2004 — 2009 |
Goodrich, James (co-PI) [⬀] Betterton, Meredith Perkins, Thomas [⬀] |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Nirt: Watching Proteins Bend Dna With Subnanometer Resolution @ University of Colorado At Boulder
This proposal was received in response to Nanoscale Science and Engineering initiative, NSF 03-043, category NIRT. This interdisciplinary research effort will combine high-resolution single-molecule experiments and mathematical modeling with ensemble biochemical assays to study protein-DNA interactions that control gene expression.
The human transcription factor TATA box-binding protein (TBP) is the central protein in a larger protein complex (TFIID) that binds to DNA sequences in genes and controls how genes are transcribed into messenger RNA. The proposed project will investigate the mechanism of DNA binding by single TBP molecules and TFIID complexes to illuminate a key first step in transcription initiation. A unique optical trapping instrument with sub-nanometer resolution will be developed to enable single-molecule studies of biological complexes. The improved apparatus will allow direct detection of the binding of TBP to TATA-box sequences, via the apparent shortening of a DNA molecule due to the 100-degree kink in the DNA backbone caused by TBP. Ensemble biochemical experiments will be carefully coordinated for comparison with the innovative single-molecule results. Theoretical analysis of the experimental data will determine the bend angle, and provide testable predictions for the search time required by TBP to find the TATA box. The analysis will enable an energetic description of the binding as a function of DNA tension and will further illuminate the structure of multi-protein complexes bound to DNA, by predicting the different experimental signatures of protein-induced bending of the DNA and wrapping of the DNA around the complex. Experiments and theoretical analysis will examine how DNA length, the number of TATA-box sequences per DNA construct, and the presence of other DNA-binding obstacle proteins affect the time for TBP to find a TATA box.
The project takes a multifaceted approach to education that will include training of undergraduate and graduate students in research, mentoring students in course development and science teaching, and using a unique mechanism to explain the science to the general public. Students will develop a deep understanding of biophysics and its interrelation to other disciplines. Joint meetings of the interdisciplinary research team will bring together students and researchers with backgrounds including applied math, biology, and physics.
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0.915 |
2005 — 2008 |
Betterton, Meredith Qi, Hang (Jerry) |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
A Multiscale Modeling Approach For Large Deformation Behavior of Erythrocyte Membrane @ University of Colorado At Boulder
The goal of the proposed research is to develop a micromechanical modeling framework that links the large deformation behavior of erythrocyte (red blood cell) cytoskeleton membrane to its detailed structure and single protein macromolecule behaviors. The erythrocyte cytoskeleton membrane is an extraordinary material system that combines a fluidic lipid bilayer with a rubber-like scaffolding protein network to form a flexible membrane that can undergo large deformation. Recent studies on the diseased red blood cells indicate that the membrane structure and the single protein macromolecule behaviors play a critical role in determining the shape and deformability, and thus the physiological functions of red blood cells. However, previous studies on the shape and deformation of cytoskeletal membrane using continuum mechanics neglect the detailed information about the structure of the cytoskeleton membrane. As a consequence, the structure-deformability relationship cannot be established. In the proposed work, a micromechanical modeling framework that is based on the structure of erythrocyte cytoskeleton membrane will be developed. The micromechanically representative volume element will be modeled as a rubbery membrane (skeletal protein network) attached to two membrane layers (the lipid bilayer) via connecting elements (integral proteins). Parametric studies which simulate the structure change of red blood cell under diseased conditions will be conducted to investigate the structure-function relationship of large deformation behavior of erythrocyte cytoskeleton membrane. The proposed research will inspire new concepts for developing a structure based constitutive model to describe the large deformation behavior of red blood cells, and will greatly assist the exploration of the molecular mechanism of red blood cell deformations under diseased conditions. The methodology of combining nanomechanics with the new knowledge in life science is expected to bring in new insight into the miracle of life and eventually result in revolutionary new therapy and improvement of human health. In addition, the proposed work, together with proposed education plans, will enhance higher education in nanotechnology and biotechnology and will inspire young scientists and engineers to develop their careers in this exciting field.
