Gene expression waves. Cell cycle independent collective dynamics in cultured cells

The ergodic hypothesis, which assumes the independence of each cell of the ensemble from all the others, is a necessary prerequisite to attach single cell based explanations to the grand averages taken from population data. This was the prevailing view about the interpretation of cellular biology experiments that typically are performed on colonies of billions of cells. By analysing gene expression data of different cells going from yeast to mammalian cell cultures, we demonstrate that cell cultures display a sort of "ecology-in-a-plate" giving rise to a rich dynamics of gene expression that are independent from reproductive cycles, hence contradicting simple ergodic assumptions The aspecific character of the observed coordinated gene expression activity inhibits any simple mechanistic hypothesis and highlights the need to consider population effects in the interpretation of data coming from cell cultures.     

Polymorphisms in interleukins 17A and 17F genes and periodontitis: results from a meta-analysis

Polymorphisms in inflammatory genes such as interleukins 17A and 17F are associated with the risk of development of periodontitis, although the results remain contradictory. Hence, the aim of this study was perform a meta-analysis focusing on two polymorphisms (rs2275913 and rs763780) in interleukins 17A and 17F genes, respectively, in both chronic (CP) and aggressive periodontitis (AgP). A review in literature was performed in several databases for studies published before 25, September 2016. The meta-analysis was obtained through the review manager statistical software (version 5.2) with odds ratio (OR) calculation and funnel plot (P?<?0.05) for heterogeneity, as well as the comprehensive meta-analysis software (version 3.3.070) for the assessment of publication bias. Seven articles with 1540 participants composed the results in which the mutant allele in the rs2275913 polymorphism did not present significant association with the risk of CP or AgP (OR 1.56, 95% CI 0.77, 3.15, P?=?0.21; OR 1.12, 95% CI 0.05, 23.44, P?=?0.94, respectively) nor was the mutant allele in rs763780 associated with the risk of CP (OR 1.19, 95% CI 0.80, 1.76, P?=?0.39) or AgP (OR 1.07, 95% CI 0.63, 1.84, P?=?0.79). No bias of publication was observed by Egger’s and Begg’s tests in any allelic evaluation. This meta-analysis showed a non-significant association between the polymorphisms rs2275913 and rs763780 in interleukins 17A and 17F genes and chronic and aggressive periodontitis in the allelic evaluation.     

Opheliidae (Polychaeta) from the Southwestern Atlantic ocean, with the description of Travisia amadoi n. sp., Ophelina gaucha n. sp. and Ophelina alata n. sp.

The diet of the brackish water tilapia Sarotherodon melanotheron is studied in various riverine and lacustrine systems of the Bia River basin (Côte d'Ivoire). Comparison of the diet between sampling sites (upper course, lower course and man-made Lake Ayame) shows significant differences. In the man-made lake, prey described as preferential include Asterionella (Bacillariophyceae) and Bosmina(Cladocera). In the lower course, the preferential preys are represented by Lyngbya(Cyanophyceae) while in the upper course Lyngbya and chironomid larvae are preferential. These differences are related to the altered environmental conditions generated by the construction of the dam on the Bia river main stream. In the man-made lake, there is no shift in diet either with the seasons (dry and rainy seasons) or with size.     

Determination of a large number of kinase activities using peptide substrates,P81 phosphocellulose paper arrays and phosphor imaging

To perform phosphoproteomics and signal transduction studies, a number of protein kinase activities and levels must be simultaneously analyzed in different cell samples and correlated with phosphoprotein patterns to obtain conclusions with regard to the regulation of kinase networks. We describe here a miniaturized format of the classical phosphocellulose (P81) paper binding assay with which up to 594 kinase reactions can be simultaneously analyzed. Kinase peptide substrates possessing a minimum of three consecutive basic residues were subjected to phosphorylation in 96-well plates and aliquots of the phosphorylation reactions were spotted on arrays printed on P81 papers. Phosphorylation levels were quantified using a storage phosphor system imager. The versatility of the procedure was validated by analyzing casein kinase 2, protein kinase C, and p34cdc2/cyclin B in cell extracts and testing the effect of known inhibitors and activators on kinase activities. This improved, miniaturized version of the classical P81 paper method combines simplicity, high sensitivity, high reproducibility, high reliability, and optimal Z factors and takes into account possible sources of background signals. We discuss the possibility of automation and the advantages over other methods.     

