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Telisotuzumab vedotin (formerly ABBV‐399) is an antibody‐drug conjugate targeting c‐Met–overexpressing tumor cells, irrespective of MET gene amplification status. Safety, pharmacokinetics, and preliminary efficacy of telisotuzumab vedotin were evaluated outside of Japan. This phase 1 open‐label study evaluated the safety, tolerability, pharmacokinetics, and preliminary antitumor activity of telisotuzumab vedotin in Japanese patients with advanced solid tumors. Telisotuzumab vedotin was administered intravenously at either 2.4 mg/kg (n = 3) or 2.7 mg/kg (n = 6) every 3 weeks, following a 3 + 3 design. Maximum tolerated dose was not reached on the basis of the study design; no dose‐limiting toxicity events were observed. The most common treatment‐emergent adverse events related to telisotuzumab vedotin were peripheral sensory neuropathy (44%), and nausea, decreased appetite, and decreased white blood cell count (33% each). Most frequent grade ≥3 treatment‐emergent adverse events, irrespective of relationship to telisotuzumab vedotin, were decreased neutrophil count and hypoalbuminemia, reported in two patients (22%) each. Systemic exposure of telisotuzumab vedotin at both dose levels was approximately dose proportional. Pharmacokinetic profile in Japanese patients was similar to that previously reported in non‐Japanese patients. Two (22%) patients achieved a partial response, six (67%) had stable disease, one (11%) had progressive disease. Overall disease control rate was 89% (eight of nine patients; 95% confidence interval: 51.8%–99.7%]). Median progression‐free survival was 7.1 months (95% confidence interval: 1.2–10.4). In conclusion, telisotuzumab vedotin demonstrated a manageable safety profile, with antitumor activity in Japanese patients with advanced solid tumors; the recommended phase 2 dose was confirmed as 2.7 mg/kg every 3 weeks. ClinicalTrials.gov registration number: NCT03311477. [ABSTRACT FROM AUTHOR]

We investigated the birds in the diet of the bird‐like noctule (Nyctalus aviator) through DNA amplification from feather remains found in faecal pellets. Our goal was to confirm whether N. aviator preys on nocturnally migratory species, as does its European relative N. lasiopterus, and to gain insight into this hunting strategy (e.g. on the wing vs. from cavities). The diversity and the characteristics of the birds found in the faecal remains indicate that in Japan N. aviator employs a similar hunting strategy on songbirds as N. lasiopterus in Iberia. Both noctules are primarily generalist insectivores that prey seasonally on songbirds of 5‐25 g body mass during their migration and probably hunt them at high altitude. Accordingly, predation on birds seems to be a strategy that appears in distant points across the Palaearctic and is not the result of local specialization. We hypothesize that the bird hunting behaviour appeared during evolution as a trophic jump from a pre‐existing hunting behaviour on the many insects that carry out seasonal nocturnal migrations in temperate zones at high altitude. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: The dispersal of alien species is tightly coupled to human activities such as trade and transport. Trade is known to spread troublesome weeds from countries exporting, to those importing, grain. Glyphosate resistant (GR) Amaranthus palmeri is one of the most problematic weeds in the US, which is the largest grain exporter to Japan. We demonstrate that GR A. palmeri has become established in a Japanese port in less than 10 years from the first report of GR A. palmeri in the US. The initial detection of alien species is critical to enable effective control measures to be undertaken, before problematic species are able to spread more widely. Summary: The US is the largest source to Japan of crops genetically modified to be glyphosate resistant (GR). The intensive use of glyphosate in the US has led to the evolution of GR Amaranthus palmeri, one of the most problematic weeds in the US. Here, we investigated the initial invasion and establishment of GR A. palmeri at grain‐importing ports in Japan.The primary glyphosate resistance mechanism is a copy‐number amplification of the 297‐kb region containing the herbicide target site gene 5‐enolpyruvylshikimate‐3‐phosphate synthase (EPSPS). We used quantitative PCR to measure the EPSPS genomic copy number and used PCR to confirm the presence of the other amplified region. We used microsatellite marker analysis to compare the genetic similarities between Japanese populations and US accessions.We detected GR A. palmeri at three ports: although present as a casual plant at two of the three ports, GR populations were established at one of the ports investigated. The port populations were found to be genetically similar to the US accessions and showed no geographical genetic structure.This study shows that GR A. palmeri has naturalized in Japan in less than 10 years from the first report of GR A. palmeri in the US. [ABSTRACT FROM AUTHOR]

Objective: Prevention of recurrent pressure ulcers (PU) is one of the most important challenges in wound care, furthermore, the risk factors for recurrent PUs are still not fully understood. This study aimed to explore the risk factors for recurrent PU development within two weeks, including biophysical skin properties, pro-inflammatory cytokine (tumour necrosis factor [TNF]-α) levels and bacterial species, in older patients. Method: This prospective study was conducted in a long-term care facility with patients whose PU had healed within two months. Biophysical skin properties were evaluated by stratum corneum hydration, pH, sebum content and transepidermal water loss. TNF-α level was measured using skin blotting. Skin bacteria were collected using tape stripping and determined by species-specific gene amplification. These parameters, along with Braden scale and interface pressure, were evaluated every two weeks for a total period of eight weeks. A penalised generalised estimating equation analysis was used to determine the risk factors for recurrent PUs. Results: In total, 20 patients were included in this study, with 57 observations. Of these, recurrent PU was seen in eight observations. Elevation of pH (p=0.049; odds ratio [OR] per 1 unit=3.91, 95% confidence interval [CI]:1.01–15.15), presence of Acinetobacter spp. (p=0.039; OR versus culture-negative=6.28, 95%CI:1.10–35.86) and higher interface pressure (p=0.008; OR per 1 mmHg=1.06, 95%CI:1.01–1.10) on the healed PU were significantly related to the development of recurrent PU. Conclusion: Higher pH, existence of Acinetobacter spp. and higher interface pressure on the site of the healed PU were associated with the development of recurrent PUs in older patients undergoing conservative treatments. [ABSTRACT FROM AUTHOR]

Since late 2013, after an absence of seven years, outbreaks of porcine epidemic diarrhea virus (PEDV) infection have reemerged and swept rapidly across Japan, resulting in significant economic losses. In this study, we report the emergence, mixed infection, and genetic characterization of 15 novel field PEDV variants with large genomic deletions. The sizes of deletion varied between 582 nt (194 aa) and 648 nt (216 aa) at positions 28–714 (10–238) on the S gene (protein). Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94.1% of them were found to consist of strains with an intact S gene. These variants were found in eight primary and nine recurrent outbreaks, and they might be associated with persistent PEDV infection in the farms. Full-length S and ORF3 genes of eight variants derived from 2 samples were characterized. This is the first report of mixed infections caused by various genotypes of PEDV and would be important for the studies of viral isolation, pathogenesis, and molecular epidemiology of the disease. [ABSTRACT FROM AUTHOR]

