DIYBio and Bioart: liberating the laboratory

Life is becoming like raw material, waiting to be engineered – Oron Catts

What is the biolab used for today? Discovering pharma-cures, creating the next pest-resistant crop, synthesizing recombinant bacteria to glow, sense, detect, digest…? We see something slightly different: where artists work alongside scientists to create universally beautiful sculptures, where a public laboratory performance is held to question Monsanto’s patented crops, and where biologists take respite from their day-jobs to conduct experiments they truly care about, but have limited funding to do. Most importantly, we are witnessing technology liberated from these laboratories, and biology becoming more and more accessible to the average citizen.

We as creators of DIYsect: Filming Biotinkering for the Web, seek to document these game-changing people and put them all on a single web-series where each episode focuses on a different theme within biotechnology. We don’t plan to profit from these episodes, nor do we plan to charge a single penny to our viewers. Like our subjects, we believe that knowledge should be open to all.

Stay tuned for our release in early 2014, and support us on Kickstarter:

http://www.kickstarter.com/projects/260055886/diysect-filming-biotinkering-for-the-web

LEGO Robots in a Research Lab

On a related note:

The Free Universal Construction Kit offers adapters between LegoDuploFischertechnik,Gears! Gears! Gears!K’NexKrinkles (Bristle Blocks), Lincoln LogsTinkertoysZome, and Zoob. Our adapters can be downloaded from Thingiverse.com and other sharing sites as a set of 3D models in .STL format, suitable for reproduction by personal manufacturing devices like the Makerbot (an inexpensive, open-source 3D printer).

 

Cheapass science – Build a pipette stand from PVC pipe for $3.47+tax

I wanted to purchase a pipette stand but it seems like such a frivolous purchase.  I am expected to spend $20 (eBay) to $60 (venders) to hold my pipettes vertically?  Really?  Ugh.  As much as I wanted a pretty acrylic stand I just could not pull the trigger and buy one.  This post will briefly go over how I built a pipette stand out of PVC pipe.

These instructions are for a linear pipette stand.  The circular/revolving stands are an annoyance and an example of bad design.  If you are suffering through one of the revolving stands I urge you to abandon it for a linear stand. Continue reading

Tuur Van Balen hacks Lactobacillus

Designer Tuur Van Balen gives an interesting presentation where he hacks the yogurt producing bacteria, LactoBacillus, using DNA pulled from the Parts Registry.

If you’re interested in hacking yogurt yourself, I’d recommend starting with Cathals “Beginners Guide to Yogurt Hacking“.

Note: Tuur Van Balen has done some pretty crazy science/design experiments, I highly recommend checking out his past works.

Cheapass science – DIY Vortex Mixer Tube Holder

 

The protocol I use for collecting human DNA samples requires tubes to be vortexed for 10 minutes.  Standing around for a sixth of an hour is not my idea of fun so I decided to get a foam tube holder.  Unsurprisingly a piece of foam with holes in it costs 50 dollars.  As per my usual I wanted to be a cheapass and thus I built my own foam tube holder with some things I had lying around.  If you want to see the DIY tube holder in action, watch the youtube video below and scroll further down for instructions for building your own.

 

Guide

 

Compatibility

Before attempting this guide make sure your vortexer will work with this method.  Check the type of head piece present on your vortexer, consult the diagram below for an example of two different types (#12+13 and #14).  This guide works for vortexers with head pieces that match #14. New vortexers usually come with both of these pieces and used vortexers (like the one I bought) may only come with one type.

Materials

The tools and consumables I list are not absolute. Use your noggin and substitute if necessary.

  • Tools
    • Dremel (a drill can be used for some steps but not for carving foam)
      • Sanding bits are needed for foam carving (see image below)
      • Cutting tool
      • Drill bit
  • Ruler or measuring tape
  • Hand saw
  • Marker
  • Compass (optional)
  • Consumables
    • Foam block
    • plastic box (I used a large pipette tip box that was 4”x5”)
    • Rubber bands

These are the two dremel tips I used to carve the foam.

