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.     

<i>In Vitro</i>-Propagation of <i>Agave tequilana</i> Weber cv. azul in a Temporary Immersion System

In Mexico, there is a need to produce large quantities of plantlets for the establishment and replanting of blue (cv. azul) agave production areas. Most of these plots are within the origin denomination area (DOT, Spanish acronym) of the distilled product of this plant, known as tequila. The objective of this study was to develop an in vitro-propagation protocol for Agave tequilana Weber cv. azul using segmented stems in both: solid and liquid media. A disinfection and in vitro technique were developed to obtain shoots, through plantlets collected in commercial plots, which attained 100% surface-disinfection and budding rate. At the multiplication stage, the effects of 6-Benzylaminopurine (BA) (0.0, 4.4 and 13.2 μM) and kinetin (0.0, 9.4, 18.8 and 37.6 μM) were evaluated on lateral-shoot production of segmented sagittal stems. These were cultivated on Murashige & Skoog (MS) medium, with the addition of 3.0% sucrose and 8 g L⁻¹ agar. It was observed that BA and kinetin increased the number of shoots per explant, obtaining up to 18 and 26, respectively. Furthermore, it was found that just the sagittal segmentation of explants increased axillary budding. On the other hand, segmented-stem bases were grown in MS liquid medium with 3.0% sucrose, inside a RITA® system, programmed by a 5 min immersion step with a frequency of every 4 h. The effect of Indole−3-Acetic acid (IAA) (0.57, 2.9, 5.7 μM) was evaluated, while maintaining a concentration of BA (13.2 μM). It was observed that the greatest concentration of IAA led to the formation of more than 20 buds per explant. These results offer a new methodology to increase the efficiency of A. tequilana Weber cv. azul-in vitro multiplication by sagittal segmentation of stems and the addition of BA and/or IAA.     

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.     

Predicting chromatin organization using histone marks

Genome-wide mapping of three dimensional chromatin organization is an important yet technically challenging task. To aid experimental effort and to understand the determinants of long-range chromatin interactions, we have developed a computational model integrating Hi-C and histone mark ChIP-seq data to predict two important features of chromatin organization: chromatin interaction hubs and topologically associated domain (TAD) boundaries. Our model accurately and robustly predicts these features across datasets and cell types. Cell-type specific histone mark information is required for prediction of chromatin interaction hubs but not for TAD boundaries. Our predictions provide a useful guide for the exploration of chromatin organization.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0740-z) contains supplementary material, which is available to authorized users.     

Biliverdin reductase-A protein levels and activity in the brains of subjects with Alzheimer disease and mild cognitive impairment

Biliverdin reductase-A is a pleiotropic enzyme involved not only in the reduction of biliverdin-IX-alpha into bilirubin-IX-alpha, but also in the regulation of glucose metabolism and cell growth secondary to its serine/threonine/tyrosine kinase activity. Together with heme oxygenase, whose metabolic role is to degrade heme into biliverdin-IX-alpha, it forms a powerful system involved in the cell stress response during neurodegenerative disorders. In this paper, an up-regulation of the biliverdin reductase-A protein levels was found in the hippocampus of the subjects with Alzheimer disease and arguably its earliest form, mild cognitive impairment. Moreover a significant reduction in the phosphorylation of serine, threonine and tyrosine residues of biliverdin reductase-A was found, and this was paralleled by a marked reduction in its reductase activity. Interestingly, the levels of both total and phosphorylated biliverdin reductase-A were unchanged as well as its enzymatic activity in the cerebella. These results demonstrated a dichotomy between biliverdin reductase-A protein levels and activity in the hippocampus of subjects affected by Alzheimer disease and mild cognitive impairment, and this effect likely is attributable to a reduction in the phosphorylation of serine, threonine and tyrosine residues of biliverdin reductase-A. Consequently, not just the increased levels of biliverdin reductase-A, but also its changed activity and phosphorylation state, should be taken into account when considering potential biomarkers for Alzheimer disease and mild cognitive impairment.     

Effect of impeller type and stirring frequency on the behavior of an AnSBBR in the treatment of low-strength wastewater

The influence of impeller type and stirring frequency on the performance of a mechanically stirred anaerobic sequencing batch reactor containing immobilized biomass on an inert support (AnSBBR - Anaerobic Sequencing Batch Biofilm Reactor) was evaluated. The biomass was immobilized on polyurethane foam cubes placed in a stainless-steel basket inside a glass cylinder. Each 8-h batch run consisted of three stages: feed (10 min), reaction (460 min) and discharge (10 min) at 30 °C. Experiments were performed with four impeller types, i.e., helical, flat-blade, inclined-blade and curved-blade turbines, at stirring frequencies ranging from 100 to 1100 rpm. Synthetic wastewater was used in all experiments with an organic-matter concentration of 530 ± 37 mg/L measured as chemical oxygen demand (COD). The reactor achieved an organic-matter removal efficiency of around 87% under all investigated conditions. Analysis of the four impeller types and the investigated stirring frequencies showed that mass transfer in the liquid phase was affected not only by the applied stirring frequency but also by the agitation mode imposed by each impeller type. The best reactor performance at all stirring frequencies was obtained when agitation was provided by the flat-blade turbine impeller.     

Inter-limb coordination, strength, jump, and sprint performances following a youth men's basketball game

This study aimed to verify whether basketball players are able to maintain strength (handgrip), jump (countermovement jump [CMJ]), sprint (10 m and 10 m bouncing the ball [10 mBB]), and interlimb coordination (i.e., synchronized hand and foot flexions and extensions at 80, 120, and 180 bpm) performances at the end of their game. Ten young (age 15.7 ± 0.2 years) male basketball players volunteered for this study. During the friendly game, heart rate (HR), rate of perceived exertion (RPE), and rate of muscle pain (RMP) were assessed to evaluate the exercise intensity. Overall, players spent 80% of the time playing at intensities higher than 85% HRmax. Main effects (p < 0.05) for game periods emerged for HR and the number of players involved in a single action, with lower occurrence of maximal efforts and higher involvement of teammates after the first 2 periods. At the end of the game, players reported high (p < 0.05) RPE (15.7 ± 2.4) and RMP (5.2 ± 2.3) values; decreased (p < 0.05) sprint capabilities (10 m: pre = 1.79 ± 0.09 seconds, post = 1.84 ± 0.08 seconds; 10 mBB: pre = 1.81 ± 0.11 seconds, post = 1.96 ± 0.08 seconds); increased (p < 0.05) interlimb coordination at 180 bpm (pre = 33.3 ± 20.2 seconds, post = 43.9 ± 19.8 seconds); and maintained jump (pre = 35.2 ± 5.2 cm, post = 35.7 ± 5.2 cm), handgrip (pre = 437 ± 73 N, post = 427 ± 55 N), and coordinative performances at lower frequencies of executions (80 bpm: pre = 59.7 ± 1.3 seconds, post = 60.0 ± 0.0 seconds; 120 bpm: pre = 54.7 ± 12.3 seconds, post = 57.3 ± 6.7 seconds). These findings indicate that the heavy load of the game exerts beneficial effects on the efficiency of executive and attentive control functions involved in complex motor behaviors. Coaches should structure training sessions that couple intense physical exercises with complex coordination tasks to improve the attentional capabilities of the players.