Biomedical subjects

M Shoda

Publications and source records attributed to M Shoda.

At least 19 recordsLinked to original sources

PubMed2006

Genetic mapping of the pear scab resistance gene Vnk of Japanese pear cultivar Kinchaku.

Pear scab (caused by Venturia nashicola) is one of the most harmful diseases of pears, especially Japanese and Chinese pear species. The molecular identification and early selection of resistant plants could greatly improve pear breeding. We have identified the position of the scab resistance gene, designated Vnk in an indigenous Japanese pear cultivar Kinchaku, within the pear genome by using simple sequence repeat (SSR) markers derived from pear and apple. The position of Vnk was identified in the central region of linkage group 1 of Kinchaku. Several amplified fragment length polymorphism (AFLP) markers linked to Vnk were obtained by bulked segregant analysis. Among them, the AFLP marker closest to Vnk was converted into a sequence tagged site (STS) marker. Four random amplified polymorphic DNA (RAPD) markers previously found to be loosely associated with Vnk (Iketani et al. 2001) were successfully converted into STS markers. Six markers (one SSR Hi02c07 and five STSs converted from AFLP and RAPD) showed tight linkages to Vnk, being mapped with distances ranging from 2.4 to 12.4 cM. The SSR CH-Vf2, which was isolated from a BAC clone of the contig containing the apple scab gene Vf, was mapped at the bottom of linkage group 1 in Kinchaku, suggesting that the Vnk and Vf loci are located in different genomic regions of the same homologous linkage group.

Ascomycota↗

PubMed2006

Production of lipopeptide antibiotic iturin A using soybean curd residue cultivated with Bacillus subtilis in solid-state fermentation.

Bacillus subtilis RB14-CS, which suppresses the growth of various plant pathogens in vitro by producing the lipopeptide antibiotic iturin A, was cultured using soybean curd residue, okara, a by-product of tofu manufacture in solid-state fermentation. After 4 days incubation, iturin A production reached 3,300 mg/kg wet solid material (14 g/kg dry solid material), which is approximately tenfold higher than that in submerged fermentation. When the okara product cultured with RB14-CS was introduced into soil infested with Rhizoctonia solani, which is a causal agent of damping-off of tomato, the disease occurrence was significantly suppressed. After 14 days, the number of RB14-CS cells remained in soil at the initial level, whereas almost no iturin A was detected in soil. As the okara cultured with RB14-CS exhibited functions of both plant disease suppression and nutritional effect on tomato seedlings, this product is expected to contribute to the recycling of the soybean curd residue.

Bacillus subtilis↗

PubMed2006

DHMEQ, a new NF-kappaB inhibitor, induces apoptosis and enhances fludarabine effects on chronic lymphocytic leukemia cells.

Chronic lymphocytic leukemia (CLL) is a low-grade lymphoid malignancy incurable with conventional modalities of chemotherapy. Strong and constitutive nuclear factor kappa B (NF-kappaB) activation is a characteristic of CLL cells. We examined the effects of a new NF-kappaB inhibitor, dehydroxymethylepoxyquinomicin (DHMEQ), on CLL cells. Dehydroxymethylepoxyquinomicin completely abrogated constitutive NF-kappaB activity and induced apoptosis of CLL cells. Apoptosis induced by DHMEQ was accompanied by downregulation of NF-kappaB-dependent antiapoptotic genes: c-IAP, Bfl-1, Bcl-X(L) and c-FLIP. Dehydroxymethylepoxyquinomicin also inhibited NF-kappaB induced by CD40 and enhanced fludarabine-mediated apoptosis of CLL cells. Results of this study suggest that inhibition of constitutive and inducible NF-kappaB by DHMEQ in combination with fludarabine is a promising strategy for the treatment of CLL.

Aged↗

PubMed2005

Enhancement of styrene removal by Pseudomonas sp. SR-5 in mixed culture with a benzoic acid-degrading bacterium in biofilter.

