Team:NYU Abu Dhabi/description.html
A non-invasive, point-of-care diagnostics technology platform which incorporates the most novel isothermal rapid DNA amplification and detection techniques coupled with a carefully engineered microfluidic system and integrated database for effective management of communicable diseases.
D E T E C T
Novel Nucleic Acid Amplification and Detection
Thorough exploration and in-depth research into the specificity and sensitivity of nucleic acid amplification techniques and combined CRISPR detection solutions including Polymerase Chain Reaction (PCR), Loop-mediated isothermal Amplification (LAMP), Recombinase Polymerase Amplification (RPA), Specific High-sensitivity Enzymatic Reporter un-LOCKing (SHERLOCK) and DNA Endonuclease Targeted CRISPR Trans Reporter (DETECTR), revealed that DETECTR was the best suited for our applications. DETECTR combines the RPA DNA amplification technique with CRISPR cas12a technology and custom fluorescence quenching sequence for the fluorescent amplification of disease specific gene sequences.
Primer and crRNA Design
Endogenous, non-pathogenic, non-coding gene sequences specific to target pathogens were selected according to extensive research of existing diagnostics literature. Primers and crRNA specific to these gene sequences were designed to meet optimal parameters for recognition, amplification and binding. PCR, LAMP and RPA primers were optimised and designed using NCBI Primer-BLAST, Primer Explorer and PrimedRPA software programs respectively, whilst crRNA was determined using Benchling. The targeted gene sequences and their associated pathogens were:
Multiplex Microfluidic System
Microfluidic technologies not only allows for the efficient usage of reagents and sample specimen, but also enable the possibility of multiplex diagnosis. With multiple microchannels that flow concurrently, a single sample can be used to test for up to fourfive pathogens creating a labour-saving and cost-efficient system.
P R O T E C T
Non-invasive, Point-of-care Diagnostics
With quick and easy sample collection involving only saliva specimens, Volatect is a user-friendly device that aims to provide a comfortable experience for both the technician and individuals being tested. Disposable microfluidic chips contribute to the ease-of-use and ready compliance to biosafety concerns whilst the rapidity of the suite of bioengineering techniques ensures fast diagnosis.
Integrated Database
A seamless management system is achieved with an integrated database that allows for the potential of global disease tracking, out-break alert processes, research and prevention programs. This database will gather diagnostic results from the device as well as relevant patient details, analytic tools may then be used on this data to extrapolate potential trends or disease insights.
Target Diseases
The selection of diseases diagnosable with Volatect is far ranging and customisable due to the possibility of designing primers and crRNA for most given gene sequences and the ability to simply load the microfluidic chips with new sets of reagents. However, the selection of communicable disease causing pathogens targeted by our research project and their respective diseases are: Bordetella pertussis (whooping cough), Yersinia pestis (plague), Hepatitis B and Mycobacterium tuberculosis (tuberculosis).
V O L A T E C T
Inspiration and Legacy
Continuing on three years of iGEM research at NYU Abu Dhabi on pathogen detection and diagnostics seemed obvious when we were struck by the fact that our main campus in New York City was experiencing the largest measles outbreak in 30 years. All over the airports and subway stations of New York City there were posters and banners prompting travellers to report any measles related symptoms. With the wealth of knowledge and feedback we had gained over the past few years working on pathogen detection, we had identified and were prepared for our next challenge, stopping and preventing the spread of communicable diseases.
Looking forward
Due to the limitation of the amplification technique allowing only amplification of DNA sequences, efforts could be made to incorporate the use of reverse transcriptase so that identifiable RNA sequences can be detected and amplified, widening the detection potential to RNA viruses such as the Measles virus.
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