The dynamic proteome of Lyme disease Borrelia

The proteome of the spirochete bacterium Borrelia burgdorferi, the tick-borne agent of Lyme disease, has been characterized by two different approaches using mass spectrometry, providing a launching point for future studies on the dramatic changes in protein expression that occur during transmission of the bacterium between ticks and mammals

Genetic diversity in Treponema pallidum: Implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws

AbstractPathogenic uncultivable treponemes, similar to syphilis-causing Treponema pallidum subspecies pallidum, include T. pallidum ssp. pertenue, T. pallidum ssp. endemicum and Treponema carateum, which cause yaws, bejel and pinta, respectively. Genetic analyses of these pathogens revealed striking similarity among these bacteria and also a high degree of similarity to the rabbit pathogen, Treponema paraluiscuniculi, a treponeme not infectious to humans. Genome comparisons between pallidum and non-pallidum treponemes revealed genes with potential involvement in human infectivity, whereas comparisons between pallidum and pertenue treponemes identified genes possibly involved in the high invasivity of syphilis treponemes. Genetic variability within syphilis strains is considered as the basis of syphilis molecular epidemiology with potential to detect more virulent strains, whereas genetic variability within a single strain is related to its ability to elude the immune system of the host. Genome analyses also shed light on treponemal evolution and on chromosomal targets for molecular diagnostics of treponemal infections

Fully broadband vAPP coronagraphs enabling polarimetric high contrast imaging

We present designs for fully achromatic vector Apodizing Phase Plate (vAPP) coronagraphs, that implement low polarization leakage solutions and achromatic beam-splitting, enabling observations in broadband filters. The vAPP is a pupil plane optic, inducing the phase through the inherently achromatic geometric phase. We discuss various implementations of the broadband vAPP and set requirements on all the components of the broadband vAPP coronagraph to ensure that the leakage terms do not limit a raw contrast of 1E-5. Furthermore, we discuss superachromatic QWPs based of liquid crystals or quartz/MgF2 combinations, and several polarizer choices. As the implementation of the (broadband) vAPP coronagraph is fully based on polarization techniques, it can easily be extended to furnish polarimetry by adding another QWP before the coronagraph optic, which further enhances the contrast between the star and a polarized companion in reflected light. We outline several polarimetric vAPP system designs that could be easily implemented in existing instruments, e.g. SPHERE and SCExAO.Comment: 11 pages, 5 figures, presented at SPIE Astronomical Telescopes and Instrumentation 201

A retrospective study on genetic heterogeneity within Treponema strains: Subpopulations are genetically distinct in a limited number of positions

Pathogenic uncultivable treponemes comprise human and animal pathogens including agents of syphilis, yaws, bejel, pinta, and venereal spirochetosis in rabbits and hares. A set of 10 treponemal genome sequences including those of 4 Treponema pallidum ssp. pallidum (TPA) strains (Nichols, DAL-1, Mexico A, SS14), 4 T. p. ssp. pertenue (TPE) strains (CDC-2, Gauthier, Samoa D, Fribourg-Blanc), 1 T. p. ssp. endemicum (TEN) strain (Bosnia A) and one strain (Cuniculi A) of Treponema paraluisleporidarum ecovar Cuniculus (TPLC) were examined with respect to the presence of nucleotide intrastrain heterogeneous sites.The number of identified intrastrain heterogeneous sites in individual genomes ranged between 0 and 7. Altogether, 23 intrastrain heterogeneous sites (in 17 genes) were found in 5 out of 10 investigated treponemal genomes including TPA strains Nichols (n = 5), DAL-1 (n = 4), and SS14 (n = 7), TPE strain Samoa D (n = 1), and TEN strain Bosnia A (n = 5). Although only one heterogeneous site was identified among 4 tested TPE strains, 16 such sites were identified among 4 TPA strains. Heterogeneous sites were mostly strain-specific and were identified in four tpr genes (tprC, GI, I, K), in genes involved in bacterial motility and chemotaxis (fliI, cheC-fliY), in genes involved in cell structure (murC), translation (prfA), general and DNA metabolism (putative SAM dependent methyltransferase, topA), and in seven hypothetical genes.Heterogeneous sites likely represent both the selection of adaptive changes during infection of the host as well as an ongoing diversifying evolutionary process

Intact flagellar motor of Borrelia burgdorferi revealed by cryo-electron tomography: evidence for stator ring curvature and rotor/C-ring assembly flexion.

