Posts
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New paper / Dear Reviewer #2
Our new paper - Trajectories for the evolution of bacterial CO2-concentrating mechanisms - aims to understand how bacterial CO2 concentrating mechanisms evolved. -
(Relatively) new preprints and publications
Since I last updated this site, I've published a few papers and preprints. Here's quick overview. -
Don't be a postdoctoral fellow, be a postdoctoral employee
Among many things no one ever explained to me about academia, postdocs awarded fellowships are often not employees of their host institutions. -
On bad terminology: up- and down-regulated
Today I read a paper I enjoyed and learned from about the physiology of bacterial lag phase. I do recommend the paper - Rolfe et al., J Bac. 2012 - it is very good, but it nonetheless reminded me of something that has bothered me for a long time: I despise the terms "up-regulated" and "down-regulated." -
Five years
This year marks the fifth anniversary of my father Jack's death. His fifth yahrzeit. Around the time of his first, we held an event in his honor at Drisha in NYC. These are some words I wrote to introduce that event, which was on the theme of "Judaism in America." Unbelievable that five years have past. For context, this speech was delivered in fall 2017. President Trump was newly elected. My Daddy, forever the gallows humorist, told me he was happy he would never see the man elected. Jack Flamholz died on erev erev Rosh Hashana of 2016, which was the evening of Sept. 30th that year. I miss him. -
#AviLovesYourPaper #1 - Jinich et al. PNAS 2020
This week on #AviLovesYourPaper I re-read @champiDicty's "A thermodynamic atlas of carbon redox chemical space" - a really pleasing application of recent advances in computational chemistry to probe the origin and structure of cellular metabolism. -
Functional reconstitution of a bacterial CO2 concentrating mechanism
Many photosynthetic organisms have evolved CO2-concentrating mechanisms (CCMs) that compensate for the relative inefficiencies of rubisco by elevating CO2 levels near the enzyme. Elevated CO2 is doubly beneficial, bringing rubisco closer to CO2-saturation and also excluding O2 from the active site. CCMs are very significant on the global scale, responsible for perhaps 50% of global photosynthesis. CCMs are also very significant to the organisms harboring them. CCM mutants typically entirely fail to grow in ambient levels of CO2 (0.04%) and require CO2 supplementation to enable robust growth. -
Ballotsplaining: the Propositioning
Last week Rachel and I had a Zoom ballot-splanation-athon with some friends. A lot of people contributed to that conversation and I took copious notes. Sharing my thoughts on the statewide propositions here. -
DABs are inorganic carbon pumps
Using RB-TNSeq we compared the phenotypes of 70,000 knockout mutants between ambient air, where the CCM is required for growth, and elevated CO2 (where the CCM is dispensable). 17 genes appear to be required for CCM function, including all known carboxysome genes, three transcriptional regulators, a putative Rubisco chaperone, and a pair of candidate transporters. -
Revisiting tradeoffs between rubisco kinetic parameters
All plants, algae and cyanobacteria rely on the Calvin-Benson-Bassham (CBB) cycle for growth. Rubisco is the central enzyme of the CBB cycle and the most abundant enzyme on the planet. It does the tricky bit where CO2 gets "fixed" onto a soluble sugar. While it is often said that rubisco is "slow," it is actually an average enzyme in terms of "turnover number" (maximum rate per active site, kcat). The true rate of rubisco carboxylation is much slower than its kcat, however, because rubisco can react non-specifically with O2. I certainly think it's surprising that rubisco is not faster or more specific given how important and abundant it is. -
Bike boulevards are fiction
I have opinions about bike infrastructure for sure. I wrote about the insufficiencies fo Berkeley’s “bike boulevards” for Berkeleyside here. Many thanks to Rachel Shipps, Leslie Gordon and Emeric Charles for editing and important substantive comments on the article.
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The fungal-mammalian emergence hypothesis
My friend Andrew sent me a nice Reddit thread with the charmingly long title "It’s hypothesized that warm-bloodedness evolved in mammals and birds because it provided defense against fungal infections. Very few fungi can survive the body temperatures of warm-blooded animals. By comparison, insects, reptiles, and amphibians are plagued by fungal infections." -
Applying to the UC Berkeley MCB PhD program
This year I had the privilege of sitting on our department's PhD admissions comittee as a student representative... -
New preprint! A novel class of carbonic anhydrase-like inorganic carbon transporters
I'm pretty excited about this new preprint - Jack Desmarais and I worked on it up until the crack of Thanksgiving. -
New preprint: Revisiting Tradeoffs in Rubisco Kinetic Parameters
I just posted my first preprint to bioRxiv - Revisiting Tradeoffs in Rubisco Kinetic Parameters. -
2018 Ballot Prop Recs AF *Updated*
Thanks to conversations with a number of friends, I've firmed up my thoughts on the statewide propositions. Here's an updated overview with some details below. -
2018 Ballot Prop Recs AF
I've spent a bunch of time in the last couple weeks learning about the ballot initiatives in front of me for the November 6th election. These are my notes on how I'm thinking of voting, though I remain (evermore) open to compelling contrary arguments. Contact me up in person if you know me or on Twitter if you don't. I'll write something about local measures, candidates etc. later. -
City of Gold
I find myself surprisingly saddened that Jonathan Gold is no longer with us. He died yesterday (Saturday night) of pancreatic cancer. He was 57. Maybe it's the ineffable similarities to my father - a quiet subtle-minded lover of cars and odd foods - that are grabbing at my heart now. -
2018 Photosynthesis, Carbon Fixation & the Environment Symposium @ UC Berkeley
Next Wednesday 6/27/18 we are hosting the second (annual?) UC Berkeley Symposium on "Photosynthesis, Carbon Fixation and the Environment"... -
eQuilibrator: Enzymes by Name & Reaction
One consequence of the 100+ year legacy of biochemistry research, is that some enzymes have truly inconvenient names... -
eQuilibrator: Redox Reactions
An electron carrier is a molecule that can stably occupy reduced and oxidized states - like NAD+ and NADH diagrammed below. Most biological redox reactions involve the enzyme-catalyzed transfer of electrons to or from an electron carrier... -
eQuilibrator: Balancing Reactions
The more I study biology the more I realize that *I am not a chemist*. I studied computer science and applied math in college and made my way into biology slowly. After 8 years, I am comfortable with biology. But *I am not a chemist*... -
eQuilibrator update
Elad just pushed some nice updates to our biochemical thermodynamics calculator eQuilibrator... -
Just bury the algae?
The word "fossil", I think, conjurs images of dinosaurs. Maybe also fossilized leaves and coelacanths. But fossil fuels like petroleum are not formed from dinosaurs of course. They are mostly formed from algae, cyanobacteria and other small photosynthetic organisms... -
On the nature of cytoplasm pt. 1: crowding & excluded volume
Usually when we do "in-vitro" experiments with purified proteins, AKA "biochemistry," the only protein in the tube is the one we are studying. OK, perhaps the tube contains our favorite protein and a few others... -
I made a website.
And you found it. Nice work!
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