602 research outputs found
Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication
<p>Abstract</p> <p>Background</p> <p>Positions of spliceosomal introns are often conserved between remotely related genes. Introns that reside in non-conserved positions are either novel or remnants of frequent losses of introns in some evolutionary lineages. A recent gain of such introns is difficult to prove. However, introns verified as novel are needed to evaluate contemporary processes of intron gain.</p> <p>Results</p> <p>We identified 25 unambiguous cases of novel intron positions in 31 Drosophila genes that exhibit near intron pairs (NIPs). Here, a NIP consists of an ancient and a novel intron position that are separated by less than 32 nt. Within a single gene, such closely-spaced introns are very unlikely to have coexisted. In most cases, therefore, the ancient intron position must have disappeared in favour of the novel one. A survey for NIPs among 12 Drosophila genomes identifies intron sliding (migration) as one of the more frequent causes of novel intron positions. Other novel introns seem to have been gained by regional tandem duplications of coding sequences containing a proto-splice site.</p> <p>Conclusions</p> <p>Recent intron gains sometimes appear to have arisen by duplication of exonic sequences and subsequent intronization of one of the copies. Intron migration and exon duplication together may account for a significant amount of novel intron positions in conserved coding sequences.</p
The Genome of the Stick Insect Medauroidea extradentata Is Strongly Methylated within Genes and Repetitive DNA
BACKGROUND: Cytosine DNA methylation has been detected in many eukaryotic organisms and has been shown to play an important role in development and disease of vertebrates including humans. Molecularly, DNA methylation appears to be involved in the suppression of initiation or of elongation of transcription. Resulting organismal functions are suggested to be the regulation of gene silencing, the suppression of transposon activity and the suppression of initiation of transcription within genes. However, some data concerning the distribution of methylcytosine in insect species appear to contradict such roles. PRINCIPAL FINDINGS: By comparison of MspI and HpaII restriction patterns in genomic DNA of several insects we show that stick insects (Phasmatodea) have highly methylated genomes. We isolated methylated DNA fragments from the Vietnamese Walking Stick Medauroidea extradentata (formerly known as Baculum extradentatum) and demonstrated that most of the corresponding sequences are repetitive. Bisulfite sequencing of one of these fragments and of parts of conserved protein-coding genes revealed a methylcytosine content of 12.6%, mostly found at CpG, but also at CpT and CpA dinucleotides. Corresponding depletions of CpG and enrichments of TpG and CpA dinucleotides in some highly conserved protein-coding genes of Medauroidea reach a similar degree as in vertebrates and show that CpG methylation has occurred in the germline of these insects. CONCLUSIONS: Using four different methods, we demonstrate that the genome of Medauroidea extradentata is strongly methylated. Both repetitive DNA and coding genes appear to contain high levels of methylcytosines. These results argue for similar functions of DNA methylation in stick insects as those already known for vertebrates
Multidifferential study of identified charged hadron distributions in -tagged jets in proton-proton collisions at 13 TeV
Jet fragmentation functions are measured for the first time in proton-proton
collisions for charged pions, kaons, and protons within jets recoiling against
a boson. The charged-hadron distributions are studied longitudinally and
transversely to the jet direction for jets with transverse momentum 20 GeV and in the pseudorapidity range . The
data sample was collected with the LHCb experiment at a center-of-mass energy
of 13 TeV, corresponding to an integrated luminosity of 1.64 fb. Triple
differential distributions as a function of the hadron longitudinal momentum
fraction, hadron transverse momentum, and jet transverse momentum are also
measured for the first time. This helps constrain transverse-momentum-dependent
fragmentation functions. Differences in the shapes and magnitudes of the
measured distributions for the different hadron species provide insights into
the hadronization process for jets predominantly initiated by light quarks.Comment: All figures and tables, along with machine-readable versions and any
supplementary material and additional information, are available at
