Orphaning Regimes: The Missing Link Between Flattened and Penetrating Slab Morphologies

Slab orphaning is a newly discovered phenomenological behavior, where the slab tip breaks off at the top of the lower mantle (~660 km depth) and is abandoned by its parent slab. Upon orphaning, subduction continues uninterrupted through the lateral motion of the parent slab above 660 km depth. In this work, we present a regime diagram for the range of conditions under which slabs can orphan at the top of the lower mantle. Our models show that a viscosity jump at 1,000 km depth not coincident with the endothermic phase change responsible for the 660 km seismic discontinuity, is necessary for orphaning as is the presence of a low viscosity channel between 660 and 1,000 km depth. We show that orphan slabs, similar to other deep slab morphologies, can be the end result for a wide range of physical parameters governing slab dynamics: slab orphaning persists across wide variations in slab dip, slab yield stress/strength, Clapeyron slope values, and overriding plate nature. The diversity in orphan slab sizes and orphaning periods is tied to the orphaning regime space, which describes a hitherto unexplored region between deflected and penetrating deep-subduction modes. Orphaning provides a simple dynamic link between the well-known deflection and penetration, and provides one possible way for slabs to switch from direct penetration to deflection, littering the mantle with abandoned fragments. Orphan slabs are therefore the intermediary between these two extensively studied slab morphologies

Geodynamic diagnostics, scientific visualisation and StagLab 3.0

Today's geodynamic models can, often do and sometimes have to become very complex. Their underlying, increasingly elaborate numerical codes produce a growing amount of raw data. Post-processing such data is therefore becoming more and more important, but also more challenging and time-consuming. In addition, visualising processed data and results has, in times of coloured figures and a wealth of half-scientific software, become one of the weakest pillars of science, widely mistreated and ignored. Efficient and automated geodynamic diagnostics and sensible scientific visualisation preventing common pitfalls is thus more important than ever. Here, a collection of numerous diagnostics for plate tectonics and mantle dynamics is provided and a case for truly scientific visualisation is made. Amongst other diagnostics are a most accurate and robust plate-boundary identification, slab-polarity recognition, plate-bending derivation, surface-topography component splitting and mantle-plume detection. Thanks to powerful image processing tools and other elaborate algorithms, these and many other insightful diagnostics are conveniently derived from only a subset of the most basic parameter fields. A brand new set of scientific quality, perceptually uniform colour maps including devon, davos, oslo and broc is introduced and made freely available (http://www.fabiocrameri.ch/colourmaps, last access: 25 June 2018). These novel colour maps bring a significant advantage over misleading, non-scientific colour maps like rainbow, which is shown to introduce a visual error to the underlying data of up to 7.5 %. Finally, StagLab (http://www.fabiocrameri.ch/StagLab, last access: 25 June 2018) is introduced, a software package that incorporates the whole suite of automated geodynamic diagnostics and, on top of that, applies state-of-the-art scientific visualisation to produce publication-ready figures and movies, all in the blink of an eye and all fully reproducible. StagLab, a simple, flexible, efficient and reliable tool made freely available to everyone, is written in MATLAB and adjustable for use with geodynamic mantle convection codes.</p

Abrupt upper-plate tilting during slab-transition-zone collision

The sinking remnant of a surface plate crosses and interacts with multiple boundaries in Earth's interior. Here, we specifically investigate the prominent dynamic interaction of the sinking plate portion with the upper-mantle transition zone and its corresponding surface elevation signal. We unravel, for the first time, that the collision of the sinking slab with the transition zone induces a sudden, dramatic downward tilt of the upper plate towards the subduction trench. Unraveling this crucial interaction was only possible thanks to state-of-the-art numerical modelling and post-processing. The new model that is introduced here to study the dynamically self-consistent temporal evolution of subduction features accurate subduction-zone topography, robust single-sided plate sinking, stronger plates close to laboratory values, an upper-mantle phase transition, and simple continents at a free surface. To distinguish the impact of the new physical model features, three different setups are used: the simplest model setup includes a basic high-viscosity lower mantle, the second adds a 660-km phase transition, and the third includes, additionally, a continental upper plate. Common to all models is the clear topographic signal upon slab-transition-zone interaction: the upper plate tilts abruptly towards the subduction trench by about 0.05° and over around 10. Ma. This dramatic increase in upper-plate tilt can be related to the slab-induced excitation of the high-viscosity lower mantle, which introduces a wider flow pattern. A large change in horizontal extent of inundation of up to 900. km is observed as a direct consequence of the upper-plate tilting. Such an abrupt variation in surface topography and inundation extent should be clearly visible in temporal records of large-scale surface elevation and might explain continental tilting as observed in Australia since the Eocene and North America during the Phanerozoic

