Structure of the Pyoverdin PVD 2908 – a new Pyoverdin from Pseudomonas sp. 2908

An unknown siderophore (pyoverdin) was isolated from the strain Pseudomonas sp. 2908. The structure of the pyoverdin – called PVD 2908 – was elucidated by spectroscopic methods and degradation studies. Some other siderophores were identified by LC/ESI-MS-screening based on the knowledge of PVD 2908.     

Optimization of cell growth and poly(3-hydroxybutyrate) accumulation on date syrup by a Bacillus megaterium strain

Optimal growth and PHB accumulation in Bacillus megaterium occurred with 5% (w/v) date syrup or beet molasses supplemented with NH₄Cl. When date syrup and beet molasses were used alone without an additional nitrogen source, a cell density of about 3gl^–1 with a PHB content of the cells of 50% (w/w) was achieved. NH₄NO₃ followed by ammonium acetate and then NH₄Cl supported cell growth up to 4.8gl^–1, whereas PHB accumulation was increased with NH₄Cl followed by ammonium acetate, NH₄NO₃ and then (NH₄)₂SO₄ to a PHB content of nearly 42% (w/w). Cultivation of B.megaterium at 30l scale gave a PHB content of 25% (w/w) of the cells and a cell density of 3.4gl^–1 after 14h growth.     

An Ensemble Method for Predicting Subnuclear Localizations from Primary Protein Structures

Background

Predicting protein subnuclear localization is a challenging problem. Some previous works based on non-sequence information including Gene Ontology annotations and kernel fusion have respective limitations. The aim of this work is twofold: one is to propose a novel individual feature extraction method; another is to develop an ensemble method to improve prediction performance using comprehensive information represented in the form of high dimensional feature vector obtained by 11 feature extraction methods.

Methodology/Principal Findings

A novel two-stage multiclass support vector machine is proposed to predict protein subnuclear localizations. It only considers those feature extraction methods based on amino acid classifications and physicochemical properties. In order to speed up our system, an automatic search method for the kernel parameter is used. The prediction performance of our method is evaluated on four datasets: Lei dataset, multi-localization dataset, SNL9 dataset and a new independent dataset. The overall accuracy of prediction for 6 localizations on Lei dataset is 75.2% and that for 9 localizations on SNL9 dataset is 72.1% in the leave-one-out cross validation, 71.7% for the multi-localization dataset and 69.8% for the new independent dataset, respectively. Comparisons with those existing methods show that our method performs better for both single-localization and multi-localization proteins and achieves more balanced sensitivities and specificities on large-size and small-size subcellular localizations. The overall accuracy improvements are 4.0% and 4.7% for single-localization proteins and 6.5% for multi-localization proteins. The reliability and stability of our classification model are further confirmed by permutation analysis.

Conclusions

It can be concluded that our method is effective and valuable for predicting protein subnuclear localizations. A web server has been designed to implement the proposed method. It is freely available at http://bioinformatics.awowshop.com/snlpred_page.php.     

Effect of modifiers of natural biological response on the functional activity of macrophages (oncological aspect)

Induction of cytotoxicity by biological response modifiers (BRMs) is only one aspect of macrophage activation. After the use of BRMs there were other changes in the functional activity of cells and in particular their increased production or secretion of a number of growth factors. Thus, activation of macrophage antitumor activity induced by BCG vaccine was transitory while activation of growth factor production was more stable in time which finally led to increased proliferation of tumor cells. Combined use of cyclophosphamide and BCG vaccine significantly increased not only the toxicity induced by BCG vaccine but also their liberation of the growth factors. Such macrophages lost their ability to control the growth of a small number of the tumor cells cultivated in their presence. Development of ways for directed activation of macrophages aimed at elimination of the tumor cells which survived the chemotherapy should include evaluation of the combined effect of various BRMs and chemotherapeutics on both antitumor and protumor activity i. e. ability to produce the factors stimulating the tumor growth.     

Computer analysis of two-dimensional gels

New methods and computer programs are described which enable one to analyze autoradiograms produced by two-dimensional gel electrophoresis. These programs are completely automatic with respect to finding spots resolved by such gels and quantitating the radioactivity in them. Semiautomatic programs have also been developed to match the spot patterns of different autoradiograms, and to follow the synthesis of any individual polypeptide through a series of gels.     

Decomposing trends in bird populations: Climate,life histories and habitat affect different aspects of population change

Aim

Despite the complexity of population dynamics, most studies concerning current changes in bird populations reduce the trajectory of population change to a linear trend. This may hide more complex patterns reflecting responses of bird populations to changing anthropogenic pressures. Here, we address this complexity by means of multivariate analysis and attribute different components of bird population dynamics to different potential drivers.

Location

Czech Republic.

Methods

We used data on population trajectories (1982–2019) of 111 common breeding bird species, decomposed them into independent components by means of the principal component analysis (PCA), and related these components to multiple potential drivers comprising climate, land use change and species' life histories.

Results

The first two ordination axes explained substantial proportion of variability of population dynamics (42.0 and 12.5% of variation in PC1 and PC2 respectively). The first axis captured linear population trend. Species with increasing populations were characterized mostly by long lifespan and warmer climatic niches. The effect of habitat was less pronounced but still significant, with negative trends being typical for farmland birds, while positive trends characterized birds of deciduous forests. The second axis captured the contrast between hump-shaped and U-shaped population trajectories and was even more strongly associated with species traits. Species migrating longer distances and species with narrower temperature niches revealed hump-shaped population trends, so that their populations mostly increased before 2000 and then declined. These patterns are supported by the trends of total abundances of respective ecological groups.

Main Conclusion

Although habitat transformation apparently drives population trajectories in some species groups, climate change and associated species traits represent crucial drivers of complex population dynamics of central European birds. Decomposing population dynamics into separate components brings unique insights into non-trivial patterns of population change and their drivers, and may potentially indicate changes in the regime of anthropogenic effects on biodiversity.     

Dependence of protective effect of alpha-tocopherol on its concentration and time of action on PC12 cell under conditions of oxidative stress

At the short-term incubation (0.5 and 1.5 h) of cells of the PC12 neuronal line with alpha-tocopherol, its protective effect against the cytotoxic hydrogen peroxide action was increased with rise of its concentration in samples; the protection was practically absent at action of nanomolar antioxidant concentrations, but was well expressed at its micromolar concentrations. These data agree with the concept that alpha-tocopherol increases the cell living activity by reacting directly with free radicals, which leads to formation of the less reactive compounds deprived of non-paired electron. The evidence is obtained that at the long-term action on PC12 cells, alpha-tocopherol not only in micro-, but also in nanomolar concentrations increases statistically significantly the cell living activity under conditions of oxidative stress. As follows from the obtained data, an important role in realization of the alpha-tocopherol protective effect at the long-term incubation with it seems to be played by modulation by this antioxidant of activity of protein kinase activated by extracellular signaling, phosphatidylinosite 3-kinase, and protein kinase C.