Probing the nucleotide-binding activity of a redox sensor: two-component regulatory control in chloroplasts

Two-component signal transduction systems mediate adaptation to environmental changes in bacteria, plants, fungi, and protists. Each two-component system consists of a sensor histidine kinase and a response regu- lator. Chloroplast sensor kinase (CSK) is a modified sensor histidine kinase found in chloroplasts—photosynthetic organelles of plants and algae. CSK regulates the tran- scription of chloroplast genes in response to changes in photosynthetic electron transport. In this study, the full- length and truncated forms of Arabidopsis CSK proteins were overexpressed and purified in order to characterise their kinase and redox sensing activities. Our results show that CSK contains a modified kinase catalytic domain that binds ATP with high affinity and forms a quinone adduct that may confer redox sensing activity

Nanoindentation Of Si Nanostructures: Buckling And Friction At Nanoscales

A nanoindentation system was employed to characterize mechanical properties of silicon nanolines (SiNLs), which were fabricated by an anisotropic wet etching (AWE) process. The SiNLs had the linewidth ranging from 24 nm to 90 nm, having smooth and vertical sidewalls and the aspect ratio (height/linewidth) from 7 to 18. During indentation, a buckling instability was observed at a critical load, followed by a displacement burst without a load increase, then a full recovery of displacement upon unloading. This phenomenon was explained by two bucking modes. It was also found that the difference in friction at the contact between the indenter and SiNLs directly affected buckling response of these nanolines. The friction coefficient was estimated to be in a range of 0.02 to 0.05. For experiments with large indentation displacements, irrecoverable indentation displacements were observed due to fracture of Si nanolines, with the strain to failure estimated to be from 3.8% to 9.7%. These observations indicated that the buckling behavior of SiNLs depended on the combined effects of load, line geometry, and the friction at contact. This study demonstrated a valuable approach to fabrication of well-defined Si nanoline structures and the application of the nanoindentation method for investigation of their mechanical properties at the nanoscale.Microelectronics Research Cente

Oligomeric states in sodium ion-dependent regulation of cyanobacterial histidine kinase-2

Two-component signal transduction systems (TCSs) consist of sensor histidine kinases and response regulators. TCSs mediate adaptation to environmental changes in bacteria, plants, fungi and protists. Histidine kinase 2 (Hik2) is a sensor histidine kinase found in all known cyanobacteria and as chloroplast sensor kinase in eukaryotic algae and plants. Sodium ions have been shown to inhibit the autophosphorylation activity of Hik2 with precedes phosphoryl transfer to response regulators, but the mechanism of inhibition has not been determined. We report on the mechanism of Hik2 activation and inactivation probed by chemical cross-linking and size exclusion chromatography together with direct visualisation of the kinase using negative-stain transmission electron microscopy of single particles. We show that the functional form of Hik2 is a higher-order oligomer such as a hexamer or octamer. Increased NaCl concentration converts the active hexamer into an inactive tetramer. The action of NaCl appears to be confined to the Hik2 kinase domain

Langevin Trajectories between Fixed Concentrations

We consider the trajectories of particles diffusing between two infinite baths of fixed concentrations connected by a channel, e.g. a protein channel of a biological membrane. The steady state influx and efflux of Langevin trajectories at the boundaries of a finite volume containing the channel and parts of the two baths is replicated by termination of outgoing trajectories and injection according to a residual phase space density. We present a simulation scheme that maintains averaged fixed concentrations without creating spurious boundary layers, consistent with the assumed physics

Scaling in Complex Systems: Analytical Theory of Charged Pores

In this paper we find an analytical solution of the equilibrium ion distribution for a toroidal model of a ionic channel, using the Perfect Screening Theorem (PST). The ions are charged hard spheres, and are treated using a variational Mean Spherical Approximation (VMSA) . Understanding ion channels is still a very open problem, because of the many exquisite tuning details of real life channels. It is clear that the electric field plays a major role in the channel behaviour, and for that reason there has been a lot of work on simple models that are able to provide workable theories. Recently a number of interesting papers have appeared that discuss models in which the effect of the geometry, excluded volume and non-linear behaviour is considered. We present here a 3D model of ionic channels which consists of a charged, deformable torus with a circular or elliptical cross section, which can be flat or vertical (close to a cylinder). Extensive comparisons to MC simulations were performed. The new solution opens new possibilities, such as studying flexible pores, and water phase transformations inside the pores using an approach similar to that used on flat crystal surfaces

Evolution in the Disks and Bulges of Group Galaxies since z=0.4

We present quantitative morphology measurements of a sample of optically selected group galaxies at 0.3 < z < 0.55 using the Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS) and the GIM2D surface brightness--fitting software package. The group sample is derived from the Canadian Network for Observational Cosmology Field Redshift survey (CNOC2) and follow-up Magellan spectroscopy. We compare these measurements to a similarly selected group sample from the Millennium Galaxy Catalogue (MGC) at 0.05 < z < 0.12. We find that, at both epochs, the group and field fractional bulge luminosity (B/T) distributions differ significantly, with the dominant difference being a deficit of disk--dominated (B/T < 0.2) galaxies in the group samples. At fixed luminosity, z=0.4 groups have ~ 5.5 +/- 2 % fewer disk--dominated galaxies than the field, while by z=0.1 this difference has increased to ~ 19 +/- 6 %. Despite the morphological evolution we see no evidence that the group environment is actively perturbing or otherwise affecting the entire existing disk population. At both redshifts, the disks of group galaxies have similar scaling relations and show similar median asymmetries as the disks of field galaxies. We do find evidence that the fraction of highly asymmetric, bulge--dominated galaxies is 6 +/- 3 % higher in groups than in the field, suggesting there may be enhanced merging in group environments. We replicate our group samples at z=0.4 and z=0 using the semi-analytic galaxy catalogues of Bower et al (2006). This model accurately reproduces the B/T distributions of the group and field at z=0.1. However, the model does not reproduce our finding that the deficit of disks in groups has increased significantly since z=0.4.Comment: Accepted for publication in MNRAS. 20 pages, 17 figure

