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Bradyrhizobium is thought to be the largest and most diverse rhizobial genus, but this is not reflected in the number of described species. Although it was one of the first rhizobial genera recognised, its taxonomy remains complex. Various contemporary studies are showing that genome sequence information may simplify taxonomic decisions. Therefore, the growing availability of genomes for Bradyrhizobium will likely aid in the delineation and characterization of new species. In this study, we addressed two aims: first, we reviewed the availability and quality of available genomic resources for Bradyrhizobium. This was achieved by comparing genome sequences in terms of sequencing technologies used and estimated level of completeness for inclusion in genome-based phylogenetic analyses. Secondly, we utilized these genomes to investigate the taxonomic standing of Bradyrhizobium in light of its diverse lifestyles. Although genome sequences differed in terms of their quality and completeness, our data indicate that the use of these genome sequences is adequate for taxonomic purposes. By using these resources, we inferred a fully resolved, well-supported phylogeny. It separated Bradyrhizobium into seven lineages, three of which corresponded to the so-called supergroups known for the genus. Wide distribution of key lifestyle traits such as nodulation, nitrogen fixation and photosynthesis revealed that these traits have complicated evolutionary histories. We present the first robust Bradyrhizobium species phylogeny based on genome sequence information for investigating the evolution of this important assemblage of bacteria. Furthermore, this study provides the basis for using genome sequence information as a resource to make important taxonomic decisions, particularly at the species and genus levels. [ABSTRACT FROM AUTHOR]

Abstract Many gene flow barriers associated with genetic isolation during eukaryotic species divergence, are lacking in prokaryotes. In these organisms the processes associated with horizontal gene transfer (HGT) may provide both the homogenizing force needed for genetic cohesion and the genetic variation essential to speciation. This is because HGT events can broadly be grouped into genetic conversions (where endogenous genetic material are replaced with homologs acquired from external sources) and genetic introductions (where novel genetic material is acquired from external sources). HGT-based genetic conversions therefore causes homogenization, while genetic introductions drive divergence of populations upon fixation of genetic variants. The impact of HGT in different prokaryotic species may vary substantially and can range from very low levels to rampant HGT, producing chimeric groups of isolates. Combined with other evolutionary processes, these varying levels of HGT causes diversity space to be occupied by unique groups that are mostly incomparable in terms of genetic similarity, genomic cohesion and evolutionary age. As a result, the conventional, cut-off based metrics for species delineation are not adequate. Rather, a pluralistic approach to prokaryotic species recognition is required to accommodate the unique evolutionary ages and tendencies, population dynamics, and evolutionary fates of individual prokaryotic species. Following this approach, all prokaryotic species may be regarded as unique and each of their own kind (sui generis). Taxonomic decisions thus require evolutionary information that integrates vertical inheritances with all possible sources of genetic heterogeneity to ultimately produce robust and biologically meaningful classifications. [ABSTRACT FROM AUTHOR]

Highlights • Anisotropic elastic half-space. • Use of method of images. • Image point is not at mirror-image point. Abstract The effects of the traction-free boundary of a half-space can often be incorporated using images. In the simplest situations, a point force in the half-space induces an image force at the mirror-image point outside the half-space. However, for antiplane deformations of anisotropic media, the image point has a different location, as shown by T. C. T. Ting for static problems. This observation leads to formulas for a time-harmonic half-space fundamental solution and for time-harmonic half-space multipole solutions. [ABSTRACT FROM AUTHOR]

Abstract Mating is central to many fungal life cycles and is controlled by genes at the mating-type (MAT) locus. These genes determine whether the fungus will be self-sterile (heterothallic) or self-fertile (homothallic). Species in the ascomycete family Ceratocystidaceae have different mating strategies, making them interesting to consider with regards to their MAT loci. The aim of this study was to compare the composition of the MAT locus flanking regions in 11 species of Ceratocystidaceae representing four genera. Genome assemblies for each species were examined to identify the MAT locus and determine the structure of the flanking regions. Large contigs containing the MAT locus were then functionally annotated and analysed for the presence of transposable elements. Genes typically flanking the MAT locus in sordariomycetes were found to be highly conserved in the Ceratocystidaceae. The different genera in the Ceratocystidaceae displayed little synteny outside of the immediate MAT locus flanking genes. Even though species of Ceratocystis did not show much synteny outside of the immediate MAT locus flanking genes, species of Huntiella and Endoconidiophora were comparatively syntenic. Due to the high number of transposable elements present in Ceratocystis MAT flanking regions, we hypothesise that Ceratocystis species may have undergone recombination in this region. [ABSTRACT FROM AUTHOR]

