MiR‐342 controls Mycobacterium tuberculosis susceptibility by modulating inflammation and cell death

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb) that places a heavy strain on public health. Host susceptibility to Mtb is modulated by macrophages, which regulate the balance between cell apoptosis and necrosis. However, the role of molecular switches that modulate apoptosis and necrosis during Mtb infection remains unclear. Here, we show that Mtb‐susceptible mice and TB patients have relatively low miR‐342‐3p expression, while mice with miR‐342‐3p overexpression are more resistant to Mtb. We demonstrate that the miR‐342‐3p/SOCS6 axis regulates anti‐Mtb immunity by increasing the production of inflammatory cytokines and chemokines. Most importantly, the miR‐342‐3p/SOCS6 axis participates in the switching between Mtb‐induced apoptosis and necrosis through A20‐mediated K48‐linked ubiquitination and RIPK3 degradation. Our findings reveal several strategies by which the host innate immune system controls intracellular Mtb growth via the miRNA‐mRNA network and pave the way for host‐directed therapies targeting these pathways.     

Co‐substrate composition is critical for enrichment of functional key species and for process efficiency during biogas production from cattle manure

Cattle manure has a low energy content and high fibre and water content, limiting its value for biogas production. Co‐digestion with a more energy‐dense material can improve the output, but the co‐substrate composition that gives the best results in terms of degree of degradation, gas production and digestate quality has not yet been identified. This study examined the effects of carbohydrate, protein and fat as co‐substrates for biogas production from cattle manure. Laboratory‐scale semi‐continuous mesophilic reactors were operated with manure in mono‐digestion or in co‐digestion with egg albumin, rapeseed oil, potato starch or a mixture of these, and chemical and microbiological parameters were analysed. The results showed increased gas yield for all co‐digestion reactors, but only the reactor supplemented with rapeseed oil showed synergistic effects on methane yield. The reactor receiving potato starch indicated improved fibre degradation, suggesting a priming effect by the easily accessible carbon. Both these reactors showed increased species richness and enrichment of key microbial species, such as fat‐degrading Syntrophomonadaceae and families known to include cellulolytic bacteria. The addition of albumin promoted enrichment of known ammonia‐tolerant syntrophic acetate‐ and potential propionate‐degrading bacteria, but still caused slight process inhibition and less efficient overall degradation of organic matter in general, and of cellulose in particular.

The study investigated co‐digestion of cattle manure with different categories of co substrates, e.g. starch, albumin, rapeseed oil or a mix of these. The processes were evaluated using both chemical parameters and analysis of microbial communities. Results showed clear correlations between process efficiency and the applied co‐substrates, and enrichment key microbial taxa.     

Intracellular Mycobacterium tuberculosis Exploits Host-derived Fatty Acids to Limit Metabolic Stress

Recent data indicate that the nutrients available to Mycobacterium tuberculosis (Mtb) inside its host cell are restricted in their diversity. Fatty acids and cholesterol appear more favored; however, their degradation can result in certain metabolic stresses. Their breakdown can generate propionyl-CoA, which gives rise to potentially toxic intermediates. Detoxification of propionyl-CoA relies on the activity of the methylcitrate cycle, the methylmalonyl pathway, or incorporation of the propionyl-CoA into methyl-branched lipids in the cell wall. The current work explores carbon flux through these pathways, focusing primarily on those pathways responsible for the incorporation of propionyl-CoA into virulence-associated cell wall lipids. Exploiting both genetic and biochemical rescue, we demonstrate that these metabolic pressures are experienced by Mtb inside its host macrophage and that the bacterium accesses host fatty acid stores. The metabolism of these host lipids expands the acetyl-CoA pool and alleviates the pressure from propionyl-CoA. These data have major implications for our appreciation of central metabolism of Mtb during the course of infection.     

Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion

Adaptive laboratory evolution has proven highly effective for obtaining microorganisms with enhanced capabilities. Yet, this method is inherently restricted to the traits that are positively linked to cell fitness, such as nutrient utilization. Here, we introduce coevolution of obligatory mutualistic communities for improving secretion of fitness‐costly metabolites through natural selection. In this strategy, metabolic cross‐feeding connects secretion of the target metabolite, despite its cost to the secretor, to the survival and proliferation of the entire community. We thus co‐evolved wild‐type lactic acid bacteria and engineered auxotrophic Saccharomyces cerevisiae in a synthetic growth medium leading to bacterial isolates with enhanced secretion of two B‐group vitamins, viz., riboflavin and folate. The increased production was specific to the targeted vitamin, and evident also in milk, a more complex nutrient environment that naturally contains vitamins. Genomic, proteomic and metabolomic analyses of the evolved lactic acid bacteria, in combination with flux balance analysis, showed altered metabolic regulation towards increased supply of the vitamin precursors. Together, our findings demonstrate how microbial metabolism adapts to mutualistic lifestyle through enhanced metabolite exchange.     

