Vitamin D receptor gene variability as a factor influencing bone mineral density in pediatric patients

To determine the relationship between the polymorphism of vitamin D receptor gene and the bone mineral density in children. The study group consisted of 395 children aged 6–18 years. All patients underwent genotyping using the PCR-RFLP method within polymorphic loci BsmI (rs1544410), FokI (rs2228570), ApaI (rs7975232) and Taq I (rs731236) of the VDR gene. The BMD (g/cm², Z score) and BMC (g, Z score) by DXA method, as well as Z scores of the BUA, SOS and Stiffness ultrasound parameters were evaluated. Based on densitometry results, children were divided into 3 groups: I—Z score ± 1.0; II—Z score from −1.1 to −2.0; and III—Z score ≤ −2.1. A control group numbering 294 children was used for the purpose of allele frequency comparisons. The occurrence of studied polymorphism alleles in the control group did not significantly differ from the values expected according to the Hardy–Weinberg equilibrium (p values: 0.1224 for BsmI; 0.5958 for TaqI; 0.0817 for ApaI; and 0.8901 for FokI). Allele a ApaI carrier status in group III children was associated with an increased BMD (x = 0.8 vs 0.69, p = 0.0296) and BMC value (x = 28.76 vs 22.14, p = 0.0565) in spine projection results, Stiffness (x = −1.12 vs −1.91, p = 0.0347) and SOS (x = −1.43 vs −2.27, p = 0.0319) ultrasound parameters. In group II, significantly increased SOS values (−1.13 vs −1.73, p = 0.0378) were noted in f (FokI) carriers. The presence of aa ApaI and ff FokI polymorphisms favours a higher bone mass and better bone structure (decreased bone mass loss) in the analysed group.     

Production of bioactive phenolic acids and furanocoumarins in in vitro cultures of Ruta graveolens L. and Ruta graveolens ssp. divaricata (Tenore) Gams. under different light conditions

Extracts from the biomass of Ruta graveolens and Ruta graveolens ssp. divaricata cultured in vitro under different light conditions (far-red, red and blue light, UV-A irradiation, in darkness and white light) were tested for the amounts of free phenolic acids and cinnamic acid (twelve compounds) as well as furanocoumarins and umbelliferone (seven compounds) using HPLC methods. Total amounts of the investigated groups of compounds in the cultures of both plants increased from 2.6 to 6.7 times, depending on light quality, and the maximum values reached were 106.50 and 1,276.74?mg?100?g^?1 DW (in R. graveolens), and 106.97 and 262.54?mg?100?g^?1 DW (in the subspecies), respectively. Both white light and blue light were equally beneficial for the total production of phenolic acids in cultures of both plants, whereas the total production of furanocoumarins was clearly better stimulated by blue light in R. graveolens and by darkness in the subspecies (i.e. the amounts were respectively 1.44 and 1.7 times higher than in the biomass cultivated under white light). The amounts of individual compounds in both plant cultures increased from about 2.2 to 26.3 times depending on light quality. The following bioactive compounds were obtained in quantities which are of interest from a practical perspective: in R. graveolens culture??protocatechuic acid (45?mg?100?g^?1 DW), isopimpinellin (about 500?mg?100?g^?1 DW) and bergapten (about 270?mg?100?g^?1 DW), and in the subspecies culture: p-coumaric acid (70?mg?100?g^?1 DW) and isopimpinellin (about 210?mg?100?g^?1 DW).     

Oriented immobilization of the tobacco etch virus protease for the cleavage of fusion proteins

The tobacco etch virus (TEV) protease is a useful tool for the removal of fusion tags from recombinant proteins. The difficulty in obtaining this enzyme led us to look for an optimal method for its use. In this work, we produced both the wild-type and the S219V mutant TEV proteases fused to the Streptag II affinity sequence (Streptag II-TEV(WT), and Streptag II-TEV(S219V), respectively). The two enzymes were affinity immobilized on a streptavidin-agarose matrix and compared to their respective free forms. Both immobilized Streptag II-TEV(WT) and Streptag II-TEV(S219V) were active on the 74-kDa Streptag II substrate with a retained activity of 83.5% and 81%, respectively compared to their free corresponding forms. The slight enzyme activity decrease caused by the immobilization was balanced by the enhanced stability and the successful repetitive use of the proteolytic columns. Thus, the wild-type and the mutant immobilized proteases were used, during a period of 18 months, for nine batch reactions with retention of 38% and 51% of their initial activities, respectively. The present results demonstrate that immobilized TEV protease on streptavidin-agarose is an attractive and efficient tool for fusion protein cleavage, especially when the target protein is fused to a streptagged fusion partner. Using this strategy, the total process can be shortened by performing the cleavage and the recovery of the purified target protein in one step.     

