Category 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…

-BZ

Crohn’s and Colitis

I recently went to an event hosted by the Crohn’s and Colitis Foundation (CCF)’s Northern California chapter. The event was an educational symposium for patients and families with IBD, and I was impressed with the CCF organization as well as the amazing community of patients and caregivers. I want to thank Kayla Kraich for all of her hard work organizing such a nice and welcoming event.

I went to the CCF event to learn more about IBD, and specifically biologic treatments for IBD, their benefits, as well as their limitations. Our startup is developing a new small-molecule treatment of IBD, so I would like to stay on top of the standard of care and see what else is going on in the field.

I grabbed a cup of coffee, sat down, and waited for the talks to start. The people sitting around me all looked like happy and healthy adults leading vibrant lives. The guy in front of me looked about my age, well dressed, clean-cut, and maybe a touch sciencey. I thought, hey, maybe he is another researcher? The first talk focused on biologics for IBD, when they are indicated, pros and cons, etc. At the end of the talk the MD invited up a panel of patients to talk about their experience with biologics. The man in front of me stood up and joined the patient panel. When he shared his story of battling IBD since he was 15, it was eye-opening. I have heard that IBD is one of the most disruptive diseases that can be largely hidden from the outside world.

At the first break, the woman sitting next to me introduced herself. Right after her name, she launched into her history with ulcerative colitis, her multiple surgeries, and how she ultimately tamed her disease with a balance of diet and medications. At the end of her quick life story, she then said, “what about you Brandon?”

I have to admit that I felt like a poser. I don’t have IBD. I haven’t had multiple surgeries. I haven’t seen numerous doctors, received infusions of antibodies, worried about infections from a suppressed immune system. I haven’t struggled to knock down GI flares with steroids, and then dealing with their crazy side effects. Nor have I endured the never-ending visits to the bathroom (a metric for ulcerative colitis activity is the number of daily bowel movements, with the highest tier being anything over 10 times a day).

I told her that I’m just a researcher, but we are working on IBD and have a new drug that we are rapidly advancing to the clinic. She put me at ease with her genuine appreciation for my research, and although I felt insignificant and like I didn’t belong, she welcomed me to the event and wished me the best of luck in our work.

At this point, I may have drank a couple cups of coffee trying to remain alert and sharp during the morning talks, so I made my first trip to the men’s room.

What I encountered in the men’s room was subtle at first, but after recounting the experience and putting it into context with the diseases of the colon, it started to make sense. On my first trip to the men’s room I noticed a number of people coming and going, but the notable interaction was with someone who introduced himself while walking from the urinal to the sinks. The man was very extroverted, and the tone and content of the conversation could have taken place in any setting. Only this time, it was in the men’s room. And that level of forward communication in the men’s room seemed a little odd to me.

Back to the talks, the next speaker gave a nice overview of IBD (the MD and I overlapped as undergrads at UC Davis- go Ags!). After this second talk, my bladder was losing the battle to the coffee and water I was drinking, so I made my second trip to the men’s room. This trip, there was another very genuine introduction and discussion that started in the bathroom. I chatted, and eventually made my way back to the conference room, and didn’t think much of it.

After the talks I headed home, and during the drive I reflected on the great talks and on my interactions with the amazing members of the CCF community. And of course those very genuine interactions that I had in the men’s room…

And then it hit me.

For a patient population that uses the restroom so much, the CCF community is very, very comfortable in the bathroom. Especially at an event filled with fellow patients, doctors, and caregivers, and when it is hard to tell who has what disease, everyone wearing a CCF nametag must seem like an ally. I laughed out loud when I put it together. And then the realization actually felt heavy on my face and my chest. There was a lifelong struggle that was underneath the interactions with the people in the bathroom. I have now attended two CCF events, at which the first item of business was telling everyone the location of the bathrooms. My gastrointestinal health is something I have always taken for granted, but I am now looking at it with a new perspective.

The more that I learn about Crohn’s and Colitis, it just kills me to think of what IBD sufferers are going through. As we are so preoccupied with the pharmacology and interactions of our drug compounds in lab, we don’t often think about of these complications that IBD patients suffer daily. I am extremely grateful for how welcoming and open the CCF community has been with me. It leaves me feeling hungry for our upcoming clinical trials, and it reaffirms that IBD is a worthy cause that I am grateful to be working on.

-BZ

Biohacking


I have an opinion piece on Biohacking in the Innovation Edition of¬†Comstock’s Magazine. As a scientist, I like things to be referenced and annotated, so here is my effort to support the claims and information included in the piece.

  • Good intro to garage¬† biohacking with Josiah Zayner : Link
  • Article on Liz Parrish and her telomere self-experiment: Link
  • Article on Brian Hanley and his personal gene therapy work: Link
  • Article in Outside Magazine on Josiah Zayner with the FBI interview and comment: Link
  • Self-administration of a HIV therapy on a home couch, while live-streaming on Facebook: Link
  • Companies are offering RFID implant chips to their employees: Link
  • The Open Discovery Institute, aka The Odin, DIY Bacterial Gene Engineering CRISPR Kit: Link
  • Makerspaces that offer science classes and lab equipment for community based projects:
    Oakland, Counter Culture Labs
    Seattle, Sound Bio
    New York, Genspace
    Los Angeles, The Lab
    A more complete list can be found over at DIYbio.org
  • Article on the rising cost of prescription drugs: Link
  • An article on biohackers responding to the rising price of the EpiPen: Link
  • The Four Thieves Vinegar Collective that is behind the EpiPencil, Daraprim synthesis, and is currently working on an at-home mini chemical reactor. Link
  • A project to combat the high price of insulin: Link
  • The Sacramento startup and science scene:
    Hackerlab
    UC Davis Venture Catalyst
    HM Clause / UC Davis Life Science Innovation Center
    Inventopia

As for a biohacking scene in Sacramento, there are currently two good resources for fledgling biotechs to get shared lab space with the HM Clause Innovation center and Inventopia, both linked above. But for hacking together ideas, teaching classes, or playing with DNA, Eric Ullrich over at Hackerlab has expressed interest in facilitating biohacking classes and even setup of some wet lab space. There is definitely energy around the idea in Sacramento, but it has yet to reach critical mass. The opinion piece in Comstock’s was intended to share the topic of biohacking with the broader business community in our region, but also to send up a flare to any other scientists that are interested in getting something going.

So if you are interested in setting up local biohacking meetings or joining up for some projects, shoot me an email over at biohacksac.org. Let’s make something happen!

-BZ

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…