Background: Human epidermal growth factor (HER) 2 positivity and its association with clinicopathological factors remain unclear in Japanese gastric cancer (GC) patients. We performed a prospective, multicenter, observational cohort study to evaluate HER2 protein expression and gene amplification in Japanese metastatic and recurrent GC patients, and explored its correlations with clinicopathological features. Methods: HER2 protein expression and gene amplification were centrally assessed in formalin-fixed, paraffin-embedded GC tissue by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). Patient information was collected, and associations between clinicopathological factors and HER2 positivity (IHC score 3+ and/or FISH positive) and low HER2 expression (IHC score 0/FISH positive or IHC score 1+/FISH positive) were examined. Results: From September 2011 to June 2012, 1461 patients were registered across 157 sites, and the HER2 status of 1427 patients was evaluated. The rate of HER2 positivity was 21.2 %, whereas the rate of high HER2 expression (IHC score 2+/FISH positive or IHC score 3+) was 15.6 % and that of low HER2 expression was 7.0 %. Multiple logistic regression analysis identified intestinal type, absence of peritoneal metastasis, and hepatic metastasis as significant independent factors related to HER2 positivity. The intestinal type was confirmed to be the GC subtype predominantly associated with lower HER2 expression. Sampling conditions including number of biopsy samples, formalin concentration, and formalin-fixation time did not significantly affect HER2 positivity. Conclusions: HER2 expression in Japanese patients was comparable to that in other populations examined. Intestinal type was an independent factor related to HER2 positivity and low HER2 expression. [ABSTRACT FROM AUTHOR]

In Japan, ciguatera fish poisoning (CFP) has been increasingly reported not only in subtropical areas but also in temperate areas in recent years, causing a serious threat to human health. Ciguatera fish poisoning is caused by the consumption of fish that have accumulated toxins produced by an epiphytic/benthic dinoflagellate, genus Gambierdiscus . Previous studies revealed the existence of five Gambierdiscus species/phylotypes in Japan: Gambierdiscus australes , Gambierdiscus scabrosus , Gambierdiscus sp. type 2, Gambierdiscus sp. type 3, and Gambierdiscus ( Fukuyoa ) cf. yasumotoi . Among these, G . australes , G . scabrosus , and Gambierdiscus sp. type 3 strains exhibited toxicities in mice, whereas Gambierdiscus sp. type 2 strains did not show any toxicity. Therefore, it is important to monitor the cell abundance and dynamics of these species/phylotypes to identify and characterize CFP outbreaks in Japan. Because it is difficult to differentiate these species/phylotypes by observation under a light microscope, development of a rapid and reliable detection and enumeration method is needed. In this study, a quantitative PCR assay was developed using a TaqMan probe that targets unique SSU rDNA sequences of four Japanese Gambierdiscus species/phylotypes and incorporates normalization with DNA recovery efficiency. First, we constructed standard curves with high linearity ( R 2 = 1.00) and high amplification efficiency (≥1.98) using linearized plasmids that contained SSU rDNA of the target species/phylotypes. The detection limits for all primer and probe sets were approximately 10 gene copies. Further, the mean number of SSU rDNA copies per cell of each species/phylotype was determined from single cells in culture and from those in environmental samples using the qPCR assay. Next, the number of cells of each species/phylotype in the mixed samples, which were spiked with cultured cells of the four species/phylotypes, was calculated by division of the total number of rDNA copies of each species/phylotype in each sample by the number of rDNA copies per cell. The numbers of cells of each species/phylotype quantified by qPCR assay were similar to the number of cells of each species/phylotype that were spiked. Finally, the cell densities of the target species/phylotypes were quantified using the qPCR assay in 30 environmental samples collected from Japanese coastal areas. Total cell densities of the four Gambierdiscus species/phylotypes quantified by qPCR assay were similar to those of Gambierdiscus spp. quantified by direct counting under a light microscope. The qPCR assay developed in this study is expected to be a powerful new tool for determining detailed distribution patterns and for monitoring the cell abundance and dynamics of each Japanese Gambierdiscus species/phylotype in the coastal areas of Japan. [ABSTRACT FROM AUTHOR]

Objective: Resistance to trastuzumab is a problem that remains to be solved in HER2-positive breast cancer. We aimed to characterize profiles of genetic and epigenetic alterations in cancer-related pathways in HER2-positive breast cancers, using biopsy tissue samples obtained from patients enrolled in a prospective neoadjuvant clinical trial. Methods: HER2-positive breast cancer tissue samples were collected and processed with the PAXgene Tissue System. A total of 24 breast cancers were analyzed. Genetic alterations of 409 cancer-related genes were analyzed by a bench-top next-generation sequencer. DNA methylation statuses were analyzed by a bead array with 485,512 probes. Results: The WNT pathway was potentially activated by aberrant methylation of its negative regulators, such as DKK3 and SFRP1, in 9 breast cancers. The AKT/mTOR pathway was activated by mutations of PIK3CA in 5 breast cancers. The Notch pathway was potentially activated by mutations of NOTCH1 and NOTCH2 in 4 breast cancers. The p53 pathway was inactivated by mutations of TP53 in 13 breast cancers and potentially by aberrant methylation of its downstream genes in 10 breast cancers. Cell adhesion was affected by mutations of CDH1 in 1 breast cancer. Conclusion: Genes involved in cancer-related pathways were frequently affected not only by genetic but also by epigenetic alterations in HER2-positive breast cancer. © 2015 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Certain genetically defined cancers are dependent on a single overactive oncogene for their proliferation and survival, a phenomenon known as "oncogene addiction". A new generation of drugs that selectively target such "driver oncogenes" manifests a clinical efficacy greater than that of conventional chemotherapy in appropriate genetically defined patients. MET is a proto-oncogene that encodes a receptor tyrosine kinase, and aberrant activation of MET signaling occurs in a subset of advanced cancers as result of various genetic alterations including gene amplification, polysomy, and gene mutation. Our preclinical studies have shown that inhibition of MET signaling either with the small-molecule MET inhibitor crizotinib or by RNA interference targeted to MET mRNA resulted in marked antitumor effects in cancer cell lines with MET amplification both in vitro and in vivo. Furthermore, patients with non-small cell lung cancer or gastric cancer positive for MET amplification have shown a pronounced clinical response to crizotinib. Accumulating preclinical and clinical evidence thus suggests that MET amplification is an "oncogenic driver" and therefore a valid target for treatment. However, the prevalence of MET amplification has not been fully determined, possibly in part because of the difficulty in evaluating gene amplification. In this review, we provide a rationale for targeting this genetic alteration in cancer therapy. [ABSTRACT FROM AUTHOR]

Background The Jr(a-) phenotype is rare in European and North American populations but is not so rare in Japanese and other Asian populations. Recently, two groups have established the connection between the Jr(a-) phenotype and the ATP-binding cassette, member G2 ( ABCG2) gene and concluded that ABCG2-null alleles encode the Jr(a-) phenotype. In Japanese Red Cross Blood Centers, the Jr(a-) phenotype is found with a prevalence of 0.05% among blood donors, and we applied DNA-based genotyping to investigate the molecular basis of the Jr(a-) phenotype in Japan, in addition to serologic typing. Study Design and Methods Purified genomic DNA extracts of Japanese donor samples [500 Jr(a+) and 85 Jr(a-) phenotypes] were amplified using specific amplification primers for the c.376 C> T mutation, which is the most common mutation in the Asian JRnull allele. Polymerase chain reaction products were examined by high-resolution melt techniques and DNA sequence analyses. Results Seventy-nine of 85 Jr(a-) samples were homozygous for the single-nucleotide polymorphism c.376 C> T ( Gln126 Stop) change. In other samples, two novel null alleles were detected: c.2 T> C and c.421 C> A: c.1515 delC. Conclusion In this study, more than 90% of the Japanese Jr(a-) phenotypes had c.376 C> T ( Gln126 Stop) nucleotide change. In the other Jr(a-), a new mutation ( c.2T> C) in the start codon encoding Thr instead of Met, c.1515 delC encoding Ala505 Alafs Stop and heterozygous for c.337 C/ T and c.736 C/ T were detected. DNA-based genotyping is accurate and useful for Jr(a-) donor typing. [ABSTRACT FROM AUTHOR]

