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.

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.

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.

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.

Adjustment of trehalose metabolism in wine Saccharomyces cerevisiae strains to modify ethanol yields.

The ability of Saccharomyces cerevisiae to efficiently produce high levels of ethanol through glycolysis has been the focus of much scientific and industrial activity. Despite the accumulated knowledge regarding glycolysis, the modification of flux through this pathway to modify ethanol yields has proved difficult. Here, we report on the systematic screening of 66 strains with deletion mutations of genes encoding enzymes involved in central carbohydrate metabolism for altered ethanol yields. Five of these strains showing the most prominent changes in carbon flux were selected for further investigation. The genes were representative of trehalose biosynthesis (TPS1, encoding trehalose-6-phosphate synthase), central glycolysis (TDH3, encoding glyceraldehyde-3-phosphate dehydrogenase), the oxidative pentose phosphate pathway (ZWF1, encoding glucose-6-phosphate dehydrogenase), and the tricarboxylic acid (TCA) cycle (ACO1 and ACO2, encoding aconitase isoforms 1 and 2). Two strains exhibited lower ethanol yields than the wild type (tps1Δ and tdh3Δ), while the remaining three showed higher ethanol yields. To validate these findings in an industrial yeast strain, the TPS1 gene was selected as a good candidate for genetic modification to alter flux to ethanol during alcoholic fermentation in wine. Using low-strength promoters active at different stages of fermentation, the expression of the TPS1 gene was slightly upregulated, resulting in a decrease in ethanol production and an increase in trehalose biosynthesis during fermentation. Thus, the mutant screening approach was successful in terms of identifying target genes for genetic modification in commercial yeast strains with the aim of producing lower-ethanol wines.

Multipolar plasmonic resonances in silver nanowire antennas imaged with a subnanometer electron probe.

We detect short-range surface plasmon-polariton (SR-SPP) resonances setup in individual silver nanoantenna structures at high-spatial resolution with a scanning, subnanometer electron probe. Both even and odd multipolar resonant modes are resolved up to sixth order, and we measure their spatial distribution in relation to nanoantenna structures at energies down to 0.55 eV. Fabry-Perot type SR-SPP reflection phase shifts are calculated from direct measurements of antinode spacings in high-resolution plasmonic field maps. We observe resonant SR-SPP antinode bunching at nanoantenna terminals in high-order resonant modes, and antinode shifts in nonhomogeneous local environments. Finally, we achieve good agreement of our experimental SR-SPP maps with numerical calculations of photon excited near fields, using a novel integrated photon excitation geometry.

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.

Liposarcoma. An ultrastructural study of 15 cases.

Fifteen liposarcomas from 13 patients were examined by electron microscopy. These included nine primary tumors, four recurrent tumors after primary surgery or irradiation, and two metastatic lesions. Twelve of the liposarcomas were located in the thigh, and 11 were of the myxoid variety. All neoplasms were composed of cells having the ultrastructural characteristics of some stage of lipoblastic differentiation, i.e., lipid droplets, micropinocytotic vesicles, glycogen, external lamina, intermediate filaments, Golgi apparatuses, rough and smooth endoplasmic reticulum, and mitochondria. The nuclear-cytoplasmic ratio and nuclear pleomorphism were related inversely to the size and number of lipid droplets. Lipoblasts were frequently in close association with capillaries and pericytes, and in four cases lipid droplets were found in pericytes. Multivacuolated, mitochondria-rich lipoblasts, resembling brown fat cells, also were seen. Most tumors contained lipid-free, poorly differentiated mesenchymal cells that showed a continuum of morphologic differentiation to cells that closely resembled early lipoblasts that contained nonmembrane-bound lipid vacuoles. Fibrolipoblasts, cells containing lipid droplets and abundant rough endoplasmic reticulum, were observed only in well-differentiated liposarcomas. Some soft tissue sarcomas contain vacuolated cells that simulate lipoblasts by light microscopy but prove to be reactive or malignant fibroblasts, histiocytes, or smooth muscle cells ultrastructurally. Therefore, use of electron microscopy may be necessary to establish the line of differentiation in these neoplasms.

Lafora-body disease with optic atrophy, macular degeneration and cardiac failure.

A 17-year-old boy was admitted to hospital in acute cardiac failure and psychosis. The clinical course, EEG records and tissue diagnosis, including biopsies of brain, skin, skeletal muscle, peripheral nerve and liver were compatible with Lafora-body disease (LBD). Unusual features were those of optic atrophy and macular degeneration, signs generally regarded as negative criteria for the diagnosis of this disease. We also present the findings on endomyocardial biopsy which was performed because cardiac failure as an early symptom of LBD has not been previously described. The patient died in status epilepticus a few months after discharge from hospital.

