Complex gas hydrate from the Cascadia margin

Natural gas hydrates are a potential source of energy and may play a role in climate change and geological hazards. Most natural gas hydrate appears to be in the form of 'structure I', with methane as the trapped guest molecule, although 'structure II' hydrate has also been identified, with guest molecules such as isobutane and propane, as well as lighter hydrocarbons. A third hydrate structure, 'structure H', which is capable of trapping larger guest molecules, has been produced in the laboratory, but it has not been confirmed that it occurs in the natural environment. Here we characterize the structure, gas content and composition, and distribution of guest molecules in a complex natural hydrate sample recovered from Barkley canyon, on the northern Cascadia margin. We show that the sample contains structure H hydrate, and thus provides direct evidence for the natural occurrence of this hydrate structure. The structure H hydrate is intimately associated with structure II hydrate, and the two structures contain more than 13 different hydrocarbon guest molecules. We also demonstrate that the stability field of the complex gas hydrate lies between those of structure II and structure H hydrates, indicating that this form of hydrate is more stable than structure I and may thus potentially be found in a wider pressure-temperature regime than can methane hydrate deposits.     

Fluctuating valence in a correlated solid and the anomalous properties of delta-plutonium

Although the nuclear properties of the late actinides (plutonium, americium and curium) are fully understood and widely applied to energy generation, their solid-state properties do not fit within standard models and are the subject of active research. Plutonium displays phases with enormous volume differences, and both its Pauli-like magnetic susceptibility and resistivity are an order of magnitude larger than those of simple metals. Curium is also highly resistive, but its susceptibility is Curie-like at high temperatures and orders antiferromagnetically at low temperatures. The anomalous properties of the late actinides stem from the competition between itinerancy and localization of their f-shell electrons, which makes these elements strongly correlated materials. A central problem in this field is to understand the mechanism by which these conflicting tendencies are resolved in such materials. Here we identify the electronic mechanisms responsible for the anomalous behaviour of late actinides, revisiting the concept of valence using a theoretical approach that treats magnetism, Kondo screening, atomic multiplet effects and crystal field splitting on the same footing. We find that the ground state in plutonium is a quantum superposition of two distinct atomic valences, whereas curium settles into a magnetically ordered single valence state at low temperatures. The f(7) configuration of curium is contrasted with the multiple valences of the plutonium ground state, which we characterize by a valence histogram. The balance between the Kondo screening and magnetism is controlled by the competition between spin-orbit coupling, the strength of atomic multiplets and the degree of itinerancy. Our approach highlights the electronic origin of the bonding anomalies in plutonium, and can be applied to predict generalized valences and the presence or absence of magnetism in other compounds starting from first principles.     

Exploitation of structural and regulatory diversity in glutamate racemases

Glutamate racemase is an enzyme essential to the bacterial cell wall biosynthesis pathway, and has therefore been considered as a target for antibacterial drug discovery. We characterized the glutamate racemases of several pathogenic bacteria using structural and biochemical approaches. Here we describe three distinct mechanisms of regulation for the family of glutamate racemases: allosteric activation by metabolic precursors, kinetic regulation through substrate inhibition, and D-glutamate recycling using a d-amino acid transaminase. In a search for selective inhibitors, we identified a series of uncompetitive inhibitors specifically targeting Helicobacter pylori glutamate racemase that bind to a cryptic allosteric site, and used these inhibitors to probe the mechanistic and dynamic features of the enzyme. These structural, kinetic and mutational studies provide insight into the physiological regulation of these essential enzymes and provide a basis for designing narrow-spectrum antimicrobial agents.     

Functional diversification of closely related ARF-GEFs in protein secretion and recycling

Guanine-nucleotide exchange factors on ADP-ribosylation factor GTPases (ARF-GEFs) regulate vesicle formation in time and space by activating ARF substrates on distinct donor membranes. Mammalian GBF1 (ref. 2) and yeast Gea1/2 (ref. 3) ARF-GEFs act at Golgi membranes, regulating COPI-coated vesicle formation. In contrast, their Arabidopsis thaliana homologue GNOM (GN) is required for endosomal recycling, playing an important part in development. This difference indicates an evolutionary divergence of trafficking pathways between animals and plants, and raised the question of how endoplasmic reticulum-Golgi transport is regulated in plants. Here we demonstrate that the closest homologue of GNOM in Arabidopsis, GNOM-LIKE1 (GNL1; NM_123312; At5g39500), performs this ancestral function. GNL1 localizes to and acts primarily at Golgi stacks, regulating COPI-coated vesicle formation. Surprisingly, GNOM can functionally substitute for GNL1, but not vice versa. Our results suggest that large ARF-GEFs of the GBF1 class perform a conserved role in endoplasmic reticulum-Golgi trafficking and secretion, which is done by GNL1 and GNOM in Arabidopsis, whereas GNOM has evolved to perform an additional plant-specific function of recycling from endosomes to the plasma membrane. Duplication and diversification of ARF-GEFs in plants contrasts with the evolution of entirely new classes of ARF-GEFs for endosomal trafficking in animals, which illustrates the independent evolution of complex endosomal pathways in the two kingdoms.     