The Evolution of X-ray Clusters of Galaxies

Considerable progress has been made over the last decade in the study of the evolutionary trends of the population of galaxy clusters in the Universe. In this review we focus on observations in the X-ray band. X-ray surveys with the ROSAT satellite, supplemented by follow-up studies with ASCA and Beppo-SAX, have allowed an assessment of the evolution of the space density of clusters out to z~1, and the evolution of the physical properties of the intra-cluster medium out to z~0.5. With the advent of Chandra and Newton-XMM, and their unprecedented sensitivity and angular resolution, these studies have been extended beyond redshift unity and have revealed the complexity of the thermodynamical structure of clusters. The properties of the intra-cluster gas are significantly affected by non-gravitational processes including star formation and Active Galactic Nucleus (AGN) activity. Convincing evidence has emerged for modest evolution of both the bulk of the X-ray cluster population and their thermodynamical properties since redshift unity. Such an observational scenario is consistent with hierarchical models of structure formation in a flat low density universe with Omega_m=0.3 and sigma_8=0.7-0.8 for the normalization of the power spectrum. Basic methodologies for construction of X-ray-selected cluster samples are reviewed and implications of cluster evolution for cosmological models are discussed.Comment: 40 pages, 15 figures. Full resolution figures can be downloaded from http://www.eso.org/~prosati/ARAA

Optimality of mutation and selection in germinal centers

The population dynamics theory of B cells in a typical germinal center could play an important role in revealing how affinity maturation is achieved. However, the existing models encountered some conflicts with experiments. To resolve these conflicts, we present a coarse-grained model to calculate the B cell population development in affinity maturation, which allows a comprehensive analysis of its parameter space to look for optimal values of mutation rate, selection strength, and initial antibody-antigen binding level that maximize the affinity improvement. With these optimized parameters, the model is compatible with the experimental observations such as the ~100-fold affinity improvements, the number of mutations, the hypermutation rate, and the "all or none" phenomenon. Moreover, we study the reasons behind the optimal parameters. The optimal mutation rate, in agreement with the hypermutation rate in vivo, results from a tradeoff between accumulating enough beneficial mutations and avoiding too many deleterious or lethal mutations. The optimal selection strength evolves as a balance between the need for affinity improvement and the requirement to pass the population bottleneck. These findings point to the conclusion that germinal centers have been optimized by evolution to generate strong affinity antibodies effectively and rapidly. In addition, we study the enhancement of affinity improvement due to B cell migration between germinal centers. These results could enhance our understandings to the functions of germinal centers.Comment: 5 figures in main text, and 4 figures in Supplementary Informatio

Estimating High Spatial Resolution Air Temperature for Regions with Limited in situ Data Using MODIS Products

The use of land surface temperature and vertical temperature profile data from Moderate Resolution Imaging Spectroradiometer (MODIS), to estimate high spatial resolution daily and monthly maximum and minimum 2 m above ground level (AGL) air temperatures for regions with limited in situ data was investigated. A diurnal air temperature change model was proposed to consider the differences between the MODIS overpass times and the times of daily maximum and minimum temperatures, resulting in the improvements of the estimation in terms of error values, especially for minimum air temperature. Both land surface temperature and vertical temperature profile data produced relatively high coefficient of determination values and small Mean Absolute Error (MAE) and Root Mean Square Error (RMSE) values for air temperature estimation. The correction of the estimates using two gridded datasets, National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) reanalysis and Climate Research Unit (CRU), was performed and the errors were reduced, especially for maximum air temperature. The correction of daily and monthly air temperature estimates using the NCEP/NCAR reanalysis data, however, still produced relatively large error values compared to existing studies, while the correction of monthly air temperature estimates using the CRU data significantly reduced the errors; the MAE values for estimating monthly maximum air temperature range between 1.73 degrees C and 1.86 degrees C. Uncorrected land surface temperature generally performed better for estimating monthly minimum air temperature and the MAE values range from 1.18 degrees C to 1.89 degrees C. The suggested methodology on a monthly time scale may be applied in many data sparse areas to be used for regional environmental and agricultural studies that require high spatial resolution air temperature data.open

Simulational study of anomalous tracer diffusion in hydrogels

In this article, we analyze different factors that affect the diffusion behavior of small tracer particles (as they are used e.g.in fluorescence correlation spectroscopy (FCS)) in the polymer network of a hydrogel and perform simulations of various simplified models. We observe, that under certain circumstances the attraction of a tracer particle to the polymer network strands might cause subdiffusive behavior on intermediate time scales. In theory, this behavior could be employed to examine the network structure and swelling behavior of weakly crosslinked hydrogels with the help of FCS.Comment: 11 pages, 11 figure