Achimota Pararubulavirus 3: A New Bat-Derived Paramyxovirus of the Genus Pararubulavirus

Bats are an important source of viral zoonoses, including paramyxoviruses. The paramyxoviral Pararubulavirus genus contains viruses mostly derived from bats that are common, diverse, distributed throughout the Old World, and known to be zoonotic. Here, we describe a new member of the genus Achimota pararubulavirus 3 (AchPV3) and its isolation from the urine of African straw-coloured fruit bats on primary bat kidneys cells. We sequenced and analysed the genome of AchPV3 relative to other Paramyxoviridae, revealing it to be similar to known pararubulaviruses. Phylogenetic analysis of AchPV3 revealed the failure of molecular detection in the urine sample from which AchPV3 was derived and an attachment protein most closely related with AchPV2—a pararubulavirus known to cause cross-species transmission. Together these findings add to the picture of pararubulaviruses, their sources, and variable zoonotic potential, which is key to our understanding of host restriction and spillover of bat-derived paramyxoviruses. AchPV3 represents a novel candidate zoonosis and an important tool for further study

The dynamical control of subduction parameters on surface topography

he long-wavelength surface deflection of Earth's outermost rocky shell is mainly controlled by large-scale dynamic processes like isostasy or mantle flow. The largest topographic amplitudes are therefore observed at plate boundaries due to the presence of large thermal heterogeneities and strong tectonic forces. Distinct vertical surface deflections are particularly apparent at convergent plate boundaries mostly due to the convergence and asymmetric sinking of the plates. Having a mantle convection model with a free surface that is able to reproduce both realistic single-sided subduction and long-wavelength surface topography self-consistently, we are now able to better investigate this interaction. We separate the topographic signal into distinct features and quantify the individual topographic contribution of several controlling subduction parameters. Results are diagnosed by splitting the topographic signal into isostatic and residual components, and by considering various physical aspects like viscous dissipation during plate bending. Performing several systematic suites of experiments, we are then able to quantify the topographic impact of the buoyancy, rheology, and geometry of the subduction-zone system to each and every topographic feature at a subduction zone and to provide corresponding scaling laws. We identify slab dip and, slightly less importantly, slab buoyancy as the major agents controlling surface topography at subduction zones on Earth. Only the island-arc high and the back-arc depression extent are mainly controlled by plate strength. Overall, his modeling study sets the basis to better constrain deep-seated mantle structures and their physical properties via the observed surface topography on present-day Earth and back through time

In the light of directed evolution: Pathways of adaptive protein evolution

Directed evolution is a widely-used engineering strategy for improving the stabilities or biochemical functions of proteins by repeated rounds of mutation and selection. These experiments offer empirical lessons about how proteins evolve in the face of clearly-defined laboratory selection pressures. Directed evolution has revealed that single amino acid mutations can enhance properties such as catalytic activity or stability and that adaptation can often occur through pathways consisting of sequential beneficial mutations. When there are no single mutations that improve a particular protein property experiments always find a wealth of mutations that are neutral with respect to the laboratory-defined measure of fitness. These neutral mutations can open new adaptive pathways by at least 2 different mechanisms. Functionally-neutral mutations can enhance a protein's stability, thereby increasing its tolerance for subsequent functionally beneficial but destabilizing mutations. They can also lead to changes in “promiscuous” functions that are not currently under selective pressure, but can subsequently become the starting points for the adaptive evolution of new functions. These lessons about the coupling between adaptive and neutral protein evolution in the laboratory offer insight into the evolution of proteins in nature

A comparison of numerical surface topography calculations in geodynamic modelling: an evaluation of the ‘sticky air' method

