Biomedical subjects

Pekka Ojala

Publications and source records attributed to Pekka Ojala.

3 recordsLinked to original sources

PubMed2006

Automated pattern ranking in differential display data analysis.

Gene expression analysis by differential display (DD) is limited by the labor-intensive visual evaluation of the electrophoretic data traces. We describe a flexible method for computer-assisted ranking of expression patterns in data from DD experiments. The method is based on a pairwise alignment and comparison of the quantitative trace data with respect to specific expression patterns defined by the investigator. The observed patterns are ranked according to a score value that identifies the most potential findings to be confirmed visually instead of the vast amount of original results. This two-step approach, enabled by the efficient computer algorithm for gene expression pattern comparison, will increase the percentage of true-positive findings chosen for the tedious downstream processing, while minimizing the cost and labor involved in large scale DD data analysis.

Algorithms↗

PubMed2002

mRNA differential display of gene expression in colonic carcinoma.

We analyzed changes in gene expression in human colonic carcinoma by fluorescent mRNA differential display. RNA isolated from two samples of normal colon and four cases of colonic adenocarcinoma were amplified with a 15 x 32 set of primers resulting in 2880 cDNAs analyzed with an automated sequencer. Electrophoretic patterns implying constitutive gene expression as well as upregulated and downregulated expression in carcinomas were identified. Forty such cDNA fragments were purified by a novel fluorescent polyacrylamide gel electrophoresis (PAGE)-based method and identified by cyclic sequencing. Most genes showing differential expression were upregulated in colonic carcinoma. Upregulated genes included those for various ribosomal and mitochondrial proteins, heat shock proteins, nucleolar RNA-helicase and phosphoserine aminotransferase. Downregulated genes included histone H3.3. In conclusion, genes associated with vital cellular functions such as transcription, protein synthesis and mitochondrial metabolism were upregulated in colonic carcinoma. Fluorescent mRNA differential display can be applied to the identification of novel cancer-related genes for diagnostic, prognostic and therapeutic purposes.

Adenocarcinoma↗

PubMed2002

Contralateral non-operated nerve to transected rat sciatic nerve shows increased expression of IL-1beta, TGF-beta1, TNF-alpha, and IL-10.

Recent reports indicate that after a peripheral nerve injury, the uninjured contralateral nerve is also affected. Because cytokines play an important role in the peripheral nerve injury, we studied the expression of five different mRNAs (interleukin-1beta (IL-1beta), tumor necrosis factor-alpha (TNF-alpha), interleukin-10 (IL-10), transforming growth factor-beta1 (TGF-beta1) and interleukin-4 (IL-4)) in the contralateral, non-operated, left sciatic nerve when the right rat sciatic nerve was transected. This study extended up to 42 days after the transection. No IL-4 expression was noted. During the first 3 days, high expression of the other studied cytokines was noted in the endoneurium. At day 7, the expression diminished to the control levels. After this, a cyclic expression pattern appeared, which was most pronounced in the endoneurium at 35 days. We also show that the expression pattern in the endoneurium is different from that in the surrounding epi- and perineurium. Also, our present study shows clearly that contralateral nerves are poor controls after injury.

Animals↗