Works and Days

LBPA Bacteria Lab at ENS Cachan: Kerry Jones, Winter Shadow 2016

Imagine you’re me. You’re 20 years old and you love DNA, but have very little on your resume to show for it, save a former lab tech job and a prayer that your future employer can detect your enthusiasm. You’re dragging a conspicuously neon suitcase down the street of a Parisian suburb following the signs to École Normale Supérieure de Cachan, a private University with a reputation for its scientific prestige. Not surprisingly, your three days of 1990s-era in-car-insta-French CDs have done nothing to prepare you for the conversation with the security guard explaining what you’re doing there. For the next two weeks, you’ll be having these conversations with everyone you meet by courtesy of the immediate observation that you are out of your element. Your comfort zone is 6667 km away, and you are really excited not to be in it.

For my Winter Shadow Internship, I was working under the supervision of Bianca Sclavi, a biophysicist in charge of the Bacteria Lab at ENS Cachan. Suffice it to say that my Winter Shadow experience was a learning opportunity, but also an experience of exposure on many counts.

LBPA is an interdisciplinary lab, so projects not only pass through the hands of biologists, but chemists, mathematicians, and physicists as well. In addition, Bianca often seeks the assistance of collaborators around the world from Minneapolis to Cambridge to other side of Paris. Coming from Reed, where the Bio Department and the Physics Department ironically feel miles away from one other, this was one of the first surprises about LBPA: how scientific inquiry in its raw form refused to stay in one place. With this in mind, as well as Bianca’s tendency to work on multiple things at once, it was often easiest to follow the development of individual experiments.

The majority of projects worked with various bacterial promoters, usually including multiple forms of P1, a self-regulating promoter that’s sensitive to DNA supercoiling and growth rate, and P5, a promoter that’s not sensitive to supercoiling, but binds well to RNA polymerase, and transcribes a lot. Bianca proposed to use these promoters, and another one called DnaA for an experiment with a Masters student aiming to answer questions on when the cell decides to start and stop DNA replication, and how this changes in different growth media.

One of the more unique challenges I faced throughout the weeks was navigating a space that seemed to permanently straddle both the English and French languages unconsciously. Though all scientific papers were in English, the comfortable default vernacular of the lab was all in French; often there would be lab equipment with English protocols and French annotations, and the workers, well acquainted with the disorder of the lab, didn’t seem to notice. On the second day of my visit, I attended a seminar entitled “Polarizable Molecular Mechanics/Dynamics Potentials: Addressing the Issues of Non-isotropy and Non-additivity” in which the speaker presented in French but pointed to English Powerpoint slides.

Despite my inability to speak in the casual dialect of the students and lab workers, I found that they were eager to talk to me about their experiments. I followed Qing, a postdoc who is studying how E. coli gene expression changes with growth rate in the presence of chloramphenicol, an antibiotic that results in the increase of ribosome synthesis. I also asked Cyriane a lot of questions about a project she’s contributing to which involves the insertion of three different promoters at six different insertion points on the genome to compare relative expression levels and supercoiling. I also assisted Malik, who was using FLP recombinase experiments to create libraries of bacteria containing different P1 promoters but lacking the antibiotic kanamycin. He taught me how to patch colonies from one LB agar plate to another using a toothpick, which was not as easy as it first appeared.

One of the best takeaways from this experience was the ability to converse with accomplished scientists without being star-struck by their unfathomable genius. Bianca, besides being a data analysis guru, is a professor, PhD advisor, and trilingual badass, and has the habit of trailing off in the middle of her sentences as if lost in some faraway thought. But in the face of her achievements, it comforted me to see a side of her that was indescribably Reed-ish. We bonded over old Reed professors and the best Patti Smith book. “Of course you have a picture of Karl Marx on your desktop,” she would joke while setting up my wifi. Then one day we were talking about her salamander tattoo and she told me about the fascinating side experiments she had been working on.

One of the coolest things about modern science, Bianca taught me, was the ability to do publishable research for free without having anything but online materials. With genomic databases and data software at her disposal, Bianca ventured outside her field to research salamander evolution in relation to genome size. Salamanders, she explained, have a high variation in genome size, but the same number of coding genes, so she postulated that there was a correlation between genome size and capacity for DNA repair, which she measured by examining phylogenies of ribosomal DNA. Though her publishing process was fraught with challenges from other experts, it was beautiful to see that just as the LBPA projects never stayed within one field, so scientific curiosity resisted the same disciplinary confinement.

Hearing Bianca talk about doing research out of her area of expertise reminded me how much of science is just diving into something with fascination. Before this trip, one of the things that intimidated me about applying for graduate programs after leaving Reed was the anxiety of being inexperienced and irrevocably under qualified. Somehow it never occurred to me that accomplished scientists—professors, seminar presenters, the paper-publishing biology elite—must have started from places of inexperience as well. What’s more, they continue to dabble in areas outside of their forte because they don’t let the intimidation of the unknown interfere with the thrill of figuring it out.

Between this cheesy realization and the conversations I had with PhD students and a postdoc at the Institute Pasteur, the possibility of graduate education began to seem less unattainable and more inviting. I’m now so much more excited to figure out where I will fit into the scientific community. Throughout the trip— from the French to microscopy to the metro system— I felt so lucky to be learning it all for the first time.

Tags: winter shadow, externship, biology, dna, lab, research, international travel