Systemic Risks from Different Perspectives.

Systemic risks are characterized by high complexity, multiple uncertainties, major ambiguities, and transgressive effects on other systems outside of the system of origin. Due to these characteristics, systemic risks are overextending established risk management and create new, unsolved challenges for policymaking in risk assessment and risk governance. Their negative effects are often pervasive, impacting fields beyond the obvious primary areas of harm. This article addresses these challenges of systemic risks from different disciplinary and sectorial perspectives. It highlights the special contributions of these perspectives and approaches and provides a synthesis for an interdisciplinary understanding of systemic risks and effective governance. The main argument is that understanding systemic risks and providing good governance advice relies on an approach that integrates novel modeling tools from complexity sciences with empirical data from observations, experiments, or simulations and evidence-based insights about social and cultural response patterns revealed by quantitative (e.g., surveys) or qualitative (e.g., participatory appraisals) investigations. Systemic risks cannot be easily characterized by single numerical estimations but can be assessed by using multiple indicators and including several dynamic gradients that can be aggregated into diverse but coherent scenarios. Lastly, governance of systemic risks requires interdisciplinary and cross-sectoral cooperation, a close monitoring system, and the engagement of scientists, regulators, and stakeholders to be effective as well as socially acceptable.

Endangering the integrity of science by misusing unvalidated models and untested assumptions as facts: General considerations and the mineral and phosphorus scarcity fallacy.

There is increasing demand for science to contribute to solving societal problems (solutionism). Thereby, scientists may become normative activists for solving certain problems (advocacy). When doing this, they may insufficiently differentiate between scientific and political modes of reasoning and validation (de-differentiationism), which is sometimes linked to questionable forms of utilizing the force of facts (German: Faktengewalt). Scientific findings are simplified and communicated in such a way that they acquire a status as unfalsifiable and absolutely true (truth to power). This becomes critical if the consistency and validation of the findings are questionable and scientific models underlying science activists' actions are doubtful, oversimplified, or incorrect. Herein, we exemplarily elaborate how the integrity of science is endangered by normative solutionist and sociopolitically driven transition management and present mineral scarcity claims that ignore that reserves or resources are dynamic geotechnological-socioeconomic entities. We present the main mineral scarcity models and their fallacious assumptions. We then discuss the phosphorus scarcity fallacy, which is of particular interest as phosphorus is non-substitutable and half of all current food production depends on fertilizers (and thus phosphorus). We show that phosphorus scarcity claims are based on integrating basic geoeconomic knowledge and discuss cognitive and epistemological barriers and motivational and sociopolitical drivers promoting the scarcity fallacy, which affects high-level public media. This may induce unsustainable environmental action. Scientists as honest knowledge brokers should communicate the strengths but also the constraints and limits of scientific modeling and of applying it in reality. Supplementary Information: The online version contains supplementary material available at 10.1007/s11625-021-01006-w.

Characterization of the Citrobacter rodentium Cpx regulon and its role in host infection.

Envelope-localized proteins, such as adhesins and secretion systems, play critical roles in host infection by Gram-negative pathogens. As such, their folding is monitored by envelope stress response systems. Previous studies demonstrated that the Cpx envelope stress response is required for virulence of Citrobacter rodentium, a murine pathogen used to model infections by the human pathogens enteropathogenic and enterohemorrhagic Escherichia coli; however, the mechanisms by which the Cpx response promotes host infection were previously unknown. Here, we characterized the C. rodentium Cpx regulon in order to identify genes required for host infection. Using transcriptomic and proteomic approaches, we found that the Cpx response upregulates envelope-localized protein folding and degrading factors but downregulates pilus genes and type III secretion effectors. Mouse infections with C. rodentium strains lacking individual Cpx-regulated genes showed that the chaperone/protease DegP and the disulfide bond oxidoreductase DsbA were essential for infection, but Cpx regulation of these genes did not fully account for attenuation of C. rodentium ΔcpxRA. Both deletion of dsbA and treatment with the reducing agent dithiothreitol activated the C. rodentium Cpx response, suggesting that it may sense disruption of disulfide bonding. Our results highlight the importance of envelope protein folding in host infection by Gram-negative pathogens.

Salmonella Rapidly Regulates Membrane Permeability To Survive Oxidative Stress.

