Interconnectivity of habitats in soil:combining X-ray micro tomography and thin sectioning to reveal fungal-soil structure interactions

The extreme heterogeneity and interconnectivity of the 3-dimensional pore space within soil makes it a unique habitat for the diverse microbial population and has a pivotal role in microbial interactions. Manipulation and quantification of the 3-dimensional pore space and the spatial distribution of micro-organisms is therefore essential if we are to fully understand microbial interactions. Here we pack soil microcosms at different bulk-densities to manipulate soil structure and use x-ray micro tomography and soil thin sections to analyse the effect on the connectivity of the pore volume and on fungal exploration

Applications of percolation theory to fungal spread with synergy

There is increasing interest in the use of the percolation paradigm to analyze and predict the progress of disease spreading in spatially-structured populations of animals and plants. The wider utility of the approach has been limited, however, by several restrictive assumptions, foremost of which is a strict requirement for simple nearest-neighbour transmission, in which the disease history of an individual is in uenced only by that of its neighbours. In a recent paper the percolation paradigm has been generalised to incorporate synergistic interactions in host infectivity and susceptibility and the impact of these interactions on the invasive dynamics of an epidemic has been demonstrated. In the current paper we elicit evidence that such synergistic interactions may underlie transmission dynamics in real-world systems by rst formulating a model for the spread of a ubiquitous parasitic and saprotrophic fungus through replicated populations of nutrient sites and subsequently tting and testing the model using data from experimental microcosms. Using Bayesian computational methods for model tting, we demonstrate that synergistic interactions are necessary to explain the dynamics observed in the replicate experiments. The broader implications of this work in identifying disease control strategies that de ect epidemics from invasive to non-invasive regimes are discussed

Direct cell-to-cell exchange of matter in synthetic clostridium syntrophies enabling CO2 fixation and an expanded metabolic space.

In microbial fermentations to produce metabolites, at least 33% of the sugar-substrate carbon is lost as CO2 during pyruvate decarboxylation to acetyl-CoA. Previous attempts to reduce this carbon loss focused on engineering a single organism. In nature, microorganisms live in complex communities where syntrophic interactions result in superior resource utilization. Microbial communities are ubiquitous in nature and have a wide range of applications, including production of biofuels and chemicals. Syntrophic and other microbial co-cultures/consortia carry out efficient bio-transformations that are the result of multiple complementary metabolic systems working together. It is now well appreciated that the capabilities of multi-microorganism systems cannot be predicted by the sum of their parts. Rather, synergistic interactions at different levels often result in better overall performance of these systems. Importantly, integration of diverse metabolic systems through syntrophic dependencies make co-culture systems robust to environmental fluctuations. Clostridium organisms are of major importance for developing new technologies to produce biofuels and chemicals. Three major types of Clostridium organisms have been the focus of studies for the sustainable production of fuels and chemicals. Solventogenic clostridia utilize a large variety of biomass-derived carbohydrates (hexoses, pentoses, disaccharides, and hemicellulose), and can produce C2-C4 chemicals. Acetogenic clostridia can fix inorganic H2, CO2, and CO to generate C2 acids and alcohols. Other specialized clostridia possess diverse biosynthetic capabilities for production of a wide variety of metabolites including C4 – C8 carboxylic acids and alcohols, which could serve as commodity chemicals, biofuels, or biofuel precursors. Here, we first examined a synthetic syntrophy consisting of the solventogen Clostridium acetobutylicum, which converts simple and complex carbohydrates into a variety of chemicals, and the acetogen C. ljungdahlii, which fixes CO2. This synthetic co-culture achieved carbon recoveries into C2-C4 alcohols almost to the limit of substrate-electron availability, with minimal H2 and CO2 release. The syntrophic co-culture produced robust metabolic outcomes over a broad range of starting population ratios of the two organisms. Significantly, the co-culture exhibited unique direct cell-to-cell interactions and material exchange among the two microbes, which enabled unforeseen rearrangements in the metabolism of the individual species that resulted in the production of non-native metabolites, namely isopropanol and 2,3-butanediol. Next, we expanded this co-culture system to include C. kluyveri, which can metabolite ethanol and acetate to produce C6 and C8 carboxylic acids. Both C. acetobutylicum and C. ljungdahlii produce ethanol and acetate, which makes C. kluyveri and ideal partner for a triple synthetic co-culture system capable to converting biomass-derived carbohydrates to C6 and C8 chemicals. Supported by the National Science Foundation through the US Army Research Office (ARO; Award No. W911NF-17-1-0343) and the US Department of Energy (DOE; Award No. DE-SC0019155)

