Dynamic cofilin phosphorylation in the control of lamellipodial actin homeostasis

During animal cell chemotaxis, signalling at the plasma membrane induces actin polymerisation to drive forward cell movement. Since the cellular pool of actin is limited, efficient protrusion formation also requires the coordinated disassembly of pre-existing actin filaments. To search for proteins that can monitor filamentous and globular actin levels to maintain the balance of polymerisation and disassembly, we followed changes in the proteome induced by RNA interference (RNAi)mediated alterations in actin signalling. This unbiased approach revealed an increase in the levels of an inactive, phosphorylated form of the actin-severing protein cofilin in cells unable to generate actin-based lamellipodia. Conversely, an increase in F-actin levels induced the dephosphorylation and activation of cofilin via activation of the Ssh phosphatase. Similarly, in the context of acute phosphoinositide 3-kinase (PI3K) signalling, dynamic changes in cofilin phosphorylation were found to depend on the Ssh phosphatase and on changes in lamellipodial Factin. These results indicate that changes in the extent of cofilin phosphorylation are regulated by Ssh in response to changes in the levels and/or organisation of F-actin. Together with the recent finding that Ssh phosphatase activity is augmented by F-actin binding, these results identify Ssh-dependent regulation of phosphorylated cofilin levels as an important feedback control mechanism that maintains actin filament homeostasis during actin signalling

Shock Deformation in Zircon, a Comparison of Results from Shock-Reverberation and Single-Shock Experiments

The utility of the mineral zircon, ZrSiO4, as a shock-metamorphic geobarometer and geochronometer, has been steadily growing within the planetary science community. Zircon is an accessory phase found in many terrestrial rock types, lunar samples, lunar meteorites, martian meteorites and various other achondrites. Because zircon is refractory and has a high closure temperature for Pb diffusion, it has been used to determine the ages of some of the oldest material on Earth and elsewhere in the Solar System. Furthermore, major (O) and trace-element (REE, Ti, Hf) abundances and isotope compositions of zircon help characterize the petrogenetic environments and sources from which they crystallized. The response of zircon to impact-induced shock deformation is predominantly crystallographic, including dislocation creep and the formation of planar and sub-planar, low-angle grain boundaries; the formation of mechanical {112} twins; transformation to the high pressure polymorph reidite; the development of polycrystalline microtextures; and dissociation to the oxide constituents SiO2 and ZrO2. Shock microstructures can also variably affect the U- Pb isotope systematics of zircon and, in some instances, be used to constrain the impact age. While numerous studies have characterized shock deformation in zircon recovered from a variety of terrestrial impact craters and ejecta deposits and Apollo samples, experimental studies of shock deformation in zircon are limited to a handful of examples in the literature. In addition, the formation conditions (e.g., P, T) of various shock microstructures, such as planar-deformation bands, twins, and reidite lamellae, remain poorly con-strained. Furthermore, previous shocked-zircon experimental charges have not been analyzed using modern analytical equipment. This study will therefore under-take an new set of zircon shock experiments, which will then be microstructurally characterized using state-of-the-art instrumentation within the Astromaterials Research and Exploration Science Division (ARES), NASA Johnson Space Center

Rapid hydration and weakening of anhydrite under stress: implications for natural hydration in the Earth's crust and mantle

Mineral hydration is an important geological process that influences the rheology and geochemistry of rocks and the fluid budget of the Earth's crust and mantle. Constant-stress differential compaction (CSDC) tests, dry and "wet"tests under confining pressure, and axial-stress tests were conducted for the first time to investigate the influence of triaxial stress on hydration in anhydrite-gypsum aggregates. Characterization of the samples before and after triaxial experiments was performed with optical and scanning electron microscopy, including energy-dispersive spectroscopy and electron backscatter diffraction mapping. Stress-strain data reveal that samples that underwent constant-stress differential compaction in the presence of fluids are g1/4g14g% to g1/4g41g% weaker than samples deformed under wet conditions. The microstructural analysis shows that there is a strong temporal and spatial connection between the geometry, distribution, and evolution of fractures and hydration products. The increasing reaction surface area in combination with pre-existing gypsum in a gypsum-bearing anhydrite rock led to rapid gypsification. The crystallographic orientations of newly formed vein gypsum have a systematic preferred orientation for long distances along veins, beyond the grain boundaries of wall-rock anhydrite. Gypsum crystallographic orientations in {100} and {010} are systematically and preferentially aligned parallel to the direction of maximum shear stress (45g to σ1). Gypsum is also not always topotactically linked to the wall-rock anhydrite in the immediate vicinity. This study proposes that the selective inheritance of crystal orientations from favourably oriented wall-rock anhydrite grains for the minimization of free energy for nucleation under stress leads to the systematic preferred orientation of large, new gypsum grains. A sequence is suggested for hydration under stress that requires the development of fractures accompanied by localized hydration. Hydration along fractures with a range of apertures up to 120gμm occurred in under 6gh. Once formed, gypsum-filled veins represent weak surfaces and are the locations of further shear fracturing, brecciation, and eventual brittle failure. These findings imply that non-hydrostatic stress has a significant influence on hydration rates and subsequent mechanical strength of rocks. This phenomenon is applicable across a wide range of geological environments in the Earth's crust and upper mantle

