Nucleosome compaction facilitates HP1γ binding to methylated H3K9

The α, β and γ isoforms of mammalian heterochromatin protein 1 (HP1) selectively bind to methylated lysine 9 of histone H3 via their chromodomains. Although the phenotypes of HP1-knockout mice are distinct for each isoform, the molecular mechanisms underlying HP1 isoform-specific function remain elusive. In the present study, we found that in contrast to HP1α, HP1γ could not bind tri-methylated H3 lysine 9 in a reconstituted tetra-nucleosomes when the nucleosomes were in an uncompacted state. The hinge region connecting HP1''s chromodomain and chromoshadow domain contributed to the distinct recognition of the nucleosomes by HP1α and HP1γ. HP1γ, but not HP1α, was strongly enhanced in selective binding to tri-methylated lysine 9 in histone H3 by the addition of Mg²⁺ or linker histone H1, which are known to induce compaction of nucleosomes. We propose that this novel property of HP1γ recognition of lysine 9 in the histone H3 tail in different nucleosome structures plays a role in reading the histone code.     

Isolation of soil bacteria able to hydrolyze both organophosphate and carbamate pesticides

Two bacteria identified as Pseudomonas putida and Acinetobacter rhizosphaerae able to rapidly degrade the organophosphate (OP) fenamiphos (FEN) were isolated. Denaturating gradient gel electrophoresis analysis revealed that the two isolates were dominant members of the enrichment culture. Clone libraries further showed that bacteria belonging to α-, β-, γ-proteobacteria and Bacteroidetes were also present in the final enrichment but were not isolated. Both strains hydrolyzed FEN to fenamiphos phenol which was further transformed, only by P. putida. The two strains were using FEN as C and N source. Cross-feeding studies with other pesticides showed that P. putida degraded OPs with a P-O-C linkage and unexpectedly degraded the carbamates oxamyl and carbofuran being the first wild-type bacterial strain able to degrade both OPs and carbamates. The same isolate exhibited high bioremediation potential against spillage-level concentrations of aged residues of FEN and its oxidized derivatives.     

The effect of rapamycin on DNA synthesis in multiple tissues from late gestation fetal and postnatal rats

Rapamycin is a potent antiproliferative agent that arrests cells in the G1 phase of the cell cycle through a variety of mechanisms involving the inhibition of the mammalian target of rapamycin (mTOR) pathway. The majority of normal cells in culture are sensitive to the cytostatic effects of rapamycin, whereas the growth of many malignant cells and tumors is rapamycin resistant. We had shown previously that hepatic DNA synthesis in the late gestation rat fetus is rapamycin resistant even though signaling through the mTOR/S6 kinase (S6K) pathway is attenuated. On the basis of this finding, we went on to characterize the response to rapamycin in a spectrum of tissues during late gestation and the early postnatal period in the rat. We found that rapamycin had no effect on DNA synthesis in major organs such as heart, intestine, and kidney in the fetal and early postnatal rat despite a marked attenuation in the phosphorylation of ribosomal protein S6. In contrast, the proliferation of mature hepatocytes during liver regeneration was highly sensitive to rapamycin. These data indicate that basal cellular proliferation in a wide variety of tissues is rapamycin resistant and occurs independently of mTOR/S6K signaling. Furthermore, the well-characterized effects of rapamycin in tissue culture systems are not recapitulated in the asynchronous cell proliferation that accompanies normal growth and tissue remodeling.     

Isolation and characterization of a biosurfactant from Deinococcus caeni PO5 using jackfruit seed powder as a substrate

Biosurfactant-producing bacteria were isolated from various sources in the south of Thailand. Isolates were screened for biosurfactant production using jackfruit seed powder (JSP) as a novel and promising substrate. The highest biosurfactant activity was obtained with a bacterial strain which was identified by 16S rRNA gene sequence analysis as Deinococcus caeni PO5. D. caeni PO5 was able to grow and reduce the surface tension of the culture supernatant from 67.0 to 25.0 mN/m after 87 h of cultivation when 40 g/l of JSP and 1 g/l of commercial monosodium glutamate were used as carbon and nitrogen sources, respectively. The biosurfactant obtained by ethyl acetate extraction showed high surface tension reduction (47.0 mN/m), a small critical micelle concentration value (8 mg/l), thermal and pH stability with respect to surface tension reduction and emulsification activity, and a high level of salt tolerance. Chemical characterization by biochemical testing, Fourier transform infrared spectroscopy, and mass spectra revealed that the obtained biosurfactant was a glycolipid-type biosurfactant. The obtained biosurfactant was capable of forming stable emulsions with various hydrocarbons and had the ability to enhance oil recovery, the solubility of polyaromatic hydrocarbons, heavy metal removal, and antimicrobial activity.     