The growth of a styrene-degrading bacterium, Pseudomonas sp. SR-5, was inhibited by benzoic acid (BA), one of the styrene degradation intermediates, in liquid culture. A benzoic acid-degrading microorganism, Raoultella sp. strain A, was isolated from a peat biofilter inoculated with a wastewater. The styrene removal efficiencies of the two laboratory-scale biofilters inoculated with only strain SR-5 and a mixed culture of strains SR-5 and A were compared using a mixed packing material of peat and ceramic (1:1) for 45 days. The biofilter with the mixed culture showed a higher removal efficiency than that with a single culture of SR-5. The maximum elimination capacities of the biofilters with the mixed culture and the single culture were 141 g m(-3)h(-1) and 106 g m(-3)h(-1), respectively. In the biofilter with the single culture, 136 g of benzoic acid (m3 of dry packing material)(-1) was accumulated at the end of the experiment. However, no accumulation of benzoic acid was observed in the biofilter with the mixed culture.

Air Pollutants↗

PubMed2004

Production of bacterial cellulose by Acetobacter xylinum BPR2001 using molasses medium in a jar fermentor.

Bacterial cellulose (BC) production by Acetobacter xylinum subsp. sucrofermentans BPR2001 using molasses medium was carried out in a jar fermentor. When molasses was subjected to H(2)SO(4)-heat treatment, the maximum BC concentration increased to 76% more than that achieved using untreated molasses, and the specific growth rate increased 2-fold. When the initial sugar concentrations in the H(2)SO(4)-heat treated molasses were varied from 23 g/l to 72 g/l, BC concentration, production rate, and yield were maximum at sugar concentrations of 23 g/l and 37 g/l, and production of by-products, such as polysaccharides and CO(2), was lower than at sugar concentrations of 48 g/l and 72 g/l, indicating that maintaining a lower molasses concentration is essential for efficient BC production in jar fermentors, this being due mainly to the complex nature of molasses. Molasses has a clear advantage over pure sugars as a carbon source from an economic viewpoint.

Bioreactors↗

PubMed2004

Styrene degradation by Pseudomonas sp. SR-5 in biofilters with organic and inorganic packing materials.

Pseudomonas sp. SR-5 was isolated as a styrene-degrading bacterium. In liquid culture containing 1% (v/v) styrene, more than 90% styrene was degraded in 53 h and the doubling time of SR-5 was 2 h. The removal of styrene gas was investigated in biofilters for 31 days using an organic packing material of peat and an inorganic packing material of ceramic inoculated with SR-5. The maximum-styrene-elimination capacities for peat and ceramic packing materials were 236 and 81 g m(-3) h(-1), respectively. The percentage of styrene converted to low molecular weight compounds including CO(2) in the peat and ceramic biofilters during a 10-day operation were estimated to be 90.4 and 36.7%, respectively. As the pressure drop in the peat bioflter at the end of experiment was significantly higher than that in ceramic biofilter, a biofilter using a mixture of peat and ceramic was tested. We determined that the maximum elimination capacity was 170 g m(-3) h(-1) and the production of low molecular weight compounds was 95% at a low pressure drop for this mixed packing material filter.

Biodegradation, Environmental↗

PubMed2004

Features of bacterial cellulose synthesis in a mutant generated by disruption of the diguanylate cyclase 1 gene of Acetobacter xylinum BPR 2001.

