Browsing by Subject "Kinesin"
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Item Modeling and analysis of microtubule-mediated chromosome transport during mitosis.(2008-08) Gardner, Melissa KleinDuring mitosis, dynamic arrays of kinetochore-associated microtubules (kMTs) and molecular motors are organized into a mitotic spindle that serves to accurately segregate chromosomes into daughter cells. Understanding the dynamics and organization of mitotic spindle components could ultimately apply to clinical applications, such as in cancer treatment, because of the centrality of the mitotic spindle in mediating cell mitosis. Computer simulation can provide a bridge between mitotic spindle phenotypes and the individual dynamic spindle components that produce these phenotypes. I have found that by simulating the dynamics of kMTs mediating chromosome segregation during mitosis, it is possible to build a model for their regulation which results in specific predictions for molecular functions within the mitotic spindle. Specifically, by simulating the dynamics of molecular motors and chromosomes relative to kMT dynamics, and by comparing these simulations to experiments using fluorescent proteins and cryo-electron tomography, major mechanisms regulating proper chromosome congression in yeast have been uncovered. I have shown (1) that tension generated via the stretch of chromosomes between sister kinetochores is important in regulating the proper separation of sister kinetochores during metaphase, and (2) that a molecular motor, specifically the Kinesin-5 molecular motor Cin8p, is responsible for mediating a gradient in kMT catastrophe frequency that is required for proper chromosome congression. Dynamic microtubule plus-ends are responsible for the proper segregation of chromosomes during mitosis, as well as for other critical cellular functions. By performing molecular-level Monte Carlo simulations of microtubule assembly and comparing these simulations to in vitro measurements of microtubule assembly, I have found that microtubule assembly at the nanoscale is highly variable. This result supports a model for microtubule dynamic instability in which there is exists a substantial and dynamic GTP-cap during microtubule assembly that is critical for microtubule growth.Item Novel tools for biophysics research.(2012-01) Aggarwal, TanujThis dissertation is aimed toward furthering biophysical studies using novel instrumentation techniques and algorithms. This work describes the development of optical tweezers as an instrumentation platform to study single bio-molecules. Algorithms for signal processing, data analysis are also developed in this thesis within the purview of single molecule experiments but also extensible to a wide array of applications. These tools are tested on experimental data obtained from samples prepared using protocols that are also a part of this work. Key contributions of the thesis includes the following: (i) Construction of optical tweezers with an emphasis on measures taken to reduce the unwanted extrinsic noise in the measurements. (ii) Development of an artificial neural network based technique to increase the measurement range of the instrument by twice the previously reported value. (iii) Application of a recursive least squares based approach to estimate the persistence length of a double stranded DNA molecule in real-time. (iv) Theoretically analyzing a coupled oscillator system as a sensor compared to a single oscillator system. (v) Development of analysis tools and experimental schemes to extract parameters that model kinesin flexibility. (vi) Development of a three-dimensional, multi-motor simulation environment to understand complicated dynamics of multi-motor transport and better interpretation of experimental data. (vii) Development and analysis of an algorithm to fit step signal to a noisy data from single molecule experiments that give better fitting than existing algorithms. The step detection algorithm is further extended to detect events like sudden changes in the parameters of the system in presence of non-linearities.