OpenLH: Automating Biology for Everyone

When we took a biology lab, you had to use a mouth pipette to transfer liquids around. That always seemed odd to use your mouth to pick up something that could be dangerous. It’s also not very efficient. A modern lab will use a liquid handling robot, but these aren’t exactly cheap. Sometimes these are called pipettors and even a used one on eBay will set you back an average of $1,000 — and many of them much more than that. Now there’s an open source alternative, OpenLH, that can be built for under $1,000 that leverages an open source robot arm. You can find a video about the system below.

The robot arm, a uArm Swift Pro, is the bulk of the cost.  The Pro can also operate as a 3D printer or a laser engraver with a little work. In fact, we wondered if you could use the arm to make a 3D printer and then print the parts you need to convert it to a liquid handler. Seems like it should work.

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A Lecture By A Fun Guy

Many people hear “fungus” and think of mushrooms. This is akin to hearing “trees” and thinking of apples. Fungus makes up 2% of earth’s total biomass or 10% of the non-plant biomass, and ranges from the deadly to the delicious. This lecture by [Justin Atkin] of [The Thought Emporium] is slightly shorter than a college class period but is like a whole semester’s worth of tidbits, and the lab section is about growing something (potentially) edible rather than a mere demonstration. The video can also be found below the break.

Let’s start with the lab where we learn to grow fungus in a mason jar on purpose for a change. The ingredient list is simple.

  • 2 parts vermiculite
  • 1 part brown rice flour
  • 1 part water
  • Spore syringe

Combine, sterilize, cool, inoculate, and wait. We get distracted when cool things are happening so shopping around for these items was definitely hampered by listening to the lecture portion of the video.

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Cyborg, Or Leafy Sensor Array?

Some plants react quickly enough for our senses to notice, such as a Venus flytrap or mimosa pudica. Most of the time, we need time-lapse photography at a minimum to notice while more exotic sensors can measure things like microscopic pores opening and closing. As with any sensor reading, those measurements can be turned into action through a little trick we call automation. [Harpreet Sareen] and [Pattie Maes] at MIT brought these two ideas together in a way which we haven’t seen before where a plant has taken the driver’s seat in a project called Elowan. Details are sparse but the concept is easy enough to grasp.

We are not sure if this qualifies as a full-fledged cyborg or if this is a case of a robot using biological sensors. Maybe it all depends on which angle you present this mixture of plant and machine. Perhaps it is truly is the symbiotic relationship that the project claims it to be. The robot would not receive any instructions without the plant and the plant would receive sub-optimal light without the robot. What other ways could plants be integrated into robotics to make it a bona fide cyborg?

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Biology Lab on Your Christmas List

We hope you have been good this year because we have a list to start your own biology lab and not everything will fit into Santa’s bag (of holding). If you need some last minute goodie points, Santa loves open-source and people who share on our tip line. Our friends at [The Thought Emporium] have compiled a list of the necessary equipment for a biology lab. Chemistry labs-in-a-box have been the inspiration for many young chemists, but there are remarkable differences between a chemistry lab and a biology lab which are explained in the Youtube video linked above and embedded after the break.

If you are preparing to start a laboratory or wondering what to add to your fledging lab, this video is perfect. It comes from the perspective of a hacker not afraid to make tools like his heat block and incubator which should absolutely be built rather than purchased but certain things, like a centrifuge, should be purchased when the lab is mature. In the middle we have the autoclave where a used pressure cooker may do the trick or you may need a full-blown commercial model with lots of space and a high-pressure range.

Maybe this will take some of the mystique out of starting your own lab and help you understand what is happening with a gel dock or why a spectrophotometer is the bee’s knees. There are a handful of other tools not mentioned here so if this is resonating, it will be worth a watch.

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Cyborg Mushrooms

Of all the fictional cyborgs who turn against humanity to conquer the planet, this is as far from that possibility as you can get. These harmless mushrooms seem more interested in showing off their excellent fashion sense with a daring juxtaposition of hard grid lines with playful spirals. But the purpose of this bacteria-fungus-technology hybrid is to generate electricity. The mushrooms are there to play nurse to a layer of cyanobacteria, the green gel in the photo, while the straight black lines harvest electricity.

Cyanobacteria do not live very long under these kinds of conditions, so long-term use is out of the question, but by giving the cyanobacteria somewhere it can thrive, the usefulness grows. The interplay between bacterial and supportive organics could lead to advances in sensors and hydrogels as well. At some point, we may grow some of our hardware and a green thumb will be as useful as a degree in computer science.

Hydrogels could be the next medical revolution, and we’ve already made hydrogels into tattoos, used them as forms for artificial muscles, and hydrogels can be a part of soft tissue printing.

Alice Evans: Brucellosis, or Why We Pasteurize Milk

It’s easy to forget how much illness and death was caused by our food and drink just one hundred years ago. Our modern food systems, backed by sound research and decent regulation, have elevated food safety to the point where outbreaks of illness are big news. If you get sick from a burger, or a nice tall glass of milk, it’s no longer a mystery what happened. Instead we ask why, and “who screwed up?”

In the early 20th century though, many food-borne illnesses were still a mystery, and microbiology was a scientific endeavor that was just getting started. Alice Catherine Evans was an unlikely figure to make a dent in this world at the time, but through her research at the United States Department of Agriculture’s (USDA), and later at the Hygienic Laboratory (now the National Institute of Health) she had a huge impact on the field of bacteriology, the dairy industry, and consumer safety. Continue reading “Alice Evans: Brucellosis, or Why We Pasteurize Milk”

Hacked Heating Instruments for the DIY Biology Lab

[Justin] from The Thought Emporium takes on a common molecular biology problem with these homebrew heating instruments for the DIY biology lab.

The action at the molecular biology bench boils down to a few simple tasks: suck stuff, spit stuff, cool stuff, and heat stuff. Pipettes take care of the sucking and spitting, while ice buckets and refrigerators do the cooling. The heating, however, can be problematic; vessels of various sizes need to be accommodated at different, carefully controlled temperatures. It’s not uncommon to see dozens of different incubators, heat blocks, heat plates, and even walk-in environmental chambers in the typical lab, all acquired and maintained at great cost. It’s enough to discourage any would-be biohacker from starting a lab.

[Justin] knew It doesn’t need to be that way, though. So he tackled two common devices:  the incubator and the heating block. The build used as many off-the-shelf components as possible, keeping costs down. The incubator is dead simple: an insulated plastic picnic cooler with a thermostatically controlled reptile heating pad. That proves to be more than serviceable up to 40°, at the high end of what most yeast and bacterial cultures require.

The heat block, used to heat small plastic reaction vessels called Eppendorf tubes, was a little more complicated to construct. Scrap heat sinks yielded aluminum stock, which despite going through a bit of a machinist’s nightmare on the drill press came out surprisingly nice. Heat for the block is provided by a commercial Peltier module and controller; it looks good up to 42°, a common temperature for heat-shocking yeast and tricking them into taking up foreign DNA.

We’re impressed with how cheaply [Justin] was able to throw together these instruments, and we’re looking forward to seeing how he utilizes them. He’s already biohacked himself, so seeing what happens to yeast and bacteria in his DIY lab should be interesting.

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