A new type of Na+-driven ATP synthase membrane rotor with a two-carboxylate ion-coupling motif

Abstract: The anaerobic bacterium Fusobacterium nucleatum uses glutamate decarboxylation to generate a transmembrane gradient of Na+. Here, we demonstrate that this ion-motive force is directly coupled to ATP synthesis, via an F1Fo-ATP synthase with a novel Na+ recognition motif, shared by other human pathogens. Molecular modeling and free-energy simulations of the rotary element of the enzyme, the c-ring, indicate Na+ specificity in physiological settings. Consistently, activity measurements showed Na+ stimulation of the enzyme, either membrane-embedded or isolated, and ATP synthesis was sensitive to the Na+ ionophore monensin. Furthermore, Na+ has a protective effect against inhibitors targeting the ion-binding sites, both in the complete ATP synthase and the isolated c-ring. Definitive evidence of Na+ coupling is provided by two identical crystal structures of the c11 ring, solved by X-ray crystallography at 2.2 and 2.6 Å resolution, at pH 5.3 and 8.7, respectively. Na+ ions occupy all binding sites, each coordinated by four amino acids and a water molecule. Intriguingly, two carboxylates instead of one mediate ion binding. Simulations and experiments demonstrate that this motif implies that a proton is concurrently bound to all sites, although Na+ alone drives the rotary mechanism. The structure thus reveals a new mode of ion coupling in ATP synthases and provides a basis for drug-design efforts against this opportunistic pathogen. Author Summary: Essential cellular processes such as biosynthesis, transport, and motility are sustained by the energy released in the hydrolysis of ATP, the universal energy carrier in living cells. Most ATP in the cell is produced by a membrane-bound enzyme, the ATP synthase, through a rotary mechanism that is coupled to the translocation of ions across the membrane. The majority of ATP synthases are energized by transmembrane electrochemical gradients of protons (proton-motive force), but a number of organisms, including some important human pathogens, use gradients of sodium ions instead (sodium-motive force). The ion specificity of ATP synthases is determined by a membrane-embedded sub-complex, the c-ring, which is the smallest known biological rotor. The functional mechanism of the rotor ring and its variations among different organisms are of wide interest, because of this enzyme's impact on metabolism and disease, and because of its potential for nanotechnology applications. Here, we characterize a previously unrecognized type of Na+-driven ATP synthase from the opportunistic human pathogen Fusobacterium nucleatum, which is implicated in periodontal diseases. We analyzed this ATP synthase and its rotor ring through a multi-disciplinary approach, combining cell-growth and biochemical assays, X-ray crystallography and computer-simulation methods. Two crystal structures of the membrane rotor were solved, at low and high pH, revealing an atypical ion-recognition motif mediated by two carboxylate side-chains. This motif is shared by other human pathogens, such as Mycobacterium tuberculosis or Streptococcus pneumonia, whose ATP synthases are targets of novel antibiotic drugs. The implications of this ion-recognition mode on the mechanism of the ATP synthase and the cellular bioenergetics of F. nucleatum were thus examined. Our results provide the basis for future pharmacological efforts against this important pathogen

Innovation platforms: experiences with their institutional embedding in agricultural research for development

Innovation Platforms (IPs) are seen as a promising vehicle to foster a paradigm shift in agricultural research for development (AR4D). By facilitating interaction, negotiation and collective action between farmers, researchers and other stakeholders, IPs can contribute to more integrated, systemic innovation that is essential for achieving agricultural development impacts. However, successful implementation of IPs requires institutional change within AR4D establishments. The objective of this paper is to reflect on the implementation and institutionalisation of IPs in present AR4D programmes. We use experiences from sub-Saharan Africa to demonstrate how the adoption and adaptation of IPs creates both opportunities and challenges that influence platform performance and impact. Niche-regime theory is used to understand challenges, and anticipate on how to deal with them. A key concern is whether IPs in AR4D challenge or reinforce existing technology-oriented agricultural innovation paradigms. For example, stakeholder representation, facilitation and institutional embedding determine to a large extent whether the IP can strengthen systemic capacity to innovate that can lead to real paradigm change, or are merely ‘old wine in new bottles’ and a continuation of ‘business as usual’. Institutional embedding of IPs and – more broadly – the transition from technology-oriented to system-oriented AR4D approaches requires structural changes in organisational mandates, incentives, procedures and funding, as well as investments in exchange of experiences, learning and capacity development

Pre-breakup magmatism on the Vøring margin: Insight from new sub-basalt imaging and results from Ocean Drilling program hole 642E