UNLABELLED: The outer membrane (OM) of Gram-negative bacteria provides protection against toxic molecules, including reactive oxygen species (ROS). Decreased OM permeability can promote bacterial survival under harsh circumstances and protects against antibiotics. To better understand the regulation of OM permeability, we studied the real-time influx of hydrogen peroxide in Salmonella bacteria and discovered two novel mechanisms by which they rapidly control OM permeability. We found that pores in two major OM proteins, OmpA and OmpC, could be rapidly opened or closed when oxidative stress is encountered and that the underlying mechanisms rely on the formation of disulfide bonds in the periplasmic domain of OmpA and TrxA, respectively. Additionally, we found that a Salmonella mutant showing increased OM permeability was killed more effectively by treatment with antibiotics. Together, these results demonstrate that Gram-negative bacteria regulate the influx of ROS for defense against oxidative stress and reveal novel targets that can be therapeutically targeted to increase bacterial killing by conventional antibiotics. IMPORTANCE: Pathogenic bacteria have evolved ways to circumvent inflammatory immune responses. A decrease in bacterial outer membrane permeability during infection helps protect bacteria from toxic molecules produced by the host immune system and allows for effective colonization of the host. In this report, we reveal molecular mechanisms that rapidly alter outer membrane pores and their permeability in response to hydrogen peroxide and oxidative stress. These mechanisms are the first examples of pores that are rapidly opened or closed in response to reactive oxygen species. Moreover, one of these mechanisms can be targeted to artificially increase membrane permeability and thereby increase bacterial killing by the antibiotic cefotaxime during in vitro experiments and in a mouse model of infection. We envision that a better understanding of the regulation of membrane permeability will lead to new targets and treatment options for multidrug-resistant infections.

Quantitative Mass Spectrometry Identifies Novel Host Binding Partners for Pathogenic Escherichia coli Type III Secretion System Effectors.

Enteropathogenic and enterohemorrhagic Escherichia coli cause enteric diseases resulting in significant morbidity and mortality worldwide. These pathogens remain extracellular and translocate a set of type III secreted effector proteins into host cells to promote bacterial virulence. Effectors manipulate host cell pathways to facilitate infection by interacting with a variety of host targets, yet the binding partners and mechanism of action of many effectors remain elusive. We performed a mass spectrometry screen to identify host targets for a library of effectors. We found five known effector targets and discovered four novel interactions. Interestingly, we identified multiple effectors that interacted with the microtubule associated protein, ensconsin. Using co-immunoprecipitations, we confirmed that NleB1 and EspL interacted with ensconsin in a region that corresponded to its microtubule binding domain. Ensconsin is an essential cofactor of kinesin-1 that is required for intracellular trafficking, and we demonstrated that intracellular trafficking was severely disrupted during wild type EPEC infections but not during infections with ΔnleB1 or ΔespL mutants. Our findings demonstrate the efficacy of quantitative proteomics for identifying effector-host protein interactions and suggest that vesicular trafficking is a crucial cellular process that may be targeted by NleB1 and EspL through their interaction with ensconsin.

A Highly Effective Component Vaccine against Nontyphoidal Salmonella enterica Infections.

UNLABELLED: Nontyphoidal Salmonella enterica (NTS) infections are a major burden to global public health, as they lead to diseases ranging from gastroenteritis to systemic infections and there is currently no vaccine available. Here, we describe a highly effective component vaccine against S. enterica serovar Typhimurium in both gastroenteritis and systemic murine infection models. We devised an approach to generate supernatants of S. enterica serovar Typhimurium, an organism that is highly abundant in virulence factors. Immunization of mice with this supernatant resulted in dramatic protection against a challenge with serovar Typhimurium, showing increased survival in the systemic model and decreased intestinal pathology in the gastrointestinal model. Protection correlated with specific IgA and IgG levels in the serum and specific secretory IgA levels in the feces of immunized mice. Initial characterization of the protective antigens in the bacterial culture supernatants revealed a subset of antigens that exhibited remarkable stability, a highly desirable characteristic of an effective vaccine to be used under suboptimal environmental conditions in developing countries. We were able to purify a subset of the peptides present in the supernatants and show their potential for immunization of mice against serovar Typhimurium resulting in a decreased level of colonization. This component vaccine shows promise with regard to protecting against NTS, and further work should significantly help to establish vaccines against these prevalent infections. IMPORTANCE: Salmonella enterica infections other than typhoid and paratyphoid fever are a major global health burden, as they cause high morbidity and mortality worldwide. Strategies that prevent Salmonella-related diseases are greatly needed, and there is a significant push for the development of vaccines against nontyphoidal Salmonella enterica serovars. In this work, we describe an S. Typhimurium supernatant-derived vaccine that is effective in reducing bacterial colonization in mouse models of gastroenteritis as well as invasive disease. This is a component vaccine that shows high stability to heat, a feature that is important for use under suboptimal conditions, such as those found in sub-Saharan Africa.

