Lead-free MCP to improve coincidence time resolution and reduce MCP direct interactions.

Achieving direct imaging of the annihilation position of a positron on an event-by-event basis using an ultrafast detector would have a great impact on the field of nuclear medicine. Cherenkov emission is the most attractive physical phenomenon for realizing such an ultrafast timing performance. Moreover, a microchannel-plate photomultiplier tube (MCP-PMT) is one of the most promising photodetectors for fully exploiting the fast timing properties of Cherenkov emission owing to its excellent single photon time resolution of 25 ps full width at half maximum (FWHM). However, as the MCP structure generally contains a lead compound, the gamma rays frequently and directly interact with the MCP, resulting in the degradation of its timing performance and generation of undesirable side peaks in its coincidence timing histogram. To overcome this problem, we have developed a new MCP-PMT based on an MCP consisting of borosilicate glass, thus drastically reducing the probability of the photoelectric effect occurring in the MCP. To evaluate its insensitivity to gamma rays and its timing performance, a coincidence experiment was performed and showed that the probability of direct interactions was reduced by a factor of 3.4. Moreover, a coincidence time resolution of 35.4 ± 0.4 ps FWHM, which is equivalent to a position resolution of 5.31 mm, was obtained without any pulse height/area cut, improving to 28.7 ± 3.0 ps when selecting on the highest amplitude events by careful optimization of the voltage divider circuit of the new MCP-PMT. The timing performance of this new MCP-PMT presents an important step toward making direct imaging possible.

Analysis of 'Fuji' apple somatic variants from next-generation sequencing.

The domesticated apple (Malus x domestica Borkh.) is a major fruit crop of temperate regions of the world. 'Fuji' apple (Ralls Genet x Delicious), a famous apple cultivar in Korea, has been very popular since its promotion in Japan in 1958. 'Fuji' and its bud mutant cultivars possess variable levels of genetic diversity. Nonetheless, the phenotypes of each group, which are classified into the bud mutation groups: early season, fruiting spur, and coloring, are similar. Despite attempts to identify these bud mutation cultivars, molecular markers, which were developed before the emergence of next-generation sequencing technology, have not been able to distinguish each cultivar easily. In this study, we adopted the resequencing technique using the 'Golden Delicious' (Grimes Golden x Unknown) apple genome as a reference. SNPs (single nucleotide polymorphisms) and InDels (insertions or deletions) of 'Fuji' apple and its bud mutant cultivar were detected and SNPs and unique InDels distinct to each cultivar were identified. Data from this study may be used to identify bud mutant cultivars of 'Fuji' apples and be useful for further breeding of apples.

Assessment of apple core collections constructed using phenotypic and genotypic data.

Several types of information can be used to select core collections, including passport data, agronomic data, and molecular data. However, little is known about the ability of core collections to retain the genetic diversity and structure of the whole collection for characters that were not considered during the selection, particularly when molecular markers are used. In this study, two core subsets were established for the apple (Malus spp) germplasm bank curated at the Apple Research Station, National Institute of Horticultural and Herbal Science, Korea, based upon genetic diversity estimated with 14 simple sequence repeat markers, and phenotypic diversity based on 23 traits. Comparisons between these two subsets and with the whole collection were used to determine the effect of the data used in the selection on phenotypic and genetic diversity, and population structure. The two subsets had a similar diversity and did not differ from the original collection, according to the Nei and Shannon diversity indices. Allele and class frequencies were also maintained in the two subsets. Overall, the type of data used to construct the core collection had little influence on the phenotypic and genetic diversity retained. Therefore, in the case of apple collections, the use of molecular markers is preferable, because they allow rapid and reliable characterization.

Expression analysis of rice VQ genes in response to biotic and abiotic stresses.

