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PubMed2004

Square vortex solitons with a large angular momentum.

We show the existence of square-shaped optical vortices with a large value of the angular momentum hosted in finite-size laser beams which propagate in nonlinear media with a cubic-quintic nonlinearity. The light profiles take the form of rings with sharp boundaries and variable sizes depending on the power carried. Our stability analysis shows that these light distributions remain stable when they propagate, probably for unlimited values of the angular momentum, provided the hosting beam is wide enough. This happens if the peak amplitude approaches a critical value which only depends on the nonlinear refractive index of the material. A variational approach allows us to calculate the main parameters involved. Our results add extra support to the concept of surface tension of light beams that can be considered as a trace of the existence of a liquid of light.

Journal Article↗
PubMed1994

DNA binding specificity of the bovine papillomavirus E1 protein is determined by sequences contained within an 18-base-pair inverted repeat element at the origin of replication.

Bovine papillomavirus type 1 (BPV-1) DNA replicates episomally and requires two virally expressed proteins, E1 and E2, for this process. Both proteins bind to the BPV-1 genome in the region that functions as the origin of replication. The binding sequences for the E2 protein have been characterized previously, but little is known about critical sequence requirements for E1 binding. Using a bacterially expressed E1 fusion protein, we examined binding of the BPV-1 E1 protein to the origin region. E1 strongly protected a 28-bp segment of the origin (nucleotides 7932 to 15) from both DNase I and exonuclease III digestion. Additional exonuclease III protection was observed beyond the core region on both the 5' and 3' sides, suggesting that E1 interacted with more distal sequences as well. Within the 28-bp protected core, there were two overlapping imperfect inverted repeats (IR), one of 27 bp and one of 18 bp. We show that sequences within the smaller, 18-bp IR element were sufficient for specific recognition of DNA by E1 and that additional BPV-1 sequences beyond the 18-bp IR element did not significantly increase origin binding by E1 protein. While the 18-bp IR element contained sequences sufficient for specific binding by E1, E1 did not form a stable complex with just the isolated 18-bp element. Formation of a detectable E1-DNA complex required that the 18-bp IR be flanked by additional DNA sequences. Furthermore, binding of E1 to DNA containing the 18-bp IR increased as a function of overall increasing fragment length. We conclude that E1-DNA interactions outside the boundaries of the 18-bp IR are important for thermodynamic stabilization of the E1-DNA complex. However, since the flanking sequences need not be derived from BPV-1, these distal E1-DNA interactions are not sequence specific. Comparison of the 18-bp IR from BPV-1 with the corresponding region from other papillomaviruses revealed a symmetric conserved consensus sequence, T-RY--TTAA--RY-A, that may reflect the specific nucleotides critical for E1-DNA recognition.

Base Sequence↗
PubMed1988

A discrete element 3' of human immunodeficiency virus 1 (HIV-1) and HIV-2 mRNA initiation sites mediates transcriptional activation by an HIV trans activator.

An important point of regulation in the reproductive growth and latency of the human and simian immunodeficiency viruses (HIV and SIV, respectively) is provided by virally encoded trans-activators (tat), proteins capable of dramatically increasing viral gene expression. The mechanism of this autostimulatory pathway has remained unclear, however, with substantial effects having been reported at the level of either mRNA accumulation, translational efficiency, or both. Our previous findings indicated that trans-activation results primarily from induction of RNA levels but could not distinguish between the roles of transcriptional rate, RNA stabilization, and RNA transport in this event. In addition, the boundaries of tat-responding elements, which would be valuable in elucidating the mode of tat action, are not precisely known. In this study, HIV-1 and HIV-2 long terminal repeat-directed expression was characterized by using an in vitro nuclear transcription assay to clarify this mechanism, and a detailed mutational analysis was undertaken to localize precisely the sequences participating in this process. Two key findings were revealed: an increased transcription rate was the primary event in tat-mediated activation of HIV-1 and HIV-2, and trans-activation was impaired by mutations in two regions, the TATA box and sequences between +19 to +42, a region lacking enhancer activity. These results implicate a discrete 3' regulatory element in the transcriptional activation of the HIVs.