Loop-mediated isothermal amplification (LAMP) is an established technology that continues to attract the attention of researchers in many fields. Research and development efforts on LAMP technology in recent years have focused on two major areas; first, the study of its clinical application as an approved in vitro diagnostics tool in Japan and certain other countries; and second, research aimed at further simplifying the LAMP test process. This review provides an overview of the status of LAMP on these two topics by summarizing research work conducted, in the main, after our previous review article. [ABSTRACT FROM AUTHOR]

The relationship between Y-chromosome single-nucleotide polymorphisms (SNPs) registered in the Japanese SNP (JSNP) database (http://snp.ims.u-tokyo.ac.jp) and Y-binary haplogroup lineages was investigated to identify new Y-chromosomal binary haplogroup markers and further refine Y-chromosomal haplogroup classification in the Japanese population. We used SNPs for which it was possible to construct primers to make Y-specific PCR product sizes small enough to obtain amplification products even from degraded DNA, as this would allow their use not only in genetic but also in archeological and forensic studies. The genotype of 35 JSNP markers were determined, of which 14 were assigned to appropriate positions on the Y-chromosomal haplogroup tree, together with 5 additional new non-JSNP markers. These markers defined 14 new branches (C3/64562+13, C3/2613-27, D2a1b/006841*, D2a1b/119166-11A, D2a/022456*, D2a/119166-11A, D2a/119167rec/119167-40rec*, D2a/75888-GC, O3a3c/075888-9T/10T*, O3a3c/075888-9T/9T, O3a3/8425+6, O3a3/119166-13A*, O3a3/008002 and O3a4/037852) and 21 new internal markers on the 2008 Y-chromosome haplogroup tree. These results will provide useful information for Y-chromosomal polymorphic studies of East Asian populations, particularly those in and around Japan, in the fields of anthropology, genetics and forensics. [ABSTRACT FROM AUTHOR]

Abstract: Background: Hepatitis A virus (HAV) is still one of the most common causative agents of acute hepatitis in Japan. Although a relatively small number of annual acute hepatitis A cases (approximately 100–150, 0.78–1.17 per million) were recently reported, a larger number of cases (346, 2.71 per million) were reported in 2010. Objectives: To investigate the causes of the 2010 HAV resurgence in Japan by using molecular epidemiological and genetic analyses. Study design: HAV specimens were obtained from 61 cases from 22 different prefectures. These viral specimens were genotyped by PCR amplification and sequencing of the VP1/2A region of HAV genome. Results: Phylogenetic analysis revealed that 61 HAV strains could be divided into three genotypes: IA (44 cases), IB (1 case) and IIIA (16 cases). The IA genotype consisted of two genomic sub-lineages. The sequences of one of the two IA sub-lineages (corresponding to 31 cases) were very similar, 26 of these 31 isolates had 100% identity. The other IA sub-lineage corresponded to strains endemic to Japan. The sequences of Japanese IIIA strains were similar to those of strains that caused a large epidemic in the Republic of Korea from 2007 to 2009. Conclusions: The resurgence of HAV in 2010 can be attributed to importation of two newly emerged HAV genotypes. [Copyright &y& Elsevier]

Bovine leukemia virus (BLV) infection in cattle causes persistent lymphocytosis, and a few percent of infected animals develop lymphoid tumors, namely enzootic bovine leukosis (EBL). In this study, a 440-bp fragment of the env gene was amplified from 204 tumor samples collected from different regions of Japan and analyzed by restriction fragment length polymorphism (RFLP) to determine the association of BLV with EBL. Of the seven RFLP types defined, types I, II, and III were dominant and found in 12.7, 75.0, and 8.3% of tumor samples, respectively. Cattle harboring type III virus were significantly older than other animals at the time of diagnosis of EBL. Type III viruses were found in approximately 33% and 5.5% of Japanese Black and Holstein cattle, respectively, with EBL. These findings indicate that genetically distinct BLV was associated with EBL in Japan and that the genetic profile may influence the leukemogenicity of the virus. [ABSTRACT FROM AUTHOR]

To clarify transfusion incidence of hepatitis B virus (HBV) infected blood negative for mini pool-nucleic acid amplification testing (MP-NAT). Japanese Red Cross (JRC) blood centres screen donated blood to avoid contamination with HBV. However, a low copy number of HBV may be overlooked. In Hyogo-Prefecture, JRC blood centres screened 787 695 donations for HBV from April 2005 to March 2009. Of these, 685 844 were donations from the repeat donors. To detect the donors with HBV, serological tests, MP-NAT and/or individual donation (ID)-NAT were performed. To detect the recipients with transfusion-transmitted HBV infection (TTHBI), serological analysis and/or ID-NAT were performed. In this study, 265 of the 685 844 repeat donations were serologically and/or MP-NAT positive for HBV. Their repository samples from the previous donation were examined in a look-back study; 13 of the 265 repository samples proved ID-NAT positive. Twelve recipients were transfused with HBV-infected blood components derived from 10 of the 13 HBV-infected donors. Only 1 of the 12 recipients was identified as TTHBI case. Seven of the 12 recipients escaped from our follow-up study and 4 recipients were negative for HBV during the observation period. On the basis of the look-back study among the repeat donors in Hyogo-Prefecture, Japan, donations with HBV-infected blood negative for MP-NAT occurred with a frequency of 13 in 685 844 donations (∼1/53 000 donations). However, more than half of the recipients transfused with HBV-infected blood negative for MP-NAT could not be followed up. It is necessary to establish a more cautious follow-up system. [ABSTRACT FROM AUTHOR]

Phenylketonuria (PKU) is a heterogeneous metabolic disorder caused by a deficiency in hepatic phenylalanine hydroxylase (PAH). On the basis of phenotype/genotype correlations, determination of phenylketonuric genotype is important for classification of the clinical phenotype and treatment of PKU, including tetrahydrobiopterin therapy. We characterized the genotypes of 203 Japanese patients with PKU and hyperphenylalaninemia using the following systems: (1) denaturing high-performance liquid chromatography with a GC-clamped primer; (2) direct sequencing; and, (3) multiplex ligation-dependent probe amplification. Of 406 mutant alleles, 390 (96%) were genotyped; 65 mutations were identified, including 22 new mutations. R413P, R241C, IVS4-1g>a, R111X and R243Q were prevalent mutations. Mutations prevalent in the Japanese cohort are also common in Korean and Northern Chinese populations, suggesting same origin. The spectrum of prevalent mutations was not significantly different among six Japanese districts, indicating that Japan comprises a relatively homogeneous ethnic group. We classified the mutations by clinical phenotypes and in vivo PAH activity and estimated the mutations with potential tetrahydrobiopterin (BH4) responsiveness. The frequency of BH4 responsiveness based on the genotype was 29.1% in Japanese PKU patients. A catalog of PKU genotypes would be useful for predicting clinical phenotype, deciding on the subsequent treatment of PKU including BH4 therapy, and genetic counseling in East Asia. [ABSTRACT FROM AUTHOR]

The article discusses a research study on zoonotic onchocerciasis in Hiroshima, Japan and analyzes parraffin section for reliably identifying the agent. Collected were tissue samples of zoonotic onchocerciasis in Japan then were examined based on morphology for identifying female Onchocerca devittei japonica and the deoxyribonucleic acid (DNA) extracted for the polymerase chain reaction (PCR) and sequencing through the amplification of the mitochondrial CO1 gene. Results of the study proved the effectivity of mitochondrial CO1 gene regrion and DNA analysis for accurately identifying causative species of zoonotic onchocerciasis in the area where Onchocerca species reside.

