Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and ...where the plethora of industrial strains originates from. Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts. Our analyses reveal that today’s industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence. Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts. Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains.
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•We sequenced and phenotyped 157 S. cerevisiae yeasts•Present-day industrial yeasts originate from only a few domesticated ancestors•Beer yeasts show strong genetic and phenotypic hallmarks of domestication•Domestication of industrial yeasts predates microbe discovery
The history and domestication of yeast used for making beer and other types of alcohol are revealed through genomic and phenotypic analyses.
Cells constantly adapt to environmental fluctuations. These physiological changes require time and therefore cause a lag phase during which the cells do not function optimally. Interestingly, past ...exposure to an environmental condition can shorten the time needed to adapt when the condition re-occurs, even in daughter cells that never directly encountered the initial condition. Here, we use the molecular toolbox of
to systematically unravel the molecular mechanism underlying such history-dependent behavior in transitions between glucose and maltose. In contrast to previous hypotheses, the behavior does not depend on persistence of proteins involved in metabolism of a specific sugar. Instead, presence of glucose induces a gradual decline in the cells' ability to activate respiration, which is needed to metabolize alternative carbon sources. These results reveal how trans-generational transitions in central carbon metabolism generate history-dependent behavior in yeast, and provide a mechanistic framework for similar phenomena in other cell types.
The perception and appreciation of food flavor depends on many interacting chemical compounds and external factors, and therefore proves challenging to understand and predict. Here, we combine ...extensive chemical and sensory analyses of 250 different beers to train machine learning models that allow predicting flavor and consumer appreciation. For each beer, we measure over 200 chemical properties, perform quantitative descriptive sensory analysis with a trained tasting panel and map data from over 180,000 consumer reviews to train 10 different machine learning models. The best-performing algorithm, Gradient Boosting, yields models that significantly outperform predictions based on conventional statistics and accurately predict complex food features and consumer appreciation from chemical profiles. Model dissection allows identifying specific and unexpected compounds as drivers of beer flavor and appreciation. Adding these compounds results in variants of commercial alcoholic and non-alcoholic beers with improved consumer appreciation. Together, our study reveals how big data and machine learning uncover complex links between food chemistry, flavor and consumer perception, and lays the foundation to develop novel, tailored foods with superior flavors.
Abstract
Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A ...thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Project engagement metrics have continued to grow over the last 2 years, including source code contributions, publications, software packages wrapped as tools, registered users and their daily analysis jobs, and new independent specialized servers. Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools. Important scientific developments enabled by Galaxy include Vertebrate Genome Project (VGP) assembly workflows and global SARS-CoV-2 collaborations.
Graphical Abstract
Graphical Abstract
The Galaxy Project is represented by a combination of software, managed services, application of the software for solving scientific analyses, and vibrant world-wide community. In turn, each area is characterized by new depicted capabilities.
To examine the nature of asthma in the elderly, we compared older (group 1: 65 years or older, n = 50) with younger patients (group 2: <40 years, n = 99) and to determine the influence of ...long-standing disease, elderly asthmatics with early onset (group A: onset before 40, n = 22) were compared with patients developing symptoms later in their lives (group B: onset after 40, n = 22). Blood eosinophilia and IgE value >/=100 IU/l were more frequent in younger patients. Short symptom-free periods were more frequent among older asthmatics (78.5 vs. 45.4%, p < 0.001). Only 31.2% of older patients had only mild symptoms. Requirement of systemic steroids was higher in the elderly population. The worst FEV1 was lower in older patients (54.4 +/- 17.3 vs. 71.8 +/- 18.5%, p </= 0.001). Patients with early-onset asthma showed more frequently shorter symptom-free periods (93.3 vs. 53.3%, p <0.05), higher emergency admissions/year, and hospitalizations/year. Best FEV1 (group 1: 66.7 +/- 13.7% vs. group 2: 90.3 +/- 15.1%, p < 0.005) and worst FEV1 (46.2 +/- 13.1 vs. 61.0 +/- 13.2%, p < 0.01) were lower in early-onset patients. A higher systemic steroid requirement, a lower best and worst FEV1, shorter symptom-free periods and a lesser proportion of patients with only mild symptoms were observed in patients older than 65 with early-onset asthma compared with those younger than 40 years. Elderly patients with a shorter duration of asthma were not different from young patients. Our study strongly suggests that severity of asthma and development of irreversible airflow obstruction depend on the duration of disease.