Blue light plays an important role in the growth and development of fungi. Environmental cues enable plant pathogenic fungi to synchronise essential metabolic pathways to that of their hosts to gain a competitive advantage. Phylogenetic analysis of the LOV domain present in blue light receptors across all three kingdoms suggests that these receptors in fungal lineages have undergone convergent evolution to use the same domain for control and regulation of similar cellular and metabolic processes. In this review, the genetic basis of blue light photoperception in fungi, and the functions it regulates, will be discussed. Furthermore, the evolution of the light sensing domain and its role in pathogenesis is hypothesised concluding with how knowledge of conserved LOV domains may be exploited for fungal disease control in crop plants. [ABSTRACT FROM AUTHOR]

Babinet's principle is established for certain problems in antiplane anisotropic elasticity. For example, the scattered field behind a finite straight crack is exactly cancelled by the total field behind an aperture in an infinite flat rigid screen, where the crack and the aperture have the same length and the incident wave is the same for both problems. The method used involves Fourier integrals and dual integral equations. • Scattering by cracks and coplanar screens. • Scalar problems with antiplane (SH) motions in anisotropic elastic media. • Babinet's principle established. [ABSTRACT FROM AUTHOR]

Understanding intrasalt structure may elucidate the fundamental kinematics and, ultimately, the mechanics of diapir growth. However, there have been relatively few studies of the internal structure of salt diapirs outside the mining industry because their cores are only partly exposed in the field and poorly imaged on seismic reflection data. This study uses 3D seismic reflection and borehole data from the São Paulo Plateau, Santos Basin, offshore Brazil to document the variability in intrasalt structural style in natural salt diapirs. We document a range of intrasalt structures that record: (i) initial diapir rise; (ii) rise of lower mobile halite through an arched and thinned roof of denser, layered evaporites, and emplacement of an intrasalt sheet or canopy; (iii) formation of synclinal flaps kinematically linked to emplacement of the intrasalt allochthonous bodies; and (iv) diapir squeezing. Most salt walls contain simple internal anticlines. Only a few salt walls contain allochthonous bodies and breakout-related flaps. The latter occur in an area having a density inversion within the autochthonous salt layer, such that upper, anhydrite-rich, layered evaporites are denser than lower, more halite-rich evaporites. We thus interpret that most diapirs rose through simple fold amplification of internal salt stratigraphy but that locally, where a density inversion existed in the autochthonous salt, Rayleigh–Taylor overturn within the growing diapir resulted in the ascent of less dense evaporites into the diapir crest by breaching of the internal anticline. This resulted in the formation of steep salt-ascension zones or feeders and the emplacement of high-level intrasalt allocthonous sheets underlain by breakout-related flaps. Although regional shortening undoubtedly occurred on the São Paulo Plateau during the Late Cretaceous, we suggest this was only partly responsible for the complex intrasalt deformation. We suggest that, although based on the Santos Basin, our kinematic model may be more generally applicable to other salt-bearing sedimentary basins. [ABSTRACT FROM AUTHOR]

Jackson et al. ( this volume ) used 3D seismic reflection data to describe intrasalt deformation in salt walls in the Santos Basin. They focused on the origin of enigmatic allochthonous salt sheets of older evaporites (A1 unit) emplaced above overlying stratified evaporites (A2–A4 units). Their kinematic model incorporates: (i) initial inward flow and thickening of A1 salt within the rising wall, and arching of A2–A4 overburden; (ii) breaching of the arched overburden, ascent of mobile A1 evaporites along single or multiple feeders, and emplacement of upper-wall sheets or canopies; and (iii) a component of regional shortening within the salt. This companion paper uses physical modelling to explain how and why these structures occur and proposes a mechanical basis for the kinematic model. Our first two models simulated salt having uniform internal density, with walls growing by (i) initially symmetric differential loading and (ii) initially symmetric differential loading plus shortening. These models reproduced anticlines and injection folds seen in the simpler deformed walls in the Santos Basin. However, neither model reproduced the most complex structures within the Santos evaporites, which are: (i) allochthonous intrusions, (ii) steep feeders, and (iii) recumbent synclines. Thus, differential loading and shortening alone are insufficient to generate these complex structures. In our third model, a less-dense lower evaporite (A1) was overlain by denser upper evaporites (A2–A4), similar to the density structure found by Santos Basin wellbores. The wall rose solely by differential loading. In this model, A1 breached the overlying evaporites to form vertical diapirs feeding salt sheets and salt wings in the upper part of the salt wall. Breakthrough of A1 folded A2–A4 evaporites into recumbent synclines. Model sections closely resemble Santos seismic examples, suggesting that the key to forming these complex intrasalt structures is a density inversion within the evaporite sequence that creates a Rayleigh–Taylor instability. [ABSTRACT FROM AUTHOR]

