Protein multi-scale organization through graph partitioning and robustness analysis: Application to the myosin-myosin light chain interaction

Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the intricate coupling between the different scales. Starting from a physico-chemical atomistic network of interactions that encodes the structure of the protein, we introduce a methodology based on multi-scale graph partitioning that can uncover partitions and levels of organization of proteins that span the whole range of scales, revealing biological features occurring at different levels of organization and tracking their effect across scales. Additionally, we introduce a measure of robustness to quantify the relevance of the partitions through the generation of biochemically-motivated surrogate random graph models. We apply the method to four distinct conformations of myosin tail interacting protein, a protein from the molecular motor of the malaria parasite, and study properties that have been experimentally addressed such as the closing mechanism, the presence of conserved clusters, and the identification through computational mutational analysis of key residues for binding.Comment: 13 pages, 7 Postscript figure

Precipitation Water Stable Isotopes in the South Tibetan Plateau: Observations and Modeling

International audienceMeasurements of precipitation isotopic composition have been conducted on a daily basis for 1 yr at Bomi, in the southeast Tibetan Plateau, an area affected by the interaction of the southwest monsoon, the westerlies, and Tibetan high pressure systems, as well as at Lhasa, situated west of Bomi. The measured isotope signals are analyzed both on an event basis and on a seasonal scale using available meteorological information and airmass trajectories. The processes driving daily and seasonal isotopic variability are investigated using multidecadal climate simulations forced by twentieth-century boundary conditions and conducted with two different isotopic atmospheric general circulation models [the isotopic version of the Laboratoire de Meteorologie Dynamique GCM (LMDZiso) and the ECHAM4iso model]. Both models use specific nudging techniques to mimic observed atmospheric circulation fields. The models simulate a wet and cold bias on the Tibetan Plateau together with a dry bias in its southern part. A zoomed LMDZ simulation conducted with similar to 50-km local spatial resolution dramatically improves the simulation of isotopic compositions of precipitation on the Tibetan Plateau. Simulated water isotope fields are compared with new data and with previous observations, and regional differences in moisture origins are analyzed using back-trajectories. Here, the focus is on relationships between the water isotopes and climate variables on an event and seasonal scale and in terms of spatial and altitudinal isotopic gradients. Enhancing the spatial resolution is crucial for improving the simulation of the precipitation isotopic composition

Mutations in Hydin impair ciliary motility in mice

Chlamydomonas reinhardtii hydin is a central pair protein required for flagellar motility, and mice with Hydin defects develop lethal hydrocephalus. To determine if defects in Hydin cause hydrocephalus through a mechanism involving cilia, we compared the morphology, ultrastructure, and activity of cilia in wild-type and hydin mutant mice strains. The length and density of cilia in the brains of mutant animals is normal. The ciliary axoneme is normal with respect to the 9 + 2 microtubules, dynein arms, and radial spokes but one of the two central microtubules lacks a specific projection. The hydin mutant cilia are unable to bend normally, ciliary beat frequency is reduced, and the cilia tend to stall. As a result, these cilia are incapable of generating fluid flow. Similar defects are observed for cilia in trachea. We conclude that hydrocephalus in hydin mutants is caused by a central pair defect impairing ciliary motility and fluid transport in the brain

Improved Procedures for Purification of the Bandeiraea simplicifolia I Isolectins and Bandeiraea simplicifolia II Lectin by Affinity Chromatography

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66350/1/j.1432-1033.1980.tb07197.x.pd

Identification of the First Oomycete Mating-type Locus Sequence in the Grapevine Downy Mildew Pathogen, Plasmopara viticola

