Detection of GST1 gene deletion by the polymerase chain reaction and its possible correlation with stomach cancer in Japanese

Summary A homozygous gene deletion at the GST1 locus of genomic DNA isolated from peripheral blood was investigated for its relationship with several types of cancer using the polymerase chain reaction (PCR) technique. DNA samples were prepared from blood obtained from 128 healthy blood donors and 150 patients with cancer or chronic hepatitis. PCR primers were prepared based on the human cDNA sequence and the intron/exon sequences of the rat Yb2 gene. The amplified sequence between exons 5 and 6 including intron 5 showed very clearly the presence of absence of the GST1 gene, after electrophoresis in a 2% agarose gel. Segregation of the presence and absence of PCR product from samples of twins and their parents indicated that presence involves homozygous or heterozygous normal GST1 genotypes while absence invovles only homozygous gene deletion. The patients with stomach cancer had a significantly higher frequency of gene deletion than did the healthy controls (P< 0.005). Thus, GST1 deletion may be a possible genetic marker for early detection of a group at high risk of stomach cancer.     

A novel copper(II) coordination at His186 in full-length murine prion protein

To explore Cu(II) ion coordination by His¹⁸⁶ in the C-terminal domain of full-length prion protein (moPrP), we utilized the magnetic dipolar interaction between a paramagnetic metal, Cu(II) ion, and a spin probe introduced in the neighborhood of the postulated binding site by the spin labeling technique (SDSL technique). Six moPrP mutants, moPrP(D143C), moPrP(Y148C), moPrP(E151C), moPrP(Y156C), moPrP(T189C), and moPrP(Y156C,H186A), were reacted with a methane thiosulfonate spin probe and a nitroxide residue (R1) was created in the binding site of each one. Line broadening of the ESR spectra was induced in the presence of Cu(II) ions in moPrP(Y148R1), moPrP(Y151R1), moPrP(Y156R1), and moPrP(T189R1) but not moPrP(D143R1). This line broadening indicated the presence of electron-electron dipolar interaction between Cu(II) and the nitroxide spin probe, suggesting that each interspin distance was within 20 Å. The interspin distance ranges between Cu(II) and the spin probes of moPrP(Y148R1), moPrP(Y151R1), moPrP(Y156R1), and moPrP(T189R1) were estimated to be 12.1 Å, 18.1 Å, 10.7 Å, and 8.4 Å, respectively. In moPrP(Y156R1,H186A), line broadening between Cu(II) and the spin probe was not observed. These results suggest that a novel Cu(II) binding site is involved in His186 in the Helix2 region of the C-terminal domain of moPrP^C.     

Among-population variation in resistance traits of a nettle and its relationship with deer habitat use frequency

Because leaf hairs serve as resistance against herbivores, among-population variation in hair production may arise from adaptation to local herbivore communities. It is possible that Japanese nettle (Urtica thunbergiana) shows among-population variation in stinging hair abundance that is associated with the frequency of habitat use by sika deer (Cervus nippon). We examined 31–32 individuals of each of 19 populations for leaf area, stinging hair number (/leaf) and stinging hair density (per square centimeter) in and away from Nara Park (6.6 km²), where many deer have been protected for 1,200 years. At each site we also measured deer habitat use frequency, light intensity and soil fertility as environmental factors potentially affecting leaf traits. We analyzed our hierarchical data at the levels of individuals and populations using multilevel structural equation modeling. Leaf area had a positive direct effect on stinging hair number at the individual level but no significant effect at the population level. At the population level, deer habitat use frequency had a negative direct effect on leaf area and positive direct effects on stinging hair number and density, generating a negative indirect correlation between leaf area and stinging hair number. Light intensity had a negative direct effect on leaf area, while soil fertility had no significant effect on any trait. These results suggest that the relationships between leaf area and stinging hair number at the two levels do not align. We discussed what processes were involved in the effects of environmental factors on leaf traits.     

