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

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

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

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

Mapping local structural perturbations in the native state of stefin B (cystatin B) under amyloid forming conditions

Unlike a number of amyloid-forming proteins, stefins, and in particular stefin B (cystatin B) form amyloids under conditions where the native state predominates. In order to trigger oligomerization processes, the stability of the protein needs to be compromised, favoring structural re-arrangement however, accelerating fibril formation is not a simple function of protein stability. We report here on how optimal conditions for amyloid formation lead to the destabilization of dimeric and tetrameric states of the protein in favor of the monomer. Small, highly localized structural changes can be mapped out that allow us to visualize directly areas of the protein which eventually become responsible for triggering amyloid formation. These regions of the protein overlap with the Cu (II)-binding sites which we identify here for the first time. We hypothesize that in vivo modulators of amyloid formation may act similarly to painstakingly optimized solvent conditions developed in vitro. We discuss these data in the light of current structural models of stefin B amyloid fibrils based on H-exchange data, where the detachment of the helical part and the extension of loops were observed

Kinetics of immersion nucleation driven by surface tension

Immersion nucleation is the nuclei formation mechanism for wet granulation systems where the liquid drops are large relative to the primary particles. The process of immersion nucleation has been examined in many studies, however the kinetics of nuclei formation are not well understood, and there is a distinct lack of experimentally validated models for this process. A kinetic model has been proposed by Hounslow et al. (2009) which describes surface tension driven immersion nucleation. This paper presents the results from a series of experiments measuring the kinetics of immersion nucleation, and these results are compared with the model predictions. Drops of model liquids (aqueous HPMC solution and silicone oil) are placed on static powder beds of zeolite and lactose. Nuclei granules are carefully excavated at different times and the change in granule mass with time is measured. As predicted by Hounslow et al.'s model, the granule mass increases with the square root of time to a maximum granule size at a time tmax after an initial adjustment period. The critical packing factor is shown to be a function of powder properties, and not dependent on the liquid properties. The model captures well the measured effects of liquid and powder properties. However, the kinetics of the nucleation process are much slower than predicted by the model. It is believed this is due to continued percolation of the liquid within the powder bed, after the liquid drop is fully immersed. This secondary liquid movement may have an important effect on granule growth kinetics, and influence final granule product properties

Decoration of the enterococcal polysaccharide antigen EPA is essential for virulence, cell surface charge and interaction with effectors of the innate immune system

Enterococcus faecalis is an opportunistic pathogen with an intrinsically high resistance to lysozyme, a key effector of the innate immune system. This high level of resistance requires a complex network of transcriptional regulators and several genes (oatA, pgdA, dltA and sigV) acting synergistically to inhibit both the enzymatic and cationic antimicrobial peptide activities of lysozyme. We sought to identify novel genes modulating E. faecalis resistance to lysozyme. Random transposon mutagenesis carried out in the quadruple oatA/pgdA/dltA/sigV mutant led to the identification of several independent insertions clustered on the chromosome. These mutations were located in a locus referred to as the enterococcal polysaccharide antigen (EPA) variable region located downstream of the highly conserved epaA-epaR genes proposed to encode a core synthetic machinery. The epa variable region was previously proposed to be responsible for EPA decorations, but the role of this locus remains largely unknown. Here, we show that EPA decoration contributes to resistance towards charged antimicrobials and underpins virulence in the zebrafish model of infection by conferring resistance to phagocytosis. Collectively, our results indicate that the production of the EPA rhamnopolysaccharide backbone is not sufficient to promote E. faecalis infections and reveal an essential role of the modification of this surface polymer for enterococcal pathogenesis

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

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