Gene expression and neovascularization: analysis of mouse retinae by gene microarray

2006 ◽  
Vol 1 (S 1) ◽  
Author(s):  
J Lin ◽  
S Zeller ◽  
J Huber ◽  
N Dietrich ◽  
Y Feng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Microarray

scholarly journals Patterns of Gene Expression Upon Infection of Soybean Plants by Phytophthora sojae

2004 ◽  
Vol 17 (10) ◽  
pp. 1051-1062 ◽  
Author(s):  
Pat Moy ◽  
Dinah Qutob ◽  
B. Patrick Chapman ◽  
Ian Atkinson ◽  
Mark Gijzen
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Phytophthora Sojae ◽  
Gene Microarray ◽  
Pathogenesis Related ◽  
Soybean Plants ◽  
Related Proteins ◽  
Phytoalexin Biosynthesis ◽  
Host Tissues ◽  
Mixed Samples

To investigate patterns of gene expression in soybean (Glycine max) and Phytophthora sojae during an infection time course, we constructed a 4,896-gene microarray of host and pathogen cDNA transcripts. Analysis of rRNA from soybean and P. sojae was used to estimate the ratio of host and pathogen RNA present in mixed samples. Large changes in this ratio occurred between 12 and 24 h after infection, reflecting the rapid growth and proliferation of the pathogen within host tissues. From the microarray analysis, soybean genes that were identified as strongly upregulated during infection included those encoding enzymes of phytoalexin biosynthesis and defense and pathogenesis-related proteins. Expression of these genes generally peaked at 24 h after infection. Selected lipoxygenases and peroxidases were among the most strongly downregulated soybean genes during the course of infection. The number of pathogen genes expressed during infection reached a maximum at 24 h. The results show that it is possible to use a single microarray to simultaneously probe gene expression in two interacting organisms. The patterns of gene expression we observed in soybean and P. sojae support the hypothesis that the pathogen transits from biotrophy to necrotrophy between 12 and 24 h after infection.

scholarly journals The inflammation-resolution promoting molecule resolvin-D1 prevents atrial proarrhythmic remodelling in experimental right heart disease

2020 ◽  
Author(s):  
Roddy Hiram ◽  
Feng Xiong ◽  
Patrice Naud ◽  
Jiening Xiao ◽  
Martin Sirois ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heart Disease ◽  
M2 Macrophages ◽  
Gene Microarray ◽  
Resolvin D1 ◽  
Right Heart ◽  
M1 Macrophages ◽  
Anti Inflammatory ◽  
Inflammation Resolution ◽  
Inflammatory Signalling

Abstract Aims Inflammation plays a role in atrial fibrillation (AF), but classical anti-inflammatory molecules are ineffective. Recent evidence suggests that failure of inflammation-resolution causes persistent inflammatory signalling and that a novel drug-family called resolvins promotes inflammation-resolution. Right heart disease (RHD) is associated with AF; experimental RHD shows signs of atrial inflammatory-pathway activation. Here, we evaluated resolvin-therapy effects on atrial arrhythmogenic remodelling in experimental RHD. Methods and results Pulmonary hypertension and RHD were induced in rats with an intraperitoneal injection of 60 mg/kg monocrotaline (MCT). An intervention group received daily resolvin-D1 (RvD1), starting 1 day before MCT administration. Right atrial (RA) conduction and gene-expression were analysed respectively by optical mapping and qPCR/gene-microarray. RvD1 had no or minimal effects on MCT-induced pulmonary artery or right ventricular remodelling. Nevertheless, in vivo transoesophageal pacing induced atrial tachyarrhythmias in no CTRL rats vs. 100% MCT-only rats, and only 33% RvD1-treated MCT rats (P < 0.001 vs. MCT-only). Conduction velocity was significantly decreased by MCT, an effect prevented by RvD1. RHD caused RA dilation and fibrosis. RvD1 strongly attenuated RA fibrosis but had no effect on RA dilation. MCT increased RA expression of inflammation- and fibrosis-related gene-expression pathways on gene-microarray transcriptomic analysis, effects significantly attenuated by RvD1 (334 pathways enriched in MCT-rats vs. control; only 177 dysregulated by MCT with RvD1 treatment). MCT significantly increased RA content of type 1 (proinflammatory) CD68-positive M1 macrophages without affecting type 2 (anti-inflammatory) M2 macrophages. RvD1-treated MCT-rat RA showed significant reductions in proinflammatory M1 macrophages and increases in anti-inflammatory M2 macrophages vs. MCT-only. MCT caused statistically significant increases in protein-expression (western blot) of COL3A1, ASC, CASP1, CASP8, IL1β, TGFβ3, CXCL1, and CXCL2, and decreases in MMP2, vs. control. RvD1-treatment suppressed all these MCT-induced protein-expression changes. Conclusion The inflammation-resolution enhancing molecule RvD1 prevents AF-promoting RA remodelling, while suppressing inflammatory changes and fibrotic/electrical remodelling, in RHD. Resolvins show potential promise in combating atrial arrhythmogenic remodelling by suppressing ongoing inflammatory signalling.