Base Sequence↗
PubMed2006

Violations and migrations in health care: a framework for understanding and management.

Violations are deliberate deviations from standard procedure. The usual reaction is to attempt to eliminate them and reprimand those concerned. However, the situation is not that simple. Firstly, violations paradoxically may be markers of high levels of safety because they need constraints and defences to exist. They may even become more frequent than errors in ultrasafe systems. Secondly, violations have both positive and negative aspects. On the one hand they occur frequently, increase system performance and individual satisfaction, are mostly limited to practices with limited safety consequences, and therefore are often tolerated or even encouraged by the hierarchy. On the other hand, extreme violations can lead to real danger or actual harm. This paper proposes a three phase model derived from Rasmussen's theory of migration to boundaries to explain the mechanism by which the deviance occurs, stabilizes, regresses, or progresses to harm. The model suggests that violations are unavoidable because system dynamics and deviances are markers of adaptation to this dynamicity. Violations cannot be eliminated but they can be managed. Solutions are specific to each step of the model, with a mix of relaxing constraints, increasing peer control (staff), and constraining dangerous individuals.

Attitude of Health Personnel↗
PubMed1998

Evolving reaction-diffusion ecosystems with self-assembling structures in thin films.

Recently, new types of coupled isothermal polynucleotide amplification reactions for the investigation of in vitro evolution have been established that are based on the multi-enzyme 3SR reaction. Microstructured thin-film open bioreactors have been constructed in our laboratory to run these reactions spatially resolved in flow experiments. Artificial DNA/RNA chemistries close to the in vitro biochemistry of these systems have been developed, which we have studied in computer simulations in configurable hardware (NGEN). These artificial chemistries are described on the level of individual polynucleotide molecules, each with a defined sequence, and their complexes. The key feature of spatial pattern formation provides a weak stabilization of cooperative catalytic properties of the evolving molecules. Of great interest is the step to include extended self-assembly processes of flexible structures-allowing the additional stabilization of cooperation through semipermeable, flexible, self-organizing membrane boundaries. We show how programmable matter simulations of experimentally relevant molecular in vitro evolution can be extended to include the influence of self-assembling flexible membranes.

Bioreactors↗
PubMedDate not supplied

[Modeling of swarm formation as a consequence of autotaxis].

The simple model of school and swarm formation is proposed within the frameworks of Eulerian space models (reaction-diffusion-advection system). Assuming that the schooling and the processes of birth-and-death act on different time scales, we have excluded the local kinetics of species (the reaction term) from the model. The spatial dynamics of animals is circumscribed by scalar field of density and vector field of velocity. The basis of animal aggregation in space is the ability of animals to move in certain direction, i.e. taxis. As an example of swarming strategy the behavior of midges is taken: we presume that individuals accelerate towards higher swarm density but change direction when the density exceeded some maximum. In other words, acceleration of movement is assumed to be proportional (with density-dependent coefficient of proportionality) to the gradient of species density. This statement poses the equation for species velocity. Thus, our model adds the differential equation for velocity of autotaxis to the standard advection-diffusion model. The linear analysis of 1D problem with zero-flux boundary conditions has showed that homogeneous nonzero equilibrium looses its stability when the movement rate of animals (coefficient of proportionality in velocity equation) overpasses some bifurcation value. The numerical experiments have confirmed analytical results, displaying stationary spatially heterogeneous solution (standing waves) for the detected supercritical value of the movement rate.

Animals↗
PubMed1992

The electrocardiographic inverse problem.

Using the boundary element method in conjunction with Tikhonov zero-order regularization, we have computed epicardial potentials from body surface potential data in a realistic geometry heart-torso system. The inverse-reconstructed epicardial potentials were compared to the actual measured potentials throughout a normal cardiac cycle. Potential features (maxima, minima) were recovered with an accuracy better than 1 cm in their location. In this chapter, we use these data to illustrate and discuss computational issues related to the inverse-reconstruction procedure. These include the boundary element method, the choice of a regularization scheme to stabilize the inversion, and the effects of incorporating a priori information on the accuracy of the solution. In particular, emphasis is on the use of temporal information in the regularization procedure. The sensitivity of the solution to geometrical errors and to the spatial and temporal resolution of the data is discussed.