WRKY transcription factors are encoded by a large gene superfamily with a broad range of roles in plants. Proteins containing a short VQ (FxxxVQxLTG) motif have been recently shown to interact with WRKY transcription factors, implying that AtVQ proteins are important in the plant defense responses in Arabidopsis, either as positive or negative cofactors of WRKY transcription factors. Thirty-nine Oryza sativa genes containing the VQ motif (OsVQs) were identified and the genome structures of OsVQ proteins were characterized through genome-wide analysis in rice. Also, phylogenetic tree analysis was performed with the VQ domain of Arabidopsis and rice. The expression patterns of these OsVQ genes in plants under several stress treatments were assessed, specifically, following infection with the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo), treatment with abscisic acid (ABA), or exposure to drought. The cellular localization of a few OsVQ proteins was examined using rice protoplast system. Based on our results, we suggest that OsVQ proteins function as important co-regulators during the plant defense response to biotic and abiotic stresses.

Decline in extractable antibiotics in manure-based composts during composting.

A wide variety of antibiotics have been detected in natural water samples and this is of potential concern because of the adverse environmental effects of such antibiotic residues. One of the main sources of antibiotics effluence to the surrounding environment is livestock manures which often contain elevated concentrations of veterinary antibiotics (VAs) which survive digestion in the animal stomach following application in animal husbandry practices. In Korea, livestock manures are normally used for compost production indicating that there is potential for antibiotic release to the environment through compost application to agricultural lands. Therefore, reduction of the amount of VAs in composts is crucial. The purpose of this study was to understand the influence of the composting process and the components of the compost on the levels of three common classes of antibiotics (tetracyclines, sulfonamides, and macrolides). Composted materials at different stages of composting were collected from compost manufacturing plants and the variation in antibiotic concentrations was determined. Three different antibiotics, chlortetracycline (CTC), sulfamethazine (SMZ), and tylosin (TYL) at three different concentrations (2, 10, and 20mgkg(-1)) were also applied to a mixture of pig manure and sawdust and the mixtures incubated using a laboratory scale composting apparatus to monitor the changes in antibiotic concentrations during composting together with the physicochemical properties of the composts. During composting, in both field and lab-scale investigations, the concentrations of all three different antibiotics declined below the relevant Korean guideline values (0.8mgkg(-1) for tetracyclines, 0.2mgkg(-1) for sulfonamides and 1.0mgkg(-1) for macrolides). The decline of tetracycline and sulfonamide concentrations was highly dependent on the presence of sawdust while there was no influence of sawdust on TYL decline.

Applicability of the Charm II system for monitoring antibiotic residues in manure-based composts.

The effluence of veterinary antibiotics (VAs) to aquatic and terrestrial environments is of concern due to the potential adverse effects on human health, such as the production of antibiotic resistant bacteria. One of the main pathways for antibiotics to enter the environment is via the application of manure and/or manure-based composts as an alternative organic fertilizer to agricultural lands. While a wide diversity of manure-based composts are produced in Korea, there is currently no regulatory guideline for VA residues. Hence, monitoring and limiting the concentration of VA residues in manure and/or manure-based composts prior to application to the lands is important to mitigate any environmental burden. The current study was conducted to examine the applicability of the Charm II antibiotic test system for monitoring tetracyclines, sulfonamides and macrolides in manure-based composts. The Charm II system was a highly reproducible method for determining whether VA residue concentrations in manure-based compost exceeded specific guideline values. A wide range of manure-based composts and liquid fertilizers commercially available in Korea were examined using the Charm II system to monitor the residues of the target VAs. For this, the guideline concentrations of VA residues (0.8 mg kg(-1) for tetracyclines, 0.2 mg kg(-1) for sulfonamides, and 0.1 mg kg(-1) for macrolides) stated in 'Official Standard of Feeds' under the 'Control of Livestock and Fish Feed Act' in Korea were adopted to establish control points. Of the 70 compost samples examined 12 exceeded 0.8 mg kg(-1) for tetracyclines and 21 exceeded 0.2 mg kg(-1) for sulfonamides. Of the 25 liquid fertilizer samples examined most samples exceeded these prospective guidelines.

