A Transcriptomic Analysis of Higher-Order Ecological Interactions in a Eukaryotic Model Microbial Ecosystem.

Nonlinear ecological interactions within microbial ecosystems and their contribution to ecosystem functioning remain largely unexplored. Higher-order interactions, or interactions in systems comprised of more than two members that cannot be explained by cumulative pairwise interactions, are particularly understudied, especially in eukaryotic microorganisms. The wine fermentation ecosystem presents an ideal model to study yeast ecosystem establishment and functioning. Some pairwise ecological interactions between wine yeast species have been characterized, but very little is known about how more complex, multispecies systems function. Here, we evaluated nonlinear ecosystem properties by determining the transcriptomic response of Saccharomyces cerevisiae to pairwise versus tri-species culture. The transcriptome revealed that genes expressed during pairwise coculture were enriched in the tri-species data set but also that just under half of the data set comprised unique genes attributed to a higher-order response. Through interactive protein-association network visualizations, a holistic cell-wide view of the gene expression data was generated, which highlighted known stress response and metabolic adaptation mechanisms which were specifically activated during tri-species growth. Further, extracellular metabolite data corroborated that the observed differences were a result of a biotic stress response. This provides exciting new evidence showing the presence of higher-order interactions within a model microbial ecosystem. IMPORTANCE Higher-order interactions are one of the major blind spots in our understanding of microbial ecosystems. These systems remain largely unpredictable and are characterized by nonlinear dynamics, in particular when the system is comprised of more than two entities. By evaluating the transcriptomic response of S. cerevisiae to an increase in culture complexity from a single species to two- and three-species systems, we were able to confirm the presence of a unique response in the more complex setting that could not be explained by the responses observed at the pairwise level. This is the first data set that provides molecular targets for further analysis to explain unpredictable ecosystem dynamics in yeast.

The ecology of wine fermentation: a model for the study of complex microbial ecosystems.

The general interest in microbial ecology has skyrocketed over the past decade, driven by technical advances and by the rapidly increasing appreciation of the fundamental services that these ecosystems provide. In biotechnology, ecosystems have many more functionalities than single species, and, if properly understood and harnessed, will be able to deliver better outcomes for almost all imaginable applications. However, the complexity of microbial ecosystems and of the interactions between species has limited their applicability. In research, next generation sequencing allows accurate mapping of the microbiomes that characterise ecosystems of biotechnological and/or medical relevance. But the gap between mapping and understanding, to be filled by "functional microbiomics", requires the collection and integration of many different layers of complex data sets, from molecular multi-omics to spatial imaging technologies to online ecosystem monitoring tools. Holistically, studying the complexity of most microbial ecosystems, consisting of hundreds of species in specific spatial arrangements, is beyond our current technical capabilities, and simpler model systems with fewer species and reduced spatial complexity are required to establish the fundamental rules of ecosystem functioning. One such ecosystem, the ecosystem responsible for natural alcoholic fermentation, can provide an excellent tool to study evolutionarily relevant interactions between multiple species within a relatively easily controlled environment. This review will critically evaluate the approaches that are currently implemented to dissect the cellular and molecular networks that govern this ecosystem. KEY POINTS: • Evolutionarily isolated fermentation ecosystem can be used as an ecological model. • Experimental toolbox is gearing towards mechanistic understanding of this ecosystem. • Integration of multidisciplinary datasets is key to predictive understanding.

Combinatorial analysis of population dynamics, metabolite levels and malolactic fermentation in Saccharomyces cerevisiae/ Lachancea thermotolerans mixed fermentations.

The outcome of co- or sequential inoculation of Lachancea thermotolerans in winemaking remains unpredictable due to a lack of integrated data regarding the impact of grape juice composition on L. thermotolerans fermentation behaviour. Here, we investigate the impact of nitrogen composition on fermentation characteristics and aroma compound production in grape juice sequentially inoculated with commercial L. thermotolerans and S. cerevisiae strains. Subsequently, all treatments were subjected to malolactic fermentation (MLF) using two commercial strains of Oenococcus oeni. Addition of amino acids led to faster growth for S. cerevisiae fermentations, compared to the nitrogen-equivalent addition of diammonium phosphate (DAP). L. thermotolerans persistence in the mixed fermentations was significantly higher following DAP addition, with higher glycerol and lactic acid production. Interestingly, the lower total Nitrogen content in DAP-treated musts compared to other treatments did not alter the subsequent growth of S. cerevisiae. MLF was more similar between musts fermented with L. thermotolerans, regardless of nutrient regime, whereas significant differences in MLF completion times were observed for different nitrogen treatments in S. cerevisiae fermentations. Collectively, the data present an integrated view of the impact of nitrogen treatment on multispecies co-inoculation (growth kinetics and aromatic outcomes) and the downstream impact on MLF.

