Delayed adenosine A1 receptor preconditioning in rat myocardium is MAPK dependent but iNOS independent

Adenosine A1 receptor delayed preconditioning (PC) against myocardial infarction has been well described; however, there have been limited investigations of the signaling mechanisms that mediate this phenomenon. In addition, there are multiple conflicting reports on the role of inducible nitric oxide synthase (iNOS) in mediating A1 late-phase PC. The purpose of this study was to determine the roles of the p38 and extracellular signal-regulated kinase (ERK) mitogen-activated protein kinases (MAPKs) in in vivo delayed A1 receptor PC and whether this protection at the myocyte level is due to upregulation of iNOS. Myocardial infarct size was measured in open-chest anesthetized rats 24 h after treatment with vehicle or the adenosine A1 agonist 2-chloro-N6-cyclopentyladenosine (CCPA; 100 microg/kg ip). Additional rats receiving CCPA were pretreated with the p38 inhibitor SB-203580 (1 mg/kg ip) or the MAPK/ERK kinase (MEK) inhibitor PD-098059 (0.5 mg/kg ip). At 24 h after CCPA administration, a group of animals was given the iNOS inhibitor 1400 W 10 min before ischemia. Treatment with CCPA reduced infarct size from 48 +/- 2 to 28 +/- 2% of the area at risk, an effect that was blocked by both SB-203580 and PD-098059 but not 1400 W. Ventricular myocytes isolated 24 h after CCPA injection exhibited significantly reduced oxidative stress during H2O2 exposure compared with myocytes from vehicle-injected animals, and this effect was not blocked by the iNOS inhibitor 1400 W. Western blot analysis of whole heart and cardiac myocyte protein samples revealed no expression of iNOS 6 or 24 h after CCPA treatment. These results indicate that adenosine A1 receptor delayed PC in rats is mediated by MAPK-dependent mechanisms, but this phenomenon is not associated with the early or late expression of iNOS.     

Nucleotide dependent motion and mechanism of action of p97/VCP

The AAA (ATPases associated with a variety of cellular activities) family of proteins bind, hydrolyze, and release ATP to effect conformational changes, assembly, or disassembly upon their binding partners and substrate molecules. One of the members of this family, the hexameric p97/valosin-containing protein p97/VCP, is essential for the dislocation of misfolded membrane proteins from the endoplasmic reticulum. Here, we observe large motions and dynamic changes of p97/VCP as it proceeds through the ATP hydrolysis cycle. The analysis is based on crystal structures of four representative ATP hydrolysis states: APO, AMP-PNP, hydrolysis transition state ADP x AlF3, and ADP bound. Two of the structures presented herein, ADP and AMP-PNP bound, are new structures, and the ADP x AlF3 structure was re-refined to higher resolution. The largest motions occur at two stages during the hydrolysis cycle: after, but not upon, nucleotide binding and then following nucleotide release. The motions occur primarily in the D2 domain, the D1 alpha-helical domain, and the N-terminal domain, relative to the relatively stationary and invariant D1alpha/beta domain. In addition to the motions, we observed a transition from a rigid state to a flexible state upon loss of the gamma-phosphate group, and a further increase in flexibility within the D2 domains upon nucleotide release. The domains within each protomer of the hexameric p97/VCP deviate from strict 6-fold symmetry, with the more flexible ADP state exhibiting greater asymmetry compared to the relatively rigid ADP x AlF3 state, suggesting a mechanism of action in which hydrolysis and conformational changes move about the hexamer in a processive fashion.     

Assessing the generality of global leaf trait relationships

Global-scale quantification of relationships between plant traits gives insight into the evolution of the world's vegetation, and is crucial for parameterizing vegetation-climate models. A database was compiled, comprising data for hundreds to thousands of species for the core 'leaf economics' traits leaf lifespan, leaf mass per area, photosynthetic capacity, dark respiration, and leaf nitrogen and phosphorus concentrations, as well as leaf potassium, photosynthetic N-use efficiency (PNUE), and leaf N : P ratio. While mean trait values differed between plant functional types, the range found within groups was often larger than differences among them. Future vegetation-climate models could incorporate this knowledge. The core leaf traits were intercorrelated, both globally and within plant functional types, forming a 'leaf economics spectrum'. While these relationships are very general, they are not universal, as significant heterogeneity exists between relationships fitted to individual sites. Much, but not all, heterogeneity can be explained by variation in sample size alone. PNUE can also be considered as part of this trait spectrum, whereas leaf K and N : P ratios are only loosely related.     

CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes

Background  

Online Mendelian Inheritance in Man (OMIM) is a computerized database of information about genes and heritable traits in human populations, based on information reported in the scientific literature. Our objective was to establish an automated text-mining system for OMIM that will identify genetically-related cancers and cancer-related genes. We developed the computer program CGMIM to search for entries in OMIM that are related to one or more cancer types. We performed manual searches of OMIM to verify the program results.     

Ubiquitinated proteins including uH2A on the human and mouse inactive X chromosome: enrichment in gene rich bands

The inactive X chromosome (Xi) forms a heterochromatic structure in the nucleus that is known to have several modifications to specific histones involving acetylation or methylation. Using three different antibodies in four different cell lines, we demonstrate that the Xi in human and mouse cells is highly enriched in ubiquitinated protein(s), much of which is polyubiquitinated. This ubiquitination appears specific for the Xi as it was not observed for centromeres or other regions of heterochromatin. Results using an antibody specific to ubiquitinated H2A provide a clear link between H2A ubiquitination and gene repression, as visualized across an entire inactive chromosome. Interestingly, the ubiquitination of the chromosome persists into mitosis and can be seen in a reproducible banded pattern. This pattern matches that of Xist RNA which forms bands as it detaches from the mitotic X chromosome. Both ubiquitination and Xist RNA appear enriched in gene dense regions and depleted in gene poor bands, but do not correlate with L1 LINE elements which have been suggested as key to X-inactivation. These results provide evidence that ubiquitination along with Xist RNA plays an important role in the formation of facultative heterochromatin during X-inactivation.     

Effects of the geometry of the immunological synapse on the delivery of effector molecules

Recent experiments focusing on the function of the immunological synapse formed between a T cell and an antigen-presenting cell raise many questions about its purpose. We examine the proposal that the close apposition of the cell membranes in the central region of the synapse acts to focus T-cell secretions on the target cell, thus reducing the effect on nearby cells. We show that the efficiency of targeted T-cell responses to closely apposed cells is only weakly dependent on the distance between the cells. We also calculate effective (diffusion-limited) rates of binding and unbinding for molecules secreted within the synapse. We apply our model to the stimulation of B cells by secreted interleukin-4 (IL-4), and find that very few molecules of IL-4 need be released to essentially saturate the IL-4 receptors on the B-cell surface.     

The solution structure and oligomerization behavior of two bacterial toxins: pneumolysin and perfringolysin O

Pneumolysin (PLY), an important protein virulence factor of the human bacterial pathogen Streptococcus pneumoniae, could be a candidate for inclusion in a new anti-streptococcal vaccine. PLY solution species from monomer via multimeric intermediates to ring-shaped oligomers were studied with time-dependent sedimentation velocity in the analytical ultracentrifuge (AUC). Hydrodynamic bead modeling was used to interpret the data obtained. PLY remained mostly monomeric in solution; intermediate PLY multimers were detected in small quantities. Current understanding of PLY molecular mechanism is guided by a model built on the basis of its homology with perfringolysin O (PFO) for which there is an atomic structure. PFO, a virulence factor of the organism Clostridium perfringens, has almost the same molecular mass as PLY and shares 48% sequence identity and 60% sequence similarity with PLY. We report a comparative low-resolution structural study of PLY and PFO using AUC and small-angle x-ray scattering (SAXS). AUC data demonstrate that both proteins in solution are mostly monodisperse but PLY is a monomer whereas PFO is mostly dimeric. Ab initio dummy atom and dummy residue models for PFO and PLY were restored from the distance distribution function derived from experimental small-angle x-ray scattering curves. In solution, PLY is elongated, consistent with the shape predicted by its high-resolution homology model. The PFO dimer is also an elongated particle whose shape and volume are consistent with a staggered antiparallel dimer.     

Low-resolution reconstruction of a synthetic DNA holliday junction

We have studied the low-resolution solution conformation of a Holliday (or four-way) DNA junction by using small-angle x-ray scattering, sedimentation velocity, and computational modeling techniques. The scattering data were analyzed in two independent ways: firstly, by rigid-body modeling of the scattering data using previously suggested models for the Holliday junction (HJ), and secondly, by ab initio reconstruction methods. The models found by both methods agree with experimentally determined sedimentation coefficients and are compatible with the results of previous studies using different techniques, but provide a more direct and accurate determination of the solution conformation of the HJ. Our results show that addition of Mg(2+) alters the conformation of the HJ from an extended to a stacked arrangement.