Protein-Protein Interactions: The Interaction Factor

As the result of a collaboration with members of Dr. Eli Rothenburg's laboratory in Dr. David Fenyo's laboratory we have developed an algorithm in Python and ImageJ called the "Interaction Factor" to quantify protein-protein interactions by stochastic modeling of super-resolution fluorescence microscopy images. The Interaction Factor indicates if the close proximity of the two proteins is greater than that observed by random chance. It can be used to determine if two proteins interact and to determine if experimental manipulations affect the degree of interaction between the two proteins. The manuscript was accepted in the journal Scientific Reports on October 19 2017.

Interaction Factor Package ImageJ Plugin

These are screeenshots of the a user-friendly ImageJ plugin package called Interaction Factor. There are two plugins in the Interaction Factor Package that may be used to analyze an image. The first version, simply called “Interaction Factor”, allows you to calculate the Interaction Factor of the image as well as other measures such as overlap area. The second version, called “Interaction Factor Simulations” allows you to run any number of simulations against the image.

Cell Tracking

As the result of a collaboration with members of Dr. Michele Pagano's laboratory I developed a custom Python module to track cell movement and measure mean intensity levels over time.

Automation of Foci Quantification

As the result of a collaboration with members of Dr. Michele Pagano's laboratory I developed a custom module script to quantify yH2AX foci.

Dankert, J.F., Rona, G., Geter, P., Clijsters, L., Skaar, J.S., Bermudez-Hernandez, K., Fenyo, D., Ueberheide, B., Schneider, R., Pagano, M. (2016) Cyclin F-mediated degradation of SLBP limits H2A.X accumulation and apoptosis upon genotoxic stress in G2. Mol. Cell.

Automation of Cell Classification

As the result of a collaboration with Dr.Eric Schafler and Dr.Susan Logan I developed a custom algorithm in Python to classify germ cells in green that express Ki67 in red.The cells marked in red are the cells that were classified as cells that expressed Ki67.

Schafler, E., Thomas, P., Bermudez-Hernandez, K., Tang, Z., Fenyo, D., Vigodner, M., Logan, S. (In review) ART-27 regulates mammalian spermatogonial stem cell survival and differentiation. Dev. Biol.

Automation of Immunoreactive Cell Quantification

One of the challenges I encountered during my thesis work was being able to quantify immunoreactive cells in a determined region of the brain for hundreds of images. In addition, I needed a way to calculate cell density. If I wanted to manually count cells, it would have taken me months, but instead, I decided to automate the process by writing macros and scripts, making the process of counting faster and unbiased. To automate the process, I wrote scripts in JavaScript that automated image processing in Adobe Photoshop CC; for counting cells and density, I wrote macros for ImageJ; and finally, I organized all the data using Python scripts. You can learn more about the scripts by visiting my project webiste.

Hilar granule cells in the hilus of the mouse dentate gyrus: effects of age, septotemporal location, strain, and selective deletion of the proapoptotic gene BAX.

Bermudez-Hernandez, K., Lu, Y., Moretto, J., Jain, S., LaFrancois, J., Duffy, A.M.,Scharfman, H. E. (2017) Brain Struct. Func.

As part of this project, I was in charge of planning and executing all the experiments, analyzing, and writing the paper. In this project I had to troubleshoot and develop technical skills like developing a new way of sectioning the hippocampus of mice, a technique that has never been done before. In addition of developing technical skills, I developed a great partnership with the animal caretakers and the administrative staff, ensuring we executed effectively the importation of mice, the breeding scheme, and the chemical purchases.

Entorhinal cortical defects in Tg2576 mice are present as early as 2-4 months of age.

Duffy AM, Morales-Corraliza J, Bermudez-Hernandez K, Schaner MJ, Magagna-Poveda A, Mathews PM, Scharfman HE (2014) Neurbiol. Aging

I contributed to this project by doing immunocythochemistry and histochemistry. Among the histological stainings I did were: myelin, cresyl, and thioflavin-s staining.

The influence of ectopic migration of granule cells into the hilus on dentate gyrus-CA3 function.

Myers CE, Bermudez-Hernandez K, Scharfman HE (2013) PLoS One 8:e68208.

In this project I was in charge of purchasing, breeding, and genotyping a portion of the mice that were used in the study, as well as immunocytochemistry for different markers.