Students awarded Dissertation Year Fellowships

Two graduate students at the Jacobs School of Engineering were selected by the UC San Diego Graduate Fellowship and Award Review Committee to receive UC President's Dissertation Year Fellowship awards. Alexander Chen, a chemical engineering PhD candidate, and Phoebe Valdes, a bioengineering PhD candidate, were among the five students honored with the fellowship this year. 

Alexander Chen and Phoebe Valdes
were awarded Dissertation Year Fellowships

The UC President's Dissertation Year Fellowship is awarded to promising students in the final stages of their doctoral work, who demonstrate strong potential for university teaching and research. Recipients receive a $23,500 stipend plus tuition and fees. 

Alexander Chen is advised by nanoengineering Professor Darren Lipomi. He studies a class of materials called semiconducting polymers, which are plastic materials that can conduct electricity.

"My research focuses on understanding and improving the mechanical properties of semiconducting polymers, particularly for enabling new applications in energy technologies," he said. "For example, one of my projects focuses on improving the mechanical robustness and survivability of organic solar cells to enable solar energy harvesting from human-transformed surfaces (e.g., rooftops, buildings, painted and coated surfaces)."

Outside of this research, Chen founded the Graduate Application Mentorship Program (GradAMP) at UC San Diego in 2019. The organization's goal is to help make the graduate education pathway more accessible by pairing undergraduate applicants with a PhD student mentor in their field of study to help guide them through the graduate application process.

With research interests in the fields of energy, materials and healthcare, Chen is leaving his future options open, but hopes to continue conducting research that interests and motivates him, and that has a positive impact on society. 

Phoebe Valdes is advised by bioengineering Professor Shankar Subramaniam and conducts research in his Systems Biology and Systems Medicine laboratory. She uses computational methods to study different forms of Alzheimer's Disease (AD) in order to better understand the mechanisms behind the disease. 

"I want to look into the full progression of early to late stages of AD development by assessing key mechanistic endotypes (i.e. disease substate characteristics) in patient-derived neurons and postmortem patient brain samples," she said. "To investigate what these endotypes could be and how to better formulate mechanisms responsible for AD, I want to analyze large multi-omics data sets at both the gene and chromatin levels (RNA-seq and ATAC-seq) using various computational methods." 

Valdes plans to travel and sightsee for a few months after completing her PhD, and then hopes to secure a post-doctoral research position in the biotech industry or academia to pursue a career as a data science or bioinformatics scientist. 

"I am a big fan of looking into analyzing big data generated from diseases (open to going beyond neurodegenerative diseases after my PhD)," she said. "Otherwise, we will see where life takes me after I complete my doctoral studies."

Valdes is a second-generation Filipino-American whose parents immigrated from the Philippines, and is the only bioengineer in her family. She hopes her research will help direct new avenues of treatment for patients with different forms of AD, as there is no cure yet. 

"I am completely thrilled and honored to be receiving this fellowship as it will help support my own research endeavors. Thank you Graduate Division for supporting me on my graduate school journey."

Bioengineering students create prototype lymph node for cancer patients

Yuxuan Zhou, Sonia Singh, Riyam Al-Msari and
 Arielle Hancko present their award-winning research. 

By Kiran Kumar

Four UC San Diego undergraduate bioengineering students designed a prototype of a decellularized lymph node for individuals who have had their original lymph nodes surgically removed during head and neck squamous cell carcinomas (HNSCCs) treatment. The students– Sonia Singh, Yuxuan Zhou, Riyam Al-Msari and Arielle Hancko – completed the project for their Jacobs School of Engineering bioengineering capstone senior design project. Their work was awarded the Best Overall Poster designation at the student-run Bioengineering Day 2022.

Ninety percent of head and neck cancers originate from squamous cells: cells in the surface of the skin, and the linings of many organs in the body. These are referred to as HNSCCs. Standard treatment of HNSCCs involves surgical removal of lymph nodes in the neck. However, these lymph nodes carry a host of immune cells, which can be vital to the success of several cancer therapies, including cancer immunotherapies and radiotherapies. Without these lymph nodes, these therapies can sometimes prove ineffective.

This team of bioengineering students wanted to help those individuals who have had their lymph nodes removed still experience the benefit of immunotherapies and radiotherapies. They used tissue engineering to design decellularized lymph nodes which can be surgically implanted in place of the removed lymph nodes. Ex vivo experiments were conducted on mouse models to establish that these engineered lymph nodes had an adaptive immune response, restoring immune function. The results were promising.

“We spent most of our time on the decellularization aspect of the lymph nodes since that is the foundational aspect of tissue engineering, removing the double stranded DNA” said the team. Decellularization is very important to maintain the morphology of the tissue. Non-decellularized tissue can lead to rejection of the lymph node.

To engineer these replacement lymph nodes,  cervical lymph nodes were harvested from mice, and then washed in a phosphate buffered saline solution.  Then, sodium dodecyl sulfate was used for decellularizing the mouse lymph nodes. The tissue was recellularized using dendritic cells from the bone marrow of mice. They also attached chemokine proteins to the lymph nodes.

The team is excited that this research will be taken to the next level with in vivo experiments in mice.

“It will be completed by a senior design team next year,” the students said. “We have now completed the handover work. They will test how the mice fare with our lymph nodes, and then test the immune function of the lymph nodes.”