Open-Source Biology And Biohacking Hack Chat

February 11, 2019 by Dan Maloney 16 Comments

Join us on Wednesday at noon Pacific time for the open-source biology and biohacking Hack Chat!

Justin Atkin‘s name might not ring a bell, but you’ve probably seen his popular YouTube channel The Thought Emporium, devoted to regular doses of open source science. Justin’s interests span a wide range, literally from the heavens above to the microscopic world.

His current interest is to genetically modify yeast to produce spider silk, and to perhaps even use the yeast for brewing beer. He and the Thought Emporium team have been busy building out a complete DIY biology lab to support the effort, and have been conducting a variety of test experiments along the way.

Please join us for this Hack Chat, in which we’ll cover:

The how’s and why’s of yeast genetic engineering;
What it takes to set up an effective biology lab from scratch;
An update on the current status of the spider-silk yeast project; and
Where the open-source biology field is, and where it’s going.

You are, of course, encouraged to add your own questions to the discussion. You can do that by leaving a comment on the Open-Source Biology and Biohacking Hack Chat event page and we’ll put that in the queue for the Hack Chat discussion.

Our Hack Chats are live community events on the Hackaday.io Hack Chat group messaging. This week we’ll be sitting down on Wednesday, February 13, at noon, Pacific time. If time zones have got you down, we have a handy time zone converter.

Click that speech bubble to the right, and you’ll be taken directly to the Hack Chat group on Hackaday.io. You don’t have to wait until Wednesday; join whenever you want and you can see what the community is talking about.

Open Source Biological Gear For The Masses

February 3, 2019 by Tom Nardi 8 Comments

At the risk of putting too fine a point on it, Hackaday exists because people are out there building and documenting open source gadgets. If the person who built a particular gizmo is willing to show the world how they did it, consider us interested. Since you’re reading this, we’ll assume you are as well. Over the years, this mentality has been spreading out from the relatively niche hacker community into the greater engineering world, and we couldn’t be happier.

Case in point, the Poseidon project created at the California Institute of Technology. Developed by students [Sina Booeshaghi], [Eduardo Beltrame], and [Dylan Bannon], along with researcher [Jase Gehring] and professor [Lior Pachter], Poseidon consists of an open source digital microscope and syringe pump which can be used for microfluidics experiments. The system is not only much cheaper than commercial offerings, but is free from the draconian modification and usage restrictions that such hardware often comes with.

Of course, one could argue that major labs have sufficient funding to purchase this kind of gear without having to take the DIY route. That’s true enough, but what benefit is there to limiting such equipment to only the established institutions? As in any other field, making the tools available to a wider array of individuals (from professionals to hobbyists alike) can only serve to accelerate progress and move the state of the art forward.

The Poseidon microscope consists of a Raspberry Pi, touch screen module, and commercially available digital microscope housed in a 3D printed stage. This device offers a large and clear view of the object under the microscope, and by itself makes an excellent educational tool. But when running the provided Python software, it doubles as a controller for the syringe pumps which make up the other half of the Poseidon system.

Almost entirely 3D printed, the pumps use commonly available components such as NEMA 17 stepper motors, linear bearings, and threaded rods to move the plunger on a syringe held in the integrated clamp. Controlled by an Arduino and CNC shield, these pumps are able to deliver extremely precise amounts of liquid which is critical for operations such as Single-cell RNA sequencing. All told a three pump system can be built for less than $400 USD, compared to the tens of thousands one might pay for commercially available alternatives.

The Poseidon project joins a relatively small, but very exciting, list of DIY biology projects that we’ve seen over the years. From the impressive open source CO2 incubator we saw a few years ago to the quick and dirty device for performing polymerase chain reaction experiments, there’s little doubt about it: biohacking is slowly becoming a reality.

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Tiny Voltmeter Uses DNA

January 28, 2019 by Al Williams 4 Comments

We use a lot of voltmeters and we bet you do too. We have some big bench meters and some panel meters and even some tiny pocket-sized meters. But biological researchers at the University of Chicago and Northwestern University have even smaller ones. They’ve worked out a way to use a DNA-based fluorescent reporter to indicate the voltage across cellular membranes.

We don’t know much about biology, but apparently measuring the voltage on the membrane around a cell is easy, but measuring the voltages across membranes inside the cell isn’t. Previous work disrupted cells and measured potentials on isolated organelles.

The indicator — called Voltair — can target specific parts of a cell and includes a reference indicator so that a ratiometric measurement is possible. In fact, there are three main parts to the 38-base pair DNA duplex. One module contains a voltage-sensing dye that fluoresces in a way that indicates voltage. The second module is a reference dye that allows researchers to judge the voltage level. The final module identifies where the probe should attach.

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The Short And Tragic Story Of Life On The Moon

January 23, 2019 by Tom Nardi 66 Comments

The Moon is a desolate rock, completely incapable of harboring life as we know it. Despite being our closest celestial neighbor, conditions on the surface couldn’t be more different from the warm and wet world we call home. Variations in surface temperature are so extreme, from a blistering 106 C (223 F) during the lunar day to a frigid -183 C (-297 F) at night, that even robotic probes struggle to survive. The Moon’s atmosphere, if one is willing to call the wispy collection of oddball gasses including argon, helium, and neon at nearly negligible concentrations an atmosphere, does nothing to protect the lunar surface from being bombarded with cosmic radiation.

Yet for a brief time, very recently, life flourished on the Moon. Of course, it did have a little help. China’s Chang’e 4 lander, which made a historic touchdown in the Von Kármán crater on January 3rd, brought with it an experiment designed to test if plants could actually grow on the lunar surface. The device, known as the Lunar Micro Ecosystem (LME), contained air, soil, water, and a collection of seeds. When it received the appropriate signal, LME watered the seeds and carefully monitored their response. Not long after, Chinese media proudly announced that the cotton seeds within the LME had sprouted and were doing well.

Unfortunately, the success was exceptionally short-lived. Just a few days after announcing the success of the LME experiment, it was revealed that all the plants which sprouted had died. The timeline here is a bit hazy. It was not even immediately clear if the abrupt end of the LME experiment was intentional, or due to some hardware failure.

So what exactly do we know about Chang’e 4’s Lunar Micro Ecosystem, and the lifeforms it held? Why did the plants die? But perhaps most importantly, what does all this have to do with potential future human missions to that inhospitable rock floating just a few hundred thousand kilometers away from us?

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OpenLH: Automating Biology For Everyone

December 16, 2018 by Al Williams 9 Comments

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

December 14, 2018 by Brian McEvoy 9 Comments

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?

December 12, 2018 by Brian McEvoy 17 Comments

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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