94 research outputs found
The problem of the acceleration of electrons of the outer radiation belt and magnetospheric substorms
Transcriptomic Characterization of a Synergistic Genetic Interaction during Carpel Margin Meristem Development in Arabidopsis thaliana
In flowering plants the gynoecium is the female reproductive structure. In Arabidopsis thaliana ovules initiate within the developing gynoecium from meristematic tissue located along the margins of the floral carpels. When fertilized the ovules will develop into seeds. SEUSS (SEU) and AINTEGUMENTA (ANT) encode transcriptional regulators that are critical for the proper formation of ovules from the carpel margin meristem (CMM). The synergistic loss of ovule initiation observed in the seu ant double mutant suggests that SEU and ANT share overlapping functions during CMM development. However the molecular mechanism underlying this synergistic interaction is unknown. Using the ATH1 transcriptomics platform we identified transcripts that were differentially expressed in seu ant double mutant relative to wild type and single mutant gynoecia. In particular we sought to identify transcripts whose expression was dependent on the coordinated activities of the SEU and ANT gene products. Our analysis identifies a diverse set of transcripts that display altered expression in the seu ant double mutant tissues. The analysis of overrepresented Gene Ontology classifications suggests a preponderance of transcriptional regulators including multiple members of the REPRODUCTIVE MERISTEMS (REM) and GROWTH-REGULATING FACTOR (GRF) families are mis-regulated in the seu ant gynoecia. Our in situ hybridization analyses indicate that many of these genes are preferentially expressed within the developing CMM. This study is the first step toward a detailed description of the transcriptional regulatory hierarchies that control the development of the CMM and ovule initiation. Understanding the regulatory hierarchy controlled by SEU and ANT will clarify the molecular mechanism of the functional redundancy of these two genes and illuminate the developmental and molecular events required for CMM development and ovule initiation
Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions
<p>Abstract</p> <p>Background</p> <p>Reliable transcription factor binding site (TFBS) prediction methods are essential for computer annotation of large amount of genome sequence data. However, current methods to predict TFBSs are hampered by the high false-positive rates that occur when only sequence conservation at the core binding-sites is considered.</p> <p>Results</p> <p>To improve this situation, we have quantified the performance of several Position Weight Matrix (PWM) algorithms, using exhaustive approaches to find their optimal length and position. We applied these approaches to bio-medically important TFBSs involved in the regulation of cell growth and proliferation as well as in inflammatory, immune, and antiviral responses (NF-ÎșB, ISGF3, IRF1, STAT1), obesity and lipid metabolism (PPAR, SREBP, HNF4), regulation of the steroidogenic (SF-1) and cell cycle (E2F) genes expression. We have also gained extra specificity using a method, entitled SiteGA, which takes into account structural interactions within TFBS core and flanking regions, using a genetic algorithm (GA) with a discriminant function of locally positioned dinucleotide (LPD) frequencies.</p> <p>To ensure a higher confidence in our approach, we applied resampling-jackknife and bootstrap tests for the comparison, it appears that, optimized PWM and SiteGA have shown similar recognition performances. Then we applied SiteGA and optimized PWMs (both separately and together) to sequences in the Eukaryotic Promoter Database (EPD). The resulting SiteGA recognition models can now be used to search sequences for BSs using the web tool, SiteGA.</p> <p>Analysis of dependencies between close and distant LPDs revealed by SiteGA models has shown that the most significant correlations are between close LPDs, and are generally located in the core (footprint) region. A greater number of less significant correlations are mainly between distant LPDs, which spanned both core and flanking regions. When SiteGA and optimized PWM models were applied together, this substantially reduced false positives at least at higher stringencies.</p> <p>Conclusion</p> <p>Based on this analysis, SiteGA adds substantial specificity even to optimized PWMs and may be considered for large-scale genome analysis. It adds to the range of techniques available for TFBS prediction, and EPD analysis has led to a list of genes which appear to be regulated by the above TFs.</p
The formation of human populations in South and Central Asia
