Gordon Conference

I was in Ventura, California from January 8 - 13, 2017 to present a poster titled Resource Sharing Controls Gene Expression Bursting at the Stochastic Physics in Biology Gordon Research Conference: Landscapes, Stochastic Dynamics and Heterogeneity in Biology. The research is now published open access at ACS Synthetic Biology. The Gordon Conferences are unique. Everyone signs an NDA and no photos are allowed, so very new results are presented and discussed. The conference topics are very specific so the audience is small and mostly the world experts in the field. Because the conferences are small, discussion is encouraged from everyone, even grad students. Finally the conferences are in remote locations and there is an early afternoon break every day where people are encouraged to hang out. During this time I played soccer, tennis, biked and ran with professors, post docs, and other grad students. It was a great way to get to know people in a less academic, less intimidating way. I was very fortunate to meet Dr. Daniel Gillespie and his wife Carol Gillespie. He created the Gillespie algorithm which I use to make stochastic simulations of my experimental system. He spoke about how the algorithm was created and how he received great skepticism when he first presented it. 

Resource Sharing

My first first-author paper, Resource Sharing Controls Gene Expression Bursting, has been published [PDF]! 

Genes express proteins in bursts of activity with periods of no activity between bursts. Burst dynamics are characterized by a burst size (duration of a burst) and burst frequency (number of bursts per time). During a burst the gene draws on a limited pool of reusable resource. Little is known about the relationship between burst dynamics and resource sharing. Here we made cell-sized reaction chambers (both PDMS plastic and POPC lipid vesicles) and observed bursting dynamics as the size of the resource pools was varied. When the size of the resource pool was increased, the number of protein made increased. This increase in protein was achieved by increasing the burst size not burst frequency. This may be due to the fact that the 100 different molecules needed to make protein became localized. Localized components suggest large transcriptional burst sizes are correlated with large translational burst sizes. This correlation is confirmed with in vivo E.coli data. Our results demonstrate the link between bursting dynamics and resource sharing.

 
 

Caveney, Patrick M., S. Elizabeth Norred, Charles W. Chin, Jonathan B. Boreyko, Brandon S. Razooky, Scott T. Retterer, C. Patrick Collier, and Michael L. Simpson. "Resource Sharing Controls Gene Expression Bursting." ACS Synthetic Biology (2016).

SEED 2016

I presented a poster titled “Effects of Resource Sharing on Gene Expression Dynamics” at the 2016 Synthetic Biology: Engineering, Evolution & Design (SEED) Conference in Chicago.

Dr. Julius Lucks, Associate Professor at Northwestern University, won the ACS Synthetic Biology Young Investigator Award and presented “Uncovering How RNA Molecules ‘Make Decisions’ On the Fly: Towards Understanding and Engineering CoTranscriptional RNA Folding." This was an amazing lecture about visualizing RNA folding as it is being transcribed. He described their SHAPE-Seq technology to protect RNA from degradation and measure the reactivity with nucleotide resolution. This allowed them to see hairpin loops fold and unfold as the RNA was transcribed.

Watters, Kyle E., et al. "Cotranscriptional folding of a riboswitch at nucleotide resolution." Nature structural & molecular biology 23.12 (2016): 1124.

SEED 2015

I presented a poster titled “Noise in Confined Cell-free Reactions” at the 2015 Synthetic Biology: Engineering, Evolution & Design (SEED) Conference in Boston. We then toured Ginkgo Bioworks. Their labs were beautiful. Every sample is barcoded, and every time a sample is manipulated a record is made. What a wonderful thing!

This was my first time in Boston. I walked around MIT and saw the finish line for the Boston Marathon.

JOVE

March 2015 we open-source published Sealable Femtoliter Chamber Arrays for Cell-free Biology, our experimental setup, in the Journal of Visualized Experiments to allow other researchers to confine reactions in femtoliter chambers. We use this technique to observe cell-free protein synthesis.

SynBioBeta 2014

This week I attended SynBioBeta 2014. This is a biotech/synthetic biology industry conference. I saw presentations from many new biotech startups. This is a rapidly growing space. Many companies were focusing on the foundations needed for a biotech revolution: DNA sequencing, DNA writing (Cambrian Genomics), easy genetic manipulations in organisms (Ginkgo Bioworks). One of my favorite parts was a tour of Cambrian Genomics led by founder Austen Heinz. Austen and his company were inspiring because they were pushing the edge on a shoestring budget. He talked about modifying all kinds of organisms often in playful, but useful ways. He had an almost “we can do this fun thing so why not” attitude. This reminded me of the attitudes of the founders of early computer companies, and it was exciting to see the same attitude in biology.

I also met with researchers at the Gladstone Institute who are frequent collaborators of our group.

This was my first time in San Francisco. The city had a very cool atmosphere and it seemed like everyone was focused on building their own company and releasing the next product.

Caltech Workshop

This week I attended a cell-free synthetic biology workshop at Dr. Richard Murray's lab at Caltech. We learned how they make cell-free extracts for their experiments and made a batch ourselves. Cell-free extracts start with whole cells (in most cases E.coli), remove the cell membranes, centrifuge out genome, and dialyze to remove salts. What is left is a pared down set of proteins that are used to make proteins from any desired gene. Salts, nucleotides, amino acids, and energy molecules are added back to sustain protein synthesis. The goal of their work is to make cell-free systems more predictable and reliable. They mostly use cell-free extract to test genetic circuits before putting them in cells.

Their protocol is published in the Journal of Visualized Experiments (JOVE). Sun, Zachary Z., et al. "Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology.Journal of visualized experiments: JoVE 79 (2013).