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0.915 |
2005 — 2006 |
Betterton, Meredith Clark, Noel Glaser, Matthew [⬀] Maclennan, Joseph Walba, David (co-PI) [⬀] |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Ner: Design and Synthesis of Light-Driven Molecular Motors @ University of Colorado At Boulder
In this award, funded by the Experimental Physical Chemistry Program of the Chemistry Division, Profs. Matthew A. Glaser, Meredith D. Betterton, Noel A. Clark, Joseph E. Maclennan and David M. Walba of the University of Colorado and their graduate research students will design and synthesize light-driven molecular motors. The work will be based upon specific small-molecule versions of Brownian ratchets. The specific systems to be employed will be photolabile molecules deposited on well-characterized, low-symmetry substrates. These systems are analogous to biological motor systems.
The potential impact of working, light-driven molecular motors is significant. They might find use in nanoscale rotors, shuttles and switches, artificial muscle systems, chiral separation and detection systems, and ratchet-based force microscopies. The students working on this project will gain experience working on a potentially high-impact project in an intensely interdisciplinary environment.
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0.915 |
2009 — 2015 |
Betterton, Meredith |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Career: Molecular Motors and Protein Motion: From Mechanisms to Collective Effects @ University of Colorado At Boulder
This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).
TECHNICAL SUMMARY This CAREER award will support an integrated research and education program in the field of theoretical biophysics, with interdisciplinary support from the Division of Materials Research, the Division of Molecular and Cellular Biosystems, and the Division of Mathematical Sciences. The research component will address addresses the theory of directed and diffusive protein motion, active gels, and DNA target recognition, with emphasis on incorporating polymer elasticity effects into models of protein motion on DNA and crowding and collective effects in protein motion.
The research will have applications in important biological problems such as gene expression, DNA copying, DNA repair, and cell division. It will contribute to the broader effort in the community studying molecular motors to understand diverse motor proteins, and to develop theoretical tools to predict the behavior of systems of interacting proteins. It will also contribute to understanding both the function of motor proteins in crowded cellular environments, and the role of nucleic-acid motors in macromolecular complexes. This work is strongly interdisciplinary, because the research bridges statistical physics, theoretical chemistry, and molecular biophysics.
The education component aims to increase the connection between physics and biology in introductory physics courses at CU-Boulder. Integrating biologically relevant course materials will help students understand that physics is important in many fields, including biology and medicine. The second education aim is to integrate biophysics into the undergraduate physics curriculum at CU-Boulder by developing a biophysics course. The physics department does not currently teach a biophysics course, so this aim will enhance the education of students at CU-Boulder. The proposed education work will be carried out in collaboration with the Physics Education Research group at the University of Colorado to incorporate cutting-edge educational methods and assessment.
NONTECHNICAL SUMMARY This CAREER award will support an integrated research and education program in the field of theoretical biophysics, with interdisciplinary support from the Division of Materials Research, the Division of Molecular and Cellular Biosystems, and the Division of Mathematical Sciences. The research component of this award addresses novel problems in theoretical biophysics involving the directed and random motions of proteins and related biomolecular systems.
The research will have applications in important biological problems such as gene expression, DNA copying, DNA repair, and cell division. It will contribute to the broader effort in the community studying molecular motors to understand diverse motor proteins, and to develop theoretical tools to predict the behavior of systems of interacting proteins. It will also contribute to understanding both the function of motor proteins in crowded cellular environments, and the role of nucleic-acid motors in macromolecular complexes. This work is strongly interdisciplinary, because the research bridges statistical physics, theoretical chemistry, and molecular biophysics.
