Disclaimer: No clinical weight will or should be placed on these protocols and their test results. Only public health certified labs should be relied upon. No testing of anyone else’s samples apart from your own should be done (for multiple reasons, ethical, practical and legal). If Corona Virus was as fatal as SARS but as contagious as the flu we would have a major problem. Thankfully it is not*. Conservative guesses at the moment are probably pointless as we don’t have enough information. However it’s looking like it will infect hundreds of millions. At 1%** fatality rate that’s a lot of “avoidable” deaths and suffering. To break the cycle, as with all public health initiatives, early detection is not necessary but it is incredibly powerful. Because the flu has similar symptoms (albeit probably more runny noses) then it’s difficult for some one infected to tell them apart. And if they are symptomless then it will be impossible for them to tell. We will need to move to a society where in situations like this, everyone has ready access to a test, and preferably one performed once or more per day. You could imagine waking up and putting a nasal and saliva sample in a tube. Then having breakfast, getting ready for work, and before you leave the front door you get the all clear or you know you are infectious and can call in sick / work from home. If we had such a system in place now we’d send the genetic code over the wire, your device would synthesis you the correct primers, and run the diagnostic. The system would need a supply of cartridges containing freeze dried reagents, preferably in single pot reactions. Where can DIT (Do It Together) DIY Biology help out? Well beyond being a...

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Whilst doing a lab clear out a couple of years ago we found this amazingly symmetrical formation of mould growing on top of some buffer. We called it the Hammer Head and then, alas, we autoclaved it.

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Ok so perhaps that’s a stretch but we’ve got some plans which are made a lot easier by being able to programmatically produce designs for the laser cutter in the HackSpace. After a little work we had the following designs: These can be put straight into InkScape and converted to .dxf file format as is. However after cutting on all the lines, half of these designs would fall apart into many pieces. Instead it might be interesting to cut to leave the lines. Something like this: To do this we want to change this SVG: Into this: Where we cut on the red and blue which will leave the black lines intact. To do this: A. Grab the SVG and open it in InkScape. B. Under Edit > Preferences > Behaviour > Steps , change “Inset/Outset by” from 2px to 0.8px C. Select the shape and use ctrl+d to duplicate it D. Down the bottom, change the stroke colour to red E. Use “ctrl+shift+9” ( “ctrl+(” ) to Inset this F. Same as C G. Same as D but change colour to blue H. Same as E but “ctrl+)” (“ctrl+shift+0”) to outset Once you’re happy you may wish to delete the black line, save as a dxf and carve out of your favourite laser cutter material! Note on InkScapes Inset/Outset: it’s very good but it’s not perfect. Below is an example of 1, 2 and 3 mm distances and you can see some pretty weird artefacts brought up: For less uniform shapes like the spirals this “randomness” adds to its natural look but for things like squares it is obviously conspicuous and not in a good way. Note on our laser cutter software. It has a feature called “unite lines” when this is used it appears that the software...

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George and team from Darigov Research provided an excellent introduction to the open source, microscopes and then step by step guidance on how to build the FoldScope microscope. We actually had a few more people that this turn up after we took this photo: The first item on the menu for microscopic inspection were some Sweet & Salty Crystals™ 😉 which we’d grown in the lab over the last few days. The sugar may have provided a nucleation point that the salt then crystalised around, whatever the reason they had these interesting crosses through them (not very obvious in the photo below): Up close you can see they have a strange cross shaped indentation We moved on to look at some of our hairs, and skin detritus from ears. We also found our algae in a bottle look much more magical up close (collected from Cambridge) And finally took a closer look at our Daphnia (collected from near Highbury and Islington, London). There was a Rotifer moving around too but we couldn’t find it after a while… probably ended up as afternoon tea for the Daphnia! To compare and contrast with our lab microscope we took some more pictures. These were on a different phone and we managed to get them into focus more easily so it’s not like for like comparison… the images you can see through the foldscope are actually better than those above but we didn’t take time to fine tune the setup. Included below are also some stained cheek cells from last week. Thanks to everyone who attended!