The variation and visualisation of elastic anisotropy in rock forming minerals

Acknowledgements David Healy thanks John Wheeler (Liverpool) for discussions and Ross Angel (Padua) for discussions and a reprint. This paper is dedicated to the memory of John Frederick Nye (1923–2019), whose seminal text book, first published in 1957 (Physical Properties of Crystals: Their Representation by Tensors and Matrices; reprinted as Nye, 1985), has had a huge influence on the lead author. Financial support This research has been supported by the NERC (grant no. NE/N003063/1).Peer reviewedPublisher PD

A cancer cell-line titration series for evaluating somatic classification.

BackgroundAccurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated with normal cells confounding the available evidence for the somatic variants. Furthermore, tumours are heterogeneous so sub-clonal variants are observed at reduced allele frequencies. We present here a cell-line titration series dataset that can be used to evaluate somatic variant calling pipelines with the goal of reliably calling true somatic mutations at low allele frequencies.ResultsCell-line DNA was mixed with matched normal DNA at 8 different ratios to generate samples with known tumour cellularities, and exome sequenced on Illumina HiSeq to depths of >300×. The data was processed with several different variant calling pipelines and verification experiments were performed to assay >1500 somatic variant candidates using Ion Torrent PGM as an orthogonal technology. By examining the variants called at varying cellularities and depths of coverage, we show that the best performing pipelines are able to maintain a high level of precision at any cellularity. In addition, we estimate the number of true somatic variants undetected as cellularity and coverage decrease.ConclusionsOur cell-line titration series dataset, along with the associated verification results, was effective for this evaluation and will serve as a valuable dataset for future somatic calling algorithm development. The data is available for further analysis at the European Genome-phenome Archive under accession number EGAS00001001016. Data access requires registration through the International Cancer Genome Consortium's Data Access Compliance Office (ICGC DACO)

Enhanced diffusion of Uranium and Thorium linked to crystal plasticity in zircon

The effects of crystal-plasticity on the U-Th-Pb system in zircon is studied by quantitative microstructural and microchemical analysis of a large zircon grain collected from pyroxenite of the Lewisian Complex, Scotland. Electron backscatter diffraction (EBSD) mapping reveals a c.18° variation in crystallographic orientation that comprises both a gradual change in orientation and a series of discrete low-angle (<4°) boundaries. These microstructural data are consistent with crystal-plastic deformation of zircon associated with the formation and migration of dislocations. A heterogeneous pattern of dark cathodoluminescence, with the darkest domains coinciding with low-angle boundaries, mimics the deformation microstructure identified by EBSD. Geochemical data collected using the Sensitive High Resolution Ion MicroProbe (SHRIMP) shows a positive correlation between concentrations of the elements U, Th and Pb (ranging from 20–60 ppm, 30–110 ppm, and 14–36 ppm, respectively) and Th/U ratio (1.13 – 1.8) with the deformation microstructure. The highest measured concentrations and Th/U coincide with low-angle boundaries. This enrichment is interpreted to reflect enhanced bulk diffusion of U and Th due to the formation and migration of high-diffusivity dislocations. (207)Pb/(206)Pb ages for individual analyses show no significant variation across the grain, and define a concordant, combined mean age of 2451 ± 14 Ma. This indicates that the grain was deformed shortly after initial crystallization, most probably during retrograde Inverian metamorphism at amphibolite facies conditions. The elevated Th over U and consistent (207)Pb/(206)Pb ages indicates that deformation most likely occurred in the presence of a late-stage magmatic fluid that drove an increase in the Th/U during deformation. The relative enrichment of Th over U implies that Th/U ratio may not always be a robust indicator of crystallization environment. This study provides the first evidence of deformation-related modification of the U-Th system in zircon and has fundamental implications for the application and interpretation of zircon trace element data