 

Instructions

Two types of modifications need to be done to the plastic box.  First, a hole needs to be made in the center that will allow the vortexer head to poke through.  This alteration will prevent the tube holder from wobbling off of the vortexer head.  For my vortexer the size of the required hole was 1-1/4”.  The second modification is the addition of 4 grooves to the top of the box so that the rubber bands do not slip.

Prior to drilling and cutting grooves.  Yellow circles indicate approximate target locations for the grooves.

After drilling and cutting grooves

 

Close-up of the grooves

How the box fits onto the vortexer head.

Now it is time to carve the block of foam.  My box was not perfectly square; the top of the box (the opening) is larger than the bottom of the box.  This odd shape can be ignored but do make sure to use the top of the box for determining the foam block size.  I made a block that was 4-1/4” x 5-1/4” x 2”.  It is very important that the width and length match or slightly exceed the size of the box so that the foam sits tightly inside the box.

My block

My original block was too tall.  Rather than cut grooves in the foam for the rubber bands and have a tall block (which is preferable for large tubes), I decided to cut the foam down so that it was flush with the box.

Carving and cutting the holes in the foam can be frustrating. Make as few cuts and holes as possible because with each tear the foam becomes more likely to get caught on the Dremel bit and then it will twist and tear the foam block.  Also note that the edges of the foam block are likely to get caught by the Dremel bits.

I used sanding bits to make the holes you see below.  I started with the cylindrical dremel bit I pictured in the materials section.  I went into the block about 0.5” with the cylindrical drill bit (this made the cleanest looking hole opening) and then I switched to the conical bit which I used to go straight down to the bottom of the tray.  Use tubes to test each hole you make to ensure they fit.  A snug fitting tube is better than a loose fitting tube.

When the Dremel grabs the foam and twists some areas of the block will be torn.

Another view of the finished block.

 

All that is left is to attach the box to the vortexer and for that we just need rubber bands.  The way the rubber bands rest on the vortexer head and on the box is important, consult the images below.

The first rubber band is hooked under the left side of the vortexer head and hooked over the right side of the box.

The second rubber band is a mirror of the first rubber band.

 

That is it, the attachment is finished.

Before

After

Glamour shot

If you build a vortexer attachment send me a picture and let me know how it turns out.

 

How to make glow-in-the-dark or Flourescent Yoghurt

Photoshop Mockup.

Glow in the dark yoghurt is something that has been floating around the DIYbio community for a while now, though to my knowledge no one has actually made a batch. Hopefully that will change now that Cathal Garvey of IndieBiotech has released a “Beginners” guide to hacking yoghurt. As you can see from the excerpt below beginner here is code for you are going to learn alot.

For our project then, we want DNA that resembles the following:

A diagram showing the format of the desired DNAColourised and labelled sections of the DNA, presented with the unnamed section of target DNA. This assumes the simplest scenario where no “cleanup” mechanisms are included to remove the resistance gene.

The promoter (Prom) should be a constantly “on” promoter, termed “constitutive”. The terminator (Term) is a region of DNA that prevents the gene from transcribing beyond its normal context, which could cause unintended interruptions of cellular functions; unhappy bacteria could result, and the gene could end up unstable. The antibiotic should be chosen to avoid medically significant antibiotics such as ampicillin; this is a civic responsibility matter, as otherwise your yoghurt could end up assisting dangerous pathogens in becoming resistant to medicines. Ideally your antibiotics would be self-excising once they become unnecessary, leaving a yoghurt containing only harmless fluorescent proteins and nothing else.

Cheapass science – How to build a $21 gel box

Gel Electrophoresis is a very popular technique in biology. Used for the separation of DNA, RNA and even proteins based on molecular. The Gel box is a very simple tool allowing one to run a charge through the gel to separate.

Disclaimer

The techniques used to make the gel box and the operation of this gel box may be hazardous.  Follow this instruction and use these gel boxes at your own risk.

Cost

Below is a rough break down of the cost per gel box.  The actual cost could be more because  some of the supplies below are not sold separately and the vendors force you to buy them in packs.  Try and plan around making a couple gel boxes to get the most out of your money.

