Tag Archives: biochemistry

Fraction Collector

I haven’t posted much about my builds- mostly because I’m swamped with work and family. But I can’t resist with this one.

Our flash chromatography system was acting up, and so the saying goes: necessity is the mother of invention. Rather than try to coax the equipment to keep eeking out 48 samples with the occasional hardware failure, I just decided to program my own system that could do exactly what I wanted. More sample collection capacity, more control, and more arduino!

I hijacked my XY plotter (purchased a few years ago to build a microbial biopointilism plotter), and coded a relatively simple XY coordinate grid that was based on a cheap test tube rack (Amazon/Ebay). In doing so, I now have 5 racks of 24 tubes, for a whopping 120 tubes at 50ml each. That’s a grand total of 6 liters of fractionation capacity. Oh yeah.

The plotter already had simple limit switches on the X+/X- and Y+/Y- planes, so I started out writing a simple “homing” sketch to get to (0,0) at the bottom left, then basically just placed the first tube rack under that first coordinate. The collector head will stay over the tube for a defined period of time, which is linearly proportional to the volume that we want to collect. Once that time is up, it moves a specified number of steps to the next tube. The spacing between the row of 8 tubes is constant, but then it needs to move to the next row like a typewriter- same movement between racks. The movement is actually pretty easy, and it only took some minor tweaking to get all of the tube racks aligned with the code.

Next I implemented a 12vdc pinch valve to be able to close the flow while the collector head moves between rows and racks. Tube to tube didn’t suffer any sample losses, so it only turns off the flow while zig-zagging from one row to the next.

I then made a custom 25-pin din cable end to plug into a masterflex digital peristaltic pump, and this allows us to remotely control the solvent flow on vs off. No need to change the flowrate, just keep it at a nice simple isocratic flow. (or one thing I am considering is altering the flowrate based on the column backpressure, so the fraction volume doesn’t tail off as pressure increases).

There is a serial interface with a computer, so the collector head can be steered manually, the valves and the pumps activated, etc.¬†The software/code is arduino-based, and I hosted it over on Github here. Please be kind, I’m a biochemist not a programmer. ūüėČ

Regarding the code… Right now it is only using a delay function to set the time for each sample. I have a draft program coded that uses the system clock to keep track of the fraction time, so the microprocessor can actually think and do other things- like pause, or modify the program while it is running. I’ll upload that when I get it working, but for now the delay is working well. Also I have considered abandoning the laptop and just using a LCD screen or some form of readout, with buttons or some human interface to control the robotic arm and program, but the serial interface is easy and convenient, and it works. Done is better than perfect!

Hardware involved:

  • Makeblock XY plotter kit- with electronics
  • BioChemValve Pinch valve, normally closed, 12vdc
  • A masterflex peristaltic pump and tubing
  • Chromatography column of your liking
  • Luer lock fittings for the pump tubing
  • Zipties to hold the tubing to the cables and the fraction head
  • 5vdc 2x Relay board (or suitable setup to control the pinch valve)
  • 25 pin din, male, solder cup adapter (or as needed for the pump interface)
  • rj11 6 wire data cables to tap into the MakeBlock Orion (Arduino) board
  • A 12vdc 2A power source for the pinch valve
  • And a laptop or computer with Arduino IDE installed on it

I have programmed our Tecan and have done some other small robotics projects in lab, but this is my first project that has become a workhorse of the lab. With my initial success, I’m now trying to hijack a $22 ebay robot kit for fraction collection.

The number of fraction collectors that one needs is always n+1…


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.


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.


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…