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.     

HIV-1 down-modulates gamma signaling chain of Fc gamma R in human macrophages: a possible mechanism for inhibition of phagocytosis

HIV-1 infection impairs a number of macrophage effector functions, thereby contributing to development of opportunistic infections and the pathogenesis of AIDS. FcgammaR-mediated phagocytosis by human monocyte-derived macrophages (MDM) is inhibited by HIV-1 infection in vitro, and the underlying mechanism was investigated in this study. Inhibition of phagocytosis directly correlated with the multiplicity of HIV-1 infection. Expression of surface FcgammaRs was unaffected by HIV-1 infection, suggesting that inhibition of phagocytosis occurred during or after receptor binding. HIV-1 infection of MDM markedly inhibited tyrosine phosphorylation of the cellular proteins, which occurs following engagement of FcgammaRs, suggesting a defect downstream of initial receptor activation. FcgammaR-mediated phagocytosis in HIV-infected MDM was associated with inhibition of phosphorylation of tyrosine kinases from two different families, Hck and Syk, defective formation of Syk complexes with other tyrosine-phosphorylated proteins, and inhibition of paxillin activation. Down-modulation of protein expression but not mRNA of the gamma signaling subunit of FcgammaR (a docking site for Syk) was observed in HIV-infected MDM. Infection of MDM with a construct of HIV-1 in which nef was replaced with the gene for the gamma signaling subunit augmented FcgammaR-mediated phagocytosis, suggesting that down-modulation of gamma-chain protein expression in HIV-infected MDM caused the defective FcgammaR-mediated signaling and impairment of phagocytosis. This study is the first to demonstrate a specific alteration in phagocytosis signal transduction pathway, which provides a mechanism for the observed impaired FcgammaR-mediated phagocytosis in HIV-infected macrophages and contributes to the understanding of how HIV-1 impairs cell-mediated immunity leading to HIV-1 disease progression.     

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.     

Activation of the interleukin 2 receptor: a possible role for tyrosine phosphatases

Engagement of interleukin-2 (IL-2) mediates the heterodimeridation of the common beta chain (beta(c)) and common gamma chain (gamma(c)) of the IL-2 receptor (IL-2R). This is sufficient and necessary for receptor activation and signal transduction. It is generally held that the IL-2R is activated by the trans-activity of the protein tyrosine kinases (PTKs) Jak1 and Jak3 associated with beta(c) and gamma(c) respectively. Transduction of proliferative signals requires Jak3 activity. A Jak3 independent signalling pathway involving p56(lck), generating anti-apoptotic signals, can be observed and requires the PROX domain of gamma(c). p56(lck) can be activated by dephosphorylation of an inhibitory carboxyl terminal phosphorylated tyrosine residue (Y505). We propose that this is mediated by a PROX domain associated protein tyrosine phosphatase (PTP). Activation of p56(lck) alone is insufficient for transduction of proliferative signals and thus works in concert with Jak3 mediated receptor activation. This indicates that both gamma(c) domains are vital for signal transduction.     

ELEVENTH ANNUAL GENERAL MEETING OF THE LIMNOLOGICAL SOCIETY OF SOURTHERN AFRICA

SUMMARY

The classification of highveld pans by Geldenhuys (1982) emphasized the spatial diversity of morphology, vegetation and fauna. However, since the characteristics of individual pans also change seasonally and over longer term wet/dry cycles, he called for more detailed limnological studies to improve predictive and management potential. Marked changes occurred in the physical, chemical and biological characteristics of Rolfes pan in response to winter drawdown following dry (1983) and wet (1986) summers. The constancy of physical and chemical conditions during 1986 contrasted with rapid changes in temperature, turbidity, conductivity and salinity as benthic plants disappeared in 1983. The abundance of emergent vegetation provided breeding sites for certain wetland birds in 1986 but shallow water and submerged plants attracted wading birds in 1983. Changes within and between years highlighted the importance of three distinctive limnological characteristics of pans; large surface area to volume ratio, large littoral zone to open water ratio and an endorheic hydrological regime. Conservation of pans, beginning with inventory and classification, must focus on describing systems on the basis of these three characteristics, recognizing that activities in the catchment act through them to alter ecosystem properties.     

Plant community and landscape patterns of a floodplain wetland in Maputaland, Northern KwaZulu-Natal, South Africa

The lower Mkuze River floodplain is located east of the Lebombo Mountains on the Maputaland Coastal Plain in northern KwaZulu‐Natal, South Africa. The vegetation ecology of the floodplain was examined using the hierarchical framework described by landscape ecology theory. The smallest spatial scale to which the vegetation of the floodplain was described was the relatively homogeneous units of plant communities. From a landscape ecology perspective this level of analysis is referred to as the grain. Six plant communities were identified using two‐way indicator species analysis (TWINSPAN) classification. The distribution of these plant communities were correlated to an underlying inundation‐sedimentation gradient using the ordination technique, detrended correspondence analysis (DCA). This correlation provided a useful foundation for the examination of ecological processes and phenomena at the next higher, spatially coarser level within the landscape hierarchy, namely the reference level. This reference level was described by three functional types delimited by differing flooding and sedimentation regimes. The use of landscape ecology theory guided the interpretation of results by explicitly recognizing the importance of spatial heterogeneity, hierarchical organization and dynamics, and proved invaluable in developing process‐based understanding of the vegetation ecology of the lower Mkuze River floodplain.