HapMap SNP Scanner: an online program to mine SNPs responsible for cell phenotype.

Minor histocompatibility (H) antigens are targets of graft-vs-host disease and graft-vs-tumor responses after human leukocyte antigen matched allogeneic hematopoietic stem cell transplantation. Recently, we reported a strategy for genetic mapping of linkage disequilibrium blocks that encoded novel minor H antigens using the large dataset from the International HapMap Project combined with conventional immunologic assays to assess recognition of HapMap B-lymphoid cell line by minor H antigen-specific T cells. In this study, we have constructed and provide an online interactive program and demonstrate its utility for searching for single-nucleotide polymorphisms (SNPs) responsible for minor H antigen generation. The website is available as 'HapMap SNP Scanner', and can incorporate T-cell recognition and other data with genotyping datasets from CEU, JPT, CHB, and YRI to provide a list of candidate SNPs that correlate with observed phenotypes. This method should substantially facilitate discovery of novel SNPs responsible for minor H antigens and be applicable for assaying of other specific cell phenotypes (e.g. drug sensitivity) to identify individuals who may benefit from SNP-based customized therapies.

Salmonella in healthy pigs: prevalence, serotype diversity and antimicrobial resistance observed during 1998-1999 and 2004-2005 in Japan.

To determine prevalence, serotype diversity and antimicrobial resistance of Salmonella in healthy pigs, faecal samples from 6771 pigs on 73 farms collected during 1998-1999 and 2004-2005 were examined. Salmonella isolates were serotyped and tested for susceptibility to 22 antimicrobials: benzylpenicillin, ampicillin, amoxicillin, cefazolin, cephaloridine, gentamicin, kanamycin, streptomycin, fradiomycin, colistin, tetracycline, chlortetracycline, oxytetracycline, chloramphenicol, thiamphenicol, sulfadimethoxine, sulfamethoxazole, sulfamethoxypyridazine, trimethoprim, sulfamethoxazole/trimethoprim, norfloxacin and ofloxacin. Farm-level and pig-level Salmonella prevalences were 35.5% and 2.2% in 1998-1999, and 35.7% and 3.3% in 2004-2005. Prevalence by growth stage was 2.4% for sows, 3.3% for weaned pigs, 2.7% for fattening pigs and 3.8% for finishing pigs. The predominant serotypes identified were Agona (28.4%), Typhimurium (17.9%) and Infantis (16.4%) in 1998-1999, and Typhimurium (32.5%), Anatum (24.6%) and Infantis (13.5%) in 2004-2005. Compared with the 1998-1999 isolates, the 2004-2005 isolates showed significantly higher rates of resistance to all the antimicrobials except tetracyclines (P<0.01 to P<0.05) and resistance to 2 antimicrobials [19.4% (13/67) vs. 39.7% (50/126), P<0.01]. This study provides national estimates of Salmonella prevalence in healthy pigs of different growth stages in Japan.

In hydrolyzed cow's milk Helicobacter pylori becomes nonculturable and the growth of Salmonella typhi and Escherichia coli is inhibited.

The colony forming unit (CFU) of H. pylori is reduced rapidly in lipase hydrolyzed cow's milk and a similar reduction was found in a physiological saline solution when it was supplemented with soluble C4 to C10 fatty acids of milk fat composition. Slight CFU decreases were observed for E. coli and S. typhi in hydrolyzed milk buffered to pH 3, while the counts in milk and physiological saline solution at pH 3 stayed almost unchanged for 24 h. E. coli proliferated in glucose-peptone medium, better at pH 4.7 than at pH 3. On the other hand, supplementation of the medium with soluble fatty acids of milk composition completely inhibited growth for 32 h. Supplementation of the medium with fatty acids reduced the growth of S. typhi to approximately 1/20 at pH 4.7. Therefore, milk hydrolyzed by gastric lipase may damage H. pylori, producing a nonculturable state. With E. coli and S. typhi, hydrolyzed milk does not induce inactivation to a nonculturable state but inhibits their proliferation potently. The latter is considered to be a state prior to VBNC (viable but nonculturable). However, the antibiotic effect will disappear when the fatty acids are absorbed by the intestine.

Effect of oxygen-enriched aeration on regeneration of rice (Oryza sativa L.) cell culture.

The effect of the oxygen concentration in the aeration gas on regeneration from rice cells in bioreactor cultures was investigated. The efficiency of regeneration in cultures aerated with over 40% oxygen was higher than that in a flask culture. In the case of a culture in which the dissolved oxygen(DO) was saturated by aeration with air, the efficiency of regeneration was less than the half that of cultures aerated with 40% oxygen. In cultures with the DO levels controlled at 8,10 and 12 mg/ℓ, the efficiency of regeneration was highest at 12 mg/ℓ. In the oxygenenriched cultures, although cell aggregation was observed and the color of plantlets was relatively pale, more than 90% of them grew into healthy plants.

Effect of culture methods on the regeneration of albino rice (Oryza sativa L.) plantlets.

In our study, we investigated the effects of regeneration conditions on both green and albino rice plants (Oryza sativa L.). The regeneration frequency of an albino cell line was compared to a normal cell line obtained from mature seed under two kinds of culture conditions; namely, the static culture on semi-solid regeneration medium and the suspension culture in liquid regeneration medium. The albino cell line, from which only albino plantlets were regenerated, was induced from the albino leaf segments. There were no significant differences in the regeneration frequencies between normal and albino calli on the semisolid regeneration medium. On the other hand, the frequency of regeneration of albino calli was significantly lower than that of the control specifically in the liquid regeneration medium.

Simple dehydration treatment promotes plantlet regeneration of rice (Oryza sativa L.) callus.

To increase plantlet regeneration frequency, rice callus was dehydrated in a Petri dish with a single layer of filter paper prior to transfer to the regeneration medium. With a 24 h dehydration treatment, the regeneration frequency was increased to 47 %, while the regeneration frequency of the untreated control was less than 5 %. This relatively simple method provides an alternative method for improving the regeneration frequency of rice callus.

[Prevention of renal toxicity of cisplatin by administration of bismuth subnitrate].

The effect of pretreatment with bismuth subnitrate (BSN) for prevention of the renal toxicity of cisplatin (CDDP) was examined in 44 patients with lung cancer (43 non-small cell and one small cell lung cancer). In non-small cell lung cancer cases, the effect of the antitumor activity of chemotherapeutic drugs was observed in 62% of patients pretreated with BSN, and 42% in the group without pretreatment with BSN. No antitumoral activity of chemotherapeutic drugs was suppressed by treatment with BSN. In the group without pretreatment of BSN, serum creatinine and BUN were in proportion to the number of administrations of chemotherapeutic drugs. On the other hand, no renal toxicity was shown in the group with pretreatment by BSN. No protective effect against myelosuppression with pretreatment by BSN was demonstrated, perhaps because of the influence of anti-cancer drugs apart from CDDP.

[An autopsy case of lung cancer in a young adult dwarf].

A 31-year-old man with peripheral squamous cell carcinoma is reported. By nature he was very small. On admission he was 140 cm tall, weighed 28 kg, and was complaining of chest pain of five years duration. A giant tumor in the right lung was found to be moderately differentiated squamous cell carcinoma. He also had congenital anomalies, such as crossed ectopic kidney with fusion, café-au-lait spots, inguinal hernia, simian line, etc. He had never been exposed to cancer-causing agents. In conclusion, genetic factors related to intrauterine growth retardation might have been linked to his oncodevelopmental mechanisms.