363 research outputs found
Guided-wave photodetectors in germanium on optical chips in silicon-on-insulator
We report the integration of near-infrared waveguide photodetectors in polycrystalline Germanium with Silicon on Insulator optical chips for power monitor applications. We discuss design and fabrication of the devices as well as their characterization in terms of dark current, responsivity and signal to noise ratio
Non-equilibrium raft-like membrane domains under continuous recycling
We present a model for the kinetics of spontaneous membrane domain (raft)
assembly that includes the effect of membrane recycling ubiquitous in living
cells. We show that the domains have a broad power-law distribution with an
average radius that scales with the 1/4 power of the domain lifetime when the
line tension at the domain edges is large. For biologically reasonable
recycling and diffusion rates the average domain radius is in the tens of nm
range, consistent with observations. This represents one possible link between
signaling (involving rafts) and traffic (recycling) in cells. Finally, we
present evidence that suggests that the average raft size may be the same for
all scale-free recycling schemes.Comment: 8 pages, 5 figure
Genome-wide mapping of the distribution of CarD, RNAP σA, and RNAP β on the Mycobacterium smegmatis chromosome using chromatin immunoprecipitation sequencing
CarD is an essential mycobacterial protein that binds the RNA polymerase (RNAP) and affects the transcriptional profile of Mycobacterium smegmatis and Mycobacterium tuberculosis [6]. We predicted that CarD was directly regulating RNAP function but our prior experiments had not determined at what stage of transcription CarD was functioning and at which genes CarD interacted with the RNAP. To begin to address these open questions, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. The distribution of RNAP subunits β and σA were also profiled. We expected that RNAP β would be present throughout transcribed regions and RNAP σA would be predominantly enriched at promoters based on work in Escherichia coli [3], however this had yet to be determined in mycobacteria. The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA. The colocalization of σA and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. Here we describe in detail the data from the ChIP-seq experiments associated with the study published by Srivastava and colleagues in the Proceedings of the National Academy of Science in 2013 [5] as well as discuss the findings from this dataset in relation to both CarD and mycobacterial transcription as a whole.
The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164)
Flat histogram simulation of lattice polymer systems
We demonstrate the use of a new algorithm called the Flat Histogram sampling
algorithm for the simulation of lattice polymer systems. Thermodynamics
properties, such as average energy or entropy and other physical quantities
such as end-to-end distance or radius of gyration can be easily calculated
using this method. Ground-state energy can also be determined. We also explore
the accuracy and limitations of this method.
Key words: Monte Carlo algorithms, flat histogram sampling, HP model, lattice
polymer systemsComment: 7 RevTeX two-column page
Compact phases of polymers with hydrogen bonding
We propose an off-lattice model for a self-avoiding homopolymer chain with
two different competing attractive interactions, mimicking the hydrophobic
effect and the hydrogen bond formation respectively. By means of Monte Carlo
simulations, we are able to trace out the complete phase diagram for different
values of the relative strength of the two competing interactions. For strong
enough hydrogen bonding, the ground state is a helical conformation, whereas
with decreasing hydrogen bonding strength, helices get eventually destabilized
at low temperature in favor of more compact conformations resembling
-sheets appearing in native structures of proteins. For weaker hydrogen
bonding helices are not thermodynamically relevant anymore.Comment: 5 pages, 3 figures; revised version published in PR
Folding, Design and Determination of Interaction Potentials Using Off-Lattice Dynamics of Model Heteropolymers
We present the results of a self-consistent, unified molecular dynamics study
of simple model heteropolymers in the continuum with emphasis on folding,
sequence design and the determination of the interaction parameters of the
effective potential between the amino acids from the knowledge of the native
states of the designed sequences.Comment: 8 pages, 3 Postscript figures, uses RevTeX. Submitted to Physical
Review Letter
Modeling study on the validity of a possibly simplified representation of proteins
The folding characteristics of sequences reduced with a possibly simplified
representation of five types of residues are shown to be similar to their
original ones with the natural set of residues (20 types or 20 letters). The
reduced sequences have a good foldability and fold to the same native structure
of their optimized original ones. A large ground state gap for the native
structure shows the thermodynamic stability of the reduced sequences. The
general validity of such a five-letter reduction is further studied via the
correlation between the reduced sequences and the original ones. As a
comparison, a reduction with two letters is found not to reproduce the native
structure of the original sequences due to its homopolymeric features.Comment: 6 pages with 4 figure
Viscosity Dependence of the Folding Rates of Proteins
The viscosity dependence of the folding rates for four sequences (the native
state of three sequences is a beta-sheet, while the fourth forms an
alpha-helix) is calculated for off-lattice models of proteins. Assuming that
the dynamics is given by the Langevin equation we show that the folding rates
increase linearly at low viscosities \eta, decrease as 1/\eta at large \eta and
have a maximum at intermediate values. The Kramers theory of barrier crossing
provides a quantitative fit of the numerical results. By mapping the simulation
results to real proteins we estimate that for optimized sequences the time
scale for forming a four turn \alpha-helix topology is about 500 nanoseconds,
whereas the time scale for forming a beta-sheet topology is about 10
microseconds.Comment: 14 pages, Latex, 3 figures. One figure is also available at
http://www.glue.umd.edu/~klimov/seq_I_H.html, to be published in Physical
Review Letter
Islet isolation assessment in man and large animals
Recent progress in islet isolation from the pancreas of large mammals including man, accentuated the need for the development of precise and reproducible techniques to assess islet yield. In this report both quantitative and qualitative criteria for islet isolation assessment were discussed, the main topics being the determination of number, volume, purity, morphologic integrity and in vitro and in vivo function tests of the final islet preparations. It has been recommended that dithizone should be used as a specific stain for immediate detection of islet tissue making it possible to estimate both the total number of islets (dividing them into classes of 50 μ diameter range increments) and the purity of the final preparation. Appropriate morphological assessment should include confirmation of islet identification, assessment of the morphological integrity and of the purity of the islet preparation. The use of fluorometric inclusion and exclusion dyes together have been suggested as a viability assay to simultaneously quantitate the proportion of cells that are intact or damaged. Perifusion of islets with glucose provides a dynamic profile of glucose-mediated insulin release and of the ability of the cells to down regulate insulin secretion after the glycemic challenge is interrupted. Although perifusion data provides a useful guide to islet viability the quantity and kinetics of insulin release do not necessarily predict islet performance after implantation. Therefore, the ultimate test of islet viability is their function after transplantation into a diabetic recipient. For this reason, in vivo models of transplantation of an aliquot of the final islet preparation into diabetic nude (athymic) rodents have been suggested. We hope that these general guidelines will be of assistance to standardize the assessment of islet isolations, making it possible to better interpret and compare procedures from different centers. © 1990 Casa Editrice il Ponte
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