Cohen Lab

Posts tagged #big-ideas-night

Big Ideas Night

Aaaand we’re back for round three. This time with some new faces! Ah, time ticks on and people come and go. Fortunately for us, whiskey and science persist.

Back at the Scottish Arms, we tackled the problem of detecting simultaneous binding of two proteins to DNA; the proteins each must bind to the DNA and thus are not co-localized due to protein-protein interactions. In Barak’s words…imagine the TF a cowboy. Once on its DNA horse, it can lasso other TFs around it, but only those TFs also on horses. A wild west of a genome, indeed.

Some ideas included FRET-seq, 2-dimensional gels, and combination usage of accessibility and binding footprints. Without a clear winner, we’ll wait another day before discarding the lassos hanging from our bench top shelves. Until next time, keep thinking big, you crazy scientists.

Big Ideas Night

Following the smashing success of our first big ideas night, big ideas coated our benches just as Barak’s wool sweater once did. Ideas so big that we contemplated moving into a building with even higher ceilings. But alas, we shan’t desert our loyal coffee maker, so we stay put.

The second gathering of Big Idea’s Night took place at Retreat Gastropub. Amidst some fries and whiskey, we pitched ideas for how we can utilize our Center’s newest sequencing technologies. PacBio’s ultra-long sequencing reads and the 10x single-cell method both provide new avenues for innovative research. And to not exclude our friends in imaging, we discussed a new application of FISH, called clampFISH. This technology generates a FISH signal strong enough to be detected by FACS.

The idea most discussed utilizes ultra-long reads to query chromatin interactions. In our lab, we have identified strong regional effects on gene expression. How far do these regions stretch? With our landing pad in place, we can integrate reporter genes at variable distances and ask how the length relates to the coordinated expression between the reporter gene at the LP and at distance. If we see discordance at a certain distance, it may be possible to restore the similar expression with looping-related proteins, such as CTCF or YY1. As team landing pad ventures further into the mechanisms of this strong regional effect, we will draw from these discussions and this big idea.

Big Ideas Night

The inaugural Cohen Lab Big Ideas Night! Barak loves to tell the story of the discovery of transfer RNA. Our scientific forefathers kicked around ideas over tea, scones, and maybe some beers too. Through this sort of brainstorming, the idea that there must be some molecule shuttling around amino acids was borne. Once our forefathers convinced themselves of the specifics of the idea, and how the experiment would work, actually conducting it became trivial. And thus tRNA was discovered. If such great biological discovery can be made over scones and ales, then lets indulge!

Settled into our lab’s old haunts, The Scottish Arms, we bounced around big ideas focused on master regulators. With new graduate students patrolling the benches, the lab has taken up new vocabulary as well: pioneer factors. Discussion flitted between definition, mechanism, and proof of these special transcription factors; perhaps we leave this discussion for our graduate students’ future presentations.

And so big idea #1 was not as much an idea but an open question: what would result from treating cells with two different master regulator cocktails? What type of cell would the transcriptome resemble? Would we see a random assortment of cell A and cell B, or would we see a monster, with the head of cell A and the body of cell B? With Halloween on the horizon, we’ll incubate this spooky idea until a rainy day comes along, ripe with time for a big idea experiment.