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P J Boender

Publications and source records attributed to P J Boender.

5 recordsLinked to original sources
PubMed2003

Effect of secondary structure on single nucleotide polymorphism detection with a porous microarray matrix; implications for probe selection.

Oligonucleotide arrays capable of detecting single nucleotide polymorphisms (SNPs) from amplified nucleic acid have many applications. The expected SNP is usually placed approximately in the center of the probe to ensure the maximum shift in Tm between complementary and SNP sequences. Unfortunately, different short probes (< 30 bases) selected using widely accepted criteria do not perform consistently in this type of assay. Here we present a systematic study on the effect of secondary structure on the ability of oligonucleotide probes to detect an SNP, using real-time array monitoring of a porous microarray substrate that incorporates a novel intra-array mixing system. These results demonstrate that, although positioning of an SNP in the middle of the probe is highly destabilizing, the effect of stable secondary structure on the signal obtained is so dramatic that such probes may be very insensitive. Therefore, if the SNP flanking sequence contains significant secondary structure, then more sensitive probes with good specificity may be obtained by positioning the mutation towards one end of the probe.

Artifacts↗
PubMed1989

Inhibition of human hemopoiesis by non-A, non-B hepatitis virus.

All etiologies of acute viral hepatitis are associated with a transient suppression of hemopoiesis and, rarely, with the development of aplastic anemia. Both hepatitis A and hepatitis B viruses directly inhibit the growth and differentiation of human bone marrow progenitor cells in vitro. We now report a similar effect of a non-A, non-B (NANB) hepatitis agent on human bone marrow progenitor cells. Three chimpanzees were inoculated with a putative NANB agent. Coded sera were blindly evaluated for their ability to affect human bone marrow colony formation in vitro. Sera obtained during the acute phase of NANB hepatitis inhibited the in vitro growth of human erythroid (CFU-E, BFU-E) and granulocyte-macrophage (CFU-GM) progenitor cells, compared with sera obtained before inoculation. Sera obtained after remission of both the biochemical and histological hepatitis and sera obtained from a chimpanzee who underwent biochemical but not histological remission did not inhibit the stem cell assays as much as the acute phase sera. These results suggest an approach to identifying the viremic phase of NANB hepatitis. Inhibition of human bone marrow proliferation appears to be a common property of all known hepatitis viruses.

Animals↗
PubMed1989

Nucleosomal fragments in serum may directly reflect cell-mediated cytotoxic activity in vivo.

In in vitro experiments the activity of cytotoxic T-cells and natural killer cells has been shown to cause nuclear DNA fragmentation leading to the release of nucleosomal multimers from the target cells. These multimers form a ladder-like pattern with a periodicity of approximately 200 bp during gel electrophoresis. The objective of the present study was to show the relevance of the presence of these nucleosomal multimers in vivo during diseases that show cell-mediated cytotoxicity. Nucleosomal multimers (n greater than 5) could be detected using nick translation followed by electrophoresis in a series of sera of a chimpanzee infected with hepatitis A virus and in sera drawn from several hepatitis B patients. The multimers were present during periods expected to show an increased activity of cell-mediated cytotoxicity in the liver. During these periods the injury of the liver cells was also mirrored by the classical parameter, the release of a specific liver enzyme into the serum. The liver enzyme activity in the serum and the detection of the nucleosomal multimers did not completely overlap, however. It is postulated that the proposed nick translation assay is useful as a simple diagnostic test for cell-mediated cytotoxicity since it reflects this activity under different in vivo situations.

Alanine Transaminase↗
PubMed1985

Detection of integration during active replication of hepatitis B virus in the liver.

A method is described that enables the unequivocal detection of the integration of hepatitis B virus DNA (HBV-DNA) into the genomic DNA of the host cell, while at the same time the virus exhibits active replication. This detection was achieved by separating the low molecular weight replicating HBV-DNA from the high molecular weight genomic DNA of the host by electrophoresis of the total undigested cellular DNA through low melting agarose. The high molecular weight DNA was isolated from this gel and electrophoresed after digestion with restriction enzyme(s) on a second agarose gel. Transfer of the DNA content of both gels and hybridization of these blots with 32P-labelled HBV-DNA will reveal whether any integrated and/or actively replicating DNA is present. By using this method the presence of a single copy of HBV-DNA integrated in host DNA was demonstrated in hepatocellular carcinoma tissue of a patient with active HBV replication.

Carcinoma, Hepatocellular↗