Modeling tight junction dynamics and oscillations

Tight junction (TJ) permeability responds to changes of extracellular Ca(2+) concentration. This can be gauged through changes of the transepithelial electrical conductance (G) determined in the absence of apical Na(+). The early events of TJ dynamics were evaluated by the fast Ca(2+) switch assay (FCSA) (Lacaz-Vieira, 2000), which consists of opening the TJs by removing basal calcium (Ca(2+)(bl)) and closing by returning Ca(2+)(bl) to normal values. Oscillations of TJ permeability were observed when Ca(2+)(bl) is removed in the presence of apical calcium (Ca(2+)(ap)) and were interpreted as resulting from oscillations of a feedback control loop which involves: (a) a sensor (the Ca(2+) binding sites of zonula adhaerens), (b) a control unit (the cell signaling machinery), and (c) an effector (the TJs). A mathematical model to explain the dynamical behavior of the TJs and oscillations was developed. The extracellular route (ER), which comprises the paracellular space in series with the submucosal interstitial fluid, was modeled as a continuous aqueous medium having the TJ as a controlled barrier located at its apical end. The ER was approximated as a linear array of cells. The most apical cell is separated from the apical solution by the TJ and this cell bears the Ca(2+) binding sites of zonula adhaerens that control the TJs. According to the model, the control unit receives information from the Ca(2+) binding sites and delivers a signal that regulates the TJ barrier. Ca(2+) moves along the ER according to one-dimensional diffusion following Fick's second law. Across the TJ, Ca(2+) diffusion follows Fick's first law. Our first approach was to simulate the experimental results in a semiquantitative way. The model tested against experiment results performed in the frog urinary bladder adequately predicts the responses obtained in different experimental conditions, such as: (a) TJ opening and closing in a FCSA, (b) opening by the presence of apical Ca(2+) and attainment of a new steady-state, (c) the escape phase which follows the halt of TJ opening induced by apical Ca(2+), (d) the oscillations of TJ permeability, and (e) the effect of Ca(2+)(ap) concentration on the frequency of oscillations.     

Structure and function of a protein folding machine: the eukaryotic cytosolic chaperonin CCT

Coupled translocation of tRNA and mRNA in the ribosome during protein synthesis is one of the most challenging and intriguing problems in the field of translation. We highlight several key questions regarding the mechanism of translocation, and discuss possible mechanistic models in light of the recent crystal structures of the ribosome and its subunits.     

Comparative cytogenetics of three species of Dichotomius (Coleoptera, Scarabaeidae)

Meiotic and mitotic chromosomes of Dichotomius nisus, D. semisquamosus and D. sericeus were analyzed after conventional staining, C-banding and silver nitrate staining. In addition, Dichotomius nisus and D. semisquamosus chromosomes were also analyzed after fluorescent in situ hybridization (FISH) with an rDNA probe. The species analyzed had an asymmetrical karyotype with 2n = 18 and meta-submetacentric chromosomes. The sex determination mechanism was of the Xy(p) type in D. nisus and D. semisquamosus and of the Xy (r) type in D. sericeus. C-banding revealed the presence of pericentromeric blocks of constitutive heterochromatin (CH) in all the chromosomes of the three species. After silver staining, the nucleolar organizer regions (NORs) were located in autosomes of D. semisquamosus and D. sericeus and in the sexual bivalent of D. nisus. FISH with an rDNA probe confirmed NORs location in D. semisquamosus and in D. nisus. Our results suggest that chromosome inversions and fusions occurred during the evolution of the group.     

Kinetic characterization of P-type membrane ATPase from Streptococcus mutans

The proton translocating membrane ATPase of oral streptococci has been implicated in cytoplasmatic pH regulation, acidurance and cariogenicity. Studies have confirmed that Streptococcus mutans is the most frequently detected species in dental caries. A P-type ATPase that can act together with F₁F_o-ATPase in S. mutans membrane has been recently described. The main objective of this work is to characterize the kinetic of ATP hydrolysis of this P-type ATPase. The optimum pH for ATP hydrolysis is around 6.0. The dependence of P-type ATPase activity on ATP concentration reveals high (K_0.5=0.27 mM) and low (K_0.5=3.31 mM) affinity sites for ATP, exhibiting positive cooperativity and a specific activity of about 74 U/mg. Equimolar concentrations of ATP and magnesium ions display a behavior similar to that described for ATP concentration in Mg²⁺ saturating condition (high affinity site, K_0.5=0.10 mM, and low affinity site, K_0.5=2.12 mM), exhibiting positive cooperativity and a specific activity of about 68 U/mg. Sodium, potassium, ammonium, calcium and magnesium ions stimulate the enzyme, showing a single saturation curve, all exhibiting positive cooperativities, whereas inhibition of ATPase activity is observed for zinc ions and EDTA. The kinetic characteristics reveal that this ATPase belongs to type IIIA, like the ones found in yeast and plants.     

