Simple Fluorometer Makes Nucleic Acid Detection Cheap And Easy

December 18, 2024 by Dan Maloney 8 Comments

Back in the bad old days, dealing with DNA and RNA in a lab setting was often fraught with peril. Detection technologies were limited to radioisotopes and hideous chemicals like ethidium bromide, a cherry-red solution that was a fast track to cancer if accidentally ingested. It took time, patience, and plenty of training to use them, and even then, mistakes were commonplace.

Luckily, things have progressed a lot since then, and fluorescence detection of nucleic acids has become much more common. The trouble is that the instruments needed to quantify these signals are priced out of the range of those who could benefit most from them. That’s why [Will Anderson] et al. came up with DIYNAFLUOR, an open-source nucleic acid fluorometer that can be built on a budget. The chemical principles behind fluorometry are simple — certain fluorescent dyes have the property of emitting much more light when they are bound to DNA or RNA than when they’re unbound, and that light can be measured easily. DIYNAFLUOR uses 3D-printed parts to hold a sample tube in an optical chamber that has a UV LED for excitation of the sample and a TLS2591 digital light sensor to read the emitted light. Optical bandpass filters clean up the excitation and emission spectra, and an Arduino runs the show.

The DIYNAFLUOR team put a lot of effort into making sure their instrument can get into as many hands as possible. First is the low BOM cost of around $40, which alone will open a lot of opportunities. They’ve also concentrated on making assembly as easy as possible, with a solder-optional design and printed parts that assemble with simple fasteners. The obvious target demographic for DIYNAFLUOR is STEM students, but the group also wants to see this used in austere settings such as field research and environmental monitoring. There’s a preprint available that shows results with commercial fluorescence nucleic acid detection kits, as well as detailing homebrew reagents that can be made in even modestly equipped labs.

Rainwater From The Road To The Garden

December 15, 2024 by Bryan Cockfield 59 Comments

Most small-scale, residential rainwater harvesting systems we’ve seen rely on using an existing roof and downspout to collect water that would otherwise be diverted out into the environment. These are accessible for most homeowners since almost all of the infrastructure needed for it is already in place. [SuburbanBiology] already built one of these systems to take care of his potable water, though, and despite its 30,000 gallon capacity it’s not even close to big enough to also water his garden. But with some clever grading around his yard and a special rainwater system that harvests rain from the street instead of his roof, he’s capable of maintaining a lush food forest despite living through a drought in Texas.

For this build there are actually two systems demonstrated, one which is gravity-fed from the road and relies on one’s entire property sloping away from the street, and a slightly more complex one that’s more independent of elevation. Both start with cutting through a section of sidewalk to pass a 4″ PVC pipe through to the street where the stormwater runoff can be collected. The gravity-fed system simply diverts this into a series of trenches around the property while the second system uses a custom sump pump to deliver the water to the landscaping.

For a system like this a holding tank is not necessary; [SuburbanBiology] is relying on the soil on his property itself to hold onto the rainwater. Healthy, living soil can hold a tremendous amount of water for a very long time, slowly releasing it to plants when they need it. And, at least where he lives, a system like this is actually helpful for the surrounding environment as a whole since otherwise all of the stormwater runoff has to be diverted out of the city or cause a flood, and it doesn’t end up back in an aquifer. If you’re more curious about a potable water system instead, take a look at [SuburbanBiology]’s previous system.

Continue reading “Rainwater From The Road To The Garden” →

A researcher in a safety harness pollinates an American chestnut tree from a lift. Another researcher is on the other side of the lift and appears to be taking notes. The tree has bags over some of its branches, presumably to control the pollen that gets in. The lift has a grey platform and orange arm.

Hacking Trees To Bring Back The American Chestnut

November 29, 2024 by Navarre Bartz 34 Comments

“Chestnuts Roasting on an Open Fire” is playing on the radio now in the Northern Hemisphere which begs the question, “What happened to the American chestnut?” Would you be surprised to hear there’s a group dedicated to bringing it back from “functional extinction?” [via Inhabitat]

Between logging and the introduction of chestnut blight, the once prevalent American chestnut became increasingly uncommon throughout its traditional range in the Appalachians. While many trees in the southern range were killed by Phytophthora root rot (PRR), the chestnut blight leaves roots intact, so many chestnuts have been surviving by growing back from the roots only to succumb to the blight and be reborn again. Now, scientists are using a combination of techniques to develop blight-resistant trees from this remaining population.