scholarly journals Changes in gene expression linked with adult reproductive diapause in a northern malt fly species: a candidate gene microarray study

BMC Ecology ◽  
2010 ◽  
Vol 10 (1) ◽  
pp. 3 ◽  
Author(s):  
Maaria Kankare ◽  
Tiina Salminen ◽  
Asta Laiho ◽  
Laura Vesala ◽  
Anneli Hoikkala
Keyword(s):  
Gene Expression ◽  
Candidate Gene ◽  
Gene Microarray ◽  
Reproductive Diapause ◽  
Microarray Study

scholarly journals Metatranscriptome Analysis for Insight into Whole-Ecosystem Gene Expression during Spontaneous Wheat and Spelt Sourdough Fermentations

2010 ◽  
Vol 77 (2) ◽  
pp. 618-626 ◽  
Author(s):  
Stefan Weckx ◽  
Joke Allemeersch ◽  
Roel Van der Meulen ◽  
Gino Vrancken ◽  
Geert Huys ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Pathways ◽  
Fermented Foods ◽  
Gene Microarray ◽  
Organoleptic Properties ◽  
Redox Equilibrium ◽  
Flavor Compound ◽  
Approaches To Study ◽  
Microarray Analyses ◽  
Insight Into

ABSTRACTLactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, including sourdough-derived products. Despite their limited metabolic capacity, LAB contribute considerably to important characteristics of fermented foods, such as extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Triggered by the considerable amount of LAB genomic information that became available during the last decade, transcriptome and, by extension, metatranscriptome studies have become one of the most appropriate research approaches to study whole-ecosystem gene expression in more detail. In this study, microarray analyses were performed using RNA sampled during four 10-day spontaneous sourdough fermentations carried out in the laboratory with an in-house-developed LAB functional gene microarray. For data analysis, a new algorithm was developed to calculate a net expression profile for each of the represented genes, allowing use of the microarray analysis beyond the species level. In addition, metabolite target analyses were performed on the sourdough samples to relate gene expression with metabolite production. The results revealed the activation of different key metabolic pathways, the ability to use carbohydrates other than glucose (e.g., starch and maltose), and the conversion of amino acids as a contribution to redox equilibrium and flavor compound generation in LAB during sourdough fermentation.

Gene Microarray Analysis of Human Brain Arteriovenous Malformations

Neurosurgery ◽  
2004 ◽  
Vol 54 (2) ◽  
pp. 410-425 ◽  
Author(s):  
Tomoki Hashimoto ◽  
Michael T. Lawton ◽  
Gen Wen ◽  
Guo-Yuan Yang ◽  
Thomas Chaly ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Brain ◽  
Microarray Data ◽  
Arteriovenous Malformations ◽  
Gene Expression Pattern ◽  
Protein Product ◽  
Published Data ◽  
Gene Microarray ◽  
Control Brain ◽  
Microarray Technique

