Category Archives: Proteins

Cannabis sativa

I work on cannabis.

As a PhD biochemist and former cancer researcher, it feels a little dirty to admit. But let me explain…

I love plants. My favorite plant is Sarcodes sanguinea, a native of the high Sierras that is a brilliant red hue because it lost it’s chlorophyll and parasitizes fungi for food:

A fabulous Sarcodes seen while riding my cyclocross bike on the East side of Lake Davis before the Lost and Found Gravel Grinder, June 2017.

I planted lemon, lime, fig, pomegranate, olive, pear, and apple trees in my back yard. I also have a rockin’ garden, and I love teaching my kids where their food comes from:

My main garden in full force, June 2017.

I also have a soft spot for interesting plant chemistries. While at U.C. Davis I worked with antioxidants produced from broccoli and other cruciferous vegetables. I have worked with the biochemical pathways producing the stevia sweetener, and contrast that with working on the genetics of noxious plants that are toxic to humans.

I am an  endurance athlete, and I like to cycle or trail run for hours. Mostly from the health benefits, but I do enjoy the endorphin rush from an epic workout. I’m generally risk-averse, and I’m an Eagle Scout in most senses of the stereotype.

But I work on cannabis. Or more specifically, cannabinoids that originate from the cannabis plant.

Cannabis sativa. Pot. Weed. Marijuana. Ganja. Reefer. (Insert your favorite slang here). Yeah, that cannabis.

It is weird to me how some people think that I am part of a counter-culture movement full of pot-smoking hippies (or whatever the equivalent is for the millenial generation – pot smoking, avocado-toast-eating, millenials?). In actuality, we are a bunch of over-educated, lab-coat clad nerds, drinking coffee and geeking out about the amazing chemistry of cannabinoids and the corresponding human cannabinoid receptor system.

Nerds!!!

As Alexander Shulgin wrote in PiHKAL, “Among the drugs that are currently illegal, I have chosen not to use marijuana, as I feel the light-headed intoxication, and benign alteration of consciousness does not adequately compensate for an uncomfortable feeling that I am wasting time.”

None of us partake in cannabis for recreational or medicinal uses, and whenever a question on human use comes up- we are forced to consult Google to learn about typical usage and exposures. I personally, and our startup are fully compliant with all state and federal regulations, and we have all necessary approvals to perform our research. When it comes down to it, we are just doing science. Some plant biochemistry, some mammalian receptor biology. But our work could have an impact on inflammatory bowel disorders, colon cancer, and some other potential applications that could be pretty damn cool.

A friend from grad school was concerned that by researching cannabis, I may be a marked scientist- unable to rejoin the ranks of the normal scientists hard at work on cancer, neurobiology, and other respectable areas of study. I completely disagree. What I have found is that the cannabinoid and cannabinoid-receptor research field has been stifled by undue regulatory pressure for so many years, so instead of being a dead-end for science, it is ripe for discovery.

Pharmacological uses of non-psychotropic cannabinoids

The cannabinoid receptor is the most abundant G-protein coupled receptor in the brain, hence, people get really high with THC exposure (an agonist). CBD on the other hand is an inverse-agonist, so it has somewhat of an opposite effect on our receptors and doesn’t get people “high”. It is on the fast-track to be approved for treatment of specific epilepsy subtypes, is in multiple clinical studies for schizophrenia, and has tremendous potential as an anti-inflammatory. So the pharmaceutical applications are real, and have even been vetted by the Food and Drug Administration.

Cannabinoid receptors are also found throughout the body, and to use the “lock and key” analogy for enzymes- we have discovered locked doors throughout the body- now we just need to figure out the keys, and what doors we can open with this new knowledge. The therapeutic  potential for cannabinoids is unmistakable. I look forward to seeing what doors we can open with our work.

