Hardware support for real-time reconfigurable system-on-chip

This paper introduces a computer architecture suitable for embedded real-time applications where low power consumption is a requirement. This is achieved through the use of a hybrid hardware-software system. A system architecture is proposed which allows for modules of a system to be implemented at run-time in either hardware or software. Implementation choices may be made dynamically based on the loading of the host microprocessor, in a multi-tasking environment. An approach to inter-module communication is described, along with how this is affected by dynamic configuration. Some research goals are identified, including investigating the effects on real-time performance, power consumption and the design process involved in reconfigurable systems

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

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 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 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 agreemen

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

MHz Unidirectional Rotation of Molecular Rotary Motors

A combination of cryogenic UV-vis and CD spectroscopy and transient absorption spectroscopy at ambient temperature is used to study a new class of unidirectional rotary molecular motors. Stabilization of unstable intermediates is achieved below 95 K in propane solution for the structure with the fastest rotation rate, and below this temperature measurements on the rate limiting step in the rotation cycle can be performed to obtain activation parameters. The results are compared to measurements at ambient temperature using transient absorption spectroscopy, which show that behavior of these motors is similar over the full temperature range investigated, thereby allowing a maximum rotation rate of 3 MHz at room temperature under suitable irradiation conditions

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

The mTORC1 inhibitor everolimus prevents and treats Eμ-Myc lymphoma by restoring oncogene-induced senescence

MYC deregulation is common in human cancer. IG-MYC translocations that are modeled in EμMyc mice occur in almost all cases of Burkitt lymphoma as well as in other B-cell lymphoproliferative disorders. Deregulated expression of MYC results in increased mTOR complex 1 (mTORC1) signaling. As tumors with mTORC1 activation are sensitive to mTORC1 inhibition, we used everolimus, a potent and specific mTORC1 inhibitor, to test the requirement for mTORC1 in the initiation and maintenance of EμMyc lymphoma. Everolimus selectively cleared premalignant B cells from the bone marrow and spleen, restored a normal pattern of B-cell differentiation, and strongly protected against lymphoma development. Established EμMyc lymphoma also regressed after everolimus therapy. Therapeutic response correlated with a cellular senescence phenotype and induction of p53 activity. Therefore, mTORC1-dependent evasion of senescence is critical for cellular transformation and tumor maintenance by MYC in B lymphocytes