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Abstract Background Elevations in the gut metabolite trimethylamine-N-oxide (TMAO) have been linked to cardiovascular and metabolic diseases. Whether elevated TMAO levels reflect early mechanistic involvement or a sequela of evolving disease awaits elucidation. The purpose of this study was to further explore these potential associations. Methods We investigated relationships between circulating levels of TMAO and its pre-cursor substrates, dietary factors, gut microbiome profiles and disease risk in individuals with a Healthy BMI (18.5 30, n = 27) and Metabolic Syndrome (MetS; ≥ 3 ATPIII report criteria, n = 39). Results Unexpectedly, plasma [TMAO] did not vary substantially between groups (means of 3–4 µM; p > 0.05), although carnitine was elevated in participants with MetS. Gut microbial diversity and Firmicutes were also significantly reduced in the MetS group (p

Summary The yeast Saccharomyces cerevisiae uses the pyruvate dehydrogenase‐bypass for acetyl‐CoA biosynthesis. This relatively inefficient pathway limits production potential for acetyl‐CoA‐derived biochemical due to carbon loss and the cost of two high‐energy phosphate bonds per molecule of acetyl‐CoA. Here, we attempted to improve acetyl‐CoA production efficiency by introducing heterologous acetylating aldehyde dehydrogenase and phosphoketolase pathways for acetyl‐CoA synthesis to enhance production of the sesquiterpene trans‐nerolidol. In addition, we introduced auxin‐mediated degradation of the glucose‐dependent repressor Mig1p to allow induced expression of GAL promoters on glucose so that production potential on glucose could be examined. The novel genes that we used to reconstruct the heterologous acetyl‐CoA pathways did not sufficiently complement the loss of endogenous acetyl‐CoA pathways, indicating that superior heterologous enzymes are necessary to establish fully functional synthetic acetyl‐CoA pathways and properly explore their potential for nerolidol synthesis. Notwithstanding this, nerolidol production was improved twofold to a titre of ˜ 900 mg l−1 in flask cultivation using a combination of heterologous acetyl‐CoA pathways and Mig1p degradation. Conditional Mig1p depletion is presented as a valuable strategy to improve the productivities in the strains engineered with GAL promoters‐controlled pathways when growing on glucose.

Acetogenic bacteria can convert waste gases into fuels and chemicals. Design of bioprocesses for waste carbon valorization requires quantification of steady-state carbon flows. Here, steady-state quantification of autotrophic chemostats containing Clostridium autoethanogenum grown on CO2 and H2 revealed that captured carbon (460 ± 80 mmol/gDCW/day) had a significant distribution to ethanol (54 ± 3 C-mol% with a 2.4 ± 0.3 g/L titer). We were impressed with this initial result, but also observed limitations to biomass concentration and growth rate. Metabolic modeling predicted culture performance and indicated significant metabolic adjustments when compared to fermentation with CO as the carbon source. Moreover, modeling highlighted flux to pyruvate, and subsequently reduced ferredoxin, as a target for improving CO2 and H2 fermentation. Supplementation with a small amount of CO enabled co-utilization with CO2, and enhanced CO2 fermentation performance significantly, while maintaining an industrially relevant product profile. Additionally, the highest specific flux through the Wood-Ljungdahl pathway was observed during co-utilization of CO2 and CO. Furthermore, the addition of CO led to superior CO2-valorizing characteristics (9.7 ± 0.4 g/L ethanol with a 66 ± 2 C-mol% distribution, and 540 ± 20 mmol CO2/gDCW/day). Similar industrial processes are commercial or currently being scaled up, indicating CO-supplemented CO2 and H2 fermentation has high potential for sustainable fuel and chemical production. This work also provides a reference dataset to advance our understanding of CO2 gas fermentation, which can contribute to mitigating climate change.

