Software Extensions to UCSF Chimera for Interactive Visualization of Large Molecular Assemblies

SummaryMany structures of large molecular assemblies such as virus capsids and ribosomes have been experimentally determined to atomic resolution. We consider four software problems that arise in interactive visualization and analysis of large assemblies: how to represent multimers efficiently, how to make cartoon representations, how to calculate contacts efficiently, and how to select subassemblies. We describe techniques and algorithms we have developed and give examples of their use. Existing molecular visualization programs work well for single protein and nucleic acid molecules and for small complexes. The methods presented here are proposed as features to add to existing programs or include in next-generation visualization software to allow easy exploration of assemblies containing tens to thousands of macromolecules. Our approach is pragmatic, emphasizing simplicity of code, reliability, and speed. The methods described have been distributed as the Multiscale extension of the UCSF Chimera (www.cgl.ucsf.edu/chimera) molecular graphics program

Duality Invariant Magnetohydrodynamics And Dyons

The theory of magnetohydrodynamics is extended to the cases of a plasma of separate magnetic and electric charges, as well as to a plasma of dyons respectively. In both these cases the system possesses electric-magnetic duality symmetry. In the former case we find that because of the existence of two independent generalized Ohm's law equations, the limit of infinite electric and magnetic conductivity results in the vanishing of both electric and magnetic fields, as well as the corresponding currents. In the dyonic case, we find that the resulting duality-invariant system of equations are equivalent to those of ordinary MHD, after suitable field redefinitions.Comment: 11 pages, late

Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions

Cryo-electron microscopy produces 3D density maps of molecular machines, which consist of various molecular components such as proteins and RNA. Segmentation of individual components in such maps is a challenging task, and is mostly accomplished interactively. We present an approach based on the immersive watershed method and grouping of the resulting regions using progressively smoothed maps. The method requires only three parameters: the segmentation threshold, a smoothing step size, and the number of smoothing steps. We first apply the method to maps generated from molecular structures and use a quantitative metric to measure the segmentation accuracy. The method does not attain perfect accuracy, however it produces single or small groups of regions that roughly match individual proteins or subunits. We also present two methods for fitting of structures into density maps, based on aligning the structures with single regions or small groups of regions. The first method aligns centers and principal axes, whereas the second aligns centers and then rotates the structure to find the best fit. We describe both interactive and automated ways of using these two methods. Finally, we show segmentation and fitting results for several experimentally-obtained density maps.National Institutes of Health (U.S.) (Grant PN2EY016525)National Institutes of Health (U.S.) (Grant R01GM079429)National Institutes of Health (U.S.) (Grant P41RR02250)National Science Foundation (U.S.) (IIS-0705644

The weak imprint of environment on the stellar populations of galaxies

We investigate the environmental dependence of the stellar populations of galaxies in SDSS DR7. Echoing earlier works, we find that satellites are both more metal-rich (<0.1dex) and older (<2Gyr) than centrals of the same stellar mass. However,after separating star-forming, green valley and passive galaxies, we find that the true environmental dependence of both stellar metallicity (<0.03dex) and age (<0.5Gyr) is in fact much weaker. We show that the strong environmental effects found when galaxies are not differentiated result from a combination of selection effects brought about by the environmental dependence of the quenched fraction of galaxies, and thus we strongly advocate for the separation of star-forming, green valley and passive galaxies when the environmental dependence of galaxy properties are investigated.We also study further environmental trends separately for both central and satellite galaxies. We find that star-forming galaxies show no environmental effects, neither for centrals nor for satellites. In contrast, the stellar metallicities of passive and green valley satellites increase weakly with increasing halo mass, increasing local overdensity and decreasing projected distance from their central; this effect is interpreted in terms of moderate environmental starvation (‘strangulation’) contributing to the quenching of satellite galaxies. Finally, we find a unique feature in the stellar mass–stellar metallicity relation for passive centrals, where galaxies in more massive haloes have larger stellar mass at constant stellar metallicity; this effect is interpreted in terms of dry merging of passive central galaxies and/or progenitor bias.ERC STF

Assessment of the feasibility of the use of conductive polymers in the fabrication of ion mobility spectrometers

The development of an ion mobility spectrometer with an injection molded plastic drift tube made from carbon-loaded nylon and the cyclo-olefinpolymer Zeonex is described. Thermogravimetric assessment combined with headspace analysis by ion mobility spectrometry and gas chromatography−mass spectrometry indicated that Zeonex encapsulated carbon-loaded nylon could be used to fabricate a snap-together injection molded stacked ring drift tube, 4.25 cm long that could be substituted for a conventional wire-wound heated ceramic drift tube of the same length into a high temperature ion mobility spectrometer. Temperature stability experiments indicated that such a combination of polymers produced stable water-based reactant ion peaks [(H2O)nH]+ up to a temperature of approximately 50 °C. Above this temperature, ammonia appeared to outgas, resulting in the production of [(H2O)n(NH4)mH]+ type species before, at higher temperatures, the release of oligomeric entities suppressed resolved ion responses. Surface charging effects were also observed, and over a period of continuous operation of 4 h, these caused suppression of the signal intensity (1.11−0.954 V) and an apparent mobility shift in the observed responses (K0 = 1.86−1.90 cm2 V−1 s−1). Substituting nylon, a polymer with a significantly lower surface resistivity, for the Zeonex demonstrated how surface charging phenomena could be managed though control of surface resistivity in future polymer formulations. The device was challenged successfully with test atmospheres of hexan-1-ol (K0 = 1.66 cm2 V−1 s−1 (monomer) and 1.32 cm2 V−1 s−1(dimer)) and dimethylmethyl phosphonate (K0 = 1.70 cm2 V−1 s−1 (monomer) and 1.44 cm2 V−1 s−1 (dimer)). The potential advantages of developing polymeric systems using more advanced polymer formulations are discussed

