Cholera disease produces vomiting and severe diarrhea and causes approximately 100,000 deaths per... more Cholera disease produces vomiting and severe diarrhea and causes approximately 100,000 deaths per year worldwide. The disease is caused by the bacterium Vibrio cholerae colonizing the lining of the small intestine. V. cholerae ’s ability to swim is known to increase its infectivity, but the underlying mechanisms are not known.
How motile bacteria navigate environmental chemical gradients has implications ranging from healt... more How motile bacteria navigate environmental chemical gradients has implications ranging from health to climate science, but the underlying behavioral mechanisms are unknown for most species. The well-studied navigation strategy of Escherichia coli forms a powerful paradigm that is widely assumed to translate to other bacterial species. This assumption is rarely tested because of a lack of techniques capable of bridging scales from individual navigation behavior to the resulting population-level chemotactic performance. Here, we present such a multiscale 3D chemotaxis assay by combining high-throughput 3D bacterial tracking with microfluidically created chemical gradients. Large datasets of 3D trajectories yield the statistical power required to assess chemotactic performance at the population level, while simultaneously resolving the underlying 3D navigation behavior for every individual. We demonstrate that surface effects confound typical 2D chemotaxis assays, and reveal that, cont...
Many eukaryotic cell functions depend on dynamic instability, meaning the nucleotide-driven assem... more Many eukaryotic cell functions depend on dynamic instability, meaning the nucleotide-driven assembly and disassembly of microtubules. Assembly requires the constituent tubulin dimers to bind the nucleotide GTP, and its subsequent hydrolysis to GDP induces disassembly. The underlying structural mechanisms, however, are not well understood. Here, we determine the strength of contacts in the microtubule lattice by combining high precision measurements of the bending stiffness of analogues of GTP and GDP microtubules with a recent theoretical model. While previous structural studies have focussed on how the curvature of the tubulin dimer is affected by nucleotide binding, we present evidence of a dramatic regulation of the lateral interactions between the parallel protofilaments that dimers form in the microtubule. We conclude that the shear coupling between neighboring protofilaments is at least two orders of magnitude stronger in the GTP state than in the GDP state, and discuss the im...
The mechanical properties of microtubules have been the subject of intense study during recent de... more The mechanical properties of microtubules have been the subject of intense study during recent decades because of their importance to the many cell functions that they are involved in. Observations of microtubule thermal fluctuations have proven to be a reliable method to extract mechanical properties because they provide intrinsic calibration. While analysis of the entire microtubule shape is limited by spatial resolution to very long microtubules, we show that even for short microtubules, one can obtain high-precision fluctuation information from one point along the contour by the use of tracer particles attached to the microtubule. The information is sufficient to extract key mechanical parameters such as stiffness and first mode relaxation time. In this article, we discuss sample preparation as well as measurements and data analysis.
Environmental changes can not only trigger a regulatory response, but also impose evolutionary pr... more Environmental changes can not only trigger a regulatory response, but also impose evolutionary pressures that can modify the underlying regulatory network. Here, we review recent approaches that are beginning to disentangle this complex interplay between regulatory and evolutionary responses. Systematic genetic reconstructions have shown how evolutionary constraints arise from epistatic interactions between mutations in fixed environments. This approach is now being extended to more complex environments and systems. The first results suggest that epistasis is affected dramatically by environmental changes and, hence, can profoundly affect the course of evolution. Thus, external environments not only define the selection of favored phenotypes, but also affect the internal constraints that can limit the evolution of these phenotypes. These findings also raise new questions relating to the conditions for evolutionary transitions and the evolutionary potential of regulatory networks.
At timescales once deemed immeasurably small by Einstein, the random movement of Brownian particl... more At timescales once deemed immeasurably small by Einstein, the random movement of Brownian particles in a liquid is expected to be replaced by ballistic motion. So far, an experimental verification of this prediction has been out of reach due to a lack of instrumentation fast and precise enough to capture this motion. Here we report the observation of the Brownian
High precision position measurements often involve the detection of a laser beam that interacts w... more High precision position measurements often involve the detection of a laser beam that interacts with various components of an experimental setup. In order to achieve the highest precision, instabilities that contribute to a decrease in precision must be identified and quantified. Instabilities include fluctuations in the laser power, fluctuations in the laser pointing and fluctuations in the phase, as well as vibrating mechanical components that are susceptible to excitations and drift. Instabilities lead to unwanted resonances and band structures in the power spectral density of the detector signals. Typically, the most important instabilities are identified by the magnitude and location of resonances or bands in the power spectral density. However, power spectral density plots can be misleading if the width or shape of a resonance or a band are not correctly accounted for. This is especially true for measurements that span a large bandwidth. Here, we discuss Power Spectral Density Integration Analysis as a more intuitive and accurate method for identifying and quantifying instabilities. Resonances and bands are readily identified as step-like features with heights that correctly represent their contribution to the error in the position measurement.