Highlights • Sub-basalt imaging improvement on the Vøring Margin • Definition of a new seismic facies unit: the Lower Series Flows • Significant organic carbon content within the melting crustal segment • Apectodinium augustum marker for the PETM is reworked into the Lower Series Flows • The Lower Series Flows, early Eocene in age, predate the Vøring Margin breakup Abstract Improvements in sub-basalt imaging combined with petrological and geochemical observations from the Ocean Drilling Program (ODP) Hole 642E core provide new constraints on the initial breakup processes at the Vøring Margin. New and reprocessed high quality seismic data allow us to identify a new seismic facies unit which we define as the Lower Series Flows. This facies unit is seismically characterized by wavy to continuous subparallel reflections with an internal disrupted and hummocky shape. Drilled lithologies, which we correlate to this facies unit, have been interpreted as subaqueous flows extruding and intruding into wet sediments. Locally, the top boundary of this facies unit is defined as a negative in polarity reflection, and referred as the K-Reflection. This reflection can be correlated with the spatial extent of pyroclastic deposits, emplaced during transitional shallow marine to subaerial volcanic activities during the rift to drift transition. The drilled Lower Series Flows consist of peraluminous, cordierite bearing peperitic basaltic andesitic to dacitic flows interbedded with thick volcano-sedimentary deposits and intruded sills. The peraluminous geochemistry combined with available C (from calcite which fills vesicles and fractures), Sr, Nd, and Pb isotopes data point towards upper crustal rock-mantle magma interactions with a significant contribution of organic carbon rich pelagic sedimentary material during crustal anatexis. From biostratigraphic analyses, Apectodinium augustum was found in the The Lower Series Flows. This species is a marker for the Paleocene – Eocene Thermal Maximum (PETM). However, the absence of very low carbon isotope values (from bulk organic matter), that characterize the PETM, imply that A.augustum was reworked into the early Eocene sediments of this facies unit which predate the breakup time of the Vøring Margin. Finally, a plausible conceptual emplacement model for the Lower Series Flows facies unit is proposed. This model comprises several stages: (1) the emplacement of subaqueous peperitic basaltic andesitic flows intruding and/or extruding wet sediments; (2) a subaerial to shallow marine volcanism and extrusion of dacitic flows; (3) a proto-breakup phase with intense shallow marine to subaerial explosive volcanism responsible for pyroclastic flow deposits which can be correlated with the seismic K-Reflection and (4) the main breakup stage with intense transitional tholeiitic MORB-type volcanism and large subsidence concomitant with the buildup of the Seaward Dipping Reflector wedge

Online Reviews Generated Through Product Testing: Can More Favorable Reviews Be Enticed with Free Products?

Online reviews have profound impacts on firm success in terms of sales volume and how much customers are willing to pay, yet firms remain highly dependent on customers' voluntary contributions. A popular way to increase the number of online reviews is to use product testing programs, which offer participants free products in exchange for writing reviews. Firms that employ this practice generally hope to increase review quality and secure higher product rating scores. However, a qualitative study, experimental study, and multilevel analysis of a field study dataset of more than 200,000 online reviews by product testers combine to reveal that product testing programs do not necessarily generate higher quality reviews, nor better product ratings. Only in certain circumstances (e.g., higher priced products) does offering a product testing program generate these benefits for the firm. Therefore, companies should consider carefully if and when they want to offer product testing programs

High resolution 2-D fluorescence imaging of the mass boundary layer thickness at free water surfaces

A novel 2-D fluorescence imaging technique has been developed to visualize the thickness of the aqueous mass boundary layer at a free water surface. Fluorescence is stimulated by high-power LEDs and is observed from above with a low noise, high resolution and high-speed camera. The invasion of ammonia into water leads to an increase in pH (from a starting value of 4), which is visualized with the fluorescent dye pyranine. The flux of ammonia can be controlled by controlling its air side concentration. A higher flux leads to basic pH values (pH > 7) in a thicker layer at the water surface from which fluorescent light is emitted. This allows the investigation of processes affecting the transport of gases in different depths in the aqueous mass boundary layer. In this paper, the chemical system and optical components of the measurement method are presented and its applicability to a wind-wave tank experiment is demonstrated

The interplay between metabolic stochasticity and cAMP-CRP regulation in single E. coli cells

The inherent stochasticity of metabolism raises a critical question for understanding homeostasis: are cellular processes regulated in response to internal fluctuations? Here, we show that, in E. coli cells under constant external conditions, catabolic enzyme expression continuously responds to metabolic fluctuations. The underlying regulatory feedback is enabled by the cyclic AMP (cAMP) and cAMP receptor protein (CRP) system, which controls catabolic enzyme expression based on metabolite concentrations. Using single-cell microscopy, genetic constructs in which this feedback is disabled, and mathematical modeling, we show how fluctuations circulate through the metabolic and genetic network at sub-cell-cycle timescales. Modeling identifies four noise propagation modes, including one specific to CRP regulation. Together, these modes correctly predict noise circulation at perturbed cAMP levels. The cAMP-CRP system may thus have evolved to control internal metabolic fluctuations in addition to external growth conditions. We conjecture that second messengers may more broadly function to achieve cellular homeostasis