The education component aims to increase the connection between physics and biology in introductory physics courses at CU-Boulder. Integrating biologically relevant course materials will help students understand that physics is important in many fields, including biology and medicine. The second education aim is to integrate biophysics into the undergraduate physics curriculum at CU-Boulder by developing a biophysics course. The physics department does not currently teach a biophysics course, so this aim will enhance the education of students at CU-Boulder. The proposed education work will be carried out in collaboration with the Physics Education Research group at the University of Colorado to incorporate cutting-edge educational methods and assessment.
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0.915 |
2011 — 2015 |
Betterton, Meredith |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Collaborative Research: Hydrodynamic Theories of the Dynamics, Fluctuations, Boundaries, and Shapes of Flocks @ University of Colorado At Boulder
This proposal will develop the theory of "flocking": the collective, coherent motion of large numbers of organisms or biomolecules. This ubiquitous biological phenomenon occurs for organisms (flocks of birds, schools of fish), cells (collections of swimming bacteria, migration of cancer cells in tumors) and subcellular molecules (long molecules such as microtubules and actin filaments involved in the operation and reproduction of cells). The project will apply ideas originally developed for fluid dynamics (air flow over airplane wings, weather forecasting, and plumbing) to flocks.
This project will extend that approach to investigating what holds flocks together at their boundaries; to study the effects of birth and death of organisms or molecules (which is very important for molecules inside living cells, which are constantly created and destroyed as they move), and to compare predictions of the theory with experiments on diverse biological systems. Among these are experiments on the mitotic spindle, a spindle-shaped structure of long, rigid molecules called microtubules that forms inside cells when they divide, and which acts to separate the chromosomes into the two daughter cells. This work will also address flocks of organisms (such as birds and fish) to study their shapes and how those shapes fluctuate as the flock moves.
This work is strongly interdisciplinary and will advance condensed-matter physics, molecular biophysics, cellular biology, fluid mechanics, organismal biology, and medicine (through a deeper understanding of processes that impact cancer cell migration and wound healing). The proposed work will integrate research and learning by involving students and postdoctoral fellows in the research, and through the development of new course materials at CU-Boulder and the University of Oregon.
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0.915 |
2012 — 2017 |
Betterton, Meredith Lladser, Manuel Cech, Thomas [⬀] Anseth, Kristi (co-PI) [⬀] Dowell, Robin |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Igert: Interdisciplinary Quantitative Biology Program @ University of Colorado At Boulder
This Integrative Graduate Education and Research Traineeship (IGERT) award will provide graduate students with the mathematical and computational training necessary to excel in the collaborative world of quantitative bioscience and make a positive impact on society through the application of their research. Quantitative biology is a transformative approach to bioscience and bioengineering research, which embraces a combination of quantitative skills and biological insight applied to previously intractable research problems.
Intellectual Merit: Led by the University of Colorado Biofrontiers Institute, eight science, engineering and math departments will collaborate to address the national need for both interdisciplinary and quantitative training at the graduate level. IQ Biology will create new infrastructure for interdisciplinary graduate programs by providing a mechanism to bring trainees directly into interdisciplinary cohorts and remove hurdles for trainees participating in courses and research that cross departmental and college boundaries. Additionally, trainees will participate in innovation training activities through industry internships, non-academic mentors, symposia, and multidisciplinary team collaborations with faculty and business school colleagues.
Broader Impacts: This IGERT project will help define a new approach to graduate education, catalyze institutional change, foster innovation, encourage global thinking and engage the public in scientific discovery. IQ Biology will create cohorts of graduate students who have disciplinary depth and are uniquely qualified to cross academic boundaries throughout their careers. Building on the University?s commitment to increase diversity in STEM disciplines, IQ Biology works with CU-Boulder?s successful programs to recruit and retain students from underrepresented groups.
