685 research outputs found
Orientational correlations in confined DNA
We study how the orientational correlations of DNA confined to nanochannels
depend on the channel diameter D by means of Monte Carlo simulations and a
mean-field theory. This theory describes DNA conformations in the
experimentally relevant regime where the Flory-de Gennes theory does not apply.
We show how local correlations determine the dependence of the end-to-end
distance of the DNA molecule upon D. Tapered nanochannels provide the necessary
resolution in D to study experimentally how the extension of confined DNA
molecules depends upon D. Our experimental and theoretical results are in
qualitative agreement.Comment: Revised version including supplemental material, 7 pages, 8 figure
Extension of nano-confined DNA: quantitative comparison between experiment and theory
The extension of DNA confined to nanochannels has been studied intensively
and in detail. Yet quantitative comparisons between experiments and model
calculations are difficult because most theoretical predictions involve
undetermined prefactors, and because the model parameters (contour length, Kuhn
length, effective width) are difficult to compute reliably, leading to
substantial uncertainties. Here we use a recent asymptotically exact theory for
the DNA extension in the "extended de Gennes regime" that allows us to compare
experimental results with theory. For this purpose we performed new
experiments, measuring the mean DNA extension and its standard deviation while
varying the channel geometry, dye intercalation ratio, and ionic buffer
strength. The experimental results agree very well with theory at high ionic
strengths, indicating that the model parameters are reliable. At low ionic
strengths the agreement is less good. We discuss possible reasons. Our approach
allows, in principle, to measure the Kuhn length and effective width of a
single DNA molecule and more generally of semiflexible polymers in solution.Comment: Revised version, 6 pages, 2 figures, 1 table, supplementary materia
Nanoconfined circular and linear DNA - equilibrium conformations and unfolding kinetics
Studies of circular DNA confined to nanofluidic channels are relevant both
from a fundamental polymer-physics perspective and due to the importance of
circular DNA molecules in vivo. We here observe the unfolding of DNA from the
circular to linear configuration as a light-induced double strand break occurs,
characterize the dynamics, and compare the equilibrium conformational
statistics of linear and circular configurations. This is important because it
allows us to determine to which extent existing statistical theories describe
the extension of confined circular DNA. We find that the ratio of the
extensions of confined linear and circular DNA configurations increases as the
buffer concentration decreases. The experimental results fall between
theoretical predictions for the extended de Gennes regime at weaker confinement
and the Odijk regime at stronger confinement. We show that it is possible to
directly distinguish between circular and linear DNA molecules by measuring the
emission intensity from the DNA. Finally, we determine the rate of unfolding
and show that this rate is larger for more confined DNA, possibly reflecting
the corresponding larger difference in entropy between the circular and linear
configurations.Comment: 21 pages, 7 figures, 1 tabl
Advancing Genomics with OrthoDB, BUSCO, and the LEM Framework
The rapid growth of genomics data necessitates continuous advancements in bioinformatics
tools. This presentation highlights the latest updates to our toolbox, including OrthoDB v11,
BUSCO v5, and the LEM benchmarking framework.
OrthoDB (https://www.orthodb.org) is a leading resource for gene orthology and
functional annotations across diverse eukaryotes, prokaryotes, and viruses. Orthology
facilitates precise bridging of gene function knowledge within the genomics sphere.
OrthoDB v11 encompasses over 100 million genes from 18,000 prokaryotes and nearly
2,000 eukaryotes, providing extensive species coverage. The open-source OrthoLoger
software (https://orthologer.ezlab.org) allows mapping of novel gene sets to precomputed
orthologs, linking them to relevant annotations.
BUSCO (https://busco.ezlab.org) serves as a standard tool for assessing the completeness
of genome assemblies, transcriptomes, and predicted gene sets, complementing
assembly contiguity measures like N50 values. A spin-off of OrthoDB, BUSCO evaluates
the presence and coverage of marker genes, offering an evolutionarily-grounded
expectation of gene content completeness. BUSCO v5 now automatically selects the most
suitable dataset for evaluation, outperforming the popular CheckM tool. Its efficiency is
particularly evident in large eukaryotic genomes, and it is uniquely capable of assessing
both eukaryotic and prokaryotic species, making it applicable to metagenome-assembled
genomes of unknown origin.