Abstract Background Propionic acid is used primarily as a food preservative with smaller applications as a chemical building block for the production of many products including fabrics, cosmetics, drugs, and plastics. Biological production using propionibacteria would be competitive against chemical production through hydrocarboxylation of ethylene if native producers could be engineered to reach near-theoretical yield and good productivity. Unfortunately, engineering propionibacteria has proven very challenging. It has been suggested that activation of the sleeping beauty operon in Escherichia coli is sufficient to achieve propionic acid production. Optimising E. coli production should be much easier than engineering propionibacteria if tolerance issues can be addressed. Results Propionic acid is produced in E. coli via the sleeping beauty mutase operon under anaerobic conditions in rich medium via amino acid degradation. We observed that the sbm operon enhances amino acids degradation to propionic acid and allows E. coli to degrade isoleucine. However, we show here that the operon lacks an epimerase reaction that enables propionic acid production in minimal medium containing glucose as the sole carbon source. Production from glucose can be restored by engineering the system with a methylmalonyl-CoA epimerase from Propionibacterium acidipropionici (0.23 ± 0.02 mM). 1-Propanol production was also detected from the promiscuous activity of the native alcohol dehydrogenase (AdhE). We also show that aerobic conditions are favourable for propionic acid production. Finally, we increase titre 65 times using a combination of promoter engineering and process optimisation. Conclusions The native sbm operon encodes an incomplete pathway. Production of propionic acid from glucose as sole carbon source is possible when the pathway is complemented with a methylmalonyl-CoA epimerase. Although propionic acid via the restored succinate dissimilation pathway is considered a fermentative process, the engineered pathway was shown to be functional under anaerobic and aerobic conditions.

The urgent need for major gains in industrial crops productivity and in biofuel production from bioenergy grasses have reinforced attention on understanding C4 photosynthesis. Systems biology studies of C4 model plants may reveal important features of C4 metabolism. Here we chose foxtail millet (Setaria italica), as a C4 model plant and developed protocols to perform systems biology studies. As part of the systems approach, we have developed and used a genome-scale metabolic reconstruction in combination with the use of multi-omics technologies to gain more insights into the metabolism of S.italica. mRNA, protein and metabolite abundances, were measured in mature and immature stem/leaf phytomers and the multi-omics data were integrated into the metabolic reconstruction framework to capture key metabolic features in different developmental stages of the plant. RNA-Seq reads were mapped to the S. italica resulting for 83% coverage of the protein coding genes of S. italica. Besides revealing similarities and differences in central metabolism of mature and immature tissues, transcriptome analysis indicates significant gene expression of two malic enzyme isoforms (NADP- ME and NAD-ME). Although much greater expression levels of NADP-ME genes are observed and confirmed by the correspondent protein abundances in the samples, the expression of multiple genes combined to the significant abundance of metabolites that participates in C4 metabolism of NAD-ME and NADP-ME subtypes suggest that S. italica may use mixed decarboxylation modes of C4 photosynthetic pathways under different plant developmental stages. The overall analysis also indicates different levels of regulation in mature and immature tissues in carbon fixation, glycolysis, TCA cycle, amino acids, fatty acids, lignin and cellulose syntheses. Altogether, the multi-omics analysis reveals different biological entities and their interrelation and regulation over plant development. With this study, we demonstrated that this systems approach is powerful enough to complement the functional metabolic annotation of bioenergy grasses.

To date, evaluating the diets of natural enemies like carabids has largely been limited to spatially explicit and short-term sampling. This leaves a knowledge gap for the intra-annual dynamics of carabid diets, and the provision and timing of delivery of natural pest control services. Season-long pitfall trapping of adult carabids was conducted in conventional winter wheat fields, from November 2018 to June 2019, in five French departments. Diagnostic Multiplex PCR of carabid gut contents was used to determine the dynamics of carabid diets. The overall detection rate of target prey DNA was high across carabid individuals (80%) but varied with the prey group. The rate of detection was low for pests, at 8.1% for slugs and 9.6% for aphids. Detection of intraguild predation and predation on decomposers was higher, at 23.8% for spiders, 37.9% for earthworms and 64.6% for springtails. Prey switching was high at the carabid community level, with pest consumption and intraguild predation increasing through the cropping season as the availability of these prey increased in the environment, while the detection of decomposer DNA decreased. Variation in diet through the cropping season was characterized by: (i) complementary predation on slug and aphid pests; and (ii) temporal complementarity in the predominant carabid taxa feeding on each pest. We hypothesize that natural pest control services delivered by carabids are determined by complementary contributions to predation by the different carabid taxa over the season.