Effect of cellulose physical characteristics, especially the water sorption value, on the efficiency of its hydrolysis catalyzed by free or immobilized cellulase

Cellulase, an enzymatic complex that synergically promotes the degradation of cellulose to glucose and cellobiose, free or adsorbed onto Si/SiO₂ wafers at 60 °C has been employed as catalyst in the hydrolysis of microcrystalline cellulose (Avicel), microcrystalline cellulose pre-treated with hot phosphoric acid (CP), cotton cellulose (CC) and eucalyptus cellulose (EC). The physical characteristics such as index of crystallinity (I_C), degree of polymerization (DP) and water sorption values were determined for all samples. The largest conversion rates of cellulose into the above-mentioned products using free cellulase were observed for samples with the largest water sorption values; conversion rates showed no correlation with either I_C or DP of the biopolymer. Cellulose with large water sorption value possesses large pore volumes, hence higher accessibility. The catalytic efficiency of immobilized cellulase could not be correlated with the physical characteristics of cellulose samples. The hydrolysis rates of the same cellulose samples with immobilized cellulase were lower than those by the free enzyme, due to the diffusion barrier (biopolymer chains approaching to the immobilized enzyme) and less effective contact between the enzyme active site and its substrate. Immobilized cellulase, unlike its free counterpart, can be recycled at least six times without loss of catalytic activity, leading to higher overall cellulose conversion.     

BIND – An algorithm for loss-less compression of nucleotide sequence data

Recent advances in DNA sequencing technologies have enabled the current generation of life science researchers to probe deeper into the genomic blueprint. The amount of data generated by these technologies has been increasing exponentially since the last decade. Storage, archival and dissemination of such huge data sets require efficient solutions, both from the hardware as well as software perspective. The present paper describes BIND-an algorithm specialized for compressing nucleotide sequence data. By adopting a unique 'block-length' encoding for representing binary data (as a key step), BIND achieves significant compression gains as compared to the widely used general purpose compression algorithms (gzip, bzip2 and lzma). Moreover, in contrast to implementations of existing specialized genomic compression approaches, the implementation of BIND is enabled to handle non-ATGC and lowercase characters. This makes BIND a loss-less compression approach that is suitable for practical use. More importantly, validation results of BIND (with real-world data sets) indicate reasonable speeds of compression and decompression that can be achieved with minimal processor/ memory usage. BIND is available for download at http://metagenomics.atc.tcs.com/compression/BIND. No license is required for academic or non-profit use.     

Klotho coreceptors inhibit signaling by paracrine fibroblast growth factor 8 subfamily ligands

It has been recently established that Klotho coreceptors associate with fibroblast growth factor (FGF) receptor tyrosine kinases (FGFRs) to enable signaling by endocrine-acting FGFs. However, the molecular interactions leading to FGF-FGFR-Klotho ternary complex formation remain incompletely understood. Here, we show that in contrast to αKlotho, βKlotho binds its cognate endocrine FGF ligand (FGF19 or FGF21) and FGFR independently through two distinct binding sites. FGF19 and FGF21 use their respective C-terminal tails to bind to a common binding site on βKlotho. Importantly, we also show that Klotho coreceptors engage a conserved hydrophobic groove in the immunoglobulin-like domain III (D3) of the "c" splice isoform of FGFR. Intriguingly, this hydrophobic groove is also used by ligands of the paracrine-acting FGF8 subfamily for receptor binding. Based on this binding site overlap, we conclude that while Klotho coreceptors enhance binding affinity of FGFR for endocrine FGFs, they actively suppress binding of FGF8 subfamily ligands to FGFR.     

Distributional change and epidemic introgression in overlapping areas of Japanese pond frog species over 30 years

Pelophylax nigromaculatus, P. porosus porosus, and P. p. brevipoda are three pond frog species distributed in Japan. Their distributions overlap at two basins in central Japan (P. nigromaculatus and P. p. porosus in the Matsumoto basin, and P. nigromaculatus and P. p. brevipoda in the Ina basin), and hybrid descendants have been found in these areas. To clarify the distribution areas and hybrid zones of the frogs, and to understand the mode of introgressive hybridization and its impact on the frog populations, we conducted exhaustive sampling at each basin and performed allozyme and mtDNA analyses of 233 individuals. Analysis using genetic markers clearly detected nine F1 hybrids and 94 hybrid descendants of P. nigromaculatus and P. porosus from the overlapping areas of both basins. Allozyme and mtDNA data suggest directional hybridization between female P. p. porosus and male P. nigromaculatus in the Matsumoto basin. Over the past 30 years, the distribution of P. p. porosus has been narrowed and fragmented by the invasion of P. nigromaculatus, seemingly because of directional hybridization in the Matsumoto basin. In the Ina basin, the "pure" P. p. brevipoda (n = 8) population was extremely reduced by gene introgression from P. nigromaculatus, yet its distribution was barely changed compared to the Matsumoto basin. Consequently, this study shows that P. porosus populations are threatened by interspecific hybridization with P. nigromaculatus, and that introgressive hybridization damaged P. porosus populations by different means in each basin.     

Floral structure and pollen morphology of two zinc violets (Viola lutea ssp. calaminaria and V. lutea ssp. westfalica) indicate their taxonomic affinity to Viola lutea

Two zinc violets, the yellow form of the Aachen–Liège area and the blue morph of Blankenrode in western Westphalia, have very restricted occurrence on heavy metal waste heaps. Their taxonomic affinities have not been finally resolved. The flower micromorphological analysis presented here indicates that both zinc violets are closely related to the alpine Viola lutea, in line with our earlier published molecular data, but not with the conclusions of other authors. The zinc violets are classed at the rank of subspecies as V. lutea: ssp. calaminaria for the yellow zinc violet and ssp. westfalica for its blue counterpart. Although the violets examined (V. lutea, V. lutea ssp. calaminaria, V. lutea ssp. westfalica) are closely related, there is no evidence that V. lutea ssp. westfalica is a descendent of V. tricolor. Here we provide the most detailed information on generative organ structure in the four violets studied.