Separation and purification of periplasmic cytochrome c553 using reversed micelles

Surfactant concentration, ionic strength, and pH were optimised for the selective separation and purification of periplasmic cytochrome c553 from recombinant E. coli TG2 cells using response surface methodology. Back-extraction was accomplished using counter-ionic surfactant addition. Optimum forward extraction conditions were: 65 mM bis(2-ethylhexyl)sulfosuccinate sodium salt (AOT), 0.07 M NaCl, and pH 8.4, while the optimum back-extraction conditions were 80 mM trioctylmethylammonium chloride, 0.85 M KCl, and pH 9.62. In comparison to a conventionally purified sample using column chromatography (10 mg cytochrome c553 l–1 with a purity of 0.66), reverse micelles achieved the same concentration and similar purity (0.50) in only two simple steps.     

The effect of demulsifiers on lysozyme extraction from hen egg white using reverse micelles

The liquid–liquid extraction of protein from buffered aqueous phases using reverse micelles (RM) has been extensively researched from a fundamental point of view. However, very little effort has been expended at scaling up this process for the extraction of real fermentation broth. When real broths are used with reverse micellar phases there are major problems with emulsion formation. In this study the effect of a variety of demulsifiers on lysozyme extraction was evaluated in terms of their influence on the separating properties of the emulsion, water content (W _o ), and, extraction yield and kinetics from both buffer and hen egg white. In addition, the use of a low shear contactor (a Graesser or `raining bucket') was assessed in terms of its suitability as a RM contactor. It was found that most of the demulsifiers reduced the settling time of the emulsion, and enhanced the yield and kinetics of lysozyme extraction from hen egg white. It was hypothesised that this was due to the demulsifier displacing the lysozyme from the interface and preventing the protein unfolding and precipitating. This effect was found to depend on both the generic type of demulsifier, and its concentration.     

Fold prediction problem: the application of new physical and physicochemical-based features

One of the most important goals in bioinformatics is the ability to predict tertiary structure of a protein from its amino acid sequence. In this paper, new feature groups based on the physical and physicochemical properties of amino acids (size of the amino acids' side chains, predicted secondary structure based on normalized frequency of β-Strands, Turns, and Reverse Turns) are proposed to tackle this task. The proposed features are extracted using a modified feature extraction method adapted from Dubchak et al. To study the effectiveness of the proposed features and the modified feature extraction method, AdaBoost.M1, Multi Layer Perceptron (MLP), and Support Vector Machine (SVM) that have been commonly and successfully applied to the protein folding problem are employed. Our experimental results show that the new feature groups altogether with the modified feature extraction method are capable of enhancing the protein fold prediction accuracy better than the previous works found in the literature.     

Gene expression and characterization of a serine proteinase inhibitor PmSERPIN8 from the black tiger shrimp Penaeus monodon

The ubiquitous SERPINs or serine proteinase inhibitors are essential for controlling proteinases in several biological processes in various organisms. A PmSERPIN8, one of eight SERPINs identified from the Penaeus monodon database, is studied and reported herein. The open reading frame of PmSERPIN8 gene derived from a genomic gene contains 5 exons of 320, 139, 244, 239 and 312 bp separated by 4 introns of 447, 657, 326 and 479 bp. The PmSERPIN8 gene is highly expressed at nauplius stage and gradually subsided as the shrimp grow through zoea, mysis and postlarva stages. At sub-adult stage, the PmSERPIN8 gene is expressed mainly in the hemocyte and epipodite. The expression in response to Vibrio harveyi and YHV injection is up-regulated, respectively, at 24 and 48 h post-injection. The number of PmSERPIN8-producing hemocytes, however, is observed highest at 48 h post V. harveyi injection. All three hemocyte cell types: hyaline, semigranular and granular hemocytes are able to produce PmSERPIN8. The recombinant mature PmSERPIN8 (rPmSERPIN8) with a predicted size of 45.5 kDa was over-produced in an Escherichia coli system, solubilized from the inclusion bodies, purified and tested for its activity. We have found that the rPmSERPIN8 is able to inhibit the growth of Gram-positive bacterium, Bacillus subtilis, but not Gram-negative bacterium, V. harveyi 639, and inhibit the shrimp prophenoloxidase system. The PmSERPIN8 is, thus, involved in the shrimp innate immunity.     

High interannual variation in the diet of a tropical forest frugivore (Hylobates lar)

Frugivores must deal with seasonal changes in fruit availability and changes from year to year, as most species of tropical forest fruiting trees have considerable interannual variation in phenology and many are mast fruiters. We quantified seasonal and interannual changes in the fruit diet in a frugivore and important seed disperser, the white‐handed gibbon, Hylobates lar, in Thailand. We used 40‐d following data during April and May replicated in six consecutive years to study interannual variability in the diet and compared it with seasonal changes measured in monthly samples of the same size collected in three successive years. The 40‐d periods of following also allowed us to measure the decline in dietary similarity with time over a finer scale. We measured fruit diet similarity between replicated 5‐d periods using the percentage overlap (Renkonen's) index and Jaccard's similarity index. Seasonally, average dietary overlap between adjacent months was low, and similarity approached zero after four months. Average rate of decline in similarity exceeded 20 percent per 5‐d period. Variation in fruit species in the diet between years was high and was correlated with interannual variation in fruiting phenology. The strongest correlation occurred in the case of Nephelium melliferum, a highly preferred species that dominated the diet in good fruiting years. It is difficult to separate changes in food species preference from changes in availability from year to year. We devised a relative measure of preference that depends on the degree to which the gibbons rely on prior knowledge to find sources.     

Silvaglins and related 2,3-secodammarane derivatives - unusual types of triterpenes from Aglaia silvestris

Lipophilic crude extracts of leaves, stem and root bark of six different provenances of Aglaia silvestris were compared to determine species-specific chemical trends as well as infraspecific variability. 3,4-Secodammarane triterpenes formed the basic chemical equipment accompanied by the 2,3-seco derivative aglasilvinic acid, probably representing the precursor of the silvaglin A and isosilvaglin A characterised by a five membered ring A. In addition, the pregnane steroid pregnacetal was isolated and identified together with the known sesquiterpenes α-muurolene and viridiflorol, and the bisamide pyramidatin. Depending on the collection site all major triterpenes showed two different stereochemical trends either towards 20R or 20S configuration, giving rise to isolation and identification of the two isomers methylisofoveolate B (20S,24R) and methylfoveolate B (20R,24S) as well as the known derivatives shoreic acid (20S,24R), isoeichlerianic acid (20R,24S), and methylisoeichleriate (20R,24S). The structures were elucidated by 2D-NMR experiments and silvaglin A additionally by X-ray diffraction. The structural diversity and distribution of triterpenoids within the genus Aglaia is highlighted with respect to chemotaxonomic implications.     

Bio-Mirror project for public bio-data distribution

Timely worldwide distribution of biosequence and bioinformatics data depends on high performance networking and advances in Internet transport methods. The Bio-Mirror project focuses on providing up-to-date distribution of this rapidly growing and changing data. It offers FTP, Web and Rsync access to many high-volume databanks from several sites around the world. Experiments with data grids and other methods offer future improvements in biology data distribution.