Protecting crops against pests is a major issue in the current agricultural production system. In particular, assessing the risk to crops can promote integrated pest management (IPM) strategies that encourage natural control mechanisms and advocate the use of pesticides as a last resort. In this study, we focused on wireworms, major soil-dwelling insect pests inflicting severe economic damage on various crops (including maize, potatoes and cereals) across Europe and North America. We have developed an original hierarchical Bayesian model that explicitly accounts for biological knowledge and uncertainty in field observations, rather than relying solely on statistical correlations, to predict the level of wireworm infestation. The model was calibrated and validated using a substantial dataset originating from an agro-environmental survey carried out over three consecutive years (2012–2014) in France, which provides the wireworm abundance in 419 maize fields, together with information on the landscape context, field history, weather conditions, soil characteristics and farming practices associated to each field. Model outcomes show good agreement with current knowledge from literature and field expertise in terms of the effects of variables on wireworm abundance, and provide fairly good predictive capacity. Subsequently, the model was encapsulated as a software (R shiny application) to predict the risk of wireworm infestation in any field of interest, and can be used by farmers or agricultural advisors as a decision support system for the implementation of IPM strategies. The conceptual framework that we implemented can be adapted to a wide range of similar situations involving other crops and pests.

Sowing of wildflower strips has been integrated in agri-environment schemes of several European countries. Their beneficial effects on natural enemies of pest insects are well documented but (1) the desired spill-over into crop fields has not always been demonstrated, and (2) the need to adapt sown mixtures to regional climatic differences has been rarely addressed.We set up a multi-site experiment in different French climatic regions to compare effects of a wildflower strip with a grass mixture and spontaneous vegetation. The design included five regions, three to five fields per region and the three strip treatments being repeated in each field. We tested strip treatment effects on vegetation (plant species richness, plant and flower cover) and on natural enemies (hoverflies, ladybirds, aphid predation). In a subset, we further analysed the spill-over into winter wheat fields including natural enemies and pest insects (cereal aphids, leaf beetles).The wildflower strip mixture developed well in all regions and increased plant species richness and flower cover compared with grass strips and spontaneous vegetation. We found a corresponding higher hoverfly abundance and aphid predation in wildflower strips that were consistent in all regions, whereas ladybird abundance was not affected. A significantly higher hoverfly abundance, aphid predation and aphid parasitism in wheat fields close to wildflower strips indicated a spill-over. No corresponding margin treatment effects were observed for aphid and leaf beetle abundance in the field. A multivariate analysis comparing the influence of climate and vegetation parameters showed that floral cover better explained variation in natural enemy abundance and predation than climate. Our results demonstrated that similar mixtures of native plants can be used over large climatic gradients to improve biocontrol. Further research is needed to improve spill-over into crop fields and to obtain consistently strong effects in different climate zones.

Adoption of practices that reduce the risk of pest outbreaks is one of the pillars of agroecology and is largely based on biological control. Multiple infield and landscape parameters affect biocontrol, but the effects of conservation soil management on biological control have been poorly investigated over crop season. By comparing winter wheat fields within the same landscape but with different soil management, the direct and indirect effects of soil management (conservation and conventional systems) on natural enemies’ communities and their biological control on aphids was studied from the tillering stage to the harvest. In addition to aphid infestation, two families of the main natural enemies’ guilds were monitored, as well as their associated services: aphid parasitoid, a specialist and flying natural enemy, with parasitism service, and carabid beetles, a generalist and ground-dwelling predator, with aphidophagy service. Soil conservation system hosted more abundant and diverse carabid beetles’ assemblages, and received higher aphidophagy service in June than conventional system. However, neither parasitoid abundance, nor parasitism rates, were affected by soil management. Aphid infestation and its associated damage did not depend on soil management either. Our results suggest that ground-dwelling natural enemies are more impacted by soil management than foliage-dwelling natural enemies, which is partly reflected in aphid biocontrol. In agricultural systems with reduced soil perturbation, direct mortality on ground-dwelling communities due to tillage may be lower than in a conventional system, but habitat heterogeneity is also greater, increasing the number of ecological niches for natural enemies. Both factors are supposed to favor an early presence of natural enemies and a tendency toward a precocious aphidophagy service is indeed observed in conservation system.