Distinct Leaf‐trait Syndromes of Evergreen and Deciduous Trees in a Seasonally Dry Tropical Forest

In seasonally dry tropical forests, tree species can be deciduous, remaining without leaves throughout the dry season, or evergreen, retaining their leaves throughout the dry season. Deciduous and evergreen trees specialize in habitats that differ in water availability (hillside and riparian forest, respectively) and in their exposure to herbivore attack (seasonal and continuous, respectively). We asked whether syndromes of leaf traits in deciduous and evergreen trees were consistent with hypothesized abiotic and biotic selective pressures in their respective habitat. We measured seven leaf traits in 19 deciduous and 11 evergreen tree species in a dry tropical forest in Western Mexico, and measured rates of herbivory on 23 of these species. We investigated the covariance of leaf traits in syndromes related to phenology and associated physiology, and to anti‐herbivory defense. We found evidence for syndromes that separated phenological strategies among four traits: toughness, water content, specific leaf area, and carbon:nitrogen (C:N) ratios. We found a trade‐off between two other traits: trichomes and latex. Overall, evergreen species exhibited lower rates of herbivory than deciduous species. Lower rates of herbivory were explained by a syndrome of higher toughness, lower water content, and higher C:N ratios, which are traits representative of evergreen trees. Phenology and trait syndromes did not exhibit significant phylogenetic signal, consistent with the hypothesis of evolutionary convergence among phenologies and associated leaf‐trait syndromes. Our results suggest that deciduous and evergreen trees could respond to differential water availability and herbivory in their respective habitats by converging on distinct leaf‐trait syndromes. Abstract in Spanish is available at http://www.blackwell‐synergy.com/loi/btp .     

The spontaneously hyperlipoproteinaemic rabbit

It is possible to detect among New Zealand rabbits some animals (A. N.Z.) whose plasma lipoproteins patterns are quite different from those of normal rabbits (N.N.Z.). The differences involve VLDL (< 1.006), LDL₁ (1.006–1.019), LDL₂ (1.019–1.063), HDL (1.063–1.210), VHDL (> 1.210) and plasma cholesterol, triglycerides and phospholipids. This lipoprotein pattern seems to resemble human type IIb hyperlipoproteinaemia. A rapid screening procedure for detecting these animals is proposed.     

The dimerization interface of initiator RctB governs chaperone and enhancer dependence of Vibrio cholerae chromosome 2 replication

Protein function often requires remodeling of protein structure. In the well-studied iteron-containing plasmids, the initiator of replication has a dimerization interface that undergoes chaperone-mediated remodeling. This remodeling reduces dimerization and promotes DNA replication, since only monomers bind origin DNA. A structurally homologs interface exists in RctB, the replication initiator of Vibrio cholerae chromosome 2 (Chr2). Chaperones also promote Chr2 replication, although both monomers and dimers of RctB bind to origin, and chaperones increase the binding of both. Here we report how five changes in the dimerization interface of RctB affect the protein. The mutants are variously defective in dimerization, more active as initiator, and except in one case, unresponsive to chaperone (DnaJ). The results indicate that chaperones also reduce RctB dimerization and support the proposal that the paradoxical chaperone-promoted dimer binding likely represents sequential binding of monomers on DNA. RctB is also activated for replication initiation upon binding to a DNA site, crtS, and three of the mutants are also unresponsive to crtS. This suggests that crtS, like chaperones, reduces dimerization, but additional evidence suggests that the remodelling activities function independently. Involvement of two remodelers in reducing dimerization signifies the importance of dimerization in limiting Chr2 replication.     

Punto de corte de espesor de tejido adiposo epicárdico para predecir síndrome metabólico en población venezolana

ObjectiveTo define an echocardiographically-assessed cut-off point for epicardial adipose tissue (EAT) thickness associated to metabolic syndrome (MS) components in Venezuelan subjects.MethodsFifty-two subjects aged 20-65 years diagnosed with MS according to International Diabetes Federation criteria and 45 sex- and age-matched controls were selected. Blood glucose and plasma lipids were tested; EAT thickness and left ventricular mass were measured by echocardiography.ResultsNo significant age and sex differences were found between the two groups. Body weight, body mass index, waist circumference, and systolic and diastolic blood pressure were significantly higher (P = .0001) in the MS group. This group showed significantly higher levels of fasting blood glucose (P = .0001), total cholesterol (P = .002), LDL-C (P = .007), non-HDL-C (P = .0001), triglycerides (P = .0001), Tg-HDL-C ratio (P = .0001), and lower HDL-C levels (P = .0001) as compared to the control group. EAT thickness (P = .0001) and left ventricular mass (P = .017) were significantly higher in the MS group. The ROC curve showed an AUC of 0.852 (P = .0001) with a power of the test of 0.99. A 5-mm EAT thickness showed a sensitivity of 84.62% (95% CI: 71.9-93.1) and a specificity of 71.11% (95% CI: 55.7-83.6) for predicting MS. The odds ratio of this population for experiencing MS due to an EAT ≥ 5 mm was 8.25 (95% CI: 3.15-21.56; P = .0001).ConclusionAn EAT value ≥ 5 mm has good sensitivity and specificity for predicting MS in the Venezuelan population.