Example of an extended UTR bridging the gap to a distant full-length cDNA

<p><b>Copyright information:</b></p><p>Taken from "Beyond the 3′ end: experimental validation of extended transcript isoforms"</p><p></p><p>Nucleic Acids Research 2007;35(6):1947-1957.</p><p>Published online 4 Mar 2007</p><p>PMCID:PMC1874610.</p><p>© 2007 The Author(s)</p> Screenshot from the Riken genomic element viewer () displaying both full-length cDNAs and CAGE tags (transcription starts) for gene Tmem33. The stop codon position is indicated with a yellow triangle. The bottom red strip represents the RT-PCR validated transcript (5′ end is not determined). We located a putative poly(A) site for gene Tmem33 at around 5.2 kb from the stop codon, supported by a single full-length cDNA (highlighted). The 2.35 kb gap between this unique cDNA and the longest Tmem33 transcript caused Riken to predict two independent transcription units (TUs) for these entities

Additional file 1: Table S1. of Gene expression comparison reveals distinct basal expression of HOX members and differential TNF-induced response between brain- and spinal cord-derived microvascular endothelial cells

TNF-α modulated expression of genes involved in the TNF-α signaling pathway in BMECs and SCMECs. (DOC 53 kb

Enzymatic activities involved in the TCA cycle.

<p>Tg and WT astrocytes were treated or not with pantethine, then exposed or not to oAβ. Enzymatic activities were determined on mitochondrial preparations. (A) α-Ketoglutarate dehydrogenase (KGDH) activity. (B) succinate dehydrogenase (SDH) activity. Results are the mean values ± SD from three independent experiments (n = 3 per group) and are expressed as nmol/min/mg protein (*, significant difference with the WT group; §, significant difference with the corresponding group not exposed to oAβ; #, significant difference with the corresponding group untreated with pantethine; <i>p</i><0.05). (C) Schematic representation of the TCA cycle enzymes and metabolites involved in HIF-1α hydroxylation (α-KG: α-ketoglutarate; HIF-1α: hypoxia inducible factor-1α; HIF-1α (-OH): hydroxylated HIF-1α).</p

Relative abundance of distinct metabolites in Tg and WT astrocytes, treated or not with pantethine.

<p>Intracellular levels of different metabolites were determined. The table shows normalized data expressed relative to the abundance of the untreated WT group and are shown as the mean values ± SD from three independent experiments (n = 3 per group); (*, values significantly different between Tg and WT astrocytes; #, values significantly different compared to the corresponding untreated groups; <i>p</i>≤0.05).</p

APP is expressed in astrocytes.

<p>(A) Western blot analysis of full-length APP, C99 and C83 CTF fragments in Tg and WT cortices (upper panel) and in astrocytes (bottom panel), using a CTF (C-terminal fragment) antibody specifically recognizing the C-terminal end of APP. Graphs on the right represent the mean ± SD of actin-normalized values of the percentage of variation in optical density (O.D.) relative to WT. (B) mRNA expression levels of human APP (<i>APP</i>) and presenilin-1 (<i>PS1</i>) in Tg and WT astrocytes. Values were obtained from three independent experiments (n = 3 per group) (*, significant difference between Tg and WT groups; <i>p</i><0.05).</p

Kinetics of HIF-1α protein expression and proteasome activity in Tg and WT astrocytes following oAβ exposure.

<p>(A) Western blot analysis of HIF-1α expression. (B) Densitometry analysis. Data were normalized to β-actin and are displayed as fold increase relative to control untreated WT astrocytes. (C) Proteasomal enzymatic activity assayed using a chymotrypsin substrate. The data are displayed as percent of control untreated WT astrocytes. As a control, enzyme activity was determined in the presence of 0.5 μM of the inhibitor MG132 for 24 h. Bars represent the mean ± SD from three independent experiments (n = 3 per group) (*, significant difference with the corresponding WT control; §, significant difference with the corresponding control; #, significant difference with groups untreated with pantethine; <i>p</i><0.05).</p

Enzymatic activities involved in the glycolytic pathway.

<p>Tg and WT astrocytes were treated or not with pantethine and then exposed or not to exogenous oligomeric Aβ (oAβ). Enzymatic activity and NADPH levels were determined on cell extracts. (A) Glucose-6-phosphate dehydrogenase (G6PD) activity. (B) Pyruvate kinase (PK) activity. (C) NADPH levels. Results are the mean values ± SD from three independent experiments (n = 3 per group). Enzyme activities are expressed as nmol/min/mg protein and NADPH levels are expressed as nmol/mg protein (*, significant difference between experimental groups; <i>p</i><0.05). (D) Schematic representation of glucose metabolism enlightening the hexose monophosphate shunt (HMS) and PK (G6-P, glucose-6P; G-3P, glyceraldehyde-3P; PEP, phosphoenoylpyruvate; pyr, pyruvate).</p

HIF-1α protein levels in Tg and WT astrocytes.

<p>(A) Western blot analysis of HIF-1α expression in astrocytes treated or not with pantethine. (B) Densitometric analysis of western blots. Data were normalized to β-actin and are displayed as fold increase relative to untreated WT astrocytes (black diagram). The results represent the mean ± SD from three independent experiments (n = 3 per group) (*, significant difference with the WT control group; #, significant difference with the corresponding group untreated with pantethine; <i>p</i><0.05).</p

Tg and WT astrocyte activation status.

<p>Tg and WT astrocytes were treated or not with pantethine, then exposed or not to oAβ. (A) Confocal microscopy images of astrocyte morphology monitored by GFAP labeling (green); nuclei are labeled with Hoechst (blue). a, Quiescent astrocytes; b, astrocytes exposed to oAβ; P, pantethine treatment. Each picture is representative of images obtained from at least three independent cultures. (B) Astrocyte activation quantified by counting the number of activated cells (stellar shape) as a percent of the total number of cells in 10 randomly selected 10⁵ μm² fields from all the pictures obtained. (C) Astrocyte viability determined using the MTT assay. The diagrams are mean values ± SD from three independent experiments (n = 3 per group) (*, significant difference between WT and Tg groups; §, significant difference with groups not exposed to oAβ; #, significant difference with the corresponding group untreated with pantethine; <i>p</i><0.05). Scale bars: 100 μm.</p

This Venn diagrams show the number of overlapping genes with significant expression changes on days 2, 5, and 7 post-infection with PbA, for C57BL/6 mice (and ), CBA/J mice (and ) and BALB/c mice (and )

<p><b>Copyright information:</b></p><p>Taken from "Gene expression analysis reveals early changes in several molecular pathways in cerebral malaria-susceptible mice versus cerebral malaria-resistant mice"</p><p>http://www.biomedcentral.com/1471-2164/8/452</p><p>BMC Genomics 2007;8():452-452.</p><p>Published online 6 Dec 2007</p><p>PMCID:PMC2246131.</p><p></p> Genes that are either induced or suppressed by infection are distinguished for each strain: the number of genes induced is shown in , , and , while the number of genes suppressed is shown in , , and