IGERT is an NSF-wide program intended to meet the challenges of educating U.S. Ph.D. scientists and engineers with the interdisciplinary background, deep knowledge in a chosen discipline, and the technical, professional, and personal skills needed for the career demands of the future. The program is intended to establish new models for graduate education and training in a fertile environment for collaborative research that transcends traditional disciplinary boundaries, and to engage students in understanding the processes by which research is translated to innovations for societal benefit.
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0.915 |
2014 — 2016 |
Betterton, Meredith |
K25Activity Code Description: Undocumented code - click on the grant title for more information. |
Assessing the Contributions of Microtubule Dynamic Instability and Microtubule Ro
DESCRIPTION (provided by applicant): The PI of this Mentored Career Development Award proposal has significant experience in biophysics theory, and a long history of working closely in collaboration with experimentalists. However, her lack of direct experimental training has proved to be a severe limitation in her progress toward her long-term career objective: to advance the understanding of chromosome motions and mitosis, and related human-health issues, through an integrated experimental and theoretical approach. This grant will provide protected training time in order for the PI to: (1) Learn to design and conduct experiments. This will require practical laboratory training in a range of techniques in biophysics, cell biology, molecular biology, genetics, and biochemistry. (2) Educate herself in biology to complement her physics training and to allow her to formulate cutting-edge, biologically relevant research questions. This will require participation in conferences, workshops, seminars, and journal clubs. (3) Develop her expertise as she manages an experimental laboratory. This will require training in lab safety, grant writing, and the responsible conduct of research. The research component of the project will address the capture of kinetochores (KCs) by microtubules (MTs) in cell division. For years the primary mechanism of KC capture in mitosis was believed to be microtubule search and capture, in which dynamic MTs grow in different directions from centrosomes and make end-on attachments with KCs. However, recent work found that lateral KC attachment to rotationally diffusing MTs enabled rapid KC capture even with significantly reduced MT dynamics. Previous work has focused exclusively on MT dynamic instability or rotational diffusion and therefore has been unable to compare the two mechanisms and determine their relative importance. The specific aims are: 1: Evaluate the importance of microtubule dynamic instability and rotational diffusion to kinetochore capture using quantitative imaging and a first-generation model. The preliminary model developed for this proposal is believed to be the first model of KC capture that includes both MT dynamic instability and MT and KC diffusion. Measurements will be made of the fraction of lost KCs and polar MT lengths as a function of time after recovery from cold block will determine the time course of KC capture; the data will be used to fit unknown parameters in the model. The model will allow assessment the importance of MT rotation and dynamic instability, separately and together, for KC capture. 2: Measure the dynamics of mitotic nuclear polar microtubules and use the measured parameters to create a second-generation kinetochore capture model. The study in Aim 1 requires fitting key model parameters for MT dynamic instability. Because uncertainty in model parameters leads to uncertainty in model predictions, for a reliable and accurate model it is best to use measured values of MT dynamic instability parameters, rather than relying on estimates or fits. However, dynamics of nuclear polar MTs in mitosis have not previously been measured in sufficient detail to build a quantitative model without unknown parameters. Because these MTs are short-lived, several live-cell imaging approaches will be compared to determine MT dynamics parameters. 3: Predict and measure how alterations in microtubule dynamics affect the time course of kinetochore capture. Biological perturbations such as disease states can lead to alterations in MT dynamics, but it is not understood how these alterations affect KC capture. Current models are not able to predict how MT dynamics affect KC. The model will be used to find sensitive regions of parameter space where small changes in MT dynamics parameters lead to relatively large changes in the time course of KC capture. Multiple experimental perturbations are available to perturb MT dynamics in fission yeast. The results will test the understanding of the contributions of MT dynamic instability and rotational diffusion to KC capture. The PI will be mentored under this grant by J. Richard McIntosh, an esteemed scientist whose work has focused on cell division in the model organism S. pombe. He will provide lab space and equipment to allow the PI to fulfill the aims of this grant. This will be an ideal training environment, as McIntosh has recently retired from teaching, though still maintains an active research lab. The PI is an associate professor at the University of Colorado, Boulder. There are several initiatives in place at CU Boulder that have fostered a strong interdisciplinary research environment. The PI is part of the Biofrontiers Institute, and attends monthly meetings with her biophysics colleagues from a range of departments. The institution is committed to fully supporting the PI as she learns techniques in cell biology.