Glacier shrinkage opens new proglacial terrain with pronounced environmental gradients along longitudinal and lateral chronosequences. Despite the environmental harshness of the streams that drain ...glacier forelands, their benthic biofilms can harbor astonishing biodiversity spanning all domains of life. Here, we studied the spatial dynamics of prokaryotic and eukaryotic photoautotroph diversity within braided glacier-fed streams and tributaries draining lateral terraces predominantly fed by groundwater and snowmelt across three proglacial floodplains in the Swiss Alps. Along the lateral chronosequence, we found that benthic biofilms in tributaries develop higher biomass than those in glacier-fed streams, and that their respective diversity and community composition differed markedly. We also found spatial turnover of bacterial communities in the glacier-fed streams along the longitudinal chronosequence. These patterns along the two chronosequences seem unexpected given the close spatial proximity and connectivity of the various streams, suggesting environmental filtering as an underlying mechanism. Furthermore, our results suggest that photoautotrophic communities shape bacterial communities across the various streams, which is understandable given that algae are the major source of organic matter in proglacial streams. Overall, our findings shed new light on benthic biofilms in proglacial streams now changing at rapid pace owing to climate-induced glacier shrinkage.
The seasonal abundance of Botryosphaeriaceae spp. spores was studied in California vineyards by using glass microscope slides covered with petroleum jelly placed on grapevine cordons and Burkard ...volumetric spore traps at seven and two different locations, respectively. Correlation analysis was used to determine which meteorological variables (precipitation, relative humidity, temperature, and wind speed) influenced Botryosphaeriaceae spp. spore release. Among all variables, regression analysis resulted in a strong relationship between spore release and precipitation. Additionally, a positive relationship between irrigation and spore release was also observed in the Riverside County vineyard. During the study period, spore discharge of Botryosphaeriaceae spp. occurred from the first fall rain through the last spring rains, coinciding with September to April. However, based on the results obtained from the spore traps, most spores (over 60%) were trapped following rain events during the winter months of December, January, and February, which coincides with the grapevine pruning season. Botryosphaeriaceae spp. spore release was much lower in fall and early spring (22%) and very few or no spores were trapped in late spring and summer (3%). This work suggests that a delay of pruning time in California may be warranted to reduce grapevine infection because the current timing coincides with the greatest period of spore discharge.
The aim of this study was to define the most useful index of expressing bronchodilator response and to distinguish between asthma and COPD.
A prospective study was carried out of bronchodilator ...response in 142 asthmatics and 58 COPD patients in a university hospital.
Reversibility was expressed as: 1. absolute change (Δabs); 2. % of initial (Δ%init); 3. % of predicted (Δ%pred) and 4. % of maximum possible response (Δ%max). Dependence on forced expirations volume in 1 sec (FEV
1) as % of predicted and sensitivity and specificity for diagnosis of asthma were established.
A relationship between Δabs and initial FEV
1 was not found in asthma (Δabs
vs. % initial FEV
1.
r = 0·07) or COPD (
r = 0·02). Δ%pred did not show a correlation in asthma (
r = 0·10) or COPD (
r = 0·06). Δ%init was dependent on the baseline value in asthma (
r = 0·38,
P ≤ 0·001) but not in COPD (
r = 0·18,
P = n.s.). Δmax was dependent in both. The combination of best sensitivity and specificity to separate asthma and COPD was obtained with Δabs (70·4 or 70·6%). The worst specificity for asthma diagnosis was obtained with Δ% init (50%). The best likelihood ratios were obtained with Δabs and Δ%pred and the worst likelihood ratio with Δ%init
Δ%init is not recommended as an index for differential diagnosis between asthma and COPD; 2) Δ%init overscores bronchodilator response in patients with low FEV
1. The independence of each bronchodilator response index should be verified in clinical trials for each selected sample.
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