Engineering for the 21st century: synthetic biology.

For years, scientists have hoped that biology would find its engineering counterpart--a series of principles that could be used as reliably as chemical engineering is for chemistry. Thanks to major advances in synthetic biology, those hopes may soon be realized.

Development of a perfusion chamber assay to study in real time the kinetics of thrombosis and the antithrombotic characteristics of antiplatelet drugs.

BACKGROUND: Arterial thrombosis triggered by vascular injury is a balance between thrombus growth and thrombus fragmentation (dethrombosis). Unbalance towards thrombus growth can lead to vascular occlusion, downstream ischemia and tissue damage.Here we describe the development of a simple methodology that allows for continuous real time monitoring and quantification of both processes during perfusion of human blood under arterial shear rate conditions. Using this methodology, we have studied the effects of antiplatelet agents targeting COX-1 (aspirin), P2Y12 (2-MeSAMP, clopidogrel), GP IIb-IIIa (eptifibatide) and their combinations on the kinetics of thrombosis over time. RESULTS: Untreated samples of blood perfused over type III collagen at arterial rates of shear promoted the growth of stable thrombi. Modulation by eptifibatide affected thrombus growth, while that mediated by 2-MeSAMP and aspirin affected thrombus stability. Using this technique, we confirmed the primacy of continuous signaling by the ADP autocrine loop acting on P2Y12 in the maintenance of thrombus stability. Analysis of the kinetics of thrombosis revealed that continuous and prolonged analysis of thrombosis is required to capture the role of platelet signaling pathways in their entirety. Furthermore, studies evaluating the thrombotic profiles of 20 healthy volunteers treated with aspirin, clopidogrel or their combination indicated that while three individuals did not benefits from either aspirin or clopidogrel treatments, all individuals displayed marked destabilization profiles when treated with the combination regimen. CONCLUSIONS: These results show the utility of a simple perfusion chamber technology to assess in real time the activity of antiplatelet drugs and their combinations. It offers the opportunity to perform pharmacodynamic monitoring of arterial thrombosis in clinical trials and to investigate novel strategies directed at inhibiting thrombus stability in the management of cardiovascular disease.

miRNA profiling on high-throughput OpenArray™ system.

Micro RNA (miRNAs) are a class of 17-25 nucleotides noncoding RNAs that have been shown to have critical functions in a wide variety of biological processes. Measuring quantity of miRNAs in tissues of different physiological and pathological conditions is an important first step to investigate the functions of miRNAs. To this date, the number of identified miRNA consists of around 850 different species, and more sequence-predicted miRNA genes are awaiting experimental confirmation. The need for high-throughput technologies allowing to profile all known miRNAs with power similar to microarray and precision/specificity of qPCR is evident. The example of such system based on high-density array of nanoliter PCR assays is described here. Functionally equivalent to a microtiter plate, a single OpenArray™ nanoplate makes possible to do up to 3,072 real-time PCRs at a single experiment. Methods for miRNA profiling using the dual-label probe chemistry (Taqman(®)) are outlined in this chapter, and experimental data illustrating system performance are provided.

A nanoliter fluidic platform for large-scale single nucleotide polymorphism genotyping.

Discovery, evaluation, and understanding the biological relevance of single nucleotide polymorphisms (SNPs) and their associated phenotypes is relevant to many applications, including human disease diagnostics, pathogen detection, and identification of genetic traits impacting agricultural practices, both in terms of food quality and production efficiency. Validation of putative SNP associations in large-scale cohorts is currently impeded by the technical challenges and high cost inherent in analyzing large numbers of samples using available SNP genotyping platforms. We describe in this report the implementation of the 5'-exonuclease, biallelic PCR assay for SNP genotyping (TaqMan) in a nanofluidic version of a high-density microplate. System performance was assessed using a panel of 32 TaqMan SNP genotyping assays targeted to human polymorphisms. This functional test of the nanoliter fluidic SNP genotyping platform delivered genotyping call rates and accuracies comparable to the same larger volume reactions in microplate systems.

Agonist-induced calcium response in single human platelets assayed in a microfluidic device.

To facilitate drug discovery directed toward platelet-specific targets, we developed a platelet isolation and fluorophore-loading method that yields functionally responsive platelets in which we were able to detect agonist-induced calcium flux using a microfluidics-based screening platform. The platelet preparation protocol was designed to minimize preparation-induced platelet activation and to optimize signal strength. Measurement of platelet activation, as monitored by ratiometric determination of agonist-induced calcium flux in fluor-loaded human platelets, was optimized in a macrosample cuvette format in preparation for detection in a microfluidic chip-based assay. For the microfluidic device used in these studies, a cell density of 1 to 2 x 10(6) platelets per milliliter and a nominal flow rate of 5 to 10 nl per second provided optimal event resolution of 5 to 20 platelets traversing the detection volume per unit time. Platelets responded in a dose-dependent manner to adenosine diphosphate and protease-activating peptide (PAR) 1 thrombin receptor-activating peptide (TRAP). The work presented here constitutes proof-of-principle experiments demonstrating the enabling application of a microfluidic device to conduct high-throughput signaling studies and drug discovery screening against human platelet targets.