Calculating surface topography in geodynamic models is a common numerical problem. Besides other approaches, the so-called ‘sticky air' approach has gained interest as a free-surface proxy at the top boundary. The often used free slip condition is thereby vertically extended by introducing a low density, low viscosity fluid layer. This allows the air/crust interface to behave in a similar manner to a true free surface. We present here a theoretical analysis that provides the physical conditions under which the sticky air approach is a valid approximation of a true free surface. Two cases are evaluated that characterize the evolution of topography on different timescales: (1) isostatic relaxation of a cosine perturbation and (2) topography changes above a rising plume. We quantitatively compare topographies calculated by six different numerical codes (using finite difference and finite element techniques) using three different topography calculation methods: (i) direct calculation of topography from normal stress, (ii) body-fitting methods allowing for meshing the topography and (iii) Lagrangian tracking of the topography on an Eulerian grid. It is found that the sticky air approach works well as long as the term (ηst/ηch)/(hst/L)3 is sufficiently small, where ηst and hst are the viscosity and thickness of the sticky air layer, and ηch and L are the characteristic viscosity and length scale of the model, respectively. Spurious lateral fluctuations of topography, as observed in some marker-based sticky air approaches, may effectively be damped by an anisotropic distribution of markers with a higher number of markers per element in the vertical than in the horizontal directio

A transdisciplinary and community-driven database to unravel subduction zone initiation

Subduction zones are pivotal for the recycling of Earth’s outer layer into its interior. However, the conditions under which new subduction zones initiate are enigmatic. Here, we constructed a transdisciplinary database featuring detailed analysis of more than a dozen documented subduction zone initiation events from the last hundred million years. Our initial findings reveal that horizontally forced subduction zone initiation is dominant over the last 100 Ma, and that most initiation events are proximal to pre-existing subduction zones. The SZI Database is expandable to facilitate access to the most current understanding of subduction zone initiation as research progresses, providing a community platform that establishes a common language to sharpen discussion across the Earth Science community

Development of a TaqMan Allelic Discrimination Assay for detection of Single Nucleotides Polymorphisms associated with anti-malarial drug resistance

<p>Abstract</p> <p>Background</p> <p>Anti-malarial drug resistance poses a threat to current global efforts towards control and elimination of malaria. Several methods are used in monitoring anti-malarial drug resistance. Molecular markers such as single nucleotide polymorphism (SNP) for example are increasingly being used to identify genetic mutations related to anti-malarial drug resistance. Several methods are currently being used in analysis of SNP associated with anti-malarial drug resistance and although each one of these methods has unique strengths and shortcoming, there is still need to improve and/or develop new methods that will close the gap found in the current methods.</p> <p>Methods</p> <p>TaqMan Allelic Discrimination assays for detection of SNPs associated with anti-malarial drug resistance were designed for analysis on Applied Biosystems PCR platform. These assays were designed by submitting SNP sequences associated with anti-malarial drug resistance to Applied Biosystems website. Eleven SNPs associated with resistance to anti-malarial drugs were selected and tested. The performance of each SNP assay was tested by creating plasmid DNAs carrying codons of interests and analysing them for analysis. To test the sensitivity and specificity of each SNP assay, 12 clinical samples were sequenced at codons of interest and used in the analysis. Plasmid DNAs were used to establish the Limit of Detection (LoD) for each assay.</p> <p>Results</p> <p>Data from genetic profiles of the <it>Plasmodium falciparum </it>laboratory strains and sequence data from 12 clinical samples was used as the reference method with which the performance of the SNP assays were compared to. The sensitivity and specificity of each SNP assay was establish at 100%. LoD for each assay was established at 2 GE, equivalent to less than 1 parasite/μL. SNP assays performed well in detecting mixed infection and analysis of clinical samples.</p> <p>Conclusion</p> <p>TaqMan Allelic Discrimination assay provides a good alternative tool in detection of SNPs associated with anti-malarial drug.</p

The Sex, Age, and Me Study: Recruitment and sampling for a large mixed-methods study of sexual health and relationships in an older Australian population

Older people are often excluded from large studies of sexual health, as it is assumed that they are not having sex or are reluctant to talk about sensitive topics, and are therefore difficult to recruit. We outline the sampling and recruitment strategies from a recent study on sexual health and relationships among older people. Sex, Age and Me was a nationwide Australian study that examined sexual health, relationship patterns, safer-sex practices, and STI knowledge of Australians aged 60 years and over. The study used a mixed-methods approach to establish baseline levels of knowledge and to develop deeper insights into older adult’s understandings and practices relating to sexual health. Data collection took place in 2015, with 2,137 participants completing a quantitative survey and 53 participating in one-on-one semi-structured interviews. As the feasibility of this type of study has been largely untested until now, we provide detailed information on the study’s recruitment strategies and methods. We also compare key characteristics of our sample with national estimates to assess its degree of representativeness. This study provides evidence to challenge the assumptions that older people will not take part in sexual health-related research and details a novel and successful way to recruit participants in this area