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0.915 |
2015 — 2017 |
Betterton, Meredith |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Eager: Biophysical Theory of Mitotic Spindle Length Instability and Self Assembly @ University of Colorado At Boulder
NONTECHNICAL SUMMARY
This award is made on an EAGER proposal, and it supports theoretical research and education on the biophysical theory of mitotic spindle length instability and self-assembly. The mitotic spindle is an important part of the cytoskeleton in eukaryotic cells. It is a self-assembled three-dimensional structure, primarily composed of tubes made from specific proteins, and it functions as a molecular machine that separates chromosomes during cell division. The ultimate goal of this research program is to provide an answer to the fundamental question: "How can the mitotic spindle, a non-equilibrium structure with constant molecular turnover i) self-assemble, and ii) maintain a fixed length." The PI intends to model the spindle length dynamics and self-assembly at multiple scales, ranging from nanometer to micron, bringing together ideas from statistical physics, molecular biophysics, structural, molecular, and cellular biology. The effort has a very substantial computational component involving a large-scale modeling framework. The PI intends to make the developed software freely available through an open-source license.
TECHNICAL SUMMARY
Cells self-organize and dynamically generate complex three-dimensional structures. Filament nucleation, polymerization, and interaction-driven rearrangement are regulated in space and time to construct a wide variety of assemblies. An important general question in the study of self-organized cytoskeletal structures is how to integrate molecular-level knowledge to predict higher-order aspects of assembly and organization. A prototypical self-assembled cytoskeletal structure is the mitotic spindle, a microtubule-based machine that segregates chromosomes during eukaryotic cell division. This project will create a physical theory of the fission yeast mitotic spindle that recapitulates spindle length stability/fluctuations and bipolar spindle assembly to address the fundamental question of how a non-equilibrium structure with constant molecular turnover can self-assemble and maintain a fixed length. This project has three components. The PI will first develop essential model ingredients including multiple species of motors/crosslinks, novel motor force-velocity relations, two-stage binding/unbinding of motors/crosslinks, and dynamic microtubules. Then the PI will determine the mechanisms underlying mitotic spindle length fluctuations and stabilization of spindle length through the integration of models that span from nanometer to micron scales. This component will lead to the development of a quantitative physical theory of dynamic stabilization of spindle length. Subsequently, the PI will determine the ingredients necessary for bipolar bundle assembly in a minimal model of the fission yeast mitotic spindle. This work will involve computational screens to find regions of model/parameter space associated with self-assembly of a stable spindle-like microtubule bundle and comparison to tomographic models. The effort has a very substantial computational component involving a large-scale modeling framework. The PI intends to make the developed software freely available through an open-source license.
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0.915 |
2016 — 2019 |
Glaser, Matthew [⬀] Betterton, Meredith |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Collaborative Research: Multiscale Study of Active Cellular Matter: Simulation, Modeling, and Analysis @ University of Colorado At Boulder
Active cellular matter is the basis of novel synthetic active fluids made of mixtures of suspended cytoskeletal filaments and molecular motors. By consuming chemical fuel, the molecular motors (e.g., kinesins) can bind to and create actively moving crosslinks between the biofilaments (e.g., microtubules) to drive their relative motion, which leads to large-scale collective motions in the filament/motor mixture through hydrodynamic coupling. Synthetic active suspensions made of small numbers of components reveal how higher-order aspects of assembly and organization are built in living cells. These systems also present new challenges to our understanding, design, and analysis of materials, and have the potential to provide valuable new technologies such as autonomously moving and self-healing materials.
