Challenging terrestrial biosphere models with data from the long‐term multifactor Prairie Heating and CO2 Enrichment experiment

Multifactor experiments are often advocated as important for advancing terrestrial biosphere models (TBMs), yet to date, such models have only been tested against single‐factor experiments. We applied 10 TBMs to the multifactor Prairie Heating and CO₂ Enrichment (PHACE) experiment in Wyoming, USA. Our goals were to investigate how multifactor experiments can be used to constrain models and to identify a road map for model improvement. We found models performed poorly in ambient conditions; there was a wide spread in simulated above‐ground net primary productivity (range: 31–390 g C m^?2 yr^?1). Comparison with data highlighted model failures particularly with respect to carbon allocation, phenology, and the impact of water stress on phenology. Performance against the observations from single‐factors treatments was also relatively poor. In addition, similar responses were predicted for different reasons across models: there were large differences among models in sensitivity to water stress and, among the N cycle models, N availability during the experiment. Models were also unable to capture observed treatment effects on phenology: they overestimated the effect of warming on leaf onset and did not allow CO₂‐induced water savings to extend the growing season length. Observed interactive (CO₂ × warming) treatment effects were subtle and contingent on water stress, phenology, and species composition. As the models did not correctly represent these processes under ambient and single‐factor conditions, little extra information was gained by comparing model predictions against interactive responses. We outline a series of key areas in which this and future experiments could be used to improve model predictions of grassland responses to global change.     

Legacy effects of individual crops affect N2O emissions accounting within crop rotations

Uruguay is pursuing renewable energy production pathways using feedstocks from its agricultural sector to supply transportation fuels, among them ethanol produced from commercial technologies that use sweet and grain sorghum. However, the environmental performance of the fuel is not known. We investigate the life cycle environmental and cost performance of these two major agricultural crops used to produce ethanol that have begun commercial production and are poised to grow to meet national energy targets for replacing gasoline. Using both attributional and consequential life cycle assessment (LCA) frameworks for system boundaries to quantify the carbon intensity, and engineering cost analysis to estimate the unit production cost of ethanol from grain and sweet sorghum, we determined abatement costs. We found 1) an accounting error in estimating N₂O emissions for a specific crop in multiple crop rotations when using Intergovernmental Panel on Climate Change(IPCC) Tier 1 methods within an attributional LCA framework, due to N legacy effects; 2) choice of baseline and crop identity in multiple crop rotations evaluated within the consequential LCA framework both affect the global warming intensity (GWI) of ethanol; and 3) although abatement costs for ethanol from grain sorghum are positive and from sweet sorghum they are negative, both grain and sweet sorghum pathways have a high potential for reducing transport fuel GWI by more than 50% relative to gasoline, and are within the ranges targeted by the US renewable transportation fuel policies.     

Inhibition of rab5 GTPase activity stimulates membrane fusion in endocytosis.

Small GTPases of the rab family control distinct steps of intracellular transport. The function of their GTPase activity is not completely understood. To investigate the role of the nucleotide state of rab5 in the early endocytic pathway, the effects of two mutants with opposing biochemical properties were tested. The Q79L mutant of rab5, analogous with the activating Q61L mutant of p21-ras, was found to have a strongly decreased intrinsic GTPase activity and was, unlike wild-type rab5, found mainly in the GTP-bound form in vivo. Expression of this protein in BHK and HeLa cells led to a dramatic change in cell morphology, with the appearance of unusually large early endocytic structures, considerably larger than those formed upon overexpression of wild-type rab5. An increased rate of transferrin internalization was observed in these cells, whereas recycling was inhibited. Cytosol containing rab5 Q79L stimulated homotypic early endosome fusion in vitro, even though it contained only a small amount of the isoprenylated protein. A different mutant, rab5 S34N, was found, like the inhibitory p21-ras S17N mutant, to have a preferential affinity for GDP. Overexpression of rab5 S34N induced the accumulation of very small endocytic profile and inhibited transferrin endocytosis. This protein inhibited fusion between early endosomes in vitro. The opposite effects of the rab5 Q79L and S34N mutants suggest that rab5:GTP is required prior to membrane fusion, whereas GTP hydrolysis by rab5 occurs after membrane fusion and functions to inactivate the protein.     

Cholesterol and fatty acids regulate dynamic caveolin trafficking through the Golgi complex and between the cell surface and lipid bodies

Caveolins are a crucial component of plasma membrane (PM) caveolae but have also been localized to intracellular compartments, including the Golgi complex and lipid bodies. Mutant caveolins associated with human disease show aberrant trafficking to the PM and Golgi accumulation. We now show that the Golgi pool of mainly newly synthesized protein is detergent-soluble and predominantly in a monomeric state, in contrast to the surface pool. Caveolin at the PM is not recognized by specific caveolin antibodies unless PM cholesterol is depleted. Exit from the Golgi complex of wild-type caveolin-1 or -3, but not vesicular stomatitis virus-G protein, is modulated by changing cellular cholesterol levels. In contrast, a muscular dystrophy-associated mutant of caveolin-3, Cav3P104L, showed increased accumulation in the Golgi complex upon cholesterol treatment. In addition, we demonstrate that in response to fatty acid treatment caveolin can follow a previously undescribed pathway from the PM to lipid bodies and can move from lipid bodies to the PM in response to removal of fatty acids. The results suggest that cholesterol is a rate-limiting component for caveolin trafficking. Changes in caveolin flux through the exocytic pathway can therefore be an indicator of cellular cholesterol and fatty acid levels.     

Review of the biology of Bordetella pertussis.

