A family tree of Markov models in systems biology

Motivated by applications in systems biology, we seek a probabilistic framework based on Markov processes to represent intracellular processes. We review the formal relationships between different stochastic models referred to in the systems biology literature. As part of this review, we present a novel derivation of the differential Chapman-Kolmogorov equation for a general multidimensional Markov process made up of both continuous and jump processes. We start with the definition of a time-derivative for a probability density but place no restrictions on the probability distribution, in particular, we do not assume it to be confined to a region that has a surface (on which the probability is zero). In our derivation, the master equation gives the jump part of the Markov process while the Fokker-Planck equation gives the continuous part. We thereby sketch a {}``family tree'' for stochastic models in systems biology, providing explicit derivations of their formal relationship and clarifying assumptions involved.Comment: 18 pages, 2 figure

Transglutaminase-catalyzed matrix cross-linking in differentiating cartilage: identification of osteonectin as a major glutaminyl substrate.

The expression of tissue transglutaminase in skeletal tissues is strictly regulated and correlates with chondrocyte differentiation and cartilage calcification in endochondral bone formation and in maturation of tracheal cartilage (Aeschlimann, D., A. Wetterwald, H. Fleisch, and M. Paulsson. 1993. J. Cell Biol. 120:1461-1470). We now demonstrate the transglutaminase reaction product, the gamma-glutamyl-epsilon-lysine cross-link, in the matrix of hypertrophic cartilage using a novel cross-link specific antibody. Incorporation of the synthetic transglutaminase substrate monodansylcadaverine (amine donor) in cultured tracheal explants reveals enzyme activity in the pericellular matrix of hypertrophic chondrocytes in the central, calcifying areas of the horseshoe-shaped cartilages. One predominant glutaminyl substrate (amine acceptor) in the chondrocyte matrix is osteonectin as revealed by incorporation of the dansyl label in culture. Indeed, nonreducible osteonectin-containing complexes of approximately 65, 90, and 175 kD can be extracted from mature tracheal cartilage. In vitro cross-linking of osteonectin by tissue transglutaminase gives similar products of approximately 90 and 175 kD, indicating that the complexes in cartilage represent osteonectin oligomers. The demonstration of extracellular transglutaminase activity in differentiating cartilage, i.e., cross-linking of osteonectin in situ, shows that tissue transglutaminase-catalyzed cross-linking is a physiological mechanism for cartilage matrix stabilization

Transglutaminase-catalyzed matrix cross-linking in differentiating cartilage: identification of osteonectin as a major glutaminyl substrate

The expression of tissue transglutaminase in skeletal tissues is strictly regulated and correlates with chondrocyte differentiation and cartilage calcification in endochondral bone formation and in maturation of tracheal cartilage (Aeschlimann, D., A. Wetterwald, H. Fleisch, and M. Paulsson. 1993. J. Cell Biol. 120:1461-1470). We now demonstrate the transglutaminase reaction product, the gamma-glutamyl-epsilon-lysine cross-link, in the matrix of hypertrophic cartilage using a novel cross-link specific antibody. Incorporation of the synthetic transglutaminase substrate monodansylcadaverine (amine donor) in cultured tracheal explants reveals enzyme activity in the pericellular matrix of hypertrophic chondrocytes in the central, calcifying areas of the horseshoe-shaped cartilages. One predominant glutaminyl substrate (amine acceptor) in the chondrocyte matrix is osteonectin as revealed by incorporation of the dansyl label in culture. Indeed, nonreducible osteonectin-containing complexes of approximately 65, 90, and 175 kD can be extracted from mature tracheal cartilage. In vitro cross-linking of osteonectin by tissue transglutaminase gives similar products of approximately 90 and 175 kD, indicating that the complexes in cartilage represent osteonectin oligomers. The demonstration of extracellular transglutaminase activity in differentiating cartilage, i.e., cross-linking of osteonectin in situ, shows that tissue transglutaminase-catalyzed cross-linking is a physiological mechanism for cartilage matrix stabilization

Heat dissipation in atomic-scale junctions

Atomic and single-molecule junctions represent the ultimate limit to the miniaturization of electrical circuits. They are also ideal platforms to test quantum transport theories that are required to describe charge and energy transfer in novel functional nanodevices. Recent work has successfully probed electric and thermoelectric phenomena in atomic-scale junctions. However, heat dissipation and transport in atomic-scale devices remain poorly characterized due to experimental challenges. Here, using custom-fabricated scanning probes with integrated nanoscale thermocouples, we show that heat dissipation in the electrodes of molecular junctions, whose transmission characteristics are strongly dependent on energy, is asymmetric, i.e. unequal and dependent on both the bias polarity and the identity of majority charge carriers (electrons vs. holes). In contrast, atomic junctions whose transmission characteristics show weak energy dependence do not exhibit appreciable asymmetry. Our results unambiguously relate the electronic transmission characteristics of atomic-scale junctions to their heat dissipation properties establishing a framework for understanding heat dissipation in a range of mesoscopic systems where transport is elastic. We anticipate that the techniques established here will enable the study of Peltier effects at the atomic scale, a field that has been barely explored experimentally despite interesting theoretical predictions. Furthermore, the experimental advances described here are also expected to enable the study of heat transport in atomic and molecular junctions, which is an important and challenging scientific and technological goal that has remained elusive.Comment: supporting information available in the journal web site or upon reques

PRELIMINARY REPORT ON GEOPHYSICAL AND MECHANICAL BOREHOLE MEASUREMENTS AT STRIPA

Four different systems of borehole instrumentation have been employed thus far at an experimental site at Stripa, Sweden where a series of hydrological and thermo-mechanical experiments are being conducted to examine the suitability of granitic rock for the storage of radioactive waste materials. Asuite of seven logs--neutron, gamma-gamma, resistivity, gamma ray, sonic, caliper, and temperature--operated in a borehole of 380-m depth located eleven zones where the rock permeability is expected to be enhanced due to the presence of open fractures. The sonic waveform record proved especially useful in this regard. Borehole measurements were also acquired in a large number of boreholes from 5- to 14-m length located in experimental drifts some 340-m underground. Here several physical properties, including the porosity, density, sonic velocity, and borehole rugosity, are generally quite uniform, with the exception of a few local chloritic zones and a few minor fractures. However, in situ determinations of the mechanical modulus with the CSM cell indicate substantial variability, with some apparent fracture control. Uranium and thorium concentrations are quite high in the Stripa granite, with local fluctuations associated with mineralogical changes as revealed by the gamma-ray log. Adifferential resistance probe appears promising as a sensitive detector of fine fracturing. Across-hole ultrasonic system indicates variations of a few percent in compressional- and shear-wave velocities, reflecting the presence of fractures and changes in fracture characteristics as the rock is heated in a simulated storage test. The geophysical and mechanical data are being compared with the results from core and television logging, with hydrological test data on static pressure and injection permeability, and with displacements induced by thermal loading

Characteristic odour in the blood reveals ovarian carcinoma

<p>Abstract</p> <p>Background</p> <p>Ovarian carcinoma represents about 4% of all cancers diagnosed in women worldwide. Mortality rate is high, over 50%, mainly due to late diagnosis. Currently there are no acceptable screening techniques available, although ovarian cancer belongs to the group of malignancies for which mortality could be dramatically reduced by early diagnosis.</p> <p>In a recently published study, we clearly demonstrated that human ovarian carcinoma tissues can be characterized by a specific odour, detectable by a trained dog. Another recent study confirmed these results using an electronic nose.</p> <p>Methods</p> <p>In the present work, we examined whether the cancer-specific odour can also be found in the blood. Two specially trained dogs were used. Both ovarian cancer tissues and blood from patients with ovarian carcinoma were tested.</p> <p>Results</p> <p>The tissue tests showed sensitivity of 100% and specificity of 95%, while the blood tests showed sensitivity of 100% and specificity of 98%.</p> <p>Conclusions</p> <p>The present study strongly suggests that the characteristic odour emitted by ovarian cancer samples is also present in blood (plasma) taken from patients with the disease. This finding opens possibilities for future screening of healthy populations for early diagnosis of ovarian carcinoma. A future challenge is to develop a sensitive electronic nose for screening of ovarian carcinoma by testing the blood/plasma to detect the disease at a stage early enough for treatment to be effective.</p

Effect of promoter architecture on the cell-to-cell variability in gene expression

According to recent experimental evidence, the architecture of a promoter, defined as the number, strength and regulatory role of the operators that control the promoter, plays a major role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effort that addresses the question of how changes in promoter architecture affect noise in gene expression in a systematic rather than case-by-case fashion. In this article, we make such a systematic investigation, based on a simple microscopic model of gene regulation that incorporates stochastic effects. In particular, we show how operator strength and operator multiplicity affect this variability. We examine different modes of transcription factor binding to complex promoters (cooperative, independent, simultaneous) and how each of these affects the level of variability in transcription product from cell-to-cell. We propose that direct comparison between in vivo single-cell experiments and theoretical predictions for the moments of the probability distribution of mRNA number per cell can discriminate between different kinetic models of gene regulation.Comment: 35 pages, 6 figures, Submitte

Trade-offs and Noise Tolerance in Signal Detection by Genetic Circuits

Genetic circuits can implement elaborated tasks of amplitude or frequency signal detection. What type of constraints could circuits experience in the performance of these tasks, and how are they affected by molecular noise? Here, we consider a simple detection process–a signal acting on a two-component module–to analyze these issues. We show that the presence of a feedback interaction in the detection module imposes a trade-off on amplitude and frequency detection, whose intensity depends on feedback strength. A direct interaction between the signal and the output species, in a type of feed-forward loop architecture, greatly modifies these trade-offs. Indeed, we observe that coherent feed-forward loops can act simultaneously as good frequency and amplitude noise-tolerant detectors. Alternatively, incoherent feed-forward loop structures can work as high-pass filters improving high frequency detection, and reaching noise tolerance by means of noise filtering. Analysis of experimental data from several specific coherent and incoherent feed-forward loops shows that these properties can be realized in a natural context. Overall, our results emphasize the limits imposed by circuit structure on its characteristic stimulus response, the functional plasticity of coherent feed-forward loops, and the seemingly paradoxical advantage of improving signal detection with noisy circuit components

Large-Scale Atomistic Simulations of Environmental Effects on the Formation and Properties of Molecular Junctions

Using an updated simulation tool, we examine molecular junctions comprised of benzene-1,4-dithiolate bonded between gold nanotips, focusing on the importance of environmental factors and inter-electrode distance on the formation and structure of bridged molecules. We investigate the complex relationship between monolayer density and tip separation, finding that the formation of multi-molecule junctions is favored at low monolayer density, while single-molecule junctions are favored at high density. We demonstrate that tip geometry and monolayer interactions, two factors that are often neglected in simulation, affect the bonding geometry and tilt angle of bridged molecules. We further show that the structures of bridged molecules at 298 and 77 K are similar.Comment: To appear in ACS Nano, 30 pages, 5 figure