TRAF6 protein couples Toll-like receptor 4 signaling to Src family kinase activation and opening of paracellular pathway in human lung microvascular endothelia

Gram-negative bacteria release lipopolysaccharide (LPS) into the bloodstream. Here, it engages Toll-like receptor (TLR) 4 expressed in human lung microvascular endothelia (HMVEC-Ls) to open the paracellular pathway through Src family kinase (SFK) activation. The signaling molecules that couple TLR4 to the SFK-driven barrier disruption are unknown. In HMVEC-Ls, siRNA-induced silencing of TIRAP/Mal and overexpression of dominant-negative TIRAP/Mal each blocked LPS-induced SFK activation and increases in transendothelial [(14)C]albumin flux, implicating the MyD88-dependent pathway. LPS increased TRAF6 autoubiquitination and binding to IRAK1. Silencing of TRAF6, TRAF6-dominant-negative overexpression, or preincubation of HMVEC-Ls with a cell-permeable TRAF6 decoy peptide decreased both LPS-induced SFK activation and barrier disruption. LPS increased binding of both c-Src and Fyn to GST-TRAF6 but not to a GST-TRAF6 mutant in which the three prolines in the putative Src homology 3 domain-binding motif (amino acids 461-469) were substituted with alanines. A cell-permeable decoy peptide corresponding to the same proline-rich motif reduced SFK binding to WT GST-TRAF6 compared with the Pro → Ala-substituted peptide. Finally, LPS increased binding of activated Tyr(P)(416)-SFK to GST-TRAF6, and preincubation of HMVEC-Ls with SFK-selective tyrosine kinase inhibitors, PP2 and SU6656, diminished TRAF6 binding to c-Src and Fyn. During the TRAF6-SFK association, TRAF6 catalyzed Lys(63)-linked ubiquitination of c-Src and Fyn, whereas SFK activation increased tyrosine phosphorylation of TRAF6. The TRAF6 decoy peptide blocked both LPS-induced SFK ubiquitination and TRAF6 phosphorylation. Together, these data indicate that the proline-rich Src homology 3 domain-binding motif in TRAF6 interacts directly with activated SFKs to couple LPS engagement of TLR4 to SFK activation and loss of barrier integrity in HMVEC-Ls.     

Responses of terrestrial ecosystems to temperature and precipitation change: a meta‐analysis of experimental manipulation

Global mean temperature is predicted to increase by 2–7 °C and precipitation to change across the globe by the end of this century. To quantify climate effects on ecosystem processes, a number of climate change experiments have been established around the world in various ecosystems. Despite these efforts, general responses of terrestrial ecosystems to changes in temperature and precipitation, and especially to their combined effects, remain unclear. We used meta‐analysis to synthesize ecosystem‐level responses to warming, altered precipitation, and their combination. We focused on plant growth and ecosystem carbon (C) balance, including biomass, net primary production (NPP), respiration, net ecosystem exchange (NEE), and ecosystem photosynthesis, synthesizing results from 85 studies. We found that experimental warming and increased precipitation generally stimulated plant growth and ecosystem C fluxes, whereas decreased precipitation had the opposite effects. For example, warming significantly stimulated total NPP, increased ecosystem photosynthesis, and ecosystem respiration. Experimentally reduced precipitation suppressed aboveground NPP (ANPP) and NEE, whereas supplemental precipitation enhanced ANPP and NEE. Plant productivity and ecosystem C fluxes generally showed higher sensitivities to increased precipitation than to decreased precipitation. Interactive effects of warming and altered precipitation tended to be smaller than expected from additive, single‐factor effects, though low statistical power limits the strength of these conclusions. New experiments with combined temperature and precipitation manipulations are needed to conclusively determine the importance of temperature–precipitation interactions on the C balance of terrestrial ecosystems under future climate conditions.     

Does the disturbance hypothesis explain the biomass increase in basin‐wide Amazon forest plot data?

Positive aboveground biomass trends have been reported from old-growth forests across the Amazon basin and hypothesized to reflect a large-scale response to exterior forcing. The result could, however, be an artefact due to a sampling bias induced by the nature of forest growth dynamics. Here, we characterize statistically the disturbance process in Amazon old-growth forests as recorded in 135 forest plots of the RAINFOR network up to 2006, and other independent research programmes, and explore the consequences of sampling artefacts using a data-based stochastic simulator. Over the observed range of annual aboveground biomass losses, standard statistical tests show that the distribution of biomass losses through mortality follow an exponential or near-identical Weibull probability distribution and not a power law as assumed by others. The simulator was parameterized using both an exponential disturbance probability distribution as well as a mixed exponential–power law distribution to account for potential large-scale blowdown events. In both cases, sampling biases turn out to be too small to explain the gains detected by the extended RAINFOR plot network. This result lends further support to the notion that currently observed biomass gains for intact forests across the Amazon are actually occurring over large scales at the current time, presumably as a response to climate change.     

