Developing Inexpensive and Portable Molecular Diagnostics Tools for DNA Analysis
Fig. 1: Contrasting a. traditional PCR-based molecular diagnostic workflow with the proposed b. novel heating mechanism. A rotating disc with embedded conductors surrounded by magnets induces eddy currents that can raise temperature of fluidic samples. The spinning platform can also leverage centrifuge-based sample preparation workflows to enable pre-PCR nucleic acid extraction. Integrating a smartphone-based fluorescence detection of post PCR analysis enables inexpensive and portable “sample-to-answer” molecular diagnostic platform.
Problem Statement
The recent global pandemic (COVID-19) has exposed some of the key limitations in our current infectious disease management systems, particularly when applied in remote underdeveloped areas. Existing approaches (like the Polymerase Chain Reaction (PCR) tests) are highly resource-intensive, relying on people depositing their biological samples to collections centers where trained personnel process these samples in dedicated laboratories for further analysis. These inefficient channels introduce a considerable time lag between sample collection, diagnosis, and implementation of countermeasures. A need, therefore, exists for developing inexpensive and simple tools that can be broadly deployed to accelerate diagnosis, and provide real-time data to better inform decision making.
Project Description
The Protégé student will work in Dr. Priye’s laboratory to develop inexpensive and simplified instruments/protocols that can replace traditional bulky, expensive and power intensive laboratory instruments required for infectious disease diagnostics. One of the major challenges associated with making PCR tests more accessible is the need for thermal cyclers which repeatedly heat and cool the biological samples using power consuming Peltier heating elements. We will explore unconventional and novel techniques of heating samples that are more efficient and inexpensive such as heat generation via eddy currents and lasers. Detection of PCR tests is accomplished using expensive fluorometers. We will explore simpler optical setups such as the use of smartphone cameras or raspberry pi cameras to read fluorescent signals from PCR tests.
Learning Outcomes
Along with gaining research experience in the laboratory, the protégé student will learn and apply 3D printing, CNC machining, Arduino and python programming, Microfluidics technology and physics-based modeling. Students are encouraged to document their results and successful completion of the project can result in a journal publication.
Director
Aashish Priye
Assistant Professor, CEAS - Chemical & Env Eng
693 Rhodes Hall
Physics of Micro-scale Flows
Fluid flow arising due to thermal gradients (thermal instability driven convective flows) is quite ubiquitous in nature (oceanic currents, cloud formation, etc.) but they can exhibit unique characteristics at the micro-scale, capable of greatly accelerating biomolecular transport and reactions. We use computational tools (Computational Fluid Dynamics) and novel experimental setups (automated microfluidic systems) to study these flow states and evaluate the conditions under which they can be harnessed to actuate biomolecular transport and assembly, accelerate DNA replication and separate cells (based on their shape and size).
Point-of-Care Detection for Global Health
The recent disease outbreaks have exposed some key limitations facing current infectious disease management strategies, particularly when applied in remote underdeveloped areas. Existing approaches are highly resource intensive, relying on dispatching specially trained personnel to isolated locations where biological samples are collected and returned to dedicated laboratories for analysis. A need therefore exists for inexpensive and robust tools that can be broadly deployed to accelerate diagnosis, enable pinpoint delivery of therapeutics, and provide real-time data to better inform decision making. We engineer simple and portable diagnostic tools (such as smartphone based DNA analyzer and lab on a drone) that can be deployed and operated outside the laboratory to address global challenges of healthcare, environmental sampling, agriculture and science outreach. Projects under this area are quite multidisciplinary and collaborative in nature.
Functional Microfluidics
Microfluidics enables large-scale automation in chemical and biological sciences, suggesting the possibility of numerous experiments performed rapidly and in parallel while consuming little reagents. This has led to the emergence of the so-called lab on chip systems, making significant strides in diverse areas ranging from grand challenges such as water purification to fundamental research such as genetic analysis. Despite significant advances, few roadblocks has hindered microfluidic systems from replacing convectional bench-top analytical tools and widely penetrate the point of care in low resource settings where they are needed most. We aim to create the next generation of microfluidic devices using rapid fabrication techniques (3D printing, micro-milling and laser cutting) that would drastically simplify the prototyping and assembly processes of microfluidics systems.
We have a few positions open for passionate postdoctoral, graduate (prospective PhD/Master’s applicants) and undergraduate students. Our research is quite multidisciplinary, involving researchers from a wide range of background including engineering (chemical, mechanical, biomedical, electrical and bioengineering), applied physics, biophysics, material science and applied mathematics. Along with frequently publishing our research, we actively explore platforms to commercialize the technologies that are developed in our lab.
If you are interested in joining our lab, please send a copy of recent CV, a brief summary of your projects and a short statement of your research interests to priyeah@uc.edu.