Abstract: The Garvin–Alterman–Loewenthal solution refers to the problem of a line blast load suddenly applied in the interior of an elastic half-space. It is expected that the long-time asymptotic limit of this solution should be equal to the solution of a related static problem. This expectation is justified here. First, the solution of the static problem is constructed. Then, the asymptotic limit of the transient problem is found, correcting previously published results. [Copyright &y& Elsevier]

Abstract: We develop an orders-of-scattering approximation, termed the “screened cylindrical void/core” (SCV) approximation, for a composite cylinder. The composite cylinder consists of a large host cylinder that contains a small, eccentrically embedded, core cylinder. The SCV approximation is developed via separation of variables in conjunction with addition theorems for cylindrical functions. We show that the SCV approximation is in good agreement with the numerically exact solution. A simple physical interpretation of the SCV approximation is also presented. [Copyright &y& Elsevier]

Abstract: Potential problems for thin elliptical plates are solved exactly with emphasis on computation of the electrostatic energy. Expansions in terms of Jacobi polynomials are used. [Copyright &y& Elsevier]

Abstract: This paper summarizes the scientific legacy of Peter C. Waterman (1928–2012) who introduced concepts and theoretical techniques that have had a major impact on the fields of scattering by particles and particle groups, optical particle characterization, radiative transfer, and remote sensing. A biographical sketch is also included. [Copyright &y& Elsevier]

Abstract: Salt can be partially removed by viscous flow from between wall rocks to form a salt weld. Welds in autochthonous and allochthonous salt can form significant structures in evaporite basins, where petroleum and mineral discovery can hinge on whether salt welds act as seals or windows for migrating hydrocarbons or brines containing dissolved metals. Despite the importance of welds, little is known about salt evacuation during welding. We investigate viscous flow during welding using analytical and numerical models, based on exact solutions to the Navier–Stokes equations for idealized geometries and boundary conditions. We explore two questions: how does salt thin during evacuation, and what are the limits of viscous flow during salt welding? Hydraulic-gradient and displacement boundary conditions are shown to drive salt evacuation, which is rate-limited by drag along the boundaries of a salt layer. Where salt flow is restricted, for example beneath a broad, prograding sediment wedge, up to ~50m salt can remain in an incomplete weld. Where salt flow is unrestricted, for example beneath a subsiding minibasin, viscous flow can remove all but a vanishingly thin (<<1m) salt layer. In both cases, any remaining salt must be dissolved to leave a weld containing no remnant salt. Evacuation rate increases with increasing differential stress and decreasing flow length and dynamic viscosity of the salt. Translation of wall rock parallel to bedding may result in a fault weld but may also inhibit evacuation if the displacement counteracts flow driven by a hydraulic gradient. Evacuation of multilayered evaporites is controlled by the distribution of layer thickness and viscosity. Multilayered evaporites can be compositionally modified during evacuation. [Copyright &y& Elsevier]

Abstract: Using data from Vaccine Adverse Event Reporting System, we identified 69 reports of Guillain–Barré Syndrome (GBS) after Gardasil vaccination that occurred in the United States between 2006 and 2009. The onset of symptoms was within 6 weeks after vaccination in 70% of the patients in whom the date of vaccination was known. The estimated weekly reporting rate of post-Gardasil GBS within the first 6 weeks (6.6 per 10,000,000) was higher than that of the general population, and higher than post-Menactra and post-influenza vaccinations. Further prospective active surveillance for accurate ascertainment and identification of high-risk groups of GBS after Gardasil vaccination is warranted. [ABSTRACT FROM AUTHOR]

Abstract: Growth faults in gravity-driven extensional provinces are dominated by coast-parallel trends, but coast-perpendicular (transverse) trends are far less documented. The Clemente–Tomas fault in the inner Texas shelf has corrugations that are transverse to the fault and that plunge downdip. A large (8500km2), high-quality, 3D seismic survey allows a uniquely encompassing perspective into hanging-wall deformation above this corrugated fault surface. Synextensional strata in the hanging wall are folded into alternating transverse ridges and synclines, typically spaced 10km apart. Forward modelling in dip profiles of an extensional fault having three ramps produces ramp basin-rollover pairs that compare with the seismically revealed ridges and synclines. As they translated down the undulose fault plane, ramp basins and rollovers were juxtaposed along strike, forming the hanging-wall ridges and synclines observed offshore Texas. Fault-surface corrugations correlate broadly with footwall structure. We infer that corrugations on the Clemente–Tomas fault formed by evacuation of an allochthonous salt canopy emplaced in the late Eocene to early Oligocene. Early salt evacuation (Oligocene) created an undulose topography that influenced incipient Clemente-Tomas fault segments as they merged to form an inherently undulose fault. Late salt evacuation (early Miocene) further deformed this fault surface. [ABSTRACT FROM AUTHOR]

