Ernesto Gamauf, COL ’24, Doylestown, PA
Upon the fusion of the sperm and egg, a zygote is formed. This single, unassuming cell will give rise to red blood cells, neurons, skin cells, retinal cells, and the myriad of other cells in our bodies. This cellular complexity is what makes organisms like us possible. But how does this occur if all those cells have the same DNA? How can they begin to differentiate themselves from one another? How are cell fates determined?
The answer is complicated. How would we even go about figuring it out? We can’t see inside an embryo. Or can we?
We could start by choosing an organism to study. Ideally, it would be one easy to work with, with limited ethical issues, and whose development is comparable that of humans. So, the fruit fly.
It turns out that the early fruit fly embryo, which looks like a white, oblong blob from the outside, is undergoing a massive transformation on the inside. It is trying to figure out which genes should be active. To do this, some proteins called transcription factors, that the mother fly deposited into the egg before she laid it, spread out across the now-embryo in defined patterns. These proteins create a concentration gradient, activating transcription differently depending on their density at a specific region of the embryo, through a process known as patterning.
One example of a patterning transcription factor is the famous Bicoid protein which forms a gradient along the anterior-posterior axis (the axis along the embryo’s head and tail). It turns on genes by binding to DNA at specific regions and then summons transcriptional machinery like RNA Polymerase to activate transcription. Another analogous protein called Dorsal does a similar thing along the dorso-ventral axis (the axis along the embryo’s back and belly), where it is present at a high concentration inside nuclei on the ventral side of the embryo and at a low concentration on dorsal nuclei. The presence of these gene-activating transcription factors on one side more than another makes it so that DNA is transcribed differently in different regions of the embryo. This difference in transcription is what distinguishes otherwise nearly identical nuclei from one another. Embryonic regions whose nuclei experienced similar concentrations of patterning transcription factors are grouped together and “assigned” similar cell fates.
So, we know that these patterning proteins like Dorsal help activate transcription in certain embryonic regions, but the nucleus is a very crowded place. It must fit thousands and thousands of proteins in a space over 200 times smaller than a pencil tip. Amid that jumble, how in the world do these specific proteins, which are required for proper development, arrive at the right time and place to bind to a specific stretch of DNA? Once that is done, how do they bring over other proteins to activate transcription?
Those were the questions I worked towards solving this summer. I worked in the Mir Lab at CHOP to delve deeper into how exactly transcription is being regulated during these early developmental stages. Specifically, I investigated how Dorsal proteins find, bind, and recruit transcriptional machinery to set in motion the patterning of the embryo, which differentiates the dorsal nuclei from the ventral ones. Using the MOSAIC lattice light sheet microscope, I observed the behavior of single molecules of the Dorsal protein within live, developing embryos. From those data, I tracked and quantified the motion of individual Dorsal molecules to understand how they find their target sites, bind to them, and ultimately activate transcription.
As with all research, my experience this summer has led to more questions than answers, but the process has allowed me to develop my imaging, fly culture, programming, wet lab, and critical thinking skills and has given me the opportunity to get to know some amazing people. Not only that, but, this summer, I was able to apply what I’ve learned in my coursework and textbooks to shine a light (I mean laser) on early development and learn about a groundbreaking and unknown field. It is just so cool to work towards the generation of new knowledge that may just end up in the next generation of textbooks.
Thank you to my PI, Dr. Mustafa Mir, my grad student mentor, S Fallacaro, and all my amazing lab mates for their advice and patience and thank you to Career Services for making this experience and work possible.
From learning about molecular kinetics to knowing how to sex random fruit flies in my kitchen, my passion for research has been further ignited. I’m excited that humanity is closer than ever to unraveling the secrets of life (one single molecule at a time), and I am thrilled and grateful to have contributed a small part in that quest.
This is part of a series of posts by recipients of the 2023 Career Services Summer Funding Grant. We’ve asked funding recipients to reflect on their summer experiences and talk about the industries in which they spent their summer. You can read the entire series here
