Practical Aspects of Automatic Orientation Analysis of Micrographs

Techniques to analyse the orientation of particulate materials as observed in the scanning electron microscope are reviewed in this paper. Emphasis is placed on digital imaging, processing, and analysis methods, but many secondary electron images are not amenable to traditional image processing as adequate thresholding is often difficult to achieve. Evaluation of the intensity gradient at each pixel offers an alternative approach, and this method is described in detail including the latest developments to generalize the technique. Practical points in the acquisition, processing and analysis of the images are considered and several images, including both synthetically generated and actual back-scattered images of soil particle arrangements are presented. A discussion of methods to display the results is included as are possible future developments

Subduction flux modulates the geomagnetic polarity reversal rate

© 2018 The Authors Ascertaining the cause of variations in the frequency of geomagnetic polarity reversals through the Phanerozoic has remained a primary research question straddling paleomagnetism and geodynamics for decades. Numerical models suggest the primary control on geomagnetic reversal rates on 10 to 100 Ma timescales is the changing heat flux across the core-mantle boundary and that this is itself expected to be strongly influenced by variations in the flux of lithosphere subducted into the mantle. A positive relationship between the time-dependent global subduction flux and magnetic reversal rate is expected, with a time delay to transmit the thermal imprint into the lowermost mantle. We perform the first test of this hypothesis using subduction flux estimates and geomagnetic reversal rate data back to the early Paleozoic. Subduction area flux estimates are derived from global, full-plate tectonic models, and are evaluated against independent subduction flux proxies based on the global age distribution of detrital zircons and strontium isotopes. A continuous Phanerozoic reversal rate model is built from pre-existing compilations back to ~320 Ma plus a new reversal rate model in the data-sparse mid-to-early Paleozoic. Cross-correlation of the time-dependent subduction flux and geomagnetic reversal rate series reveals a significant correlation with a time delay of ~120 Ma (with reversals trailing the subduction flux). This time delay represents a value intermediate between the seismologically constrained time expected for a subducted slab to transit from the surface to the core-mantle boundary (~150–300 Ma), and the much shorter lag time predicted by some numerical models of mantle flow (~30–60 Ma). While the reason for this large discrepancy remains unclear, it is encouraging that our novel estimate of lag time represents a compromise between them. Although important uncertainties in our proposed relationship remain, these results cast new light on the dynamic connections between the surface and deep Earth, and will help to constrain new models linking mantle convection, the thermal evolution of the lowermost mantle and the geodynamo

Characterizing the self‐potential response to concentration gradients in heterogeneous subsurface environments

Self‐potential (SP) measurements can be used to characterize and monitor, in real‐time, fluid movement and behavior in the subsurface. The electrochemical exclusion‐diffusion (EED) potential, one component of SP, arises when concentration gradients exist in porous media. Such concentration gradients are of concern in coastal and contaminated aquifers and oil and gas reservoirs. It is essential that estimates of EED potential are made prior to conducting SP investigations in complex environments with heterogeneous geology and salinity contrasts, such as the UK Chalk coastal aquifer. Here we report repeatable laboratory estimates of the EED potential of chalk and marls using natural groundwater (GW), seawater (SW), deionized (DI) water, and 5 M NaCl. In all cases, the EED potential of chalk was positive (using a GW/SW concentration gradient the EED potential was ca. 14 to 22 mV), with an increased deviation from the diffusion limit at the higher salinity contrast. Despite the relatively small pore size of chalk (ca. 1 μm), it is dominated by the diffusion potential and has a low exclusion efficiency, even at large salinity contrasts. Marl samples have a higher exclusion efficiency which is of sufficient magnitude to reverse the polarity of the EED potential (using a GW/SW concentration gradient the EED potential was ca. −7 to −12 mV) with respect to the chalk samples. Despite the complexity of the natural samples used, the method produced repeatable results. We also show that first order estimates of the exclusion efficiency can be made using SP logs, supporting the parameterization of the model reported in Graham et al. (2018, https://doi.org/10.1029/2018WR022972), and that derived values for marls are consistent with the laboratory experiments, while values derived for hardgrounds based on field data indicate a similarly high exclusion efficiency. While this method shows promise in the absence of laboratory measurements, more rigorous estimates should be made where possible and can be conducted following the experimental methodology reported here

Loss of residues 119 – 136, including the first β-strand of human prion protein, generates an aggregation-competent partially “open” form