Enhanced effect of recombinant adenoviruses co‐expression of ING4 and OSM on anti‐tumour activity of laryngeal cancer

The inhibitor of growth family member 4 (ING4) is one of the ING family genes, serves as a repressor of angiogenesis or tumour growth and suppresses loss of contact inhibition. Oncostatin M (OSM) is a multifunctional cytokine that belongs to the interleukin (IL)‐6 subfamily with several biological activities. However, the role of recombinant adenoviruses co‐expressing ING4 and OSM (Ad‐ING4‐OSM) in anti‐tumour activity of laryngeal cancer has not yet been identified. Recombinant Ad‐ING4‐OSM was used to evaluate their combined effect on enhanced anti‐tumour activity in Hep‐2 cells of laryngeal cancer in vivo. Moreover, in vitro function assays of co‐expression of Ad‐ING4‐OSM were performed to explore impact of co‐expression of Ad‐ING4‐OSM on biological phenotype of laryngeal cancer cell line, that is Hep‐2 cells. In vitro, Ad‐ING4‐OSM significantly inhibited the growth, enhanced apoptosis, altered cell cycle with G1 and G2/M phase arrest, and upregulated the expression of P21, P27, P53 and downregulated survivin in laryngeal cancer Hep‐2 cells. Furthermore, in vivo functional experiments of co‐expressing of Ad‐ING4‐OSM demonstrated that solid tumours in the nude mouse model were significantly suppressed, and the co‐expressing Ad‐ING4‐OSM showed a significant upregulation expression of P21, P53, Bax and Caspase‐3 and a downregulation of Cox‐2, Bcl‐2 and CD34. This study for the first time demonstrated the clinical value and the role of co‐expressing Ad‐ING4‐OSM in biological function of laryngeal cancer. This work suggested that co‐expressing Ad‐ING4‐OSM might serve as a potential therapeutic target for laryngeal cancer patients.     

Attenuation of SARS‐CoV‐2 replication and associated inflammation by concomitant targeting of viral and host cap 2'‐O‐ribose methyltransferases

The SARS‐CoV‐2 infection cycle is a multistage process that relies on functional interactions between the host and the pathogen. Here, we repurposed antiviral drugs against both viral and host enzymes to pharmaceutically block methylation of the viral RNA 2''‐O‐ribose cap needed for viral immune escape. We find that the host cap 2''‐O‐ribose methyltransferase MTr1 can compensate for loss of viral NSP16 methyltransferase in facilitating virus replication. Concomitant inhibition of MTr1 and NSP16 efficiently suppresses SARS‐CoV‐2 replication. Using in silico target‐based drug screening, we identify a bispecific MTr1/NSP16 inhibitor with anti‐SARS‐CoV‐2 activity in vitro and in vivo but with unfavorable side effects. We further show antiviral activity of inhibitors that target independent stages of the host SAM cycle providing the methyltransferase co‐substrate. In particular, the adenosylhomocysteinase (AHCY) inhibitor DZNep is antiviral in in vitro, in ex vivo, and in a mouse infection model and synergizes with existing COVID‐19 treatments. Moreover, DZNep exhibits a strong immunomodulatory effect curbing infection‐induced hyperinflammation and reduces lung fibrosis markers ex vivo. Thus, multispecific and metabolic MTase inhibitors constitute yet unexplored treatment options against COVID‐19.     

Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mapping

Anaerobic ammonium-oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving anammox bacterial anabolism and use of different carbon and energy substrates beyond genome-based predictions. Here, we experimentally resolved the central carbon metabolism of the anammox bacterium Candidatus ‘Kuenenia stuttgartiensis’ using time-series ¹³C and ²H isotope tracing, metabolomics, and isotopically nonstationary metabolic flux analysis. Our findings confirm predicted metabolic pathways used for CO₂ fixation, central metabolism, and amino acid biosynthesis in K. stuttgartiensis, and reveal several instances where genomic predictions are not supported by in vivo metabolic fluxes. This includes the use of the oxidative branch of an incomplete tricarboxylic acid cycle for alpha-ketoglutarate biosynthesis, despite the genome not having an annotated citrate synthase. We also demonstrate that K. stuttgartiensis is able to directly assimilate extracellular formate via the Wood–Ljungdahl pathway instead of oxidizing it completely to CO₂ followed by reassimilation. In contrast, our data suggest that K. stuttgartiensis is not capable of using acetate as a carbon or energy source in situ and that acetate oxidation occurred via the metabolic activity of a low-abundance microorganism in the bioreactor’s side population. Together, these findings provide a foundation for understanding the carbon metabolism of anammox bacteria at a systems-level and will inform future studies aimed at elucidating factors governing their function and niche differentiation in natural and engineered ecosystems.Subject terms: Environmental microbiology, Metabolism     

