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An aggregation-induced emission chromophore, vinylpyrrole, was prepared from a formylpyrrole derivative, Meldrum's acid, and 1,3-dimethylbarbituric acid. The optical properties of the chromophore both in the solution and solid states were investigated by UV-vis and fluorescence spectroscopy. Single crystal X-ray diffraction measurements revealed that the dimethylbarbituric acid adduct formed a J-aggregate in the solid and resulted in higher fluorescence quantum yield compared to the Meldrum's acid adduct. Emission enhancement was found to occur by the restriction of molecular rotation in the solid state.

Polyhydroxyalkanoate (PHA) synthase from the bacterium Bacillus cereus YB-4 (PhaRC YB4 ), a Class IV PHA synthase, shows both PHA polymerization and alcoholysis activities. In PhaRC YB4 -expressing Escherichia coli in the presence of ethanol, biosynthesized PHA is subjected to an ethyl-esterification at the carboxy terminus as a result of alcoholytic cleavage of the PHA chain by PhaRC YB4 . In this study, we investigated the range of alcohol species available for alcoholysis by PhaRC YB4 using E. coli JM109 as an assay host by monitoring the molecular weight of PHA during the second step of a two-step cultivation. PhaRC YB4 utilized various alcohols other than ethanol for alcoholysis. Through the use of bifunctional compounds for alcoholysis, the PHA carboxy terminus could be modified with thiol, alkynyl, hydroxy, and benzyl groups, resulting in the functionalization of the PHA carboxy terminus. Furthermore, one-step production of carboxy-terminal functionalized PHA was developed using E. coli XL1-Blue as a production host.

Polyhydroxyalkanoates (PHAs) are a group of microbial intracellular biopolyesters that have wide potential applications for the plastics industry. Here, we report the results of molecular analyses of PHA synthases from Halomonas species, which are halophilic eubacteria known as promising industrial PHA producers, but the PHA synthase gene of Halomonas has not been cloned previously. In this study, the putative PHA synthase genes (phaC1 and phaC2) from two Halomonas strains (a new isolate, Halomonas sp. O-1, and the genome-sequenced strain, Halomonas elongata DSM2581) were cloned and characterized. We identified a gene related to the H. elongata DSM2581 PHA synthase gene (phaC1He) in the Halomonas sp. O-1 genome (phaC1HO1). PHA synthases usually contain a lipase box-like sequence Gly-X-Cys-X-Gly in their active sites. However, the equivalent sequence found in PhaC1HO1 and PhaC1He was determined to be Ser-X-Cys-X-Gly, with serine replacing the first glycine. The cloned phaC1HO1 and phaC1He genes were found to be functional when expressed in Escherichia coli JM109 and Ralstonia eutropha PHB-4. Site-directed mutagenesis studies showed that the cysteine in the Ser-X-Cys-X-Gly sequence was the catalytic center of Halomonas PhaC1 proteins and that replacement of serine with glycine slightly affected PHA biosynthesis and copolymer composition. In addition, a second potential PHA synthase gene (phaC2) was cloned and its polymerization activity was evaluated. The results herein provide an important molecular basis for PHA production by Halomonas species.

Polyhydroxyalkanoate (PHA)-producing Bacillus strains express class IV PHA synthase, which is composed of the subunits PhaR and PhaC. Recombinant Escherichia coli expressing PHA synthase from Bacillus cereus strain YB-4 (PhaRC YB-4 ) showed an unusual reduction of the molecular weight of PHA produced during the stationary phase of growth. Nuclear magnetic resonance analysis of the low-molecular-weight PHA revealed that its carboxy end structure was capped by ethanol, suggesting that the molecular weight reduction was the result of alcoholytic cleavage of PHA chains by PhaRC YB-4 induced by endogenous ethanol. This scission reaction was also induced by exogenous ethanol in both in vivo and in vitro assays. In addition, PhaRC YB-4 was observed to have alcoholysis activity for PHA chains synthesized by other synthases. The PHA synthase from Bacillus megaterium (PhaRC Bm ) from another subgroup of class IV synthases was also assayed and was shown to have weak alcoholysis activity for PHA chains. These results suggest that class IV synthases may commonly share alcoholysis activity as an inherent feature.

