Occurrence, distribution, and trends of volatile organic compounds in urban rivers and their estuaries in Osaka, Japan, 1993-2006.

Fifty-five volatile organic compounds (VOCs) in 738 water samples collected from 33 monitoring sites in the rivers of highly industrialized urban area in Osaka, Japan, 1993-2006 were analyzed. VOCs could be classified into three groups by the detection frequency and levels of mean concentrations detected. Firstly, for 30 compounds, almost all data were non detection or were around the detection limits.

Winners of CASMI2013: Automated Tools and Challenge Data.

CASMI (Critical Assessment of Small Molecule Identification) is a contest in which participants identify the molecular formula and chemical structure of challenging molecules using blind mass spectra as the challenge data. Seven research teams participated in CASMI2013. The winner of CASMI2013 was the team of Andrew Newsome and Dejan Nikolic, the University of Illinois at Chicago, IL, USA.

Sensitive Detection of Aromatic Hydrophobic Compounds in Water and Perfluorooctane Sulfonate in Human Serum by Surface-Assisted Laser Desorption/Ionization Mass Spectrometry (SALDI-MS) with Amine Functionalized Graphene-Coated Cobalt Nanoparticles.

In this article, we describe the application of surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) with the use of amine functionalized graphene-coated cobalt nanoparticles (CoC-NH2 nanoparticles) to analyse aromatic hydrophobic compounds that are known environmental contaminants, including polycyclic aromatic hydrocarbons (PAHs) and pentachlorophenol (PCP). Our results demonstrated that SALDI-MS can detect PCP, anthracene, and pyrene in water. In particular, the CoC-NH2 nanoparticles proved to be an efficient means of capturing PCP in water because of the high adsorption capacity of the nanoparticles for PCP, which resulted in a detectability of 100 ppt.

Suppression of phosphorus release from sediments using water clarifier sludge as capping material.

Water clarifier sludge was assessed as a capping material for preventing release of phosphorus from eutrophic pond sediments. Sediment incubation experiments were carried out over two months using five capping materials (sludge, sludge sintered respectively at 200, 400 and 600 degrees C, and sea sand) to evaluate the effect of sintering temperature. We also examined reduction in the nitrogen eluted from the sludge.

Effects of popping on nutrient contents of amaranth seed.

Amaranth seeds can be popped by heating. The traditional method of popping in a skillet is simple, but it is difficult to control the heating time and temperature. To overcome these disadvantages, we developed a fluidized bed continuous processing system based on hot air heating for producing popped amaranth seeds in bulk.

Biofilm formation and resistance to benzalkonium chloride in Listeria monocytogenes isolated from a fish processing plant.

Listeria monocytogenes is a foodborne pathogen that causes the potentially life-threatening illness listeriosis. Previously, a few clones of L. monocytogenes persisting in a cold-smoked fish processing plant were isolated from the plant's products continuously.

[Determination of uranium in spinach].

After the severe accident at the Fukushima-1 Nuclear Power Plant in March 2011, radioactive contamination of food has become a matter of serious concern in Japan. There is considerable information about radioactive iodine and cesium, but little is known about uranium contamination. We determined uranium content in spinach by the Japanese official method (Manual on Radiation Measurement of Food in Emergency Situations).

Molecular characterization of kudoid parasites (Myxozoa: Multivalvulida) from somatic muscles of Pacific bluefin (Thunnus orientalis) and yellowfin (T. albacores) tuna.

The public health importance of Kudoa infection in fish remains unclear. Recently in Japan a Kudoa species, K. septempunctata, was newly implicated as a causative agent of unidentified food poisoning related to the consumption of raw olive flounder.

Multi-locus variable number tandem repeat analysis for Clostridium botulinum type B isolates in Japan: comparison with other isolates and genotyping methods.

Clostridium botulinum produces botulinum neurotoxin (BoNT) and causes botulism in humans and animals. Recently, 15-loci multi-locus variable number tandem repeat analysis (MLVA) for C. botulinum was developed for high-resolution and inter-lab comparative genotyping.

Bayesian estimation for the effectiveness of pesticides and repellents.

In the quantitative estimation of the effectiveness of pesticides and repellents, Abbott's correction and similar methods have been used for nearly a century. However, the formulas for such corrections have some disadvantages in performing range estimations and being used in batched experiments. These disadvantages also exist in the estimation of EC50, the chemical concentration that produces 50% mortality.

[Discrimination of mushrooms causing food-poisoning incidents by using DNA sequence analysis].

In this study, the identification of mushrooms by using DNA analysis was investigated. Our analysis of internal transcribed spacer (ITS) regions revealed that a DNA-based method could be applicable for samples that are difficult to distinguish in terms of the morphological characteristics. PCR amplification using templates extracted from cooked samples gave sufficient fragments to analyze the sequence.

Detection of five rash-associated viruses using multiplex real-time PCR during 2006-2011.

Many viruses have been reported to be associated with rash development. Multiplex real-time PCR was used to investigate the presence of 5 viruses associated with rashes: measles virus (MV), rubella virus (RV), human parvovirus B19 (PVB19), human herpes virus 6 (HHV-6), and HHV-7. A total of 187 clinical specimens from 169 patients with erythema were collected between January 2006 and December 2011.

Molecular characterization of Giardia psittaci by multilocus sequence analysis.