Abstract Bile duct injury (BDI) is a dangerous complication of cholecystectomy, with significant postoperative sequelae for the patient in terms of morbidity, mortality, and long-term quality of life. BDIs have an estimated incidence of 0.4–1.5%, but considering the number of cholecystectomies performed worldwide, mostly by laparoscopy, surgeons must be prepared to manage this surgical challenge. Most BDIs are recognized either during the procedure or in the immediate postoperative period. However, some BDIs may be discovered later during the postoperative period, and this may translate to delayed or inappropriate treatments. Providing a specific diagnosis and a precise description of the BDI will expedite the decision-making process and increase the chance of treatment success. Subsequently, the choice and timing of the appropriate reconstructive strategy have a critical role in long-term prognosis. Currently, a wide spectrum of multidisciplinary interventions with different degrees of invasiveness is indicated for BDI management. These World Society of Emergency Surgery (WSES) guidelines have been produced following an exhaustive review of the current literature and an international expert panel discussion with the aim of providing evidence-based recommendations to facilitate and standardize the detection and management of BDIs during cholecystectomy. In particular, the 2020 WSES guidelines cover the following key aspects: (1) strategies to minimize the risk of BDI during cholecystectomy; (2) BDI rates in general surgery units and review of surgical practice; (3) how to classify, stage, and report BDI once detected; (4) how to manage an intraoperatively detected BDI; (5) indications for antibiotic treatment; (6) indications for clinical, biochemical, and imaging investigations for suspected BDI; and (7) how to manage a postoperatively detected BDI.

There are many different practices that contribute to conservation biological control, but little is known about their complementarity. We tested the effects of providing food and alternative hosts to parasitoids by intercropping a plum orchard with companion plants. Oats and vetch were intercropped into the orchard either as single-species (oats or vetch) or two-species (oats and vetch combined) intercrops within an inter-row. The trophic resources provided by these intercrops were assessed, along with the incidences of aphids and their parasitoids in plum trees. We found up to ten alternative host species provided by oats and vetch, and extrafloral nectar was available from the vetch and mixed strips. An effect of intercrop type and distance to plum trees was observed on aphid incidence during one sampling period. Parasitism rates in exclusion cages were affected by intercrop type, reaching almost 60% close to the mixed intercrop. However, no general tendency was observed upon whether oats, vetch or their mixture was associated with a lower incidence of aphids. We found no evidence that providing effective sources of food and alternative hosts for parasitoids increased aphid mortality in this study. The context-dependent efficiency of intercropping is discussed.

Wireworms, the soil-dwelling larvae of click beetles (Coleoptera: Elateridae), comprise major pests of several crops worldwide, including maize and potatoes. The current trend towards the reduction in pesticides use has resulted in strong demand for alternative methods to control wireworm populations. This review provides a state-of-the-art of current theory and practice in order to develop new agroecological strategies. The first step should be to conduct a risk assessment based on the production context (e.g., crop, climate, soil characteristics, and landscape) and on adult and/or larval population monitoring. When damage risk appears significant, prophylactic practices can be applied to reduce wireworm abundance (e.g., low risk rotations, tilling, and irrigation). Additionally, curative methods based on natural enemies and on naturally derived insecticides are, respectively, under development or in practice in some countries. Alternatively, practices may target a reduction in crop damage instead of pest abundance through the adoption of selected cultural practices (e.g., resistant varieties, planting and harvesting time) or through the manipulation of wireworm behavior (e.g., companion plants). Practices can be combined in a global Integrated Pest Management (IPM) framework to provide the desired level of crop protection.