The diguanylate cyclase 1 (DGC1) (dgc1) gene in Acetobacter xylinum BPR 2001--a bacterial cellulose (BC) producer--was cloned and sequenced, and a DGC1 gene-disrupted mutant, strain DD, was constructed. The production and structural characteristics of the BC formed by DD were compared with those of the parental strain BPR 2001. BC production by DD was almost the same as that by BPR 2001 in static cultivation and in shake flask cultivation. However, in a jar fermentor DD produced about 36% more BC than the parental strain. DD produced suspended particle materials that cannot aggregate owing to their random structural characteristics in static cultivation; more uniformly dispersed BC pellicles and smaller BC pellets are produced on average in a jar fermentor, as reflected by the higher BC production by DD than by the parental strain in a jar fermentor. Micrographs of BC produced by DD revealed that the width of cellulose ribbons assemblies decreased as a result of differences in the ultrastructure and mechanism of formation of BC between the two strains. These results reveal that disruption of the dgc1 gene, which catalyzes synthesis of c-di-GMP (an effector of BC synthase), is not fatal for BC synthesis, although it affects BC structure.

Cellulose↗

PubMed2003

Utilization of the buffering capacity of corn steep liquor in bacterial cellulose production by Acetobacter xylinum.

Acetobacter xylinum BPR2001 produces water-insoluble bacterial cellulose (BC). Using a pH sensor for the accurate control of pH, which is one of the most critical factors for efficient BC production, is difficult especially in a baffled shake-flask and an airlift reactor. The buffering capacity of corn steep liquor (CSL) was estimated by measuring beta (buffering capacity) values in advance and was used to maintain the pH within the optimal range during the production of BC. When CSL was added to either a shake-flask, a stirred-tank reactor or an airlift reactor, BC production was almost the same as that in cultivations where pH was controlled manually or by a pH sensor.

Bioreactors↗

PubMed2003

Functional electrical stimulation (FES) for spinal cord injury.

Restoration of respiratory motion by stimulation of the phrenic nerve was investigated. Respiratory motion was restored successfully by introducing a breathing pacemaker to a patient with respiratory disturbance due to upper cervical spinal cord injury. Breathing pacemakers are considered to be more similar to physiological conditions compared to mechanical ventilators. Although the system is very expensive, its cost effectiveness may be excellent, provided that it can be used for long hours each day over an extended period. The system is effective in improving patient QOL because it dramatically increases patient mobility. From these findings, it is concluded that breathing pacemakers should be used more frequently in Japan, and that various forms of support are necessary to cope with economic and other concerns.

Adult↗

PubMed2003

Characteristics of a newly isolated fungus Geotrichum candidum Dec 1 with broad degradation spectrum of xenobiotic compounds.

A newly isolated fungus, Geotrichum candidum Dec 1 (abbreviated as Dec 1), was found to have the ability to degrade many xenobiotic compounds such as synthetic dyes, food coloring agents, molasses, organic halogens, lignin and kraft pulp effluents. The broad spectrum of the degradation of these compounds are associated mainly with peroxidases produced by the fungus.

Aspergillus oryzae↗

PubMed2002

Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears.

Genetic linkage maps of the European pear ( Pyrus communis L.) cultivar 'Bartlett' and the Japanese pear ( Pyrus pyrifolia Nakai) cultivar 'Housui' were constructed based on AFLPs, SSRs from pear, apple and Prunus, isozymes and phenotypic traits by using their F(1) progenies. The map of the female parent Bartlett consisted of 226 loci including 175 AFLPs, 49 SSRs, one isozyme and one S locus on 18 linkage groups over a total length of 949 cM, while that for 'Housui' contained 154 loci including 106 AFLPs, 42 SSRs, two phenotypic traits and the other four markers on 17 linkage groups encompassing a genetic distance of 926 cM. These maps were partially aligned using 20 codominant markers which showed segregating alleles in both parents. Compared with the reports of apple genetic maps, these pear maps were not saturated but were near saturation. Distorted segregation was observed in two and one regions of the genome of Bartlett and Housui, respectively. The position of 14 SSRs originating from apple could be successfully determined in pear maps, which enabled us to compare the two maps. Some SSRs developed from Prunus (peach, cherry) were also mapped. The relationships between pear and the other species belonging to the Rosaceae were discussed based on the position of SSRs.

Chromosome Mapping↗

PubMed2001

Bacterial cellulose production under oxygen-enriched air at different fructose concentrations in a 50-liter, internal-loop airlift reactor.

