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.     

Protective effect of ε-viniferin on β-amyloid peptide aggregation investigated by electrospray ionization mass spectrometry

Abnormal β-amyloid peptide accumulation and aggregation is considered to be responsible for the formation and cerebral deposition of senile plaques in the brains of patients with Alzheimer's disease (AD). Inhibition of the formation of β-amyloid (Aβ) fibrils would be an attractive therapeutic target for the treatment of AD. Resveratrol and its derivatives exhibit a broad range of pharmacological properties such as protection against cardiovascular diseases and cancers, as well as promoting antiaging effects. We reported previously that ε-viniferin glucoside (VG), a resveratrol-derived dimer, strongly inhibits Aβ (25-35) fibril formation in vitro. In this study, we investigated the effects of VG on the aggregation of the full-length peptides (Aβ (1-40) and Aβ (1-42)) and on the β-amyloid-induced toxicity in PC12 cells. VG inhibited Aβ cytotoxicity and the non-covalent complex between VG and Aβ was observed by electrospray ionization mass spectrometry.     

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.     

Identification of metabolic network models from incomplete high-throughput datasets

MOTIVATION: High-throughput measurement techniques for metabolism and gene expression provide a wealth of information for the identification of metabolic network models. Yet, missing observations scattered over the dataset restrict the number of effectively available datapoints and make classical regression techniques inaccurate or inapplicable. Thorough exploitation of the data by identification techniques that explicitly cope with missing observations is therefore of major importance. RESULTS: We develop a maximum-likelihood approach for the estimation of unknown parameters of metabolic network models that relies on the integration of statistical priors to compensate for the missing data. In the context of the linlog metabolic modeling framework, we implement the identification method by an Expectation-Maximization (EM) algorithm and by a simpler direct numerical optimization method. We evaluate performance of our methods by comparison to existing approaches, and show that our EM method provides the best results over a variety of simulated scenarios. We then apply the EM algorithm to a real problem, the identification of a model for the Escherichia coli central carbon metabolism, based on challenging experimental data from the literature. This leads to promising results and allows us to highlight critical identification issues.     

Characterization of a novel immobilized biocatalyst obtained by matrix-assisted refolding of recombinant polyhydroxyoctanoate depolymerase from <Emphasis Type="Italic">Pseudomonas putida</Emphasis> KT2442 isolated from inclusion bodies

Purification and matrix-assisted refolding of recombinant His-tagged polyhydroxyalkanoate (PhaZ) depolymerase from Pseudomonas putida KT2442 was carried out. His-tagged enzyme was overproduced as inclusion bodies in recombinant E. coli M15 (pREP4, pPAZ3), which were denatured by 8 M urea, immobilized on Ni²⁺-nitrilotriacetate-agarose matrix, and refolded by gradual removal of the chaotropic agent. The refolded enzyme could not be eluted with 1 M imidazole buffer, leading to an immobilized biocatalyst where PhaZ depolymerase was homogeneously distributed in the agarose support as shown by confocal scanning microscopy. Polyhydroxyoctanoate could not be hydrolyzed by this novel immobilized biocatalyst, whereas the attached enzyme was active in the hydrolysis of p-nitrophenyl alkanoate esters, which differed in their alkyl chain length. Taking advantage of the observed esterase activity on p-nitrophenylacetate, functional characterization of immobilized PhaZ depolymerase was carried out. The immobilized enzyme was more stable than its soluble counterpart and showed optimal hydrolytic activity at 37°C and 50 mM phosphate buffer pH 8.0. Kinetic parameters were obtained with both p-nitrophenylacetate and p-nitrophenyloctanoate, which had not been described so far for the soluble enzyme, representing an attractive and alternative chromogenic assay for the study of this paradigmatic enzyme.