Jerry Jenkins

Automated refinement and inference of analytical models for metabolic networks

The reverse engineering of metabolic networks from experimental data is traditionally a labor-intensive task requiring a priori systems knowledge. Using a proven model as a test system, we demonstrate an automated method to simplify this process by modifying an existing or related model--suggesting nonlinear terms and structural modifications--or even constructing a new model that agrees with the systems time series observations. In certain cases, this method can identify the full dynamical model from scratch without prior knowledge or structural assumptions. The algorithm selects between multiple candidate models by designing experiments to make their predictions disagree. We performed computational experiments to analyze a nonlinear seven-dimensional model of yeast glycolytic oscillations. This approach corrected mistakes reliably in both approximated and overspecified models. The method performed well to high levels of noise for most states, could identify the correct model de novo, and make better predictions than ordinary parametric regression and neural network models. We identified an invariant quantity in the model, which accurately derived kinetics and the numerical sensitivity coefficients of the system. Finally, we compared the system to dynamic flux estimation and discussed the scaling and application of this methodology to automated experiment design and control in biological systems in real time.

Mefloquine induces oxidative stress and neurodegeneration in primary rat cortical neurons.

Mefloquine is an effective antimalarial that can cause adverse neurological events including headache, nausea, fatigue, insomnia, anxiety and depression. In this study, we examined the oxidative stress response in primary rat cortical neurons treated with mefloquine by quantifying oxidative stress markers glutathione (GSH) and F(2)-isoprostanes (F(2)-isoPs). Furthermore, we examined whether mefloquine induces synaptodendritic degeneration of primary rat cortical neurons. GSH was quantified in cortical neurons after 24-h treatment with mefloquine (0, 1, 5, 10 microM) using monochlorobimane. F(2)-isoPs were quantified in cortical neurons after 24-h treatment with mefloquine (0, 1, 5, 10 microM) using a stable isotope dilution method with detection by gas chromatography/mass spectrometry and selective ion monitoring. The concentration dependent decrease in GSH and the concomitant increase of F(2)-isoPs indicates the presence of oxidative stress in primary rat cortical neurons treated with mefloquine. Following a 24-h treatment with mefloquine, primary rat cortical neurons (0, 5, 10 microM) were fixed with 4% paraformaldehyde. Images from eight optical sections covering a distance of 2.88 microm on the z-axis were acquired using a confocal laser scanning unit. Traced images were analyzed with NeuroExplorer, a neurophysiological data analysis package. Mefloquine induces a concentration dependent decrease in the number of spines per neuron and the spine density, suggesting that mefloquine induced oxidative stress may be associated with the synaptodendritic degeneration. Together with previous work, there is strong evidence that a relationship exists between calcium homeostasis disruption, ER stress response, the oxidative stress response, and neurodegeneration. Understanding how oxidative stress alters the morphology of cortical neurons treated with mefloquine will provide further insight into the mechanism(s) related to clinically observed adverse neurological events.

Mefloquine neurotoxicity is mediated by non-receptor tyrosine kinase.

Among several available antimalarial drugs, mefloquine has proven to be effective against drug-resistant Plasmodium falciparum and remains the drug of choice for both therapy and chemoprophylaxis. However, mefloquine is known to cause adverse neurological and/or psychiatric symptoms, which offset its therapeutic advantage. The exact mechanisms leading to the adverse neurological effects of mefloquine are poorly defined. Alterations in neurotransmitter release and calcium homeostasis, the inhibition of cholinesterases and the interaction with adenosine A(2A) receptors have been hypothesized to play prominent roles in mediating the deleterious effects of this drug. Our recent data have established that mefloquine can also trigger oxidative damage and subsequent neurodegeneration in rat cortical primary neurons. Furthermore, we have utilized a system biology-centered approach and have constructed a pathway model of cellular responses to mefloquine, identifying non-receptor tyrosine kinase 2 (Pyk2) as a critical target in mediating mefloquine neurotoxicity. In this study, we sought to establish an experimental validation of Pyk2 using gene-silencing techniques (siRNA). We have examined whether the downregulation of Pyk2 in primary rat cortical neurons alters mefloquine neurotoxicity by evaluating cell viability, apoptosis and oxidative stress. Results from our study have confirmed that mefloquine neurotoxicity is associated with apoptotic response and oxidative injury, and we have demonstrated that mefloquine affects primary rat cortical neurons, at least in part, via Pyk2. The implication of these findings may prove beneficial in suppressing the neurological side effects of mefloquine and developing effective therapeutic modalities to offset its adverse effects.

Simulation and Design of E. Coli-Based Rotary Micropump for Use in Microfluidic Systems: Integration of Micro-Nano-Bio

This paper presents the results of the computational fluid dynamic (CFD) modeling of viscous fluid flow in a novel cell motor actuated micropump. A cell motor is a bacterial flagellar cell tethered to a surface by a single flagellum, this flagellum acts as a pivot around which the cell body rotates. As a test case for investigation, the micropump consisted of two Escherichia coli cell motors tethered to the bottom of a microchannel with fixed dimensions. The CFD modeling of the micropump was performed using CFD-ACE+ simulation software (CFD Research Corporation). The biological cell motor was modeled as an ellipse with constant rotational speed of 10 Hz clockwise. The results of this model demonstrated the effect of the biological cell motor placement within the microchannel, as well as the rotational phase between the two biological cell motors, on the volumetric flowrate. Pumping action was observed as the cell motor location was moved adjacent to the sidewall of the microchannel. The rates of fluid pumping were of the order of 11 pL/hr when the cell motors were rotating in phase and their placement was close to the sidewall of the microchannel.Copyright