361 research outputs found
Three-dimensional organization of the human interphase nucleus
To approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic
properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics
methods. The 30 nm chromatin fibre was folded according to the Multi-Loop-Subcompartment (MLS) model, in
which ~100 kbp loops form rosettes, connected by a linker, and the Random-Walk/Giant-Loop (RW/GL)
topology, in which 1-5 Mbp loops are attached to a flexible backbone. Both the MLS and the RW/GL model
form chromosome territories but only the MLS rosettes result in distinct subcompartments visible with light
microscopy and low overlap of chromosomes, -arms and subcompartments. This morphology and the size of
subcompartments agree with the morphology found by expression of histone auto-fluorescent protein fusions
and fluorescence in situ hybridization (FISH) experiments. Even small changes of the model parameters induced
significant rearrangements of the chromatin morphology. Thus, pathological diagnoses based on this
morphology, are closely related to structural changes on the chromatin level. The position of interphase
chromosomes depends on their metaphase location, and suggests a possible origin of current experimental
findings. The chromatin density distribution of simulated confocal (CLSM) images agrees with the MLS model
and with recent experiments. The scaling behaviour of the chromatin fiber topology and morphology of CLSM
stacks revealed fine-structured multi-scaling behaviour in agreement with the model prediction. Review and
comparison of experimental to simulated spatial distance measurements between genomic markers as function of
their genomic separation also favour an MLS model with loop and linker sizes of 63 to 126 kbp. Visual
inspection of the morphology reveals also big spaces allowing high accessibility to nearly every spatial location,
due to the chromatin occupancy <30% and a mean mesh spacing of 29 to 82 nm for nuclei of 6 to 12 µm
diameter. The simulation of diffusion agreed with this structural prediction, since the mean displacement for 10
nm sized particles of ~1 to 2 µm takes place within 10 ms. Therefore, the diffusion of biological relevant tracers
is only moderately obstructed, with the degree of obstruction ranging from 2.0 to 4.0 again in experimental
agreement
Three-dimensional organization of the human interphase nucleus
To approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic
properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics
methods. The 30 nm chromatin fibre was folded according to the Multi-Loop-Subcompartment (MLS) model, in
which ~100 kbp loops form rosettes, connected by a linker, and the Random-Walk/Giant-Loop (RW/GL)
topology, in which 1-5 Mbp loops are attached to a flexible backbone. Both the MLS and the RW/GL model
form chromosome territories but only the MLS rosettes result in distinct subcompartments visible with light
microscopy and low overlap of chromosomes, -arms and subcompartments. This morphology and the size of
subcompartments agree with the morphology found by expression of histone auto-fluorescent protein fusions
and fluorescence in situ hybridization (FISH) experiments. Even small changes of the model parameters induced
significant rearrangements of the chromatin morphology. Thus, pathological diagnoses based on this
morphology, are closely related to structural changes on the chromatin level. The position of interphase
chromosomes depends on their metaphase location, and suggests a possible origin of current experimental
findings. The chromatin density distribution of simulated confocal (CLSM) images agrees with the MLS model
and with recent experiments. The scaling behaviour of the chromatin fiber topology and morphology of CLSM
stacks revealed fine-structured multi-scaling behaviour in agreement with the model prediction. Review and
comparison of experimental to simulated spatial distance measurements between genomic markers as function of
their genomic separation also favour an MLS model with loop and linker sizes of 63 to 126 kbp. Visual
inspection of the morphology reveals also big spaces allowing high accessibility to nearly every spatial location,
due to the chromatin occupancy <30% and a mean mesh spacing of 29 to 82 nm for nuclei of 6 to 12 ÎĽm
diameter. The simulation of diffusion agreed with this structural prediction, since the mean displacement for 10
nm sized particles of ~1 to 2 ÎĽm takes place within 10 ms. Therefore, the diffusion of biological relevant tracers
is only moderately obstructed, with the degree of obstruction ranging from 2.0 to 4.0 again in experimental
agreemen
Three-dimensional organization of the human interphase nucleus: Experiments compared to simulations.