Diet and specific microbial exposure trigger features of environmental enteropathy in a novel murine model.

Environmental enteropathy (EE) is a subclinical chronic inflammatory disease of the small intestine and has a profound impact on the persistence of childhood malnutrition worldwide. However, the aetiology of the disease remains unknown and no animal model exists to date, the creation of which would aid in understanding this complex disease. Here we demonstrate that early-life consumption of a moderately malnourished diet, in combination with iterative oral exposure to commensal Bacteroidales species and Escherichia coli, remodels the murine small intestine to resemble features of EE observed in humans. We further report the profound changes that malnutrition imparts on the small intestinal microbiota, metabolite and intraepithelial lymphocyte composition, along with the susceptibility to enteric infection. Our findings provide evidence indicating that both diet and microbes combine to contribute to the aetiology of EE, and describe a novel murine model that can be used to elucidate the mechanisms behind this understudied disease.

Novel Host Proteins and Signaling Pathways in Enteropathogenic E. coli Pathogenesis Identified by Global Phosphoproteome Analysis.

Enteropathogenic Escherichia coli (EPEC) uses a type III secretion system (T3SS) to directly translocate effector proteins into host cells where they play a pivotal role in subverting host cell signaling needed for disease. However, our knowledge of how EPEC affects host protein phosphorylation is limited to a few individual protein studies. We employed a quantitative proteomics approach to globally map alterations in the host phosphoproteome during EPEC infection. By characterizing host phosphorylation events at various time points throughout infection, we examined how EPEC dynamically impacts the host phosphoproteome over time. This experimental setup also enabled identification of T3SS-dependent and -independent changes in host phosphorylation. Specifically, T3SS-regulated events affected various cellular processes that are known EPEC targets, including cytoskeletal organization, immune signaling, and intracellular trafficking. However, the involvement of phosphorylation in these events has thus far been poorly studied. We confirmed the MAPK family as an established key host player, showed its central role in signal transduction during EPEC infection, and extended the repertoire of known signaling hubs with previously unrecognized proteins, including TPD52, CIN85, EPHA2, and HSP27. We identified altered phosphorylation of known EPEC targets, such as cofilin, where the involvement of phosphorylation has so far been undefined, thus providing novel mechanistic insights into the roles of these proteins in EPEC infection. An overlap of regulated proteins, especially those that are cytoskeleton-associated, was observed when compared with the phosphoproteome of Shigella-infected cells. We determined the biological relevance of the phosphorylation of a novel protein in EPEC pathogenesis, septin-9 (SEPT9). Both siRNA knockdown and a phosphorylation-impaired SEPT9 mutant decreased bacterial adherence and EPEC-mediated cell death. In contrast, a phosphorylation-mimicking SEPT9 mutant rescued these effects. Collectively, this study provides the first global analysis of phosphorylation-mediated processes during infection with an extracellular, diarrheagenic bacterial pathogen.

The recruitment of AMP-activated protein kinase to glycogen is regulated by autophosphorylation.

The mammalian AMP-activated protein kinase (AMPK) is an obligatory αßγ heterotrimeric complex carrying a carbohydrate-binding module (CBM) in the ß-subunit (AMPKß) capable of attaching AMPK to glycogen. Nonetheless, AMPK localizes at many different cellular compartments, implying the existence of mechanisms that prevent AMPK from glycogen binding. Cell-free carbohydrate binding assays revealed that AMPK autophosphorylation abolished its carbohydrate-binding capacity. X-ray structural data of the CBM displays the central positioning of threonine 148 within the binding pocket. Substitution of Thr-148 for a phospho-mimicking aspartate (T148D) prevents AMPK from binding to carbohydrate. Overexpression of isolated CBM or ß1-containing AMPK in cellular models revealed that wild type (WT) localizes to glycogen particles, whereas T148D shows a diffuse pattern. Pharmacological AMPK activation and glycogen degradation by glucose deprivation but not forskolin enhanced cellular Thr-148 phosphorylation. Cellular glycogen content was higher if pharmacological AMPK activation was combined with overexpression of T148D mutant relative to WT AMPK. In summary, these data show that glycogen-binding capacity of AMPKß is regulated by Thr-148 autophosphorylation with likely implications in the regulation of glycogen turnover. The findings further raise the possibility of regulated carbohydrate-binding function in a wider variety of CBM-containing proteins.

