Some of the projects I worked on during my academic years..
The effects of macromolecular crowding in enzyme kinetics
Studies of diffusion controlled biochemical reactions have been carried out in dilute solutions (in vitro). However, in an intracellular environment (in vivo), there is a high concentration of macromolecules, which results in nonspecific interactions (macromolecular crowding). Over the years, researchers have explored the effects of crowding on enzyme catalysis in vitro. Generally, the process consists in the addition of a particular concentration of enzyme to a sample mixture of substrate and crowding agents in a buffer. The reaction progress is followed by monitoring the release of product. In a particular set of conditions, the Michaelis-Menten equation (a simplification of the law of mass action equations used to describe the rate at which chemical species change in the solution) can be used to describe the rate of product formation. This quasi-steady state approximation produces a time independent description of the reaction kinetics, based on two parameters: Vmax, maximum rate of product formation; and Km, the concentration of substrate at which the reaction reaches half of the maximum rate. Published literaturein in vitro studies of enzymatic reactions indicates Vmax and Km dependence on macromolecular crowding. However, they also show a wide range of behaviors for the Michaelis-Menten parameters. Both Vmax and Km parameters have been shown to increase, decrease or roughly maintain the same value in increasing crowding density conditions. We want to understand how this diversity of outcomes can be obtained in a spatial heterogeneous environment as well as the specific conditions for which the quasi-steady state approximation is valid.
Collaborators: Dr. Santiago Schnell and Doree Kreitmann (Undergraduate student)
Studies of diffusion controlled biochemical reactions have been carried out in dilute solutions (in vitro). However, in an intracellular environment (in vivo), there is a high concentration of macromolecules, which results in nonspecific interactions (macromolecular crowding). Over the years, researchers have explored the effects of crowding on enzyme catalysis in vitro. Generally, the process consists in the addition of a particular concentration of enzyme to a sample mixture of substrate and crowding agents in a buffer. The reaction progress is followed by monitoring the release of product. In a particular set of conditions, the Michaelis-Menten equation (a simplification of the law of mass action equations used to describe the rate at which chemical species change in the solution) can be used to describe the rate of product formation. This quasi-steady state approximation produces a time independent description of the reaction kinetics, based on two parameters: Vmax, maximum rate of product formation; and Km, the concentration of substrate at which the reaction reaches half of the maximum rate. Published literaturein in vitro studies of enzymatic reactions indicates Vmax and Km dependence on macromolecular crowding. However, they also show a wide range of behaviors for the Michaelis-Menten parameters. Both Vmax and Km parameters have been shown to increase, decrease or roughly maintain the same value in increasing crowding density conditions. We want to understand how this diversity of outcomes can be obtained in a spatial heterogeneous environment as well as the specific conditions for which the quasi-steady state approximation is valid.
Collaborators: Dr. Santiago Schnell and Doree Kreitmann (Undergraduate student)
Understanding the steady state of microtubule arrays in plant cells
Microtubules, one of the main components of the cytoskeleton, are rigid hollow rods of tubulin dimers approximately 25 nm in diameter. They are dynamic structures that undergo continual assembly and disassembly within the cell, in a process denominated dynamic instability. Microtubules influence cell shape and a variety of cell movements, including some forms of cell locomotion, intracellular transport of organelles and the separation of chromosomes during mitosis. Contrary to their counterpart in animal cells, nucleation of microtubules in a plant cell is centrosome independent and occurs infrequently throughout the plant cell cortex. The relative higher dynamics of a microtubule plus end in relation to the minus end lead to a process denominated treadmilling, in which the microtubule appears to be moving in the plus end direction. We want to understand (1) how the system comes to a steady state of free versus bound tubulin dimer; (2) the role of microtubule dynamic parameters, nucleation and extinction in achieving that steady state; (3) how microtubule interact in space to produce particular organizations. We are currently developing a spatio-temporal model of microtubule dynamics of plant cells at the interphase cell cycle stage.
