responsiveness of a carcinoma and DC to a TLR agonist. For this purpose we used the mammary carcinoma 4T1 and CD11c+ DC. Both 4T1 and DC expressed genes encoding multiple TLR and secreted the proinflammatory chemokines CCL2 and CXCL1 in response to the TLR4 agonist lipopo

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Sironen, Reijo, Mika Elo, Kai Kaarniranta, Heikki J. Helminen, and Mikko J. Lammi. "Transcriptional activation in chondrocytes submitted to hydrostatic pressure." Biorheology: The Official Journal of the International Society of Biorheology 37, no. 1-2 (2000): 85–93. http://dx.doi.org/10.1177/0006355x2000037001002005.

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At present, only a little is known about the transcriptional regulation in chondrocytes submitted to various physicomechanical factors known to exist in articular cartilage. Recently, we have investigated the effects of hydrostatic pressure on transcriptional control in chondrocytes using human chondrosarcoma and immortalized chondrocyte cell lines for the experiments. Hydrostatic pressure was applied on the cells in a special computer‐controlled, water‐filled pressure chamber, where cyclic and static pressures up to 32 MPa can be created. Differential display RT‐PCR and probing of cDNA arrays

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Urbanova, Maria, Verona Buocikova, Lenka Trnkova, et al. "DNA Methylation Mediates EMT Gene Expression in Human Pancreatic Ductal Adenocarcinoma Cell Lines." International Journal of Molecular Sciences 23, no. 4 (2022): 2117. http://dx.doi.org/10.3390/ijms23042117.

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Due to abundant stroma and extracellular matrix, accompanied by lack of vascularization, pancreatic ductal adenocarcinoma (PDAC) is characterized by severe hypoxia. Epigenetic regulation is likely one of the mechanisms driving hypoxia-induced epithelial-to-mesenchymal transition (EMT), responsible for PDAC aggressiveness and dismal prognosis. To verify the role of DNA methylation in this process, we assessed gene expression and DNA methylation changes in four PDAC cell lines. BxPC-3, MIA PaCa-2, PANC-1, and SU.86.86 cells were exposed to conditioned media containing cytokines and inflammatory

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Rodriguez-Menocal, Luis, Si M. Pham, Dania Mateu, et al. "Aging increases p16INK4a expression in vascular smooth-muscle cells." Bioscience Reports 30, no. 1 (2009): 11–18. http://dx.doi.org/10.1042/bsr20080128.

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Alteration of VSMC (vascular smooth-muscle cell) physiology is associated with the development of atherosclerosis and restenosis. We hypothesize that aging up-regulates the expression of p16INK4a in VSMCs, which may increase the susceptibility of blood vessels to vascular occlusive diseases. Aortic VSMCs were obtained from young and aged mice. Cells from aged mice grew more slowly than those from their younger counterparts. Progression of cell cycle in response to serum stimulation was significantly inhibited in those cells with aging, as determined by FACS after propidium iodide staining. A s

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Godel, Martina, Deborah Morena, Preeta Ananthanarayanan, et al. "Small Nucleolar RNAs Determine Resistance to Doxorubicin in Human Osteosarcoma." International Journal of Molecular Sciences 21, no. 12 (2020): 4500. http://dx.doi.org/10.3390/ijms21124500.

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Doxorubicin (Dox) is one of the most important first-line drugs used in osteosarcoma therapy. Multiple and not fully clarified mechanisms, however, determine resistance to Dox. With the aim of identifying new markers associated with Dox-resistance, we found a global up-regulation of small nucleolar RNAs (snoRNAs) in human Dox-resistant osteosarcoma cells. We investigated if and how snoRNAs are linked to resistance. After RT-PCR validation of snoRNAs up-regulated in osteosarcoma cells with different degrees of resistance to Dox, we overexpressed them in Dox-sensitive cells. We then evaluated Do

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