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Hackaday Links: July 30, 2023

A couple of weeks ago, we noted with interest that the space shuttle Endeavour (OV85) would be set up as a full-stack launch configuration display, complete with external fuel tank and solid rocket boosters. We predicted that this would result in some interesting engineering, not least of which will be making the entire 20-story stack safe from seismic activity. Looks like we were right on all counts, with this story about the foundation upon which the display will stand, which has been under construction for quite a while now. The base has six seismic isolators that support the 2.4-m thick slab of reinforced concrete that will serve as a perch for the full stack. The 1,800-ton slab will be able to move a meter or so from its resting position during earthquakes. Or perhaps more accurately, the foundation will allow Los Angeles to move as much as it wants while Endeavour rides it out.

If like us you’re worried that seismic loads are vastly different than the loads the spacecraft was actually designed for, relax — it turns out that the flight loads are far in excess of predicted loads from seismic stress. The plan is to build the booster stacks first — the aft skirts, which will support the entire stack, were just bolted in place — then lift the external tank in place between the boosters, and finally hoist the actual orbiter into place. After the stack is complete, the rest of the building will be built around it. We’re really looking forward to seeing some video on this project.

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Open-Source LAMP Instrument Aimed At Clinicians And Biohackers Alike

Over the last few years, we’ve all been given a valuable lesson in both the promise and limitations of advanced molecular biology methods for clinical diagnostics. Polymerase chain reaction (PCR) was held up as the “gold standard” of COVID-19 testing, but the cost, complexity, and need for advanced instrumentation and operators with specialized training made PCR difficult to scale to the levels demanded by a pandemic.

There are other diagnostic methods, of course, some of which don’t have all the baggage of PCR. RT-LAMP, or reverse transcriptase loop-mediated amplification, is one method with a lot of promise, especially when it can be done on a cheap open-source instrument like qLAMP. For about 50€, qLAMP makes amplification and detection of nucleic acids, like the RNA genome of the SARS-CoV-2 virus, a benchtop operation that can be performed by anyone. LAMP is an isothermal process; it can be done at one single temperature, meaning that no bulky thermal cycler is required. Detection is via the fluorescent dye SYTO 9, which layers into the base pairs inside the amplified DNA strands, using a 470-nm LED for excitation and a photodiode with a filter to detect the emission. Heating is provided by a PCB heater and a 3D-printed aluminum block that holds tubes for eight separate reactions. Everything lives in a 3D-printed case, including the ESP32 which takes care of all the housekeeping and data analysis duties.

With the proper test kits, which cost just a couple of bucks each, qLAMP would be useful for diagnosing a wide range of diseases, and under less-than-ideal conditions. It could also be a boon to biohackers, who could use it for their own citizen science efforts. We saw a LAMP setup at the height of the pandemic that used the Mark 1 eyeball as a detector; this one is far more quantitative.

Broken Genes And Scrambled Proteins: How Radiation Causes Biological Damage

If decades of cheesy sci-fi and pop culture have taught us anything, it’s that radiation is a universally bad thing that invariably causes the genetic mutations that gifted us with everything from Godzilla to Blinky the Three-Eyed Fish. There’s a kernel of truth there, of course. One only needs to look at pictures of what happened to Hiroshima survivors or the first responders at Chernobyl to see extreme examples of what radiation can do to living tissues.

But as is usually the case, a closer look at examples a little further away from the extremes can be instructive, and tell us a little more about how radiation, both ionizing and non-ionizing, can cause damage to biochemical structures and processes. Doing so reveals that, while DNA is certainly in the crosshairs for damage by radiation, it’s not the only target — proteins, carbohydrates, and even the lipids that form the membranes within cells are subject to radiation damage, both directly and indirectly. And the mechanisms underlying all of this end up revealing a lot about how life evolved, as well as being interesting in their own right.

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Logic Via DNA

We often say you can make logic gates out of nearly anything. [Steve Mould] would agree as he just finished playing naughts and crosses (tic tac toe if you are an American) with a tray full of DNA. You can see the resulting game and how it works in the video below.