Recent advances in understanding enteric pathogenic Escherichia coli.

Although Escherichia coli can be an innocuous resident of the gastrointestinal tract, it also has the pathogenic capacity to cause significant diarrheal and extraintestinal diseases. Pathogenic variants of E. coli (pathovars or pathotypes) cause much morbidity and mortality worldwide. Consequently, pathogenic E. coli is widely studied in humans, animals, food, and the environment. While there are many common features that these pathotypes employ to colonize the intestinal mucosa and cause disease, the course, onset, and complications vary significantly. Outbreaks are common in developed and developing countries, and they sometimes have fatal consequences. Many of these pathotypes are a major public health concern as they have low infectious doses and are transmitted through ubiquitous mediums, including food and water. The seriousness of pathogenic E. coli is exemplified by dedicated national and international surveillance programs that monitor and track outbreaks; unfortunately, this surveillance is often lacking in developing countries. While not all pathotypes carry the same public health profile, they all carry an enormous potential to cause disease and continue to present challenges to human health. This comprehensive review highlights recent advances in our understanding of the intestinal pathotypes of E. coli.

Sustainable use of phosphorus: a finite resource.

Phosphorus is an essential element of life and of the modern agricultural system. Today, science, policy, agro-industry and other stakeholder groups are increasingly concerned about the sustainable use of this resource, given the dissipative nature of phosphorus and difficulties in assessing, evaluating, and coping with phosphorus pollution in aquatic and terrestrial systems. We argue that predictions about a forthcoming peak, followed by a quick reduction (i.e., physical phosphate rock scarcity) are unreasoned and stress that access to phosphorus (economic scarcity) is already, and may increasingly become critical, in particular for smallholders farmers in different parts of the world. The paper elaborates on the design, development, goals and cutting-edge contributions of a global transdisciplinary process (i.e. mutual learning between science and society including multiple stakeholders) on the understanding of potential contributions and risks related to the current mode of using phosphorus on multiple scales (Global TraPs). While taking a global and comprehensive view on the whole phosphorus-supply chain, Global TraPs organizes and integrates multiple transdisciplinary case studies to better answer questions which inform sustainable future phosphorus use. Its major goals are to contribute to four issues central to sustainable resource management: i) long-term management of biogeochemical cycles, in particular the challenge of closing the phosphorus cycle, ii) achieving food security, iii) avoiding environmental pollution and iv) sustainability learning on a global level by transdisciplinary processes.

EscE and EscG are cochaperones for the type III needle protein EscF of enteropathogenic Escherichia coli.

Type III secretion systems (T3SSs) are central virulence mechanisms used by a variety of Gram-negative bacteria to inject effector proteins into host cells. The needle polymer is an essential part of the T3SS that provides the effector proteins a continuous channel into the host cytoplasm. It has been shown for a few T3SSs that two chaperones stabilize the needle protein within the bacterial cytosol to prevent its premature polymerization. In this study, we characterized the chaperones of the enteropathogenic Escherichia coli (EPEC) needle protein EscF. We found that Orf2 and Orf29, two poorly characterized proteins encoded within the EPEC locus of enterocyte effacement (LEE), function as the needle protein cochaperones. Our finding demonstrated that both Orf2 and Orf29 are essential for type III secretion (T3S). In addition, we found that Orf2 and Orf29 associate with the bacterial membrane and form a complex with EscF. Orf2 and Orf29 were also shown to disrupt the polymerization of EscF in vitro. Prediction of the tertiary structures of Orf2 and Orf29 showed high structural homology to chaperones of other T3SS needle proteins. Overall, our data suggest that Orf2 and Orf29 function as the chaperones of the needle protein, and therefore, they have been renamed EscE and EscG.

Science with society in the anthropocene.

Interdisciplinary scientific knowledge is necessary but not sufficient when it comes to addressing sustainable transformations, as science increasingly has to deal with normative and value-related issues. A systems perspective on coupled human-environmental systems (HES) helps to address the inherent complexities. Additionally, a thorough interaction between science and society (i.e., transdisciplinarity = TD) is necessary, as sustainable transitions are sometimes contested and can cause conflicts. In order to navigate complexities regarding the delicate interaction of scientific research with societal decisions these processes must proceed in a structured and functional way. We thus propose HES-based TD processes to provide a basis for reorganizing science in coming decades.

Context-specific energy strategies: coupling energy system visions with feasible implementation scenarios.