In prion replication, the cellular form of prion protein (PrPC) must undergo a full conformational transition to its disease-associated fibrillar form. Transmembrane forms of PrP have been implicated in this structural conversion. The cooperative unfolding of a structural core in PrPC presents a substantial energy barrier to prion formation, with membrane insertion and detachment of parts of PrP presenting a plausible route to its reduction. Here, we examined the removal of residues 119 - 136 of PrP, a region which includes the first β-strand and a substantial portion of the conserved hydrophobic region of PrP, a region which associates with the ER membrane, on the structure, stability and self-association of the folded domain of PrPC. We see an "open" native-like conformer with increased solvent exposure which fibrilises more readily than the native state. These data suggest a stepwise folding transition, which is initiated by the conformational switch to this "open" form of PrPC

Reconstructing palaeoclimate and hydrological fluctuations in the Fezzan Basin (southern Libya) since 130 ka: a catchment-based approach

We propose a novel method to evaluate regional palaeoclimate that can be used to alleviate the problems caused by the discontinuous nature of palaeoenvironmental data found in deserts. The technique involves processing satellite imagery and DEM’s to map past rivers, catchments and evaluate the areas and volumes of palaeolakes. This information is used to determine the new Lake Evaluation Index (LEI) that allows a qualitative estimate of the amount of sediment received by lakes and how long-lived those lakes are. Lakes with considerable longevity and large sediment stores are selected for study. Validation is performed using image interpretation of remote sensing data, UltraGPR surveys and fieldwork. These techniques are also used to identify and study spring deposits and fluvial landforms that provide valuable palaeoclimate information. The method is applied to the Fezzan Basin in southern Libya focusing on the Wadi ash Shati and Wadi el-Agial catchments. Results indicate that the palaeohydrology is accurately mapped except within dune fields. We analysed the sedimentology of the key deposits identified by this methodology, developing a chronology using optically stimulated luminescence (OSL) and radiocarbon dating. We find evidence for relatively humid conditions during MIS 5c/d and e, as well as during the early to middle Holocene. Larger lakes and more extensive river systems were present during MIS 5 than are found during the Holocene, suggestive of greater humidity. The Holocene humid period started at ~11 ka and continued until ~5 ka being interrupted by abrupt periods of aridity at ~8.2 ka and ~6 ka that coincide with North Atlantic cooling. After each of these arid events the climate was less humid than previously, suggesting that they were superimposed upon an overall drying trend. The termination of the Holocene humid period in the Sahara has received much scrutiny in recent years, and sediments of Palaeolake Shati provide a continuous record of this. We do not find evidence to support the hypothesis of either sudden or gradual aridification of the Sahara at ~5 ka, instead we find that that aridity started to develop at ~6.5 ka, whereupon the lake levels oscillated until finally drying-up by 5.3 ka. Most of the other lakes in the Fezzan also dried up at ~ 5ka. We suggest that thousands of years of aridification prior to 5 ka shrunk these lakes so that additional aridity at this time led to their final desiccation. Because lakes are prodigious dust sources this mechanism potentially explains the rapid rise in dust flux to the Atlantic at 5 ka, with this final drying being the culmination of longer term aridity, albeit overprinted with considerable climate variability

Obligate Heterodimerization of the Archaeal Alba2 Protein with Alba1 Provides a Mechanism for Control of DNA Packaging

SummaryOrganisms growing at elevated temperatures face a particular challenge to maintain the integrity of their genetic material. All thermophilic and hyperthermophilic archaea encode one or more copies of the Alba (Sac10b) gene. Alba is an abundant, dimeric, highly basic protein that binds cooperatively and at high density to DNA. Sulfolobus solfataricus encodes a second copy of the Alba gene, and the Alba2 protein is expressed at ∼5% of the level of Alba1. We demonstrate by NMR, ITC, and crystallography that Alba2 exists exclusively as a heterodimer with Alba1 at physiological concentrations and that heterodimerization exerts a clear effect upon the DNA packaging, as observed by EM, potentially by changing the interface between adjacent Alba dimers in DNA complexes. A functional role for Alba2 in modulation of higher order chromatin structure and DNA condensation is suggested

Molecular basis for bacterial peptidoglycan recognition by LysM domains.

Carbohydrate recognition is essential for growth, cell adhesion and signalling in all living organisms. A highly conserved carbohydrate binding module, LysM, is found in proteins from viruses, bacteria, fungi, plants and mammals. LysM modules recognize polysaccharides containing N-acetylglucosamine (GlcNAc) residues including peptidoglycan, an essential component of the bacterial cell wall. However, the molecular mechanism underpinning LysM-peptidoglycan interactions remains unclear. Here we describe the molecular basis for peptidoglycan recognition by a multimodular LysM domain from AtlA, an autolysin involved in cell division in the opportunistic bacterial pathogen Enterococcus faecalis. We explore the contribution of individual modules to the binding, identify the peptidoglycan motif recognized, determine the structures of free and bound modules and reveal the residues involved in binding. Our results suggest that peptide stems modulate LysM binding to peptidoglycan. Using these results, we reveal how the LysM module recognizes the GlcNAc-X-GlcNAc motif present in polysaccharides across kingdoms