Animals↗
PubMed2001

Atlantic water flow pathways revealed by lead contamination in Arctic basin sediments.

Contaminant lead in sediments underlying boundary currents in the Arctic Ocean provides an image of current organization and stability during the past 50 years. The sediment distributions of lead, stable lead isotope ratios, and lead-210 in the major Arctic Ocean basins reveal close coupling of the Eurasian Basin with the North Atlantic during the 20th century. They indicate that the Atlantic water boundary current in the Eurasian Basin has been a prominent pathway, that contaminant lead from the Laptev Sea supplies surface water in the transpolar drift, and that the Canadian and Eurasian basins have been historically decoupled.

Journal Article↗
PubMed1987

[Preservation of the blood of slaughter animals by the non-diaphragmatic use of solidified carbon dioxide. III. Effect of blood preservation. Practical blood stability].

The preservation effectivity of slaughter animal blood for consumptive purposes was studied by a method of non-phrenic action with solidified CO2. The material for studies was full pig blood stabilized with sodium citrate. The course of the changes of the blood properties studied has been described by regression equations. Blood stabilization with solidified CO2 was found to reduce the rate of aerobic microflora growth and of proteolytic changes and to extend the stability period of the coagulation system. The results of sensory studies were related to the boundary values of the studied physicochemical and microbiological quality factors. The admissible periods of blood storage were determined from the results of the studies. It was found that practical preservation of blood stabilized with solidified CO2 was 15 full days at 5 degrees C, 6 days at 10 degrees C and 4 days at 15 degrees C, and it was two, three and four times greater at the three successive temperatures, as compared with the preservation of control blood.

Animals↗
PubMedDate not supplied

[Stability of spatially-nonhomogeneous stationary conditions of a diffuse system. Positional differentiation].

The results of general investigation presented at the previous paper [9] are applied to interpreting the spatial ordering upon positional differentiation at the development of multicellular organisms. The very form of local dynamics is not specified for the lack of sufficient information about the mechanisms of biosynthesis regulation in multicellular organisms. Instead of the dynamics of intercellular processes is supposed to provide the existence of two stable stationary states. These stable regimes are interpreted as the different specialisations of individual cell (differentiations). There are accepted the boundary conditions in the form of non-zero morphogen fluxes. The requirement of stability of the exfoliated structure at the multicellular ensemble connects some physical chemical parameters of the system (the permeability of the boundaries, characteristic time of intercellular dynamics, the diffusion coefficient of morphogen and some others) in the form of inequality. Within the framework of dynamical model the ability of morphogenetic system to the regulative development is discussed.

Cell Communication↗
PubMed1995

Estimation of PCNA mRNA stability in cell cycle by a serum-deprivation method.

A simple scheme was developed to study the mRNA stability of the proliferating cell nuclear antigen (PCNA) gene during cellular transition from the G1/S boundary to a quiescent state. By this scheme, CHO.K1 cells were grown to about 80% confluence and then serum-starved for 40 h for synchronization in a quiescent state. The quiescent cells were serum-stimulated for a period of time (between 8 h and 12 h) and then grown in serum-free medium until being harvested for further analyses. The cellular PCNA mRNA level was analyzed by Northern blotting. As compared with that in cells which were continuously incubated in serum-containing medium, the decline of the mRNA level, after reaching the peak, in these serum-deprived cells was virtually devoid of mRNA synthesis. Thus, this mRNA decay was taken for the measurement of mRNA stability. The advantage of the scheme is that, unlike the treatment of transcription inhibitors, it does not prevent the cells from completing the rest of the cell cycle before returning to the resting state, and so the mRNA stability observed is cell cycle dependent. In contrast with the previous report that the stability of PCNA mRNA in quiescent cells is less by severalfold than that in S phase cells, our study shows that the mRNA stability of PCNA remained constant during the cellular transition from G1/S boundary to quiescent state.