-BZ

Best Biochemists in Movies

I don’t know of many movies that actually portray a biochemist, but there are a handful out there. In most of them, the biochemist is somewhat dorky, but either hardens up and uses a gun, or gets thrown in prison for embezzlement and lying to the FBI. These are my personal favorites:

1. Nicolas Cage as Stanley Goodspeed in The Rock.

Stanley Goodspeed

“Listen, I’m just a bio-chemist. Most of the time I work in a glass jar and lead a very uneventful life. I drive a Volvo. A beige one. But what I’m dealing with here, is one of the deadliest substances the earth has ever known so whaddaya say you cut me some friggin’ slack?”

My personal favorite, especially the quote about biochemists being boring and driving beige volvos.

2. Matt Damon as Marc Whitacre in The Informant.

Marc Whitacre

“Archer Daniels Midland. Most people have never head of us, but chances are, they’ve never had a meal we’re not a part of. Just read the side of the package. That’s us. Now ADM is taking dextrose from the corn and turning it into an amino acid called lysine. It’s all very scientific, but if you’re a stockholder, all that matters is corn goes in one end and profit comes out the other.”

A quirky movie about the real life Marc Whitacre (Nutritional Biochemistry PhD) who exposed price fixing at ADM, but also got caught embezzling from the company and thrown in prison. After serving 8 years, Whitacre is now out and serving as COO of a company in California.

I love his inner monologue. It reminds me of my own inner monologue…

3. Rachel Weisz as Marta Shearing in the Bourne Legacy.

Marta Shearing

“Well, if you’re going to reprogram human genetic material, you need a delivery system, and nothing works better than virus. It’s like a suitcase.”

Dr. Marta Shearing is a biochemist involved in hacking Jason Bourne’s metabolism, requiring him and the other covert operatives to take a special nutrient pill or their body will shut down.  A built in self-destruct of sorts. Thinking about this approach in real life- knock out a gene involved in a core metabolic pathway, and then supplement the final metabolite of that pathway. Feasible on the surface, and a virus would be the best way to do it. Hmm…

Builds I’ll get to eventually

So I’m swamped with work right now, but I have a number of projects that I want to write up and share. For now I’ll just show some of my old pictures and give a quick overview, and hopefully it motivates me to finish everything. Hopefully…

Mini bioreactor controller
Arduino controlled peristaltic pumps via relays with 20x4 LCD
I tried making a mini bioreactor unit to support smaller spinflasks with feeding and to operate the mini flowcell spectrophotometer, and got it to work decently well. There were two peristaltic pumps from Adafruit, a 20×4 LCD to show the time and culture status info, and some buttons for manual advance of the pumps.

Temp display and datalogger
High temperature display and SD datalogger
To monitor vessel temperature while running processes, I used a DS18B20 digital temp sensor with my perma/proto Uno. I now use Arduino pro mini’s for my embedded projects, but back then I didn’t know what was up.

Millisecond light timer switch
arduino, ds1307 RTC module, and relays to switch things quickly
I did a project that required turning a light on for one second every 24 hours. Conventional analog light timers give you half hour resolution, and some digital light timers can get down to the minute. We needed seconds, so I turned to an arduino with a DS1307 real time clock module to keep time, and relays to handle the heavy lifting.

Light sensor and datalogger
photoresistors via arduino to micro sd datalog
To make sure I was switching the lights at the correct time and duration, I used a different arduino to measure the light levels and datalog them to a micro SD card on an ethernet shield. Photoresistors, arduino, sd card. Boom.

Bioreactor datalogging and sending to the cloud
BioFlo 3000 arduino connection
Old bioreactors are cheap and capable, but they’re not very digitally advanced. But the old data access ports can be tapped into for datalogging and triggering alarms through an arduino. This is a custom cable with Cat5 cable soldered to a 9 pin din connector to a New Brunswick BioFlo 3000 bioreactor. Different iterations had different capabilities, but pulling the data off the machine and either datalogging, or uploading the data to an M2X server, or email alerts were used for different experiments.

3D printed protein crystal structure models
3D protein model crystal structure
I know it has been done before, but I had to include a picture of my 3D printed protein model. They are just too cool!

I’ll try to sit down one of these days and start to write things up, but if there is something you want more information about, email me or leave a message in the comments section!

-BZ