The bacterial flagellar motor is a remarkable nanomachine that provides motility through flagellar rotation. Prior structural studies have revealed the stunning complexity of the purified rotor and C-ring assemblies from flagellar motors. In this study, we used high-throughput cryo-electron tomography and image analysis of intact Borrelia burgdorferi to produce a three-dimensional (3-D) model of the in situ flagellar motor without imposing rotational symmetry. Structural details of B. burgdorferi, including a layer of outer surface proteins, were clearly visible in the resulting 3-D reconstructions. By averaging the 3-D images of approximately 1,280 flagellar motors, a approximately 3.5-nm-resolution model of the stator and rotor structures was obtained. flgI transposon mutants lacked a torus-shaped structure attached to the flagellar rod, establishing the structural location of the spirochetal P ring. Treatment of intact organisms with the nonionic detergent NP-40 resulted in dissolution of the outermost portion of the motor structure and the C ring, providing insight into the in situ arrangement of the stator and rotor structures. Structural elements associated with the stator followed the curvature of the cytoplasmic membrane. The rotor and the C ring also exhibited angular flexion, resulting in a slight narrowing of both structures in the direction perpendicular to the cell axis. These results indicate an inherent flexibility in the rotor-stator interaction. The FliG switching and energizing component likely provides much of the flexibility needed to maintain the interaction between the curved stator and the relatively symmetrical rotor/C-ring assembly during flagellar rotation

The Nucleotide Excision Repair Pathway Protects Borrelia burgdorferi from Nitrosative Stress in Ixodes scapularis Ticks

The Lyme disease spirochete Borrelia burgdorferi encounters a wide range of environmental conditions as it cycles between ticks of the genus Ixodes and its various mammalian hosts. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are potent antimicrobial molecules generated during the innate immune response to infection, however, it is unclear whether ROS and RNS pose a significant challenge to B. burgdorferi in vivo. In this study, we screened a library of B. burgdorferi strains with mutations in DNA repair genes for increased susceptibility to ROS or RNS in vitro. Strains with mutations in the methyl-directed mismatch repair (MMR) gene mutS1 are hypersensitive to killing by ROS, while strains lacking the nucleotide excision repair (NER) gene uvrB show increased susceptibility to both ROS and RNS. Therefore, mutS1-deficient and uvrB-deficient strains were compared for their ability to complete their infectious cycle in Swiss Webster mice and I. scapularis ticks to help identify sites of oxidative and nitrosative stresses encountered by B. burgdorferi in vivo. Both mutS1¬ and uvrB were dispensable for infection of mice, while uvrB promoted the survival of spirochetes in I. scapularis ticks. The decreased survival of uvrB-deficient B. burgdorferi was associated with the generation of RNS in I. scapularis midguts and salivary glands during feeding. Collectively, these data suggest that B. burgdorferi must withstand cytotoxic levels of RNS produced during infection of I. scapularis ticks

Potential migration of buoyant LNAPL from Intermediate Level Waste (ILW) emplaced in a geological disposal facility (GDF) for UK radioactive waste