Dietary citrate supplementation enhances longevity,metabolic health,and memory performance through promoting ketogenesis

Citrate is an essential substrate for energy metabolism that plays critical roles in regulating cell growth and survival. However, the action of citrate in regulating metabolism, cognition, and aging at the organismal level remains poorly understood. Here, we report that dietary supplementation with citrate significantly reduces energy status and extends lifespan in Drosophila melanogaster. Our genetic studies in fruit flies implicate a molecular mechanism associated with AMP‐activated protein kinase (AMPK), target of rapamycin (TOR), and ketogenesis. Mice fed a high‐fat diet that supplemented with citrate or the ketone body β‐hydroxybutyrate (βOHB) also display improved metabolic health and memory. These results suggest that dietary citrate supplementation may prove to be a useful intervention in the future treatment of age‐related dysfunction.     

Sodium butyrate reverses lipopolysaccharide‐induced mitochondrial dysfunction in lymphoblasts

Butyrate is a short‐chain fatty acid that is produced by commensal microbes within the intestinal microbiome through fermentation of dietary fibre. Microbial‐derived butyrate has been shown to promote immunologic and metabolic homeostasis, in part through its beneficial effects on mitochondrial function, and thus has been proposed as a possible anti‐inflammatory therapy. We tested the hypothesis that butyrate could mitigate the decrease in mitochondrial respiration in immune cells under septic conditions as a preliminary step towards better understanding the potential for butyrate as a novel therapy in sepsis. Mitochondrial respiration and content (measured as citrate synthase activity) were compared within four Epstein–Barr virus‐transformed lymphoblast (LB) cell lines exposed to either control media or lipopolysaccharide (LPS) 100 ng/ml. Both co‐incubation of LBs with LPS + butyrate and treatment with butyrate after LPS stimulation reversed the decrease in mitochondrial respiration observed in LBs exposed to LPS without butyrate. Neither LPS nor butyrate led to significant changes in citrate synthase activity. The preliminary findings support further investigation of a potential mitochondrial‐based mechanism through which butyrate may help to mitigate the immuno‐inflammatory response in sepsis.     

Building integral projection models with nonindependent vital rates

Population dynamics are functions of several demographic processes including survival, reproduction, somatic growth, and maturation. The rates or probabilities for these processes can vary by time, by location, and by individual. These processes can co‐vary and interact to varying degrees, e.g., an animal can only reproduce when it is in a particular maturation state. Population dynamics models that treat the processes as independent may yield somewhat biased or imprecise parameter estimates, as well as predictions of population abundances or densities. However, commonly used integral projection models (IPMs) typically assume independence across these demographic processes. We examine several approaches for modelling between process dependence in IPMs and include cases where the processes co‐vary as a function of time (temporal variation), co‐vary within each individual (individual heterogeneity), and combinations of these (temporal variation and individual heterogeneity). We compare our methods to conventional IPMs, which treat vital rates independent, using simulations and a case study of Soay sheep (Ovis aries). In particular, our results indicate that correlation between vital rates can moderately affect variability of some population‐level statistics. Therefore, including such dependent structures is generally advisable when fitting IPMs to ascertain whether or not such between vital rate dependencies exist, which in turn can have subsequent impact on population management or life‐history evolution.     

Mixed infection,risk projection,and misdirection: Interactions among pathogens alter links between host resources and disease

