New Asgard archaea capable of anaerobic hydrocarbon cycling, bioRxiv, 2019-01-24
Large reservoirs of natural gas in the oceanic subsurface sustain a complex biosphere of anaerobic microbes, including recently characterized archaeal lineages that extend the potential to mediate hydrocarbon oxidation (methane and butane) beyond the Methanomicrobia. Here we describe a new archaeal phylum, Helarchaeota, belonging to the Asgard superphylum with the potential for hydrocarbon oxidation. We reconstructed Helarchaeota genomes from hydrothermal deep-sea sediment metagenomes in hydrocarbon-rich Guaymas Basin, and show that these encode novel methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea. Based on these results as well as the presence of several alkyl-CoA oxidation and Wood-Ljungdahl pathway genes in the Helarchaeota genomes, we suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize short-chain hydrocarbons. These findings link a new phylum of Asgard archaea to the microbial utilization of hydrothermally generated hydrocarbons, and extend this genomic blueprint further through the archaeal domain.
biorxiv microbiology 0-100-users 2019Parallel control of mechanosensory hair cell orientation by the PCP and Wnt pathways, bioRxiv, 2019-01-24
Cell polarity plays a crucial role during development of vertebrates and invertebrates. Planar Cell Polarity (PCP) is defined as the coordinated polarity of cells within a tissue axis and is essential for processes such as gastrulation, neural tube closure or hearing. Wnt ligands can be instructive or permissive during PCP-dependent processes, and Wnt pathway mutants are often classified as PCP mutants due to the complexity and the similarities between their phenotypes. Our studies of the zebrafish sensory lateral line reveal that disruptions of the PCP and Wnt pathways have differential effects on hair cell orientations. While mutations in PCP genes cause random orientations of hair cells, mutations in Wnt pathway members induce hair cells to adopt a concentric pattern. We show that PCP signaling is normal in hair cells of Wnt pathway mutants and that the concentric hair cell phenotype is due to altered organization of the surrounding support cells. Thus, the PCP and Wnt pathways work in parallel, as separate pathways to establish proper hair cell orientation. Our data suggest that coordinated support cell organization is established during the formation of lateral line primordia, much earlier than the appearance of hair cells. Together, these finding reveal that hair cell orientation defects are not solely explained by defects in PCP signaling and that some hair cell phenotypes warrant reevaluation.
biorxiv developmental-biology 100-200-users 2019Postdoc X-ray in Europe 2017 Work conditions, productivity, institutional support and career outlooks, bioRxiv, 2019-01-24
1.Executive SummaryThis survey and data analysis were conducted by the European Network of Postdoctoral Associations (ENPA) with the aim of assessing the current research and work conditions, aspirations and support received by postdoctoral researchers working in Europe.The Results section is structured into three main parts. The first one describes the study sample of European postdoctoral researchers, including participants’ demographics, funding sources and income, research outputs, and teaching opportunities. The second section focuses on their professional aspirations and institutional support provided. The third part describes the level of engagement of postdoctoral researchers and their institutions in working towards better research conditions and career development, and what initiatives are emerging within this community.Our Conclusions section pulls together this comprehensive analysis, highlighting some of the most concerning issues currently affecting postdoctoral researchers in Europe. We also make a number of recommendations that would significantly improve the career expectations and aspirations of postdoctoral researchers. These are listed below.Conclusions and recommendations<jatslist list-type=order><jatslist-item>Longer postdoctoral periods in Southern Europe despite higher publication metricsRecommendation Institutions in Southern Europe should develop clear criteria to support postdoctoral researchers’ career progression.<jatslist-item><jatslist-item>Southern and Eastern Europe pay the lowest salaries and have the lowest number of foreign postdoctoral researchersRecommendation The salary differences across European countries should be addressed as this could be a barrier to mobility and knowledge exchange from higher to lower pay regions.<jatslist-item><jatslist-item>Lack of access to funding is a significant concern of postdoctoral researchersRecommendation Discrepancies in access to funding should be minimized across the different European areas.<jatslist-item><jatslist-item>Postdoctoral researchers in Europe work longer hours than required by contractRecommendation The culture of overwork in the research environment should be addressed in order to protect researchers against the risks associated with long hours at work.<jatslist-item><jatslist-item>The majority of full-time postdoctoral work contracts includes an exclusivity clauseRecommendation Inclusion of exclusivity clauses in contracts for postdoctoral researchers should be optional in order to allow them to enhance their employability outside academia.