520 research outputs found
: a cis antisense RNA operates in trans in S. aureus
International audienceAntisense RNAs (asRNAs) pair to RNAs expressed from the complementary strand, and their functions are thought to depend on nucleotide overlap with genes on the opposite strand. There is little information on the roles and mechanisms of asRNAs. We show that a cis asRNA acts in trans, using a domain outside its target complementary sequence. SprA1 small regulatory RNA (sRNA) and SprA1(AS) asRNA are concomitantly expressed in S. aureus. SprA1(AS) forms a complex with SprA1, preventing translation of the SprA1-encoded open reading frame by occluding translation initiation signals through pairing interactions. The SprA1 peptide sequence is within two RNA pseudoknots. SprA1(AS) represses production of the SprA1-encoded cytolytic peptide in trans, as its overlapping region is dispensable for regulation. These findings demonstrate that sometimes asRNA functional domains are not their gene-target complementary sequences, suggesting there is a need for mechanistic re-evaluation of asRNAs expressed in prokaryotes and eukaryotes
Growth Parameter Components of Adaptive Specificity during Experimental Evolution of the UVR-Inducible Mutator Pseudomonas cichorii 302959
BACKGROUND: Mutagenic DNA repair (MDR) transiently increases mutation rate through the activation of low-fidelity repair polymerases in response to specific, DNA-damaging environmental stress conditions such as ultraviolet radiation (UVR) exposure. These repair polymerases also confer UVR tolerance, intimately linking mutability and survival in bacteria that colone habitats subject to regular UVR exposure. METHODOLOGY/PRINCIPAL FINDINGS: Here, we investigate adaptive specificity in experimental lineages of the highly UVR-mutable epiphytic plant pathogen Pseudomonas cichorii 302959. Relative fitness measurements of isolates and population samples from replicate lineages indicated that adaptive improvements emerged early in all lineages of our evolution experiment and specific increases in relative fitness correlated with distinct improvements in doubling and lag times. Adaptive improvements gained under UVR and non-UVR conditions were acquired preferentially, and differentially contributed to relative fitness under varied growth conditions. CONCLUSIONS: These results support our earlier observations that MDR activation may contribute to gains in relative fitness without impeding normal patterns of adaptive specificity in P. cichorii 302959
High performance computing for haplotyping: Models and platforms
\u3cp\u3eThe reconstruction of the haplotype pair for each chromosome is a hot topic in Bioinformatics and Genome Analysis. In Haplotype Assembly (HA), all heterozygous Single Nucleotide Polymorphisms (SNPs) have to be assigned to exactly one of the two chromosomes. In this work, we outline the state-of-the-art on HA approaches and present an in-depth analysis of the computational performance of GenHap, a recent method based on Genetic Algorithms. GenHap was designed to tackle the computational complexity of the HA problem by means of a divide-et-impera strategy that effectively leverages multi-core architectures. In order to evaluate GenHap’s performance, we generated different instances of synthetic (yet realistic) data exploiting empirical error models of four different sequencing platforms (namely, Illumina NovaSeq, Roche/454, PacBio RS II and Oxford Nanopore Technologies MinION). Our results show that the processing time generally decreases along with the read length, involving a lower number of sub-problems to be distributed on multiple cores.\u3c/p\u3
Measurement of the mass and lifetime of the baryon
A proton-proton collision data sample, corresponding to an integrated
luminosity of 3 fb collected by LHCb at and 8 TeV, is used
to reconstruct , decays. Using the , decay mode for calibration, the lifetime ratio and absolute
lifetime of the baryon are measured to be \begin{align*}
\frac{\tau_{\Omega_b^-}}{\tau_{\Xi_b^-}} &= 1.11\pm0.16\pm0.03, \\
\tau_{\Omega_b^-} &= 1.78\pm0.26\pm0.05\pm0.06~{\rm ps}, \end{align*} where the
uncertainties are statistical, systematic and from the calibration mode (for
only). A measurement is also made of the mass difference,
, and the corresponding mass, which
yields \begin{align*} m_{\Omega_b^-}-m_{\Xi_b^-} &= 247.4\pm3.2\pm0.5~{\rm
MeV}/c^2, \\ m_{\Omega_b^-} &= 6045.1\pm3.2\pm 0.5\pm0.6~{\rm MeV}/c^2.