In this work, the investigators study active cellular matter composed of microtubules and molecular motors through multiscale methods, and tightly coupled modeling, analysis, and simulation. The project aims to understand the fundamental interactions underlying stress generation within bundles of rigid/flexible biofilaments that undergo dynamic instability, as well as the nonlinear dynamics and hierarchical pattern formation in large-scale collective motions. The project will also predict key material properties including its coherent structures, local heterogeneity, time- and length-scales, and material rheology. To resolve the physics at different length- and time-scales, several methods will be developed and integrated: (1) microtubule-motor interactions will be simulated using a kinetic Monte Carlo method; (2) the hydrodynamic interactions between objects of various shapes will be modeled using a nonlocal slender body/boundary integral method, together with fast summation methods; (3) a pseudo-spectral method will be implemented to simulate the collective motion through a continuous active liquid-crystal type model.
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0.915 |
2018 — 2021 |
Betterton, Meredith |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Mechanisms of Kinesin-5 Motors in Mitotic Spindle Assembly
Summary The mitotic spindle segregates chromosomes prior to eukaryotic cell division. Motor proteins, crosslinkers, and associated proteins organize spindle microtubules to assemble the bipolar spindle. Among spindle proteins, kinesin-5 motors are particularly important because they are essential to establish a bipolar spindle in most or- ganisms. Tetrameric kinesin-5s are known to crosslink overlapping antiparallel microtubules in the center of the spindle, then step toward plus ends of each microtubule in the pair. This generates force to slide apart antipar- allel microtubules and thereby separate mitotic spindle poles. Contradicting this model are observations that kinesin-5s traf?c in both directions along microtubules and localize near microtubule minus ends, in part by binding -tubulin. Both of these poorly understood mechanisms may be important for spindle-pole separation to establish a bipolar spindle, but whether they are essential is unknown. Additionally, kinesin-5 C-terminal tails are a phosphorylation hotspot important for spindle assembly, but the properties altered by phosphoryla- tion are unclear. This evidence points to a key gap in our understanding of spindle-assembly mechanisms. In preliminary work, we made two key observations: ?rst, kinesin-5/Cut7 moves bidirectionally on ?ssion- yeast spindle microtubules at speeds similar to those measured in vitro. Second, mitotic-spindle-pole separation can occur when Cut7 remains localized at one spindle pole. Thus kinesin-5's two unusual properties may play key roles in positioning the motor to enable proper force generation for spindle pole separation. Further, phos- phorylation of the C-terminal tails may regulate these functions. We hypothesize that kinesin-5 bidirectional movement and spindle-pole localization enable force generation to separate spindle poles, and that cells regu- late this motor's directionality and localization. To test these hypotheses, we will use an interdisciplinary approach combining kinesin-5 perturbation dur- ing mitosis in ?ssion yeast, quantitative light microscopy and image analysis, and computational modeling. To determine the cellular cues that bias kinesin-5/Cut7 directionality toward either plus or minus ends of spindle microtubules, we will test the hypotheses that (1) crowding on the microtubule lattice by binding proteins, (2) motor crosslinking state, and/or (3) phosphorylation alter Cut7 directional bias in vivo. The result will be a sys- tematic comparison of proposed handles cells might use to direct Cut7 on the spindle. To identify the relative contributions of kinesin-5/Cut7 spindle-pole tethering and bidirectional motility to spindle-pole separation, we will measure and model spindle assembly and kinesin-5 localization in cells with speci?c perturbations to motor spindle-pole tethering and directional bias. Further, we will de?ne the role of the Cut7 tail and its phos- phorylation in spindle-pole tethering. This work will systematically test the hypotheses that direct spindle-pole binding and/or bidirectional motility are essential for spindle assembly. The results of this project will de?ne the kinesin-5 properties required for spindle-pole separation during mitotic spindle assembly.
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0.915 |