Join Team Hackaday To Crunch COVID-19 Through Folding@Home

March 18, 2020 by Mike Szczys 85 Comments

Donate your extra computer cycles to combat COVID-19. The Folding@Home project uses computers from all over the world connected through the Internet to simulate protein folding. The point is to generate the data necessary to discover treatments that can have an impact on how this virus affects humanity. The software models protein folding in a search for pharmaceutical treatments that will weaken the virus’ ability to attack the human immune system. Think of this like mining for bitcoin but instead we’re mining for a treatment to Coronavirus.

Initially developed at Standford University and released in the year 2000, this isn’t the first time Hackaday has advocated for Folding@Home. The “Team Hackaday” folding group was started by readers back in 2005 and that team number is still active, so let’s pile on and work our way up the rankings. At the time of writing, we’re ranked 267 in the world, can we get back up to number 30 like we were in 2008? To use the comparison to bitcoin once again, this is like a mining pool except what we end up with is a show of goodwill, something I think we can all use right about now.

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Augmented Reality Aids In The Fight Against COVID-19

March 12, 2020 by Dan Maloney 3 Comments

“Know your enemy” is the essence of one of the most famous quotes from [Sun Tzu]’s Art of War, and it’s as true now as it was 2,500 years ago. It also applies far beyond the martial arts, and as the world squares off for battle against COVID-19, it’s especially important to know the enemy: the novel coronavirus now dubbed SARS-CoV-2. And now, augmented reality technology is giving a boost to search for fatal flaws in the virus that can be exploited to defeat it.

The video below is a fascinating mix of 3D models of viral structures, like the external spike glycoproteins that give coronaviruses their characteristic crown appearance, layered onto live video of [Tom Goddard], a programmer/analysts at the University of California San Francisco. The tool he’s using is called ChimeraX, a molecular visualization program developed by him and his colleagues. He actually refers to this setup as “mixed reality” rather than “augmented reality”, to stress the fact that AR tends to be an experience that only the user can fully appreciate, whereas this system allows him to act as a guide on a virtual tour of the smallest of structures.

Using a depth-sensing camera and a VR headset, [Tom] is able to manipulate 3D models of the SARS virus — we don’t yet have full 3D structure data for the novel coronavirus proteins — to show us exactly how SARS binds to its receptor, angiotensin-converting enzyme-2 (ACE-2), a protein expressed on the cell surfaces of many different tissue types. It’s fascinating to see how the biding domain of the spike reaches out to latch onto ACE-2 to begin the process of invading a cell; it’s also heartening to watch [Tom]’s simulation of how the immune system responds to and blocks that binding.

It looks like ChimeraX and similar AR systems are going to prove to be powerful tools in the fight against not just COVID-19, but in all kinds of infectious diseases. Hats off to [Tom] and his team for making them available to researchers free of charge.

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Weird Substances: Hagfish Slime

December 10, 2019 by Kristina Panos 27 Comments

In the cold, dark recesses of ocean floors around the world, hagfish slither around like sea snakes, searching for food. When a hagfish finds a suitable carcass, it devours the dead fish in two different ways. As it burrows face-first through the tissue, eating with its jaw-less, tentacled mouth, the hagfish also absorbs nutrients through its skin.

Hagfish are not the unholy result of dumping toxic waste in the ocean. They’re one of the oldest creatures on Earth, having been around for more than 300 million years. How have they lasted this long?

A coiled hagfish reveals its slime ports. Image via Oregon Coast Aquarium

These ancient creatures have no eyes, no backbones, and no scales. They are often misidentified as eel, and often called ‘slime eels’, but they are definitely fish. They just don’t look like conventional fish. In fact, when conventional, gill-faced fish come after hagfish, those guys are in for a surprise, because hagfish have a disgusting but ingenious defense mechanism.

Whenever hagfish are attacked or even just stressed by nearby fish or curious grabby humans, they immediately emit amazing amounts of mucus at an alarming rate. At the same time, the hagfish shoots out silky strands of protein that hold the slime together in a cohesive blob. Any predator that tries to bite down on one of these velvety frankfurters of the deep sea will find its mouth and gills covered in a wad of suffocating slime.

How is it that hagfish haven’t slimed themselves out of existence? Whenever they get get a taste of their own medicine, these boneless noodles quickly twist themselves into a pretzel. In the same motion, they use their paddle-shaped tails to squeegee off the slime.