Multilocus sequence analyses targeting small subunit ribosomal DNA (SSU rDNA), elongation factor 1 alpha (ef1α), glutamate dehydrogenase (gdh), and beta giardin (β-giardin) were performed on Giardia psittaci isolates from three Budgerigars (Melopsittacus undulates) and four Barred parakeets (Bolborhynchus lineola) kept in individual households or imported from overseas. Nucleotide differences and phylogenetic analyses at four loci indicate the distinction of G. psittaci from the other known Giardia species: Giardia muris, Giardia microti, Giardia ardeae, and Giardia duodenalis assemblages.

Safer DNA extraction from plant tissues using sucrose buffer and glass fiber filter.

For some plant species, DNA extraction and downstream experiments are inhibited by various chemicals such as polysaccharides and polyphenols. This short communication proposed an organic-solvent free (except for ethanol) extraction method. This method consists of an initial washing step with STE buffer (0.

Scanning of genetic diversity of evolutionarily sequential Mycobacterium tuberculosis Beijing family strains based on genome wide analysis.

The Beijing family is an endemic lineage of Mycobacterium tuberculosis in eastern Asia. In Japan, five evolutionarily sequential sublineages composing the lineage have predominated. Comparative genomic sequencing based on a microarray technique was conducted for five representative strains of those respective sublineages.

Stability of toxigenicity in proteolytic Clostridium botulinum type B upon serial passage.

Proteolytic Clostridium botulinum type B strains were investigated for stability of toxigenicity and bont/b gene upon serial passage. Strains with bont/b gene located on their plasmids showed loss or decrease of toxigenicity during serial passage. Some strains lost the bont/b gene-encoding plasmid.

Increase of GII.2 norovirus infections during the 2009-2010 season in Osaka City, Japan.

During the 2009-2010 season, a significant numerical increase of genotype GII.2 norovirus (NoV)-associated outbreaks was observed in Osaka City, Japan. The most common genotype in that season was GII.

DNA-based identification of fish species implicated in Puffer fish poisoning.

A method for identification of fish species using three different mitochondrial DNA regions, 16S rRNA, cytochrome b and cytochrome c gene fragments, was investigated. The combined use of all three regions enabled reliable species identification in not only raw fish, but also dried, seasoned and boiled fish, products. Furthermore, the method was applicable even to vomitus from a patient involved in a puffer fish poisoning incident.

Molecular characterization and surfactant utilization of Scolecobasidium isolates from detergent-rich indoor environments.

Scolecobasidium, generally found in outdoor samples, were isolated from detergent-rich indoor environments. The isolates from bathrooms and washing machines, because of their exposure to detergents, might be genetically and biologically distinct from outdoor isolates. In this study, 11 Scolecobasidium isolates from detergent-rich indoor environments were examined to find the genetic and biological differences between the indoor and outdoor isolates.

Molecular epidemiology of human rhinovirus C in patients with acute respiratory tract infections in Osaka City, Japan.

Human rhinovirus (HRV) is a causative agent of acute respiratory tract infection (ARTI). In 2007, a novel HRV group, HRV-C, was discovered. This study, which assessed whether HRV-C is epidemic among patients with ARTI, was aimed at analyzing the seasonal prevalence of HRV-C in Osaka City, Japan.

Enterovirus 68 in children with acute respiratory tract infections, Osaka, Japan.

Enterovirus 68 strains were detected in 14 specimens from children with respiratory tract infections and 1 specimen from a child with febrile convulsions during 2010 in Osaka, Japan. These strains had deletions in the 5' untranslated region and were genetically different from reported strains. This virus is associated with respiratory tract infections in Japan.

Molecular evidence for person-to-person transmission of a novel subtype in Giardia duodenalis assemblage B at the rehabilitation institution for developmentally disabled people.

Giardia duodenalis was found in three patients and a health care worker at a rehabilitation institution for developmentally disabled people. The four isolates were genotyped and subtyped by multilocus homology searching and phylogenetic analyses of the following four loci: glutamate dehydrogenase (gdh), triosephosphate isomerase (tpi), and β-giardin (bg) as variable loci, and elongation factor 1 alpha (ef1α) as a conserved locus. The partial sequences, gdh (709 bp), tpi (526 bp), bg (724 bp), and ef1α (680 bp) of four isolates obtained were mutually identical, and the isolates were found to be a novel subtype in sub-assemblage BIV, strongly indicating that person-to-person transmission by a single subtype occurred at the institution.

Is advanced treated water truly high quality?: the answer from a viewpoint of cancer risk induced by trihalomethane class.

Before and after switching to the advanced treatment, a total of 48 trihalomethanes measurements was made at household taps in the specific distribution area in Osaka City, Japan. An average of total trihalomethanes concentrations in advanced treated water was three-fifths of that in conventionally treated water. The average lifetime cancer risks for total trihalomethanes were 48.

[Molecular epidemiology of Mycobacterium tuberculosis and its prospect based on variable number of tandem repeat (VNTR) genotyping--a strategy in Osaka City, Japan].

The methodological establishment of variable number of tandem repeat(s) (VNTR) genotyping of Mycobacterium tuberculosis has opened a new era of molecular epidemiology against tuberculosis (TB). The method can provide simple, rapid and accurate identification of clinical isolates from TB patients that makes it possible to compare the isolates among different laboratories. Such advantages of VNTR not only help us certify the identification of isolates in putative outbreaks easily but also promote the reasonable estimation of unidentified transmissions in surveillance studies.