Robot Vs. Superbug

November 30, 2019 by Bryan Cockfield 6 Comments

Working in a university or research laboratory on interesting, complicated problems in the sciences has a romanticized, glorified position in our culture. While the end results are certainly worth celebrating, often the process of new scientific discovery is underwhelming, if not outright tedious. That’s especially true in biology and chemistry, where scaling up sample sizes isn’t easy without a lot of human labor. A research group from Reading University was able to modify a 3D printer to take some of that labor out of the equation, though.

This 3D printer was used essentially as a base, with the printing head removed and replaced with a Raspberry Pi camera. The printer X/Y axes move the camera around to all of the different sample stored in the print bed, which allows the computer attached to the printer to do most of the work that a normal human would have had to do. This allows them to scale up massively and cheaply, presumably with less tedious inputs from a large number of graduate students.

While the group hopes that this method will have wide applicability for any research group handling large samples, their specific area of interest involves researching “superbugs” or microbes which have developed antibiotic resistance. Their recently-published paper states that any field which involves bacterial motility, colony growth, microtitre plates or microfluidic devices could benefit from this 3D printer modification.

Disrupting Cell Biology Hack Chat With Incuvers

June 3, 2019 by Dan Maloney No comments

Join us on Wednesday 5 June 2019 at noon Pacific for the Disrupting Cell Biology Hack Chat with Incuvers!

A lot of today’s most successful tech companies have creation myths that include a garage in some suburban neighborhood where all the magic happened. Whether there was literally a garage is not the point; the fact that modest beginnings can lead to big things is. For medical instrument concern Incuvers, the garage was actually a biology lab at the University of Ottawa, and what became the company’s first product started as a simple incubator project consisting of a Styrofoam cooler, a space blanket, and a Soda Stream CO2 cylinder controlled by an Arduino.

From that humble prototype sprang more refined designs that eventually became marketable products, setting the fledgling company on a course to make a huge impact on the field of cell biology with innovative incubators, including one that can image cell growth in real time. What it takes to go from prototype to product has been a common theme in this year’s Hack Chats, and Noah, Sebastian, and David from Incuvers will drop by Wednesday to talk about that and more.

Our Hack Chats are live community events in the Hackaday.io Hack Chat group messaging. This week we’ll be sitting down on Wednesday June 5 at 12:00 PM 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.

Artificial Neural Networks Help Hack Biological Counterparts

May 12, 2019 by Roger Cheng 16 Comments

Eyes are windows into the soul, the old saying goes. They are also pathways into the mind, as much of our brain is involved in processing visual input. This dedication to vision is partly why much of AI research is likewise focused on machine vision. But do artificial neural networks (ANN) actually work like the gray matter that inspired them? A recently published research paper (DOI: 10.1126/science.aav9436) builds a convincing argument for “yes”.

Neural nets were named because their organization was inspired by biological neurons in the brain. But as we learned more and more about how biological neurons worked, we also discovered artificial neurons aren’t very faithful digital copies of the original. This cast doubt whether machine vision neural nets actually function like their natural inspiration, or if they worked in an entirely different way.

This experiment took a trained machine vision network and analyzed its internals. Armed with this knowledge, images were created and tailored for the purpose of triggering high activity in specific neurons. These responses were far stronger than what occurs when processing normal visual input. These tailored images were then shown to three macaque monkeys fitted with electrodes monitoring their neuron activity, which picked up similarly strong neural responses atypical of normal vision.

Manipulating neural activity beyond their normal operating range via tailored imagery is the Hollywood portrayal of mind control, but we’re not at risk of input injection attacks on our brains. This data point gives machine learning researchers confidence their work still has relevance to biological source material, and neuroscientists are excited about the possibility of exploring brain functions without invasive surgical implants. Artificial neural networks could end up help us better understand what happens inside our brain, bringing the process full circle.

[via Science News]

This Kerosene Lantern Becomes A Compact Bioreactor

February 15, 2019 by Lewin Day 1 Comment

A bioreactor is a useful thing to have in any biology lab. Fundamentally, it’s a tank in which biological activity can be nurtured and controlled. [The Thought Emporium] needed a visual aid for an upcoming video on bioluminescent bacteria, but figured a single test tube full of the little critters just wasn’t visually striking enough. Thus began the build to turn a kerosene lantern into a full-featured bioreactor.

The ideal bioreactor for the project needed to be visually appealing, biologically safe, and to have the possibility for continuous operation. First, the lantern’s base was sealed with aluminium plate and silicone sealant. The top was then fitted with a plastic plug, which contained passthroughs for air and fluid feeds, UV LEDs for luminescence tests, as well as potential sterilization purposes. Wiring was neatly passed through the arms of the lantern, and an air pump hidden in the top. A battery compartment was also installed so the reactor can be portable, even when fully loaded.

The bioreactor was first filled with highlighter ink, and the UV lights switched on, confirming that the reactor does look the part when filled with glowing fluid. Then, it was flushed with hydrogen peroxide, before being refilled with growth medium and an E. Coli strain which produces a fluorescent red protein. Growth was successful, and there are future plans to use the bioreactor for other projects, too.

It goes without saying that it’s important to take the proper precautions when hacking on biological projects, lest you inadvertently create the zombie virus and take down half the population of the eastern seaboard. Regardless, it’s an impressive build that showcases various techniques for working with biological matter that may not be familiar to the home hacker. If you’re looking for more automation for your home biology hacks, perhaps the OpenLH project may interest you. Video after the break.

[Thanks to Baldpower for the tip!]

Continue reading “This Kerosene Lantern Becomes A Compact Bioreactor” →

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.

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.

Continue reading “Open Source Biological Gear For The Masses” →

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.

Continue reading “Tiny Voltmeter Uses DNA” →