ElowitzLab

@sethbannon @fiftyyears Awesome

@ElowitzLab @fiftyyears You got it.

Goodies for 5050 gift boxes going out to labs. If you want one for your lab, let us know below!

Excited to co-found @Merge Labs! TLDR: We’re developing a new paradigm for BCI using molecules instead of electrodes. If you’re excited about this and want to contribute in protein engineering, synbio, delivery, immunology, ultrasound, devices, neuroscience, or data/ML/AI, we’d love to hear from you. merge.io/blog merge.io/careers 🧵

Amazing work!

Some things I believe about writing: > It is the best, most efficient way to transmit ideas. (Brain-to-brain BCIs may surpass it someday.) Even the best YouTube videos or podcasts usually only convey a fraction of the ideas contained in an excellent essay. > It is faster to write than to make a video or record a podcast. Therefore, you should usually default to writing when exploring an idea. (And videos and podcasts usually involve a fair amount of writing anyway.) > Using AI to write for you (not research, or explaining a paper to you, but actually **writing**) will make you dumb. > Writing is a form of telepathy across space and time. Here's a passage from Stephen King that I love, about a table on which there is "a cage the size of a small fish aquarium. In the cage is a white rabbit with a pink nose and pink-rimmed eyes. In its front paws is a carrot-stub upon which it is contendedly munching. On its back, clearly marked in blue ink, is the numeral 8.... Do we see the same thing? We'd have to get together and compare notes to make absolutely sure, but I think we do." (King wrote this in 1999, and his thought of this rabbit, and what it looks like, shall remain firmly established for all time. Similarly, I can still read Pliny today and know exactly what he was thinking 2,000 years ago.) > It is the best way to make sure you, yourself, understand something. > If you can write something using simpler words, without distorting your meaning, then you should do so. > Adverbs are almost always your enemy; akin to a gentle lullaby that will strangle you into the passive tense. (And readers do not enjoy the passive tense.) This list will expand over time. Brief bibliography: - The Elements of Style by Strunk and White is the only book on writing worth reading. But Stephen King's "On Writing" is also nice. - "Always Bet on Text" by graydon2: graydon2.dreamwidth.org/193447.html

This experiment came to life when I realized the negative control (two genes, same regulation) was intrinsically more interesting—and easier!—than the "real" experiment I had been planning... Thanks @NikoMcCarty!

⏰Tick-tock!⏰ Abstract deadline for SynBio for Future Health Jan 17th #synbio Heads up to @MoKhalilLab @RosserLab @barbara_synbio @LeonardoMorsut @rjerala @XueSherryGao @SynBioGaoLab @ElowitzLab @genegirl007 @BintuLacra @TheLeonardLab @Geneticdesigner @kunjapur @ProfTomEllis

This work had wonderful contributions from Jordan Lay, James Linton, @ChadlyDuncan, @Y0shiki_2019, Ron Hadas, @AndrewPerez9201, Mario Blanco, @PaolaLaurino, @mitchguttman

“What’s past is prologue” — excited about chromatin recording by synthetically engineering recruitment of adenine methyltransferases in living cells. Will enable one to correlate past states with subsequent fate decisions. New work from the virtuosic @yodai_takei See thread.

In 2000, a physicist named Michael Elowitz published one of the first synthetic gene circuits, called the "repressilator." By stitching three genes together, he endowed living cells with an artificial rhythm, coaxing them to flash green. Learn how he built it, and even play around with its parameters, in our interactive article from the archives: "The Making of a Gene Circuit." press.asimov.com/articles/gene-…

I’ve always been interested in the stories behind BioNumbers. Textbooks say DNA polymerase, for example, replicates 220 nucleotides per second. But how do we know this? How can one actually measure the speed of a single enzyme? A fast typist, for comparison, types ~80 words per minute or ~5-7 characters per second. This means that DNA polymerase (in this case, from T7 phage) “types” letters 30-40 times faster than a skilled typist. Measuring the speed of a single enzyme is not so simple. In this case, one cannot simply time how long it takes for a cell to divide, say, and then divide that time by the cell's genome length to arrive at an estimate of DNA polymerase speeds. That is because division rates are not bottlenecked by DNA division times, and bacterial cells initiate multiple rounds of DNA replication on their genomes simultaneously. Therefore, we need another way. Ideally, there would be a “single molecule” way to observe DNA replication happening without relying upon highly indirect measurements. In 2006, a group of Harvard biochemists figured out a way to do exactly that. Before explaining their experiment, though, it’s important to note that these biochemists took advantage of length differences between single-stranded and double-stranded DNA. Double-stranded DNA has a rigid, helical structure (which we learn about in school) and, therefore, also a consistent length of about 0.34 nanometers per base pair. Single-stranded DNA, for comparison, is far more flexible and disordered. It doesn’t have stabilizing hydrogen bonds like double-stranded DNA does, so it tends to coil and collapse on itself. Under experimental conditions, and outside of cells, single-stranded DNA has a short length of only about 0.03 nanometers per nucleotide. Now, here’s how this experiment worked: First, the researchers took a long, single-stranded thread of DNA and stretched it between a glass surface and a tiny bead, floating in liquid. Next, they added a short piece of DNA, called a primer, which latched onto the DNA near the glass surface. This gave the enzyme a starting point to begin copying DNA. Then, they added the T7 DNA polymerase to the liquid. As the enzyme added new nucleotides, it turned the single-stranded DNA into stiff, double-stranded DNA. The DNA began to uncoil and stretch out. And since one end was fixed to the glass and the other to the bead, the bead slowly moved as the DNA extended. Finally, the researchers watched this movement using a microscope and camera. By tracking the bead’s movements, and measuring its distance further and further from the glass slide, they figured out that polymerase was copying about 220 nucleotides of DNA per second. From this experiment, the researchers could ALSO see that the DNA polymerase enzyme moves in "bursts;" it doesn't copy DNA continuously. This is just one “Behind the BioNumbers” experiments that I really enjoy. I’ll plan to write more about these in the future if you enjoy them.

Congratulations @ShiyuXia and @ucberkeley!

Added some tiny improvements to the flowcytometry app I made during my time in @ElowitzLab. Now it supports exporting gated events as npy and mat. So you can gate data in your favorite graphic interface, then analyze them with python or Matlab! ym3141.github.io/EasyFlowQ/Raw%…

Congratulations to @ShiyuXia and all of the outstanding CASI recipients!

This work was led by brilliant students: @andreww_lu, @lkmoeller, and Stephen Moore, and is a collaboration with @Zhu_Lab and @DJSiegwart. If you have experience in animal cancer models and are interested in circuit therapeutics, please reach out.

In a mouse model of Ras-driven liver cancer, systemic treatment with the circuits (lower row) reduced tumor burden compared to untreated controls (upper row). Much more to explore.

Synthetic biology could enable new types of programmable therapeutics. Our new preprint introduces synthetic protein circuits that selectively trigger cell death in Ras-mutant cancer cells, with interesting advantages compared to existing approaches. biorxiv.org/content/10.110…