Effectiveness of proactive telephone counselling for smoking cessation in parents: Study protocol of a randomized controlled trial

Contains fulltext : 99284.pdf (publisher's version ) (Open Access)Background Smoking is the world's fourth most common risk factor for disease, the leading preventable cause of death, and it is associated with tremendous social costs. In the Netherlands, the smoking prevalence rate is high. A total of 27.7% of the population over age 15 years smokes. In addition to the direct advantages of smoking cessation for the smoker, parents who quit smoking may also decrease their children's risk of smoking initiation. Methods/Design A randomized controlled trial will be conducted to evaluate the effectiveness of proactive telephone counselling to increase smoking cessation rates among smoking parents. A total of 512 smoking parents will be proactively recruited through their children's primary schools and randomly assigned to either proactive telephone counselling or a control condition. Proactive telephone counselling will consist of up to seven counsellor-initiated telephone calls (based on cognitive-behavioural skill building and Motivational Interviewing), distributed over a period of three months. Three supplementary brochures will also be provided. In the control condition, parents will receive a standard brochure to aid smoking cessation. Assessments will take place at baseline, three months after start of the intervention (post-measurement), and twelve months after start of the intervention (follow-up measurement). Primary outcome measures will include sustained abstinence between post-measurement and follow-up measurement and 7-day point prevalence abstinence and 24-hours point prevalence abstinence at both post- and follow-up measurement. Several secondary outcome measures will also be included (e.g., smoking intensity, smoking policies at home). In addition, we will evaluate smoking-related cognitions (e.g., attitudes towards smoking, social norms, self-efficacy, intention to smoke) in 9-12 year old children of smoking parents. Discussion This study protocol describes the design of a randomized controlled trial to evaluate the effectiveness of proactive telephone counselling in smoking cessation. It is expected that, in the telephone counseling condition, parental smoking cessation rates will be higher and children's cognitions will be less favorable about smoking compared to the control condition. Trial registration The protocol for this study is registered with the Netherlands Trial Register NTR2707.6 p

Prevention of Rectal SHIV Transmission in Macaques by Daily or Intermittent Prophylaxis with Emtricitabine and Tenofovir

Using a repeat-exposure macaque model, Walid Heneine and colleagues find that pre-exposure prophylaxis with combination antiretroviral drugs provides protection against rectal challenge with a SHIV virus

De Novo Reconstruction of Consensus Master Genomes of Plant RNA and DNA Viruses from siRNAs

Virus-infected plants accumulate abundant, 21–24 nucleotide viral siRNAs which are generated by the evolutionary conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids. Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in both sense and antisense orientations. This implies pervasive transcription of both coding and non-coding viral DNA in the nucleus, which generates double-stranded RNA precursors of viral siRNAs. Consistent with our finding and hypothesis, we demonstrate that the complete genomes of DNA viruses from Caulimoviridae and Geminiviridae families can be reconstructed by deep sequencing and de novo assembly of viral siRNAs using bioinformatics tools. Furthermore, we prove that this ‘siRNA omics’ approach can be used for reliable identification of the consensus master genome and its microvariants in viral quasispecies. Finally, we utilized this approach to reconstruct an emerging DNA virus and two viroids associated with economically-important red blotch disease of grapevine, and to rapidly generate a biologically-active clone representing the wild type master genome of Oilseed rape mosaic virus. Our findings show that deep siRNA sequencing allows for de novo reconstruction of any DNA or RNA virus genome and its microvariants, making it suitable for universal characterization of evolving viral quasispecies as well as for studying the mechanisms of siRNA biogenesis and RNAi-based antiviral defense