RNA polymerase II CTD S2P is dispensable for embryogenesis but mediates exit from developmental diapause in C. elegans.

Serine 2 phosphorylation (S2P) within the CTD of RNA polymerase II is considered a Cdk9/Cdk12-dependent mark required for 3'-end processing. However, the relevance of CTD S2P in metazoan development is unknown. We show that cdk-12 lesions or a full-length CTD S2A substitution results in an identical phenotype in Caenorhabditis elegans Embryogenesis occurs in the complete absence of S2P, but the hatched larvae arrest development, mimicking the diapause induced when hatching occurs in the absence of food. Genome-wide analyses indicate that when CTD S2P is inhibited, only a subset of growth-related genes is not properly expressed. These genes correspond to SL2 trans-spliced mRNAs located in position 2 and over within operons. We show that CDK-12 is required for maximal occupancy of cleavage stimulatory factor necessary for SL2 trans-splicing. We propose that CTD S2P functions as a gene-specific signaling mark ensuring the nutritional control of the C. elegans developmental program.

Evolution of mutualistic behaviour between Chlorella sorokiniana and Saccharomyces cerevisiae within a synthetic environment.

Yeast and microalgae are microorganisms with widely diverging physiological and biotechnological properties. Accordingly, their fields of applications diverge: yeasts are primarily applied in processes related to fermentation, while microalgae are used for the production of high-value metabolites and green technologies such as carbon capture. Heterotrophic-autotrophic systems and synthetic ecology approaches have been proposed as tools to achieve stable combinations of such evolutionarily unrelated species. We describe an entirely novel synthetic ecology-based approach to evolve co-operative behaviour between winery wastewater isolates of the yeast Saccharomyces cerevisiae and microalga Chlorella sorokiniana. The data show that biomass production and mutualistic growth improved when co-evolved yeast and microalgae strains were paired together. Combinations of co-evolved strains displayed a range of phenotypes, including differences in amino acid profiles. Taken together, the results demonstrate that biotic selection pressures can lead to improved mutualistic growth phenotypes over relatively short time periods.

Real-time monitoring of population dynamics and physical interactions in a synthetic yeast ecosystem by use of multicolour flow cytometry.

Ecological interactions between different species of yeasts have been observed and described extensively, but the mechanisms of interaction remain poorly understood. A hindrance to the characterization of multispecies yeast ecosystems is the lack of accurate methods for rapid real-time analysis of population dynamics in synthetic multispecies consortia. Here, we sought to accelerate and improve the sensitivity of ecological modelling and characterization of a synthetic yeast ecosystem by developing a flow cytometry-based method that tracks and sorts fluorescently tagged individual yeast species in real time during growth in model multispecies consortia. A protocol for integrative genetic modification of non-conventional yeasts was developed. The application of the method was demonstrated in a model four-species synthetic wine-yeast ecosystem that consisted of species commonly isolated from natural wine fermentations. The data show that this method allows for rapid generation of meaningful ecological data that contributes to our understanding of multispecies synthetic yeast ecosystems. Furthermore, interspecies interactions have been shown to impact the evolution of yeasts in natural ecosystems, and this platform will provide an ideal tool to better evaluate the impact of biotic selection pressures.Key Points• Fluorescent labelling of yeast species in a consortium for multicolour flow cytometry• Method developed to track population dynamics of multispecies yeast consortia• Enables real-time visualization, manipulation and response analyses of population dynamics• Produces accurate, reproducible data with powerful visual analyses potential at a rapid rate.

A giant exoplanet orbiting a very-low-mass star challenges planet formation models.

Surveys have shown that super-Earth and Neptune-mass exoplanets are more frequent than gas giants around low-mass stars, as predicted by the core accretion theory of planet formation. We report the discovery of a giant planet around the very-low-mass star GJ 3512, as determined by optical and near-infrared radial-velocity observations. The planet has a minimum mass of 0.46 Jupiter masses, very high for such a small host star, and an eccentric 204-day orbit. Dynamical models show that the high eccentricity is most likely due to planet-planet interactions. We use simulations to demonstrate that the GJ 3512 planetary system challenges generally accepted formation theories, and that it puts constraints on the planet accretion and migration rates. Disk instabilities may be more efficient in forming planets than previously thought.

Peer pressure: evolutionary responses to biotic pressures in wine yeasts.

In the macroscopic world, ecological interactions between multiple species of fauna and flora are recognised as major role-players in the evolution of any particular species. By comparison, research on ecological interactions as a driver of evolutionary adaptation in microbial ecosystems has been neglected. The evolutionary history of the budding yeast Saccharomyces cerevisiae has been extensively researched, providing an unmatched foundation for exploring adaptive evolution of microorganisms. However, in most studies, the habitat is only defined by physical and chemical parameters, and little attention is paid to the impact of cohabiting species. Such ecological interactions arguably provide a more relevant evolutionary framework. Within the genomic phylogenetic tree of S. cerevisiae strains, wine associated isolates form a distinct clade, also matched by phenotypic evidence. This domestication signature in genomes and phenomes suggests that the wine fermentation environment is of significant evolutionary relevance. Data also show that the microbiological composition of wine fermentation ecosystems is dominated by the same species globally, suggesting that these species have co-evolved within this ecosystem. This system therefore presents an excellent model for investigating the origins and mechanisms of interspecific yeast interactions. This review explores the role of biotic stress in the adaptive evolution of wine yeast.

Beam Energy and Centrality Dependence of Direct-Photon Emission from Ultrarelativistic Heavy-Ion Collisions.

The PHENIX collaboration presents first measurements of low-momentum (0.41 GeV/c) direct-photon yield dN_{γ}^{dir}/dη is a smooth function of dN_{ch}/dη and can be well described as proportional to (dN_{ch}/dη)^{α} with α≈1.25. This scaling behavior holds for a wide range of beam energies at the Relativistic Heavy Ion Collider and the Large Hadron Collider, for centrality selected samples, as well as for different A+A collision systems. At a given beam energy, the scaling also holds for high p_{T} (>5 GeV/c), but when results from different collision energies are compared, an additional sqrt[s_{NN}]-dependent multiplicative factor is needed to describe the integrated-direct-photon yield.

A magnetar-powered X-ray transient as the aftermath of a binary neutron-star merger.

Mergers of neutron stars are known to be associated with short γ-ray bursts1-4. If the neutron-star equation of state is sufficiently stiff (that is, the pressure increases sharply as the density increases), at least some such mergers will leave behind a supramassive or even a stable neutron star that spins rapidly with a strong magnetic field5-8 (that is, a magnetar). Such a magnetar signature may have been observed in the form of the X-ray plateau that follows up to half of observed short γ-ray bursts9,10. However, it has been expected that some X-ray transients powered by binary neutron-star mergers may not be associated with a short γ-ray burst11,12. A fast X-ray transient (CDF-S XT1) was recently found to be associated with a faint host galaxy, the redshift of which is unknown13. Its X-ray and host-galaxy properties allow several possible explanations including a short γ-ray burst seen off-axis, a low-luminosity γ-ray burst at high redshift, or a tidal disruption event involving an intermediate-mass black hole and a white dwarf13. Here we report a second X-ray transient, CDF-S XT2, that is associated with a galaxy at redshift z = 0.738 (ref. 14). The measured light curve is fully consistent with the X-ray transient being powered by a millisecond magnetar. More intriguingly, CDF-S XT2 lies in the outskirts of its star-forming host galaxy with a moderate offset from the galaxy centre, as short γ-ray bursts often do15,16. The estimated event-rate density of similar X-ray transients, when corrected to the local value, is consistent with the event-rate density of binary neutron-star mergers that is robustly inferred from the detection of the gravitational-wave event GW170817.

The exceptional X-ray evolution of SN 1996cr in high resolution.

We present X-ray spectra spanning 18 yr of evolution for SN 1996cr, one of the five nearest SNe detected in the modern era. Chandra HETG exposures in 2000, 2004, and 2009 allow us to resolve spectrally the velocity profiles of Ne, Mg, Si, S, and Fe emission lines and monitor their evolution as tracers of the ejecta-circumstellar medium interaction. To explain the diversity of X-ray line profiles, we explore several possible geometrical models. Based on the highest signal-to-noise 2009 epoch, we find that a polar geometry with two distinct opening angle configurations and internal obscuration can successfully reproduce all of the observed line profiles. The best-fitting model consists of two plasma components: (1) a mildly absorbed (2 × 1021 cm-2), cooler (≈2 keV) with high Ne, Mg, Si, and S abundances associated with a wide polar interaction region (half-opening angle ≈58°); (2) a moderately absorbed (2 × 1022 cm-2), hotter (≳20 keV) plasma with high Fe abundances and strong internal obscuration associated with a narrow polar interaction region (half-opening angle ≈20°). We extend this model to seven further epochs with lower signal-to-noise ratio and/or lower spectral-resolution between 2000 and 2018, yielding several interesting trends in absorption, flux, geometry, and expansion velocity. We argue that the hotter and colder components are associated with reflected and forward shocks, respectively, at least at later epochs. We discuss the physical implications of our results and plausible explosion scenarios to understand the X-ray data of SN 1996cr.

