25 research outputs found
Whole-Genome Immunoinformatic Analysis of F. tularensis: Predicted CTL Epitopes Clustered in Hotspots Are Prone to Elicit a T-Cell Response
The cellular arm of the immune response plays a central role in the defense against intracellular pathogens, such as F. tularensis. To date, whole genome immunoinformatic analyses were limited either to relatively small genomes (e.g. viral) or to preselected subsets of proteins in complex pathogens. Here we present, for the first time, an unbiased bacterial global immunoinformatic screen of the 1740 proteins of F. tularensis subs. holarctica (LVS), aiming at identification of immunogenic peptides eliciting a CTL response. The very large number of predicted MHC class I binders (about 100,000, IC50 of 1000 nM or less) required the design of a strategy for further down selection of CTL candidates. The approach developed focused on mapping clusters rich in overlapping predicted epitopes, and ranking these “hotspot” regions according to the density of putative binding epitopes. Limited by the experimental load, we selected to screen a library of 1240 putative MHC binders derived from 104 top-ranking highly dense clusters. Peptides were tested for their ability to stimulate IFNγ secretion from splenocytes isolated from LVS vaccinated C57BL/6 mice. The majority of the clusters contained one or more CTL responder peptides and altogether 127 novel epitopes were identified, of which 82 are non-redundant. Accordingly, the level of success in identification of positive CTL responders was 17–25 fold higher than that found for a randomly selected library of 500 predicted MHC binders (IC50 of 500 nM or less). Most proteins (ca. 2/3) harboring the highly dense hotspots are membrane-associated. The approach for enrichment of true positive CTL epitopes described in this study, which allowed for over 50% increase in the dataset of known T-cell epitopes of F. tularensis, could be applied in immunoinformatic analyses of many other complex pathogen genomes
ExoClock Project III: 450 new exoplanet ephemerides from ground and space observations
The ExoClock project has been created with the aim of increasing the
efficiency of the Ariel mission. It will achieve this by continuously
monitoring and updating the ephemerides of Ariel candidates over an extended
period, in order to produce a consistent catalogue of reliable and precise
ephemerides. This work presents a homogenous catalogue of updated ephemerides
for 450 planets, generated by the integration of 18000 data points from
multiple sources. These sources include observations from ground-based
telescopes (ExoClock network and ETD), mid-time values from the literature and
light-curves from space telescopes (Kepler/K2 and TESS). With all the above, we
manage to collect observations for half of the post-discovery years (median),
with data that have a median uncertainty less than one minute. In comparison
with literature, the ephemerides generated by the project are more precise and
less biased. More than 40\% of the initial literature ephemerides had to be
updated to reach the goals of the project, as they were either of low precision
or drifting. Moreover, the integrated approach of the project enables both the
monitoring of the majority of the Ariel candidates (95\%), and also the
identification of missing data. The dedicated ExoClock network effectively
supports this task by contributing additional observations when a gap in the
data is identified. These results highlight the need for continuous monitoring
to increase the observing coverage of the candidate planets. Finally, the
extended observing coverage of planets allows us to detect trends (TTVs -
Transit Timing Variations) for a sample of 19 planets. All products, data, and
codes used in this work are open and accessible to the wider scientific
community.Comment: Recommended for publication to ApJS (reviewer's comments
implemented). Main body: 13 pages, total: 77 pages, 7 figures, 7 tables. Data
available at http://doi.org/10.17605/OSF.IO/P298