Collaborators: Dr. Sidney Shaw
Microtubules, one of the main components of the cytoskeleton, are rigid hollow rods of tubulin dimers approximately 25 nm in diameter. They are dynamic structures that undergo continual assembly and disassembly within the cell, in a process denominated dynamic instability. Microtubules influence cell shape and a variety of cell movements, including some forms of cell locomotion, intracellular transport of organelles and the separation of chromosomes during mitosis. Contrary to their counterpart in animal cells, nucleation of microtubules in a plant cell is centrosome independent and occurs infrequently throughout the plant cell cortex. The relative higher dynamics of a microtubule plus end in relation to the minus end lead to a process denominated treadmilling, in which the microtubule appears to be moving in the plus end direction. We want to understand (1) how the system comes to a steady state of free versus bound tubulin dimer; (2) the role of microtubule dynamic parameters, nucleation and extinction in achieving that steady state; (3) how microtubule interact in space to produce particular organizations. We are currently developing a spatio-temporal model of microtubule dynamics of plant cells at the interphase cell cycle stage.
Collaborators: Dr. Sidney Shaw
Deciphering the mechanisms of pheromone transmission and its effects in the lifespan of flies
The effects of social interactions on human health are well known, but poorly understood. For example, recent findings demonstrate that social interactions affect human health in aging populations by slowing the onset of dementia or cognitive decline. However, no molecular mechanisms have been proposed. Dr. Scott Pletcher’s lab has recently shown that exposure of Drosophila flies to pheromones of the opposite sex, without mating, is sufficient to decrease lifespan, starvation resistance and triacylglyceride (TAG) levels. These phenotypes are reversible and occur in both males and females, providing a great framework to investigate potential mechanisms of well known effects of social interactions on health. We want to understand (1) how interactions between flies may explain the lifespan and mortality rates experimentally observed; (2) how pheromone sensing and mating affects the evolution of populations over long time spans.
Collaborators: Dr. Scott Pletcher and Zach Harvanek (PhD Student)
The effects of social interactions on human health are well known, but poorly understood. For example, recent findings demonstrate that social interactions affect human health in aging populations by slowing the onset of dementia or cognitive decline. However, no molecular mechanisms have been proposed. Dr. Scott Pletcher’s lab has recently shown that exposure of Drosophila flies to pheromones of the opposite sex, without mating, is sufficient to decrease lifespan, starvation resistance and triacylglyceride (TAG) levels. These phenotypes are reversible and occur in both males and females, providing a great framework to investigate potential mechanisms of well known effects of social interactions on health. We want to understand (1) how interactions between flies may explain the lifespan and mortality rates experimentally observed; (2) how pheromone sensing and mating affects the evolution of populations over long time spans.
Collaborators: Dr. Scott Pletcher and Zach Harvanek (PhD Student)
Understanding the dynamics of mRNA inhibition by miRNA
MicroRNA (miRNA) bound messenger RNAs (mRNAs) localize to processing bodies (PBs), sub-cellular foci enriched in RNA processing enzymes, as a cause or consequence of post-transcriptional gene silencing. Regardless, PBs play an important role in miRNA mediated mRNA repression by, at the very least, sequestering previously repressed mRNAs and subjecting them to (further) degradation. To gain a deeper understanding on the, hitherto unidentified, dynamic and possibly heterogeneous nature of miRNA:PB interactions, we are developing a spatio-temporal model to predict the effect of different miRNA-PB interactions and miRNP/PB composition on gene expression, with the ultimate goal of mapping the dynamic interaction network of the RNA silencing pathway.
Collaborators: Dr. Nils Walter and Dr. Sethuramaundaram Pitchiaya (Postdoctoral researcher)
MicroRNA (miRNA) bound messenger RNAs (mRNAs) localize to processing bodies (PBs), sub-cellular foci enriched in RNA processing enzymes, as a cause or consequence of post-transcriptional gene silencing. Regardless, PBs play an important role in miRNA mediated mRNA repression by, at the very least, sequestering previously repressed mRNAs and subjecting them to (further) degradation. To gain a deeper understanding on the, hitherto unidentified, dynamic and possibly heterogeneous nature of miRNA:PB interactions, we are developing a spatio-temporal model to predict the effect of different miRNA-PB interactions and miRNP/PB composition on gene expression, with the ultimate goal of mapping the dynamic interaction network of the RNA silencing pathway.
Collaborators: Dr. Nils Walter and Dr. Sethuramaundaram Pitchiaya (Postdoctoral researcher)