Poecilus cupreus (L.) (Coleoptera: Carabidae) is a typical polyphagous predator species on arable lands. In this study, 11 polymorphic microsatellite markers were developed from genomic DNA of P. cupreus. Genotypes of 87 individuals sampled from three localities in Western France were analyzed to characterize the polymorphism at each locus. The number of alleles ranged from 3 to 20. All pairs of loci were in linkage equilibrium. The expected and observed heterozygosity ranged from 0.165 to 0.890 and 0.103 to 0.926, respectively. From the northern to the southern sites, six, three, and six loci showed significant deviations from Hardy-Weinberg equilibrium, respectively. At one locus, null alleles were suspected as occuring at high frequency in the three populations. A weak genetic differentiation among populations was found, suggesting intense and large scale gene flow coupled with large population size in P. cupreus. These polymorphic microsatellite markers could be used in future population genetics studies of P. cupreus.

We investigated, over the course of two years, the association between the abundance of aphids and their natural carabid enemies and landscape, which may help in the development of effective strategies for reducing the incidence of aphid outbreaks in agricultural crops. This was undertaken in 12 wheat and 12 maize fields each year in an agricultural landscape in western France. Our study area was characterized by hedgerows surrounding arable fields and permanent grassland. Some areas have not changed much for several decades, while field enlargement and removal of hedges occurred in some areas following agricultural intensification. This paper aims to determine if the abundance of aphids in crops (either directly, or indirectly via their natural enemies) is associated with the landscape around fields and if so, is it dependent on the landscape scale considered. We observed that the abundance of aphids in fields was associated with landscape composition at a large scale (500 m and 800 m). There was a positive correlation between the abundance of aphids and the proportion of the area under woodland and grassland at these scales. There was a negative correlation between the abundance of carabids and the proportion of grassland and hedgerow around crop fields. The species richness of carabids was positively correlated with the proportion of hedgerows. We found that the abundance of aphids in wheat fields was negatively and in maize fields positively associated with the proportion under grass strips. At a large scale carabid abundance in both types of culture was positively correlated with the proportion under grass strips.

Winter ecology of natural enemies has a great influence on the level and efficiency of biological control at spring. The hoverfly Episyrphus balteatus (DeGeer) (Diptera: Syrphidae) is one of the most important natural predators of crop aphids in Europe. Three different overwintering strategies coexist in this species which makes it a good model in order to study ecologically-based speciation processes. The purpose of this study was to determine whether E. balteatus populations with alternative overwintering strategies are genetically differentiated. To that aim, we developed 12 specific microsatellite markers and evaluated the level of neutral genetic differentiation between E. balteatus field populations that overwinter in the three different ways described in this species (i.e. migration, local overwintering at a pre-imaginal stage, and local overwintering at adult stage). Results showed a lack of neutral genetic differentiation between individuals with different overwintering strategies although there are strong ecological differences between them. All pair-wise FST values are below 0.025 and non-significant, and Bayesian clustering showed K=1 was the most likely number of genetic clusters throughout our sample. The three overwintering strategies form one unique panmictic population. This suggests that all the individuals may have genetic material for the expression of different overwintering phenotypes, and that their commitment in one particular overwintering strategy may depend on environmental and individual factors. Consequently, the prevalence of the different overwintering strategies would be potentially modified by landscape engineering and habitat management which could have major implications for biological control.

El artículo analiza las repercusiones de la revolución de 1910-1920 sobre la cuestión agraria en La Laguna y sostiene, cuando examina las fuentes locales y nacionales, que el villismo favoreció el asentamiento de pequeños aparceros en las haciendas tras la confiscación en 1914 y modificó los mecanismos de arrendamiento por medio de contratos de aparcería en productos. La actuación de varias "comisiones" villistas consiguió dar una respuesta al descontento social de la región y condicionó la política de restitución de las haciendas de 1916 por parte de los gober­nantes carrancistas; el trabajo concluye que la movilización social de 1911 y el dominio villista en 1914-1915, determinaron cambios en la estructura social y en la esfera productiva de la hacienda al­godonera de La Laguna.