Abstract: To reveal whether bats serve as an amplifying host for Yokose virus (YOKV), we conducted a serological survey and experimentally infected fruit bats with YOKV isolated from microbats in Japan. YOKV belongs to the Entebbe bat virus group of vector unknown group within the genus Flavivirus and family Flaviviridae. To detect antibodies against YOKV, we developed an enzyme-linked immunosorbent assay (ELISA) using biotinylated anti-bat IgG rabbit sera. Serological surveillance was conducted with samples collected in the Philippines and the sera supplied from Malaysia. One of the 36 samples from the Philippines (2.7%) and 5 of the 26 samples from Malaysia (19%) had detectable ELISA antibodies. In the experimental infections, no clinical signs of disease were observed. Moreover, no significant viral genome amplification was detected. These findings revealed that YOKV replicates poorly in the fruit bat, suggesting that fruit bats do not seem to serve as an amplifying host for YOKV. [Copyright &y& Elsevier]

Abstract: Spatial distribution, diversity, and composition of bacterial communities within the shallow sub-seafloor at the deep-sea hydrothermal field of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific Ocean, were investigated. Fluids were sampled from four boreholes in this area. Each borehole was located near or away from active vents, the distance ranging 2–40m from active vents. In addition, fluids discharging from a natural vent and ambient seawater were sampled in this area. We extracted DNA from each sample, amplified bacterial 16S rRNA genes by PCR, cloned the PCR products and sequenced. The total number of clones analyzed was 348. Most of the detected phylotypes were affiliated with the phylum Proteobacteria, of which the detection frequency in each clone library ranged from 84.6% to 100%. The bacterial community diversity and composition were different between hydrothermal fluids and seawater, between fluids from the boreholes and the vent, and even among fluids from each borehole. The relative abundances of the phylotypes related to Thiomicrospira, Methylobacterium and Sphingomonas were significantly different among fluids from each borehole. The phylotypes related to Thiomicrospira and Alcanivorax were detected in all of the boreholes and vent samples. Our findings provide insights into bacterial communities in the shallow sub-seafloor environments at active deep-sea hydrothermal vent fields. [Copyright &y& Elsevier]

Cholangiocarcinoma is an intractable cancer, with no effective therapy other than surgical resection. Elevated vascular endothelial growth factor (VEGF) and epidermal growth factor receptor (EGFR) expressions are associated with the progression of cholangiocarcinoma. We therefore examined whether inhibition of VEGFR and EGFR could be a potential therapeutic target for cholangiocarcinoma. Vandetanib (ZD6474, ZACTIMA), a VEGFR-2/EGFR inhibitor, was evaluated. Four human cholangiocarcinoma cell lines were molecularly characterised and investigated for their response to vandetanib. In vitro, two cell lines (OZ and HuCCT1), both of which harboured KRAS mutation, were refractory to vandetanib, one cell line (TGBC24TKB) was somewhat resistant, and another cell line (TKKK) was sensitive. The most sensitive cell line (TKKK) had EGFR amplification. Vandetanib significantly inhibited the growth of TKKK xenografts at doses > or = 12.5 mg kg(-1) day(-1) (P<0.05), but higher doses (50 mg kg(-1) day(-1), P<0.05) of vandetanib were required to inhibit the growth of OZ xenografts. Vandetanib (25 mg kg(-1) day(-1)) also significantly (P=0.006) prolonged the time to metastasis in an intravenous model of TKKK metastasis. Inhibiting both VEGFR and EGFR signalling appears a promising therapeutic approach for cholangiocarcinoma. The absence of KRAS mutation and the presence of EGFR amplification may be potential predictive molecular marker of sensitivity to EGFR-targeted therapy in cholangiocarcinoma. [ABSTRACT FROM AUTHOR]

Sequencing amplification fragments produced using simple-sequence repeat (SSR) primer pairs pchgms2 and UDP96008 in 'Dayezhugan' japanese apricot showed that SSRs obtained included a microsatellite locus originally identified in peach. The microsatellite sequence homogeneity between UDP96008 in japanese apricot in this study and UDP96008 in the peach in GenBank was 98%. Twenty-four japanese apricot genotypes originating in diverse geographic areas had been identified with 14 SSR primer pairs developed in different species of Prunus. In total, 129 alleles were obtained and per primer pairs detected 2.5 alleles on the average. The results from cluster analysis showed that the genetic distance between 'Nanhong' and 'Zhonghong' was the closest, and cultivars from China and from Japan could not be separated completely. [ABSTRACT FROM AUTHOR]

Reports on the development of a novel bioluminescence assay of ATP by researchers from Japan. Use of ATP amplification technique on the development of the novel medical screening; Sensitivity of the bioluminescence assay on the detection of a single cell bacteria; Advantages of using the novel method over conventional bioluminescence assay in detecting bacterial contamination.

Although adjuvant tegafur/uracil (UFT) is recommended for patients with completely resected stage I non-small-cell lung cancer (NSCLC) in Japan, only one-third of cases has received adjuvant chemotherapy (ADJ) according to real-world data. Therefore, robust predictive biomarkers for selecting ADJ or observation (OBS) without ADJ are needed. Patients who underwent complete resection of stage I lung adenocarcinoma with or without adjuvant UFT were enrolled. The status of ACTN4 gene amplification was analyzed by FISH. Statistical analyses to determine whether the status of ACTN4 gene amplification affected recurrence-free survival (RFS) were carried out. Formalin-fixed, paraffin-embedded samples from 1136 lung adenocarcinomas were submitted for analysis of ACTN4 gene amplification. Ninety-nine (8.9%) of 1114 cases were positive for ACTN4 gene amplification. In the subgroup analysis of patients aged 65 years or older, the ADJ group had better RFS than the OBS group in the ACTN4-positive cohort (hazard ratio [HR], 0.084, 95% confidence interval [CI], 0.009-0.806; P = .032). The difference in RFS between the ADJ group and the OBS group was not significant in ACTN4-negative cases (all ages: HR, 1.214; 95% CI, 0.848-1.738; P = .289). Analyses of ACTN4 gene amplification contributed to the decision regarding postoperative ADJ for stage I lung adenocarcinomas, preventing recurrence, improving the quality of medical care, preventing the unnecessary side-effects of ADJ, and saving medical costs., (© 2022 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.)

[Display omitted] • The first development of a LAMP assay for detecting alveolar echinococcosis in horses. • The results of the developed LAMP assay were completely consistent with those of PCR testing. • The developed LAMP assay has a potential alternative to conventional PCR testing to diagnose equine alveolar echinococcosis. Alveolar echinococcosis, which is caused by a larval-stage infection of Echinococcus multilocularis , is a zoonosis with public health importance. Recently, alveolar echinococcosis in slaughtered horses has been reported in Japan and Poland. In terms of public health, a highly sensitive and specific diagnostic method is essential for early detection during meat inspection. In this study, the loop-mediated isothermal amplification (LAMP) assay was developed and validated to target the mitochondrial cytochrome b (cob) gene of E. multilocularis. Forty-one hepatic solid nodules obtained from each horse were evaluated based on histopathological examination and cob -targeted PCR and then submitted to the LAMP assay. The optimal condition of the developed LAMP assay was 64℃ for 30 min. The results of the developed LAMP assay were completely consistent with those of cob PCR. In addition, the detection limit for the number of copies of the cob gene was 135 copies/μL in the LAMP assay. These findings suggest that the ability of the LAMP assay developed in this study is equivalent to that of the conventional PCR testing. The LAMP assay developed in this study can be used as an alternative to PCR testing for the routine genetic diagnosis of alveolar echinococcosis in horses. [ABSTRACT FROM AUTHOR]