Abstract: Gravity spreading of a buried salt canopy produces thrust faults around the canopy rim. These thrusts may form by shear along the base of the salt, by frontal rolling of the canopy, by expulsion of underlying sediments, or by submarine landsliding off the canopy''s frontal escarpment. Each mechanism has a characteristic structural style, providing clues to processes of shortening in canopy-margin thrust systems. Canopy-margin thrust systems along the Sigsbee Escarpment in the deepwater Gulf of Mexico may have three parts. First, nearly all canopy-margin systems include a roof-edge thrust, which cuts upsection from the tip of the salt canopy and separates condensed strata in the canopy roof from thicker sections on the adjoining peripheral plain. Second, roughly one-third of roof-edge thrusts overlie an imbricate wedge, which telescopes sediments on the peripheral plain above a bedding-plane décollement. Third, in a few areas, salt-roof thrusts shorten the roof of the salt sheet. Because roof-edge thrusts and imbricate wedges both form by shear along the base of the salt allochthon, their abundance along the Sigsbee Escarpment implies that basal shear is the primary mode of advance there. Despite the dominance of basal shear, however, the Sigsbee Escarpment exhibits a wide range of structural styles. We speculate that this range reflects variations in relief on the canopy margin, thickness of the roof above the canopy toe, strength of the base-salt zone, and strength of sediments on the peripheral plain. [Copyright &y& Elsevier]

Abstract: We used scaled physical models to investigate how buried, dormant diapirs are rejuvenated by lateral squeezing. In Stage 1, regional shortening increased the pressure of the source layer, causing an inward plume of source-layer salt to intrude the dilating diapir and arch its roof. In Stage 2, the thrust front jumped forward to the salt stock, forming a major salient toward the foreland, and the stock roof was arched. Salt inflation still dominated, but a small outward plume of diapiric salt began to intrude the source layer on the foreland side of the diapir. With continued shortening in Stage 3, the converging diapir walls deflated the diapir, while a major overthrust prevented surface extrusion. Compressional uplift of the overburden created space for downward intrusion of diapiric salt into the source layer and diapiric pedestal. The models document a newly recognized type of active diapir that inflates under compression. The models also show how a salt diapir can weld shut where surface extrusion of salt is inhibited. [Copyright &y& Elsevier]

Abstract: Ramp syncline basins filled with synkinematic sediments record the incremental translation history and translation rates of strata transported over basement ramps. On passive margins, movement of strata over a stratabound salt detachment is stratigraphically recorded as an isopach thick on the seaward side of a monoclinal ramp. This growth syncline gradually moves seaward down and then off the monocline, as if on a conveyor belt. This shift creates accommodation space for a new isopach thick to form just landward of the older one. Repetition of this cycle creates a shingled series of isopach thicks within the ramp syncline basin. Kinematic forward models and restored cross sections from the Kwanza Basin, Angola, show that the stratigraphic pattern of ramp syncline basins is most influenced by three factors. (1) The relative rates of translation and aggradation control the curvature of the axial trace of the growth synclines. (2) Bathymetric scarps above basement ramps can create spectacular seaward-dipping onlap surfaces >30km long downdip; adjoining ramps generate stacked, interfering onlap surfaces. (3) Salt diapirs or anticlines are commonly shortened at the top of the ramp, especially where this coincides with the base of the continental slope. Diapir shortening provides a buffer to absorb sliding from its landward side and impede sliding on its seaward side. This buffering can have a major control on the entire gravity-spreading system containing the diapirs. [Copyright &y& Elsevier]

Abstract: A rod theory is developed for long waves in an elastic circular cylinder with cylindrical anisotropy. Detailed results for flexural waves and cylindrical orthotropy are given. The theory uses the method of Frobenius in the radial direction so that the equation of motion is satisfied exactly. Then, the equations arising from the lateral boundary condition are truncated properly, leading to a rod theory. [Copyright &y& Elsevier]

The problem of a point force acting in a composite, two-dimensional, isotropic elastic half-plane is considered. An exact solution is obtained, using Mellin transforms and the Melan solution for a point force in a homogeneous half-plane. [Copyright &y& Elsevier]

Abstract: An inhomogeneous layer is sandwiched between homogeneous half-spaces. The layer contains a defect. There are incident waves and the problem is to calculate the scattered waves. Five recent publications are criticised, mainly because of their misuse of the method of images. [Copyright &y& Elsevier]