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

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

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

Reprogramming of Escherichia coli K-12 Metabolism during the Initial Phase of Transition from an Anaerobic to a Micro-Aerobic Environment

Background: Many bacteria undergo transitions between environments with differing O2 availabilities as part of their natural lifestyles and during biotechnological processes. However, the dynamics of adaptation when bacteria experience changes in O2 availability are understudied. The model bacterium and facultative anaerobe Escherichia coli K-12 provides an ideal system for exploring this process. Methods and Findings: Time-resolved transcript profiles of E. coli K-12 during the initial phase of transition from anaerobic to micro-aerobic conditions revealed a reprogramming of gene expression consistent with a switch from fermentative to respiratory metabolism. The changes in transcript abundance were matched by changes in the abundances of selected central metabolic proteins. A probabilistic state space model was used to infer the activities of two key regulators, FNR (O2 sensing) and PdhR (pyruvate sensing). The model implied that both regulators were rapidly inactivated during the transition from an anaerobic to a micro-aerobic environment. Analysis of the external metabolome and protein levels suggested that the cultures transit through different physiological states during the process of adaptation, characterized by the rapid inactivation of pyruvate formate-lyase (PFL), a slower induction of pyruvate dehydrogenase complex (PDHC) activity and transient excretion of pyruvate, consistent with the predicted inactivation of PdhR and FNR. Conclusion: Perturbation of anaerobic steady-state cultures by introduction of a limited supply of O2 combined with time-resolved transcript, protein and metabolite profiling, and probabilistic modeling has revealed that pyruvate (sensed by PdhR) is a key metabolic signal in coordinating the reprogramming of E. coli K-12 gene expression by working alongside the O2 sensor FNR during transition from anaerobic to micro-aerobic conditions

High‐resolution rock magnetic cyclostratigraphy in an Eocene flysch, Spanish Pyrenees

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95346/1/ggge1746.pd