Animals↗
PubMed1993

Identification of the Shiga toxin A-subunit residues required for holotoxin assembly.

Recent X-ray crystallographic analyses have demonstrated that the receptor-binding (B) subunits of Shiga toxin (STX) are arranged as a doughnut-shaped pentamer. The C terminus of the enzymatic (A) subunit presumably penetrates the nonpolar pore of the STX B pentamer, and the holotoxin is stabilized by noncovalent interactions between the polypeptides. We identified a stretch of nine nonpolar amino acids near the C terminus of StxA which were required for subunit association by using site-directed mutagenesis to introduce progressive C-terminal deletions in the polypeptide and assessing holotoxin formation by a receptor analog enzyme-linked immunosorbent assay, immunoprecipitation, and a cytotoxicity assay. Tryptophan and aspartic acid residues which form the N-terminal boundary, as well as two arginine residues which form the C-terminal boundary of the nine-amino-acid sequence, were implicated as the stabilizers of subunit association. Our model proposes that residues 279 to 287 of the 293-amino-acid STX A subunit penetrate the pore while the tryptophan, aspartic acid, and 2 arginine residues interact with other charged or aromatic amino acids outside the pore on the planar surfaces of the STX B pentamer.

Amino Acid Sequence↗
PubMedDate not supplied

[Molecular mechanisms of senescence in cell culture].

Clones of non-transformed human cells are mortal, that is, the cells divide only a limited number of times before they approach a state of proliferative senescence. This state has long been regarded as a cellular model of organismal aging or as aging in vitro because of its close relationship to the aging process of the donor of the cells. The underlying molecular mechanisms of this particular aging process have only been recently understood and are reviewed in the present paper. Cell division is accompanied by progressive telomere shortening, which is due both to properties of the replicative apparatus (the "end-replication problem") and to oxidative damage to telomere DNA under conventional cell culture conditions. If shortening of telomeres reaches a certain critical level, it is recognized as DNA damage by the cell's "guardian of the genome", the tumor suppressor p53. Stabilization of p53 activates the well characterized cell cycle checkpoint at the G1/S phase boundary and blocks the cell cycle irreversibly. Two recent results prove that telomere shortening is in fact the trigger of the checkpoint control in cellular senescence: First, acceleration of telomere shortening by increased oxidative stress results in accelerated proliferative senescence. Second, stabilization of telomere length, typically by activation of telomere, appears to be a necessary prerequisite for the immortalization of cells. Proliferative senescence, therefore, should be understood as an important means to counteract genetic instability and cancer.

Aged↗
PubMed1985

Effect of imposed step-movements and pulse-movements of the retinal image on perception of hue with coloured targets.

There is strong experimental evidence that colour discrimination depends upon signals originating at colour boundaries. Controlled movements were imposed on a boundary between an illuminated coloured area and a dark area in a previously stabilized image. Red, yellow, green and blue fields were used. Step-movements of amplitude M min arc and pulse-movements of amplitude M min arc and pulse width tau s were studied. The movement M50 to produce 50% positive responses for perception of hue was measured as a function of retinal illuminance, boundary length and speed for step-movements and pulse-width (tau) for pulse movements. Signal/photon-noise ratios were calculated.

Color Perception↗
PubMed1978

Stability of local rings of dimension 2.

The notion of stability of a local ring arises naturally in investigating completed moduli spaces via geometric invariant theory. A scheme corresponding to a boundary point of a moduli space of nonsingular varieties cannot have unstable singular points. This paper reports some results concerning the stability of surface singularities. If a two-dimensional Cohen-Macaulay local ring R is semistable, its multiplicity must be less than seven and either equal to or 1 less than its embedding dimension. If the multiplicity of R is equal to its embedding dimension, the singularity of R must be a simple or cyclic elliptic singularity or the nonnormal limit of such a singularity. The results for the case when the multiplicity of R is less than its embedding dimension are still incomplete; the possible singularities that may arise when the multiplicity of R is equal to 2 or 3 are described.

Journal Article↗
PubMed2005

Stability analysis of three-dimensional colloidal domains: quadratic fluctuations.

Three-dimensional domain patterns can self-assemble in a charged colloidal suspension with competing short-range attraction and long-range Yukawa repulsion. Following the investigation of the ground-state domain shapes in our previous paper, we study the stability of isolated spherical, cylindrical, and lamellar domains with respect to shape fluctuations on boundaries. In the framework of the continuum model, we expand the free energy variation to quadratic terms under the constraint of constant volume. For the three shapes (sphere, cylinder, and lamella) discussed, domains with equilibrium sizes are stable with respect to shape fluctuations, and the stability of domains decreases as the spatial symmetry decreases.

Journal Article↗
PubMed2004

The cell cycle checkpoint kinase Chk2 is a negative regulator of mitotic catastrophe.

Fusion between nonsynchronized cells leads to the formation of heterokarya which transiently activate Cyclin-dependent kinase 1 (Cdk1)/cyclin B1 and enter the prophase of the cell cycle, where they arrest due to a loss of Cdk1/cyclin B1 activity, activate p53, disorganize centrosomes, and undergo apoptosis. Here, we show that the down regulation of Cdk1/cyclin B is secondary to the activation of the DNA structure checkpoint kinase Chk2. Thus, syncytia generated by the fusion of asynchronous HeLa cells contain elevated levels of active Chk2 but not Chk1. Chk2 bearing the activating phosphorylation on threonine-68 accumulates in BRCA1 nuclear bodies when the cells arrest at the G2/M boundary. Inhibition of Chk2 by transfection of a dominant-negative Chk2 mutant or a chemical inhibitor, debromohymenialdesine, stabilizes centrosomes, maintains high cyclin B1 levels, and allows for a prolonged activation of Cdk1. Under these conditions, multinuclear HeLa syncytia do not arrest at the G2/M boundary and rather enter mitotis and subsequently die during the metaphase of the cell cycle. This mitotic catastrophe is associated with the activation of the pro-apoptotic caspase-3. Inhibition of caspases allows the cells to go beyond the metaphase arrest, indicating that apoptosis is responsible for cell death by mitotic catastrophe. In another, completely different model of mitotic catastrophe, namely 14.3.3 sigma-deficient HCT116 colon carcinoma cells treated with doxorubicin, Chk2 activation was also found to be deficient as compared to 14.3.3 sigma-sufficient controls. Inhibition of Chk2 again facilitated the induction of mitotic catastrophe in HCT116 wild-type cells. In conclusion, a conflict in cell cycle progression or DNA damage can lead to mitotic catastrophe, provided that the checkpoint kinase Chk2 is inhibited. Inhibition of Chk2 thus can sensitize proliferating cells to chemotherapy-induced apoptosis.

14-3-3 Proteins↗
PubMed1993

Helix capping propensities in peptides parallel those in proteins.

Helix content of peptides with various uncharged nonaromatic amino acids at either the N-terminal or C-terminal position has been determined. The choice of N-terminal amino acid has a major effect on helix stability: asparagine is the best, glycine is very good, and glutamine is the worst helix-stabilizing amino acid at this position. The rank order of helix stabilization parallels the frequencies of these amino acids at the N-terminal boundary (N-cap) position of helices in proteins found by Richardson and Richardson [Richardson, J. S. & Richardson, D. C. (1988) Science 240, 1648-1652], and the N-terminal amino acid in a peptide composed of helix-forming amino acids may be considered as the N-cap residue. The choice of C-terminal amino acid has only a minor effect on helix stability. N-capping interactions may be responsible for the asymmetric distribution of helix content within a given peptide found by various workers. An acetyl group on the N-terminal alpha-amino function cancels the N-cap effect and the acetyl group is equivalent to N-terminal asparagine in an unacetylated peptide. Our results demonstrate a close relationship between the mechanisms of alpha-helix formation in peptides and in proteins.

Acetylation↗