https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2022-013.html (LHCb
public pages
Study of the decay
The decay is studied
in proton-proton collisions at a center-of-mass energy of TeV
using data corresponding to an integrated luminosity of 5
collected by the LHCb experiment. In the system, the
state observed at the BaBar and Belle experiments is
resolved into two narrower states, and ,
whose masses and widths are measured to be where the first uncertainties are statistical and the second
systematic. The results are consistent with a previous LHCb measurement using a
prompt sample. Evidence of a new
state is found with a local significance of , whose mass and width
are measured to be and , respectively. In addition, evidence of a new decay mode
is found with a significance of
. The relative branching fraction of with respect to the
decay is measured to be , where the first
uncertainty is statistical, the second systematic and the third originates from
the branching fractions of charm hadron decays.Comment: All figures and tables, along with any supplementary material and
additional information, are available at
https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2022-028.html (LHCb
public pages
Measurement of the ratios of branching fractions and
The ratios of branching fractions
and are measured, assuming isospin symmetry, using a
sample of proton-proton collision data corresponding to 3.0 fb of
integrated luminosity recorded by the LHCb experiment during 2011 and 2012. The
tau lepton is identified in the decay mode
. The measured values are
and
, where the first uncertainty is
statistical and the second is systematic. The correlation between these
measurements is . Results are consistent with the current average
of these quantities and are at a combined 1.9 standard deviations from the
predictions based on lepton flavor universality in the Standard Model.Comment: All figures and tables, along with any supplementary material and
additional information, are available at
https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2022-039.html (LHCb
public pages
MspI/HpaII restriction analysis of selected insect species.
<p>Equivalent amounts of insect genomic DNA were digested with MspI (black line) and HpaII (red line) and separated at adjacent lanes of an agarose gel. The ethidium bromide signals of both lanes were plotted in different colors into one plot. Results are shown for <i>Drosophila melanogaster, Bombyx mori, Apis mellifera</i> and the walking sticks <i>Sipyloidea sipylus</i> and <i>Medauroidea extradentata</i>.</p
CpG, TpG and CpA dinucleotide abundances (observed/expected) in different metazoan genes.
<p>Orthologous fragments of 5 strongly conserved, protein-coding genes were used. The species are ordered according to CpG depletion. The lengths of the analyzed sequences lie between 1846 and 3989 bp. Stars mark significant deviances from the expected relation (1.00) according to a two-sided, exact test.</p><p>*0.05≥p>0.01.</p><p>**0.01≥p>0.001.</p><p>***0.001≥p.</p
Southern blots showing methylation and repetitivity of selected DNA fragments.
<p>Both blots contain five enzyme lanes. CpG methylation is demonstrated by a partial signal shift from lower (MspI lane) to higher molecular weights (HpaII lane). The existence of more than two signals in the lanes may be due to restriction site variability between different copies of the repetitive sequences or due to methylation of the outer cytosine of some MspI sites, which renders such sites resistent to MspI. (A) The 730 bp signal corresponds to the expected internal MspI/HpaII fragment as shown below for the 1862 bp fragment 3–20 (FM985962). (B) The 615 bp signal may correspond to the longer MspI/HpaII fragment of the 835 bp fragment 5–11 (FM985964).</p
Relative dinucleotide abundances (observed/expected) in different sequence classes of the <i>Medauroidea extradentata</i> genome.
<p>Stars mark significant deviances from the expected relation (1.00) according to a two-sided, exact test.</p><p>*0.05≥p>0.01.</p><p>**0.01≥p>0.001.</p><p>***0.001≥p.</p
Differential restriction analysis of <i>Medauroidea extradentata</i>.
<p>Equivalent amounts of genomic DNA were digested and analyzed using MspI (Ms), HpaII (Hp), MboI (Mb), Bsp143I (Bs) and McrBC. For comparison, equivalent genomic digestions using McrBC and DNA from <i>Drosophila melanogaster</i> (Dr), <i>Medauroidea extradentata</i> (Me) and <i>Homo sapiens</i> (Ho) are shown. The track labelled L contains GeneRuler® Ladder Mix (Fermentas).</p
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