Developing Escherichia coli strains that are tolerant to acetate toxicity is important in light of an increased interest in the efficient utilization of lignocellulosic biomass feedstocks for the biosynthesis of value-added products. In this study, four strains known to produce polyhydroxyalkanoates (PHAs) from the typical hemicellulosic sugar xylose were tested for their tolerance to acetate. E. coli RSC10 was found to be tolerant of acetate, both in growth and fermentation studies. In the presence of acetate the strain showed a >2-fold increase in overall yields compared to using xylose alone as the feedstock. More importantly, the strain was found to be able to utilize acetate as a feedstock for biosynthesis of PHAs, with complete depletion of acetate (25 mM) at 9 h when acetate was the sole feedstock. Higher concentrations of acetate showed greater inhibition of fermentation than growth with a reduction of 90% in PHA yields at 100 mM. Additionally, the present work provides data to support the potential of acetate as a modulator for the control of composition of PHAs that incorporate lactate (LA) monomers into the copolymer from hemicellulose derived sugars.

Cells of Lactobacilli co-aggregated with Escherichia coli K-12 cells to form co-aggregates under mixed-culture conditions at 37 °C for 24 h. Co-aggregation was inhibited by sodium dodecyl sulfate but not by protease. E. coli deletion mutants of fimbriae formation and lipopolysaccharide (LPS) formation did not co-aggregate with Lactobacilli. These results showed that fimbriae and LPS are necessary for co-aggregation between Lactobacilli and E. coli.

We describe the characterization of polyhydroxyalkanoate (PHA)-producing bacteria isolated from an ammunition-polluted soil in Kitakyushu City, Japan. Over 270 strains were evaluated for PHA accumulation based on a colony staining method using Nile red. Of these, nine strains were selected based on the intensity of Nile red fluorescence and the cells were quantitatively analyzed for PHA by gas chromatography. PHA accumulation was observed in five strains, all of which are inferred to be close to the Bacillus cereus group according to 16S rDNA sequence analysis. Interestingly, these strains produced a PHA copolymer, poly(3-hydroxybutyrae-co-3-hydroxyvalerate) [P(3HB-co-3HV)], with a 3HV fraction up to 2 mol% with glucose as a carbon source. Further characterization was performed on one isolate, B. cereus YB-4. Gel permeation chromatography analysis revealed that the number of average molecular weights of PHA accumulated in B. cereus YB-4 drastically changed from 722,000 to 85,000 over a 72-h cultivation period. Furthermore, the PHA synthase genes were cloned and the deduced amino acid sequences were determined. This study provides new insights into PHA biosynthesis by members of the B. cereus group.

Polyhydroxyalkanoates (PHAs) are eco-friendly plastics that are synthesized by bacteria as an intracellular storage material. Ethanol is a key compound in molecular weight regulation of PHA during biosynthesis. In this study, three strains of Escherichia coli expressing PHA synthase (PhaCRe, PhaCAc or PhaCHe) were cultured to compare the effect of ethanol level on PHA molecular weight. As a result, it was revealed that PhaCAc tends to produce low molecular weight PHA due to its high ethanol sensitivity whereas PhaCHe produces high molecular weight PHA even in the presence of ethanol.

To investigate the possibility of applying staphylococcal catalase to eliminate H2O2 in lactic acid fermentation, an intracellular catalase from Staphylococcus warneri ISK-1 which exhibited high catalase activity was purified to homogeneity in a six-step purification procedure. The subunit molecular mass of the purified enzyme determined under denaturing conditions was 64,000. The absorption spectrum of the catalase showed a soret band at 406 nm, indicating that the enzyme is a heme protein. Km and Vmax of the catalase for H2O2 were 59 mM and 42,700 U/mg, respectively. The catalase showed a broad optimum pH (5.5–9.5) and stability to organic solvents. We cloned a catalase gene from S. warneri ISK-1 genome. Nucleotide sequence analysis of a 2.2-kb DNA fragment revealed an open reading frame of 1515 bp, called katA, encoding a protein of 504 amino acid residues. The predicted amino acid sequence showed a high homology with other typical catalases. No similarities to bacterial catalase-peroxidase type enzymes were found.