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Simple, Low-Cost Rig Lets The Budding Biohacker Run DNA Gels

December 1, 2018 by Dan Maloney 12 Comments

We all the know the basic components for building out an electronics lab: breadboards, bench power supply, a selection of components, a multimeter, and maybe an oscilloscope. But what exactly do you need when you’re setting up a biohacking lab?

That’s the question that [Justin] from The Thought Emporium is trying to answer with a series of videos where he does exactly that – build a molecular biology lab from scratch. In the current installment, [Justin] covers the basics of agarose gel electrophoresis, arguably the fundamental skill for aspiring bio-geeks. Electrophoresis is simply using an electric field to separate a population of macromolecules, like nucleic acids and proteins, based on their sizes. [Justin] covers the basics, from building a rig for running agarose gels to pouring the gels to doing the actual separation and documenting the results. Commercial grade gear for the job is priced to squeeze the most money out of a grant as possible, but his stuff is built on the cheap, from dollar-store drawer organizers and other odd bits. It all works, and it saves a ton of money that can be put into the things that make more sense to buy, like fluorescent DNA stain for visualizing the bands; we’re heartened to see that the potent carcinogen ethidium bromide that we used back in the day is no longer used for this.

We’re really intrigued with [Justin]’s bio lab buildout, and it inspires us to do the same here. This and other videos in the series, like his small incubators built on the cheap, will go a long way to helping others get into biohacking.

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How Peptides Are Made

August 22, 2017 by Will Sweatman 28 Comments

What does body building, anti-aging cream and Bleomycin (a cancer drug) have in common? Peptides of course! Peptides are large molecules that are vital to life. If you were to take a protein and break it into smaller pieces, each piece would be called a peptide. Just like proteins, peptides are made of amino acids linked together in a chain-like structure. Whenever you ingest a protein, your body breaks it down to its individual amino acids. It then puts those amino acids back together in a different order to make whatever peptide or protein your body needs. Insulin, for instance, is a peptide that is 51 amino acids long. Your body synthesizes insulin from the amino acids it gets from the proteins you eat.

Peptides and small proteins can be synthesized in a lab as well. Peptide synthesis is a huge market in the pharmaceutical and skin care industry. They’re also used, somewhat shadily, as a steroid substitute by serious athletes and body builders. In this article, we’re going to go over the basic steps of how to join amino acids together to make a peptide. The chemistry of peptide synthesis is complex and well beyond the scope of this article. But the basic steps of making a peptide are not as difficult as you might think. Join me after the break to gain a basic understanding of how peptides are synthesized in labs across the world, and to establish a good footing should you ever wish to delve deeper and make peptides on your own.

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Lost PLA Casting Brings Out The Beauty Of Macromolecules

January 2, 2017 by Dan Maloney 6 Comments

Biochemistry texts are loaded with images of the proteins, nucleic acids, and other biopolymers that make up life. Depictions of the 3D structure of macromolecules based on crystallography and models of their most favorable thermodynamic conformations are important tools. And some are just plain beautiful, which is why artist [Mike Tyka] has taken to using lost-PLA casting to create sculptures of macromolecules from bronze, copper, and glass.

We normally don’t cover strictly artistic projects here at Hackaday, although we do make exceptions, such as when the art makes a commentary on technology’s place in society. In [Mike]’s case, not only is his art beautiful and dripping with nerd street cred, but his techniques can be translated to other less artsy projects.

For “Tears”, his sculpture of the enzyme lysozyme shown in the banner image, [Mike] started with crystallographic data that pinpoints every peptide residue in the protein. A model is created for the 3D printer, with careful attention paid to how the finished print can be split apart to allow casting. Clear PLA filament is used for the positive because it burns out of the mold better than colored plastic. The prints are solvent smoothed, sprues and air vents added, and the positive is coated with a plaster mix appropriate for the sculpture medium before the plastic is melted out and the mold is ready for casting.

[Mike]’s sculpture page is well worth a look even if you have no interest in macromolecules or casting techniques. And if you ever think you’ll want to start lost-PLA casting, be sure to look over his build logs for plenty of tips and tricks. “Tears” is executed in bronze and glass, and [Mike]’s description is full of advice on how to handle casting such vastly different media.

Thanks to [Dave Z.] for the tip.