I delivery. As a student in Dr.

I am interested in pursuing a graduate degree in Biomedical Engineering. I am particularly excited about
the research experience that graduate study provides to apply fundamental principles and recent advances
to interrogate biological systems and rationally engineer solutions with translational potential. Due to the
strength of both the School of Engineering and Applied Sciences and the School of Medicine, Yale would
provide me with the opportunity to conduct meaningful translational research in the field of tissue
engineering with overlap in biomaterials, cell engineering, and drug delivery.
As a student in Dr. Joseph Loparo’s laboratory at Harvard Medical School, I studied the ParABS system,
which is involved in chromosomal segregation and the organization of newly replicated origins in
bacteria. Since bacteria do not contain nucleosomes or histones, they use nucleoid-associated proteins that
bind DNA to condense its genetic information into a subcellular length-scale. Previous work in the
Loparo laboratory demonstrated that one of these nucleoid-associated proteins, ParB, could form higherorder
interactions between distal regions of DNA to condense the bacterial chromosome.
Informed by a recent structural study, I sought to investigate interaction surfaces in ParB proteins that
could allow for the formation of higher-order interactions. By mutating highly conserved residues, I
classified more than 25 mutants using single molecule assays. Using the protein induced fluorescent
enhancement effect of Cy3 dye by which labeled DNA will undergo fluorescent enhancement upon
protein binding, I quantified the kinetics of DNA compaction. To assess DNA binding stoichiometry, I
used electrophoretic gel shift assays to characterize the DNA binding of each mutant. The impact of each
mutation on chromosomal compaction was assessed in vivo through the visualization of fluorescently
labeled ParB. To analyze the chromosomal compaction in a quantitative manner, I developed and
implemented an algorithm in MATLAB for image segmentation and dynamic thresholding to quantify
foci co-localization in multi-planar images with the bacterial nucleoid using signal processing techniques
including the watershed transform. Ultimately, this investigation allowed for the identification of residues
involved in interaction hubs and was published in Nucleic Acids Research, as “A network of cis and trans
interactions is required for ParB spreading”.
This experience exposed me to a range of research techniques used across disciplines including
polymerase chain reaction, gel electrophoresis and SDS-PAGE gels, bacterial culture and cloning, and
recombinant protein expression and purification, as well as more specialized single molecule imaging
techniques. After taking advanced bioengineering courses, particularly in biomaterials, tissue, and cellular
engineering as well as immunology, I became intrigued by the crosstalk between these fields, in part due
to the recognition that natural systems can serve as a source of inspiration to rationally break down
complex problems.
I sought to apply these research techniques in a project with translational potential. As an undergraduate
in Dr. David Mooney’s laboratory, I am involved in an immuno-materials project which seeks to use
materials to enhance the reprogramming of the immune system to target tumors. Previous work in the
Mooney laboratory has demonstrated the use of an injectable, spontaneously assembling scaffold formed
by mesoporous silica rods in a peptide-based cancer vaccine. While peptide-based vaccines have
demonstrated immune enhancement, mRNA is comparatively cheaper and faster to produce, motivating
the use of antigen-encoding mRNA. However, since RNA is susceptible to extracellular nucleases, it is
necessary to protect the mRNA from degradation. Using this scaffold in order to enhance delivery of this
mRNA to the targeted cell type, I sought to develop a delivery system to simultaneously enhance the
stability and promote sustained release of mRNA from the scaffold as my undergraduate thesis.
In particular, I engineered cationic liposomes composed of DOTAP lipids and cholesterol to stabilize the
mRNA based on previous work that demonstrated they promote endosomal disruption to release the
transcript into the cytosol where it can be translated and processed for presentation to T cells. By
screening charge ratios, I quantified mRNA association and release as well as in vitro transfection efficiency and kinetics using flow cytometry. Initially, I intended to assess encapsulation efficiency
through the quantification of free mRNA. However, since ultracentrifugation disrupted the liposomes and
dialysis-mediated separation of the free mRNA from lipoplexes would dilute the mRNA to unquantifiable
levels, I drew upon my experiences in the Loparo laboratory to quantify mRNA association in lipoplexes
using gel electrophoresis-based methods reminiscent of the electrophoretic mobility shift assay I used to
quantify DNA binding of ParB proteins.
These research experiences have motivated my interest in immunology, drug delivery, gene editing, and
single cell analysis, reflected in the work conducted by Dr. Tarek Fahmy, Dr. Mark Saltzman, Dr. Rong
Fan, and Dr. Andre Levchenko. The biologically-inspired approach taken by the Fahmy laboratory to
design systems including artificial antigen-presenting cells, vaccines, and biomaterials is one that I find
extremely powerful. In addition, I am interested in the work conducted in the Saltzman laboratory in drug
delivery and gene editing to influence tissue-level assembly and growth. The work conducted in the Fan
laboratory focuses on cell-level analysis. Cellular heterogeneity has significant applications in cancer and
is compelling because tissue-level analysis often does not account for cellular heterogeneity. The work
conducted by the Levchenko laboratory pairs the interest in immunology I developed in the Mooney
laboratory with my passion for single molecule methods and cellular-level analysis that I developed in the
Loparo laboratory.
I am dedicated and motivated to continue to conduct research. Not only have I commuted three hours to
the Loparo laboratory each day for ten weeks in a non-residential research program, but I have also
volunteered to conduct summer research in the Mooney laboratory without receiving funding. Ultimately,
I understand that research can be an iterative process, but I believe that my motivation and diverse
research experiences will uniquely enable me to contribute to interdisciplinary efforts to engineer rational,
elegant solutions with translational potential. After earning a doctoral degree, I would like to continue to
conduct research as a necessary link between engineering and medicine. This knowledge would support
my goal to engage in mentoring the next generation of scientists as a professor.

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I'm Eleanor!

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