A safety case for the disposal of Intermediate Level (radioactive) Waste (ILW) in a deep geological disposal facility (GDF) requires consideration of the potential for waste-derived light non-aqueous phase liquid (LNAPL) to migrate under positive buoyancy from disposed waste packages. Were entrainment of waste-derived radionuclides in LNAPL to occur, such migration could result in a shorter overall travel time to environmental or human receptors than radionuclide migration solely associated with the movement of groundwater. This paper provides a contribution to the assessment of this issue through multiphase-flow numerical modelling underpinned by a review of the UK's ILW inventory and literature to define the nature of the associated ILW LNAPL source term. Examination has been at the waste package-local GDF environment scale to determine whether proposed disposal of ILW would lead to significant likelihood of LNAPL migration, both from waste packages and from a GDF vault into the local host rock. Our review and numerical modelling support the proposition that the release of a discrete free phase LNAPL from ILW would not present a significant challenge to the safety case even with conservative approximations. 'As-disposed' LNAPL emplaced with the waste is not expected to pose a significant issue. 'Secondary LNAPL' generated in situ within the disposed ILW, arising from the decomposition of plastics, in particular PVC (polyvinyl chloride), could form the predominant LNAPL source term. Released high molecular weight phthalate plasticizers are judged to be the primary LNAPL potentially generated. These are expected to have low buoyancy-based mobility due to their very low density contrast with water and high viscosity. Due to the inherent uncertainties, significant conservatisms were adopted within the numerical modelling approach, including: the simulation of a deliberately high organic material - PVC content wastestream (2D03) within an annular grouted waste package vulnerable to LNAPL release; upper bound inventory estimates of LNAPLs; incorporating the lack of any hydraulic resistance of the package vent; the lack of any degradation of dissolved LNAPL; and, significantly, the small threshold displacement pressure assumed at which LNAPL is able to enter initially water-saturated pores. Initial scoping calculations on the latter suggested that the rate at which LNAPL is able to migrate from a waste package is likely to be very small and insignificant for likely representative displacement pressure data: this represents a key result. Adopting a conservative displacement pressure, however, allowed the effect of other features and processes in the system to be assessed. High LNAPL viscosity together with low density contrast with water reduces LNAPL migration potential. Migration to the host rock is less likely if waste package vent fluxes are small, solubility limits are high and path lengths through the backfill are short. The capacity of the system to dissolve all of the free LNAPL will, however, depend on groundwater availability. Even with the conservatisms invoked, the overall conclusion of model simulations of intact and compromised (cracked or corroded) waste packages, for a range of realistic ILW LNAPL scenarios, is that it is unlikely that significant LNAPL would be able to migrate from the waste packages and even more unlikely it would be sufficiently persistent to reach the host rock immediately beyond the GDF

Modification of Thermal Emission via Metallic Photonic Crystals

Photonic crystals are materials that are periodically structured on an optical length scale. It was previously demonstrated that the glow, or thermal emission, of tungsten photonic crystals that have a specific structure - known as the 'woodpile structure' - could be modified to reduce the amount of infrared radiation from the material. This ability has implications for improving the efficiency of thermal emission sources and for thermophotovoltaic devices. The study of this effect had been limited because the fabrication of metallic woodpile structures had previously required a complex fabrication process. In this project we pursued several approaches to simplify the fabrication of metallic photonic crystals that are useful for modification of thermal emission. First, we used the self-assembly of micrometer-scale spheres into colloidal crystals known as synthetic opals. These opals can then be infiltrated with a metal and the spheres removed to obtain a structure, known as an inverse opal, in which a three-dimensional array of bubbles is embedded in a film. Second, we used direct laser writing, in which the focus of an infrared laser is moved through a thin film of photoresist to form lines by multiphoton polymerization. Proper layering of such lines can lead to a scaffold with the woodpile structure, which can be coated with a refractory metal. Third, we explored a completely new approach to modified thermal emission - thin metal foils that contain a simple periodic surface pattern, as shown in Fig. 1. When such a foil is heated, surface plasmons are excited that propagate along the metal interface. If these waves strike the pattern, they can be converted into thermal emission with specific properties

Modification of Thermal Emission via Metallic Photonic Crystals

Photonic crystals are materials that are periodically structured on an optical length scale. It was previously demonstrated that the glow, or thermal emission, of tungsten photonic crystals that have a specific structure - known as the 'woodpile structure' - could be modified to reduce the amount of infrared radiation from the material. This ability has implications for improving the efficiency of thermal emission sources and for thermophotovoltaic devices. The study of this effect had been limited because the fabrication of metallic woodpile structures had previously required a complex fabrication process. In this project we pursued several approaches to simplify the fabrication of metallic photonic crystals that are useful for modification of thermal emission. First, we used the self-assembly of micrometer-scale spheres into colloidal crystals known as synthetic opals. These opals can then be infiltrated with a metal and the spheres removed to obtain a structure, known as an inverse opal, in which a three-dimensional array of bubbles is embedded in a film. Second, we used direct laser writing, in which the focus of an infrared laser is moved through a thin film of photoresist to form lines by multiphoton polymerization. Proper layering of such lines can lead to a scaffold with the woodpile structure, which can be coated with a refractory metal. Third, we explored a completely new approach to modified thermal emission - thin metal foils that contain a simple periodic surface pattern, as shown in Fig. 1. When such a foil is heated, surface plasmons are excited that propagate along the metal interface. If these waves strike the pattern, they can be converted into thermal emission with specific properties