Differentiation between reinfection and recrudescence of helicobacter pylori strains using PCR-based restriction fragment length polymorphism analysis.

The aim of this study was to evaluate whether PCR-based restriction fragment length polymorphism (RFLP) analysis was effective in differentiating between reinfection and recrudescence of H. pylori strains. Following a 1-2 week regimen of omeprazole 20 mg, amoxicillin 1.0 g, and clarithromycin 500 mg twice daily, twenty patients with duodenal ulcer were enrolled in the study. Ten patients (group 1, control) were not successfully treated, and another 10 patients (group 2) exhibited recurrence of infection 6-24 months following the therapy. Follow-up diagnosis was performed by Giemsa stain and CLO test. RFLP profiles of antral and midbody biopsy specimens were compared before and after therapy. PCR products using the ureC gene were digested with restriction enzymes Hha I, Mbo I, and Hind III, and the fragments generated were analyzed by agarose gel electrophoresis. Hha I, Mbo I, and Hind III digestion produced 13, 7, and 2 distinguishable digestion patterns, respectively. There was no difference in RFLP profiles seen before and after the therapy in 17 duodenal ulcer patients, while different RFLP profiles were discovered in 3 patients. Following treatment, one (group 2) patient differed in Mbo I, and two (one each from both groups) patients differed in Hha I and Mbo I RFLP patterns. Eight of group 2 patients showed recrudescence of previous infection and two patients had reinfection by another strain. This study supports the hypothesis that PCR-based RFLP analysis can be effective for differentiating reinfection and recrudescence of H. pylori strains following triple therapy.

Molecular cloning, characterization and expression analysis of a catalase cDNA from hot pepper (Capsicum annuum L.).

We report the cloning of a catalase cDNA from hot pepper (Capsicum annuum L.) and its expression patterns. CaCat1 is consisted of 1837 bp containing one open reading frame (ORF) of 1479 and 45 bp/313 bp of 5'/3'-untranslated region. Deduced amino acid sequence of CaCat1 showed the 95% and 78% identity with that of Nicotiana tabacum Cat1 and Nicotiana plumbaginifolia Cat2, respectively. Northern hybridization shows that CaCat1 transcripts are more abundant in stems than in leaves and roots, and in early stages than in mature stage of fruit development. In roots its transcripts are induced in response to aluminum and NaCl. In addition, its transcription levels under light (12 h)/dark (12 h) cycle and constant light conditions exhibit circadian rhythm, reaching a maximum at late in the dark period or early in the light period. The morning specific circadian regulation of CaCat1 was also observed in NpCat1, but not in NtCat1, suggesting difference in evolutionary rates between coding region and regulatory region of the catalase genes.

Catalase activities of Phanerochaete chrysosporium are not coordinately produced with ligninolytic metabolism: catalases from a white-rot fungus.

Phanerochaete chrysosporium uses hydrogen peroxide as a substrate in its ligninolytic phase. To determine how the fungus protects itself against detrimental effects of reactive oxygen species, catalase activity was examined. The fungus produced up to four different catalase isozymes, Cat A to D. Isozyme CatC was the dominant activity in all growth conditions. A minor catalase, CatD, was apparent in low-carbon culture and upon exposure of mycelium grown on high-nitrogen medium with 5-50 mm of hydrogen peroxide. In low-nitrogen culture, an increase in catalase-specific activity preceded the onset of ligninolysis by 3 days. In low-carbon culture, catalase was produced at an even higher level without development of ligninolysis. Thus, catalase activity was not coordinately produced with ligninolytic metabolism.

Analysis of Plasmodium vivax merozoite surface protein-1 gene sequences from resurgent Korean isolates.

