Incorporating prior knowledge improves detection of differences in bacterial growth rate

BACKGROUND: Robust statistical detection of differences in the bacterial growth rate can be challenging, particularly when dealing with small differences or noisy data. The Bayesian approach provides a consistent framework for inferring model parameters and comparing hypotheses. The method captures the full uncertainty of parameter values, whilst making effective use of prior knowledge about a given system to improve estimation. RESULTS: We demonstrated the application of Bayesian analysis to bacterial growth curve comparison. Following extensive testing of the method, the analysis was applied to the large dataset of bacterial responses which are freely available at the web-resource, ComBase. Detection was found to be improved by using prior knowledge from clusters of previously analysed experimental results at similar environmental conditions. A comparison was also made to a more traditional statistical testing method, the F-test, and Bayesian analysis was found to perform more conclusively and to be capable of attributing significance to more subtle differences in growth rate. CONCLUSIONS: We have demonstrated that by making use of existing experimental knowledge, it is possible to significantly improve detection of differences in bacterial growth rate

Research for policy influence : a history of IDRC intent

Part of the collection of government and miscellaneous documents relating to the history of IDRC.This paper tells the story of how the Centre's intent on linking research and policy processes has evolved over the years. There has been a persistent concern with the use of research over three decades of IDRC’s history. The task of refining a corporate strategy to foster research for policy change, and especially of putting it into practice, remains a work in progress. This study is based on analysis of IDRC planning documents, reports, internal papers, evaluations and reviews, as well as selected Board minutes. External documents were also consulted to help provide context

Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms

Harnessing chemosynthetic symbionts is a recurring evolutionary strategy. Eukaryotes from six phyla as well as one archaeon have acquired chemoautotrophic sulfur-oxidizing bacteria. In contrast to this broad host diversity, known bacterial partners apparently belong to two classes of bacteria—the Gamma- and Epsilonproteobacteria. Here, we characterize the intracellular endosymbionts of the mouthless catenulid flatworm genus Paracatenula as chemoautotrophic sulfur-oxidizing Alphaproteobacteria. The symbionts of Paracatenula galateia are provisionally classified as “Candidatus Riegeria galateiae” based on 16S ribosomal RNA sequencing confirmed by fluorescence in situ hybridization together with functional gene and sulfur metabolite evidence. 16S rRNA gene phylogenetic analysis shows that all 16 Paracatenula species examined harbor host species-specific intracellular Candidatus Riegeria bacteria that form a monophyletic group within the order Rhodospirillales. Comparing host and symbiont phylogenies reveals strict cocladogenesis and points to vertical transmission of the symbionts. Between 33% and 50% of the body volume of the various worm species is composed of bacterial symbionts, by far the highest proportion among all known endosymbiotic associations between bacteria and metazoans. This symbiosis, which likely originated more than 500 Mya during the early evolution of flatworms, is the oldest known animal–chemoautotrophic bacteria association. The distant phylogenetic position of the symbionts compared with other mutualistic or parasitic Alphaproteobacteria promises to illuminate the common genetic predispositions that have allowed several members of this class to successfully colonize eukaryote cells

A continental record of the Carnian Pluvial Episode (CPE) from the Mercia Mudstone Group (UK):palynology and climatic implications

The generally arid Late Triassic climate was interrupted by a wet phase during the mid-Carnian termed the Carnian Pluvial Episode (CPE). Quantitative palynological data from the Mercia Mudstone Group in the Wessex Basin (UK) reveal vegetation changes and palaeoclimate trends. Palynostratigraphy and bulk organic carbon isotope data allow correlation to other Carnian successions. The palynostratigraphy indicates that the Dunscombe Mudstone is Julian and the lowest part of the overlying Branscombe Mudstone Formation is Tuvalian. The Aulisporites acme characterizing the CPE in Tethyan successions and the Germanic Basin is missing in the UK. The quantitative palynological record suggests the predominance of xerophyte floral elements with a few horizons of increased hygrophytes. A humidity signal is not seen owing to the dry climate in central Pangea. Also, the signal might be masked by the overrepresentation of xerophyte regional pollen and the predominance of xerophyte hinterland flora. The bias towards regional pollen rain is enhanced by the potential increase in continental runoff related to seasonally humid conditions and differences in pollen production rates and transport mechanisms. The vegetation of British CPE successions suggests a more complex climate history during the Carnian, indicating that the CPE is not recognized by the same changes everywhere

Personal traits predict conservationists’ optimism about outcomes for nature

In the face of unprecedented biodiversity loss, the belief that conservation goals can be met could play an important role in ensuring they are fulfilled. We asked conservationists how optimistic they felt about key biodiversity outcomes over the next 10 years; 2341 people familiar with conservation in 144 countries responded. Respondents expressed optimism that enabling conditions for conservation would improve but felt pressures would continue, and the state of biodiversity was unlikely to get better. Respondents with greater general optimism about life, at early-career stages, and working in practice and policy (compared to academia) reported higher conservation optimism. But most of our biodiversity and conservation status indicators were not associated with conservation optimism. Unbounded optimism without appropriate action would be misguided in the face of growing threats to biodiversity. However, supporting those struggling to see the light at the end of the tunnel could help sustain efforts to overcome these threats

Novel (Hetero)arylalkenyl propargylamine compounds are protective in toxin-induced models of Parkinson's disease

Background: Mitochondrial dysfunction, oxidative stress and their interplay are core pathological features of Parkinson's disease. In dopaminergic neurons, monoamines and their metabolites provide an additional source of reactive free radicals during their breakdown by monoamine oxidase or auto-oxidation. Moreover, mitochondrial dysfunction and oxidative stress have a supraadditive impact on the pathological, cytoplasmic accumulation of dopamine and its subsequent release. Here we report the effects of a novel series of potent and selective MAO-B inhibitory (hetero)arylalkenylpropargylamine compounds having protective properties against the supraadditive effect of mitochondrial dysfunction and oxidative stress. Results: The (hetero)arylalkenylpropargylamines were tested in vitro, on acute rat striatal slices, pretreated with the complex I inhibitor rotenone and in vivo, using the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) induced acute, subchronic, and chronic experimental models of Parkinson's disease in mice. The compounds exhibited consistent protective effects against i) in vitro oxidative stress induced pathological dopamine release and the formation of toxic dopamine quinone in the rat striatum and rescued tyrosine hydroxylase positive neurons in the substantia nigra after rotenone treatment; ii) in vivo MPTP-induced striatal dopamine depletion and motor dysfunction in mice using acute and subchronic, delayed application protocols. One compound (SZV558) was also examined and proved to be protective in a chronic mouse model of MPTP plus probenecid (MPTPp) administration, which induces a progressive loss of nigrostriatal dopaminergic neurons. Conclusions: Simultaneous inhibition of MAO-B and oxidative stress induced pathological dopamine release by the novel propargylamines is protective in animal models and seems a plausible strategy to combat Parkinson's disease