A kilonova as the electromagnetic counterpart to a gravitational-wave source.

Gravitational waves were discovered with the detection of binary black-hole mergers and they should also be detectable from lower-mass neutron-star mergers. These are predicted to eject material rich in heavy radioactive isotopes that can power an electromagnetic signal. This signal is luminous at optical and infrared wavelengths and is called a kilonova. The gravitational-wave source GW170817 arose from a binary neutron-star merger in the nearby Universe with a relatively well confined sky position and distance estimate. Here we report observations and physical modelling of a rapidly fading electromagnetic transient in the galaxy NGC 4993, which is spatially coincident with GW170817 and with a weak, short γ-ray burst. The transient has physical parameters that broadly match the theoretical predictions of blue kilonovae from neutron-star mergers. The emitted electromagnetic radiation can be explained with an ejected mass of 0.04 ± 0.01 solar masses, with an opacity of less than 0.5 square centimetres per gram, at a velocity of 0.2 ± 0.1 times light speed. The power source is constrained to have a power-law slope of -1.2 ± 0.3, consistent with radioactive powering from r-process nuclides. (The r-process is a series of neutron capture reactions that synthesise many of the elements heavier than iron.) We identify line features in the spectra that are consistent with light r-process elements (atomic masses of 90-140). As it fades, the transient rapidly becomes red, and a higher-opacity, lanthanide-rich ejecta component may contribute to the emission. This indicates that neutron-star mergers produce gravitational waves and radioactively powered kilonovae, and are a nucleosynthetic source of the r-process elements.

CT and MR imaging in congenital cardiac malformations: Where do we come from and where are we going?

The management of patients with congenital heart disease was profoundly changed firstly by the advent of pediatric and prenatal ultrasound and then more recently by cardiac magnetic resonance imaging (MRI) and computed tomography (CT) of the heart and great vessels. The improved life expectancy of these patients has brought about new medical and imaging requirements. MRI and CT are increasing second line techniques in this group of patients. This article summarizes the advantages and limitations of CT and MRI in some frequently encountered situations in children and adults followed up for congenital heart disease.

Accuracy of mandibular reconstruction by three-dimensional guided vascularised fibular free flap after segmental mandibulectomy.

Mandibular reconstruction with a fibular free flap has become standard in specialised centres for head and neck reconstruction, particularly for defects with more than one osteotomy that are challenging even for experienced surgeons. Virtual surgical planning is a potential tool to facilitate harvesting of the fibula and the osteostomy. The purpose of this study was to compare the two methods of mandibular reconstruction - conventionally planned (conventional group) and "virtually" planned (virtual group) - with regard to accuracy, bony consolidation, complications, and operating time. Fifty patients who required mandibular reconstruction after segmental mandibulectomy were evaluated retrospectively, 24 virtually planned and 26 conventionally planned. The overall survival of flaps was 92% (46/50). The bony consolidation rate in the virtual group was significantly better than that in the conventional group (p=0.002). The difference between the angle of the mandible before and after was highly significant with a median of 11.5° (range 2°-75°) in the conventional group and 4.5° (range 0-18°) in the virtual group (p=0.0001). Operations were mean (SD) of 34 (21.2) minutes shorter in virtually-planned cases (p=0.12). The overall morbidity did not differ significantly between the groups. The use of virtual surgical planning in mandibular reconstruction by fibular free flap is beneficial for optimising accuracy, consolidation of bony segments, and operating time, while increasing the predictability of results for the surgeon. However, additional costs have to be carefully weighed against the benefits.

X-ray and radio emission from the luminous supernova 2005kd.

SN 2005kd is among the most luminous supernovae (SNe) to be discovered at X-ray wavelengths. We have re-analysed all good angular resolution (better than 20 arcsec full width at half-maximum point spread function) archival X-ray data for SN 2005kd. The data reveal an X-ray light curve that decreases as t -1.62±0.06. Our modelling of the data suggests that the early evolution is dominated by emission from the forward shock in a high-density medium. Emission from the radiative reverse shock is absorbed by the cold dense shell formed behind the reverse shock. Our results suggest a progenitor with a mass-loss rate towards the end of its evolution of ≥4.3 × 10-4 M⊙ yr-1, for a wind velocity of 10 km s-1, at 4.0 × 1016 cm. This mass-loss rate is too high for most known stars, except perhaps hypergiant stars. A higher wind velocity would lead to a correspondingly higher mass-loss rate. A luminous blue variable star undergoing a giant eruption could potentially fulfill this requirement, but would need a high mass-loss rate lasting for several hundred years, and need to explain the plateau observed in the optical light curve. The latter could perhaps be due to the ejecta expanding in the dense circum-stellar material at relatively small radii. These observations are consistent with the fact that Type IIn SNe appear to expand into high-density and high mass-loss rate environments, and also suggest rapid variability in the wind mass-loss parameters within at least the last 5000 yr of stellar evolution prior to core-collapse.