Mating types are self-incompatibility systems that promote outcrossing in plants, fungi, and oomycetes. Mating-type genes have been widely studied in plants and fungi but have yet to be identified in oomycetes, eukaryotic organisms closely related to brown algae that cause many destructive animal and plant diseases. We identified the mating-type locus of Plasmopara viticola, the oomycete responsible for grapevine downy mildew, one of the most damaging grapevine diseases worldwide. Using a genome-wide association approach, we identified a 570-kb repeat-rich non-recombining region controlling mating types, with two highly divergent alleles. We showed that one mating type was homozygous, whereas the other was heterozygous at this locus. The mating-type locus encompassed 40 genes, including one encoding a putative hormone receptor. Functional studies will, however, be required to validate the function of these genes and find the actual determinants of mating type. Our findings have fundamental implications for our understanding of the evolution of mating types, as they reveal a unique determinism involving an asymmetry of heterozygosity, as in sex chromosomes and unlike other mating-type systems. This identification of the mating-type locus in such an economically important crop pathogen also has applied implications, as outcrossing facilitates rapid evolution and resistance to harsh environmental conditions

Target atmospheric CO2: Supporting material

Additional material supporting the article "Target atmospheric CO2: Where should humanity aim?"Comment: 27 pages, 21 figures; final version accepted by Open Science Atmospheric Journal; main article separately submitted to arXiv as "Target atmospheric CO2: Where should humanity aim?", arxiv:0804.112

Temporal and spatial structure of multi‐millennial temperature changes at high latitudes during the Last Interglacial

The Last Interglacial (LIG, 129–116 thousand of years BP, ka) represents a test bed for climate model feedbacks in warmer-than-present high latitude regions. However, mainly because aligning different palaeoclimatic archives and from different parts of the world is not trivial, a spatio-temporal picture of LIG temperature changes is difficult to obtain. Here, we have selected 47 polar ice core and sub-polar marine sediment records and developed a strategy to align them onto the recent AICC2012 ice core chronology. We provide the first compilation of high-latitude temperature changes across the LIG associated with a coherent temporal framework built between ice core and marine sediment records. Our new data synthesis highlights non-synchronous maximum temperature changes between the two hemispheres with the Southern Ocean and Antarctica records showing an early warming compared to North Atlantic records. We also observe warmer than present-day conditions that occur for a longer time period in southern high latitudes than in northern high latitudes. Finally, the amplitude of temperature changes at high northern latitudes is larger compared to high southern latitude temperature changes recorded at the onset and the demise of the LIG. We have also compiled four data-based time slices with temperature anomalies (compared to present-day conditions) at 115 ka, 120 ka, 125 ka and 130 ka and quantitatively estimated temperature uncertainties that include relative dating errors. This provides an improved benchmark for performing more robust model-data comparison. The surface temperature simulated by two General Circulation Models (CCSM3 and HadCM3) for 130 ka and 125 ka is compared to the corresponding time slice data synthesis. This comparison shows that the models predict warmer than present conditions earlier than documented in the North Atlantic, while neither model is able to produce the reconstructed early Southern Ocean and Antarctic warming. Our results highlight the importance of producing a sequence of time slices rather than one single time slice averaging the LIG climate conditions

Developing a western Siberia reference site for tropospheric water vapour isotopologue observations obtained by different techniques (in situ and remote sensing)

Water stable isotopologues provide integrated tracers of the atmospheric water cycle, affected by changes in air mass origin, non-convective and convective processes and continental recycling. Novel remote sensing and in situ measuring techniques have recently offered opportunities for monitoring atmospheric water vapour isotopic composition. Recently developed infrared laser spectrometers allow for continuous in situ measurements of surface water vapour δD_v and δ¹⁸O_v. So far, very few intercomparisons of measurements conducted using different techniques have been achieved at a given location, due to difficulties intrinsic to the comparison of integrated with local measurements. Nudged simulations conducted with high-resolution isotopically enabled general circulation models (GCMs) provide a consistent framework for comparison with the different types of observations. Here, we compare simulations conducted with the ECHAM5-wiso model with two types of water vapour isotopic data obtained during summer 2012 at the forest site of Kourovka, western Siberia: hourly ground-based FTIR total atmospheric columnar δD_v amounts, and in situ hourly Picarro δD_v measurements. There is an excellent correlation between observed and predicted δD_v at surface while the comparison between water column values derived from the model compares well with FTIR estimates