Culture-independent detection of nontuberculous mycobacteria in clinical respiratory samples

Culture-based detection of nontuberculous Mycobacteria (NTM) in respiratory samples is time consuming and can be subject to overgrowth by nonmycobacterial bacteria. We describe a single-reaction TaqMan quantitative PCR assay for the direct detection of NTM species in clinical samples that is specific, sensitive, and robust

Dose-dependent genetic resistance to azole fungicides found in the apple scab pathogen

The evolution of azole resistance in fungal pathogens presents a major challenge in both crop production and human health. Apple orchards across the world are faced with the emergence of azole fungicide resistance in the apple scab pathogen Venturia inaequalis. Target site point mutations observed in this fungus to date cannot fully explain the reduction in sensitivity to azole fungicides. Here, polygenic resistance to tebuconazole was studied across a population of V. inaequalis. Genotyping by sequencing allowed Quantitative Trait Loci (QTLs) mapping to identify the genetic components controlling this fungicide resistance. Dose-dependent genetic resistance was identified, with distinct genetic components contributing to fungicide resistance at different exposure levels. A QTL within linkage group seven explained 65% of the variation in the effective dose required to reduce growth by 50% (ED50). This locus was also involved in resistance at lower fungicide doses (ED10). A second QTL in linkage group one was associated with dose-dependent resistance, explaining 34% of variation at low fungicide doses (ED10), but did not contribute to resistance at higher doses (ED50 and ED90). Within QTL regions, non-synonymous mutations were observed in several ATP-Binding Cassette and Major Facilitator SuperFamily transporter genes. These findings provide insight into the mechanisms of fungicide resistance that have evolved in horticultural pathogens. Identification of resistance gene candidates supports the development of molecular diagnostics to inform management practices

Stress in frictionless granular material: Adaptive Network Simulations

We present a minimalistic approach to simulations of force transmission through granular systems. We start from a configuration containing cohesive (tensile) contact forces and use an adaptive procedure to find the stable configuration with no tensile contact forces. The procedure works by sequentially removing and adding individual contacts between adjacent beads, while the bead positions are not modified. In a series of two-dimensional realizations, the resulting force networks are shown to satisfy a linear constraint among the three components of average stress, as anticipated by recent theories. The coefficients in the linear constraint remain nearly constant for a range of shear loadings up to about .6 of the normal loading. The spatial distribution of contact forces shows strong concentration along ``force chains". The probability of contact forces of magnitude f shows an exponential falloff with f. The response to a local perturbing force is concentrated along two characteristic rays directed downward and laterally.Comment: 8 pages, 8 figure

Can fusion coefficients be calculated from the depth rule ?

The depth rule is a level truncation of tensor product coefficients expected to be sufficient for the evaluation of fusion coefficients. We reformulate the depth rule in a precise way, and show how, in principle, it can be used to calculate fusion coefficients. However, we argue that the computation of the depth itself, in terms of which the constraints on tensor product coefficients is formulated, is problematic. Indeed, the elements of the basis of states convenient for calculating tensor product coefficients do not have a well-defined depth! We proceed by showing how one can calculate the depth in an `approximate' way and derive accurate lower bounds for the minimum level at which a coupling appears. It turns out that this method yields exact results for $\widehat{su}(3)$ and constitutes an efficient and simple algorithm for computing $\widehat{su}(3)$ fusion coefficients.Comment: 27 page

Hectospec, the MMT's 300 Optical Fiber-Fed Spectrograph

The Hectospec is a 300 optical fiber fed spectrograph commissioned at the MMT in the spring of 2004. A pair of high-speed six-axis robots move the 300 fiber buttons between observing configurations within ~300 s and to an accuracy ~25 microns. The optical fibers run for 26 m between the MMT's focal surface and the bench spectrograph operating at R~1000-2000. Another high dispersion bench spectrograph offering R~5,000, Hectochelle, is also available. The system throughput, including all losses in the telescope optics, fibers, and spectrograph peaks at ~10% at the grating blaze in 1" FWHM seeing. Correcting for aperture losses at the 1.5" diameter fiber entrance aperture, the system throughput peaks at $\sim$17%. Hectospec has proven to be a workhorse instrument at the MMT. Hectospec and Hectochelle together were scheduled for 1/3 of the available nights since its commissioning. Hectospec has returned \~60,000 reduced spectra for 16 scientific programs during its first year of operation.Comment: 68 pages, 28 figures, to appear in December 2005 PAS