The use of DNA isn’t really significant as it simply implements a logic equation for each of the nine cells. So, for example, each cell is taken by an X (the DNA) only when certain other squares have been taken by O or not taken by O. So you essentially create an AND/OR gate using the state of each cell and its inverse.

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Hacking The Wooly Mammoth

In case you can’t get enough Jurassic Park movies, you can look forward to plans a biotech company has to hybridize endangered Asian elephants with long-extinct wooly mammoths using gene splicing and other exotic techniques.

Expect a long movie, the team hopes to have calves after six years and we don’t think a theme park is in the making. The claim is that mammoth traits will help the elephants reclaim the tundra, but we can’t help but think it is just an excuse to reanimate an extinct animal. If you read popular press reports, there is some question if the ecological mission claimed by the company is realistic. However, we can’t deny it would be cool to bring an animal back from extinction — sort of.

We aren’t DNA wizards, so we only partially understand what’s being proposed. Apparently, skin cells from a modern elephant will serve as a base to accept extracted mammoth DNA. This might seem far-fetched but turns out the mammoth lived much more recently than we usually think. When they die in their natural deep-freeze environment, they are often well preserved.

Once the gene splicing is set up, a surrogate elephant will carry the embryo to term. The hope is that the improved breed would be able to further interbreed with natural species, although with the gestation and maturity times of elephants, this will be a very long time to bear fruit.

So how do you feel about it? Will we face a movie-level disaster? Will we get some lab curiosity creatures? Will it save the tundra? Let us know what you think in the comments.

DNA manipulation has gone from moon-shot-level tech to readily accessible in a very short amount of time. In particular, CRISPR, changes everything and is both exciting and scary on what it puts in the hands of nearly anyone.

Microfluidics For Biohacking Hack Chat

Join us on Wednesday, July 7 at noon Pacific for the Microfluidics for Biohacking Hack Chat with Krishna Sanka!

“Microfluidics” sounds like a weird and wonderful field, but one that doesn’t touch regular life too much. But consider that each time you fire up an ink-jet printer, you’re putting microfluidics to work, as nanoliter-sized droplets of ink are spewed across space to impact your paper at exactly the right spot.

Ink-jets may be mundane, but the principles behind them are anything but. Microfluidic mechanisms have found their way into all sorts of products and processes, with perhaps the most interesting uses being leveraged to explore and exploit the microscopic realms of life. Microfluidics can be used to recreate some of the nanoscale biochemical reactions that go on in cells, and offer not only new ways to observe the biological world, but often to manipulate it. Microfluidics devices range from “DNA chips” that can rapidly screen drug candidates against thousands of targets, to devices that can rapidly screen clinical samples for exposure to toxins or pathogens.

There are a host of applications of microfluidics in biohacking, and Krishna Sanka is actively working to integrate the two fields. As an engineering graduate student, his focus is open-source, DIY microfluidics that can help biohackers up their game, and he’ll stop by the Hack Chat to run us through the basics. Come with your questions about how — and why — to build your own microfluidics devices, and find out how modern biohackers are learning to “go with the flow.”

join-hack-chatOur Hack Chats are live community events in the Hackaday.io Hack Chat group messaging. This week we’ll be sitting down on Wednesday, July 7 at 12:00 PM Pacific time. If time zones have you tied up, we have a handy time zone converter.

[Featured image: Cooksey/NIST]

Sequencing DNA For Metagenomics

If someone brought you an odd piece of electronic hardware and you wanted to identify it, you’d probably look for markings on the outside first. If that didn’t work out, you might look under the cover and read some markings on the board or key components. However, in a tough case, you might dump the firmware and try to guess what the device is or what it does by examining the code that makes it run. That’s kind of what [Ciro] did. Wanting to determine the bacteria in a water sample led to using relatively inexpensive DNA sequencing hardware to look at the DNA present in the samples. This would have been a huge undertaking for a well-funded lab just a few short years ago. Now it just takes a USB device and some software.

Of course, inexpensive is in the eye of the beholder. The micropore sequencer costs about $500 and has a one-time use consumable cost of about $500, although that’s enough to process about 10 human genomes. The technology depends on using a small pore only large enough to pass one strand of DNA at a time. Blocks of nucelotides cause different amounts of electrical current to flow through the pore.

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