Biased Monte Carlo optimization of protein sequences

We demonstrate the application of a biased Monte Carlo method for the optimization of protein sequences. The concept of configurational-biased Monte Carlo has been used, but applied to sequence/composition rather than coordinates. Sequences of two-dimensional lattice proteins were optimized with the new approach and results compared with conventional Monte Carlo and a self-consistent mean-field (SCMF) method. Biased Monte Carlo(MC) was far more efficient than conventional MC, especially on more complex systems and with faster cooling rates. Biased MC did not converge as quickly as SCMF, but often found better sequences

A contribution to an understanding of landscape development through three-dimensional morphological analysis of a pedological cover (Paulinia, State of Sao Paulo, Brazil) = Contribution à l'analyse morphologique tridimensionnelle de la couverture pédologique à la reconstitution de l'évolution du modelé (Paulinia, Etat de Sao Paulo, Brésil)

L'organisation tridimensionnelle d'une couverture pédologique, comprenant l'étude des relations géométriques entre horizons, et particulièrement des relations de concordance ou de discordance, permet de reconstituer certaines étapes de l'évolution du modelé. Le versant étudié, situé en zone tropicale humide (Brésil atlantique), présente à l'amont une couverture ferrallitique très épaisse (> 10 m) constituée d'horizons à limites subhorizontales. La partie supérieure de cette couverture est recoupée par une différenciation pédologique moins développée. Cette dernière est concordante à la topographie actuelle et s'est développée le long du versant à partir des horizons successifs de la couverture ferrallitique jusqu'au substratum. Lorsque ce substratum est atteint, des sols lithodépendants se forment à partir des grès, siltites et argilites de la "formation Tubarao" (permo-carbonifère). Cette discordance entre la différenciation superficielle et les horizons de la couverture ferrallitique implique que la première est plus récente que la seconde. Plus à l'aval, une couverture épaisse réapparaît qui a pu être raccordée à celle de l'amont par l'étude selon le plan horizontal. En considérant que la géométrie de la couverture ferrallitique (limites entre horizons et front de structuration pédologique) est conforme à la surface topographique contemporaine de sa formation, il est possible de reconstituer cette dernière. La topographie actuelle apparaît alors comme partiellement incisée dans cette topographie ancienne. (Résumé d'auteur

Importance of food-demand management for climate mitigation

Recent studies show that current trends in yield improvement will not be sufficient to meet projected global food demand in 2050, and suggest that a further expansion of agricultural area will be required. However, agriculture is the main driver of losses of biodiversity and a major contributor to climate change and pollution, and so further expansion is undesirable. The usual proposed alternative - intensification with increased resource use - also has negative effects. It is therefore imperative to find ways to achieve global food security without expanding crop or pastureland and without increasing greenhouse gas emissions. Some authors have emphasised a role for sustainable intensification in closing global 'yield gaps' between the currently realised and potentially achievable yields. However, in this paper we use a transparent, data-driven model, to show that even if yield gaps are closed, the projected demand will drive further agricultural expansion. There are, however, options for reduction on the demand side that are rarely considered. In the second part of this paper we quantify the potential for demand-side mitigation options, and show that improved diets and decreases in food waste are essential to deliver emissions reductions, and to provide global food security in 2050.This work was funded by a grant to the University of Cambridge from BP as part of their Energy Sustainability Challenge.This is the accepted manuscript version. The final version is available from Nature Climate Change at http://www.nature.com/nclimate/journal/vaop/ncurrent/full/nclimate2353.html

Earthworm communities in organic and conventional coffee cultivation.

The objective of this work was to evaluate the effect of organic and conventional coffee crops on biomass, population density and diversity of earthworms, in Lerroville, district of Londrina County, Paraná state, Brazil. Earthworm communities were sampled in three areas with organic coffee cultivation (CO1, CO2 and CO3), two with conventional coffee (CC1 and CC2), and a native forest fragment (MT). The soil of the areas CO1, CC1, and MT was classifi ed as Nitossolo Vermelho (Rhodic Kandiudox), while CO2, CO3, and CC2 were on Latossolo Vermelho (Rhodic Hapludox). Eight samples were taken in each area on two occasions, winter and summer, using the Tropical Soil Biology and Fertility (TSBF) method in the 0–20 cm soil layer. The earthworms were handsorted and preserved in 4% formaldehyde, and were later weighed, counted and identifi ed. The highest earthworm biomass, both in winter and summer, occurred in the CO3 area. For population density, the higher numbers of individuals were found in CO1 and CO3. The highest number of species was identifi ed in the organic cultivation. The adoption of organic practices in coffee cultivation favored the diversity, density and biomass of earthworm communities

Overexpression of stathmin in breast carcinomas points out to highly proliferative tumours

We recently discovered that stathmin was overexpressed in a subgroup of human breast carcinomas. Stathmin is a cytosolic phosphoprotein proposed to act as a relay integrating diverse cell signalling pathways, notably during the control of cell growth and differentiation. It may also be considered as one of the key regulators of cell division for its ability to destabilize microtubules in a phosphorylation-dependent manner. To assess the significance of stathmin overexpression in breast cancer, we evaluated the correlation of stathmin expression, quantified by reverse transcription polymerase chain reaction, with several disease parameters in a large series of human primary breast cancer (n = 133), obtained in strictly followed up women, whose clinico-pathological data were fully available. In agreement with our preliminary survey, stathmin was found overexpressed in a subgroup of tumours (22%). In addition, overexpression was correlated to the loss of steroid receptors (oestrogen, P = 0.0006; progesterone, P = 0.008), and to the Scarff–Bloom–Richardson histopathological grade III (P = 0.002), this latter being ascribable to the mitotic index component (P = 0.02). Furthermore studies at the DNA level indicated that stathmin is overexpressed irrespective of its genomic status. Our findings raise important questions concerning the causes and consequences of stathmin overexpression, and the reasons of its inability to counteract cell proliferation in the overexpression group. © 2000 Cancer Research Campaig

Motility of an autonomous protein-based artificial motor that operates via a burnt-bridge principle

Inspired by biology, great progress has been made in creating artificial molecular motors. However, the dream of harnessing proteins – the building blocks selected by nature – to design autonomous motors has so far remained elusive. Here we report the synthesis and characterization of the Lawnmower, an autonomous, protein-based artificial molecular motor comprised of a spherical hub decorated with proteases. Its “burnt-bridge” motion is directed by cleavage of a peptide lawn, promoting motion towards unvisited substrate. We find that Lawnmowers exhibit directional motion with average speeds of up to 80 nm/s, comparable to biological motors. By selectively patterning the peptide lawn on microfabricated tracks, we furthermore show that the Lawnmower is capable of track-guided motion. Our work opens an avenue towards nanotechnology applications of artificial protein motors