Faulting and off-axis submarine massive sulfide accumulation at slow spreading mid-ocean ridges: A numerical modeling perspective

The potential of mining seafloor massive sulfide deposits for metals such as Cu, Zn, and Au is currently debated. One key challenge is to predict where the largest deposits worth mining might form, which in turn requires understanding the pattern of subseafloor hydrothermal mass and energy transport. Numerical models of heat and fluid flow are applied to illustrate the important role of fault zone properties (permeability and width) in controlling mass accumulation at hydrothermal vents at slow spreading ridges. We combine modeled mass-flow rates, vent temperatures, and vent field dimensions with the known fluid chemistry at the fault-controlled Logatchev 1 hydrothermal field of the Mid-Atlantic Ridge. We predict that the 135 kilotons of SMS at this site (estimated by other studies) can have accumulated with a minimum depositional efficiency of 5% in the known duration of hydrothermal venting (58,200 year age of the deposit). In general, the most productive faults must provide an efficient fluid pathway while at the same time limit cooling due to mixing with entrained cold seawater. This balance is best met by faults that are just wide and permeable enough to control a hydrothermal plume rising through the oceanic crust. Model runs with increased basal heat input, mimicking a heat flow contribution from along-axis, lead to higher mass fluxes and vent temperatures, capable of significantly higher SMS accumulation rates. Nonsteady state conditions, such as the influence of a cooling magmatic intrusion beneath the fault zone, also can temporarily increase the mass flux while sustaining high vent temperatures

Tectonic evolution and extension at the Møre Margin – Offshore mid-Norway

Highlights • New and reprocessed seismic data improved structural mapping at the Møre Margin. • Time-structure and thickness maps of the Cretaceous units have been constructed. • Stratigraphy reconstruction of a transect reveals 188 km extension. • Average stretching factor is 2.2–3.6 depending on assumed initial crustal thickness. Abstract Lithospheric stretching is the key process in forming extensional sedimentary basins at passive rifted margins. This study explores the stretching factors, resulting extension, and structural evolution of the Møre segment on the Mid-Norwegian continental margin. Based on the interpretation of new and reprocessed high-quality seismic, we present updated structural maps of the Møre margin that show very thick post-rift sediments in the central Møre Basin and extensive sill intrusion into the Cretaceous sediments. A major shift in subsidence and deposition occurred during mid-Cretaceous. One transect across the Møre continental margin from the Slørebotn Subbasin to the continent-ocean boundary is reconstructed using the basin modelling software TecMod. We test different initial crustal configurations and rifting events and compare our structural reconstruction results to stretching factors derived both from crustal thinning and the classical backstripping/decompaction approach. Seismic interpretation in combination with structural reconstruction modelling does not support the lower crustal bodies as exhumed and serpentinised mantle. Our extension estimate along this transect is ~ 188 ± 28 km for initial crustal thickness varying between 30 and 40 km

The interplay between metabolic stochasticity and cAMP-CRP regulation in single E. coli cells

The inherent stochasticity of metabolism raises a critical question for understanding homeostasis: are cellular processes regulated in response to internal fluctuations? Here, we show that, in E. coli cells under constant external conditions, catabolic enzyme expression continuously responds to metabolic fluctuations. The underlying regulatory feedback is enabled by the cyclic AMP (cAMP) and cAMP receptor protein (CRP) system, which controls catabolic enzyme expression based on metabolite concentrations. Using single-cell microscopy, genetic constructs in which this feedback is disabled, and mathematical modeling, we show how fluctuations circulate through the metabolic and genetic network at sub-cell-cycle timescales. Modeling identifies four noise propagation modes, including one specific to CRP regulation. Together, these modes correctly predict noise circulation at perturbed cAMP levels. The cAMP-CRP system may thus have evolved to control internal metabolic fluctuations in addition to external growth conditions. We conjecture that second messengers may more broadly function to achieve cellular homeostasis

Symbiotic status alters fungal eco-evolutionary offspring trajectories

Despite host-fungal symbiotic interactions being ubiquitous in all ecosystems, understanding how symbiosis has shaped the ecology and evolution of fungal spores that are involved in dispersal and colonization of their hosts has been ignored in life-history studies. We assembled a spore morphology database covering over 26,000 species of free-living to symbiotic fungi of plants, insects and humans and found more than eight orders of variation in spore size. Evolutionary transitions in symbiotic status correlated with shifts in spore size, but the strength of this effect varied widely among phyla. Symbiotic status explained more variation than climatic variables in the current distribution of spore sizes of plant-associated fungi at a global scale while the dispersal potential of their spores is more restricted compared to free-living fungi. Our work advances life-history theory by highlighting how the interaction between symbiosis and offspring morphology shapes the reproductive and dispersal strategies among living forms