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Applied Entomology and Zoology -     

Acetylated Histone H3K9 is associated with meiotic recombination hotspots,and plays a role in recombination redundantly with other factors including the H3K4 methylase Set1 in fission yeast

Histone modifications are associated with meiotic recombination hotspots, discrete sites with augmented recombination frequency. For example, trimethylation of histone H3 lysine4 (H3K4me3) marks most hotspots in budding yeast and mouse. Modified histones are known to regulate meiotic recombination partly by promoting DNA double-strand break (DSB) formation at hotspots, but the role and precise landscape of involved modifications remain unclear. Here, we studied hotspot-associated modifications in fission yeast and found general features: acetylation of H3 lysine9 (H3K9ac) is elevated, and H3K4me3 is not significantly enriched. Mutating H3K9 to non-acetylatable alanine mildly reduced levels of the DSB-inducing protein Rec12 (the fission yeast homologue of Spo11) and DSB at hotspots, indicating that H3K9ac may be involved in DSB formation by enhancing the interaction between Rec12 and hotspots. In addition, we found that the lack of the H3K4 methyltransferase Set1 generally increased Rec12 binding to chromatin but partially reduced DSB formation at some loci, suggesting that Set1 is also involved in DSB formation. These results suggest that meiotic DSB formation is redundantly regulated by multiple chromatin-related factors including H3K9ac and Set1 in fission yeast.     

Native-State Heterogeneity of β2-Microglobulin as Revealed by Kinetic Folding and Real-Time NMR Experiments

The kinetic folding of β₂-microglobulin from the acid-denatured state was investigated by interrupted-unfolding and interrupted-refolding experiments using stopped-flow double-jump techniques. In the interrupted unfolding, we first unfolded the protein by a pH jump from pH 7.5 to pH 2.0, and the kinetic refolding assay was carried out by the reverse pH jump by monitoring tryptophan fluorescence. Similarly, in the interrupted refolding, we first refolded the protein by a pH jump from pH 2.0 to pH 7.5 and used a guanidine hydrochloride (GdnHCl) concentration jump as well as the reverse pH jump as unfolding assays. Based on these experiments, the folding is represented by a parallel-pathway model, in which the molecule with the correct Pro32 cis isomer refolds rapidly with a rate constant of 5–6 s^? 1, while the molecule with the Pro32 trans isomer refolds more slowly (pH 7.5 and 25 °C). At the last step of folding, the native-like trans conformer produced on the latter pathway isomerizes very slowly (0.001–0.002 s^? 1) into the native cis conformer. In the GdnHCl-induced unfolding assays in the interrupted refolding, the native-like trans conformer unfolded remarkably faster than the native cis conformer, and the direct GdnHCl-induced unfolding was also biphasic, indicating that the native-like trans conformer is populated at a significant level under the native condition. The one-dimensional NMR and the real-time NMR experiments of refolding further indicated that the population of the trans conformer increases up to 7–9% under a more physiological condition (pH 7.5 and 37 °C).     

The Molten Globule of β2-Microglobulin Accumulated at pH 4 and Its Role in Protein Folding

The acid transition of β₂-microglobulin (β2m) was studied by tryptophan fluorescence, peptide circular dichroism, and NMR spectroscopy. The protein exhibits a three-state transition with an equilibrium intermediate accumulated at pH 4 (25 °C). The pH 4 intermediate has typical characteristics of the molten globule (MG) state; it showed a native-like secondary structure without specific side-chain tertiary structure, and the hydrodynamic radius determined by pulse field gradient NMR was only 20% larger than that of the native state. The accumulation of the pH 4 intermediate is very analogous to the behavior of apomyoglobin, for which the pH 4 MG has been well characterized, although β2m, a β-protein, is structurally very different from α-helical apomyoglobin. NMR pH titration of histidine residues of β2m has also indicated that His84 has an abnormally low pK_a value in the native state. From the pH dependence of the unfolding transition, the protonations of this histidine and 10 weakly abnormal carboxylates triggered the transition from the native to the MG state. This behavior is again analogous to that of apomyoglobin, suggesting a common mechanism of production of the pH 4 MG. In contrast to the folding of apomyoglobin, in which the MG was equivalent to the burst-phase kinetic folding intermediate, the burst-phase refolding intermediate of β2m, detected by stopped-flow circular dichroism, was significantly more structured than the pH 4 intermediate. It is proposed that the folding of β2m from its acid-denatured state takes place in the following order: denatured state → MG → burst-phase intermediate → native state.     