<jatslist-item><jatslist-item>Postdoctoral researchers’ career development is poorly supported by their institutionsRecommendation Postdoctoral researchers’ career prospects and career management should be much more supported by institutions in coordination with postdoctoral associations.<jatslist-item><jatslist-item>Lack of postdoctoral representation in governance is linked to unclear institutional duties and rightsRecommendation Institutional governance bodies should include postdoctoral researcher representatives. This would ensure that the views of this vital staff group are heard, as well as making postdoctoral researchers feel more engaged with their own institutions. A flexible and proactive communication strategy at the institution and research group level should be developed, taking into account the sometimes transient nature of postdoctoral researchers’ posts.<jatslist-item><jatslist-item>Researchers show higher engagement with their local postdoctoral associations than with workers’ unionsRecommendation Postdoctoral associations are an essential way to advocate for postdoctoral researchers at the governance level. Institutions should engage with, promote and support the work of postdoctoral associations.<jatslist-item>
biorxiv scientific-communication-and-education 100-200-users 2019Selection for antibiotic resistance is reduced when embedded in a natural microbial community Supplemental Figure 1-4, bioRxiv, 2019-01-24
Antibiotic resistance has emerged as one of the most pressing, global threats to public health. In single-species experiments selection for antibiotic resistance occurs at very low antibiotic concentrations. However, it is unclear how far these findings can be extrapolated to natural environments, where species are embedded within complex communities. We competed isogenic strains of Escherichia coli, differing exclusively in a single chromosomal resistance determinant, in the presence and absence of a pig fecal microbial community across a gradient of antibiotic concentration for two relevant antibiotics gentamicin and kanamycin. We show that the minimal selective concentration was increased by more than one order of magnitude for both antibiotics when embedded in the community. We identified two general mechanisms were responsible for the increase in minimal selective concentration an increase in the cost of resistance and a protective effect of the community for the susceptible phenotype. These findings have implications for our understanding of the evolution and selection of antibiotic resistance, and can inform future risk assessment efforts on antibiotic concentrations.
biorxiv microbiology 100-200-users 2019Selection for antibiotic resistance is reduced when embedded in a natural microbial community, bioRxiv, 2019-01-24
AbstractAntibiotic resistance has emerged as one of the most pressing, global threats to public health. In single-species experiments selection for antibiotic resistance occurs at very low antibiotic concentrations. However, it is unclear how far these findings can be extrapolated to natural environments, where species are embedded within complex communities. We competed isogenic strains of Escherichia coli, differing exclusively in a single chromosomal resistance determinant, in the presence and absence of a pig fecal microbial community across a gradient of antibiotic concentration for two relevant antibiotics gentamicin and kanamycin. We show that the minimal selective concentration was increased by more than one order of magnitude for both antibiotics when embedded in the community. We identified two general mechanisms were responsible for the increase in minimal selective concentration an increase in the cost of resistance and a protective effect of the community for the susceptible phenotype. These findings have implications for our understanding of the evolution and selection of antibiotic resistance, and can inform future risk assessment efforts on antibiotic concentrations.
biorxiv microbiology 100-200-users 2019C99 selectively accumulates in vulnerable neurons in Alzheimer’s disease, bioRxiv, 2019-01-23
ABSTRACTIntroductionThe levels and distribution of amyloid deposits in the brain does not correlate well with Alzheimer’s disease (AD) progression. Therefore, it is likely that Amyloid-precursor-protein proteolytic fragments other than beta-amyloid contribute to the onset of AD.MethodsWe developed a sensitive assay adapted to the detection of C99, the direct precursor of beta-amyloid. Three postmortem groups were studied control with normal and stable cognition; subjects with moderate AD, and individuals with severe AD. The amount of C99 and beta-amyloid was quantified and correlated with the severity of AD.ResultsC99 accumulates in vulnerable neurons, and its levels correlate with the degree of cognitive impairment in patients suffering from AD. In contrast, beta-amyloid levels are increased in both vulnerable and resistant brain areas.DiscussionThese results raise the possibility that C99, rather than beta-amyloid plaques, is responsible for the death of nerve cells in Alzheimer’s disease.
biorxiv neuroscience 100-200-users 2019