A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide a platform for model simulations and integrative analysis of omics data. This study introduces Yeast8 and an associated ecosystem of models that represent a comprehensive computational resource for performing simulations of the metabolism of Saccharomyces cerevisiae––an important model organism and widely used cell-factory. Yeast8 tracks community development with version control, setting a standard for how GEMs can be continuously updated in a simple and reproducible way. We use Yeast8 to develop the derived models panYeast8 and coreYeast8, which in turn enable the reconstruction of GEMs for 1,011 different yeast strains. Through integration with enzyme constraints (ecYeast8) and protein 3D structures (proYeast8DB), Yeast8 further facilitates the exploration of yeast metabolism at a multi-scale level, enabling prediction of how single nucleotide variations translate to phenotypic traits

When public action undermines public health: A critical examination of antifluoridationist literature

Background: The addition of the chemical fluorine to the water supply, called water fluoridation, reduces dental caries by making teeth more resistant to demineralisation and more likely to remineralise when initially decayed. This process has been implemented in more than 30 countries around the world, is cost-effective and has been shown to be efficacious in preventing decay across a person's lifespan. However, attempts to expand this major public health achievement in line with Australia's National Oral Health Plan 2004–2013 are almost universally met with considerable resistance from opponents of water fluoridation, who engage in coordinated campaigns to portray water fluoridation as ineffective and highly dangerous. Discussion: Water fluoridation opponents employ multiple techniques to try and undermine the scientifically established effectiveness of water fluoridation. The materials they use are often based on Internet resources or published books that present a highly misleading picture of water fluoridation. These materials are used to sway public and political opinion to the detriment of public health. Despite an extensive body of literature, both studies and results within studies are often selectively reported, giving a biased portrayal of water fluoridation effectiveness. Positive findings are downplayed or trivialised and the population implications of these findings misinterpreted. Ecological comparisons are sometimes used to support spurious conclusions. Opponents of water fluoridation frequently repeat that water fluoridation is associated with adverse health effects and studies are selectively picked from the extensive literature to convey only claimed adverse findings related to water fluoridation. Techniques such as "the big lie" and innuendo are used to associate water fluoridation with health and environmental disasters, without factual support. Half-truths are presented, fallacious statements reiterated, and attempts are made to bamboozle the public with a large list of claims and quotes often with little scientific basis. Ultimately, attempts are made to discredit and slander scientists and various health organisations that support water fluoridation. Summary: Water fluoridation is an important public health initiative that has been found to be safe and effective. Nonetheless, the implementation of water fluoridation is still regularly interrupted by a relatively small group of individuals who use misinformation and rhetoric to induce doubts in the minds of the public and government officials. It is important that public health officials are aware of these tactics so that they can better counter their negative effectJason M Armfiel

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10-20 cm and 30-40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics