124 research outputs found
Unattended automatic monitoring of bondary layer structures with cost effective lidar ceilometers
The Atmospheric Monitoring Strategy for the Cherenkov Telescope Array
The Imaging Atmospheric Cherenkov Technique (IACT) is unusual in astronomy as
the atmosphere actually forms an intrinsic part of the detector system, with
telescopes indirectly detecting very high energy particles by the generation
and transport of Cherenkov photons deep within the atmosphere. This means that
accurate measurement, characterisation and monitoring of the atmosphere is at
the very heart of successfully operating an IACT system. The Cherenkov
Telescope Array (CTA) will be the next generation IACT observatory with an
ambitious aim to improve the sensitivity of an order of magnitude over current
facilities, along with corresponding improvements in angular and energy
resolution and extended energy coverage, through an array of Large (23m),
Medium (12m) and Small (4m) sized telescopes spread over an area of order
~km. Whole sky coverage will be achieved by operating at two sites: one in
the northern hemisphere and one in the southern hemisphere. This proceedings
will cover the characterisation of the candidate sites and the atmospheric
calibration strategy. CTA will utilise a suite of instrumentation and analysis
techniques for atmospheric modelling and monitoring regarding pointing
forecasts, intelligent pointing selection for the observatory operations and
for offline data correction.Comment: 6 pages. To appear in the proceedings of the Adapting to the
Atmosphere conference 201
Three-dimensional organization of chromosome territories in the human interphase nucleus
The synthesis of proteins, maintenance of structure and duplication of the eukaryotic cell itself are all fine-tuned
biochemical processes that depend on the precise structural arrangement of the cellular components. The
regulation of genes – their transcription and replication - has been shown to be connected closely to the three-
dimensional organization of the genome in the cell nucleus. Despite the successful linear sequencing of the
human genome its three-dimensional structure is widely unknown.
The nucleus of the cell has for a long time been viewed as a 'spaghetti soup' of DNA bound to various proteins
without much internal structure, except during cell division when chromosomes are condensed into separate
entities. Only recently has it become apparent that chromosomes occupy distinct 'territories' also in the
interphase, i.e. between cell divisions. In an analogy of the Bauhaus principle that "form follows function" we
believe that analyzing in which form DNA is organized in these territories will help us to understand genomic
function. We use computer models - Monte Carlo and Brownian dynamics simulations - to develop plausible
proposals for the structure of the interphase genome and compare them to experimental data. In the work
presented here, we simulate interphase chromosomes for different folding morphologies of the chromatin fiber
which is organized into loops of 100kbp to 3 Mbp that can be interconnected in various ways. The backbone of
the fiber is described by a wormlike-chain polymer whose diameter and stiffness can be estimated from
independent measurements. The implementation describes this polymer as a segmented chain with 3000 to
20000 segments for chromosome 15 depending on the phase of the simulation. The modeling is performed on a
parallel computer (IBM SP2 with 80 nodes). We also determine genomic marker distributions within the Prader-
Willi-Region on chromosome 15q11.2-13.3. For these measurements we use a fluorescence in situ hybridisation
method (in collaboration with I. Solovai, J. Craig and T. Cremer, Munich, FRG) conserving the structure of the
nucleus. As probes we use 10 kbp long lambda clones (Prof. B. Horsthemke, Essen, FRG) covering genomic
marker distances between 8 kbp and 250 kbp. The markers are detected with confocal and standing wavefield
light microscopes (in collaboration with J.Rauch, J. Bradl, C. Cremer and E.Stelzer, both Heidelberg, FRG) and
using special image reconstruction methods developed solely for this purpose (developed by R. Eils. and W.
Jaeger, Heidelberg, FRG).
Best agreement between simulations and experiments is reached for a Multi-Loop-Subcompartment model with
a loop size of 126 kbp which are forming rosetts and are linked by a chromatin linker of 126 kbp. We also
hypothesize a different folding structure for maternal versus paternal chromosome 15. In simulations of whole
cell nuclei this modell also leads to distinct chromosome territories and subcompartments. A fractal analysis of
the simulations leads to multifractal behavior in good agreement with predictions drawn from porous network
research
Confidence levels and error bars for continuous detection of mixing layer heights by ceilometer
Temporal variation of urban mixing layer height in Mexico City and Augsburg from ceilometer and SODAR measurements
Three-dimensional organization of chromosome territories in the human interphase cell nucleus.