Directionality in protein fold prediction

Background  

Ever since the ground-breaking work of Anfinsen et al. in which a denatured protein was found to refold to its native state, it has been frequently stated by the protein fold prediction community that all the information required for protein folding lies in the amino acid sequence. Recent in vitro experiments and in silico computational studies, however, have shown that cotranslation may affect the folding pathway of some proteins, especially those of ancient folds. In this paper aspects of cotranslational folding have been incorporated into a protein structure prediction algorithm by adapting the Rosetta program to fold proteins as the nascent chain elongates. This makes it possible to conduct a pairwise comparison of folding accuracy, by comparing folds created sequentially from each end of the protein.     

Exceptionally preserved tadpoles from the Miocene of Libros,Spain: ecomorphological reconstruction and the impact of ontogeny upon taphonomy

McNamara, M.E., Orr, P.J., Kearns, S.L., Alcalá, L., Anadón, P. & Peñalver‐Mollá, E. 2010: Exceptionally preserved tadpoles from the Miocene of Libros, Spain: ecomorphological reconstruction and the impact of ontogeny upon taphonomy. Lethaia, Vol. 43, pp. 290–306. The Libros exceptional biota from the Upper Miocene of NE Spain includes abundant frog tadpoles (Rana pueyoi) preserved in finely laminated lacustrine mudstones. The tadpoles exhibit a depressed body, short tail, low tail fins, dorso‐laterally directed eyes and jaw sheaths; these features identify the Libros tadpoles as members of the benthic lentic ecomorphological guild. This, the first ecomorphological reconstruction of a fossil tadpole, supports phylogenetic evidence that this ecology is a conserved ranid feature. The soft‐tissue features of the Libros tadpoles are characterized by several modes of preservation. The space occupied previously by the brain is defined by calcium carbonate, the nerve cord is defined by calcium phosphate, and jaw sheaths and bone marrow are preserved as organic remains. Gut contents (and coprolites adjacent to specimens) comprise ingested fine‐grained sedimentary detritus and epiphyton. The body outline and the eyespots, nares, abdominal cavity, notochord, caudal myotomes and fins are defined by a carbonaceous bacterial biofilm. A similar biofilm in adult specimens of R. pueyoi from Libros defines only the body outline, not any internal anatomical features. In the adult frogs, but not in the tadpoles, calcium phosphate and calcium sulphate precipitated in association with integumentary tissues. These differences in the mode of preservation between the adult frogs and tadpoles reflect ontogenetic factors. □Anuran, ecology, soft‐tissue, tadpoles, taphonomy.     

Warming and drought alter C and N concentration,allocation and accumulation in a Mediterranean shrubland

We investigated the effects of warming and drought on C and N concentrations, nitrogen use efficiency (NUE), and C and N accumulation in different ecosystem compartments. We conducted a 6-year (1999–2005) field experiment to simulate the climate conditions projected by IPCC models for the coming decades in a Mediterranean shrubland. We studied the two dominant species, Globularia alypum and Erica multiflora, and an N-fixing species, Dorycnium pentaphyllum, also abundant in this shrubland. Warming (1 °C) decreased N leaf concentrations by 25% and increased N stem concentrations by 40% in G. alypum. Although warming changed the available ammonium in soil in some seasons, it did not increase total soil N contents. Drought (19% average reduction in soil moisture) decreased leaf N concentrations in the two dominant shrub species, E. multiflora and G. alypum by 16% and 19%, respectively, and increased stem N concentrations by 56% and 40%, respectively. Neither warming nor drought changed the leaf N concentrations in the N-fixing species D. pentaphyllum, although warming increased stem N concentration by 9%. In G. alypum, the increase of stem N concentrations contributed to the observed increase of N accumulation in stem biomass in drought treatments with respect to control plots (8 kg N ha⁻¹). Neither warming nor drought changed NUE in the period 1999–2005. Warming increased soil organic C relative to drought. The effects of warming and drought on C and N concentrations, on N accumulation and on leaf/stem N distribution were not the result of dilution or concentration effects produced by changes in biomass accumulation. Other factors such as the changes in soil N availability, photosynthetic capacity, and plant internal C and N remobilization must be involved. These changes which differed depending on the species and the plant tissue show that the climate change projected for the coming decades will have significant effects on the C and N cycle and stoichiometry, with probable implications for ecosystem structure and function, such as changes in plant–herbivore relationships, decomposition rates or community species composition.