Towards a consistent Oxfordian–Kimmeridgian global boundary: current state of knowledge

New data are presented in relation to the worldwide definition of the Oxfordian/Kimmeridgian boundary, i.e. the base of the Kimmeridgian Stage. This data, mostly acquired in the past decade, supports the 2006 proposal to make the uniform boundary of the stages in the Flodigarry section at Staffin Bay on the Isle of Skye, northern Scotland. This boundary is based on the Subboreal-Boreal ammonite successions, and it is distinguished by the Pictonia flodigarriensis horizon at the base of the Subboreal Baylei Zone, and which corresponds precisely to the base of the Boreal Bauhini Zone. The boundary lies in the 0.16 m interval (1.24–1.08 m) below bed 36 in sections F6 at Flodigarry and it is thus proposed as the GSSP for the Oxfordian/Kimmeridgian boundary. This boundary is recognized also by other stratigraphical data – palaeontological, geochemical and palaeomagnetic (including its well documented position close to the boundary between magnetozones F3n, and F3r which is placed in the 0.20 m interval – 1.28 m to 1.48 m below bed 36 – the latter corresponding to marine magnetic anomaly M26r).The boundary is clearly recognizable also in other sections of the Subboreal and Boreal areas discussed in the study, including southern England, Pomerania and the Peri-Baltic Syneclise, Russian Platform, Northern Central Siberia, Franz-Josef Land, Barents Sea and Norwegian Sea. It can be recognized also in the Submediterranean-Mediterranean areas of Europe and Asia where it correlates with the boundary between the Hypselum and the Bimmamatum ammonite zones. The changes in ammonite faunas at the boundary of these ammonite zones – mostly of ammonites of the families Aspidoceratidae and Oppeliidae – also enables the recognition of the boundary in the Tethyan and Indo-Pacific areas – such as the central part of the Americas (Cuba, Mexico), southern America, and southern parts of Asia. The climatic and environmental changes near to the Oxfordian/Kimmeridgian boundary discussed in the study relate mostly to the European areas. They show that very unstable environments at the end of the Oxfordian were subsequently replaced by more stable conditions representing a generally warming trend during the earliest Kimmeridgian. The definition of the boundary between the Oxfordian and Kimmeridgian as given in this study results in its wide correlation potential and means that it can be recognized in the different marine successions of the World

Temporal evolution of shallow marine diagenetic environments: Insights from carbonate concretions

Early diagenesis of marine organic matter dramatically impacts Earth's surface chemistry by changing the burial potential of carbon and promoting the formation of authigenic mineral phases including carbonate concretions. Marine sediment-hosted carbonate concretions tend to form as a result of microbial anaerobic diagenetic reactions that degrade organic matter and methane, some of which require an external oxidant. Thus, temporal changes in the oxidation state of Earth's oceans may impart a first-order control on concretion authigenesis mechanisms through time. Statistically significant variability in concretion carbonate carbon isotope compositions indicates changes in shallow marine sediment diagenesis associated with Earth's evolving redox landscape. This variability manifests itself as an expansion in carbon isotope composition range broadly characterized by an increase in maximum and decrease in minimum isotope values through time. Reaction transport modelling helps to constrain the potential impacts of shifting redox chemistry and highlights the importance of organic carbon delivery to the seafloor, marine sulfate concentrations, methane production and external methane influx. The first appearance of conclusively anaerobic oxidation of methane-derived concretions occurs in the Carboniferous and coincides with a Paleozoic rise in marine sulfate. The muted variability recognized in older concretions (and in particular for Precambrian concretions) likely reflects impacts of a smaller marine sulfate reservoir and perhaps elevated marine dissolved inorganic carbon concentrations. Causes of the increase in carbon isotope maximum values through time are more confounding, but may be related to isotopic equilibration of dissolved inorganic carbon with externally derived methane. Ultimately the concretion isotope record in part reflects changes in organic matter availability and marine oxidation state, highlighting connections with the subsurface biosphere and diagenesis throughout geologic time

Structural effects of the highly protective V127 polymorphism on human prion protein

Prion diseases, a group of incurable, lethal neurodegenerative disorders of mammals including humans, are caused by prions, assemblies of misfolded host prion protein (PrP). A single point mutation (G127V) in human PrP prevents prion disease, however the structural basis for its protective effect remains unknown. Here we show that the mutation alters and constrains the PrP backbone conformation preceding the PrP β-sheet, stabilising PrP dimer interactions by increasing intermolecular hydrogen bonding. It also markedly changes the solution dynamics of the β2-α2 loop, a region of PrP structure implicated in prion transmission and cross-species susceptibility. Both of these structural changes may affect access to protein conformers susceptible to prion formation and explain its profound effect on prion disease