INTELLANCE-J was a phase 1/2 study of a potent antibody-drug conjugate targeting epidermal growth factor receptor (EGFR), depatuxizumab mafodotin (Depatux-M), as a second- or first-line therapy, alone or combined with chemotherapy or chemoradiotherapy in 53 Japanese patients with World Health Organization (WHO) grade III/IV glioma. In second-line arms, patients with EGFR-amplified recurrent WHO grade III/IV glioma received Depatux-M plus chemotherapy (temozolomide) or Depatux-M alone regardless of EGFR status. In first-line arms, patients with newly diagnosed WHO grade III/IV glioma received Depatux-M plus chemoradiotherapy. The study was halted following lack of survival benefit with first-line Depatux-M in the global trial INTELLANCE-1. The primary endpoint was 6-month progression-free survival (PFS) in patients with EGFR-amplified tumors receiving second-line Depatux-M plus chemotherapy. Common nonocular treatment-emergent adverse events (TEAEs) with both second-line and first-line Depatux-M included lymphopenia (42%, 33%, respectively), thrombocytopenia (39%, 47%), alanine aminotransferase increase (29%, 47%), and aspartate aminotransferase increase (24%, 60%); incidence of grade ≥3 TEAEs was 66% and 53%, respectively. Ocular side effects (OSEs) occurred in 93% of patients receiving second-line Depatux-M plus chemotherapy and all patients receiving second-line Depatux-M alone or first-line Depatux-M plus chemoradiotherapy. Most OSEs were manageable with dose modifications and concomitant medications. The 6-month PFS estimate was 25.6% (95% confidence interval [CI] 11.4-42.6), and median PFS was 2.1 months (95% CI 1.9-3.9) with second-line Depatux-M plus chemotherapy in the EGFR-amplified subgroup. This study showed acceptable safety profile of Depatux-M alone or plus chemotherapy/chemoradiotherapy in Japanese patients with WHO grade III/IV glioma. The study was registered at ClinicalTrials.gov (NCT02590263)., (© 2021 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.)

We report the methods and results of molecular genetic identification of the species and, in some cases, geographical origins of whale and dolphin products purchased from retail markets and restaurants in Japan and South Korea. As reported previously (Baker & Palumbi 1994), we used the polymerase chain reaction (PCR) and a portable laboratory to amplify, purify and later sequence a portion of the mitochondria1 DNA control region from 16 commercial products purchased in Japan. This 'spot check' revealed a surprising variety of species for sale, including minke, fin and humpback whales and one or two species of dolphins sold as 'kujira' or whale. In the Korean survey, DNA amplifications were conducted by two of us (C.S.B. and F.C.) working with independent equipment and reagents. The two sets of DNA amplifications were returned to our respective laboratories and sequenced independently for cross-validation. Among the total of 17 species-specific sequences we found a dolphin, a beaked whale, 13 Northern Hemisphere minke whales (representing at least seven distinct individuals) and two whales which are closely related to the recognized sei and Bryde's whales but could not be identified as either using available type sequences. We suggest that these two specimens represent a currently unrecognized species or subspecies of Bryde's whale, possibly the so-called 'small-form' reported from the tropical waters of the Indo-Pacific. We conclude that molecular systematic analyses of DNA sequences have tremendous utility for the identification of whale and dolphin products. However, there are certain constraints on the application of these techniques for monitoring whaling or trade in whale products. F i t , PCR and DNA sequencing can generate misleading artefacts. These can generally be recognized or eliminated through experimental controls. Second, phylogenetic reconstructions of DNA sequences can be misinterpreted if the database of type sequences is inadequate or the taxonomy of the group is incomplete. This constraint is, at present, a more serious obstacle to molecular monitoring of whaling our results highlight uncertainties about the taxonomic status of oceanic populations and morphological forms of two species (or species complexes) targeted by legal and illegal hunting, the minke and Bryde's whales. Despite these uncertainties, it is difficult to reconcile some of the species available in Japanese and Korean commercial markets with recent catch records made available to the International Whaling Commission. It is particularly disturbing that two specimens of an unrecognized species or subspecies of baleen whale were for sale in a restaurant in South Korea in October, 1994, 8 years after the acceptance of an international moratorium on commercial whaling. [ABSTRACT FROM AUTHOR]

Objective: Fibroblast growth factor receptor 2 (FGFR2) has been proposed as a novel druggable target in unresectable gastric cancer. FGFR2 alteration has been reported as associated with poor prognosis even in patients with gastric cancer who received systemic chemotherapy. This study aimed to evaluate the frequency of FGFR2 overexpression and gene amplification in clinical specimens from Japanese patients with recurrent or unresectable gastric cancer., Methods: This observational study enrolled patients who were histologically or cytologically confirmed with unresectable HER2-negative or unknown gastric or gastroesophageal junctional adenocarcinoma treated with at least one previous chemotherapy. FGFR2 overexpression and gene amplification in the specimens were evaluated by immunohistochemical staining and fluorescence in situ hybridization methods, respectively., Results: In a total of 173 eligible cases, FGFR2 immunohistochemistry score was evaluated as 0, 1, 2, 3 and 4 for 20, 80, 35, 28 and 10 cases, respectively. In 151 evaluable cases with FGFR2 immunohistochemistry scores of 1-4, FGFR2 copy number expressed as fluorescence in situ hybridization signals were detected as <4, ≥4 < 10 and ≥10 copies for 123, 16 and 12 cases, respectively. FGFR2 copy number showed an increasing tendency along with higher FGFR2 immunohistochemistry scores in the corresponding specimen. The response rate and time to treatment failure for first line chemotherapy did not have any obvious relationship to FGFR2 immunohistochemistry score and FGFR2 copy number., Conclusions: Although FGFR2 overexpression and gene amplification were shown in Japanese patients with unresectable gastric cancer, these alterations did not impact the effects of cytotoxic agents as first line chemotherapy., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Esophageal squamous cell carcinoma (ESCC) is a malignant disease. At present, the genomic profiles of ESCC are known to a considerable extent, and DNA methylation and gene expression profiles have been mainly used for the classification of ESCC subtypes, but integrative genomic, transcriptomic, and epigenomic analyses remain insufficient. Therefore, we performed integrative analyses using whole-exome sequencing, DNA methylation, and RNA sequencing (RNA-seq) analyses of Japanese patients with ESCC. In cancer-related genes, such as NOTCH family genes, RTK/PI3K pathway genes, and NFE2L2 pathway genes, variants and copy number amplification were detected frequently. Japanese ESCC cases were clustered into two mutational signatures: an APOBEC-associated signature and an age-related signature. In imprinted genes, DNA methylation was aberrant in gene promoter regions and correlated well with gene expression profiles. Nonsynonymous single-nucleotide variants and allelic expression imbalance were detected frequently in FAT family genes. Our integrative genome-wide analyses, including DNA methylation and allele-specific gene expression profiles, revealed altered gene regulation of imprinted genes and FAT family genes in ESCC., (© 2021 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.)