Cholera disease produces vomiting and severe diarrhea and causes approximately 100,000 deaths per... more Cholera disease produces vomiting and severe diarrhea and causes approximately 100,000 deaths per year worldwide. The disease is caused by the bacterium Vibrio cholerae colonizing the lining of the small intestine. V. cholerae ’s ability to swim is known to increase its infectivity, but the underlying mechanisms are not known.
How motile bacteria navigate environmental chemical gradients has implications ranging from healt... more How motile bacteria navigate environmental chemical gradients has implications ranging from health to climate science, but the underlying behavioral mechanisms are unknown for most species. The well-studied navigation strategy of Escherichia coli forms a powerful paradigm that is widely assumed to translate to other bacterial species. This assumption is rarely tested because of a lack of techniques capable of bridging scales from individual navigation behavior to the resulting population-level chemotactic performance. Here, we present such a multiscale 3D chemotaxis assay by combining high-throughput 3D bacterial tracking with microfluidically created chemical gradients. Large datasets of 3D trajectories yield the statistical power required to assess chemotactic performance at the population level, while simultaneously resolving the underlying 3D navigation behavior for every individual. We demonstrate that surface effects confound typical 2D chemotaxis assays, and reveal that, cont...
Many eukaryotic cell functions depend on dynamic instability, meaning the nucleotide-driven assem... more Many eukaryotic cell functions depend on dynamic instability, meaning the nucleotide-driven assembly and disassembly of microtubules. Assembly requires the constituent tubulin dimers to bind the nucleotide GTP, and its subsequent hydrolysis to GDP induces disassembly. The underlying structural mechanisms, however, are not well understood. Here, we determine the strength of contacts in the microtubule lattice by combining high precision measurements of the bending stiffness of analogues of GTP and GDP microtubules with a recent theoretical model. While previous structural studies have focussed on how the curvature of the tubulin dimer is affected by nucleotide binding, we present evidence of a dramatic regulation of the lateral interactions between the parallel protofilaments that dimers form in the microtubule. We conclude that the shear coupling between neighboring protofilaments is at least two orders of magnitude stronger in the GTP state than in the GDP state, and discuss the im...
The mechanical properties of microtubules have been the subject of intense study during recent de... more The mechanical properties of microtubules have been the subject of intense study during recent decades because of their importance to the many cell functions that they are involved in. Observations of microtubule thermal fluctuations have proven to be a reliable method to extract mechanical properties because they provide intrinsic calibration. While analysis of the entire microtubule shape is limited by spatial resolution to very long microtubules, we show that even for short microtubules, one can obtain high-precision fluctuation information from one point along the contour by the use of tracer particles attached to the microtubule. The information is sufficient to extract key mechanical parameters such as stiffness and first mode relaxation time. In this article, we discuss sample preparation as well as measurements and data analysis.
Environmental changes can not only trigger a regulatory response, but also impose evolutionary pr... more Environmental changes can not only trigger a regulatory response, but also impose evolutionary pressures that can modify the underlying regulatory network. Here, we review recent approaches that are beginning to disentangle this complex interplay between regulatory and evolutionary responses. Systematic genetic reconstructions have shown how evolutionary constraints arise from epistatic interactions between mutations in fixed environments. This approach is now being extended to more complex environments and systems. The first results suggest that epistasis is affected dramatically by environmental changes and, hence, can profoundly affect the course of evolution. Thus, external environments not only define the selection of favored phenotypes, but also affect the internal constraints that can limit the evolution of these phenotypes. These findings also raise new questions relating to the conditions for evolutionary transitions and the evolutionary potential of regulatory networks.
At timescales once deemed immeasurably small by Einstein, the random movement of Brownian particl... more At timescales once deemed immeasurably small by Einstein, the random movement of Brownian particles in a liquid is expected to be replaced by ballistic motion. So far, an experimental verification of this prediction has been out of reach due to a lack of instrumentation fast and precise enough to capture this motion. Here we report the observation of the Brownian
High precision position measurements often involve the detection of a laser beam that interacts w... more High precision position measurements often involve the detection of a laser beam that interacts with various components of an experimental setup. In order to achieve the highest precision, instabilities that contribute to a decrease in precision must be identified and quantified. Instabilities include fluctuations in the laser power, fluctuations in the laser pointing and fluctuations in the phase, as well as vibrating mechanical components that are susceptible to excitations and drift. Instabilities lead to unwanted resonances and band structures in the power spectral density of the detector signals. Typically, the most important instabilities are identified by the magnitude and location of resonances or bands in the power spectral density. However, power spectral density plots can be misleading if the width or shape of a resonance or a band are not correctly accounted for. This is especially true for measurements that span a large bandwidth. Here, we discuss Power Spectral Density Integration Analysis as a more intuitive and accurate method for identifying and quantifying instabilities. Resonances and bands are readily identified as step-like features with heights that correctly represent their contribution to the error in the position measurement.
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Papers by Katja Taute