Conventional energy strategy defines an energy system vision (the goal), energy scenarios with technical choices and an implementation mechanism (such as economic incentives). Due to the lead of a generic vision, when applied in a specific regional context, such a strategy can deviate from the optimal one with, for instance, the lowest environmental impacts. This paper proposes an approach for developing energy strategies by simultaneously, rather than sequentially, combining multiple energy system visions and technically feasible, cost-effective energy scenarios that meet environmental constraints at a given place. The approach is illustrated by developing a residential heat supply strategy for a Swiss region. In the analyzed case, urban municipalities should focus on reducing heat demand, and rural municipalities should focus on harvesting local energy sources, primarily wood. Solar thermal units are cost-competitive in all municipalities, and their deployment should be fostered by information campaigns. Heat pumps and building refurbishment are not competitive; thus, economic incentives are essential, especially for urban municipalities. In rural municipalities, wood is cost-competitive, and community-based initiatives are likely to be most successful. Thus, the paper shows that energy strategies should be spatially differentiated. The suggested approach can be transferred to other regions and spatial scales.

EscA is a crucial component of the type III secretion system of enteropathogenic Escherichia coli.

The virulence of many Gram-negative pathogens is associated with type III secretion systems (T3SSs), which deliver virulence effector proteins into the cytoplasm of host cells. Components of enteropathogenic Escherichia coli (EPEC) T3SS are encoded within the locus of enterocyte effacement (LEE). While most LEE-encoded T3SS proteins in EPEC have assigned names and functions, a few of them remain poorly characterized. Here, we studied a small LEE-encoded protein, Orf15, that shows no homology to other T3SS/flagellar proteins and is only present in attaching and effacing pathogens, including enterohemorrhagic E. coli and Citrobacter rodentium. Our findings demonstrated that it is essential for type III secretion (T3S) and that it is localized to the periplasm and associated with the inner membrane. Membrane association was driven by the N-terminal 19 amino acid residues, which were also shown to be essential for T3S. Consistent with its localization, Orf15 was found to interact with the EPEC T3SS outer membrane ring component, EscC, which was previously shown to be embedded within the outer membrane and protruding into the periplasmic space. Interestingly, we found that the predicted coiled-coil structure of Orf15 is critical for the protein's function. Overall, our findings suggest that Orf15 is a structural protein that contributes to the structural integrity of the T3S complex, and therefore we propose to rename it EscA.

The crucial role of nomothetic and idiographic conceptions of time: interdisciplinary collaboration in nuclear waste management.

The disposal of nuclear waste involves extensive time scales. Technical experts consider up to 1 million years for the disposal of spent fuel and high-level waste in their safety assessment. Yet nuclear waste is not only a technical but also a so-called sociotechnical problem and, therefore, requires interdisciplinary collaboration between technical, natural, social sciences, and the humanities in its management. Given that these disciplines differ in their language, epistemics, and interests, such collaboration might be problematic. Based on evidence from cognitive psychology, we suggest that, in particular, a concept like time is presumably critical and can be understood differently. This study explores how different scientific disciplines understand extensive time scales in general and then focuses on nuclear waste. Eighteen qualitative exploratory interviews were conducted with experts for time-related phenomena of different disciplines, among them experts working in nuclear waste management. Analyses revealed two distinct conceptions of time corresponding to idiographic and nomothetic research approaches: scientists from the humanities and social sciences tend to have a more open, undetermined conception of time, whereas natural scientists tend to focus on a more determined conception that includes some undetermined aspects. Our analyses lead to reflections on potential difficulties for interdisciplinary teams in nuclear waste management. We focus on the understanding of the safety assessment, on potential implications for communication between experts from different disciplines (e.g., between experts from the humanities and engineering for risk assessment and risk communication), and we reflect on the roles of different disciplines in nuclear waste management.

The positioning of sustainability within residential property marketing.

This article investigates the evolution of sustainability positioning in residential property marketing to shed light on the specific role and responsibility of housebuilders and housing investors in urban development. To this end, an analysis is made of housing advertisements published in Basel, Switzerland, over a period of more than 100 years. The paper demonstrates how to draw successfully on advertisements to discern sustainability patterns in housing, using criteria situated along the dimensions building, location and people. Cluster analysis allows five clusters of sustainability positioning to be described­namely, good location, green building, comfort living, pre-sustainability and sustainability. Investor and builder types are differently located in these clusters. Location emerges as an issue which, to a large extent, is advertised independently from other sustainability issues.