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In their senior year, all WPI students complete a Major Qualifying Project (MQP), a professional-level research or design project that enables students to tackle, and solve, real-world problems in their fields of study. In the process, students synthesize their previous learning, hone their critical thinking and communication skills, and learn to work independently.

Under the guidance of faculty advisors, Bioinformatics and Computational Biology students apply BCB theory, tools, and techniques to make a difference in areas such as functional genomics, disease prediction, regenerative medicine, biological database mining, and biodiversity.

See some examples of the most recent Major Qualifying Projects:

Tissue Preservation Through Cryogenic Methods

Author: Alicia Howell-Munson, Kristen Dettloff, John Schwamb, and Allesandra Torres Yabar

Advisors: Marsha Rolle, Elizabeth Ryder and Destin Heilman

Focus: Identifying and solving problems in the integrity of tissue samples after cryopreservation. The effective cryopreservation of living tissue would be a significant achievement for areas ranging from medicine to space exploration. The current methods for preserving living cells and tissue are problematic due to toxic cryopreservation agents and the crystallization of water. This study used three agents with vitrification of rat smooth muscle tissue rings. The final results were compared against the commonly used 10% DMSO.

 

High Throughput Screening of C. elegans

Author: Akshaye Shah

Advisor: Elizabeth Ryder

Genetic interaction studies have identified mechanisms controlling tissue specific gene expression, but with limited scalability. A high throughput image analysis platform was designed in conjunction with a genetic construct. The construct marks the intestinal cells in Caenorhabditis elegans, using mCherry, and indicates promoter of interest expression using GFP. The computational system creates a mask using the mCherry signal and quantifies GFP fluorescence, outputting quantitative changes in intensity within the intestine.

 

Correlate Analyses for Acutely Infected HIV Individuals: Natural Disease Control Study

Author: Kylie Dickinson

Advisor: Elizabeth Ryder

The human immunodeficiency virus (HIV) infects ~5,000 new people daily. Only a small population of infected individuals are natural viral controllers. The goal of this project was to determine humoral factors that correlate to HIV controller versus progressor status. Multivariate and univariate data analyses compared HIV-specific IgG subclasses and antibody-dependent effector functions of controllers and progressors measured at acute infection. Multivariate approaches were effective in differentiating controllers from progressors, suggesting no single antibody feature is predictive of disease control.

 

PubMed AuthorMap: A Study of Research Collaboration in the Life Science Fields

 Author: Amanda Moulaison and Haylea Northcott

Advisors: Dmitry Korkin and Elizabeth Ryder 

This project incorporates the PubMed API to create a tool that builds networks representing research collaborations across life science fields. In each network, a node represents the last author on a publication, while an edge represents publications that share one or several authors. Our tool shows that most networks demonstrate characteristics of scale-free networks but cannot be statistically proven to be scale free. We performed case studies on three networks to describe the relationship between bottleneck authors and their collaborators.

 

Investigating the Unusual Gene Structure of DNA Primase in Mycobacteriophage Subclusters

Author: Daniel Champlin, Jennifer Payano, and Eoin O'Connell

Advisors: JoAnn Whitefleet-Smith and Elizabeth Ryder

In A4 and other subclusters of mycobacteriophages, DNA primase is a two-domain protein made from two genes with significant overlap that are read in different open reading frames. These genes create a functioning protein through an unknown mechanism. Our investigations using multiple sequence alignments and protein modelling do not support intein splicing, ribosomal frameshifting, or RNA polymerase slippage as mechanisms of forming a functional\nDNA primase. Preliminary RT-PCR results suggest both domains are transcribed on one transcript.

 

The Chitin Receptor Lyk5 Is Essential for Calcium-mediated Signaling in Physcomitrella patens

Author: Catherine Sherman

Advisors: Luis Vidali and Elizabeth Ryder

Plants recognize a variety of different pathogen associated molecules, like chitin, found in the walls of fungi, in order to react effectively. Chitin causes oscillations of intracellular calcium in many plants, including Physcomitrella patens. The goal of this project was to silence Lyk5 genes thought to detect chitin in P. patens and develop a program to analyze the calcium response. When the three P. patens Lyk5 genes were silenced there was no oscillatory calcium immune response which supported hypothesized functionality.

 

The Creation and Utilization of Bioinformatics Tools to Study Patterns of the Presented HIV Immunopeptidome

Author: Ann-Elizabeth Le

Advisor: Dmitry Korkin

Today, an estimated 38,000 new HIV infections still occur in the United States (CDC, 2020). During the early signs of immune recognition by T cells, virus-derived peptides are presented by MHC molecules on the cellular surface. In HIV infection, immune responses and immune protection are not very well defined. In this project, we analyze HIV-specific patterns during antigen processing and presentation and develop computational tools to aid in the process of the analyses. From this area of study, further advancement in protein degradation analyses and in immunopeptidome definition may help in identifying targets for efficient immune clearance and a future vaccine design.

 

Tracking DNA Damage Repair in Cancerous Cells

Author: Michael Corace and Alexandra Nicolella

Advisors: Dmitry Korkin and Amity Manning

This project seeks to understand the dynamics of DNA damage repair in cancerous cells utilizing preexisting software and novel analysis approaches. Current analysis tools allow biologists to independently track cell movement and count damage sites, but not simultaneously. Our methods identified a slight increase in damage frequency over time in motile cell populations. We suggest utilizing cell morphology rather than coordinate tracking for further advancements in this area.

 

Predicting DNA Damage in Fluorescent Imaging

Author: Daniel McDonough and Surya Vadivazhagu

Advisors: Dmitry Korkin and Amity Manning

There are many methods to analyze cell nuclei, but few can detect the presence of DNA damage, without labeling proteins. We have developed a process to detect and classify cell nuclei in the presence of DNA damage. This method uses the morphology of DNA-associated histone proteins, without proteins that specifically label or localize to sites of DNA damage.. We discuss how and why we address this problem, followed by the specifics of the program pipeline, then our results and how it compares to other methods, and concluding about future additions.

View additional MQP’s in our project database.

Interactive Qualifying Project

WPI undergraduates also put their problem-solving skills to use through the junior year Interactive Qualifying Project (IQP). Students work in teams to solve problems at the intersection of science, technology, and society, from designing bicycle paths in WPI’s hometown to launching a mentoring program for orphans in Morocco to creating interactive guides for a museum in London.