Molecular and physiological evidence suggests the existence of a system II-like pathway of ethylene production in non-climacteric<Emphasis Type="Italic"> Citrus</Emphasis> fruit

Mature citrus fruits, which are classified as non-climacteric, evolve very low amounts of ethylene during ripening but respond to exogenous ethylene by ripening-related pigment changes and accelerated respiration. In the present study we show that young citrus fruitlets attached to the tree produce high levels of ethylene, which decrease dramatically towards maturation. Upon harvest, fruitlets exhibited a climacteric-like rise in ethylene production, preceded by induction of the genes for 1-aminocyclopropane-1-carboxylate (ACC) synthase 1 (CsACS1), ACC oxidase 1 (CsACO1) and the ethylene receptor CsERS1. This induction was advanced and augmented by exogenous ethylene or propylene, indicating an autocatalytic system II-like ethylene biosynthesis. In mature, detached fruit, very low rates of ethylene production were associated with constitutive expression of the ACC synthase 2 (CsACS2) and ethylene receptor CsETR1 genes (system I). CsACS1 gene expression was undetectable at this stage, even following ethylene or propylene treatment, and CsERS1 gene expression remained constant, indicating that no autocatalytic response had occurred. The transition from system II-like behavior of young fruitlets to system I behavior appears to be under developmental control.Abbreviations ACC 1-Aminocyclopropane-1-carboxylate - CsACS1, CsACS2 ACC synthase - CsACO1 ACC oxidase - CsERS1, CsETR1 Ethylene receptors - DAFB Days after full bloom - 1-MCP 1-Methylcyclopropene     

The Role of Gln61 in HRas GTP hydrolysis: a quantum mechanics/molecular mechanics study

Activation of the water molecule involved in GTP hydrolysis within the HRas·RasGAP system is analyzed using a tailored approach based on hybrid quantum mechanics/molecular mechanics (QM/MM) simulation. A new path emerges: transfer of a proton from the attacking water molecule to a second water molecule, then a different proton is transferred from this second water molecule to the GTP. Gln(61) will stabilize the transient OH(-) and H(3)O(+) molecules thus generated. This newly proposed mechanism was generated by using, for the first time to our knowledge, the entire HRas-RasGAP protein complex in a QM/MM simulation context. It also offers a rational explanation for previous experimental results regarding the decrease of GTPase rate found in the HRas Q61A mutant and the increase exhibited by the HRas Q61E mutant.     

The sharing of male production among workers and queens in Scaptotrigona depilis (Moure, 1942) (Apidae, Meliponini)

The proportions of males produced by queens or workers of Scaptotrigona depilis, and the sex-ratio in the brood, were estimated. Thirteen young combs were collected; from one half of each comb the cells were opened and the number of eggs per cell was recorded. Later, upon maturation, from the other halves of the combs the individual inside each cell was classified according to sex. If from a cell containing initially two eggs a male would emerge (supposedly the son of a worker) the proportion of such cells in the comb would represent the maximum overall workers’ male production. Consequently, the difference with the number of males found in the second half of the comb would indicate the minimum contribution by the queen. In these 13 combs, on average, 7.3% of the cells contained 2 eggs, whilst in 30.9% of the cells a male developed. Males were found in 10 combs, in 2–79% of the cells. In 6 of the 13 combs 2–47% of the cells contained 2 eggs. In these 6 combs more than 40% of the cells had a male inside. In 5 of them, the frequency of males was significantly higher than the frequency of cells containing 2 eggs. Queens, therefore, produced the majority of the males. There was no correlation between worker and queen numerical investments in male production, indicating different response mechanisms of workers, compared to queens, to conditions favouring male production. There was also no correlation between the mean egg size of the queen and the percentage males in the combs.     

Multitrait Bayesian shrinkage and variable selection models with the BGLR-R package

The BGLR-R package implements various types of single-trait shrinkage/variable selection Bayesian regressions. The package was first released in 2014, since then it has become a software very often used in genomic studies. We recently develop functionality for multitrait models. The implementation allows users to include an arbitrary number of random-effects terms. For each set of predictors, users can choose diffuse, Gaussian, and Gaussian–spike–slab multivariate priors. Unlike other software packages for multitrait genomic regressions, BGLR offers many specifications for (co)variance parameters (unstructured, diagonal, factor analytic, and recursive). Samples from the posterior distribution of the models implemented in the multitrait function are generated using a Gibbs sampler, which is implemented by combining code written in the R and C programming languages. In this article, we provide an overview of the models and methods implemented BGLR’s multitrait function, present examples that illustrate the use of the package, and benchmark the performance of the software.     

Structural properties of the human respiratory syncytial virus P protein: evidence for an elongated homotetrameric molecule that is the smallest orthologue within the family of paramyxovirus polymerase cofactors

The oligomeric state and the hydrodynamic properties of human respiratory syncytial virus (HRSV) phosphoprotein (P), a known cofactor of the viral RNA-dependent RNA polymerase (L), and a trypsin-resistant fragment (X) that includes its oligomerization domain were analyzed by sedimentation equilibrium and velocity using analytical ultracentrifugation. The results obtained demonstrate that both P and fragment X are homotetrameric with elongated shapes, consistent with electron micrographs of the purified P protein in which thin rod-like molecules of approximately 12.5 +/- 1.0 nm in length were observed. A new chymotrypsin resistant fragment (Y*) included in fragment X has been identified and purified by gel filtration chromatography. Fragment Y* may represent a minimal version of the P oligomerization domain. Thermal denaturation curves based on circular dichroism data of P protein showed a complex behavior. In contrast, melting data generated for fragments X and particularly fragment Y* showed more homogeneous transitions indicative of simpler structures. A three-dimensional model of X and Y* fragments was built based on the atomic structure of the P oligomerization domain of the related Sendai virus, which is in good agreement with the experimental data. This model will be an useful tool to make rational mutations and test the role of specific amino acids in the oligomerization and functional properties of the HRSV P protein.