Effect of hydrocarbon concentration of pasture production (<i>Brachiaria humidicola</i>) in Texistepec,Veracruz

In this study, the relationship between the concentration of extra-heavy crude petroleum in a clayey material and the toxicity, field capacity, temperature, and growth of a tropical forage grass (Brachiara humidicola) was determined empirically. For this type of petroleum the acute toxicity (Microtox^®) was slight (CE₅₀ = 63200 - 76400 mg/kg) even at high hydrocarbon concentrations (29279 mg/kg). Nonetheless, serious impacts were encountered in terms of an increase in soil temperature (+ 1.3 °C), reduction in field capacity (-10.7%) and reduction in aerial biomass (-97%). The relationship between hydrocarbon concentration and biomass resulted in a typical dose-response curve (r = 0.99), where a concentration of 2626 mg/kg of hydrocarbons corresponds to a maintenance of 90% biomass. Furthermore, during the duration of this study (one year) the biodegradation was proportional to the pasture biomass production (r = 0.997) indicating a synergistic relationship between the petroleum biodegrading microorganisms in the rhizosphere and the pasture.     

Temperature dependence of acetylcholine receptor channels activated by different agonists

The temperature dependence of agonist binding and channel gating were measured for wild-type adult neuromuscular acetylcholine receptors activated by acetylcholine, carbamylcholine, or choline. With acetylcholine, temperature changed the gating rate constants (Q₁₀ ≈ 3.2) but had almost no effect on the equilibrium constant. The enthalpy change associated with gating was agonist-dependent, but for all three ligands it was approximately equal to the corresponding free-energy change. The equilibrium dissociation constant of the resting conformation (K_d), the slope of the rate-equilibrium free-energy relationship (Φ), and the acetylcholine association and dissociation rate constants were approximately temperature-independent. In the mutant αG153S, the choline association and dissociation rate constants were temperature-dependent (Q₁₀ ≈ 7.4) but K_d was not. By combining two independent mutations, we were able to compensate for the catalytic effect of temperature on the decay time constant of a synaptic current. At mouse body temperature, the channel-opening and -closing rate constants are ∼400 and 16 ms⁻¹. We hypothesize that the agonist dependence of the gating enthalpy change is associated with differences in ligand binding, specifically to the open-channel conformation of the protein.     

Structural basis of the ribosomal machinery for peptide bond formation,translocation, and nascent chain progression

Crystal structures of tRNA mimics complexed with the large ribosomal subunit of Deinococcus radiodurans indicate that remote interactions determine the precise orientation of tRNA in the peptidyl-transferase center (PTC). The PTC tolerates various orientations of puromycin derivatives and its flexibility allows the conformational rearrangements required for peptide-bond formation. Sparsomycin binds to A2602 and alters the PTC conformation. H69, the intersubunit-bridge connecting the PTC and decoding site, may also participate in tRNA placement and translocation. A spiral rotation of the 3' end of the A-site tRNA around a 2-fold axis of symmetry identified within the PTC suggests a unified ribosomal machinery for peptide-bond formation, A-to-P-site translocation, and entrance of nascent proteins into the exit tunnel. Similar 2-fold related regions, detected in all known structures of large ribosomal subunits, indicate the universality of this mechanism.     

Variation in human limb joint articular morphology

Objectives

Synovial joints in human limbs strike a balance between mobility, stability, and articular fit, yet little is known about how these conflicting demands pattern intraspecific variation in articular shape. In this study, we use geometric morphometrics to establish the apportionment and magnitude of morphological variance of the articular surfaces of the human shoulder, elbow, hip, and knee. We hypothesize that variances will be comparable between articulating surfaces within a joint and will be larger in joints with smaller ranges of motion, given their plurality of functional demands.

Materials and Methods

Three-dimensional landmarks were taken on the articular surfaces of the glenohumeral, humeroulnar, acetabulofemoral, and tibiofemoral joints from CT scans of 200 skeletons from the University of Tennessee Donated Skeletal Collection (84 females, 116 males). Root mean-squared distances between articulations calculated from Procrustes shape coordinates were used to determine variance distributions.

Results

We found no difference in variances for each articular surface between the sexes or between left and right articular surfaces. A high range of motion is associated with greater morphological variance; however, this pattern is largely driven by the concave articular surfaces of each joint, which consistently exhibit statistically greater variance than their convex counterparts.

Discussion

The striking pattern of differential variance between articulating morphologies points to potential disparities in development between them. Consistently higher variance in concave surfaces may relate to chondral modeling theory for the formation of joints. Establishing intraspecific morphological variance patterns is a first step in understanding coordinated evolution among articular features.     

In vitro development of murine T cells from prethymic and preliver embryonic yolk sac hematopoietic stem cells.