Bacterial cellulose (BC) production by Acetobacter xylinum subsp. sucrofermentans BPR2001 was carried out in a 50-1 internal-loop airlift reactor in air at an initial fructose concentration of 40 g/l. The BC production rate was 0.059 g/l per h. When oxygen-enriched air was supplied instead of air, the BC production rate increased to 0.093 g/l per h, and the BC yield was enhanced from 11% in air to 18%. When the initial fructose concentrations were varied from 30 to 70 g/l, the highest BC yield (35%) the highest production rate (0.22 g/l x per h), and the highest concentration of BC produced (10.4 g/l) were observed at 60-70 g/l fructose. From the carbon mass balance calculated at the final stage of cultivation, it was observed that enhanced BC production was reflected as a decrease in both CO2 evolution and the concentration of other unknown substances, suggesting the efficient utilization of energy for BC synthesis despite O2 limitation.

Acetobacter↗

PubMed2001

Drastic high magnetic field effect on suppression of Escherichia coli death.

When Escherichia coli B was aerobically grown in a medium containing one-fourth the concentration of the LB medium supplemented with glutamic acid at 43 degrees C under an inhomogeneous 5.2-6.1 T magnetic field, the number of cells in the stationary phase under the high magnetic field was 100,000 times higher than that under a geomagnetic field. The finding that the amount of sigma S factor encoded by the rpoS gene under the high magnetic field was larger than that under the control geomagnetic field indicated that the activity of the rpoS gene was affected by the high magnetic field.

Amino Acids↗

PubMed2001

Disappearance of growth advantage in stationary phase (GASP) phenomenon under a high magnetic field.

The phenomenon called growth advantage in stationary phase (GASP) originally discovered by Kolter et al. was confirmed using two bacterial strains, Escherichia coli ZK126Nalr and ZK126Smr, under the geomagnetic field. However, when the same experiment was conducted in an inhomogeneous high magnetic field of 5.2-6.1 T, almost no death of ZK126Smr was observed and the GASP phenomenon disappeared. When the same experiment was conducted in a homogeneous magnetic field of 7 T, the GASP was significantly delayed due to the much slower death rate of ZK126Smr than that in the geomagnetic field. These data are consistent with our previous finding that a high magnetic field reduces the death rate of bacteria and enhances their survivability in a stationary phase.

Escherichia coli↗

PubMed2001

Twelve hours exposure to inhomogeneous high magnetic field after logarithmic growth phase is sufficient for drastic suppression of Escherichia coli death.

When Escherichia coli B was aerobically grown at 43 degrees C in a medium whose concentration was one-fourth that of the Luria-Bertani (LB) medium supplemented with 1.5 g/l of glutamic acid, drastic cell death was observed after the end of the logarithmic growth phase. However, when the same experiment was conducted under inhomogeneous 5.2-6.1 T magnetic field, cell death was extremely suppressed and the ratio of viable cell number under high magnetic field to that under geomagnetic field reached as much as 100,000. When the magnetic field exposure was restricted to 12 h after the logarithmic growth phase, a similar high degree of suppressive effect on the death was observed. The findings that the amount of sigma S protein encoded by the rpoS gene under the high magnetic field was larger than that under the geomagnetic field, and that the magnetic field effect disappeared when the rpoS gene-deficient strain was cultivated under the high magnetic field, suggest the interaction of magnetic field with a stationary phase specific gene.

Bacterial Proteins↗

PubMed2001

Electrophysiological characteristic of a patient exhibiting the short-coupled variant of torsade de pointes.

