Elucidating the protein cold-adaptation: Investigation of the parameters enhancing protein psychrophilicity

To investigate the role of the critical parameters in adaptation of proteins to low temperatures, a comparative systematic analysis was performed. Several parameters were proposed to have contribution to cold adaptation of proteins. Among proposed parameters, total values of residual structure states, secondary structure states and oligomeric states were alike in both psychrophilic and mesophilic proteins. In addition, our results provided new quantitative information about the trends in the substitution preference of Ile, Phe, Tyr, Lys, Arg, His, Glu and Leu with most of amino acids and substitution avoidance of Gly, Thr and Ala with most of amino acids. These findings would help future efforts propose a strategy for designing psychrophilic proteins.     

Effect of Sugars, Surfactant, and Tangential Flow Filtration on the Freeze-Drying of Poly(lactic acid) Nanoparticles

Poly(d,l-lactic acid) nanoparticles were freeze-dried in this study. With respect to drying, effect of protective excipients and purification from excess surfactant were evaluated. The nanoparticles were prepared by the nanoprecipitation method with or without a surfactant, poloxamer 188. The particles with the surfactant were used as such or purified by tangential flow filtration. The protective excipients tested were trehalose, sucrose, lactose, glucose, poloxamer 188, and some of their combinations. The best freeze-drying results in terms of nanoparticle survival were achieved with trehalose or sucrose at concentrations 5% and 2% and, on the other hand, with a combination of lactose and glucose. Purification of the nanoparticle dispersion from the excess surfactant prior to the freeze-drying by tangential flow filtration ensured better drying outcome and enabled reduction of the amount of the protective excipients used in the process. The excess surfactant, if not removed, was assumed to interact with the protective excipients decreasing their protective mechanism towards the nanoparticles.     

Simultaneous measurement of retinol, alpha-tocopherol and six carotenoids in human plasma by using an isocratic reversed-phase HPLC method

A simple and sensitive isocratic reversed-phase high-performance liquid chromatography (HPLC) method for simultaneous determination of retinol, alpha-tocopherol and six carotenoids in human plasma was described. Sample preparation of the earlier published method was further developed by addition of ultrapure water, which enabled aqueous layer to freeze facilitating phase separation without pipetting thus also improving precision of the method. Developed method appeared to be less laborious and time consuming compared to the traditional extraction methods, which require removal of organic layer by pipetting. The recoveries (absolute and relative) were between 80% and 103%. The intra-assay CVs were 1.1-4.0% (normal level) and 3.3-9.0% (low level). Inter-assay CVs were 5.3-8.8%. Reference method for all these analytes was not available, but a comparison with another published method was carried out. The results of the comparison matched satisfactorily. The method is used routinely in our laboratory in a large population-based study.     

Biodegradation of two tetrameric lignin model compounds by a mixed bacterial culture

Summary The ability of a mixed bacterial culture to decompose two tetrameric lignin model com-pounds as a sole source of carbon and energy was investigated. The mixed bacterial culture con-sisted mainly of Gram negative rods. The tetram-ers contained two types of lignin substructures, namely the most abundant β-O-4 ether structure in lignin and also the 5-5 biphenyl structure. The tetramer (MW 638) containing two phe-nolic hydroxyls was decomposed readily; after 13 days of incubation, all intermediate products formed were almost totally decomposed. The non-phenolic tetramer (MW 666) was decom-posed much more slowly; after 53 days of incuba-tion, 5% of the substrate was unchanged. When both tetramers were degraded simultaneously, the non-phenolic tetramer was decomposed similarly to the phenolic tetramer. Determination of molecular weights of cata-bolic products showed that the degradation of the non-phenolic tetramer had proceeded at least to dimer level. SKF 525A, inhibitor of cytochrome P-450, caused one catabolic product to accumulate in the culture medium. This indicates involvement of cy-tochrome P-450 in the degradation pathway of the model compounds used. We conclude that this mixed bacterial culture was able to degrade the lignin model compounds used and that free phenolic groups seem to in-crease the biodegradability significantly.     

Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy

Vancomycin, a commonly used antibiotic, can be nephrotoxic. Known risk factors such as age, creatinine clearance, vancomycin dose / dosing interval, and concurrent nephrotoxic medications fail to accurately predict nephrotoxicity. To identify potential genomic risk factors, we performed a genome-wide association study (GWAS) of serum creatinine levels while on vancomycin in 489 European American individuals and validated findings in three independent cohorts totaling 439 European American individuals. In primary analyses, the chromosome 6q22.31 locus was associated with increased serum creatinine levels while on vancomycin therapy (most significant variant rs2789047, risk allele A, β = -0.06, p = 1.1 x 10^-7). SNPs in this region had consistent directions of effect in the validation cohorts, with a meta-p of 1.1 x 10^-7. Variation in this region on chromosome 6, which includes the genes TBC1D32/C6orf170 and GJA1 (encoding connexin43), may modulate risk of vancomycin-induced kidney injury.     

Localization of heat shock proteins in clinical Actinobacillus actinomycetemcomitans strains and their effects on epithelial cell proliferation

Actinobacillus actinomycetemcomitans is an important pathogen in periodontitis. In the present study we localized the GroEL- and DnaK-like heat shock proteins (Hsp) in subcellular fractions of 12 A. actinomycetemcomitans strains of various clinical origin and compared their effects on periodontal epithelial cell proliferation and viability. In all strains, GroEL-like protein was found in the membrane, cytoplasm, and periplasm, whereas DnaK-like protein was present in the cytoplasm and periplasm. No correlation was observed between the Hsp expression and the serotype or origin of A. actinomycetemcomitans strains. The bacterial membrane fractions that expressed the GroEL-like protein moderately or strongly induced epithelial cell proliferation more strongly than strains that expressed the protein weakly. The results suggest that GroEL-like Hsp may play a role in the virulence of A. actinomycetemcomitans by increasing epithelial proliferation.     

Studies on bucephalid digeneans parasitising molluscs and fishes in Finland. II. The description of Rhipidocotyle fennica n. sp. and its discrimination by principal components analysis

Rhipidocotyle fennica n. sp. (= Rhipidocotyle Type A of Taskinen et al., 1991) from the intestine of Esox lucius in central Finland is described and compared by means of a principal components analysis (PCA) with R. campanula (= Rhipidocotyle Type B of Taskinen et al., 1991). Its cercaria develops in the bivalve Anodonta anatina and the metacercaria occurs in the skin and fins of Rutilus rutilus. The metacercaria is discriminated from that of R. campanula by PCA and is described along with aspects of the chaetotaxy of the cercaria. The new species is distinguished from R. campanula, R. kovalae, R. papillosa and R. septpapillata.     

Dissolved iron:phosphate ratio as an indicator of phosphate release to oxic water of the inner and outer coastal Baltic Sea

Pore water concentrations and benthic fluxes of dissolved Fe, P and N were measured at two coastal basins in the Gulf of Finland, northern Baltic Sea, during a seasonal cycle. The bioturbated inner coastal basin, where exchange of near-bottom water is efficient, had a better ability to retain P in sediments than the outer basin, where near-bottom water O₂ concentration decreases during summer. Under the presence of O₂ high pore water dissolved Fe:P ratio (>3.6 w:w) in surface layer of the sediment, measured especially in winter, indicated negligible or low P-release and high N:P ratio in the efflux. On the contrary, low Fe:P ratio (<3.6), measured in summer and autumn, indicated high efflux of P and low N:P flux ratio. The low dissolved Fe:P ratio suggested that there was not enough diffusing Fe to form Fe³⁺ oxide-rich layer in the oxic surface zone of the sediments or near-bottom water to bind the P diffusing from the sediment. However, in sediments bioturbated by the abundant bivalve Macoma baltica, small efflux of P were measured almost throughout the study period. Thus, the Fe:P ratio cannot alone explain the P-release in bioturbated sediments. The low N:P ratio in the efflux measured in summer and autumn partly explains the measured low N:P ratio in the near-bottom water and thus N limitation of primary production in the Gulf. Additionally, it is evident that the release of P in the Gulf itself is of great importance for the trophic state of the Gulf of Finland.