Tag Archives: synthetic biology

The latest hardware for biology

As part of the synbio revolution lab-as-a-service providers such as Transcriptic and Emerald cloud labs are popping up, enabling researchers to perform experiments remotely. On the other hand, locally deployed low-cost setups are also gaining ground. An example is a paper published last year in Nature Biotechnology by the Riedel-Kruse lab. The authors developed a microscope coupled to a small flow chamber to observe Euglena swimming around. Via a web interface LEDs that surround the flow chamber can be turned on, so you can actually remotely control the movement of the Euglena (as they like to move to the light). The whole setup only costs $1000 a year, so an low-cost and accessible option for the educational field. The project seems a follow-up on a previous educational device from the same group called the LudusScope, a Gameboy like smartphone microscope.

In 2015 the TU Delft iGEM team won the grand prize with their biolink 3D printer. Last month a write up of an improved version was published in ACS Synthetic Biology. Instead of building a 3D printer from K’nex (as the iGEM team did), this version is a modification of the CoLiDo DIY 3D printer. Structures can be build by dissolving bacteria together with alginate and depositing this ‘bioink’ on a buildplate containing calcium. The combination of alginate and calcium triggers a cross-linking process leading to solidification of the extruded mixture. Using the technology a 14-layer high structure (of around 2 mm) containing two different bacterial strains was printed in various shapes.

Bacterial 3D printing based on the modified CoLiDo DIY framework, right a close up of the extruder head. (Source: http://pubs.acs.org/doi/abs/10.1021/acssynbio.6b00395 CC-BY-NC-ND)

Bacterial 3D printing based on the modified CoLiDo DIY framework, right a close up of the extruder head. (Source: 10.1021/acssynbio.6b00395 CC-BY-NC-ND)

The Maerkl lab published a preprint on bioRxiv last month on a microfluidic biodisplay with 768 programmable biopixels. Of this biodisplay each individual compartment (or pixel) can be inoculated with a different strain. As a proof-of-concept the pixels were loaded with previously developed arsinicum sensing strains. The WHO states a maximum of 10 μg/L of arsenite in tap water, so water spiked with various amounts of arsine were flown over the biodisplay. After 10 hours a skull-and-cross-bones symbol is visible using a microscope when as little as 20 μg/L arsinite spiked water is flow over the biodisplay. As there is room for 768 different strains, this setup can actually be used to do some pretty powerful analysis.

Response of the biodisplay to tap water after 24 hours of induction with 100 µg/l of sodium-arsenite. (Source: http://biorxiv.org/content/early/2017/02/27/112110, CC-BY 4.0)

Response of the biodisplay to tap water after 24 hours of induction with 100 µg/l of sodium-arsenite. (Source: 10.1101/112110, CC-BY 4.0)

In the Journal of Laboratory Automation an article describes an open source (although the article itself is not open access) peptide synthesizer named Pepsy. Peptide synthesizers often cost  more than $20.000, whereas Pepsy can be assembled for  less than $4000. The author put the complete  Fmoc solid phase peptide synthesis process under the control of an Arduino (an open source prototyping platform). As an example, a ten residue peptide was synthesized that can be used as a contrast agent for nuclear medicine. The source code for Pepsy is available here on Github.

The fully assembled PepSy system with the reaction syringe in the middle. Courtesy of Dr. Gali

The fully assembled PepSy system with the reaction syringe in the middle. Courtesy of Dr. Gali

Do you have more exciting examples? Let me know!

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Micropia – a microbe museum

lichensThis month I had the chance to visit the ‘smallest’ museum in the world: Micropia in Amsterdam, The Netherlands. The goal of Micropia, opened in 2014, is to distribute knowledge about microbes to the general public. The museum is part of the zoo Artis but can be visited independently and has a separate entrance. The museum offers a great introduction into the wonderful world of microorganisms. Below an impression of the exhibition.

The tree of life at the entrance showing a 'representative selection of 1500 species, 500 of each domain' the data comes from NCBI. A neat feature; the species lighting up in UV light are only visible by microscope whereas the non illuminated branches (ie. mammels in the bottom right corner) do not.

The tree of life at the entrance showing a ‘representative selection of 1500 species, 500 of each domain’ the data comes from NCBI. A neat feature; the species lighting up in UV light are only visible by microscope whereas the non illuminated branches (ie. mammals in the bottom right corner) do not.

A tardigrade ~6,000x enlarged, living tardigrades are also present and visible under the microscope

A tardigrade ~6,000x enlarged, living tardigrades are also present and visible under the microscope. I’m wondering wether its genome is also contaminated?

Micropia also features an in-house lab used to maintain the living components of the collection.

Micropia also features an in-house lab used to maintain the living components of the collection.

In a separate room a stir flask with Photobacterium phosphoreum produced a beautiful glow

In a separate room a stir flask with Photobacterium phosphoreum produced a beautiful glow.

'Wall-of-fame' with more than 100 micro organisms in large petri dishes

‘Wall of fame’ with more than 100 microorganisms in large petri dishes

Close-up on the wall of fame, Aspergillus oryzae (used to ferment soybeans to produce soy sauce), Aspergillus arachidicola (discovered on peanuts), Klebsiella (this one was only named by genus) and a specimen just named 'yeast'

Close-up on the wall of fame, Aspergillus oryzae (used to ferment soybeans to produce soy sauce), Aspergillus arachidicola (discovered on peanuts), Klebsiella (this one was only named by genus) and a specimen just named ‘yeast’

Downstairs several product were featured that could not exist without micro-organisms such as yoghurt, kimchi and 'delicious' pickled herring.

Downstairs several product were featured that could not exist without microorganisms such as yoghurt, kimchi and ‘delicious’ pickled herring.

Overall the museum does a great job in showing the presence and use of microbes in daily life. For example the ‘wall of fame’ contains all kind of household attributes together the microorganisms that are commonly found on the objects. Furthermore there is a nice collection of examples of useful microorganisms to breakdown waste or produce medicine. All this is vividly illustrated with a wealth of interactive installations.

I was a bit time constrained so I might have missed it, but there was little emphasis for potential of engineered microbes. With museum sponsors such as BASF, DSM, Galapagos, MSD, I would expect that a significant portion of the exhibition would be dedicated to GMOs and the endless possibilities of synthetic biology and metabolic engineering. For example by showcasing the bio-production of insulin, artemisinin, or biofuel using microbes. I think the museum would be a great platform to continue the discussion in society on the use of GMOs and highlight the positive aspects.

In conclusion a great way to spend a few hours and get to know more about the more invisible forms of life.

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