Radiosynthesis and in vitro stability evaluation of various radioiodine-labelled beta-iodoalkylether prosthetic groups linked to model compounds.

A systematic comparative investigation into the in vitro radiochemical stabilities of model compounds containing radioiodinated beta-iodoethoxyl units and derivatives thereof, as well as those of similar compounds lacking a beta-oxygen to serve as control references, was undertaken. The radioiodinations were carried out in fair to modest yields by means of substitution of a tosyl group by iodide. Stability evaluations were carried out by incubating the labeled compounds in human blood serum at 37 degrees C and measuring free radioiodide by means of radio-HPLC and radio-TLC. The compounds containing beta-iodoethoxyl units displayed much superior stabilities than those without, while the presence of small alkyl or aryl groups in such a unit rendered an additional degree of stability to the carbon-iodine bond, especially over a long period.

A comparative cerebral blood flow study in a baboon model with acetazolamide provocation: 99mTc-HMPAO vs 123I(IMP).

Pharmacological interactions are important when nuclear medical procedures are applied to patients under drug therapy, or drug provocation. This study compares in baboon models (regional) cerebral blood flow [(r)CBF] results from 99mTc-HMPAO and 123I-iodoamphetamine [123I(IMP)] each with and without acetazolamide, the latter a suggested drug for testing cerebrovascular reserve. Expected differences in cerebral uptake were observed between the two radio-tracers without acetazolamide. The increase in tracer uptake resulting from acetazolamide is significantly enhanced for 123I(IMP), which could have diagnostic implications.

Planar myocardial imaging in the baboon model with iodine-123-15-(iodophenyl)pentadecanoic acid (IPPA) and iodine-123-15-(P-iodophenyl)-3-R,S-methylpentadecanoic acid (BMIPP), using time-activity curves for evaluation of metabolism.

The purpose of this study was to compare by planar myocardial scintigraphy the kinetics of iodine-123-15-(iodophenyl)pentadecanoic acid (123I-pPPA and 123I-oPPA), and of iodine-123-(p-iodophenyl)-3-R,S-methyl-pentadecanoic acid (BMIPP), firstly in normal baboons, and subsequently after blocking fatty acid oxidation by a carnitine palmitoyl transferase I(CPT1) inhibitor. The induced changes in myocardial metabolism were reflected in the dynamic behaviour of the three tracers. pPPA and oPPA to a large extent, provided information on beta-oxidation changes in the myocardium: beta-oxidation participation changed from 47% and 50%, respectively to 17% and 23% after inhibition. BMIPP provided better images and reflected largely on changed tracer incorporation into the neutral lipid pools. The beta-oxidation contributed only about 10% towards the metabolic pathway of BMIPP. The information obtained in this study could help determine the tracer of choice for SPECT, whereby myocardial viability could optimally be revealed.

Biochemical and morphologic changes in rabbit lung following endotracheal instillation of zymosan particles.

In order to establish a model of lung disease in which the usefulness of potential antiinflammatory compounds can be evaluated, we have analyzed the biochemical and cellular responses of rabbits to zymosan deposition in their lungs. A suspension of zymosan particles was instilled into the lungs of rabbits using an intratracheal catheter. Because the influx of leukocytes and the transudation of plasma into affected lungs was expected to contribute to the total cellular enzyme and protein levels, lungs were homogenized and assayed after various time intervals for six cellular enzymes and for protein content. After one day, alkaline phosphatase and neutral protease levels were elevated by 90% and 50%, respectively, above normal values. After two and three days, all of the pulmonary enzymes assayed displayed maximal two- to fourfold increases in their levels of activity. After seven days, only the alkaline phosphatase and neutral protease levels remained slightly elevated by 50% and 30%, respectively. Histologic analysis revealed focal and diffuse intraalveolar, interstitial, peribronchiolar, and perivascular accumulations of macrophages, granulocytes, and lymphocytes. Severe pulmonary edema, evident microscopically after one to three days, correlated well with 100% increases in both the wet weight and protein content of the lungs. In control experiments, the intratracheal infusion of saline solution minus zymosan particles resulted in a variety of enzymatic changes in the lungs after three days, which could be distinguished both enzymatically and histologically from those following zymosan deposition; histopathologic analysis revealed a pattern of intravascular congestion with erythrocytes, edematous thickening of alveolar septa, and focal intraalveolar hemorrhages, but with no inflammatory infiltration. In summary, this study demonstrates the time course of an experimental model for acute and chronic lung inflammation, the extent of which may be quantitatively evaluated using cellular enzymatic markers.

A biomechanical evaluation of suture anchors in repair of the rotator cuff.