A growing body of literature links resources of hosts to their risk of infectious disease. Yet most hosts encounter multiple pathogens, and projections of disease risk based on resource availability could be fundamentally wrong if they do not account for interactions among pathogens within hosts. Here, we measured infection risk of grass hosts (Avena sativa) exposed to three naturally co‐occurring viruses either singly or jointly (barley and cereal yellow dwarf viruses [B/CYDVs]: CYDV‐RPV, BYDV‐PAV, and BYDV‐SGV) along experimental gradients of nitrogen and phosphorus supply. We asked whether disease risk (i.e., infection prevalence) differed in single versus co‐inoculations, and whether these differences varied with rates and ratios of nitrogen and phosphorus supply. In single inoculations, the viruses did not respond strongly to nitrogen or phosphorus. However, in co‐inoculations, we detected illustrative cases of 1) resource‐dependent antagonism (lower prevalence of RPV with increasing N; possibly due to competition), 2) resource‐dependent facilitation (higher prevalence of SGV with decreasing N:P; possibly due to immunosuppression), and 3) weak or no interactions within hosts (for PAV). Together, these within‐host interactions created emergent patterns for co‐inoculated hosts, with both infection prevalence and viral richness increasing with the combination of low nitrogen and high phosphorus supply. We demonstrate that knowledge of multiple pathogens is essential for predicting disease risk from host resources and that projections of risk that fail to acknowledge resource‐dependent interactions within hosts could be qualitatively wrong. Expansions of theory from community ecology theory may help anticipate such relationships by linking host resources to diverse pathogen communities.     

Hatching date influences winter habitat occupancy: Examining seasonal interactions across the full annual cycle in a migratory songbird

Birds experience a sequence of critical events during their life cycle, and past events can subsequently determine future performance via carry‐over effects. Events during the non‐breeding season may influence breeding season phenology or productivity. Less is understood about how events during the breeding season affect individuals subsequently in their life cycle. Using stable carbon isotopes, we examined carry‐over effects throughout the annual cycle of prairie warblers (Setophaga discolor), a declining Nearctic–Neotropical migratory passerine bird. In drier winters, juvenile males that hatched earlier at our study site in Massachusetts, USA, occupied wetter, better‐quality winter habitat in the Caribbean, as indicated by depleted carbon isotope signatures. For juveniles that were sampled again as adults, repeatability in isotope signatures indicated similar winter habitat occupancy across years. Thus, hatching date of juvenile males appears to influence lifetime winter habitat occupancy. For adult males, reproductive success did not carry over to influence winter habitat occupancy. We did not find temporally consecutive “domino” effects across the annual cycle (breeding to wintering to breeding) or interseasonal, intergenerational effects. Our finding that a male''s hatching date can have a lasting effect on winter habitat occupancy represents an important contribution to our understanding of seasonal interactions in migratory birds.     

Sex roles in nest keeping – how information asymmetry contributes to parent‐offspring co‐adaptation

Parental food provisioning and offspring begging influence each other reciprocally. This makes both traits agents and targets of selection, which may ultimately lead to co‐adaptation. The latter may reflect co‐adapted parent and offspring genotypes or could be due to maternal effects. Maternal effects are in turn likely to facilitate in particular mother‐offspring co‐adaptation, further emphasized by the possibility that mothers are sometimes found to be more responsive to offspring need. However, parents may not only differ in their sensitivity, but often play different roles in postnatal care. This potentially impinges on the access to information about offspring need. We here manipulated the information on offspring need as perceived by parents by playing back begging calls at a constant frequency in the nest‐box of blue tits (Cyanistes caeruleus). We measured the parental response in provisioning to our treatment, paying particular attention to sex differences in parental roles and whether such differences alter the perception of the intensity of our manipulation. This enabled us to investigate whether an information asymmetry about offspring need exists between parents and how such an asymmetry relates to co‐adaptation between parental provisioning and offspring begging. Our results show that parents indeed differed in the frequency how often they perceived the playback due to the fact that females spent more time with their offspring in the nest box. Correcting for the effective exposure of an adult to the playback, the parental response in provisioning covaried more strongly (positive) with offspring begging intensity, independent of the parental sex, indicating coadaptation on the phenotypic level. Females were not more sensitive to experimentally increased offspring need than males, but they were exposed to more broadcasted begging calls. Therefore, sex differences in access to information about offspring need, due to different parental roles, have the potential to impinge on family conflicts and their resolution.     

Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing

Central carbon metabolism is highly conserved across microbial species, but can catalyze very different pathways depending on the organism and their ecological niche. Here, we study the dynamic reorganization of central metabolism after switches between the two major opposing pathway configurations of central carbon metabolism, glycolysis, and gluconeogenesis in Escherichia coli, Pseudomonas aeruginosa, and Pseudomonas putida. We combined growth dynamics and dynamic changes in intracellular metabolite levels with a coarse‐grained model that integrates fluxes, regulation, protein synthesis, and growth and uncovered fundamental limitations of the regulatory network: After nutrient shifts, metabolite concentrations collapse to their equilibrium, rendering the cell unable to sense which direction the flux is supposed to flow through the metabolic network. The cell can partially alleviate this by picking a preferred direction of regulation at the expense of increasing lag times in the opposite direction. Moreover, decreasing both lag times simultaneously comes at the cost of reduced growth rate or higher futile cycling between metabolic enzymes. These three trade‐offs can explain why microorganisms specialize for either glycolytic or gluconeogenic substrates and can help elucidate the complex growth patterns exhibited by different microbial species.     