Tibetan plateau aridification linked to global cooling at the Eocene-Oligocene transition

Continental aridification and the intensification of the monsoons in Asia are generally attributed to uplift of the Tibetan plateau and to the land-sea redistributions associated with the continental collision of India and Asia, whereas some studies suggest that past changes in Asian environments are mainly governed by global climate. The most dramatic climate event since the onset of the collision of India and Asia is the Eocene-Oligocene transition, an abrupt cooling step associated with the onset of glaciation in Antarctica 34 million years ago. However, the influence of this global event on Asian environments is poorly understood. Here we use magnetostratigraphy and cyclostratigraphy to show that aridification, which is indicated by the disappearance of playa lake deposits in the northeastern Tibetan plateau, occurred precisely at the time of the Eocene-Oligocene transition. Our findings suggest that this global transition is linked to significant aridification and cooling in continental Asia recorded by palaeontological and palaeoenvironmental changes, and thus support the idea that global cooling is associated with the Eocene-Oligocene transition. We show that, with sufficient age control on the sedimentary records, global climate can be distinguished from tectonism and recognized as a major contributor to continental Asian environments.     

A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence

Plants sense potential microbial invaders by using pattern-recognition receptors to recognize pathogen-associated molecular patterns (PAMPs). In Arabidopsis thaliana, the leucine-rich repeat receptor kinases flagellin-sensitive 2 (FLS2) (ref. 2) and elongation factor Tu receptor (EFR) (ref. 3) act as pattern-recognition receptors for the bacterial PAMPs flagellin and elongation factor Tu (EF-Tu) (ref. 5) and contribute to resistance against bacterial pathogens. Little is known about the molecular mechanisms that link receptor activation to intracellular signal transduction. Here we show that BAK1 (BRI1-associated receptor kinase 1), a leucine-rich repeat receptor-like kinase that has been reported to regulate the brassinosteroid receptor BRI1 (refs 6,7), is involved in signalling by FLS2 and EFR. Plants carrying bak1 mutations show normal flagellin binding but abnormal early and late flagellin-triggered responses, indicating that BAK1 acts as a positive regulator in signalling. The bak1-mutant plants also show a reduction in early, but not late, EF-Tu-triggered responses. The decrease in responses to PAMPs is not due to reduced sensitivity to brassinosteroids. We provide evidence that FLS2 and BAK1 form a complex in vivo, in a specific ligand-dependent manner, within the first minutes of stimulation with flagellin. Thus, BAK1 is not only associated with developmental regulation through the plant hormone receptor BRI1 (refs 6,7), but also has a functional role in PRR-dependent signalling, which initiates innate immunity.     

Catastrophic flooding origin of shelf valley systems in the English Channel

Megaflood events involving sudden discharges of exceptionally large volumes of water are rare, but can significantly affect landscape evolution, continental-scale drainage patterns and climate change. It has been proposed that a significant flood event eroded a network of large ancient valleys on the floor of the English Channel-the narrow seaway between England and France. This hypothesis has remained untested through lack of direct evidence, and alternative non-catastrophist ideas have been entertained for valley formation. Here we analyse a new regional bathymetric map of part of the English Channel derived from high-resolution sonar data, which shows the morphology of the valley in unprecedented detail. We observe a large bedrock-floored valley that contains a distinct assemblage of landforms, including streamlined islands and longitudinal erosional grooves, which are indicative of large-scale subaerial erosion by high-magnitude water discharges. Our observations support the megaflood model, in which breaching of a rock dam at the Dover Strait instigated catastrophic drainage of a large pro-glacial lake in the southern North Sea basin. We suggest that megaflooding provides an explanation for the permanent isolation of Britain from mainland Europe during interglacial high-sea-level stands, and consequently for patterns of early human colonisation of Britain together with the large-scale reorganization of palaeodrainage in northwest Europe.     

Aggregation and vesiculation of membrane proteins by curvature-mediated interactions

Membrane remodelling plays an important role in cellular tasks such as endocytosis, vesiculation and protein sorting, and in the biogenesis of organelles such as the endoplasmic reticulum or the Golgi apparatus. It is well established that the remodelling process is aided by specialized proteins that can sense as well as create membrane curvature, and trigger tubulation when added to synthetic liposomes. Because the energy needed for such large-scale changes in membrane geometry significantly exceeds the binding energy between individual proteins and between protein and membrane, cooperative action is essential. It has recently been suggested that curvature-mediated attractive interactions could aid cooperation and complement the effects of specific binding events on membrane remodelling. But it is difficult to experimentally isolate curvature-mediated interactions from direct attractions between proteins. Moreover, approximate theories predict repulsion between isotropically curving proteins. Here we use coarse-grained membrane simulations to show that curvature-inducing model proteins adsorbed on lipid bilayer membranes can experience attractive interactions that arise purely as a result of membrane curvature. We find that once a minimal local bending is realized, the effect robustly drives protein cluster formation and subsequent transformation into vesicles with radii that correlate with the local curvature imprint. Owing to its universal nature, curvature-mediated attraction can operate even between proteins lacking any specific interactions, such as newly synthesized and still immature membrane proteins in the endoplasmic reticulum.     

Evolution of cooperation in a finite homogeneous graph

Recent theoretical studies of selection in finite structured populations have worked with one of two measures of selective advantage of an allele: fixation probability and inclusive fitness. Each approach has its own analytical strengths, but given certain assumptions they provide equivalent results. In most instances the structure of the population can be specified by a network of nodes connected by edges (that is, a graph), and much of the work here has focused on a continuous-time model of evolution, first described by ref. 11. Working in this context, we provide an inclusive fitness analysis to derive a surprisingly simple analytical condition for the selective advantage of a cooperative allele in any graph for which the structure satisfies a general symmetry condition ('bi-transitivity'). Our results hold for a broad class of population structures, including most of those analysed previously, as well as some for which a direct calculation of fixation probability has appeared intractable. Notably, under some forms of population regulation, the ability of a cooperative allele to invade is seen to be independent of the nature of population structure (and in particular of how game partnerships are specified) and is identical to that for an unstructured population. For other types of population regulation our results reveal that cooperation can invade if players choose partners along relatively 'high-weight' edges.