Abstract: In this study, we tried to detect protozoan blood parasites from the liver or blood of 156 Japanese black bears (Ursus thibetanus japonicus) in Iwate Prefecture of Japan by polymerase chain reaction. Two amplicons (approximately 540bp and 480bp) were detected by amplification for V4 hyper-variable regions of the 18S rRNA gene. Approximately 540-bp products were obtained in 119 samples (76.3%) and were considered to be DNA of Hepatozoon ursi. Approximately 480-bp products were obtained in 22 samples (14.1%) and were considered to be DNA of Babesia species. The nucleotide sequences (1635bp) of the 18S rRNA gene of Babesia sp. were very similar (99.3%) to those (AY190123, AY190124) of Babesia sp. detected previously from Ixodes ovatus. Phylogenetic analysis showed that Babesia sp. detected in this study closely related to Babesia sp. derived from raccoons in Japan and the U.S.A. This is the first report of Babesia species detected from Japanese black bears. [Copyright &y& Elsevier]

Abstract: We constructed a multiplex PCR and genotyping system selecting four pentanucleotide STR loci (Penta E, Penta D, Penta B and D10S2325) with multi-colored fluorescently labeled primer sets that are newly designed in order to genotype from mixed specimens, especially for degraded DNA samples, of which the amplicon sizes are smaller than about 200 bp. The allele frequencies at these four STR loci were calculated in a Japanese population. Sequence analysis was also performed for all alleles at these all STR loci observed in the Japanese population, and the allele distributions at those four loci did not deviated from HWE. The heterozygosities and the power of discriminations (PD) at all the four loci were more than 0.80 and 0.93, respectively. Furthermore, the present study provides a statistical standard to decide whether a one-repeat small peak from a main peak is the stutter peak or the peak originated from mixed individual sample. [Copyright &y& Elsevier]

Importance: Robust predictors for response to anti-programmed death 1 and its ligand (PD-1/PD-L1) immunotherapy in non-small cell lung cancer (NSCLC) are not fully characterized., Objective: To evaluate whether PD-L1 (CD274) copy number gains (CNGs), comprising amplification and polysomy, in pretreatment specimens assessed by fluorescence in situ hybridization are associated with response to nivolumab monotherapy in NSCLC., Design, Setting, and Participants: This multicenter cohort study enrolled 200 patients, of whom 194 had assessable tumors, with advanced or recurrent NSCLC who were treated with nivolumab after progression following prior treatment at 14 institutions in Japan between July 2016 and December 2018. Median (interquartile range) duration of follow-up was 12.6 (5.6-20.4) months. Data were analyzed from December 2019 to February 2020., Exposures: Sequential nivolumab was given on day 1 of a 14-day cycle. Response was assessed every 4 cycles using Response Evaluation Criteria in Solid Tumors version 1.1., Main Outcomes and Measures: Overall response rate (ORR) according to the PD-L1 copy number status. Additional end points were progression-free survival, overall survival, and PD-L1 tumor proportion score (TPS) assessed by immunohistochemistry based on PD-L1 copy number status., Results: A total of 6 of the 200 patients were excluded because of poor-quality tumor specimens for the biomarker study, resulting in 194 assessable patients. Of these, 155 (79.9%) were men, with a median (range) age of 69 (43-83) years. PD-L1 CNGs were identified in 32 patients (16.5%), including 5 (2.6%) with amplification and 27 (13.9%) with polysomy. The ORR among patients with and without PD-L1 CNGs was 28.1% (95% CI, 13.7%-46.7%) and 17.9% (95% CI, 12.3%-24.7%), respectively. Although patients with PD-L1 polysomy did not demonstrate improved ORR (18.5% [95% CI, 6.3%-38.1%]) compared with those without PD-L1 CNGs, 4 of 5 patients (80.0% [95% CI, 28.4%-99.5%]) with PD-L1 amplification showed response, among whom median duration of response was not reached. Patients with PD-L1 amplification showed excellent survival outcomes for progression-free and overall survival. Overall, 3 PD-L1-amplified tumors (60.0%) showed PD-L1 TPS of at least 80%, but 2 (40.0%) had PD-L1 TPS of 15% or less., Conclusions and Relevance: In this study, tumor PD-L1 amplification but not polysomy was associated with response to nivolumab monotherapy among patients with NSCLC. External validation with a larger sample size is warranted.

Abstract Hereditary coproporphyria (HCP) is an autosomal dominant disease characterized by a deficiency of coproporphyrinogen oxidase (CPO). Only 11 mutations of the gene have been reported to date as the mutations responsible for HCP. We report here a novel mutation of the gene responsible for the disease in a Japanese family. Analysis of the polymerase chain reaction (PCR) amplified DNA fragments of the gene by direct-sequencing and/or cloning-based sequencing methods revealed the gene abnormality responsible for the disease. The mutation found was a single base deletion of T at nt position 526, which results in frame shift and truncation of coded protein at amino acid position 204. Screening of pre-symptomatic cases seemed to be possible by PCR restriction analysis using restriction enzyme Xcm I. [ABSTRACT FROM AUTHOR]

The green microalga Botryococcus braunii produces hydrocarbon oils at 25-75% of its dry weight and is a promising source of biofuel feedstock. Few studies have examined this species' ecology in natural habitats, and few wild genetic resources have been collected due to difficulties caused by its low abundance in nature. This study aimed to develop a real-time PCR assay for specific detection and quantification of this alga in natural environments and to quantify spatiotemporal variations of wild B. braunii populations in a tropical pond. We designed PCR primers toward the hydrocarbon biosynthesis gene SSL-3 and examined amplification specificity and PCR efficiency with 70 wild strains newly isolated from various environments. The results demonstrated that this PCR assay specifically amplified B. braunii DNA, especially that of B-race strains, and can be widely used to detect wild B. braunii strains in temperate and tropical habitats. Field-testing in a tropical pond suggested a diurnal change in the abundance of B. braunii in surface water and found B. braunii not only in surface water, but also at 1-1.5 m deep and in bottom sediments. This method can contribute to efficient genetic resource exploitations and may also help elucidate the unknown ecology of B. braunii.

The present study aimed to characterize intrahepatic cholangiocarcinomas (iCCAs) with MDM2 amplification. A total of 213 cases of iCCA were examined using dual-color in situ hybridization for MDM2, immunohistochemistry for p53 and SMAD4, and gene sequencing for KRAS and IDH1/2. In situ hybridization on tissue microarrays identified MDM2 amplification in 13/213 (6%) cases. Using the recently proposed classification scheme of iCCAs (small-duct and large-duct types), all MDM2-amplified cases were of the large-duct type (13/110 cases, 12%). In whole section hybridization, MDM2 amplification appeared to be diffusely present in invasive areas. The loss of SMAD4 expression was more common in MDM2-amplified iCCAs than in those without MDM2 amplification. The relationship between MDM2 amplification and molecular alterations in p53 or KRAS was weak, with p53 overexpression and KRAS mutations only being found in 23% and 0% of cases, respectively. Overall survival was shorter in patients with MDM2-amplified iCCAs than in those with MDM2-nonamplified cancer (P=0.017); however, the lack of a prognostic impact of MDM2 amplification was confirmed in a subgroup analysis using only large-duct iCCAs. Additional studies on extrahepatic malignancies also identified MDM2 amplification in 8/68 (12%) hilar cholangiocarcinomas and 30/216 (14%) gallbladder cancers, but in 0/65 distal cholangiocarcinomas. In conclusion, MDM2 amplification in large-duct iCCAs is more common than presently considered, and it may represent a unique biliary carcinogenetic process in which KRAS and TP53 mutations are less frequent. MDM2 may become a promising drug target for not only large-duct iCCAs but also hilar and gallbladder cancers.

Studies allele frequencies of 15 loci in a population sample from Japan, using a short tandem polymerase chain reaction amplication kit from Applied BioSystems. DNA extraction from blood samples; Allelic frequencies.