Abstract OBJECTIVE Human brain arteriovenous malformations (BAVMs) display abnormal expression of various angiogenesis-related genes and their products. We examined gene expression patterns in BAVMs by the gene microarray technique. METHODS We analyzed BAVM and control brain samples obtained by temporal lobectomy for medically intractable seizure by Affymetrix Human Gene Set U95Av2 (Affymetrix, Inc., Santa Clara, CA). The gene microarray data were compared with new and previously published data that used conventional molecular biology techniques. RESULTS We analyzed six BAVM and five control brain samples. From 12,625 gene probes assayed, 1781 gene probes showed differential expression between BAVMs and controls. BAVM samples had a gene expression pattern that was distinct from those of control brain samples. Increased messenger ribonucleic acid expression of vascular endothelial growth factor A was accompanied by increased expression of its protein product. A majority of the gene data was in agreement with previously published data. The gene microarray data generated a new testable hypothesis regarding integrin, and we found increased expression of integrin αvβ3 protein in BAVMs. CONCLUSION The gene expression pattern of BAVMs was distinct from those of control brain samples. We verified the gene microarray data by demonstrating that increased gene expression levels for angiogenesis-related molecules were accompanied by increased levels of their protein product expression. The gene microarray technique may be a useful tool to study multiple pathways simultaneously in BAVM specimens.

scholarly journals Gene expression analysis of glucocorticoid-induced apoptosis by a gene microarray technique

10.1038/87108 ◽  
2001 ◽  
Vol 27 (S4) ◽  
pp. 58-58 ◽  
Author(s):  
Huiling He ◽  
Michael Malone ◽  
Steven Ostrowski ◽  
Clark Distelhorst
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Gene Microarray ◽  
Induced Apoptosis ◽  
Microarray Technique

Predicting survival and metastasis in soft tissue sarcoma: A gene microarray study using RNA derived from archival paraffin-embedded tumours

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 10074-10074
Author(s):  
K. M. Linton ◽  
Y. Hey ◽  
M. Jeziorska ◽  
C. L. Wilson ◽  
C. Miller ◽  
...  
Keyword(s):  
Gene Expression ◽  
Soft Tissue ◽  
Soft Tissue Sarcoma ◽  
Rna Extraction ◽  
Protein Detection ◽  
Outcome Data ◽  
Gene Microarray ◽  
Prognostic Information ◽  
Rank Regression ◽  
Fresh Frozen

10074 Background: The genetic determinants of survival and metastasis in soft tissue sarcoma (STS) are poorly understood and progress in this field has been limited by the rare nature of STS and the need for fresh/frozen tissue (FT) for gene microarray analyses. Our objective was to determine whether valid gene microarray data can be obtained from archival formalin-fixed paraffin-embedded tumours (FFPET) in order to retrospectively identify prognostic STS gene signatures and potential molecular targets from patients with known clinical outcome data. Methods: Total RNA was extracted from macrodissected viable tumour tissue for 34 FFPET (14 liposarcomas, 11 leiomyosarcomas and 9 synovial sarcomas) and two paired FFPET and FT primary leiomyosarcomas (modified Optimum kit, Ambion, for FFPET RNA extraction and Trizol, Invitrogen, for FT RNA extraction). One-cycle labelled cRNA was hybridised to Affymetrix U133 Plus 2 microarrays, and strict QC protocols used to identify 19 arrays for further analysis using R and BioConductor. Log rank regression and Kaplan-Meier plots of disease-specific survival were performed to identify genes predictive of survival and/or metastasis. Results: Similar fold changes in gene expression were obtained for paired cRNA samples, although the number of genes called present was lower for cRNA from FFPET. Five hundred genes (selected from FFPET cRNA arrays) were discriminatory for survival (p=0.0006 to 0.0088) across all STS subtypes and correctly assigned 17/19 cases by leave-one-out cross validation. Many are known tumour prognostic genes, significant for survival, metastasis, invasion, angiogenesis and apoptosis. Twenty-five novel and known candidate genes (with 3–10 fold differential expression) were selected for validation on 19 test and 60 independent cases by RT-PCR for relative gene expression and immunohistochemistry for protein detection. Conclusions: We have shown that prognostic information can be derived from archival FFPET, permitting the identification of candidate prognostic genes and therapeutic targets in STS, and opening the way for studies in other tumours where FT is unavailable. No significant financial relationships to disclose.

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