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We took delivery of a new power lead for the hotplate / magnetic stirrer. As half of the equipment we pick up is in a state of disrepair it was pleasantly surprising to be greeted with glowing lights, warmth (up to 300 oC) and a whirling stirrer bar! The ion exchange resin was also saturated in the water purification system. The message to “buy some more resin” was enthusiastically followed… … so if anyone wants some resin then…

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After a long wait we finally got the time to plan and build the second generation Laminar Flow Hood. We’ve been wanting to get this up and running as a necessary prerequisite of more advanced microbiology and molecular biology experiments. Keeping your cells separate from all the bugs floating around the air is really important! We started with the components from Mark 1, including the calculations which we double checked and left unchanged. There’s a soft seal on one side of the filter which we left on the output side. This is one of the only weak points we can think of in the design as we couldn’t leverage it to help seal round the top of the plastic walls as they sit inside the legs supporting the filter box: The “final” design is shown below. Notable additions or changes upon implementation: We used M5 bolts to go through the legs, polycarbonate panels and fibreboard top box. To allow the filter box to be inserted into the top box we spaced the top box panels away from the legs using 1mm spacers on all sides. This worked well: allowing us to put one edge of the filter box into the top box before lowering the other edge into place. With the side plastic walls in place it would be very hard to lower it down in one go. The front and back panels extended further to the sides to accommodate wooden battens towards the top which helped secure the top of the large box panels together. The was done as originally the structural strength of the large box was going to come from the snug fit around the filter box towards the base. The top panel was originally going to be formed from a flat piece of wood with...

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The plan was to grow harmless probiotics like lactobacillus on some agar media. We would repeat a previous experiment adding different hand washes and cleaning products to see which was most effective at sanitising them. And try a second experiment using the same yogurt brand but of different use by dates to see how many bacteria they retained (via serial dilution). The lab robot was going to be used to remotely monitor their growth on the petri dishes in the lab over the warm bank holiday weekend. This required making a now close to mythical lactose-yeast extract media made in a previous experiment. Mythical because it failed again on attempt 6 with the milk protein precipitating out. With the robot ready to roll and the media decidedly lumpy we abandoned the planned experiments, poured the media into an open plastic container and left it to nature’s devices. On returning a couple of days later it was decidedly dried out and non inhabited. We doused it with some pure water and left it again for the weekend. It was quickly investigated by some fruit flies… where do they come from?! And within 12 hours was showing some mould growth. Within a few days it was pretty unrecognisable! … and slightly too characterful… We applied a simple threshold filter on the red channel (making blue and green maximum) to the pictures to get the following data: If we assume the growth is in 3 dimensions; as the mould grows into the agar media, then we’re reminded that nature grows exponentially when given the right conditions! If you’re wondering what happened to the mould… bleach. Lots of bleach. Source code here.

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Everyone came with boundless enthusiasm and energy for the DNA workshop on Sunday in the London HackSpace.  There was great DIYBio in the new lab and people helping each other out loads to understand the fundamentals or the practicalities of pipetting, thermocycler, enzymes etc. The first step of DNA extraction started in the kitchen.  We used a small amount of slightly salty water to get some of our cheek cells… whilst trying not to laugh 😹 Then we went down to the lab and started the protocol to extract DNA from our cells. The DNA extraction didn’t use an alcohol step like ethanol or isopropyl alcohol, just centrifugation, heat and a lot of pipetting.  Here you can see the cells already starting to precipitate even before the centrifugation: Credit to Juris for taking some fantastic photos.  I saw a lot of other photos being taken so workshop attendees, please feel free to share them on the slack channel, twitter, meetup.com or the mailing list 😁 We were shortly joined by 3 more keen bio labbers and eventually had a total of 9 samples in different stages of DNA extraction.  And so commenced a lot of centrifugation, and careful pouring and pipetting to remove the supernatants (the liquid above the “pellet” of cells left in the bottom): We put it in the “thermocycler” for 99oC “cook” for 10 minutes to hopefully break open the cells and release their DNA.  Then followed even more careful pipetting!… ah the life of a biochemist: Finally after almost three hours we had our samples of DNA from everyone, and set the lactase SNP (Single Nucleotide Polymorphism) PCR running in the Bento Lab thermocycler: We broke for a well deserved lunch break and everyone washed their hands before they left the lab! 🙂  After lunch...

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As the lab has got a lot tidier and lab like recently we’ve had more opportunities to start having fun in it. We’re fortunate to own several microscopes which we have used to look at some of the local flora (green algae we got from the window shelf outside and cultured up): And an Aloe Vera stem:

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