\end{align*} These results are consistent with previous measurements.Comment: 11 pages, 5 figures, All figures and tables, along with any
supplementary material and additional information, are available at
https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2016-008.htm
Study of decays to the final state and evidence for the decay
A study of decays is performed for the first time
using data corresponding to an integrated luminosity of 3.0
collected by the LHCb experiment in collisions at centre-of-mass energies
of and TeV. Evidence for the decay
is reported with a significance of 4.0 standard deviations, resulting in the
measurement of
to
be .
Here denotes a branching fraction while and
are the production cross-sections for and mesons.
An indication of weak annihilation is found for the region
, with a significance of
2.4 standard deviations.Comment: All figures and tables, along with any supplementary material and
additional information, are available at
https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2016-022.html,
link to supplemental material inserted in the reference
Observation of resonances consistent with pentaquark states in decays
Observations of exotic structures in the channel, that we refer to
as pentaquark-charmonium states, in decays are
presented. The data sample corresponds to an integrated luminosity of 3/fb
acquired with the LHCb detector from 7 and 8 TeV pp collisions. An amplitude
analysis is performed on the three-body final-state that reproduces the
two-body mass and angular distributions. To obtain a satisfactory fit of the
structures seen in the mass spectrum, it is necessary to include two
Breit-Wigner amplitudes that each describe a resonant state. The significance
of each of these resonances is more than 9 standard deviations. One has a mass
of MeV and a width of MeV, while the second
is narrower, with a mass of MeV and a width of MeV. The preferred assignments are of opposite parity, with one
state having spin 3/2 and the other 5/2.Comment: 48 pages, 18 figures including the supplementary material, v2 after
referee's comments, now 19 figure
Model-independent evidence for contributions to decays
The data sample of decays acquired with the
LHCb detector from 7 and 8~TeV collisions, corresponding to an integrated
luminosity of 3 fb, is inspected for the presence of or
contributions with minimal assumptions about
contributions. It is demonstrated at more than 9 standard deviations that
decays cannot be described with
contributions alone, and that contributions play a dominant role in
this incompatibility. These model-independent results support the previously
obtained model-dependent evidence for charmonium-pentaquark
states in the same data sample.Comment: 21 pages, 12 figures (including the supplemental section added at the
end
Measurement of the lifetime
Using a data set corresponding to an integrated luminosity of ,
collected by the LHCb experiment in collisions at centre-of-mass energies
of 7 and 8 TeV, the effective lifetime in the
decay mode, , is measured to be ps. Assuming
conservation, corresponds to the lifetime of the light
mass eigenstate. This is the first measurement of the effective
lifetime in this decay mode.Comment: All figures and tables, along with any supplementary material and
additional information, are available at
https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2016-017.htm
Measurements of long-range near-side angular correlations in TeV proton-lead collisions in the forward region
Two-particle angular correlations are studied in proton-lead collisions at a
nucleon-nucleon centre-of-mass energy of TeV, collected
with the LHCb detector at the LHC. The analysis is based on data recorded in
two beam configurations, in which either the direction of the proton or that of
the lead ion is analysed. The correlations are measured in the laboratory
system as a function of relative pseudorapidity, , and relative
azimuthal angle, , for events in different classes of event
activity and for different bins of particle transverse momentum. In
high-activity events a long-range correlation on the near side, , is observed in the pseudorapidity range . This
measurement of long-range correlations on the near side in proton-lead
collisions extends previous observations into the forward region up to
. The correlation increases with growing event activity and is found
to be more pronounced in the direction of the lead beam. However, the
correlation in the direction of the lead and proton beams are found to be
compatible when comparing events with similar absolute activity in the
direction analysed.Comment: All figures and tables, along with any supplementary material and
additional information, are available at
https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2015-040.htm
Measurement of the branching fraction ratio
Using collision data collected by LHCb at center-of-mass energies
= 7 TeV and 8 TeV, corresponding to an integrated luminosity of 3
fb, the ratio of the branching fraction of the decay relative to that of the
decay is measured to be 0.268 0.032 (stat) 0.007 (syst) 0.006
(BF). The first uncertainty is statistical, the second is systematic, and the
third is due to the uncertainties on the branching fractions of the and decays. This
measurement is consistent with the previous LHCb result, and the statistical
uncertainty is halved.Comment: 17 pages including author list, 2 figure
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