The merozoite surface protein-1 (MSP-1) of Plasmodium vivax exhibits great antigenic diversity among different isolates of this parasite. This antigen is a useful genetic marker for studying the polymorphism of natural P. vivax parasite populations. One or more of these populations has been responsible for resurgent malaria now occurring in Korea. This paper reports the analysis of a highly polymorphic region between interspecies conserved blocks 5 and 6 of the MSP-1 gene, using the polymerase chain reaction to amplify the DNA fragment encompassing these regions from 25 Korean isolates, followed by sequencing. Almost all amino acid sequences of Korean isolates were nearly identical to that of Thai isolates TD525A (96.6-99.7%) and TD424 (96.3-99.5%), and very similar to that of the France-Belem strain when compared with other isolates (Sal-1, Sri Lanka, and Colombia). Interallelic recombination was found in the poly-Q repeat and a Sal-1 type amino acid structure was observed in all isolates. This study shows that the MSP gene nucleotide sequence of resurgent P. vivax in Korea is most similar to that of Thai isolates; however, the Korean strains are phylogenetically unique.

Isolation and characterization of the catalase gene from Rhizobium sp. SNU003, a root nodule symbiont of Canavalia lineata.

A catalase gene from Rhizobium sp. SNU003, a root nodule symbiont of Canavalia lineata, was cloned and its nucleotide sequence was determined. The Rhizobium DNA of about 280 bp was amplified using two PCR primers synthesized from the conserved sequences of the type I catalase gene. The nucleotide sequence of the amplified fragment revealed three regions that were conserved in the catalase, showing it as being part of the catalase gene. A genomic Southern hybridization using this fragment as a probe showed that the 5.5 kb PstI, 1.8 kb EcoRI, and 0.7 kb StyI fragments hybridized strongly with the probe. The Rhizobium genomic library constructed into the EMBL3 vector was screened, and one catalase clone was selected. The nucleotide sequence of the 5.5 kb PstI fragment from the clone revealed an open reading frame of 1455 bp, encoding a polypeptide of 485 amino acids with a molecular mass of 54,958 Da and a pI of 6.54. The predicted amino acid sequence of the catalase is 66.3% identical to that of Bacteroides fragilis, but was only 53.3% identical to the Rhizobium meliloti catalase.

Isolation and characterization of mitochondrial manganese superoxide dismutase (MnSOD) from Capsicum annuum L.

A cDNA clone for a mitochondrial manganese superoxide dismutase (MnSOD) was isolated and characterized from red pepper (Capsicum annuum L.). The clone consisted of 941 bp containing one open reading frame (ORF) of 687 bp, 34 bp/220 bp of 5'/3'-untranslated region. Amino acid sequence of the ORF showed the highest homology (86%) with that of Nicotiana plumbaginifolia. It encodes for a polypeptide of 228 amino acids with a molecular mass of 25.5 kDa and a pI value of 8.39. Genomic Southern hybridization suggested that more than one copy are present. Northern hybridization showed that the MnSOD transcript was more abundant in stems than in leaves and roots. When seedlings were treated with arsenate (0.1-10 mM), the MnSOD transcript level increased slightly at 0.1 mM and then dropped, while the Cu/ZnSOD transcript level increased at 1 mM, and also dropped at higher concentrations.

Isolation and characterization of cytosolic copper/zinc superoxide dismutase from Capsicum annuum L.

A cDNA clone for a cytosolic Cu/Zn superoxide dismutase (Cu/ZnSOD) was isolated and characterized from red pepper (Capsicum annuum L.). The clone consisted of 735 bp containing one open reading frame (ORF) of 459 bp, 46 bp of 5'- and 230 bp of 3'-untranslated region. The nucleotide sequence of the ORF showed 93% homology with that of Nicotiana plumbaginifolia and tomato. It encodes a polypeptide of 154 amino acids with a molecular weight of 15,300. Genomic Southern hybridization suggested that only one copy is present. During cold treatment at 4 degrees C, its expression was maintained at a similar level regardless of illumination.