In this study we attempted to control some specified metal-ion concentrations in a liquid medium and found a highly raw starch-digesting glucoamylase (RSDG) producing culture with protease-less activity, which we have called a metal-ion regulated liquid medium . Rhizopus sp. MKU 40 could not grow and produce glucoamylase (GA) in the liquid medium without metal ions (SLS medium). The addition of iron, magnesium, and zinc ions in the liquid medium was essential to growth and GA production of Rhizopus sp. MKU 40. Calcium ions also stimulated its growth and GA production. To summarize, the addition of 75 ppm calcium ions, 2 ppm iron ions, 49 ppm magnesium ions, and 0.7 ppm zinc ion to the SLS liquid medium was the best condition for producing GA and resulted in a high specific activity of GA (21.9 U/mg protein). Specific RSDG activity of the crude enzyme was 5.7 U/mg protein, and the ratio of RSDG activity to GA activity was 0.26. Since the purification was easy, the purification of GA was done in only two steps (ammonium sulfate precipitation and column chromatography on CM-Sephadex C-50) . The enzyme was purified about 4 .8-fold based on specific GA activity with an 86.0% yield based on GA activity from culture supernatant . The enzyme was proved to be homogeneous as judged by SDS-PAGE, and it has a molecular mass of about 80.4 kDa by comparison of its relative mobility on SDS-PAGE with those of standard proteins . For purified enzymes, the ratio of RSDG activity to GA activity was 0.16.

Polypeptone is widely excluded from Schizosaccharomyces pombe growth medium. However, the reasons why polypeptone should be avoided have not been documented. Polypeptone dramatically induced cell lysis in the ura4 deletion mutant when cells approached the stationary growth phase, and this phenotype was suppressed by supplementation of uracil. To determine the specificity of this cell lysis phenotype, we created deletion mutants of other genes involved in de novo biosynthesis of uridine monophosphate (ura1, ura2, ura3, and ura5). Cell lysis was not observed in these gene deletion mutants. In addition, concomitant disruption of ura1, ura2, ura3, or ura5 in the ura4 deletion mutant suppressed cell lysis, indicating that cell lysis induced by polypeptone is specific to the ura4 deletion mutant. Furthermore, cell lysis was also suppressed when the gene involved in coenzyme Q biosynthesis was deleted. This is likely because Ura3 requires coenzyme Q for its activity. The ura4 deletion mutant was sensitive to zymolyase, which mainly degrades (1,3)-beta-D glucan, when grown in the presence of polypeptone, and cell lysis was suppressed by the osmotic stabiliser, sorbitol. Finally, the induction of cell lysis in the ura4 deletion mutant was due to the accumulation of orotidine-5-monophosphate. Cell wall integrity was dramatically impaired in the ura4 deletion mutant when grown in the presence of polypeptone. Because ura4 is widely used as a selection marker in S. pombe, caution needs to be taken when evaluating phenotypes of ura4 mutants.

The biofilm degradation of Aggregatibacter actinomycetemcomitans is essential as a complete periodontal disease therapy, and here we show the effects of potential probiotic bacteria such as Lactobacillus spp. for the biofilm of several serotypes of A. actinomycetemcomitans strains. Eight of the 13 species showed the competent biofilm degradation of ≥ 90% reduction in biofilm values in A. actinomycetemcomitans Y4 (serotype b) as well as four of the seven species for the biofilm of A. actinomycetemcomitans OMZ 534 (serotype e). In contrast, the probiotic bacteria did not have a big impact for the degradation of A. actinomycetemcomitans SUNY 75 (serotype a) biofilm. The dispersed A. actinomycetemcomitans Y4 cells through the biofilm detachment were still viable and plausible factors for the biofilm degradation were not due to the lactic acid and low pH conditions. The three enzymes, protease, lipase, and amylase may be responsible for the biofilm degradation; in particular, lipase was the most effective enzyme for the biofilm degradation of A. actinomycetemcomitans Y4 along with the protease activity which should be also important for the other serotypes. Remarkable lipase enzyme activities were detected from some of the potential probiotics and a supporting result using a lipase inhibitor presented corroborating evidence that lipase activity is one of the contributing factors for biofilm degradation outside of the protease which is also another possible factor for the biofilm of the other serotype of A. actinomycetemcomitans strains. On the other hand, the biofilm of A. actinomycetemcomitans SUNY 75 (serotype a) was not powerfully degraded by the lipase enzyme because the lipase inhibitor was slightly functional for only two of potential probiotics.

