Publications

Abstract not provided.

This report provides a detailed overview of the work performed for project number 130781, 'A Systems Biology Approach to Understanding Viral Hemorrhagic Fever Pathogenesis.' We report progress in five key areas: single cell isolation devices and control systems, fluorescent cytokine and transcription factor reporters, on-chip viral infection assays, molecular virology analysis of Arenavirus nucleoprotein structure-function, and development of computational tools to predict virus-host protein interactions. Although a great deal of work remains from that begun here, we have developed several novel single cell analysis tools and knowledge of Arenavirus biology that will facilitate and inform future publications and funding proposals.

Abstract not provided.

Abstract not provided.

Single-cell analysis offers a promising method of studying cellular functions including investigation of mechanisms of host-pathogen interaction. We are developing a microfluidic platform that integrates single-cell capture along with an optimized interface for high-resolution fluorescence microscopy. The goal is to monitor, using fluorescent reporter constructs and labeled antibodies, the early events in signal transduction in innate immunity pathways of macrophages and other immune cells. The work presented discusses the development of the single-cell capture device, the iCellator chip, that isolates, captures, and exposes cells to pathogenic insults. We have successfully monitored the translocation of NF-κB, a transcription factor, from the cytoplasm to the nucleus after lipopolysaccharide (LPS) stimulation of RAW264.7 macrophages.

We present MEMS polysilicon microvalves for flow control of a rapid analytical microsystem (Micro-Gas-Analyzer, MGA). All valve components (boss, seat, springs, electrodes, and stops) are surface micromachined in the SUMMiT™ microfabrication process. The valves have been characterized at high flow rate when open (60 ml/min air), low leak rate when closed (<0.0025 ml/min Hydrogen, H2), and tunable closing pressures (1 to 35 psig). Active electrostatic valves have been shown to hold closed (voltage on) against a high pressure (>40 psig) for sample loading, open for gas chromatograph (GC) loading (voltage off), and reclose against low pressure 2-5 psig. ©2009 IEEE.

We have successfully developed a nucleic acid extraction system based on a microacoustic lysis array coupled to an integrated nucleic acid extraction system all on a single cartridge. The microacoustic lysing array is based on 36{sup o} Y cut lithium niobate, which couples bulk acoustic waves (BAW) into the microchannels. The microchannels were fabricated using Mylar laminates and fused silica to form acoustic-fluidic interface cartridges. The transducer array consists of four active elements directed for cell lysis and one optional BAW element for mixing on the cartridge. The lysis system was modeled using one dimensional (1D) transmission line and two dimensional (2D) FEM models. For input powers required to lyse cells, the flow rate dictated the temperature change across the lysing region. From the computational models, a flow rate of 10 {micro}L/min produced a temperature rise of 23.2 C and only 6.7 C when flowing at 60 {micro}L/min. The measured temperature changes were 5 C less than the model. The computational models also permitted optimization of the acoustic coupling to the microchannel region and revealed the potential impact of thermal effects if not controlled. Using E. coli, we achieved a lysing efficacy of 49.9 {+-} 29.92 % based on a cell viability assay with a 757.2 % increase in ATP release within 20 seconds of acoustic exposure. A bench-top lysing system required 15-20 minutes operating up to 58 Watts to achieve the same level of cell lysis. We demonstrate that active mixing on the cartridge was critical to maximize binding and release of nucleic acid to the magnetic beads. Using a sol-gel silica bead matrix filled microchannel the extraction efficacy was 40%. The cartridge based magnetic bead system had an extraction efficiency of 19.2%. For an electric field based method that used Nafion films, a nucleic acid extraction efficiency of 66.3 % was achieved at 6 volts DC. For the flow rates we tested (10-50 {micro}L/min), the nucleic acid extraction time was 5-10 minutes for a volume of 50 {micro}L. Moreover, a unique feature of this technology is the ability to replace the cartridges for subsequent nucleic acid extractions.

A key aspect of decision making is determining when errors or conflicts exist in information and knowing whether to continue or terminate an action. Understanding the error-conflict processing is crucial in order to emulate higher brain functions in hardware and software systems. Specific brain regions, most notably the anterior cingulate cortex (ACC) are known to respond to the presence of conflicts in information by assigning a value to an action. Essentially, this conflict signal triggers strategic adjustments in cognitive control, which serve to prevent further conflict. The most probable mechanism is the ACC reports and discriminates different types of feedback, both positive and negative, that relate to different adaptations. Unique cells called spindle neurons that are primarily found in the ACC (layer Vb) are known to be responsible for cognitive dissonance (disambiguation between alternatives). Thus, the ACC through a specific set of cells likely plays a central role in the ability of humans to make difficult decisions and solve challenging problems in the midst of conflicting information. In addition to dealing with cognitive dissonance, decision making in high consequence scenarios also relies on the integration of multiple sets of information (sensory, reward, emotion, etc.). Thus, a second area of interest for this proposal lies in the corticostriatal networks that serve as an integration region for multiple cognitive inputs. In order to engineer neurological decision making processes in silicon devices, we will determine the key cells, inputs, and outputs of conflict/error detection in the ACC region. The second goal is understand in vitro models of corticostriatal networks and the impact of physical deficits on decision making, specifically in stressful scenarios with conflicting streams of data from multiple inputs. We will elucidate the mechanisms of cognitive data integration in order to implement a future corticostriatal-like network in silicon devices for improved decision processing.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Abstract not provided.

Columbia University has developed a sensitive highly multiplexed system for genetic identification of nucleic acid targets. The primary obstacle to implementing this technology is the high rate of false positives due to high levels of unbound reporters that remain within the system after hybridization. The ability to distinguish between free reporters and reporters bound to targets limits the use of this technology. We previously demonstrated a new electrokinetic method for binary separation of kb pair long DNA molecules and oligonucleotides. The purpose of this project 99864 is to take these previous demonstrations and further develop the technique and hardware for field use. Specifically, our objective was to implement separation in a heterogeneous sample (containing target DNA and background oligo), to perform the separation in a flow-based device, and to develop all of the components necessary for field testing a breadboard prototype system.

Abstract not provided.