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

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

A continental record of the Carnian Pluvial Episode (CPE) from the Mercia Mudstone Group (UK):palynology and climatic implications

The generally arid Late Triassic climate was interrupted by a wet phase during the mid-Carnian termed the Carnian Pluvial Episode (CPE). Quantitative palynological data from the Mercia Mudstone Group in the Wessex Basin (UK) reveal vegetation changes and palaeoclimate trends. Palynostratigraphy and bulk organic carbon isotope data allow correlation to other Carnian successions. The palynostratigraphy indicates that the Dunscombe Mudstone is Julian and the lowest part of the overlying Branscombe Mudstone Formation is Tuvalian. The Aulisporites acme characterizing the CPE in Tethyan successions and the Germanic Basin is missing in the UK. The quantitative palynological record suggests the predominance of xerophyte floral elements with a few horizons of increased hygrophytes. A humidity signal is not seen owing to the dry climate in central Pangea. Also, the signal might be masked by the overrepresentation of xerophyte regional pollen and the predominance of xerophyte hinterland flora. The bias towards regional pollen rain is enhanced by the potential increase in continental runoff related to seasonally humid conditions and differences in pollen production rates and transport mechanisms. The vegetation of British CPE successions suggests a more complex climate history during the Carnian, indicating that the CPE is not recognized by the same changes everywhere

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

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

Two-site recognition of Staphylococcus aureus peptidoglycan by lysostaphin SH3b

Lysostaphin is a bacteriolytic enzyme targeting peptidoglycan, the essential component of the bacterial cell envelope. It displays a very potent and specific activity toward staphylococci, including methicillin-resistant Staphylococcus aureus. Lysostaphin causes rapid cell lysis and disrupts biofilms, and is therefore a therapeutic agent of choice to eradicate staphylococcal infections. The C-terminal SH3b domain of lysostaphin recognizes peptidoglycans containing a pentaglycine crossbridge and has been proposed to drive the preferential digestion of staphylococcal cell walls. Here we elucidate the molecular mechanism underpinning recognition of staphylococcal peptidoglycan by the lysostaphin SH3b domain. We show that the pentaglycine crossbridge and the peptide stem are recognized by two independent binding sites located on opposite sides of the SH3b domain, thereby inducing a clustering of SH3b domains. We propose that this unusual binding mechanism allows synergistic and structurally dynamic recognition of S. aureus peptidoglycan and underpins the potent bacteriolytic activity of this enzyme

THE CASE FOR THE GLOBAL STRATOTYPE SECTION AND POINT(GSSP) FOR THE BASE OF THE NORIAN STAGE

The Norian Stage is the longest stage in the Phanerozoic, and some members of the boundary working group have been evaluating suitable Carnian-Norian boundary sections for roughly two decades. This has identified two possible candidate boundary sections, at Black Bear Ridge (British Columbia, Canada) and Pizzo Mondello (Sicily, Italy). After a formal voting procedure within the working group, ending on the 26th July, 2021, the Pizzo Mondello section was selected as the global stratotype section and point for the base of the Norian. We evaluated the global correlation potential of the two proposed primary markers, the conodont Metapolygnathus parvus and the ‘flat-clam’ Halobia austriaca. Secondary markers were also evaluated around these boundary datums for correlation potential, and the veracity of the proposed sections for GSSP status. Data and arguments for the proposed sections and datums are presented here. Through a two-stage process of option elimination in voting, conforming with ICS guidelines, the working group decided by 60% majority to propose that the first occurrence datum of Halobia austriaca in the Pizzo Mondello section at the base of bed FNP135A should become the ‘golden spike’ for the base of the Norian. A secondary biotic marker for this boundary is the first occurrence of Primatella (Carnepigondolella) gulloae, in sample NA43, ca. 0 m below FNP135A, and the FA of Dimorphites noricus (sample NA42.1) ca. 3.5 m above bed FNP135 (indicating the first subzone of the Jandianus Zone). The best physical secondary marker is the magnetozone PM5n with the proposed boundary ca.40% through the thickness of PM5n. Strengths of the chosen datum are: 1) it also maintains historical priority for ammonoid zonations, which had placed the base Norian near to this level in Europe, North America and probably NE Asia; 2) Halobia austriaca is widely distributed in all paleolatitudes and is a long-established taxon

The Sail-Backed Reptile Ctenosauriscus from the Latest Early Triassic of Germany and the Timing and Biogeography of the Early Archosaur Radiation

Background Archosaurs (birds, crocodilians and their extinct relatives including dinosaurs) dominated Mesozoic continental ecosystems from the Late Triassic onwards, and still form a major component of modern ecosystems (>10,000 species). The earliest diverse archosaur faunal assemblages are known from the Middle Triassic (c. 244 Ma), implying that the archosaur radiation began in the Early Triassic (252.3–247.2 Ma). Understanding of this radiation is currently limited by the poor early fossil record of the group in terms of skeletal remains. Methodology/Principal Findings We redescribe the anatomy and stratigraphic position of the type specimen of Ctenosauriscus koeneni (Huene), a sail-backed reptile from the Early Triassic (late Olenekian) Solling Formation of northern Germany that potentially represents the oldest known archosaur. We critically discuss previous biomechanical work on the ‘sail’ of Ctenosauriscus, which is formed by a series of elongated neural spines. In addition, we describe Ctenosauriscus-like postcranial material from the earliest Middle Triassic (early Anisian) Röt Formation of Waldhaus, southwestern Germany. Finally, we review the spatial and temporal distribution of the earliest archosaur fossils and their implications for understanding the dynamics of the archosaur radiation. Conclusions/Significance Comprehensive numerical phylogenetic analyses demonstrate that both Ctenosauriscus and the Waldhaus taxon are members of a monophyletic grouping of poposauroid archosaurs, Ctenosauriscidae, characterised by greatly elongated neural spines in the posterior cervical to anterior caudal vertebrae. The earliest archosaurs, including Ctenosauriscus, appear in the body fossil record just prior to the Olenekian/Anisian boundary (c. 248 Ma), less than 5 million years after the Permian–Triassic mass extinction. These earliest archosaur assemblages are dominated by ctenosauriscids, which were broadly distributed across northern Pangea and which appear to have been the first global radiation of archosaurs