zebrafish

3 Articles

Optogenetics For 100 Euros

August 3, 2017 by 4 Comments

Larval zebrafish, Drosophila (fruit fly), and Caenorhabditis elegans (roundworm) have become key model organisms in modern neuroscience due to their low maintenance costs and easy sharing of genetic strains across labs. However, the purchase of a commercial solution for experiments using these organisms can be quite costly. Enter FlyPi: a low-cost and modular open-source alternative to commercially available options for optogenetic experimentation.

One of the things that larval zebrafish, fruit flies, and roundworms have in common is that scientists can monitor them individually or in groups in a behavioural arena while controlling the activity of select neurons using optogenetic (light-based) or thermogenetic (heat-based) tools.

FlyPi is based on a 3D-printed mainframe, a Raspberry Pi computer, and a high-definition camera system supplemented by Arduino-based optical and thermal control circuits. FlyPi features optional modules for LED-based fluorescence microscopy and optogenetic stimulation as well as a Peltier-based temperature simulator for thermogenetics. The complete version with all modules costs approximately €200 with a layman’s purchasing habits, but for those of us who live on the dark side of eBay or the depths of Taobao, it shouldn’t cost more than €100.

Once assembled, all of the functions of FlyPi can be controlled through a graphical user interface. As an example for how FlyPi can be used, the authors of the paper document its use in a series of “state-of-the-art neurogenetics experiments”, so go check out the recently published open access paper on PLOS. Everything considered the authors hope that the low cost and modular nature, as well as the fully open design of FlyPi, will make it a widely used tool in a range of applications, from the classroom all the way to research labs. Need more lab equipment hacks? Don’t worry, we’ve got you covered. And while you’re at it, why not take a spin with the RWXBioFuge.

Measuring Tiny Masses Acoustically

April 13, 2017 by 11 Comments

How do you measure the mass of something really, really tiny? Like fish-embryo tiny. There aren’t many scales with the sensitivity and the resolution to make meaningful measurements in the nanogram range, so you’ve got to turn to other methods, like measuring changes in the resonant frequency of a glass tube. And that turns out to be cheap and easy for the home gamer to reproduce.

In a recent scholarly paper, [William Grover] et al from the University of California Riverside outline the surprisingly simple and clever method of weighing zebrafish embryos, an important model organism used in all sorts of developmental biology and environmental research. [Grover]’s method is a scaled-up version of a suspended microchannel resonator (SMR), a microelectromechanical device that can measure the mass of single cells or even weigh a virus particle. Rather than etch the resonator out of silicon, a U-shaped glass tube is vibrated by a piezoelectric speaker and kept at its resonant frequency by feedback from a cheap photointerrupter. When an embryo is pumped into the tube, the slight change in mass alters the resonant frequency of the system, which is easily detected by the photointerrupter. The technique can even be leveraged to measure volume and density of the embryos, and all for about $12 in parts.

In the lab, [Grover]’s team uses a data acquisition card and LabVIEW to run the resonant loop, but there’s no reason a DIY version of this couldn’t use an Arduino. In fact, tipster [Douglas Miller] expects someone out there will try this, and would appreciate hearing the details. You can ping him on his hackaday.io page.

Are Your 3D Prints Toxic?

November 11, 2015 by 78 Comments

With the rising popularity and increasing availability of 3D printers, it was inevitable that someone would start looking into the potential environmental impact presented by them. And now we have two researchers from the University of California Riverside sounding the alarm that certain plastics are toxic to zebrafish embryos (abstract only; full paper behind a paywall).

As is often the case with science, this discovery was serendipitous. Graduate student [Shirin Mesbah Oskui] was using 3D printed tools to study zebrafish embryos, a widely used model organism in developmental biology, but she found the tools were killing her critters. She investigated further and found that prints from both a Stratasys Dimension Elite FDM printer and from a Formlabs Form 1+ stereolithography printer were “measurably toxic” to developing zebrafish embryos. The resin-based SLA printed parts were far worse for the fish than the fused ABS prints – 100% of embryos exposed to the Form 1+ prints were dead within seven days, and the few that survived that long showed developmental abnormalities before they died. Interestingly, the paper also describes a UV-curing process that reduces the toxicity of the SLA prints, which the university is patenting.

Of course what’s toxic to zebrafish is not necessarily a problem for school kids, as the video below seems to intimate. Still, this is an interesting paper that points to an area that clearly needs more investigation.

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