By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilizationâs decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages
Observation of B(s)0âJ/ÏppÂŻ decays and precision measurements of the B(s)0 masses
The first observation of the decays
B
0
(
s
)
â
J
/
Ï
p
ÂŻ
p
is reported, using proton-proton collision data corresponding to an integrated luminosity of
5.2
â
â
fb
â
1
, collected with the LHCb detector. These decays are suppressed due to limited available phase space, as well as due to Okubo-Zweig-Iizuka or Cabibbo suppression. The measured branching fractions are
B
(
B
0
â
J
/
Ï
p
ÂŻ
p
)
=
[
4.51
±
0.40
(
stat
)
±
0.44
(
syst
)
]
Ă
10
â
7
,
B
(
B
0
s
â
J
/
Ï
p
ÂŻ
p
)
=
[
3.58
±
0.19
(
stat
)
±
0.39
(
syst
)
]
Ă
10
â
6
. For the
B
0
s
meson, the result is much higher than the expected value of
O
(
10
â
9
)
. The small available phase space in these decays also allows for the most precise single measurement of both the
B
0
mass as
5279.74
±
0.30
(
stat
)
±
0.10
(
syst
)
â
â
MeV
and the
B
0
s
mass as
5366.85
±
0.19
(
stat
)
±
0.13
(
syst
)
â
â
MeV
Measurement of D s <sup>±</sup> production asymmetry in pp collisions at âs=7 and 8 TeV
The inclusive production asymmetry is measured in collisions
collected by the LHCb experiment at centre-of-mass energies of
and 8 TeV. Promptly produced mesons are used, which decay as
, with . The measurement is
performed in bins of transverse momentum, , and rapidity, ,
covering the range GeV and . No kinematic
dependence is observed. Evidence of nonzero production asymmetry is
found with a significance of 3.3 standard deviations.Comment: All figures and tables, along with any supplementary material and
additional information, are available at
https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2018-010.htm
Observation of the decay Î <sub>b</sub> <sup>0</sup> âââÏ(2S)pÏ<sup>â</sup>
International audienceThe Cabibbo-suppressed decay Î âââÏ(2S)pÏ is observed for the first time using a data sample collected by the LHCb experiment in proton-proton collisions corresponding to 1.0, 2.0 and 1.9 fb of integrated luminosity at centre-of-mass energies of 7, 8 and 13 TeV, respectively. The Ï(2S) mesons are reconstructed in the ΌΌ final state. The branching fraction with respect to that of the Î âââÏ(2S)pK decay mode is measured to b
Search for CP violation in Îb0âpKâ and Îb0âpÏâ decays
A search for CP violation in Îb0âpKâ and Îb0âpÏâ decays is presented using a sample of pp collisions collected with the LHCb detector and corresponding to an integrated luminosity of 3.0fbâ1. The CP -violating asymmetries are measured to be ACPpKâ=â0.020±0.013±0.019 and ACPpÏâ=â0.035±0.017±0.020, and their difference ACPpKââACPpÏâ=0.014±0.022±0.010, where the first uncertainties are statistical and the second systematic. These are the most precise measurements of such asymmetries to date
Evidence for an nc(1S)ff- resonance in B0 yc(1S)K+ decays
A Dalitz plot analysis of B0âηc(1S)K+Ï- decays is performed using data samples of pp collisions collected with the LHCb detector at centre-of-mass energies of s=7,8 and 13TeV , corresponding to a total integrated luminosity of 4.7fb-1 . A satisfactory description of the data is obtained when including a contribution representing an exotic ηc(1S)Ï- resonant state. The significance of this exotic resonance is more than three standard deviations, while its mass and width are 4096±20-22+18MeV and 152±58-35+60MeV , respectively. The spin-parity assignments JP=0+ and JP=1- are both consistent with the data. In addition, the first measurement of the B0âηc(1S)K+Ï- branching fraction is performed and gives B(B0âηc(1S)K+Ï-)=(5.73±0.24±0.13±0.66)Ă10-4, where the first uncertainty is statistical, the second systematic, and the third is due to limited knowledge of external branching fractions
Search for dark photons produced in 13 TeV collisions
Searches are performed for both promptlike and long-lived dark photons,
A
0
, produced in proton-proton
collisions at a center-of-mass energy of 13 TeV, using
A
0
â
Ό
ĂŸ
Ό
â
decays and a data sample corresponding
to an integrated luminosity of
1
.
6
fb
â
1
collected with the LHCb detector. The promptlike
A
0
search covers
the mass range from near the dimuon threshold up to 70 GeV, while the long-lived
A
0
search is restricted to
the low-mass region
214
<m
Ă°
A
0
Ă
<
350
MeV. No evidence for a signal is found, and 90% confidence
level exclusion limits are placed on the
Îł
â
A
0
kinetic-mixing strength. The constraints placed on promptlike
dark photons are the most stringent to date for the mass range
10
.
6
<m
Ă°
A
0
Ă
<
70
GeV, and are
comparable to the best existing limits for
m
Ă°
A
0
Ă
<
0
.
5
GeV. The search for long-lived dark photons is the
first to achieve sensitivity using a displaced-vertex signature
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