Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae

Extracytoplasmic solute receptors (ESRs) are important components of solute uptake systems in bacteria, having been studied extensively as parts of ATP binding cassette transporters. Herein we report the first crystal structure of an ESR protein from a functionally characterized electrochemical ion gradient-dependent secondary transporter. This protein, SiaP, forms part of a tripartite ATP-independent periplasmic transporter specific for sialic acid in Haemophilus influenzae. Surprisingly, the structure reveals an overall topology similar to ATP binding cassette ESR proteins, which is not apparent from the sequence, demonstrating that primary and secondary transporters can share a common structural component. The structure of SiaP in the presence of the sialic acid analogue 2,3-didehydro-2-deoxyN-acetylneuraminic acid reveals the ligand bound in a deep cavity with its carboxylate group forming a salt bridge with a highly conserved Arg residue. Sialic acid binding, which obeys simple bimolecular association kinetics as determined by stopped-flow fluorescence spectroscopy, is accompanied by domain closure about a hinge region and the kinking of an alpha-helix hinge component. The structure provides insight into the evolution, mechanism, and substrate specificity of ESR-dependent secondary transporters that are widespread in prokaryotes

From field to plate - How do bacterial enteric pathogens interact with ready-to-eat fruit and vegetables, causing disease outbreaks?

Ready-to-eat fruit and vegetables are a convenient source of nutrients and fibre for consumers, and are generally safe to eat, but are vulnerable to contamination with human enteric bacterial pathogens. Over the last decade, Salmonella spp., pathogenic Escherichia coli, and Listeria monocytogenes have been linked to most of the bacterial outbreaks of foodborne illness associated with fresh produce. The origins of these outbreaks have been traced to multiple sources of contamination from pre-harvest (soil, seeds, irrigation water, domestic and wild animal faecal matter) or post-harvest operations (storage, preparation and packaging). These pathogens have developed multiple processes for successful attachment, survival and colonization conferring them the ability to adapt to multiple environments. However, these processes differ across bacterial strains from the same species, and across different plant species or cultivars. In a competitive environment, additional risk factors are the plant microbiome phyllosphere and the plant responses; both factors directly modulate the survival of the pathogens on the leaf's surface. Understanding the mechanisms involved in bacterial attachment to, colonization of, and proliferation, on fresh produce and the role of the plant in resisting bacterial contamination is therefore crucial to reducing future outbreaks

The mass and density of the dwarf planet (225088) 2007 OR10

The satellite of (225088) 2007 OR10 was discovered on archival Hubble Space Telescope images and along with new observations with the WFC3 camera in late 2017 we have been able to determine the orbit. The orbit's notable eccentricity, e$\approx$0.3, may be a consequence of an intrinsically eccentric orbit and slow tidal evolution, but may also be caused by the Kozai mechanism. Dynamical considerations also suggest that the moon is small, D$_{eff}$ $<$ 100 km. Based on the newly determined system mass of 1.75x10$^{21}$ kg, 2007 OR10 is the fifth most massive dwarf planet after Eris, Pluto, Haumea and Makemake. The newly determined orbit has also been considered as an additional option in our radiometric analysis, provided that the moon orbits in the equatorial plane of the primary. Assuming a spherical shape for the primary this approach provides a size of 1230$\pm$50 km, with a slight dependence on the satellite orbit orientation and primary rotation rate chosen, and a bulk density of 1.75$\pm$0.07 g cm$^{-3}$ for the primary. A previous size estimate that assumed an equator-on configuration (1535$^{+75}_{-225}$ km) would provide a density of 0.92$^{+0.46}_{-0.14}$ g cm$^{-3}$, unexpectedly low for a 1000 km-sized dwarf planet.Comment: Accepted for publication in Icaru