The synthesis of proteins, maintenance of structure and duplication of the eukaryotic cell itself are all fine-tuned
biochemical processes that depend on the precise structural arrangement of the cellular components. The
regulation of genes – their transcription and replication - has been shown to be connected closely to the threedimensional
organization of the genome in the cell nucleus. Despite the successful linear sequencing of the
human genome its three-dimensional structure is widely unknown.
The nucleus of the cell has for a long time been viewed as a 'spaghetti soup' of DNA bound to various proteins
without much internal structure, except during cell division when chromosomes are condensed into separate
entities. Only recently has it become apparent that chromosomes occupy distinct 'territories' also in the
interphase, i.e. between cell divisions. In an analogy of the Bauhaus principle that "form follows function" we
believe that analyzing in which form DNA is organized in these territories will help us to understand genomic
function. We use computer models - Monte Carlo and Brownian dynamics simulations - to develop plausible
proposals for the structure of the interphase genome and compare them to experimental data. In the work
presented here, we simulate interphase chromosomes for different folding morphologies of the chromatin fiber
which is organized into loops of 100kbp to 3 Mbp that can be interconnected in various ways. The backbone of
the fiber is described by a wormlike-chain polymer whose diameter and stiffness can be estimated from
independent measurements. The implementation describes this polymer as a segmented chain with 3000 to
20000 segments for chromosome 15 depending on the phase of the simulation. The modeling is performed on a
parallel computer (IBM SP2 with 80 nodes). We also determine genomic marker distributions within the Prader-
Willi-Region on chromosome 15q11.2-13.3. For these measurements we use a fluorescence in situ hybridisation
method (in collaboration with I. Solovai, J. Craig and T. Cremer, Munich, FRG) conserving the structure of the
nucleus. As probes we use 10 kbp long lambda clones (Prof. B. Horsthemke, Essen, FRG) covering genomic
marker distances between 8 kbp and 250 kbp. The markers are detected with confocal and standing wavefield
light microscopes (in collaboration with J.Rauch, J. Bradl, C. Cremer and E.Stelzer, both Heidelberg, FRG) and
using special image reconstruction methods developed solely for this purpose (developed by R. Eils. and W.
Jaeger, Heidelberg, FRG).
Best agreement between simulations and experiments is reached for a Multi-Loop-Subcompartment model with
a loop size of 126 kbp which are forming rosetts and are linked by a chromatin linker of 126 kbp. We also
hypothesize a different folding structure for maternal versus paternal chromosome 15. In simulations of whole
cell nuclei this modell also leads to distinct chromosome territories and subcompartments. A fractal analysis of
the simulations leads to multifractal behavior in good agreement with predictions drawn from porous network
research
Unattended automatic monitoring of boundary layer structures with cost effective lidar ceilometers
Influence of mixing layer height measured by ceilometer upon traffic-related air pollution in urn ban area
Diffusion and transport in the human interphase cell nucleus - FCS experiments compared to simulations.
Despite the succesful linear sequencing of the human genome the three-dimensional arrangement of chromatin,
functional, and structural components is still largely unknown. Molecular transport and diffusion are important
for processes like gene regulation, replication, or repair and are vitally influenced by the structure. With a
comparison between fluorescence correlation spectroscopy (FCS) experiments and simulations we show here an
interdisciplinary approach for the understanding of transport and diffusion properties in the human interphase
cell nucleus.
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-model-like chromatin distribution. Simulations of fragment
distributions based on double strand breakage after carbon-ion irradiation differ in different models. Here again a
comparison with experiments favours a MLS-model.
FCS in combination with a scanning device is a suitable tool to study the diffusion characteristics of fluorescent
proteins in living cell nuclei with high spatial resolution. Computer simulations of the three-dimensional
organization of the human interphase nucleus allows a detailed test of theoretical models in comparison to
experiments. Diffusion and transport in the nucleus are most appropriately described with the concept of
obstructed diffusion. A large volume fraction of the nucleus seems to contain a cytosol-like liquid with an
apparent viscosity 5 times higher than in water. The geometry of particles and structure as well as their
interactions influence the mobilities in terms of speed and spatial coverage. A considerable amount of genomic
sites is accessible for not too large particles. FCS experiments and simulations based on the polymer model are
in a good agreement. Using recently developed in vivo chromatin markers, a detailed study of mobility vs.
structure is subject of current work
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