The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia-5

<p><b>Copyright information:</b></p><p>Taken from "The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia"</p><p>http://www.biomedcentral.com/1471-2164/8/370</p><p>BMC Genomics 2007;8():370-370.</p><p>Published online 15 Oct 2007</p><p>PMCID:PMC2194787.</p><p></p>tting CA3/CA1 ratios in ischemia vs. sham reveals deviation from the diagonal. Difference ratios are attenuated by ischemia regardless of preferential CA3 or CA1 expression (red: p< 0.05). C, Inhibin beta A displays the highest change in preference between the native and ischemic state. The gene expression preference actually reverses from higher expression in CA1 in the native brain to higher expression in CA3 in the ischemic state. Verification with quantitative PCR shows comparable values to the array-derived ratios

The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia-4

<p><b>Copyright information:</b></p><p>Taken from "The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia"</p><p>http://www.biomedcentral.com/1471-2164/8/370</p><p>BMC Genomics 2007;8():370-370.</p><p>Published online 15 Oct 2007</p><p>PMCID:PMC2194787.</p><p></p>ischemic animals and the non-ischemic controls (means of n = 4 experiments for each region). In each of the hippocampal subregions more than 5000 genes could be identified exhibiting differential expression upon ischemia. A. 5243 differentially expressed genes were detected in the CA3 region. B. 5511 differentially expressed genes were detected in the CA1 region. Red: significantly regulated genes (p< 0.05; differentially regulated genes in blue). C, A total of 97 genes is significantly different between ischemic CA3 and ischemic CA1 regions (scatterplot; blue are significantly regulated genes p< 0.05). D, Bar graph showing the 5 most different genes with preference for CA3 or CA1 with their relative enrichment factors (prdma, pr-domain containing protein 8; Inhba, Inhibin beta A; Bok, Bcl-2 related ovarian killer; Sytl4, synaptotagmin-like 4; rbp 4, retinol binding protein 4; mpped1, metallophosphoesterase domain containing 1; mrg1, myeloid ecotropic viral integration site-related gene 1, alternative names: meis2, stra10)

The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia-6

<p><b>Copyright information:</b></p><p>Taken from "The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia"</p><p>http://www.biomedcentral.com/1471-2164/8/370</p><p>BMC Genomics 2007;8():370-370.</p><p>Published online 15 Oct 2007</p><p>PMCID:PMC2194787.</p><p></p>ull hemispheric infarcts. A, TTC-stained coronal section 24 h after induction of ischemia/hypoxia demonstrate a full hemispheric infarct which fully covers the hippocampal region. B, The cutting outlines used for Laser microdissection from coronal cryosections are demonstrated on a section stained with an antibody against NeuN and a secondary Cy3-coupled antibody. Actual Laser microdissections in the experiments were performed on Thionin-stained sections. C, Scheme showing the strategy used for detection of differentially regulated genes from amplified RNA. Samples from CA3 and CA1 regions were hybridized on two-color oligonucleotide arrays (Agilent). Direct competitive hybridizations were performed for all combinations: CA3 sham vs, CA1 sham, CA3 ischemia vs CA1 ischemia, CA3 ischemia vs CA3 sham, and CA1 ischemia vs CA1 sham. All experiments were also dye-swapped, and means of the two corresponding values used for further analyses. Arrays were statistically analyzed using linear modelling (limma, R)

The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia-2

<p><b>Copyright information:</b></p><p>Taken from "The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia"</p><p>http://www.biomedcentral.com/1471-2164/8/370</p><p>BMC Genomics 2007;8():370-370.</p><p>Published online 15 Oct 2007</p><p>PMCID:PMC2194787.</p><p></p>r CA1. The upper part of the graph shows the GO category "Biological process", the lower part "Molecular function". GO analysis were performed using the web-based L2L tool [29]. For "Biological process" there is a strong emphasis on terms related to neuron differentiation, synaptic function, and energy metabolism in CA3, and to GABA-signaling in CA1. For "Molecular function" we find enrichment of groups like ephrin receptors, serin-type protease inhibitors, and carbohydrate moiety transfer activities. In contrast in CA1 we observe an enrichment in deglycosylating activity, ligand-gated ion channels, and sulfotransferase activity. Black, expected matches; red, observed matches

The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia-0

<p><b>Copyright information:</b></p><p>Taken from "The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia"</p><p>http://www.biomedcentral.com/1471-2164/8/370</p><p>BMC Genomics 2007;8():370-370.</p><p>Published online 15 Oct 2007</p><p>PMCID:PMC2194787.</p><p></p>ull hemispheric infarcts. A, TTC-stained coronal section 24 h after induction of ischemia/hypoxia demonstrate a full hemispheric infarct which fully covers the hippocampal region. B, The cutting outlines used for Laser microdissection from coronal cryosections are demonstrated on a section stained with an antibody against NeuN and a secondary Cy3-coupled antibody. Actual Laser microdissections in the experiments were performed on Thionin-stained sections. C, Scheme showing the strategy used for detection of differentially regulated genes from amplified RNA. Samples from CA3 and CA1 regions were hybridized on two-color oligonucleotide arrays (Agilent). Direct competitive hybridizations were performed for all combinations: CA3 sham vs, CA1 sham, CA3 ischemia vs CA1 ischemia, CA3 ischemia vs CA3 sham, and CA1 ischemia vs CA1 sham. All experiments were also dye-swapped, and means of the two corresponding values used for further analyses. Arrays were statistically analyzed using linear modelling (limma, R)

The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia-1

<p><b>Copyright information:</b></p><p>Taken from "The functional genome of CA1 and CA3 neurons under native conditions and in response to ischemia"</p><p>http://www.biomedcentral.com/1471-2164/8/370</p><p>BMC Genomics 2007;8():370-370.</p><p>Published online 15 Oct 2007</p><p>PMCID:PMC2194787.</p><p></p>t are differentially expressed in the CA3 and CA1 region in sham-treated animals, 566 are significantly enriched in CA3, 487 in CA1 (p< 0.05; differentially regulated genes in red). B, Bar graph showing enrichment factors for the 5 most differentially expressed genes in CA3 and CA1. The enrichment factors reflect relative abundance of gene expression in CA3 over CA1 or vice versa, and were calculated by dividing the mean of the gene abundance in CA3 by CA1 or vice versa. Bok, Bcl-2 related ovarian killer; pvrl3, poliovirus receptor-related 3; rerg, RAS-like, estrogen-regulated; dehal1, Iodotyrosine dehalogenase 1; mpped1, metallophosphoesterase domain containing 1; penk1, preproenkephalin 1