Spitzer View of Massive Star Formation in the Tidally Stripped Magellanic Bridge

The Magellanic Bridge is the nearest low-metallicity, tidally stripped environment, offering a unique high-resolution view of physical conditions in merging and forming galaxies. In this paper we present analysis of candidate massive young stellar objects (YSOs), i.e., {\it in situ, current} massive star formation (MSF) in the Bridge using {\it Spitzer} mid-IR and complementary optical and near-IR photometry. While we definitely find YSOs in the Bridge, the most massive are $\sim10 M_\odot$, $\ll45 M_\odot$ found in the Large Magellanic Cloud (LMC). The intensity of MSF in the Bridge also appears decreasing, as the most massive YSOs are less massive than those formed in the past. To investigate environmental effects on MSF, we have compared properties of massive YSOs in the Bridge to those in the LMC. First, YSOs in the Bridge are apparently less embedded than in the LMC: 81% of Bridge YSOs show optical counterparts, compared to only 56% of LMC sources with the same range of mass, circumstellar dust mass, and line-of-sight extinction. Circumstellar envelopes are evidently more porous or clumpy in the Bridge's low-metallicity environment. Second, we have used whole samples of YSOs in the LMC and the Bridge to estimate the probability of finding YSOs at a given \hi\ column density, N(HI). We found that the LMC has $\sim3\times$ higher probability than the Bridge for N(HI) $>10\times10^{20}$ cm$^{-2}$, but the trend reverses at lower N(HI). Investigating whether this lower efficiency relative to HI is due to less efficient molecular cloud formation, or less efficient cloud collapse, or both, will require sensitive molecular gas observations.Comment: 41 pages, 20 figures, 6 tables; accepted for publication in ApJ; several figures are in low resolution due to the size limit here and a high resolution version can be downloaded via http://www.astro.virginia.edu/~cc5ye/ms_bridge20140215.pd

The Emerging QCD Frontier: The Electron Ion Collider

The self-interactions of gluons determine all the unique features of QCD and lead to a dominant abundance of gluons inside matter already at moderate $x$. Despite their dominant role, the properties of gluons remain largely unexplored. Tantalizing hints of saturated gluon densities have been found in $e$+p collisions at HERA, and in d+Au and Au+Au collisions at RHIC. Saturation physics will have a profound influence on heavy-ion collisions at the LHC. But unveiling the collective behavior of dense assemblies of gluons under conditions where their self-interactions dominate will require an Electron-Ion Collider (EIC): a new facility with capabilities well beyond those In this paper I outline the compelling physics case for $e$+A collisions at an EIC and discuss briefly the status of machine design concepts. of any existing accelerator.Comment: 11 pages, 9 figures, prepared for 20th International Conference on Ultra-Relativistic Nucleus-Nucleus Collisions: Quark Matter 2008 (QM2008), Jaipur, India, 4-10 Feb. 200

Overcoming information reduced data and experimentally uncertain parameters in ptychography with regularized optimization

The overdetermination of the mathematical problem underlying ptychography is reduced by a host of experimentally more desirable settings. Furthermore, reconstruction of the sample-induced phase shift is typically limited by uncertainty in the experimental parameters and finite sample thicknesses. Presented is a conjugate gradient descent algorithm, regularized optimization for ptychography (ROP), that recovers the partially known experimental parameters along with the phase shift, improves resolution by incorporating the multislice formalism to treat finite sample thicknesses, and includes regularization in the optimization process, thus achieving reliable results from noisy data with severely reduced and underdetermined information.Comment: 18 pages, 7 figures, 3 table

Thomas rotation and Thomas precession

Exact and simple calculation of Thomas rotation and Thomas precessions along a circular world line is presented in an absolute (coordinate-free) formulation of special relativity. Besides the simplicity of calculations the absolute treatment of spacetime allows us to gain a deeper insight into the phenomena of Thomas rotation and Thomas precession.Comment: 20 pages, to appear in Int. J. Theo. Phy

Fine structure, magnetic field and heating of sunspot penumbrae

We interpret penumbral filaments as due to convection in field-free, radially aligned gaps just below the visible surface of the penumbra, intruding into a nearly potential field above. This solves the classical discrepancy between the large heat flux and the low vertical velocities observed in the penumbra. The presence of the gaps causes strong small-scale fluctuations in inclination, azimuth angle and field strength, but without strong forces acting on the gas. The field is nearly horizontal in a region around the cusp-shaped top of the gap, thereby providing an environment for Evershed flows. We identify this region with the recently discovered dark penumbral cores. Its darkness has the same cause as the dark lanes in umbral light-bridges, reproduced in numerical simulations by Nordlund and Stein (2005). We predict that the large vertical and horizontal gradients of the magnetic field inclination and azimuth in the potential field model will produce the net circular polarization seen in observations. The model also explains the significant elevation of bright filaments above their surroundings. It predicts that dark areas in the penumbra are of two different kinds: dark filament cores containing the most inclined (horizontal) fields, and regions between bright filaments, containing the least inclined field lines.Comment: submitted to A&