Grain boundary networks and shape preferred orientation : A fresh angle on pattern quantification with GBPaQ

A quantitative understanding of grain shape preferred orientation (SPO) and grain boundary networks as fundamental characteristics of rocks and other crystalline solids is of major interest in geology and material science. Grain boundary networks contain useful information on the deformation history of polycrystalline aggregates, and their diagenetic and metamorphic histories. SPO can have a major impact on material characteristics such as permeability, acoustic velocity and mechanical strength, and on reaction surfaces. The objective of this study is to present a semi-automated toolbox of MATLAB™ scripts, named Grain Boundary Pattern Quantification (GBPaQ), that incorporate different methods for grain boundary pattern quantification for their application to, for example, seismic wave attenuation estimation. GBPaQ uses grain boundary statistics and calculates radial scan line intercepts. In this paper, GBPaQ is tested on two example grain boundary patterns, a granular texture and a foam texture with equant grains, which have been digitally stretched (deformed) to analyse their SPO evolution. The results show that a combination of grain ellipse, grain boundary segment orientation, and grain boundary segment intercept density rose diagrams provide a complete, detailed quantification of grain boundary pattern anisotropy. Grain boundary segment intercept (GBSI) analysis using GBPaQ yields a new grain boundary network parameter – the minimum intensity of grain boundary intercepts (Imin) – which follows a power law relationship with the average axial ratio of grain-fitted ellipses (r) during SPO development. We propose that Imin can be used for the quantitative analysis of SPO strength as a useful tool to assess the deformation history of polycrystalline aggregates. Further studies involving a broader range of different patterns and strain histories are necessary to fully investigate the potential of Imin versus r diagrams

Rapid hydration and weakening of anhydrite under stress : Implications for natural hydration in the Earth’s crust and mantle

Acknowledgements JThis research has been supported by an Aberdeen–Curtin Alliance international postgraduate scholarship, by a Curtin publication grant, and by the Natural Environment Research Council (grant no. NE/T007826/1). Enrique Gomez-Rivas acknowledges the “Ramón y Cajal” fellowship RYC2018-026335-I, funded by the Spanish Ministry of Science and Innovation (MCIN), the State Research Agency of Spain (AEI), and the European Social Fund (ESF)/10.13039/501100011033, as well as the DGICYT research project PID2020-118999GB-I00, funded by the Spanish Ministry of Science and Innovation (MCIN) and State Research Agency of Spain (AEI)/10.13039/501100011033.Peer reviewedPublisher PD

Shocked Quartz in Polymict Impact Breccia from the Upper Cretaceous Yallalie Impact Structure in Western Australia

Yallalie is a ~12 km diameter circular structure located ~200 km north of Perth, Australia. Previous studies have proposed that the buried structure is a complex impact crater based on geophysical data. Allochthonous breccia exposed near the structure has previously been interpreted as proximal impact ejecta; however, no diagnostic indicators of shock metamorphism have been found. Here we report multiple (27) shocked quartz grains containing planar fractures (PFs) and planar deformation features (PDFs) in the breccia. The PFs occur in up to five sets per grain, while the PDFs occur in up to four sets per grain. Universal stage measurements of all 27 shocked quartz grains confirms that the planar microstructures occur in known crystallographic orientations in quartz corresponding to shock compression from 5 to 20 GPa. Proximity to the buried structure (~4 km) and occurrence of shocked quartz indicates that the breccia represents either primary or reworked ejecta. Ejecta distribution simulated using iSALE hydrocode predicts the same distribution of shock levels at the site as those found in the breccia, which supports a primary ejecta interpretation, although local reworking cannot be excluded. The Yallalie impact event is stratigraphically constrained to have occurred in the interval from 89.8 to 83.6 Ma based on the occurrence of Coniacian clasts in the breccia and undisturbed overlying Santonian to Campanian sedimentary rocks. Yallalie is thus the first confirmed Upper Cretaceous impact structure in Australia

A Comparison of Hygromycin and Paromomycin Selection Strategies in the Genetic Transformation of Seven \u3ci\u3eLolium, Festuca, Poa\u3c/i\u3e, and \u3ci\u3eAgrostis\u3c/i\u3e Species

Hygromycin selection for the hpt gene, expressed from the CaMV-35S promoter, has been successful in transgenesis of a limited number of grass species. As an alternative to hpt selection Altpeter et al., (2000) reported successful transformation using paromomycin selection for the nptII gene expressed by the maize ubiquitin promoter. We have tested the utility of a number of selection cassettes using previously sporadically transformable species which nevertheless had very good tissue culture and regeneration protocols