Technical ReportsOpen access technical reports in biomedical informaticshttp://hdl.handle.net/1803/652019-02-21T04:44:13Z2019-02-21T04:44:13ZViral flight data recorder for systems biology applicationsBoczko, Erik M.http://hdl.handle.net/1803/12222011-02-11T17:46:08Z2008-08-13T00:00:00ZViral flight data recorder for systems biology applications
Boczko, Erik M.
The paper briefly describes the construction of self organizing nanoparticles that can be designed to detect and record arbitrary intracellular events. The basic design captures nucleic acids. The design utilizes a single viral coat protein to nucleate a capsid if and only if a quantum of specific intracellular events occur.
2008-08-13T00:00:00ZAge distribution formulas for budding yeastBoczko, Erik M.Ban, Hyunjuhttp://hdl.handle.net/1803/11662011-02-11T17:45:42Z2008-08-05T18:15:41ZAge distribution formulas for budding yeast
Boczko, Erik M.; Ban, Hyunju
Yeast are an important eukaryotic model system in the study of aging.
Replicative age in budding yeast can be quantitatively determined by visualizing chitanous bud scars.
The dynamics of the process of growth and division effects the distribution of replicative age.
How much physiological information is encoded in experimental age distributions is not fully understood.
Formulas relating
the stationary age distribution to the spectrum of generational and culture doubling times
have been proposed by several authors over the past four decades.
We discuss the assumptions upon which they rest and some natural extensions.
We describe the replicative age distribution of a population growing exponentially
in terms of generational flux residence times.
We demonstrate the utility of this description and show that it produces excellent agreement with experimental data,
and describe how it compares with previous work. We demonstrate that the
age distribution in a variety of strains can be predicted by a realistic population model, and we indicate
how the age distribution is altered by perturbations and control.
2008-08-05T18:15:41ZNext-generation quantitative measurements to validate a model for yeast nitrogen catabolite repression in Saccharomyces cerevisiaeStowers, ChrisBoczko, Erik M.http://hdl.handle.net/1803/1852011-02-11T17:45:40Z2007-02-12T14:10:02ZNext-generation quantitative measurements to validate a model for yeast nitrogen catabolite repression in Saccharomyces cerevisiae
Stowers, Chris; Boczko, Erik M.
Our work is motivated by the desire to quantitatively measure biological dynamical systems. Our agenda is to describe and understand emergent behavior and to explain the observed super robustness of biological dynamics. The specific system that provides the focus for our work is an ostensibly simple stress response circuit in baker's yeast, Saccharomyces cerevisiae, that regulates the organisms' genetic response to nitrogen limitation called nitrogen catabolite repression (NCR). The circuitry of the network has been well studied for the last 40 years and comparatively much is known about its function, however, little is known about its dynamics. In order to study the dynamics at the same level of sophistication at which we formulate and reason with mathematical models, we require quantitative biophysical and biochemical techniques that are accurate at molecular dimensions on physiological timescales. Such techniques are currently in their infancy. The overall goal is to further develop the tools and techniques to measure the quantitative biological behavior of the NCR circuit well enough to refine a current NCR model and understand how to apply the model to other regulatory networks leading to advances in biology, control theory and beyond. The broader impact of our effort reaches far beyond understanding the molecular physiology of a simple fungal stress response towards a deeper understanding of the underpinnings of why some circuits persist while others do not.
2007-02-12T14:10:02ZMolecular Seismology: An inverse problem in nanobiology.Boczko, Erik M.Hinow, Peterhttp://hdl.handle.net/1803/1532011-02-11T17:55:17Z2006-09-12T19:44:22ZMolecular Seismology: An inverse problem in nanobiology.
Boczko, Erik M.; Hinow, Peter
The density profile of an elastic fiber like DNA will change in space and time as
ligands associate with it. This observation affords a new direction in single molecule
studies provided that density profiles can be measured in space and time. In fact, this
is precisely the objective of seismology, where the mathematics of inverse problems
have been employed with success. We argue that inverse problems in elastic media
can be directly applied to biophysical problems of fiber-ligand association, and demonstrate that
robust algorithms exist to perform density reconstruction in the condensed phase.
2006-09-12T19:44:22Z