A 41-year-old man was admitted because of syncope. The electrocardiogram showed torsade de pointes (Tdp) with no long QT interval and the coupling interval of the initial beat of Tdp was 240 ms. Heterogeneity of ventricular refractoriness was observed together with shortness of the effective refractory period measured at the right ventricular inflow site where the paced QRS morphology was the same as that of the initial beat of Tdp. Verapamil could suppress frequent ventricular premature complexes with a short coupling interval, which lead to Tdp. Polymorphic ventricular tachycardia was induced by triple ventricular extrastimuli. A pure potassium channel blocker was successful in inhibiting polymorphic ventricular tachycardia inducibility by prolongation of refractoriness. These results suggested that triggered ventricular premature complexes may be represent the initiating mechanism, whereas the shortness of local refractory period and heterogeneity of ventricular refractoriness may play a role in the development and the maintenance of the Tdp.

Adult↗

PubMed2001

Gene yerP, involved in surfactin self-resistance in Bacillus subtilis.

Surfactin is a cyclic lipopeptide biosurfactant. Transposon mutagenesis was performed in Bacillus subtilis strain 168, and a surfactin-susceptible mutant, strain 801, was isolated. Analysis of the region of insertion revealed that yerP was the determinant of surfactin self-resistance. YerP had homology with the resistance, nodulation, and cell division (RND) family proton motive force-dependent efflux pumps only characterized in gram-negative strains. The yerP-deficient strain 802, in which the internal region of the yerP gene of B. subtilis strain 168 was deleted, showed susceptibility to acriflavine and ethidium bromide. When strain 802 was converted to a surfactin producer by introducing a functional sfp which encodes a 4'-phosphopantetheinyl transferase and is mutated in B. subtilis strain 168, this yerP-deficient strain produced surfactin, although surfactin production was significantly reduced. The expression of yerP was at its maximum at the end of the logarithmic growth phase and was not induced by surfactin. yerP is the first RND-like gene characterized in gram-positive strains and is supposed to be involved in the efflux of surfactin.

Antibiotics, Antineoplastic↗

PubMed2001

Cloning, sequencing, and characterization of the iturin A operon.

Bacillus subtilis RB14 is a producer of the antifungal lipopeptide iturin A. Using a transposon, we identified and cloned the iturin A synthetase operon of RB14, and the sequence of this operon was also determined. The iturin A operon spans a region that is more than 38 kb long and is composed of four open reading frames, ituD, ituA, ituB, and ituC. The ituD gene encodes a putative malonyl coenzyme A transacylase, whose disruption results in a specific deficiency in iturin A production. The second gene, ituA, encodes a 449-kDa protein that has three functional modules homologous to fatty acid synthetase, amino acid transferase, and peptide synthetase. The third gene, ituB, and the fourth gene, ituC, encode 609- and 297-kDa peptide synthetases that harbor four and two amino acid modules, respectively. Mycosubtilin, which is produced by B. subtilis ATCC 6633, has almost the same structure as iturin A, but the amino acids at positions 6 and 7 in the mycosubtilin sequence are D-Ser-->L-Asn, while in iturin A these amino acids are inverted (i.e., D-Asn-->L-Ser). Comparison of the amino acid sequences encoded by the iturin A operon and the mycosubtilin operon revealed that ituD, ituA, and ituB have high levels of homology to the counterpart genes fenF (79%), mycA (79%), and mycB (79%), respectively. Although the overall level of homology of the amino acid sequences encoded by ituC and mycC, the counterpart of ituC, is relatively low (64%), which indicates that there is a difference in the amino acid sequences of the two lipopeptides, the levels of homology between the putative serine adenylation domains and between the asparagine adenylation domains in the two synthetases are high (79 and 80%, respectively), implying that there is an intragenic domain change in the synthetases. The fact that the flanking sequence of the iturin A synthetase coding region was highly homologous to the flanking sequence that of xynD of B. subtilis 168 and the fact that the promoter of the iturin A operon which we identified was also conserved in an upstream sequence of xynD imply that horizontal transfer of this operon occurred. When the promoter was replaced by the repU promoter of the plasmid pUB110 replication protein, production of iturin A increased threefold.

Amino Acid Sequence↗