1,260 research outputs found
First proof of concept of remote attendance for future observation strategies between Wettzell (Germany) and Concepción (Chile)
Current VLBI observations are controlled and attended locally at the radio telescopes on the basis of pre-scheduled session files. Operations have to deal with system specific station commands and individual setup procedures. Neither the scheduler nor the correlator nor the data-analyst gets real-time feedback about system parameters during a session. Changes in schedules after the start of a session by remote are impossible or at least quite difficult. For future scientific approaches, a more flexible mechanism would optimize the usage of resources at the sites. Therefore shared-observation control between world-wide telescope s, remote attendance/control as well as completely unattended-observations could be useful, in addition to the classic way to run VLBI observations. To reach these goals, the Geodetic Observatory Wettzell in cooperation with the Max-Planck-Institute for Radio Astronomy (Bonn) have developed a software extension to the existing NASA Field System for remote control. It uses the principle of a remotely accessible, autonomous process cell as server extension to the Field System on the basis of Remote Procedure Calls (RPC). Based on this technology the first completely remote attended and controlled geodetic VLBI session between Wettzell, Germany and Concepción, Chile was successfully performed over 24 hours. This first test was extremely valuable for gathering information about the differences between VLBI systems and measuring the performance of internet connections and automatic connection re-establishments. During the 24h-session, the network load, the number of sent/received packages and the transfer speed were monitor ed and captured. It was a first reliable test for the future wishes to control several telescopes with one graphical user interface on different data transfer rates over large distances in an efficient way. In addition, future developments for an authentication and user role management will be realized within the upcoming NEXPReS project
Cooperative housing and the American dream--examining resident participation
Thesis (M.C.P.)--Massachusetts Institute of Technology, Dept. of Urban Studies and Planning, 1993.Includes bibliographical references (leaves 182-183).by Frank S. Neidhardt.M.C.P
Thermodynamics of Heat Shock Response
Production of heat shock proteins are induced when a living cell is exposed
to a rise in temperature. The heat shock response of protein DnaK synthesis in
E.coli for temperature shifts from temperature T to T plus 7 degrees,
respectively to T minus 7 degrees is measured as function of the initial
temperature T. We observe a reversed heat shock at low T. The magnitude of the
shock increases when one increase the distance to the temperature , thereby mimicking the non monotous stability of proteins at low
temperature. Further we found that the variation of the heat shock with T
quantitatively follows the thermodynamic stability of proteins with
temperature. This suggest that stability related to hot as well as cold
unfolding of proteins is directly implemented in the biological control of
protein folding. We demonstrate that such an implementation is possible in a
minimalistic chemical network.Comment: To be published in Physical Review Letter
A Markov Chain based method for generating long-range dependence
This paper describes a model for generating time series which exhibit the
statistical phenomenon known as long-range dependence (LRD). A Markov Modulated
Process based upon an infinite Markov chain is described. The work described is
motivated by applications in telecommunications where LRD is a known property
of time-series measured on the internet. The process can generate a time series
exhibiting LRD with known parameters and is particularly suitable for modelling
internet traffic since the time series is in terms of ones and zeros which can
be interpreted as data packets and inter-packet gaps. The method is extremely
simple computationally and analytically and could prove more tractable than
other methods described in the literatureComment: 8 pages, 2 figure
The cytoplasm of living cells: A functional mixture of thousands of components
Inside every living cell is the cytoplasm: a fluid mixture of thousands of
different macromolecules, predominantly proteins. This mixture is where most of
the biochemistry occurs that enables living cells to function, and it is
perhaps the most complex liquid on earth. Here we take an inventory of what is
actually in this mixture. Recent genome-sequencing work has given us for the
first time at least some information on all of these thousands of components.
Having done so we consider two physical phenomena in the cytoplasm: diffusion
and possible phase separation. Diffusion is slower in the highly crowded
cytoplasm than in dilute solution. Reasonable estimates of this slowdown can be
obtained and their consequences explored, for example, monomer-dimer equilibria
are established approximately twenty times slower than in a dilute solution.
Phase separation in all except exceptional cells appears not to be a problem,
despite the high density and so strong protein-protein interactions present. We
suggest that this may be partially a byproduct of the evolution of other
properties, and partially a result of the huge number of components present.Comment: 11 pages, 1 figure, 1 tabl
Non-equilibrium states of a photon cavity pumped by an atomic beam
We consider a beam of two-level randomly excited atoms that pass one-by-one
through a one-mode cavity. We show that in the case of an ideal cavity, i.e. no
leaking of photons from the cavity, the pumping by the beam leads to an
unlimited increase in the photon number in the cavity. We derive an expression
for the mean photon number for all times. Taking into account leaking of the
cavity, we prove that the mean photon number in the cavity stabilizes in time.
The limiting state of the cavity in this case exists and it is independent of
the initial state. We calculate the characteristic functional of this
non-quasi-free non-equilibrium state. We also calculate the energy flux in both
the ideal and open cavity and the entropy production for the ideal cavity.Comment: Corrected energy production calculations and made some changes to
ease the readin
Systematic expression analysis of plasticity-related genes in mouse brain development brings PRG4 into play
Background: Plasticity-related genes (Prgs/PRGs) or lipid phosphate phosphatase-related proteins (LPPRs) comprise five known members, which have been linked to neuronal differentiation processes, such as neurite outgrowth, axonal branching, or dendritic spine formation. PRGs are highly brain-specific and belong to the lipid phosphate phosphatases (LPPs) superfamily, which influence lipid metabolism by dephosphorylation of bioactive lipids. PRGs, however, do not possess enzymatic activity, but modify lipid metabolism in a way that is still under investigation. Results: We analyzed mRNA expression levels of all Prgs during mouse brain development, in the hippocampus, neocortex, olfactory bulbs, and cerebellum. We found different spatio-temporal expression patterns for each of the Prgs, and identified a high expression of the uncharacterized Prg4 throughout brain development. Unlike its close family members PRG3 and PRG5, PRG4 did not induce filopodial outgrowth in non-neuronal cell lines, and does not localize to the plasma membrane of filopodia. Conclusion: We showed PRG4 to be highly expressed in the developing and the adult brain, suggesting that it is of vital importance for normal brain function. Despite its similarities to other family members, it seems not to be involved in changes of cell morphology; instead, it is more likely to be associated with intracellular signaling
Invariant Distribution of Promoter Activities in Escherichia coli
Cells need to allocate their limited resources to express a wide range of genes. To understand how Escherichia coli partitions its transcriptional resources between its different promoters, we employ a robotic assay using a comprehensive reporter strain library for E. coli to measure promoter activity on a genomic scale at high-temporal resolution and accuracy. This allows continuous tracking of promoter activity as cells change their growth rate from exponential to stationary phase in different media. We find a heavy-tailed distribution of promoter activities, with promoter activities spanning several orders of magnitude. While the shape of the distribution is almost completely independent of the growth conditions, the identity of the promoters expressed at different levels does depend on them. Translation machinery genes, however, keep the same relative expression levels in the distribution across conditions, and their fractional promoter activity tracks growth rate tightly. We present a simple optimization model for resource allocation which suggests that the observed invariant distributions might maximize growth rate. These invariant features of the distribution of promoter activities may suggest design constraints that shape the allocation of transcriptional resources
Strong negative self regulation of Prokaryotic transcription factors increases the intrinsic noise of protein expression
Background
Many prokaryotic transcription factors repress their own transcription. It is often asserted that such regulation enables a cell to homeostatically maintain protein abundance. We explore the role of negative self regulation of transcription in regulating the variability of protein abundance using a variety of stochastic modeling techniques.
Results
We undertake a novel analysis of a classic model for negative self regulation. We demonstrate that, with standard approximations, protein variance relative to its mean should be independent of repressor strength in a physiological range. Consequently, in that range, the coefficient of variation would increase with repressor strength. However, stochastic computer simulations demonstrate that there is a greater increase in noise associated with strong repressors than predicted by theory. The discrepancies between the mathematical analysis and computer simulations arise because with strong repressors the approximation that leads to Michaelis-Menten-like hyperbolic repression terms ceases to be valid. Because we observe that strong negative feedback increases variability and so is unlikely to be a mechanism for noise control, we suggest instead that negative feedback is evolutionarily favoured because it allows the cell to minimize mRNA usage. To test this, we used in silico evolution to demonstrate that while negative feedback can achieve only a modest improvement in protein noise reduction compared with the unregulated system, it can achieve good improvement in protein response times and very substantial improvement in reducing mRNA levels.
Conclusions
Strong negative self regulation of transcription may not always be a mechanism for homeostatic control of protein abundance, but instead might be evolutionarily favoured as a mechanism to limit the use of mRNA. The use of hyperbolic terms derived from quasi-steady-state approximation should also be avoided in the analysis of stochastic models with strong repressors
Toward genome editing in X-linked RP-development of a mouse model with specific treatment relevant features
Genome editing represents a powerful tool to treat inherited disorders. Highly specific endonucleases induce a DNA double strand break near the mutant site, which is subsequently repaired by cellular DNA repair mechanisms that involve the presence of a wild type template DNA. In vivo applications of this strategy are still rare, in part due to the absence of appropriate animal models carrying human disease mutations and knowledge of the efficient targeting of endonucleases. Here we report the generation and characterization of a new mouse model for X-linked retinitis pigmentosa (XLRP) carrying a point mutation in the mutational hotspot exon ORF15 of the RPGR gene as well as a recognition site for the homing endonuclease I-SceI. Presence of the genomic modifications was verified at the RNA and protein levels. The mutant protein was observed at low levels. Optical coherence tomography studies revealed a slowly progressive retinal degeneration with photoreceptor loss starting at 9 months of age, paralleling the onset of functional deficits as seen in the electroretinogram. Early changes to the outer retinal bands can be used as biomarker during treatment applications. We further show for the first time efficient targeting using the I-SceI enzyme at the genomic locus in a proof of concept in photoreceptors following adeno-associated virus mediated gene transfer in vivo. Taken together, our studies not only provide a human-XLRP disease model but also act as a platform to design genome editing technology for retinal degenerative diseases using the currently available endonucleases
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