The American Chestnut Foundation recognizes you can’t improve what you can’t measure and uses a combination of “small stem assays (SSAs) performed on potted seedlings, improved phenotype scoring methods for field-grown trees, and the use of genomic prediction models for scoring resistance based on genotype.” This allows them to more rapidly screen varieties for blight resistance to further their efforts. One approach is based on conventional plant breeding techniques and has been crossing blight and PRR-resistant Chinese chestnuts with the American type. PRR resistance has been found to be less genetically complicated, so progress has been faster on resistance to that particular problem. Continue reading “Hacking Trees To Bring Back The American Chestnut” →

A cartoon of the Sun above a windmill and a solar panel with a lightning bolt going to a big grey gear with "AAAp" written on it. A small "e-" on a circle is next to it, indicating electricity transfer. Further to the right is an ADP molecule connected to a curved arrow going through the AAAp gear to turn into ATP. Three cartoon shapes, presumably illustrating biological processes are on the right with arrows pointing from the ATP.

Powering Biology With Batteries

July 21, 2024 by Navarre Bartz 18 Comments

We’ve all been there — you forgot your lunch, but there are AC outlets galore. Wouldn’t it be so much simpler if you could just plug in like your phone? Don’t try it yet, but biologists have taken us one step further to being able to fuel ourselves on those sweet, sweet electrons.

Using an “electrobiological module” of 3-4 enzymes, the amusingly named AAA (acid/aldehyde ATP) cycle regenerates ATP in biological systems directly from electricity. The process takes place at -0.6 V vs a standard hydrogen electrode (SHE), and is compatible with biological transcription/translation processes like “RNA and protein synthesis from DNA.”

The process isn’t dependent on any membranes to foul or more complicated sets of enzymes making it ideal for in vitro synthetic biology since you don’t have to worry about keeping as many components in an ideal environment. We’re particularly interested in how this might apply to DNA computing which we keep being promised will someday be the best thing since the transistor.

Maybe in the future we’ll all jack in instead of eating our daily food pill? If this all seems like something you’ve heard of before, but in reverse, maybe you’re thinking of microbial fuel cells.

Optical Tweezers Investigate Tiny Particles

April 22, 2024 by Bryan Cockfield 1 Comment

No matter how small you make a pair of tweezers, there will always be things that tweezers aren’t great at handling. Among those are various fluids, and especially aerosolized droplets, which can’t be easily picked apart and examined by a blunt tool like tweezers. For that you’ll want to reach for a specialized tool like this laser-based tool which can illuminate and manipulate tiny droplets and other particles.

[Janis]’s optical tweezers use both a 170 milliwatt laser from a DVD burner and a second, more powerful half-watt blue laser. Using these lasers a mist of fine particles, in this case glycerol, can be investigated for particle size among other physical characteristics. First, he looks for a location in a test tube where movement of the particles from convective heating the chimney effect is minimized. Once a favorable location is found, a specific particle can be trapped by the laser and will exhibit diffraction rings, or a scattering of the laser light in a specific way which can provide more information about the trapped particle.

Admittedly this is a niche tool that might not get a lot of attention outside of certain interests but for those working with proteins, individual molecules, measuring and studying cells, or, like this project, investigating colloidal particles it can be indispensable. It’s also interesting how one can be built largely from used optical drives, like this laser engraver that uses more than just the laser, or even this scanning laser microscope.

Continue reading “Optical Tweezers Investigate Tiny Particles” →

Simulating Cellular Biology In The Browser

January 21, 2024 by Al Williams 7 Comments

[Technistuff] read a paper about simulating a “minimal” cell — apparently a cell with only 493 genes. This led to a goal: reproduce the simulation in TypeScript so it can run in a web browser. Why? We don’t know, but it is an interesting look at both in-depth biology and how to handle complex simulations. The code is available on GitHub.

For a point of reference, E. Coli has over 4,500 genes. The cell in question — JCVI-syn3A — actually has seven more genes than truly necessary. The data for this bacteria is available from a research lab, again, using GitHub.

Continue reading “Simulating Cellular Biology In The Browser” →

a) Schematic illustration of energy storage process of succulent plants by harnessing solar energy with a solar cell, and the solar cell converts the energy into electricity that can be store in APCSCs of succulent plants, and then utilized by multiple electrical appliances. b–d) The energy is stored in cactus under sunlight by solar cell and then power light strips of Christmas tree for decoration.

Succulents Into Supercapacitors

January 11, 2024 by Navarre Bartz 17 Comments

Researchers in Beijing have discovered a way to turn succulents into supercapacitors to help store energy. While previous research has found ways to store energy in plants, it often required implants or other modifications to the plant itself to function. These foreign components might be rejected by the plant or hamper its natural functions leading to its premature death.

This new method takes an aloe leaf, freeze dries it, heats it up, then uses the resulting components as an implant back into the aloe plant. Since it’s all aloe all the time, the plant stays happy (or at least alive) and becomes an electrolytic supercapacitor.

Using the natural electrolytes of the aloe juice, the supercapacitor can then be charged and discharged as needed. The researchers tested the concept by solar charging the capacitor and then using that to run LED lights.

This certainly proposes some interesting applications, although we think your HOA might not be a fan. We also wonder if there might be a way to use the photosynthetic process more directly to charge the plant? Maybe this could recharge a tiny robot that lands on the plants?