A web services choreography scenario for interoperating bioinformatics applications

Background  

Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow.     

Chitosan isolation from the chitosan-glucan complex of fungal cell wall using amylolytic enzymes

The chitosan/glucan complex isolated from the mycelia of the fungus, Gongronella butleri USDB 0201 can be cleaved with a heat-stable -amylase at 65 °C for 3 h. This results in the removal of the glucan side chain and gives a chitosan solution with 100 times lower turbidity. It is proposed that chitosan and glucan chains are bound by an (1 to 4) glucosidic bond. Both fungal chitosan and fungal glucan have been purified separately.     

Sulfated chitin and chitosan as novel biomaterials

Chitin and chitosan are known to be natural polymers and they are non-toxic, biodegradable and biocompatible. Chemical modification of chitin and chitosan with sulfate to generate new bifunctional materials is of interest because the modification would not change the fundamental skeleton of chitin and chitosan, would keep the original physicochemical and biochemical properties and finally would bring new or improved properties. The sulfated chitin and chitosan have a variety of applications, such as, adsorbing metal ions, drug delivery systems, blood compatibility, and antibacterial field. The purpose of this review is to take a closer look about the different synthetic methods and potential applications of sulfated chitin and chitosan. Based on current research and existing products, some new and futuristic approaches in this context area are discussed in detail. From the studies reviewed, we concluded that sulfated chitin and chitosan are promising materials for biomedical applications.     

Immobilized pH gradient-driven paper-based IEF: a new method for fractionating complex peptide mixtures before MS analysis

Introduction  

The vast difference in the abundance of different proteins in biological samples limits the determination of the complete proteome of a cell type, requiring fractionation of proteins and peptides before MS analysis.     

Chitosan as a growth stimulator in orchid tissue culture

The effect of shrimp and fungal chitosan on the growth and development of orchid plant meristemic tissue in culture was investigated in liquid and on solid medium. The growth of meristem explants into protocorm-like bodies in liquid medium was accelerated up to 15 times in the presence of chitosan oligomer, the optimal concentration being 15 ppm. The 1 kDa shrimp oligomer was slightly more effective compared to 10 kDa shrimp chitosan and four times more active compared to high molecular weight 100 kDa shrimp chitosan. The 10 kDa fungal chitosan was more effective compared with 1 kDa oligomer. The development of orchid protocorm into differentiated orchid tissue with primary shoots and roots was studied on solid agar medium. The optimal effect, the generation of 5–7 plantlets in 12 weeks was observed in the presence of 20 ppm using either 10 kDa fungal or 1 kDa oligomer shrimp chitosan. The data are consistent with preliminary results from field experiments and confirm unequivocally that a minor amount of chitosan has a profound effect on the growth and development of orchid plant tissue.     

Variables associated with corneal confocal microscopy parameters in healthy volunteers: implications for diabetic neuropathy screening

Diabet. Med. 29, e297-e303 (2012) ABSTRACT: Aim Corneal confocal microscopy is a promising screening method for diabetic neuropathy. Although much research in this field has been accomplished, we aimed to determine and confirm the known clinical and eyewear variables associated with the parameters of corneal confocal microscopy specifically in healthy volunteers, in particular associations with corneal nerve fibre length. Methods Clinical characteristics, electrophysiological examination and a general clinical eye history were collected from 64 healthy volunteers. Corneal confocal microscopy was performed to determine corneal nerve fibre length, corneal nerve branch density, corneal nerve fibre density and tortuosity coefficient. Univariate and multivariate linear regression analysis was used to determine clinical variables associated with corneal nerve fibre length parameters. Results We observed that corneal nerve fibre length has a broad distribution in healthy volunteers (18?±?4?mm/mm(2) , 95% confidence interval, 12.3-25.7?mm/mm(2) ). Multivariate regression analysis demonstrated that HbA(1c) was the only independent clinical factor to account for variations in corneal nerve fibre length, independent of age and status of contact lens wear. Conclusions This study does not provide convincing evidence that corneal nerve fibre length is independently associated with age or the wearing of contact lenses, and that these factors are therefore unlikely to hinder valid screening for polyneuropathies such as diabetic neuropathy. Furthermore, the strong inverse association of corneal nerve fibre length with glycaemic exposure may support the use of this parameter to detect subclinical pre-diabetic nerve injury.     

Gibberellin-like substances and indole type auxins in developing grains of normal- and high-lysine genotypes of barley

Changes in gibberellin-like activity and content of indole type auxins were investigated during grain development of the two high-lysine barley (Hordeum vulgare L.) genotypes Sv 73608 and Risø 1508, and their corresponding normal cultivars Mona and Bomi. A peak in gibberellin-like activity was found in developing grains of the normal cultivars about 18 days after anthesis, whereas the grains of the high-lysine genotypes showed a two to five times higher maximum about 3–4 days later. The auxin content of the cultivar Bomi showed a maximum between the 22nd and the 29th day after anthesis, whereas, throughout their development the grains of the mutant Risø 1508 exhibited only about ¹/10 of the maximum level of auxin found in the grains of Bomi. The normal cultivar Mona also displayed higher contents of auxin than the high-lysine genotypes Sv 73608, particularly at the later stages of grain growth, but the differences in concentration were considerable smaller than for the pair ‘Bomi’—‘Risø 1508’. It is suggested that auxins play an important role in the development of barley grains.     

Metagenomic analysis of a stable trichloroethene-degrading microbial community

Dehalococcoides bacteria are the only organisms known to completely reduce chlorinated ethenes to the harmless product ethene. However, Dehalococcoides dechlorinate these chemicals more effectively and grow more robustly in mixed microbial communities than in isolation. In this study, the phylogenetic composition and gene content of a functionally stable trichloroethene-degrading microbial community was examined using metagenomic sequencing and analysis. For phylogenetic classification, contiguous sequences (contigs) longer than 2500 bp were grouped into classes according to tetranucleotide frequencies and assigned to taxa based on rRNA genes and other phylogenetic marker genes. Classes were identified for Clostridiaceae, Dehalococcoides, Desulfovibrio, Methanobacterium, Methanospirillum, as well as a Spirochete, a Synergistete, and an unknown Deltaproteobacterium. Dehalococcoides contigs were also identified based on sequence similarity to previously sequenced genomes, allowing the identification of 170 kb on contigs shorter than 2500 bp. Examination of metagenome sequences affiliated with Dehalococcoides revealed 406 genes not found in previously sequenced Dehalococcoides genomes, including 9 cobalamin biosynthesis genes related to corrin ring synthesis. This is the first time that a Dehalococcoides strain has been found to possess genes for synthesizing this cofactor critical to reductive dechlorination. Besides Dehalococcoides, several other members of this community appear to have genes for complete or near-complete cobalamin biosynthesis pathways. In all, 17 genes for putative reductive dehalogenases were identified, including 11 novel ones, all associated with Dehalococcoides. Genes for hydrogenase components (271 in total) were widespread, highlighting the importance of hydrogen metabolism in this community. PhyloChip analysis confirmed the stability of this microbial community.