Performance prediction of deep learning applications training in GPU as a service systems

Cluster Computing - Data analysts predict that the GPU as a service (GPUaaS) market will grow to support 3D models, animated video processing, gaming, and deep learning model training. The main...     

Effect of dissolved oxygen concentration on repeated production of gluconic acid by immobilised mycelia of Aspergillus niger

Summary Gluconic acid production from corn starch hydrolysates by immobilised mycelia of Aspergillus niger was studied in a laboratory-scale stirred fermentor at different concentrations of glucose (S ₀) and dissolved oxygen (DO) in the culture broth. Its evolution was simulated quite well by applying the same unstructured model set up in previous experiments using stirred and airlift fermentors. In particular, increasing S ₀ in the range 70–160 g/l, although uninfluential upon the yield coefficient, resulted in an exponential decrease in the gluconic acid formation rate constant. Nevertheless, the greater the oxygen transfer rate used in the fermentor, the smaller the inhibitor effect of the higher concentrations of glucose on gluconate productivity became. This was achieved by enriching the inlet air with pure oxygen so as to maintain the DO level above 75% saturation throughout the fermentation. Offprint requests to: M. Moresi     

Differential detection of potentially hazardous Fusarium species in wheat grains by an electronic nose

Fungal infestation on wheat is an increasingly grave nutritional problem in many countries worldwide. Fusarium species are especially harmful pathogens due to their toxic metabolites. In this work we studied volatile compounds released by F. cerealis, F. graminearum, F. culmorum and F. redolens using SPME-GC/MS. By using an electronic nose we were able to differentiate between infected and non-infected wheat grains in the post-harvest chain. Our electronic nose was capable of distinguishing between four wheat Fusaria species with an accuracy higher than 80%.     

Endocytosis optimizes the dynamic localization of membrane proteins that regulate cortical polarity

Diverse cell types require the ability to maintain dynamically polarized membrane-protein distributions through balancing transport and diffusion. However, design principles underlying dynamically maintained cortical polarity are not well understood. Here we constructed a mathematical model for characterizing the morphology of dynamically polarized protein distributions. We developed analytical approaches for measuring all model parameters from single-cell experiments. We applied our methods to a well-characterized system for studying polarized membrane proteins: budding yeast cells expressing activated Cdc42. We found that a balance of diffusion, directed transport, and endocytosis was sufficient for accurately describing polarization morphologies. Surprisingly, the model predicts that polarized regions are defined with a precision that is nearly optimal for measured endocytosis rates and that polarity can be dynamically stabilized through positive feedback with directed transport. Our approach provides a step toward understanding how biological systems shape spatially precise, unambiguous cortical polarity domains using dynamic processes.     

Kinetic mechanism of the Zn-dependent aryl-phosphatase activity of myo-inositol-1-phosphatase

Myo-inositol-1-phosphatase (EC 3.1.3.25) is able to hydrolyze myo-inositol-1-phosphate in the presence of Mg(2+) ions at neutral pH, and also p-nitrophenyl phosphate in the presence of Zn(2+)-ions at acidic pH. This enzyme plays a role in phosphatidylinositol cell signalling and is a putative target of lithium therapy in manic depression. We elucidate here the kinetic mechanism of the Zn-dependent activity of myo-inositol-1-phosphatase. As part of this analysis it was necessary to determine the basicity constants of p-nitrophenyl phosphate and the stability constant of its metal-complex in the presence of zinc chloride. We find that the Zn-dependent reaction may be described either by a rapid-equilibrium random mechanism or an ordered steady-state mechanism in which the substrate binds to the free enzyme prior to the metal ion. In both models the Zn-substrate complex acts as a high affinity inhibitor, yielding a dead-end species through its binding to the enzyme-Zn-substrate in rapid-equilibrium or to the enzyme-phosphate complexes in a steady-state model. Phosphate is a competitive inhibitor of the enzyme with respect to the substrate and an uncompetitive inhibitor with respect to zinc ions.     

The phosphotransferase system formed by PtsP, PtsO, and PtsN proteins controls production of polyhydroxyalkanoates in Pseudomonas putida

The genome of Pseudomonas putida KT2440 encodes five proteins of the phosphoenolpyruvate-carbohydrate phosphotransferase system. Two of these (FruA and FruB) form a dedicated system for fructose intake, while enzyme I(Ntr) (EI(Ntr); encoded by ptsP), NPr (ptsO), and EII(Ntr) (ptsN) act in concert to control the intracellular accumulation of polyhydroxyalkanoates, a typical product of carbon overflow.     

A model for the recognition of protein kinases based on the entropy of 3D van der Waals interactions

The study and prediction of kinase function (kinomics) is of major importance for proteome research due to the widespread distribution of kinases. However, the prediction of protein function based on the similarity between a functionally annotated 3D template and a query structure may fail, for instance, if a similar protein structure cannot be identified. Alternatively, function can be assigned using 3D-structural empirical parameters. In previous studies, we introduced parameters based on electrostatic entropy (Proteins 2004, 56, 715) and molecular vibration entropy (Bioinformatics 2003, 19, 2079) but ignored other important factors such as van der Waals (vdw) interactions. In the work described here, we define 3D-vdw entropies (degrees theta(k)) and use them for the first time to derive a classifier for protein kinases. The model classifies correctly 88.0% of proteins in training and more than 85.0% of proteins in validation studies. Principal components analysis of heterogeneous proteins demonstrated that degrees theta(k) codify information that is different to that described by other bulk or folding parameters. In additional validation experiments, the model recognized 129 out of 142 kinases (90.8%) and 592 out of 677 non-kinases (87.4%) not used above. This study provides a basis for further consideration of degrees theta(k) as parameters for the empirical search for structure-function relationships.     

The SAUR gene family in coffee: genome-wide identification and gene expression analysis during somatic embryogenesis

Molecular Biology Reports - Small auxin-up RNA (SAUR) genes form a wide family supposedly involved in different physiological and developmental processes in plants such as leaf senescence, auxin...     

Novel pH-Stable Glycoside Hydrolase Family 3 β-Xylosidase from Talaromyces amestolkiae: an Enzyme Displaying Regioselective Transxylosylation

This paper reports on a novel β-xylosidase from the hemicellulolytic fungus Talaromyces amestolkiae. The expression of this enzyme, called BxTW1, could be induced by beechwood xylan and was purified as a glycoprotein from culture supernatants. We characterized the gene encoding this enzyme as an intronless gene belonging to the glycoside hydrolase gene family 3 (GH3). BxTW1 exhibited transxylosylation activity in a regioselective way. This feature would allow the synthesis of oligosaccharides or other compounds not available from natural sources, such as alkyl glycosides displaying antimicrobial or surfactant properties. Regioselective transxylosylation, an uncommon combination, makes the synthesis reproducible, which is desirable for its potential industrial application. BxTW1 showed high pH stability and Cu²⁺ tolerance. The enzyme displayed a pI of 7.6, a molecular mass around 200 kDa in its active dimeric form, and K_m and V_max values of 0.17 mM and 52.0 U/mg, respectively, using commercial p-nitrophenyl-β-d-xylopyranoside as the substrate. The catalytic efficiencies for the hydrolysis of xylooligosaccharides were remarkably high, making it suitable for different applications in food and bioenergy industries.