The LEMMI (https://lemmi.ezlab.org) benchmarking framework, now in version 2, facilitates
informed software tool selection. This Live Evaluation of Methods (LEM) for Metagenome
Investigation uses a container-based approach for continuous benchmarking and effective
end-user distribution. The versatile framework can be extended to other procedures,
such as gene orthology inference with LEMOrtho (https://lemortho.ezlab.org). The LEM
benchmarking approach aims to become a community-driven effort, allowing developers
to showcase novel methods and users to access standardized, easy-to-use software. We
encourage researchers to apply this framework in their domain and welcome feedback.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Lipid-Based Passivation in Nanofluidics
Stretching DNA in nanochannels is a useful tool for direct, visual studies of genomic DNA at the single molecule level. To facilitate the study of the interaction of linear DNA with proteins in nanochannels, we have implemented a highly effective passivation scheme based on lipid bilayers. We demonstrate virtually complete long-term passivation of nanochannel surfaces to a range of relevant reagents, including streptavidin-coated quantum dots, RecA proteins, and RecA-DNA complexes. We show that the performance of the lipid bilayer is significantly better than that of standard bovine serum albumin-based passivation. Finally, we show how the passivated devices allow us to monitor single DNA cleavage events during enzymatic degradation by DNase I. We expect that our approach will open up for detailed, systematic studies of a wide range of protein-DNA interactions with high spatial and temporal resolution
First Results and Status of the LHC Test String 2
After the commissioning of String 2 Phase1 and the powering of the main circuits in autumn 2001, a short yet vigorous experimental program was carried-out to validate the final design choices for the technical systems of LHC. This program included the investigation of thermo-hydraulics of quenches quench propagation, power converter controls and tracking between power converters, as well as the measurement of currents induced in the beam screen after a quench and crossing the interconnects. Parameters significant for the LHC, such as heat loads, were also measured. During the winter shutdown the String was completed to a full cell with the addition of three pre-series dipoles (Phase 2). After a short description of the layout of Phase 1 and Phase 2, the results of the experiments are presented and the future experimental program is outlined
Study of Inclusive J/psi Production in Two-Photon Collisions at LEP II with the DELPHI Detector
Inclusive J/psi production in photon-photon collisions has been observed at
LEP II beam energies. A clear signal from the reaction gamma gamma -> J/psi+X
is seen. The number of observed N(J/psi -> mu+mu-) events is 36 +/- 7 for an
integrated luminosity of 617 pb^{-1}, yielding a cross-section of
sigma(J/psi+X) = 45 +/- 9 (stat) +/- 17 (syst) pb. Based on a study of the
event shapes of different types of gamma gamma processes in the PYTHIA program,
we conclude that (74 +/- 22)% of the observed J/psi events are due to
`resolved' photons, the dominant contribution of which is most probably due to
the gluon content of the photon.Comment: 13 pages, 8 figures, Accepted by Phys. Lett.
Measurement and Interpretation of Fermion-Pair Production at LEP energies above the Z Resonance
This paper presents DELPHI measurements and interpretations of
cross-sections, forward-backward asymmetries, and angular distributions, for
the e+e- -> ffbar process for centre-of-mass energies above the Z resonance,
from sqrt(s) ~ 130 - 207 GeV at the LEP collider. The measurements are
consistent with the predictions of the Standard Model and are used to study a
variety of models including the S-Matrix ansatz for e+e- -> ffbar scattering
and several models which include physics beyond the Standard Model: the
exchange of Z' bosons, contact interactions between fermions, the exchange of
gravitons in large extra dimensions and the exchange of sneutrino in R-parity
violating supersymmetry.Comment: 79 pages, 16 figures, Accepted by Eur. Phys. J.
A Determination of the Centre-of-Mass Energy at LEP2 using Radiative 2-fermion Events
Using e+e- -> mu+mu-(gamma) and e+e- -> qqbar(gamma) events radiative to the
Z pole, DELPHI has determined the centre-of-mass energy, sqrt{s}, using energy
and momentum constraint methods. The results are expressed as deviations from
the nominal LEP centre-of-mass energy, measured using other techniques. The
results are found to be compatible with the LEP Energy Working Group estimates
for a combination of the 1997 to 2000 data sets.Comment: 20 pages, 6 figures, Accepted by Eur. Phys. J.
Study of Leading Hadrons in Gluon and Quark Fragmentation
The study of quark jets in e+e- reactions at LEP has demonstrated that the
hadronisation process is reproduced well by the Lund string model. However, our
understanding of gluon fragmentation is less complete. In this study enriched
quark and gluon jet samples of different purities are selected in three-jet
events from hadronic decays of the Z collected by the DELPHI experiment in the
LEP runs during 1994 and 1995. The leading systems of the two kinds of jets are
defined by requiring a rapidity gap and their sum of charges is studied. An
excess of leading systems with total charge zero is found for gluon jets in all
cases, when compared to Monte Carlo Simulations with JETSET (with and without
Bose-Einstein correlations included) and ARIADNE. The corresponding leading
systems of quark jets do not exhibit such an excess. The influence of the gap
size and of the gluon purity on the effect is studied and a concentration of
the excess of neutral leading systems at low invariant masses (<~ 2 GeV/c^2) is
observed, indicating that gluon jets might have an additional hitherto
undetected fragmentation mode via a two-gluon system. This could be an
indication of a possible production of gluonic states as predicted by QCD.Comment: 19 pages, 6 figures, Accepted by Phys. Lett.
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