Sandwich flaps as a feasible solution for the management of huge mandibular composite tissue defects.

In the current therapy of head and neck defects, surgical reconstruction with the aid of pedicle or free flaps is common practice. Suitable single flaps are available to solve most reconstructive challenges. However, reconstruction can become a problem in extensive mandibular defects, as they are often caused by large primary tumors or osteoradionecrosis. These composite defects often lead to large intraoral or extraoral fistulas due to the involvement of mucosa, skin, mandible and soft tissue. These issues call for a double flap approach in order to achieve adequate reconstruction. Therefore, we developed a surgical sandwich technique as presented in this study. The procedure features the acquisition and use of two vascular flaps which can be freely combined according to their desired features (for example being of high tissue volume or osteomyocutaneous). In our study we included 11 patients (ten male, one female) with a mean age of 57 years. Seven of the patients had defects due to osteoradionecrosis and four due to tumor resection. A sandwich technique was performed in a single operation in eight patients, whereas for three patients several operations were necessary. The flaps used included: fibula free flap (FFF); anterolateral thigh (ALT); radial forearm flap (RFF); deltopectoral flap (DPF) and tensor fascia lata (TFL). The following combinations were used: FFF and ALT (three cases), FFF and RFF (two), FFF and DPF (three), ALT and TFL (two), and two ALT flaps (one). The sandwich technique proved suitable for complex reconstructions and led to desirable esthetic and functional results. The flexibility in combining different free or pedicle flaps made it possible to address various defect situations and consequently offer satisfactory surgical reconstruction for complex cases.

Release of copper from embedded solid copper bullets into muscle and fat tissues of fallow deer (Dama dama), roe deer (Capreolus capreolus), and wild boar (Sus scrofa) and effect of copper content on oxidative stability of heat-processed meat.

When venison with embedded copper bullets was subjected to different culinary processing procedures, the amount of copper released from the embedded bullet was affected more by the retention period of the bullet in the meat during cool storage, than by the different heating protocols. The presence of copper fragments had no significant effect on levels of thiobarbituric acid reactive substances (TBARS). Conversely, TBARS in lean meat (fallow deer, wild boar, roe deer) were significantly affected by culinary treatment (higher TBARS in boiled and boiled-stored meat than in meat barbecued or boiled in brine). In pork-beef patties doped with up to 28mg/kg Cu, TBARS increased after dry-heating and subsequently storing the meat patties. The amount of copper doping had no effect on TBARS for 0 and 7days of storage, but a significant effect at day 14 (fat oxidation retarded at higher Cu doses). Evidence is presented that wild boar meat may be more sensitive to fat oxidation than pork-beef.

Prediction of cardiovascular events after renal transplantation.

BACKGROUND: Pulse wave velocity (PWV) is a marker of arterial stiffness and predicts cardiovascular events in the nontransplantation population. Cardiovascular events (CVE) are the leading cause of death and one of the leading causes of graft failure in renal transplant recipients. The present prospective study investigates whether there is a correlation between PWV and CVE in renal transplant recipients. METHODS: A prospective study assessing the incidence of a composite cardiovascular endpoint within ≥ 3 years after pulse wave analysis was performed in 64 stable renal transplant recipients. Measurement of PWV, augmentation index (AI75), and aortic systolic pressure was conducted using the SphygmoCor (AtCor) device. The composite endpoint of the study was the incidence of either death, myocardial infarction, stroke, or admission for symptomatic intermittent claudication or decompensated congestive heart failure. RESULTS: Fifteen patients (23%) reached the composite endpoint during a follow-up of 4.4 years. Binary logistic regression using PWV, AI75, central aortic systolic pressure, peripheral systolic pressure, and pulse pressure as covariates revealed that PWV was significantly associated with cardiovascular events (10.1 ± 3.6 m/s in subjects reaching the endpoint vs 8.5 ± 1.5 m/s in subjects not reaching the endpoint; P = .048). CONCLUSION: Increased arterial stiffness as assessed by PWV predicts CVE in renal transplant recipients and may be regarded as a footprint of accelerated arteriosclerosis for those patients.