Advances in the Diagnosis of Human Opisthorchiasis: Development of Opisthorchis viverrini Antigen Detection in Urine

Background

Many strategies to control opisthorchiasis have been employed in Thailand, but not in the other neighbouring countries. Specific control methods include mass drug administration (MDA) and health education to reduce raw fish consumption. These control efforts have greatly shifted the epidemiology of Opisthorchis viverrini (OV) infection over the last decade from presenting as densely concentrated "heavy" infections in single villages to widespread "light" OV infections distributed over wide geographical areas. Currently, the "gold standard" detection method for OV infection is formalin ethyl-acetate concentration technique (FECT), which has limited diagnostic sensitivity and diagnostic specificity for light OV infections, with OV eggs often confused with eggs of minute intestinal flukes (MIFs) in feces. In this study, we developed and evaluated the diagnostic performance of a monoclonal antibody-based enzyme-linked immunosorbent assay for the measurement of OV excretory-secretory (ES) antigens in urine (urine OV-ES assay) for the diagnosis of opisthorchiasis compared to the gold standard detection FECT method.

Methodology

We tested several methods for pre-treating urine samples prior to testing the diagnostic performance of the urine OV-ES assay. Using trichloroacetic acid (TCA) pre-treated urine, we compared detection and quantification of OV infection using the urine OV-ES assay versus FECT in OV-endemic areas in Northeastern Thailand. Receiver operating characteristic (ROC) curves were used to determine the diagnostic sensitivity and specificity of the urine OV-ES assay using TCA pre-treated urine, and to establish diagnostic positivity thresholds. The Positive Predictive Value as well as the likelihood of obtaining a positive test result (LR+) or a negative test result (LR-) were calculated for the established diagnostic positivity threshold. Diagnostic risks (Odds Ratios) were estimated using logistic regression.

Results

When urine samples were pre-treated with TCA prior to use in the urine OV-ES assay, the analytical sensitivity was significantly improved. Using TCA pre-treatment of urine, the urine OV-ES assay had a limit of detection (LoD) of 39 ng/ml compared to the LoD of 52 ng/mL reported for coprological antigen detection methods. Similarly, the urine OV-ES assay correlated significantly with intensity of OV infection as measured by FECT. The urine OV-ES assay was also able to detect 28 individuals as positive from the 63 (44.4%) individuals previously determined to be negative using FECT. The likelihood of a positive diagnosis of OV infection by urine OV-ES assay increased significantly with the intensity of OV infection as determined by FECT. With reference to FECT, the sensitivity and specificity of the urine OV-ES assay was 81% and 70%, respectively.

Conclusion

The detection of OV-infection by the urine OV-ES assay showed much greater diagnostic sensitivity and diagnostic specificity than the current "gold standard" FECT method for the detection and quantification of OV infection. Due to its ease-of-use, and noninvasive sample collection (urine), the urine OV-ES assay offers the potential to revolutionize the diagnosis of liver fluke infection and provide an effective tool for control and elimination of these tumorigenic parasites.     

Efficient concomitant production of lipids and carotenoids by oleaginous red yeast <Emphasis Type="Italic">Rhodotorula glutinis</Emphasis> cultured in palm oil mill effluent and application of lipids for biodiesel production

Rhodotorula glutinis TISTR 5159 is oleaginous red yeast that accumulates both lipids and carotenoids. It was cultured in palm oil mill effluent (POME) with only the addition of ammonium sulfate and Tween 20 as a suitable nitrogen source and surfactant, respectively. Response surface methodology (RSM) was applied to optimize initial chemical oxygen demand (COD) in POME, C/N ratio, and Tween 20 concentration for concomitant production of lipids and carotenoids. Among three investigated factors, C/N ratio contributed a significant effect upon lipid and carotenoids production. Analysis of response surface plots revealed that the optimum C/N ratio for the biomass was 140, while that for lipid content and carotenoids were higher at 180 and 170, respectively. The high level of the nitrogen source (with a low C/N ratio) enhanced the biomass, making the accumulation of lipids and carotenoids less preferable. Hence, the two-stage process was attempted as an optimal way for cell growth in the first stage and product accumulation in the second stage. The lipid yield and carotenoid production obtained in the two-stage process were higher than those in the one-stage process. In the semi-continuous fermentation, R. glutinis TISTR 5159 accumulated high lipid content and produced a considerably high concentration of carotenoids during long-term cultivation. Additionally, efficient COD removal by R. glutinis TISTR 5159 was observed. The biodiesel produced from yeast lipids was composed mainly of oleic and palmitic acids, similar to those from plant oil.