Objective: Human epidermal growth factor receptor 2 (HER2) gene amplification is a major therapeutic target in breast cancer, and has been introduced as a predictive biomarker to identify patients who may benefit from therapy with anti-human epidermal growth factor receptor 2 agents. Human epidermal growth factor receptor 2 somatic mutations have been reported in patients without human epidermal growth factor receptor 2 gene amplification. Since these are activating mutations, these patients may also benefit from human epidermal growth factor receptor 2-targeted drugs., Methods: In this study, we searched for human epidermal growth factor receptor 2 mutations in a group of 286 Japanese breast cancer patients with human epidermal growth factor receptor 2-negative tumors. The activating mutations of human epidermal growth factor receptor 2 identified were analyzed by direct Sanger sequencing of two major areas: the extracellular domain at 309-310 and the kinase domain between 755 and 781., Results: Two tumors were found to have a human epidermal growth factor receptor 2 somatic mutation; one with I767M mutation and another with D769Y. No mutation was observed in the extracellular domain. One of these patients with human epidermal growth factor receptor 2 mutation recurred early with liver metastasis., Conclusions: Better knowledge of human epidermal growth factor receptor 2 mutation status will help us to choose personalized molecular targeted therapy for use in human epidermal growth factor receptor 2-negative Japanese breast cancer patients., (© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Aims: Malignant mesothelioma (MM) results from the accumulation of a number of acquired genetic events at the onset. In MM, the most frequent changes were losses in 9p21, 1p36, 14q32 and 22q12, and gains in 5p, 7p and 8q24 by comparative genomic hybridisation analysis. Although the diagnostic utility of 9p21 homozygous deletion by fluorescence in situ hybridisation (FISH) analysis in MM has been reported recently, alterations of other genes have not been examined to any great extent. This study analysed the frequency of various genomic gains and losses in MM using FISH analysis., Materials and Methods: The authors performed a FISH analysis using paraffin-embedded tissues from 42 cases of MM., Results: Chromosomal losses in MM were found at 9p21 (83%), 1p36 (43%), 14q32 (43%) and 22q12 (38%), whereas gains were found at 5p15 (48%), 7p12 (38%) and 8q24 (45%). There were no cases of adenomatoid tumour, benign mesothelial multicystic tumour, reactive mesothelial hyperplasia or pleuritis showing any gains or losses. At least one genomic abnormality was identified in all cases of MM. Among various histological subtypes, the chromosomal abnormality tended to be more common in cases showing sarcomatous elements (biphasic or pure sarcomatoid) than in cases showing an epithelioid histology., Conclusions: The authors found various genomic gains and losses in MM by FISH analysis. The frequency of each genomic gain or loss examined in MM by FISH analysis almost agreed with the comparative genomic hybridisation technique in previous studies. This study suggests that genomic evaluation by FISH analysis might be helpful in distinguishing MM from benign mesothelial proliferation.

Our previous study demonstrated that, among ovarian carcinomas, amplification of the MET gene and overexpression of MET specifically and commonly occur in clear-cell adenocarcinoma histology. This study was conducted to address how these alterations contribute to development and progression of this highly chemoresistant form of ovarian cancer. We histologically reviewed 21 previously described MET amplification-positive clear-cell adenocarcinoma cases, and selected 11 tumors with synchronous endometriosis and 2 tumors with adjacent clear-cell adenofibroma (CCAF) components. Using double in situ hybridization and immunohistochemistry, copy number alterations of the MET gene and levels of MET protein expression were analyzed in these putative precursor lesions and the corresponding invasive carcinoma components in this selected cohort. All of the non-atypical precursor lesions analyzed (ie, non-atypical endometrioses and the benign CCAFs) were negative for MET gain. However, low-level (≥3 MET copies in ≥10% and ≥4 MET copies in 10-40% of tumor cells) gain of MET was detected in 4 (40%) of the 10 atypical endometrioses and 1 of the 2 borderline CCAFs. Moreover, high-level (≥4 MET copies in ≥40% of tumor cells) gain of MET were detected in five (50%) of the atypical endometrioses. In 4 (31%) of the 13 cases enrolled, intratumoral heterogeneity for MET gain was documented in invasive carcinoma components, wherein all the relatively differentiated carcinoma components showed low-level gain of MET and all the corresponding poorly differentiated carcinomas showed high-level gain. The overall incidence of MET overexpression gradually increased from the precursors of non-atypical form (0%), through those of atypical form (67%) and the relatively differentiated carcinoma components (92%), to the poorly differentiated carcinoma components (100%). These results suggest that accumulative MET gene copy number alterations causing MET overexpression are associated with higher tumor grade and might drive the development and progression of the MET amplification-positive ovarian clear-cell adenocarcinoma.

Background: In Japan, a major type of home-related hypersensitivity pneumonitis (HP) is summer-type HP, which is caused by Trichosporon asahii (T. asahii) or Trichosporon mucoides. Some patients with home-related HP test negative for antibodies against Trichosporon; yet, a causative mold antigen cannot be identified., Methods: We analyzed 19 patients with home-related HP, 8 healthy volunteers, and 35 patients with other diseases. We extracted DNA from cell pellets of bronchoalveolar lavage fluid (BALF), amplified the DNA by PCR using Trichosporon-specific primers or other fungus-specific primers, and cloned as well as sequenced the PCR amplicon. Other primers used were specific for Acremonium chrysogenum, Aspergillus fumigatus, Aspergillus niger, Fusarium napiforme, Humicola fuscoatra, Penicillium corylophilum, and Pezizia domiciliana., Results: We detected Trichosporon DNA (n = 17) and F. napiforme DNA (n = 2) by PCR in 19 patients with home-related HP; however, these species were not identified in healthy volunteers. After sequencing of the PCR amplicon for Trichosporon species, we identified T. asahii (n = 11), Trichosporon japonicum (n = 1), and Cryptococcus uzbekistanesis (n = 4)., Conclusion: We could detect fungal DNA in BALF cell pellets from patients with home-related HP. These data suggest that this method might be useful to detect antigens responsible for home-related HP., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Background/purpose: It has previously been shown that neuroblastomas with favorable prognosis often express a high level of nerve growth factor receptor trkA. We performed an expression analysis of trkA in 106 NB samples based on the quantitative real-time polymerase chain reaction (PCR) and reevaluated the prognostic power of trkA., Materials and Methods: A total of 106 primary tumors from NB patients treated from 1988 to 2009 were analyzed. MYCN was amplified in 13 cases. TaqMan probe method was used for quantitative PCR. Primers and probes were designed to detect trkA I and trkA II, but not the oncogenic splice variant trkA III., Results: Expression analysis by real-time PCR revealed a wide range of expression levels of trkA within neuroblastoma tissues. Extremely low levels of trkA that were undetectable by semiquantitative PCR were able to be quantified by this method. trkA was predominantly expressed in tumors with favorable outcome. Further analysis of trkA expression was performed in a cohort excluding mass-screened neuroblastomas. Strikingly, multivariate analysis containing age, MYCN status, and trkA expression identified trkA as the only variable that independently predicts the prognosis of the 44 patients who presented clinically., Conclusion: High-resolution expression analysis targeting trkA and trkA II may add more statistical power on trkA as a biological marker., (Copyright © 2010 Elsevier Inc. All rights reserved.)

