Contributors: aswin Sundarakrishnan
... The data associated with this manuscript is available here.
Contributors: Sundar Nagaswamy, Amudha j
... First set to secondary set. Secondary set to third set. Third set to fourth set.
Contributors: Sundar Nagaswamy, Amudha j
... Bonding between metals test
Contributors: Daniel Sorensen
... Raw data set for Vit 105 to titanium laser weld manuscript
Raw images for defective replication stress response is inherently linked to the cancer stem cell phenotype
Contributors: Daniel McGrail
... Raw images/blots for "Defective replication stress response is inherently linked to the cancer stem cell phenotype"
Contributors: Yungang Liu
... Raw experimental data and associate plots, primarily including results of micronucleus tests, Hprt mutagenicity assays, CCK-8 cytotoxicity assays, q-PCR, and Westernblotting assays.
Contributors: Edoardo Paluan
... The aim of the project is to create an optical interferometer which can detect the acoustic analogue of a supernova explosion. The fingerprint of an acoustic wave propagating from a diapason will be measured. A Michelson Morley interferometer1 will be used, whereby analysis of the interference pattern will allow for the calculation of the frequency of the diapason.
Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation
Contributors: Krin, Evelyne, Pierlé, Sebastian Aguilar, Sismeiro, Odile, Jagla, Bernd, Dillies, Marie-Agnès, Varet, Hugo, Irazoki, Oihane, Campoy, Susana, Rouy, Zoé, Cruveiller, Stéphane
... Background: The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment.Results: Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5'UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369–1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection.Conclusions: We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is conserved among Vibrio species. Furthermore, this specific co-localization is found in other γ-proteobacteria for genes recN-smpA and rmuC-tatABC, suggesting SOS regulon conservation in this phylum. Finally, we comment on the limitations of widespread NGS approaches for identification of all RNA species in bacteria.
Data from: Effector gene birth in plant parasitic nematodes: neofunctionalization of a housekeeping glutathione synthetase gene
Contributors: Lilley, Catherine J., Maqbool, Abbas, Wu, Duqing, Yusup, Hazijah B., Jones, Laura M., Birch, Paul R. J., Banfield, Mark J., Urwin, Peter E., Eves-van den Akker, Sebastian
... Plant pathogens and parasites are a major threat to global food security. Plant parasitism has arisen four times independently within the phylum Nematoda, resulting in at least one parasite of every major food crop in the world. Some species within the most economically important order (Tylenchida) secrete proteins termed effectors into their host during infection to re-programme host development and immunity. The precise detail of how nematodes evolve new effectors is not clear. Here we reconstruct the evolutionary history of a novel effector gene family. We show that during the evolution of plant parasitism in the Tylenchida, the housekeeping glutathione synthetase (GS) gene was extensively replicated. New GS paralogues acquired multiple dorsal gland promoter elements, altered spatial expression to the secretory dorsal gland, altered temporal expression to primarily parasitic stages, and gained a signal peptide for secretion. The gene products are delivered into the host plant cell during infection, giving rise to “GS-like effectors”. Remarkably, by solving the structure of GS-like effectors we show that during this process they have also diversified in biochemical activity, and likely represent the founding members of a novel class of GS-like enzyme. Our results demonstrate the re-purposing of an endogenous housekeeping gene to form a family of effectors with modified functions. We anticipate that our discovery will be a blueprint to understand the evolution of other plant-parasitic nematode effectors, and the foundation to uncover a novel enzymatic function.
Efficacy of different DNA and MVA prime-boost vaccination regimens against a Rift Valley fever virus (RVFV) challenge in sheep 12 weeks following vaccination
Contributors: Lorenzo, Gema, López-Gil, Elena, Ortego, Javier, Brun, Alejandro
... The aim of this work was to evaluate the immunogenicity and efficacy of DNA and MVA vaccines encoding the RVFV glycoproteins Gn and Gc in an ovine model of RVFV infection. Adult sheep of both sexes were challenged 12 weeks after the last immunization and clinical, virological, biochemical and immunological consequences, were analyzed. Strategies based on immunization with homologous DNA or heterologous DNA/MVA prime-boost were able to induce a rapid in vitro neutralizing antibody response as well as IFNγ production after in vitro virus specific re-stimulation. In these animals we observed reduced viremia levels and less clinical signs when compared with mock-immunized controls. In contrast, sheep inoculated with a homologous MVA prime-boost showed increased viremia correlating with the absence of detectable neutralizing antibody responses, despite of inducing cellular responses after the last immunization. However, faster induction of neutralizing antibodies and IFNγ production after challenge were found in this group when compared to the mock vaccinated group, indicative of a primed immune response. In conclusion, these results suggest that vaccination strategies based on DNA priming were able to mount and maintain specific anti-RVFV glycoprotein immune responses upon homologous or heterologous booster doses, warranting further optimization in large animal models of infection.