Bordetella pertussis produces a complex array of adhesins, aggressins and toxins that are presumed to be important in the colonisation of its human host and in ensuring its survival and propagation. The organism also has highly sophisticated mechanisms for regulating virulence factor expression, in response to environmental signals or by reversible mutations. Despite the rapidly increasing knowledge of these aspects of the biology of B. pertussis, our understanding of the pathogenesis of whooping cough is still far from clear. In defining the role of individual factors, reliance has to be placed on in vitro assays or animal models of the human infection, particularly in the mouse, where different conditions may prevail. Some clues to pathogenic mechanisms may be provided by considering other bordetellae, especially B. parapertussis, B. bronchiseptica and B. avium, their similar, but not identical, range of virulence factors and the common features of the diseases caused by these species in their respective hosts. The bordetellae are usually defined as obligate, non-invasive parasites of the respiratory tracts of warm-blooded animals, including birds, with a predilection for the respiratory ciliated epithelium. This definition has been challenged by a number of recent observations. For example, the ability of Bordetella spp. to regulate virulence factor expression in response to external signals strongly suggests that they have alternative habitats where such regulation would be an advantage. These habitats may be intracellular, since it has been shown that B. pertussis, B. parapertussis and B. bronchiseptica can invade and survive within host cells, or they may be in other sites within the same or different hosts. Recent DNA fingerprinting studies of B. pertussis have revealed hitherto unsuspected heterogeneity amongst isolates which could be reflected in antigenic differences between strains. Some of these new perspectives on Bordetella pathogenicity may have implications for pertussis vaccine development.     

The SARS-CoV2 envelope differs from host cells,exposes procoagulant lipids,and is disrupted in vivo by oral rinses

The lipid envelope of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an essential component of the virus; however, its molecular composition is undetermined. Addressing this knowledge gap could support the design of antiviral agents as well as further our understanding of viral-host protein interactions, infectivity, pathogenicity, and innate immune system clearance. Lipidomics revealed that the virus envelope comprised mainly phospholipids (PLs), with some cholesterol and sphingolipids, and with cholesterol/phospholipid ratio similar to lysosomes. Unlike cellular membranes, procoagulant amino-PLs were present on the external side of the viral envelope at levels exceeding those on activated platelets. Accordingly, virions directly promoted blood coagulation. To investigate whether these differences could enable selective targeting of the viral envelope in vivo, we tested whether oral rinses containing lipid-disrupting chemicals could reduce infectivity. Products containing PL-disrupting surfactants (such as cetylpyridinium chloride) met European virucidal standards in vitro; however, components that altered the critical micelle concentration reduced efficacy, and products containing essential oils, povidone-iodine, or chlorhexidine were ineffective. This result was recapitulated in vivo, where a 30-s oral rinse with cetylpyridinium chloride mouthwash eliminated live virus in the oral cavity of patients with coronavirus disease 19 for at least 1 h, whereas povidone-iodine and saline mouthwashes were ineffective. We conclude that the SARS-CoV-2 lipid envelope i) is distinct from the host plasma membrane, which may enable design of selective antiviral approaches; ii) contains exposed phosphatidylethanolamine and phosphatidylserine, which may influence thrombosis, pathogenicity, and inflammation; and iii) can be selectively targeted in vivo by specific oral rinses.     

BioWarehouse: a bioinformatics database warehouse toolkit

Background  

This article addresses the problem of interoperation of heterogeneous bioinformatics databases.     

A sensitive chemiluminescence assay for pertussis toxin and for evaluation of cell-free pertussis toxoids

Pertussis toxin (PT) inhibited luminol-enhanced chemiluminescence induced in rabbit peritoneal neutrophils by N'-formyl-L-methionyl-L-leucyl-L-phenylalanine (fMLP) at doses as low as 0.8 ng.ml-1, even in the presence of a 10-fold higher concentration of filamentous haemagglutinin (FHA). A cell-free extract of Bordetella pertussis, containing predominantly PT and FHA, suppressed the neutrophil response to fMLP. After toxoiding with carbodiimide, the inhibitory activity of the extract was abolished and an enhancement of neutrophil chemiluminescence was observed due to FHA activity. Abrogation of the chemiluminescent response of neutrophils to fMLP is proposed as a sensitive, in vitro assay for pT, and may be useful for monitoring the residual toxin activity in pertussis toxoids and for determining the anti-toxic effects of anti-PT antibodies.     

Cortactin Scaffolds Arp2/3 and WAVE2 at the Epithelial Zonula Adherens

Cadherin junctions arise from the integrated action of cell adhesion, signaling, and the cytoskeleton. At the zonula adherens (ZA), a WAVE2-Arp2/3 actin nucleation apparatus is necessary for junctional tension and integrity. But how this is coordinated with cadherin adhesion is not known. We now identify cortactin as a key scaffold for actin regulation at the ZA, which localizes to the ZA through influences from both E-cadherin and N-WASP. Using cell-free protein expression and fluorescent single molecule coincidence assays, we demonstrate that cortactin binds directly to the cadherin cytoplasmic tail. However, its concentration with cadherin at the apical ZA also requires N-WASP. Cortactin is known to bind Arp2/3 directly (Weed, S. A., Karginov, A. V., Schafer, D. A., Weaver, A. M., Kinley, A. W., Cooper, J. A., and Parsons, J. T. (2000) J. Cell Biol. 151, 29–40). We further show that cortactin can directly bind WAVE2, as well as Arp2/3, and both these interactions are necessary for actin assembly at the ZA. We propose that cortactin serves as a platform that integrates regulators of junctional actin assembly at the ZA.