Microbiology of nitrogen cycle in animal manure compost

Composting is the major technology in the treatment of animal manure and is a source of nitrous oxide, a greenhouse gas. Although the microbiological processes of both nitrification and denitrification are involved in composting, the key players in these pathways have not been well identified. Recent molecular microbiological methodologies have revealed the presence of dominant Bacillus species in the degradation of organic material or betaproteobacterial ammonia‐oxidizing bacteria on nitrification on the surface, and have also revealed the mechanism of nitrous oxide emission in this complicated process to some extent. Some bacteria, archaea or fungi still would be considered potential key players, and the contribution of some pathways, such as nitrifier denitrification or heterotrophic nitrification, might be involved in composting. This review article discusses these potential microbial players in nitrification–denitrification within the composting pile and highlights the relevant unknowns through recent activities that focus on the nitrogen cycle within the animal manure composting process.     

Validity and reliability of a visual scoring method for masticatory ability using test gummy jelly

Background: For quantitative evaluation of masticatory ability of the elderly patients, there should be a simple and reliable method without special techniques and instruments. Objective: The purpose of this study was to examine the validity and reliability of a visual scoring method for assessing masticatory performance. Materials and Methods: A 10‐stage scale for visually scoring was rated based on the range of the glucose concentration dissolved from comminuted jelly. Photographic images of comminuted jellies were produced as a standard material for each score. Fifty subjects were recruited as raters who graded the visual score for 50 photographic images of comminuted jellies on the screen of a lap‐top three times in random order. Results: There were strong correlations (rs = 0.911– 0.981, Spearman’s rank coefficient) between the actual scores determined from the glucose concentration and the visual scores graded by subjects in all three measurements. The intraclass correlation coefficients (ICCs) of the inter‐rater reliability and the ICCs of the intra‐rater reliability of the visual scoring ranged from 0.946 to 0.947 and from 0.860 to 0.987 in three measurements, respectively. Conclusions: These results indicated that the visual scoring method was valid and reliable for evaluation of masticatory performance.     

Optimisation of OPLS–UA force-field parameters for protein systems using protein data bank

We have previously proposed a method for refining force-field parameters of protein systems, which consists of minimising the summation of the square of the force acting on each atom in the proteins with the structures from the protein data bank (PDB). The results showed that the modified force-field parameters for all-atom model gave structures more consistent with the experimental implications than the original force fields. In this work, we applied this method and a new method to the OPLS–UA force field. In the new method, we perform a minimisation of the average of the root-mean-square deviation of various protein structures from the native structure. We selected some torsion-energy parameters for this optimisation, and 100 molecules from the PDB were used. The results imply that the new force-field parameters gave structures of two peptides more consistent with the experimental implications for the secondary structure-forming tendencies than the original OPLS–UA force field.     

Preparation and Reaction of Partially Benzylated 2-Azido-2-deoxy-l-xylopyranose

2-Azido-3,4-di-O-benzyl-2-deoxy-l-xylopyranose (XV) was prepared. Oxidation of XV with methyl sulfoxide and acetic anhydride was examined.     

Studies on Lotus Seed Protease

Some physicochemical and enzymic properties of the purified lotus seed protease were investigated. The molecular weight determined from sedimentation-diffusion studies and by Sephadex G-100 gel-filtration was 36,800 and 35,500, respectively. The enzyme gave a typical ultraviolet spectrum of protein and its isoelectric point was found to be in a range of pH 3~4. The enzyme was stabilized at pH 6 in Tris-hydrochloric acid buffer by the addition of cupric ion. The inhibitory function of some reagents, especially that of potassium permanganate, and acetylation of the enzyme revealed that the tyosine residue in this enzyme protein might play some important role in the enzyme activity. Lotus seed protease was found to be fairly similar to pepsin in some properties.     

Studies on the d-Xylose Series

Methyl 2-O-acetyl-3-O-methanesulfonyl-5-O-benzyl-d-xylofuranoside (X) was prepared from 1,2-O-isopropylidene-d-xylofuranose.

Solvolysis of X in methyl cellosolve in the presence of sodium acetate trihydrate gave a mixture of three pentose derivatives (xylose, arabinose and ribose). Formation of cis-2,3-diol compound (ribose) is supposed to be specific to furanose ring because solvolysis of 3-sulfonyl ester in pyranose ring, having trans-2-acetoxyl group, gave no cis-2,3-diol Compound.     