Class IV polyhydroxyalkanoate (PHA) synthase from Bacillus cereus YB-4 (PhaRC(YB4)) or B. megaterium NBRC15308(T) (PhaRC(Bm)) was expressed in Ralstonia eutropha PHB(-)4 to compare the ability to produce PHA and the substrate specificity of PhaRCs. PhaRC(YB4) produced significant amounts of PHA and had broader substrate specificity than PhaRC(Bm).

Polyhydroxyalkanoate (PHA)-producing Bacillus strains possess class IV PHA synthases composed of two subunit types, namely, PhaR and PhaC. In the present study, PHA synthases from Bacillus megaterium NBRC15308(T) (PhaRC(Bm)), B. cereus YB-4 (PhaRC(YB4)), and hybrids (PhaR(Bm)C(YB4) and PhaR(YB4)C(Bm)) were expressed in Escherichia coli JM109 to characterize the molecular weight of the synthesized poly(3-hydroxybutyrate) [P(3HB)]. PhaRC(Bm) synthesized P(3HB) with a relatively high molecular weight (M(n) = 890 × 10(3)) during 72 h of cultivation, whereas PhaRC(YB4) synthesized low-molecular-weight P(3HB) (M(n) = 20 × 10(3)). The molecular weight of P(3HB) synthesized by PhaRC(YB4) decreased with increasing culture time and temperature. This time-dependent behavior was observed for hybrid synthase PhaR(Bm)C(YB4), but not for PhaR(YB4)C(Bm). These results suggest that the molecular weight change is caused by the PhaC(YB4) subunit. The homology between PhaCs from B. megaterium and B. cereus YB-4 is 71% (amino acid identity); however, PhaC(YB4) was found to have a previously unknown effect on the molecular weight of the P(3HB) synthesized in E. coli.

The biogenic production of hydrogen sulfide is a serious problem associated with wastewater treatment. The aim of this study was to investigate the inhibitory effect of nitrate on the dynamics of sulfate-reducing bacteria (SRB) community in a laboratory-scale wastewater reactor, originating from a denitrifying plant using activated sludge. For this purpose, denaturing gradient gel electrophoresis (DGGE) analysis targeting the dsrB (dissimilatory sulfite reductase) gene was used in combination with chemical analyses and measurement of oxidation and reduction potential (ORP). The reactors were initially dosed with 1.0 and 4.0 g/L potassium nitrate and anaerobically incubated for 490 h. Addition of 4.0 g/L nitrate to the reactor was associated with a prolonged inhibition (over 300 h, i.e., 12.5 days) of sulfate reduction and this was consistent with a rapid decrease in ORP associated with nitrate depletion. The DGGE analysis revealed that nitrate addition remarkably attenuated a distinct group of dsrB related to Desulfovibrio, whereas other dsrB groups were not influenced. Furthermore, another sulfate reduction by Syntrophobacter in the later stages of the incubation period occurred in both reactors (regardless of the nitrate concentration), suggesting that different SRB groups are associated with sulfate reduction at different stages of the wastewater treatment process.

Ternary compound AlxGa1-xN thin films were grown on sapphire substrates by the dual-beam pulsed laser deposition (PLD) method in N2 atmosphere. Due to Ga re-evaporation, a compositional change of the film developed with change of the growth temperature. The activation energy of Ga re-evaporation was estimated to be 1–2 eV which was about 1 eV lower than that so far obtained for molecular-beam-epitaxy.