Carbon monoxide alleviates senescence in diabetic nephropathy by improving autophagy

ObjectivesSenescence, characterized by permanent cycle arrest, plays an important role in diabetic nephropathy (DN). However, the mechanism of renal senescence is still unclear, and the treatment targeting it remains to be further explored.Materials and MethodsThe DN mice were induced by HFD and STZ, and 3 types of renal cells were treated with high glucose (HG) to establish in vitro model. Senescence‐related and autophagy‐related markers were detected by qRT‐PCR and Western blot. Further, autophagy inhibitors and co‐immunoprecipitation were used to clarify the mechanism of CO. Additionally, the specific relationship between autophagy and senescence was explored by immunofluorescence triple co‐localization and ELISA.ResultsWe unravelled that senescence occurred in vivo and in vitro, which could be reversed by CO. Mechanistically, we demonstrated that CO inhibited the dysfunction of autophagy in DN mice partly through dissociating Beclin‐1‐Bcl‐2 complex. Further results showed that autophagy inhibitors blocked the improvement of CO on senescence. In addition, the data revealed that autophagy regulated the degradation of senescence‐related secretory phenotype (SASP) including Il‐1β, Il‐6, Tgf‐β and Vegf.ConclusionsThese results suggested that CO protects DN mice from renal senescence and function loss via improving autophagy partly mediated by dissociating Beclin‐1‐Bcl‐2 complex, which is possibly ascribed to the degradation of SASP. These findings bring new ideas for the prevention and treatment of DN and the regulation of senescence.     

A new approach to interspecific synchrony in population ecology using tail association

Standard methods for studying the association between two ecologically important variables provide only a small slice of the information content of the association, but statistical approaches are available that provide comprehensive information. In particular, available approaches can reveal tail associations, that is, accentuated or reduced associations between the more extreme values of variables. We here study the nature and causes of tail associations between phenological or population‐density variables of co‐located species, and their ecological importance. We employ a simple method of measuring tail associations which we call the partial Spearman correlation. Using multidecadal, multi‐species spatiotemporal datasets on aphid first flights and marine phytoplankton population densities, we assess the potential for tail association to illuminate two major topics of study in community ecology: the stability or instability of aggregate community measures such as total community biomass and its relationship with the synchronous or compensatory dynamics of the community''s constituent species; and the potential for fluctuations and trends in species phenology to result in trophic mismatches. We find that positively associated fluctuations in the population densities of co‐located species commonly show asymmetric tail associations; that is, it is common for two species’ densities to be more correlated when large than when small, or vice versa. Ordinary measures of association such as correlation do not take this asymmetry into account. Likewise, positively associated fluctuations in the phenology of co‐located species also commonly show asymmetric tail associations. We provide evidence that tail associations between two or more species’ population‐density or phenology time series can be inherited from mutual tail associations of these quantities with an environmental driver. We argue that our understanding of community dynamics and stability, and of phenologies of interacting species, can be meaningfully improved in future work by taking into account tail associations.     

Extensive historical and contemporary hybridization suggests premating isolation in Vermivora warblers is not strong: A reply to Confer et al.

We present comments on an article published by Confer et al. (Ecology and Evolution, 10, 2020). Confer et al. (2020) aggregate data from multiple studies of social pairing between Vermivora chrysoptera and V. cyanoptera, two wood warblers in the family Parulidae that hybridize extensively where they co‐occur. From analysis of these data, they conclude there is near‐complete reproductive isolation between these two species. In our reply, we show that this finding is not supported by other lines of evidence, and significant drawbacks of their study design preclude such strong conclusions. In our critique, we show that (a) coarse‐scale plumage classifications cannot be used to accurately estimate hybrid ancestry in Vermivora; (b) extra‐pair paternity is very high in Vermivora and is likely facilitating hybridization, yet was not considered by Confer et al. (2020), and we suggest this will have a substantial influence on the interpretation of reproductive isolation in the system; and (c) the central finding of strong total reproductive isolation is not compatible with the results of other long‐term studies, which demonstrate low isolation and high gene flow. We conclude with a more comprehensive interpretation of hybridization and reproductive isolation in Vermivora warblers.

Vermivora warblers—golden‐winged and blue‐winged warblers—hybridize extensively where they co‐occur. We discuss concerns regarding recent suggestions that this extensive hybridization takes place in the face of near complete pre‐mating isolation, which we suggest is not consistent with other data.