Our Projects

Click here to find our current student projects, and posters from previous projects!

Projects in the Lab

miRNA Detection with Ligation LAMP

Ligation LAMP (Loop-mediated Isothermal Amplification) is a molecular technique that combines nucleic acid ligation with isothermal amplification to detect specific RNA or DNA sequences. This makes ligation LAMP an effective tool for miRNA biomarker discovery and quantification in various biological samples.

Using this method, we can make point-of-care diagnostic tools that present a visual output marker when there is positive amplification. Using Phenol Red and HNB Dye we can get colorimetric outputs, and using SYBR Green, we can get a fluorescent output.

Image credit: Adane, Y., Anjum, A., Bogusch, A., Fernandes, C., Naseem, Z., Pallavajjala, R., & Vempaty, N. (2024). One-Pot Ligation LAMP Assay to Detect miRNA-222: A Glioma Biomarker. http://hdl.handle.net/1903/32412

One-Pot LAMP Portable Sensor Project

Conventional Glicoma diagnostic methods include MRI scans, CAT scans, and tissue biopsies are invasive and expensive. LAMP, Ligation Loop Mediated Isothermal Amplification, amplifies short nucleic acid sequences through amplification. It is a quicker and easier alternative to PCR, due to less lab equipment and it is a cheaper and faster point of care diagnostic tool. TRAPs, Thermally responsive alkane partitions, allow assay steps to be separated in a single tube. Changing TRAP geometry allows for magnetic beads to break without reagents mixing, which allows for a capture step.

Image credit: Zhang, M., Wang, H., Wang, H., Wang, F., & Li, Z. (2021). CRISPR/Cas12a-Assisted Ligation-Initiated Loop-Mediated Isothermal Amplification (CAL-LAMP) for Highly Specific Detection of microRNAs. Analytical Chemistry, 93(22), 7942–7948. https://doi.org/10.1021/acs.analchem.1c00686

Cal-LAMP Method

Cell-Free Extract & Biosensor

Cell-Free Expression systems aim to express proteins and RNAs in an environment independent of living cells. This removes the need to keep cells alive which lowers costs and makes many applications possible, such as biosensors designed to detect molecular targets. However, commercial cell-free kits are extremely expensive which hinders their ability to be used for low-cost application. Our project aims to optimize an in-house cell-free expression system to dramatically reduce the cost of testing biosensors and cytotoxic ribosomal proteins in collaboration with the CellEx lab. The image to the right depicts the components of a cell free expression system, as well as its functionality.

Image credit: Zhang, L., Guo, W., & Lu, Y. (2020). Advances in Cell-Free Biosensors: Principle, Mechanism, and Applications. Biotechnology Journal, 15(9), 2000187. https://doi.org/10.1002/biot.202000187

Image credit: Scoville DJ, Uhm TKB, Shallcross JA, Whelan RJ. Selection of DNA aptamers for ovarian cancer biomarker CA125 using one-pot selex and high-throughput sequencing. J Nucleic Acids. 2017;2017.

Mucin Aptamer Selection Project

Mucus is a viscous bodily fluid composed of mucin proteins, inorganic salts, and water. MUC5AC is one mucin protein that makes up airway mucus. Elevated levels of MUC5AC can indicate certain diseases, like asthma, cystic fibrosis (CF), and chronic obstructive pulmonary disease (COPD). Current treatments for mucus-associated respiratory diseases include using enzymes and chemical agents to clear mucus buildup. These existing treatments are limited in their ability to selectively target specific mucin proteins within mucus. Our research aims to select DNA aptamers that bind to MUC5AC within mucus samples. We are optimizing a One-Pot SELEX methodology with positive and negative selections previously used by other researchers, and testing binding affinity using a gel shift assay. Selected DNA aptamers with high binding affinity and specificity can detect airway mucin proteins and deliver engineered proteases to cleave and destroy them.

Image credit: FIRE MD Lab

Beta Amyloid Aptamer Selection Project

Aptamer selection, often referred to as SELEX (Systematic Evolution of Ligands by Exponential Enrichment), is a process used to identify short, single-stranded DNA or RNA molecules (aptamers) that can bind with high specificity and affinity to target molecules.

Alzheimer's disease is a chronic neurodegenerative disorder, with cases in individuals aged 65+ projected to rise by 7% by 2025. Current diagnostic methods, such as spinal taps, are invasive and not widely accessible, exacerbating public health inequities. This study aims to develop a DNA aptamer capable of binding to the β-amyloid 42 protein, a biomarker associated with Alzheimer's, for a wide range of potential diagnostic applications. We conducted positive and negative selection processes using a bead-based in vitro selection method to ensure binding specificity and strength. This research aims to further contribute to the development of non-invasive, cost-effective diagnostic tools for early Alzheimer's detection, aligning with the broader goals of improving access to diagnostic resources for all.

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