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: 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: 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
Do you have more exciting examples? Let me know!
Last week the first real novel antibiotic since the ’90 saw the light. The authors made the discovery by diluting a soil sample in agar and casting this in a matrix with tiny holes. Next this matrix chamber (called iChip) was sealed with a semi-permeable membrane and placed back in the soil. After a month colonies were picked and after co-culturing with S. aureus the authors found the new antibiotic. The compound, teixobactin is produced by a large biosynthetic gene cluster of the previously uncharacterized bacteria Eleftheria terrae. The new antibiotic is functional against S. aureus but also against M. tuberculosis and probably a whole range of other Gram positives. Back to the culturing, with the iChip the authors claim to show the growth recovery “approaches 50%, as compared to 1% of cells from soil that will grow on a nutrient Petri dish10.”
A selection of some interesting papers of the past period. Unfortunately some are only accessible for subscribers. Some topics covered; protein folding and design, antibiotic resistance genes, RNA polymerase complex and a paper on choosing the right color for your data.
Promoters and (their often forgotten partner-in-crime) operators are two key elements in the transcription of a protein sequence. A promoter sequence recruits the RNA polymerase and the status of the operator determines whether or not the adjunctive protein sequence gets translated (Figure 1). So far, biochemistry 101. Far more interesting is the diversity in promoter/operator complexes currently employed in the biotech industry and their associated efficiency rates. Not a lot of quantitative and real comparable research had been done on this topic, until March 2013…