Mature T cells are derived from prethymic stem cells, which arise at one or more extrathymic sites and enter and differentiate in the thymus. The nature of these prethymic stem cells is a critical factor for the formation of the T-cell repertoire. Although the bone marrow of adult mice can provide such stem cells, their origin during murine embryogenesis is still undetermined. Among potential sites for these progenitor cells are the fetal liver and the embryonic yolk sac. Our studies focus on the yolk sac, both because the yolk sac appears earlier than any other proposed site, and because the mammalian yolk sac is the first site of hematopoiesis. Although it has been shown that the yolk sac in midgestation contains stem cells that can enter the thymic rudiment and differentiate toward T-cell lineage, our aim was to analyze the developmental potential of cells in the yolk sac from earlier stages, prior to the formation of the liver and any other internal organ. We show here that the yolk sac from 8- and 9-day embryos (2-9 and 13-19 somites, respectively) can reconstitute alymphoid congenic fetal thymuses and acquire mature T-cell-specific characteristics. Specifically, thymocytes derived from the early embryonic yolk sac can progress to the expression of mature T lymphocyte markers including CD3/T-cell receptor (TCR), CD4 and CD8. In contrast, we have been unable to document the presence of stem cells within the embryo itself at these early stages. These results support the hypothesis that the stem cells capable of populating the thymic rudiment originate in the yolk sac, and that their presence as early as at the 2- to 9-somite stage may indicate that prethymic stem cells found elsewhere in the embryo at later times may have been derived by migration from this extra-embryonic site. Our experimental design does not exclude the possibility of multiple origins of prethymic stem cells of which the yolk sac may provide the first wave of stem cells in addition to other later waves of cells.     

Causal modeling in a multi-omic setting: insights from GAW20

Background

The GAW20 group formed on the theme of methods for association analyses of repeated measures comprised 4sets of investigators. The provided “real” data set included genotypes obtained from a human whole-genome association study based on longitudinal measurements of triglycerides (TGs) and high-density lipoprotein in addition to methylation levels before and after administration of fenofibrate. The simulated data set contained 200 replications of methylation levels and posttreatment TGs, mimicking the real data set.

Results

The different investigators in the group focused on the statistical challenges unique to family-based association analyses of phenotypes measured longitudinally and applied a wide spectrum of statistical methods such as linear mixed models, generalized estimating equations, and quasi-likelihood–based regression models. This article discusses the varying strategies explored by the group’s investigators with the common goal of improving the power to detect association with repeated measures of a phenotype.

Conclusions

Although it is difficult to identify a common message emanating from the different contributions because of the diversity in the issues addressed, the unifying theme of the contributions lie in the search for novel analytic strategies to circumvent the limitations of existing methodologies to detect genetic association.

     

Activation kinetics of recombinant mouse nicotinic acetylcholine receptors: mutations of alpha-subunit tyrosine 190 affect both binding and gating.

Affinity labeling and mutagenesis studies have demonstrated that the conserved tyrosine Y190 of the acetylcholine receptor (AChR) alpha-subunit is a key determinant of the agonist binding site. Here we describe the binding and gating kinetics of embryonic mouse AChRs with mutations at Y190. In Y190F the dissociation constant for ACh binding to closed channels was reduced approximately 35-fold at the first binding site and only approximately 2-fold at the second site. At both binding sites the association and dissociation rate constants were decreased by the mutation. Compared with wildtype AChRs, doubly-liganded alpha Y190F receptors open 400 times more slowly but close only 2 times more rapidly. Considering the overall activation reaction (vacant-closed to fully occupied-open), there is an increase of approximately 6.4 kcal/mol caused by the Y-to-F mutation, of which at least 2.1 and 0.3 kcal/mol comes from altered agonist binding to the first and second binding sites, respectively. The closing rate constant of alpha Y190F receptors was the same with ACh, carbamoylcholine, or tetramethylammonium as the agonist. This rate constant was approximately 3 times faster in ACh-activated S, W, and T mutants. The equilibrium dissociation constant for channel block by ACh was approximately 2-fold lower in alpha Y190F receptors compared with in wildtype receptors, suggesting that there are changes in the pore region of the receptor as a consequence of the mutation. The activation reaction is discussed with regard to energy provided by agonist-receptor binding contacts, and by the intrinsic folding energy of the receptor.     

Stoichiometry of Recombinant N-Methyl-d-Aspartate Receptor Channels Inferred from Single-channel Current Patterns

Single-channel currents were recorded from mouse NR1-NR2B (ζ-ε₂) receptors containing mixtures of wild-type and mutant subunits expressed in Xenopus oocytes. Mutant subunits had an asparagine-to-glutamine (N-to-Q) mutation at the N₀ site of the M2 segment (NR1:598, NR2B:589). Receptors with pure N or Q NR1 and NR2 subunits generated single-channel currents with distinctive current patterns. Based on main and sublevel amplitudes, occupancy probabilities, and lifetimes, four patterns of current were identified, corresponding to receptors with the following subunit compositions (NR1/NR2): N/N, N/Q, Q/N, and Q/Q. Only one current pattern was apparent for each composition. When a mixture of N and Q NR2 subunits was coexpressed with pure mutant NR1 subunits, three single-channel current patterns were apparent. One pattern was the same as Q/Q receptors and another was the same as Q/N receptors. The third, novel pattern presumably arose from hybrid receptors having both N and Q NR2 subunits. When a mixture of N and Q NR1 subunits was coexpressed with pure mutant NR2 subunits, six single-channel current patterns were apparent. One pattern was the same as Q/Q receptors and another was the same as N/Q receptors. The four novel patterns presumably arose from hybrid receptors having both N and Q NR1 subunits. The relative frequency of NR1 hybrid receptor current patterns depended on the relative amounts of Q and N subunits that were injected into the oocytes. The number of hybrid receptor patterns suggests that there are two NR2 subunits per receptor and is consistent with either three or five NR1 subunits per receptor, depending on whether or not the order of mutant and wild-type subunits influences the current pattern. When considered in relation to other studies, the most straightforward interpretation of the results is that N-methyl-d-aspartate receptors are pentamers composed of three NR1 and two NR2 subunits.