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Need satisfaction in intergroup contact:A multinational study of pathways toward social change

none43siFinanziamenti esterni a vari co-autoriWhat role does intergroup contact play in promoting support for social change toward greater social equality? Drawing on the needs-based model of reconciliation, we theorized that when inequality between groups is perceived as illegitimate, disadvantaged group members will experience a need for empowerment and advantaged group members a need for acceptance. When intergroup contact satisfies each group's needs, it should result in more mutual support for social change. Using four sets of survey data collected through the Zurich Intergroup Project in 23 countries, we tested several preregistered predictions, derived from the above reasoning, across a large variety of operationalizations. Two studies of disadvantaged groups (Ns = 689 ethnic minority members in Study 1 and 3,382 sexual/gender minorities in Study 2) support the hypothesis that, after accounting for the effects of intergroup contact and perceived illegitimacy, satisfying the need for empowerment (but not acceptance) during contact is positively related to support for social change. Two studies with advantaged groups (Ns = 2,937 ethnic majority members in Study 3 and 4,203 cis-heterosexual individuals in Study 4) showed that, after accounting for illegitimacy and intergroup contact, satisfying the need for acceptance (but also empowerment) is positively related to support for social change. Overall, findings suggest that intergroup contact is compatible with efforts to promote social change when group-specific needs are met. Thus, to encourage support for social change among both disadvantaged and advantaged group members, it is essential that, besides promoting mutual acceptance, intergroup contact interventions also give voice to and empower members of disadvantaged groups.mixedHässler, Tabea; Ullrich, Johannes; Sebben, Simone; Shnabel, Nurit; Bernardino, Michelle; Valdenegro, Daniel; Van Laar, Colette; González, Roberto; Visintin, Emilio Paolo; Tropp, Linda R; Ditlmann, Ruth K; Abrams, Dominic; Aydin, Anna Lisa; Pereira, Adrienne; Selvanathan, Hema Preya; von Zimmermann, Jorina; Lantos, Nóra Anna; Sainz, Mario; Glenz, Andreas; Kende, Anna; Oberpfalzerová, Hana; Bilewicz, Michal; Branković, Marija; Noor, Masi; Pasek, Michael H; Wright, Stephen C; Žeželj, Iris; Kuzawinska, Olga; Maloku, Edona; Otten, Sabine; Gul, Pelin; Bareket, Orly; Corkalo Biruski, Dinka; Mugnol-Ugarte, Luiza; Osin, Evgeny; Baiocco, Roberto; Cook, Jonathan E; Dawood, Maneeza; Droogendyk, Lisa; Loyo, Angélica Herrera; Jelić, Margareta; Kelmendi, Kaltrina; Pistella, JessicaHässler, Tabea; Ullrich, Johannes; Sebben, Simone; Shnabel, Nurit; Bernardino, Michelle; Valdenegro, Daniel; Van Laar, Colette; González, Roberto; Visintin, Emilio Paolo; Tropp, Linda R; Ditlmann, Ruth K; Abrams, Dominic; Aydin, Anna Lisa; Pereira, Adrienne; Selvanathan, Hema Preya; von Zimmermann, Jorina; Lantos, Nóra Anna; Sainz, Mario; Glenz, Andreas; Kende, Anna; Oberpfalzerová, Hana; Bilewicz, Michal; Branković, Marija; Noor, Masi; Pasek, Michael H; Wright, Stephen C; Žeželj, Iris; Kuzawinska, Olga; Maloku, Edona; Otten, Sabine; Gul, Pelin; Bareket, Orly; Corkalo Biruski, Dinka; Mugnol-Ugarte, Luiza; Osin, Evgeny; Baiocco, Roberto; Cook, Jonathan E; Dawood, Maneeza; Droogendyk, Lisa; Loyo, Angélica Herrera; Jelić, Margareta; Kelmendi, Kaltrina; Pistella, Jessic

A large-scale test of the link between intergroup contact and support for social change

Guided by the early findings of social scientists, practitioners have long advocated for greater contact between groups to reduce prejudice and increase social cohesion. Recent work, however, suggests that intergroup contact can undermine support for social change towards greater equality, especially among disadvantaged group members. Using a large and heterogeneous dataset (12,997 individuals from 69 countries), we demonstrate that intergroup contact and support for social change towards greater equality are positively associated among members of advantaged groups (ethnic majorities and cis-heterosexuals) but negatively associated among disadvantaged groups (ethnic minorities and sexual and gender minorities). Specification-curve analysis revealed important variation in the size—and at times, direction—of correlations, depending on how contact and support for social change were measured. This allowed us to identify one type of support for change—willingness to work in solidarity— that is positively associated with intergroup contact among both advantaged and disadvantaged group members

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication