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Search Results: 1 - 10 of 338 matches for " Ilka Bischofs "
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Ectopic Integration Vectors for Generating Fluorescent Promoter Fusions in Bacillus subtilis with Minimal Dark Noise
Stephanie Trauth, Ilka B. Bischofs
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0098360
Abstract: Fluorescent protein promoter reporters are important tools that are widely used for diverse purposes in microbiology, systems biology and synthetic biology and considerable engineering efforts are still geared at improving the sensitivity of the reporter systems. Here we focus on dark noise, i.e. the signal that is generated by the empty vector control. We quantitatively characterize the dark noise of a few common bacterial reporter systems by single cell microscopy. All benchmarked reporter systems generated significant amounts of dark noise that exceed the cellular autofluorescence to different extents. We then reengineered a multicolor set of fluorescent ectopic integration vectors for Bacillus subtilis by introducing a terminator immediately upstream of the promoter insertion site, resulting in an up to 2.7-fold reduction of noise levels. The sensitivity and dynamic range of the new high-performance pXFP_Star reporter system is only limited by cellular autofluorescence. Moreover, based on studies of the rapE promoter of B. subtilis we show that the new pXFP_Star reporter system reliably reports on the weak activity of the rapE promoter whereas the original reporter system fails because of transcriptional interference. Since the pXFP_Star reporter system properly isolates the promoter from spurious transcripts, it is a particularly suitable tool for quantitative characterization of weak promoters in B. subtilis.
Effect of Poisson ratio on cellular structure formation
Ilka B. Bischofs,Ulrich S. Schwarz
Physics , 2005, DOI: 10.1103/PhysRevLett.95.068102
Abstract: Mechanically active cells in soft media act as force dipoles. The resulting elastic interactions are long-ranged and favor the formation of strings. We show analytically that due to screening, the effective interaction between strings decays exponentially, with a decay length determined only by geometry. Both for disordered and ordered arrangements of cells, we predict novel phase transitions from paraelastic to ferroelastic and anti-ferroelastic phases as a function of Poisson ratio.
Self-Trapped Exciton Defects in a Charge Density Wave: Electronic Excitations of BaBiO3
Philip B. Allen,Ilka B. Bischofs
Physics , 2001, DOI: 10.1103/PhysRevB.65.115113
Abstract: In the previous paper, it was shown that holes doped into BaBiO3 self-trap as small polarons and bipolarons. These point defects are energetically favorable partly because they undo locally the strain in the charge-density-wave (Peierls insulator) ground state. In this paper the neutral excitations of the same model are discussed. The lowest electronic excitation is predicted to be a self-trapped exciton, consisting of an electron and a hole located on adjacent Bi atoms. This excitation has been seen experimentally (but not identified as such) via the Urbach tail in optical absorption, and the multi-phonon spectrum of the ``breathing mode'' seen in Raman scattering. These two phenomena occur because of the Franck-Condon effect associated with oxygen displacement in the excited state.
Polaron and Bipolaron Defects in a Charge Density Wave: a Model for Lightly Doped BaBiO3
Ilka B. Bischofs,Vladimir N. Kostur,Philip B. Allen
Physics , 2001, DOI: 10.1103/PhysRevB.65.115112
Abstract: BaBiO3 is a prototype ``charge ordering system'' forming interpenetrating sublattices with nominal valence Bi(3+) and Bi(5+). It can also be regarded as a three-dimensional version of a Peierls insulator, the insulating gap being a consequence of an ordered distortion of oxygen atoms. When holes are added to BaBiO3 by doping, it remains insulating until a very large hole concentration is reached, at which point it becomes superconducting. The mechanism for insulating behavior of more lightly-doped samples is formation of small polarons or bipolarons. These are self-organized point defects in the Peierls order parameter, which trap carriers in bound states inside the Peierls gap. We calculate properties of the polarons and bipolarons using the Rice-Sneddon model. Bipolarons are the stable defect; the missing pair of electrons come from an empty midgap state built from the lower Peierls band. Each bipolaron distortion also pulls down six localized states below the bottom of the unoccupied upper Peierls band. The activation energy for bipolaron hopping is estimated.
Effect of adhesion geometry and rigidity on cellular force distributions
Ilka B. Bischofs,Sebastian S. Schmidt,Ulrich S. Schwarz
Quantitative Biology , 2009, DOI: 10.1103/PhysRevLett.103.048101
Abstract: The behaviour and fate of tissue cells is controlled by the rigidity and geometry of their adhesive environment, possibly through forces localized to sites of adhesion. We introduce a mechanical model that predicts cellular force distributions for cells adhering to adhesive patterns with different geometries and rigidities. For continuous adhesion along a closed contour, forces are predicted to be localized to the corners. For discrete sites of adhesion, the model predicts the forces to be mainly determined by the lateral pull of the cell contour. With increasing distance between two neighboring sites of adhesion, the adhesion force increases because cell shape results in steeper pulling directions. Softer substrates result in smaller forces. Our predictions agree well with experimental force patterns measured on pillar assays.
Focal adhesions as mechanosensors: the two-spring model
Ulrich S. Schwarz,Thorsten Erdmann,Ilka B. Bischofs
Quantitative Biology , 2006,
Abstract: Adhesion-dependent cells actively sense the mechanical properties of their environment through mechanotransductory processes at focal adhesions, which are integrin-based contacts connecting the extracellular matrix to the cytoskeleton. Here we present first steps towards a quantitative understanding of focal adhesions as mechanosensors. It has been shown experimentally that high levels of force are related to growth of and signaling at focal adhesions. In particular, activation of the small GTPase Rho through focal adhesions leads to the formation of stress fibers. Here we discuss one way in which force might regulate the internal state of focal adhesions, namely by modulating the internal rupture dynamics of focal adhesions. A simple two-spring model shows that the stiffer the environment, the more efficient cellular force is built up at focal adhesions by molecular motors interacting with the actin filaments.
Memory in Microbes: Quantifying History-Dependent Behavior in a Bacterium
Denise M. Wolf, Lisa Fontaine-Bodin, Ilka Bischofs, Gavin Price, Jay Keasling, Adam P. Arkin
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0001700
Abstract: Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These “memory” effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenological measure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE) synthesis and estimate the capacity of these systems and growth dynamics to ‘remember’ 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cell history, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy.
Topological (Sliced) Doping of a 3D Peierls System: Predicted Structure of Doped BaBiO3
Ilka B. Bischofs,Philip B. Allen,Vladimir N. Kostur,Rahul Bhargava
Physics , 2002, DOI: 10.1103/PhysRevB.66.174108
Abstract: At hole concentrations below x=0.4, Ba_(1-x)K_xBiO_3 is non-metallic. At x=0, pure BaBiO3 is a Peierls insulator. Very dilute holes create bipolaronic point defects in the Peierls order parameter. Here we find that the Rice-Sneddon version of Peierls theory predicts that more concentrated holes should form stacking faults (two-dimensional topological defects, called slices) in the Peierls order parameter. However, the long-range Coulomb interaction, left out of the Rice-Sneddon model, destabilizes slices in favor of point bipolarons at low concentrations, leaving a window near 30% doping where the sliced state is marginally stable.
Collective effects in cellular structure formation mediated by compliant environments: a Monte Carlo study
I. B. Bischofs,U. S. Schwarz
Physics , 2005, DOI: 10.1016/j.actbio.2006.01.002
Abstract: Compliant environments can mediate interactions between mechanically active cells like fibroblasts. Starting with a phenomenological model for the behaviour of single cells, we use extensive Monte Carlo simulations to predict non-trivial structure formation for cell communities on soft elastic substrates as a function of elastic moduli, cell density, noise and cell position geometry. In general, we find a disordered structure as well as ordered string-like and ring-like structures. The transition between ordered and disordered structures is controlled both by cell density and noise level, while the transition between string- and ring-like ordered structures is controlled by the Poisson ratio. Similar effects are observed in three dimensions. Our results suggest that in regard to elastic effects, healthy connective tissue usually is in a macroscopically disordered state, but can be switched to a macroscopically ordered state by appropriate parameter variations, in a way that is reminiscent of wound contraction or diseased states like contracture.
Cell organization in soft media due to active mechanosensing
I. B. Bischofs,U. S. Schwarz
Quantitative Biology , 2003, DOI: 10.1073/pnas.1233544100
Abstract: Adhering cells actively probe the mechanical properties of their environment and use the resulting information to position and orient themselves. We show that a large body of experimental observations can be consistently explained from one unifying principle, namely that cells strengthen contacts and cytoskeleton in the direction of large effective stiffness. Using linear elasticity theory to model the extracellular environment, we calculate optimal cell organization for several situations of interest and find excellent agreement with experiments for fibroblasts, both on elastic substrates and in collagen gels: cells orient in the direction of external tensile strain, they orient parallel and normal to free and clamped surfaces, respectively, and they interact elastically to form strings. Our method can be applied for rational design of tissue equivalents. Moreover our results indicate that the concept of contact guidance has to be reevaluated. We also suggest that cell-matrix contacts are upregulated by large effective stiffness in the environment because in this way, build-up of force is more efficient.
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