Increased bone mass in mice after single injection of anti-receptor activator of nuclear factor-kappaB ligand-neutralizing antibody: evidence for bone anabolic effect of parathyroid hormone in mice with few osteoclasts

Receptor activator of nuclear factor-κB ligand (RANKL) is a pivotal osteoclast differentiation factor. To investigate the effect of RANKL inhibition in normal mice, we prepared an anti-mouse RANKL-neutralizing monoclonal antibody (Mab, clone OYC1) and established a new mouse model with high bone mass induced by administration of OYC1. A single subcutaneous injection of 5 mg/kg OYC1 in normal mice significantly augmented the bone mineral density in the distal femoral metaphysis from day 2 to day 28. The OYC1 treatment markedly reduced the serum level of tartrate-resistant acid phosphatase-5b (TRAP-5b, a marker for osteoclasts) on day 1, and this level was undetectable from day 3 to day 28. The serum level of alkaline phosphatase (a marker for osteoblasts) declined significantly following the reduction of TRAP-5b. Histological analysis revealed few osteoclasts in femurs of the treated mice on day 4, and both osteoclasts and osteoblasts were markedly diminished on day 14. Daily injection of parathyroid hormone for 2 weeks increased the bone mineral density in trabecular and cortical bone by stimulating bone formation in the OYC1-treated mice. These results suggest that parathyroid hormone exerted its bone anabolic activity in mice with few osteoclasts. The mouse anti-RANKL neutralizing antibody OYC1 may be a useful tool to investigate unknown functions of RANKL in vivo.     

Photomicronucleus assay of phototoxic and pseudophotoclastogenic chemicals in human keratinocyte NCTC2544 cells

Photochemical genotoxicity was evaluated in human keratinocyte NCTC2544 cells. The cells were pre-treated with photogenotoxic or pseudophotoclastogenic chemicals and irradiated with a solar-simulator for 50min at a total UV dose of 5J/cm(2) or placed in the dark for the same period. After washing, the cells were cultured for 1.5-2 cell cycles with fresh culture medium. At the end of culturing, slide specimens were prepared and examined for micronucleus formation. 8-Methoxypsoralen, a photogenotoxic chemical, strongly induced micronucleated cells with UV irradiation but not under non-irradiation conditions. Therefore, NCTC2544 cells were subjected to further investigation to evaluate the possible photogenotoxicity of other chemicals. 6-Methylcoumarin, 3,3',4',5-tetrachlorosalicylanilide and protoporphyrin IX disodium salt, which are all known phototoxic substances, induced micronucleated cells with irradiation but not in the non-irradiation state. These phototoxic substances were confirmed to be photogenotoxic. Tetrabenzoporphine and 5-aminolevulinic acid, which are used for photodynamic therapy, showed phototoxicity. However, these chemicals did not induce micronucleated cells in the irradiated or non-irradiated state, suggesting a lack of photogenotoxicity. Among 3 pseudophotoclastogenic chemicals having no light absorbance at 290-700nm, neither cycloheximide nor disulfoton induced micronucleated cells with or without irradiation; zinc oxide induced micronucleated cells with irradiation and, to a lesser extent, without irradiation. Based on the results of the photogenotoxicity assays of these 9 chemicals, NCTC2544 cells are considered to be a suitable test system to evaluate the photogenotoxic potential of chemicals.     

A protein from a parasitic microorganism, Rickettsia prowazekii, can cleave the signal sequences of proteins targeting mitochondria

The obligate intracellular parasitic bacteria rickettsiae are more closely related to mitochondria than any other microbes investigated to date. A rickettsial putative peptidase (RPP) was found to resemble the alpha and beta subunits of mitochondrial processing peptidase (MPP), which cleaves the transport signal sequences of mitochondrial preproteins. RPP showed completely conserved zinc-binding and catalytic residues compared with beta-MPP but barely contained any of the glycine-rich loop region characteristic of alpha-MPP. When the biochemical activity of RPP purified from a recombinant source was analyzed, RPP specifically hydrolyzed basic peptides and presequence peptides with frequent cleavage at their MPP-processing sites. Moreover, RPP appeared to activate yeast beta-MPP so that it processed preproteins with shorter presequences. Thus, RPP behaves as a bifunctional protein that could act as a basic peptide peptidase and a somewhat regulatory protein for other protein activities in rickettsiae. These are the first biological and enzymological studies to report that a protein from a parasitic microorganism can cleave the signal sequences of proteins targeted to mitochondria.