Adhesiveness of beta5 integrin variant lacking FNK767-769 is similar to that of the prototype containing FNKFNK764-769

Little is known about the functions of two different beta5 integrins: repeated-FNK (FNKFNK764-769) and single-FNK (FNK764-766) amino acid sequences in the cytoplasmic domain. We examined whether they occurred as germ line mutations or somatic mutations associated with neoplastic transformation, and whether there were functional alterations. Out of six cultured cell lines, only KATO-III cells had the single-FNK beta5 sequence. The single-FNK beta5 was found in 9 out of 79 patients with colon carcinoma, but no somatic mutations were detected in cancerous tissues. CHO cells were transformed with expression vectors containing single-FNK or repeated-FNK beta5 cDNA, which were derived from KATO-III cells. CHO cells transfected with single-FNK and repeated-FNK showed similar adhesiveness to, and proliferative activity on, vitronectin substrates.     

Diversity of dung-beetle community in declining Japanese subalpine forest caused by an increasing sika deer population

The Ohdaigahara subalpine plateau in Japan has recently suffered a reduction in primary forest land caused by an increasing population of sika deer (Cervus nippon). Deer have debarked many trees, causing dieback, gradually changing the primary forest first to light forest with a floor that is densely covered with sasa grass (Sasa nipponica) and then to S. nipponica grassland. To examine the effects of vegetative transformation on the dung-beetle community, we compared the diversity and abundance of dung-beetle assemblages in the primary forest, transition forest, and S. nipponica grassland using dung-baited pitfall traps. The species richness and species diversity (Shannon-Wiener index) were significantly highest in the primary forest and lowest in the S. nipponica grassland. The evenness (Smith-Wilson index) was highest in the primary forest and nearly equal in the transition forest and S. nipponica grassland. The abundance was apparently greater in the transition forest than in the primary forest and S. nipponica grassland. These results suggest that loss of primary forest resulting from an increasing deer population decreases the diversity of the dung-beetle community while increasing the abundance of dung beetles in the transition forest. Sika deer use transition forests and grasslands more frequently than primary forests as habitat, but an increase in dung supply there does not necessarily increase the diversity or abundance of dung-beetle assemblages.     

Using multiple ontologies to integrate complex biological data

The strength of the rat as a model organism lies in its utility in pharmacology, biochemistry and physiology research. Data resulting from such studies is difficult to represent in databases and the creation of user-friendly data mining tools has proved difficult. The Rat Genome Database has developed a comprehensive ontology-based data structure and annotation system to integrate physiological data along with environmental and experimental factors, as well as genetic and genomic information. RGD uses multiple ontologies to integrate complex biological information from the molecular level to the whole organism, and to develop data mining and presentation tools. This approach allows RGD to indicate not only the phenotypes seen in a strain but also the specific values under each diet and atmospheric condition, as well as gender differences. Harnessing the power of ontologies in this way allows the user to gather and filter data in a customized fashion, so that a researcher can retrieve all phenotype readings for which a high hypoxia is a factor. Utilizing the same data structure for expression data, pathways and biological processes, RGD will provide a comprehensive research platform which allows users to investigate the conditions under which biological processes are altered and to elucidate the mechanisms of disease.     

DNA-regulated arginine-specific mono(ADP-ribosyl)ation and de-ADP-ribosylation of endogenous acceptor proteins in human neutrophils

Arginine-specific mono(ADP-ribosyl)ation and de-ADP-ribosylation reactions of endogenous acceptor proteins were examined using human neutrophils. The cells contained arginine-specific ADP-ribosyltransferase, acceptor proteins and hydrolase catalyzing the release of ADP-ribose from the ADP-ribose/acceptor conjugate. One major acceptor protein with an apparent molecular mass of 27 kDa was detected in the neutrophils. The ADP-ribosylation of this protein was greatly enhanced when double-stranded DNA was added. The release of ADP-ribose from the ADP-ribosyl core-histones was suppressed. These findings provide clues as to the physiological function of neutrophil ADP-ribosyltransferase.