Denitrification in soil amended with thermophile-fermented compost suppresses nitrate accumulation in plants

NO ₃ ^? is a major nitrogen source for plant nutrition, and plant cells store NO ₃ ^? in their vacuoles. Here, we report that a unique compost made from marine animal resources by thermophiles represses NO ₃ ^? accumulation in plants. A decrease in the leaf NO ₃ ^? content occurred in parallel with a decrease in the soil NO ₃ ^? level, and the degree of the soil NO ₃ ^? decrease was proportional to the compost concentration in the soil. The compost-induced reduction of the soil NO ₃ ^? level was blocked by incubation with chloramphenicol, indicating that the soil NO ₃ ^? was reduced by chloramphenicol-sensitive microbes. The compost-induced denitrification activity was assessed by the acetylene block method. To eliminate denitrification by the soil bacterial habitants, soil was sterilized with γ irradiation and then compost was amended. After the 24-h incubation, the N₂O level in the compost soil with presence of acetylene was approximately fourfold higher than that in the compost soil with absence of acetylene. These results indicate that the low NO ₃ ^? levels that are often found in the leaves of organic vegetables can be explained by compost-mediated denitrification in the soil.     

Studies on Oxygen Transfer in Submerged Fermentations

The unsteady-state gas analysis method for the determination of oxygen transfer rate in shaken cultures was applied to the glutamic acid fermentation. This method was essentially based on the measurement of oxygen tension of gas phase in flasks. Major intentions of this application were to clarify the problems of oxygen transfer, to establish the measure of aeration effectiveness and to design the best aeration condition in the glutamic acid fermentation. Correlations of the fermentation to the level of dissolved oxygen, the rate of oxygen transfer, overall oxygen transfer coefficient and oxygen demand of cells were examined. As a measure of aeration effectiveness, the rate of oxygen transfer actually occurring in the fermentation seemed to be preferable, and was found to be above 7 × 10^?7 mol/ml-min for attaining the maximum productivity. Extremely high or low oxygen supply resulted in less productivity.     

Epiderstatin and Its Related Glutarimide Antibiotics Inhibit the Cell Growth Induced by Mitogen Stimulation

To investigate the immunosuppressive effects of glutarimide antibiotics including a new antibiotic named epiderstatin, we tested these antibiotics for inhibition of the blastogenesis of mouse spleen cells induced by mitogen stimulation (concanavalin A or lipopolysaccharide). The inhibitory activity was measured by colorimetric MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay. Among the glutarimide antibiotics tested, epiderstatin and acetoxycycloheximide especially strongly inhibited the blastogenesis of mouse spleen cells induced by concanavalin A and lipopolysaccharide, however, selectivity between T and B lymphocytes was not observed.     

Solid State 13C-NMR Analysis of Cell Wall Components of Fusarium oxysporum

An abdominal fat accumulation complicated by high blood triglycerides is regarded as a risk factor of metabolic syndrome. Feeding powdered nacre, mother of pearl, from Pinctada maxima, resulted in reduced body weight, visceral fat amount, and blood triglyceride level without influencing the food intake, body length, or amount of muscular tissue, suggesting that nacre powder specifically could decrease visceral fat.     

A New Metabolite,Parasiticolide A,from Aspergillus parasiticus

Two β-glucosidases, G1 and G2, were purified from the culture supernatant of Penicillium herquei Banier and Sartory. Both the purified enzymes were homogeneous on polyacrylamide disc gel electrophoresis. The molecular weights of G1 and G2 were estimated to be 125,000 and 122,000, respectively, by sodium dodecyl sulfate-polyacrylamide slab gel electrophoresis. G1 and G2 contained 12.7% and 16.1% carbohydrate as glucose, and had isoelectric points of 5.02 and 5.24, respectively. Both enzymes had optimum pHs of 4.0~4.5 and optimum temperatures at 60°C, but pH - and thermo-stabilities of G1 were higher than those of G2. Both enzymes were active not only on p-nitrophenyl β-d-glucopyranoside, salicin, and the p-glucobioses tested but also on laminarin. CM-Cellulose was a very poor substrate for both enzymes. The activities of G1 toward the substrates except for laminarin and CM-cellulose were apparently higher than those of G2. Both enzymes acted on cellobiose to produce a transfer product.     

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing

Background

Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast. However, SAMtools requires an additional implementation to be used in parallel with, for example, OpenMP (Open Multi-Processing) libraries. For the accumulation of next-generation sequencing data, a simple parallelization program, which can support cloud and PC cluster environments, is required.

Results

We have developed cljam using the Clojure programming language, which simplifies parallel programming, to handle SAM/BAM data. Cljam can run in a Java runtime environment (e.g., Windows, Linux, Mac OS X) with Clojure.

Conclusions

Cljam can process and analyze SAM/BAM files in parallel and at high speed. The execution time with cljam is almost the same as with SAMtools. The cljam code is written in Clojure and has fewer lines than other similar tools.