Despite the successful linear sequencing of the human genome its three-dimensional structure is widely
unknown, although it is important for gene regulation and replication. For a long time the interphase nucleus has
been viewed as a 'spaghetti soup' of DNA without much internal structure, except during cell division. Only
recently has it become apparent that chromosomes occupy distinct 'territories' also in interphase. Two models for
the detailed folding of the 30 nm chromatin fibre within these territories are under debate: In the Random-
Walk/Giant-Loop-model big loops of 3 to 5 Mbp are attached to a non-DNA backbone. In the Multi-Loop-
Subcompartment (MLS) model loops of around 120 kbp are forming rosettes which are also interconnected by
the chromatin fibre. Here we show with a comparison between simulations and experiments an interdisciplinary
approach leading to a determination of the three-dimensional organization of the human genome:
For the predictions of experiments various models of human interphase chromosomes and the whole cell nucleus
were simulated with Monte Carlo and Brownian Dynamics methods. Only the MLS-model leads to the
formation of non-overlapping chromosome territories and distinct functional and dynamic subcompartments in
agreement with experiments. Fluorescence in situ hybridization is used for the specific marking of chromosome
arms and pairs of small chromosomal DNA regions. The labelling is visualized with confocal laser scanning
microscopy followed by image reconstruction procedures. Chromosome arms show only small overlap and
globular substructures as predicted by the MLS-model. The spatial distances between pairs of genomic markers
as function of their genomic separation result in a MLS-model with loop and linker sizes around 126 kbp. With
the development of GFP-fusion-proteins it is possible to study the chromatin distribution and dynamics resulting
from cell cycle, treatment by chemicals or radiation in vivo. The chromatin distributions are similar to those
found in the simulation of whole cell nuclei of the MLS-model. Fractal analysis is especially suited to quantify
the unordered and non-euclidean chromatin distribution of the nucleus. The dynamic behaviour of the chromatin
structure and the diffusion of particles in the nucleus are also closely connected to the fractal dimension. Fractal
analysis of the simulations reveal the multi-fractality of chromosomes. First fractal analysis of chromatin
distributions in vivo result in significant differences for different morphologies and might favour a MLS-modellike
chromatin distribution. Simulations of fragment distributions based on double strand breakage after carbonion
irradiation differ in different models. Here again a comparison with experiments favours a MLS-model
Quantum kinetic description of Coulomb effects in one-dimensional nano-transistors
In this article, we combine the modified electrostatics of a one-dimensional
transistor structure with a quantum kinetic formulation of Coulomb interaction
and nonequilibrium transport. A multi-configurational self-consistent Green's
function approach is presented, accounting for fluctuating electron numbers. On
this basis we provide a theory for the simulation of electronic transport and
quantum charging effects in nano-transistors, such as gated carbon nanotube and
whisker devices and one-dimensional CMOS transistors. Single-electron charging
effects arise naturally as a consequence of the Coulomb repulsion within the
channel
Three-dimensional organization of the human interphase nucleus.
To approach the three-dimensional organization of the human cell nucleus, the structural-, scaling- and dynamic
properties of interphase chromosomes and cell nuclei were simulated with Monte Carlo and Brownian Dynamics
methods. The 30 nm chromatin fibre was folded according to the Multi-Loop-Subcompartment (MLS) model, in
which ~100 kbp loops form rosettes, connected by a linker, and the Random-Walk/Giant-Loop (RW/GL)
topology, in which 1-5 Mbp loops are attached to a flexible backbone. Both the MLS and the RW/GL model
form chromosome territories but only the MLS rosettes result in distinct subcompartments visible with light
microscopy and low overlap of chromosomes, -arms and subcompartments. This morphology and the size of
subcompartments agree with the morphology found by expression of histone auto-fluorescent protein fusions
and fluorescence in situ hybridization (FISH) experiments. Even small changes of the model parameters induced
significant rearrangements of the chromatin morphology. Thus, pathological diagnoses based on this
morphology, are closely related to structural changes on the chromatin level. The position of interphase
chromosomes depends on their metaphase location, and suggests a possible origin of current experimental
findings. The chromatin density distribution of simulated confocal (CLSM) images agrees with the MLS model
and with recent experiments. The scaling behaviour of the chromatin fiber topology and morphology of CLSM
stacks revealed fine-structured multi-scaling behaviour in agreement with the model prediction. Review and
comparison of experimental to simulated spatial distance measurements between genomic markers as function of
their genomic separation also favour an MLS model with loop and linker sizes of 63 to 126 kbp. Visual
inspection of the morphology reveals also big spaces allowing high accessibility to nearly every spatial location,
due to the chromatin occupancy <30% and a mean mesh spacing of 29 to 82 nm for nuclei of 6 to 12 ÎĽm
diameter. The simulation of diffusion agreed with this structural prediction, since the mean displacement for 10
nm sized particles of ~1 to 2 ÎĽm takes place within 10 ms. Therefore, the diffusion of biological relevant tracers
is only moderately obstructed, with the degree of obstruction ranging from 2.0 to 4.0 again in experimental
agreement
Three-dimensional organization of the human interphase nucleus
Despite the successful linear sequencing of the human genome its three-dimensional structure is widely
unknown, although it is important for gene regulation and replication. For a long time the interphase nucleus has
been viewed as a 'spaghetti soup' of DNA without much internal structure, except during cell division. Only
recently has it become apparent that chromosomes occupy distinct 'territories' also in interphase. Two models for
the detailed folding of the 30 nm chromatin fibre within these territories are under debate: In the Random-