Purpose: The hedgehog (Hh) signaling pathway is activated in some adult cancers. On the other hand, the Hh signaling pathway plays an important role in the development of the neural crest in embryos. The aim of this study is to show the activation of Hh signaling pathway in neuroblastoma (NB), a pediatric malignancy arising from neural crest cells, and to reveal the meaning of the Hh signaling pathway in NB development., Methods: This study analyzed the expression of Sonic hedgehog (Shh), GLI1, and Patched 1 (Ptch1), transactivators of Hh signaling pathway, by immunohistochemistry in 82 NB and 10 ganglioneuroblastoma cases. All 92 cases were evaluated for the status of MYCN amplification., Results: Of the 92 cases, 67 (73%) were positive for Shh, 62 cases (67%) were positive for GLI1, and 73 cases (79%) were positive for Ptch1. Only 2 (10%) of the 20 cases with MYCN amplification were positive for Shh and GLI1, and 4 cases (20%) were positive for Ptch1 (MYCN amplification vs no MYCN amplification, P ≦ .01). The percentage of GLI1-positive cells in the cases with INSS stage 1 without MYCN amplification was significantly higher than that with INSS stage 4. Of 72 cases without MYCN amplification, 60 were GLI1-positive. Twelve cases were GLI1-negative, and the prognosis of the GLI1-positive cases was significantly better than that of the GLI1-negative cases (P = .015)., Conclusions: Most of NBs without MYCN amplification were positive for Shh, GLI1, and Ptch1. In the cases without MYCN amplification, the high expression of GLI1 was significantly associated with early clinical stage and a good prognosis of the patients. In contrast to adult cancers, the activation of the Hh signaling pathway in NB may be associated with the differentiation of the NB., (Copyright © 2010 Elsevier Inc. All rights reserved.)

Molecular epidemiology analyses of the 36 clinical isolates of Pasteurella multocida from various avian hosts in Japan between 1976 to 2007 including 5 reference strains from the U.S.A., Taiwan and Indonesia were performed by employing the single-enzyme amplified fragment length polymorphism (SE-AFLP) comparison with the classical ApaI-based pulsed-field gel electrophoresis (PFGE). As the results, SE-AFLP gave 21 profiles while PFGE gave 20 profiles. The Simpson's index of diversity analysis indicated that SE-AFLP gave a high discrimination power than PFGE. This concluded that SE-AFLP is a higher discrimination power than PFGE to differentiate avian P. multocida isolates in Japan. In addition, the genetical profiles suggested that there is the evolution of somatic serotype 3 strain in the indigenous host of Japan.

Capnocytophagacanimorsus and Capnocytophagacynodegmi, fastidious gram-negative rods, are commensal microbes thriving in the oral cavities of dogs and cats. C. canimorsus can sometimes cause fatal systemic infections in humans. In the present study, we established a specific PCR which could identify and distinguish C. canimorsus from C. cynodegmi. The prevalence of Capnocytophaga spp. in dogs and cats was determined using this method. C. canimorsus was detected in 74% of dogs and 57% of cats. C. cynodegmi was detected in 86% of dogs and 84% of cats. The prevalence of Capnocytophaga spp. obtained in this study is somewhat higher than those reported previously where bacterial isolation method was used for identification. This is probably due to the fact that the PCR detection is more sensitive compared to bacterial isolation. Our findings suggest the importance of informing people who belong to high-risk groups as well as health care workers on C. canimorsus infection and its potential risk to people particularly to those who are immunocompromised., (Copyright (c) 2010 Elsevier B.V. All rights reserved.)

For three years investigations from 1996 to 1998, we tried to isolate Escherichia coli O157:H7 from fecal samples collected from dogs and cats. In results, E. coli O157:H7 was isolated from 1 out of 614 samples (0.16%). This isolate produced Stx1 and Stx2 and was isolated from a dog kept by a human patient infected with E. coli O157:H7. Excluding in this case, dogs and cats as companion animals, therefore, may not give harbor to E. coli O157:H7.

The term gastric adenoma usually refers to a flat adenoma of the intestinal type. Adenomas of the gastric type, so-called pyloric gland adenomas (PGA), which was first characterized by German and Japanese pathologists in 1990, have been regarded as exceptional until recently. In 2003, we first reported systematic clinical pathological analyses of PGA, demonstrating its unstable and precancerous nature. American gastrointestinal pathologists have finally recognized this disease entity in 2009. In this article we introduce the Japanese criteria of the gastric adenoma and review and discuss the clinical pathological and molecular aspects of PGAs.

A novel Acinetobacter strain, Ud-4, possessing a strong capacity to degrade edible, lubricating, and heavy oil was isolated from seawater in a fishing port located in Toyama, Japan. It was identified by morphological and physiological analyses and 16S rDNA sequencing. This strain could utilize five types of edible oils (canola oil, olive oil, sesame oil, soybean oil, and lard), lubricating oil, and C-heavy oil as the sole carbon source for growth in M9 medium. The strain grew well and heavily degraded edible oils in Luria-Bertani medium during a 7-day culture at 25 degrees C; it also degraded all kinds of oils in artificial seawater medium for marine bacteria. Furthermore, this strain was capable of degrading almost all C10-C25 n-alkanes in C-heavy oil during a 4-week culture. Oligonucleotide primers specific to two catabolic genes involved in the degradation of n-alkanes (Acinetobacter sp. alkM) and triglyceride (Acinetobacter sp. lipA) allowed amplification of these genes in strain Ud-4. To our knowledge, this is the first report on the isolation of a bacterium that can efficiently degrade both edible and mineral oils.

We have developed a multiplex, single nucleotide polymorphism (SNP) typing system for forensic identification, based on the Invader assay. Using this system, fluorescence data for 21 SNP loci were collected and analyzed. We used endpoint genotyping, commonly used with the Invader assay, and also developed more reliable typing criteria because endpoint typing was occasionally unable to clearly identify the genotype of some loci. Analysis of the fluorescence data identified criteria that had high reproducibility for each genotype. One such criterion is the climbing angle of the curve resulting from two-dimensional plots of the two kinds of fluorescence used for the Invader assay. The climbing angle was observed at the time during the reaction when either or both of the fluorescence intensities increased most significantly. The angles were remarkably associated with homozygous genotypes. On the other hand, all heterozygote endpoint fluorescence ratios were highly reproducible and had very little aberration. These values enabled SNP typing to be more clearly defined compared with typing using only the endpoint fluorescence ratio, which is commonly used with the Invader assay. The values suggested in this study are easily calculated from raw fluorescence data and will be useful for multiplex SNP typing based on the Invader assay.

Phylogenetic analyses were carried out on a total of 118 Listeria monocytogenes isolates from foods or food processing environments, and 7 isolates from listeriosis patients in Japan to evaluate the genetic variation in the pathogen in this country. Isolates of serotypes 1/2a, 1/2b and 4b were mainly examined to assess the risk of exposure of humans to L. monocytogenes from foods in Japan. The nucleotide sequences of the part of the iap gene that contains the region encoding the threonine-asparagine repeat units were determined in order to construct phylogenetic trees of the isolates investigated. A phylogram showed high genetic diversity among lineage 2 isolates, while the lineage 1 isolates showed clonal characteristics. The results of the genetic analyses suggested the presence of rare putative lineage 3 isolates and epidemic clone I (ECI) isolates in foods in Japan. The results showed that ECI was also isolated from listeriosis patients. The genetic variation in L. monocytogenes in Japan reported here suggests the necessity of monitoring the pathogen in foods and environments in addition to surveillance of listeriosis patients.

Purpose: To investigate the association between HLA class I antigens and Stevens-Johnson syndrome (SJS)/toxic epidermal necrolysis (TEN) with ocular complications in Japanese., Design: Case-control study., Methods: We examined the histocompatibility antigen genes HLA-A, -B, and -C of 40 Japanese SJS/TEN patients with ocular complications and 113 healthy Japanese volunteers by polymerase chain reaction amplification and subsequent hybridization with sequence-specific oligonucleotide probes (PCR-SSO)., Results: We clarified that HLA-A*0206 is strongly associated with SJS/TEN with ocular complications in the Japanese., Conclusions: Because this finding is completely different from data reported elsewhere on Taiwanese Han Chinese patients and Caucasian patients, it suggests strong ethnic differences in the HLA-SJS association and points to the need for studies in other ethnic populations in order to obtain a global picture.