Repair of the rotator cuff requires secure reattachment, but large chronic defects cause osteoporosis of the greater tuberosity which may then have insufficient strength to allow proper fixation of the tendon. Recently, suture anchors have been introduced, but have not been fully evaluated. We have investigated the strength of suture-to-anchor attachment, and the use of suture anchors in repairs of the rotator cuff either to the greater tuberosity or the lateral cortex of the humerus. The second method gave a significant increase in the strength of the repair (p = 0.014). The repairs were loaded cyclically and failed at low loads by cutting into bone and tendon, casting doubt on the integrity of the repair in early mobilisation after surgery. Repairs with suture anchors did not perform better than those with conventional transosseous attachment.

Allografted keratinocytes used to accelerate the treatment of burn wounds are replaced by recipient cells.

Cultured keratinocytes were used as allografts on burn wounds in two patients. In both patients successful covering of the wounds was obtained. DNA fingerprinting of the epidermis covering the wounds 21 days later showed that the cultured keratinocytes were replaced by the patients' cells.

Experimental reclamping of free-flap pedicles: the effect of prolonged stasis on the anastomoses and clamp sites.

The effect of static blood in direct contact with areas of microvascular anastomoses and previous clamp application for prolonged periods of time has been investigated. The free groin flap was used as a model in 27 white rabbits. The flap pedicle vessels were reclamped proximal to the anastomoses and areas of previous clamp application for periods of time varying between 30 minutes and 4 hours after 15 minutes of blood flow over these areas. A 100 percent patency rate was achieved despite the long periods of reclamping. Histologically, minor intimal damage was visible in the immediate period following anastomoses and clamping of the vessels. After 2 weeks, despite a thickened myofibroblastic intimal lesion, an intact endothelial layer was observed. No evidence of thrombosis could be demonstrated in either period. We postulate that vessels carefully treated and with technically well-performed anastomoses can be regarded as "normal" vessels after 15 minutes of blood flow over the anastomoses and clamp sites. We suggest that when required, microvascular clamps may then be reapplied without risk for prolonged periods of time despite static blood being in contact with these areas.

Semiquantitative postembedding characterization of intermediate filaments in central nervous system lesions using immunoelectron microscopy.

Standardized postembedding immunoelectron microscopy was performed to demonstrate glial fibrillary acidic protein (GFAP) and vimentin in individual intermediate filaments to determine the diagnostic value of demonstrating ultrastructural and immunophenotypic characteristics of intermediate filaments in routine brain biopsy specimens. Dual expression of GFAP and vimentin was observed in the astroblastoma and astrocytes of Alexander's disease. The antigen availability for vimentin, however, was too low to allow reliable assessment of the GFAP:vimentin ratio in individual intermediate filaments and/or filament bundles. In meningioma, only vimentin positive intermediate filaments were found. GFAP positive intermediate filaments were present in all other specimens except the oligodendroglial components of the mixed glioma, which were devoid of intermediate filaments. GFAP positivity in the filamentous periphery and electron-dense core of Rosenthal fibers was demonstrated. Technical and tissue processing factors had a significant effect on particle density values obtained for individual specimens. Although the number, distribution, and density of glial intermediate filaments varies in different astroglial entities, correlation of particle density values determined by immunoelectron microscopy with relative GFAP concentrations in different lesions requires utmost caution. Nevertheless, application of the postembedding approach to routinely fixed biopsy specimens indicated an association of different entities with the exclusive presence of GFAP and/or vimentin in individual intermediate filaments, thus emphasizing the diagnostic value of intermediate filament typing for pathological characterization.

Iodoform toxicity following the use of B.I.P.P.: a potential hazard.

1. A case of severe iodoform toxicity is presented in a patient after a total maxillectomy whose cavity was packed with B.I.P.P. The patient subsequently recovered after removal of the B.I.P.P. pack. 2. A simple spectrophotometric method for measuring plasma iodine concentration is described. Plasma iodine determinations were carried out on the toxic patient and three others with iodoform containing packs. The concentrations found correspond well with the presence or absence of iodoform toxicity. 3. From the clinical and biochemical evidence presented we suggest that B.I.P.P. gauze is a satisfactory packing for small operative cavities, but that caution should be exercised if large cavities, such as those following maxillectomies, are to be packed with the material. Another iodoform containing mixture, Whitehead's varnish, is a safer alternative to B.I.P.P. gauze.

Evaluation of nitrendipine--a new calcium channel blocker.

Nitrendipine (Baypress; Bayer-Miles), a new calcium channel blocker, was administered to 38 hypertensive patients in an oral dose of 20 mg once or twice daily. Both systolic and diastolic blood pressures were reduced to a clinically relevant extent within 2 hours of taking the medication. There was no loss of effect during the 57 days of the trial. No significant changes in heart rate were noted. On the whole, side-effects were mild and transient and consisted mainly of dizziness, headache, joint pains and oedema.