Walk/Giant-Loop-model big loops of 3 to 5 Mbp are attached to a non-DNA backbone. In the Multi-Loop-
Subcompartment (MLS) model loops of around 120 kbp are forming rosettes which are also interconnected by
the chromatin fibre. Here we show with a comparison between simulations and experiments an interdisciplinary
approach leading to a determination of the three-dimensional organization of the human genome:
For the predictions of experiments various models of human interphase chromosomes and the whole cell nucleus
were simulated with Monte Carlo and Brownian Dynamics methods. Only the MLS-model leads to the
formation of non-overlapping chromosome territories and distinct functional and dynamic subcompartments in
agreement with experiments. Fluorescence in situ hybridization is used for the specific marking of chromosome
arms and pairs of small chromosomal DNA regions. The labelling is visualized with confocal laser scanning
microscopy followed by image reconstruction procedures. Chromosome arms show only small overlap and
globular substructures as predicted by the MLS-model. The spatial distances between pairs of genomic markers
as function of their genomic separation result in a MLS-model with loop and linker sizes around 126 kbp. With
the development of GFP-fusion-proteins it is possible to study the chromatin distribution and dynamics resulting
from cell cycle, treatment by chemicals or radiation in vivo. The chromatin distributions are similar to those
found in the simulation of whole cell nuclei of the MLS-model. Fractal analysis is especially suited to quantify
the unordered and non-euclidean chromatin distribution of the nucleus. The dynamic behaviour of the chromatin
structure and the diffusion of particles in the nucleus are also closely connected to the fractal dimension. Fractal
analysis of the simulations reveal the multi-fractality of chromosomes. First fractal analysis of chromatin
distributions in vivo result in significant differences for different morphologies and might favour a MLS-modellike
chromatin distribution. Simulations of fragment distributions based on double strand breakage after carbonion
irradiation differ in different models. Here again a comparison with experiments favours a MLS-model
Simulation of Radiation-Induced Damage Distribution to evaluate Models for Higher-Order Chromosome Organisation
The structure of chromatin at the level of the 30 nm fibre has been studied in considerable detail, but little is
known about how this fibre is arranged within the interphase chromosome territory. Over the years, various
polymer models were developed to simulate chromosome structure, for example the random-walk/giant-loop
(RWGL) model, the multi-loop subcompartment (MLS) model, and the interconnected-fibre-loop model
(Friedland et al., 1999). These models differ mainly in the size and arrangement of the chromatin loops and,
correspondingly, in the predicted distribution of chromatin density within the nucleus. It occurred to us that
densely ionising radiation can be used to probe the actual distribution of chromatin density in human interphase
cells. In contrast to sparsely ionising radiation (e.g. X-rays), which induces DNA double-strand breaks (DSB)
that are distributed randomly within the nucleus, irradiation with densely ionising accelerated ions leads to
spatial clustering of DSB. This inhomogeneity in DSB localisation, together with an inhomogeneity of DNA
density within the nucleus, causes an over-dispersion in the resulting distribution of DNA fragment sizes that can
be detected by pulsed-field gel electrophoresis.
Using the above-mentioned chromosome models, we performed computer simulations to predict the DNA
fragment size distributions resulting from irradiation with accelerated ions, and compared the predicted
distributions with those obtained experimentally. We found that simulations based on the MLS model, in which
local variations in chromatin density are higher than in the other models, resulted in the best agreement between
calculation and experiment
In vivo characterization of protein-protein interactions in the AP1 system with fluorescence correlation spectroscopy (FCS).
The aim of these studies is the quantitative investigation of protein-protein interactions in the AP1 system in
vivo. First results of FCS measurements show an exchange in the nucleus of the proteins Fos-CFP and Jun-YFP
in the stably mono-transfected HeLa-Cells. This is also shown by fitting the bleaching curves measured in the
nucleus with an appropriate model. We obtained dissociation times between 10 and 20 seconds in the nucleus. In
the autocorrelation function a free and an obstructed component of diffusion are shown. For further studies
doubly transfected cells with both proteins, Fos-CFP and Jun-YFP, were prepared. These cells will now be
characterized with FCCS to investigate the protein-protein interactions. In order to obtain the dissociation rates
of the complex in the cell nucleus bleaching curves will be recorded on these cell lines. We also overexpressed
and purified Jun-YFP and Fos-CFP for in vitro studies
Biasing the perception of ambiguous vocal affect: a TMS study on frontal asymmetry
Several sources of evidence point toward a link between asymmetry of prefrontal brain activity and approach–withdrawal tendencies. Here, we tested the causal nature of this link and examined if the categorization of an ambiguous approach- or withdrawal-related vocal signal can be biased by manipulating left and right frontal neural activity. We used voice morphing of affective non-verbal vocalizations to create individually tailored affectively ambiguous stimuli on an Anger–Fear continuum—two emotions that represent extremes on the approach–withdrawal dimension. We tested perception of these stimuli after 10 min of low-frequency repetitive transcranial magnetic stimulation over left or right dorsolateral prefrontal cortex or over the vertex (control), a technique that has transient inhibitory effects on the targeted brain region. As expected, ambiguous stimuli were more likely perceived as expressing Anger (approach) than Fear (withdrawal) after right prefrontal compared with left prefrontal or control stimulation. These results provide the first evidence that the manipulation of asymmetrical activity in prefrontal cortex can change the explicit categorization of ambiguous emotional signals
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