Functional Traits of Tropical Trees and Lianas Explain Spatial Structure across Multiple Scales

Dispersal and density dependence are major determinants of spatial structure, population dynamics and coexistence for tropical forest plants. However, because these two processes can jointly influence spatial structure at similar scales, analysing spatial patterns to separate and quantify them is often difficult. Species functional traits can be useful indicators of dispersal and density dependence. However, few methods exist for linking functional traits to quantitative estimates of these processes that can be compared across multiple species. We analysed static spatial patterns of woody plant populations in the 50 ha Forest Dynamics Plot on Barro Colorado Island, Panama with methods that distinguished scale‐specific differences in species aggregation. We then tested how these differences related to seven functional traits: growth form, dispersal syndrome, tree canopy layer, adult stature, seed mass, wood density and shade tolerance. Next, we fit analytically tractable spatial moment models to the observed spatial structure of species characterized by similar trait values, which allowed us to estimate relationships of functional traits with the spatial scale of dispersal, and the spatial scale and intensity of negative density dependence. Our results confirm that lianas are more aggregated than trees, and exhibit increased aggregation within canopy gaps. For trees, increased seed mass, wood density and shade tolerance were associated with less intense negative density dependence, while higher canopy layers and increased stature were associated with decreased aggregation and better dispersal. Spatial structure for trees was also strongly determined by dispersal syndrome. Averaged across all spatial scales, zoochory was more effective than wind dispersal, which was more effective than explosive dispersal. However, at intermediate scales, zoochory was associated with more aggregation than wind dispersal, potentially because of differences in short‐distance dispersal and the intensity of negative density dependence. Synthesis. We develop new tools for identifying significant associations between functional traits and spatial structure, and for linking these associations to quantitative estimates of dispersal scale and the strength and scale of density dependence. Our results help clarify how these processes influence woody plant species on Barro Colorado, and demonstrate how these tools can be applied to other sites and systems

Genetic diversity for nitrogen use efficiency in Arabidopsis thaliana.

Meyer RC, Gryczka C, Neitsch C, et al. Genetic diversity for nitrogen use efficiency in Arabidopsis thaliana. Planta. 2019;250(1):41-57.MAIN CONCLUSION: The plasticity of plant growth response to differing nitrate availability renders the identification of biomarkers difficult, but allows access to genetic factors as tools to modulate root systems to a wide range of soil conditions. Nitrogen availability is a major determinant of crop yield. While the application of fertiliser substantially increases the yield on poor soils, it also causes nitrate pollution of water resources and high costs for farmers. Increasing nitrogen use efficiency in crop plants is a necessary step to implement low-input agricultural systems. We exploited the genetic diversity present in the worldwide Arabidopsis thaliana population to study adaptive growth patterns and changes in gene expression associated with chronic low nitrate stress, to identify biomarkers associated with good plant performance under low nitrate availability. Arabidopsis accessions were grown on agar plates with limited and sufficient supply of nitrate to measure root system architecture as well as shoot and root fresh weight. Differential gene expression was determined using Affymetrix ATH1 arrays. We show that the response to differing nitrate availability is highly variable in Arabidopsis accessions. Analyses of vegetative shoot growth and root system architecture identified accession-specific reaction modes to cope with limited nitrate availability. Transcription and epigenetic factors were identified as important players in the adaption to limited nitrogen in a global gene expression analysis. Five nitrate-responsive genes emerged as possible biomarkers for NUE in Arabidopsis. The plasticity of plant growth in response to differing nitrate availability in the substrate renders the identification of morphological and molecular features as biomarkers difficult, but at the same time allows access to a multitude of genetic factors which can be used as tools to modulate and adjust root systems to a wide range of soil conditions