    • $2.5 – 4 banana plugs
    • $7 – 2 banana jacks
    • $6.75 – 3” of platinum wire (0.005” diameter)
    • $1 – steel leader
    • $2 – gel box
    • $0.434 – gel mold
    • $1 – plexiglass (for comb)
    • 20.68 (27.43 if all platinum)

A note on electrodes:

Platinum can work as either the cathode or the anode.  Steel and other materials can be used for the anode (using them as a cathode will cause them to break apart and dissolve into solution).  Since platinum is expensive, I chose to use it only as a cathode.

Steel leaders are coated in plastic, to fix this minor problem melt the plastic off with a lighter.

Melting plastic off of a steel leader

 

What you will need

Tools

      • Dremel
      • Drill + drill bits
      • Screw drivers (assorted)
      • Fire (ex: lighter), if using steel leaders.

Supplies

      • Piece of acrylic
      • Plastic storage boxes (I used “lock tight” and “inter lock” by the Darice company )
      • Banana Jack (also called “music binding post”)
      • Banana Plug
      • Platinum Wire, 0.005” diameter
      • 25 gauge wire (other sizes can work, I am not an electrical engineer and do not know what size is best)
      • Super glue
      • Optional:  Hot glue gun and glue sticks
      • 6” Steel leaders (used for fishing, can use sterling silver or platinum instead)
      • Clear tape
      • Marker

 

How to assemble the components

 

Make the cables

Cut two 16” pieces of 25 gauge wire (or whatever length and gauge suits you), remove 3/4” of insulation from each end of the wire, and then attach each end to a banana plug per the instructions on the packaging.

The plugs I bought were solder-free and use two screws to pinch and hold the wire inside of the plug (see image below).

Inner workings of a wire

 

Assembled wire

 

Make the gel comb

One side of the plexiglass will have a thin plastic film (both sides may have the protective film, use either side), use a marker to draw the desired comb.  The spacing and size of the comb will vary depending on the box size and application.  Below is a diagram and explanation for the comb design I used.

Comb diagram

I started out by cutting a 40mm x 30mm piece of plexiglass.  Then I drew lines 5mm apart and 15mm long across the length of this square.  I then used a dremel to cut along these guidelines.  The thickness of the cutting tool was 1mm and so it removed  0.5mm from each side of each tooth of the comb. I was left with a gel comb that had six 4mm wide teeth with a 1mm gap between each.

The comb needs a support bar and it is simple to make, simply cut out the shape shown below.

Comb bracket diagram

Once this support bar is cut, super glue it to the back of the gel comb.  The length of this plexiglass bar should be longer than the width of the gel mold.

Making the comb was the hardest part for me because my hands shake when I concentrate but I nevertheless was able to cut a usable comb after a few tries.  Below are a couple of comb examples, some made with and others without a dremel.

My first attempt, I used a razor blade

 

Gel comb 2

 

Gel comb 3


Make the casting tray 

Casting tray + comb

The casting tray is simple.  Two grooves are going to be cut such that when the gel-comb bar is placed in the grooves, the bottom of the gel comb is suspended 4-5mm above the bottom of the tray.

Casting tray, top view

In my case, the grooves ended 13mm above the bottom of the tray and sat 6mm from the end of the tray.

Casting tray, side view

Below is what the casting tray looks like with a comb and comb bar inside.

Casting tray + comb

When I purchased the plastic box that was to become the gel box, it was clear from the packaging that each inner surface was flat and straight.  You may have already noticed that this was not the case for the casting tray (see image below).  The box I used for the casting tray was molded with two indentations to increase structural strength.  Fortunately these indentations were not huge and only reduced the effective width of the gel by a couple of millimeters.

Agarose slab inside of the gel box

Make the gel box

Using the banana plug jack as a template, trace the circumference of the jack onto the gel box (the image below shows this in red).  Now we are going to start drilling.  When making the holes, start with a small drill bit and make a pilot hole.  To make the hole larger, it is best to incrementally move to larger and larger bit sizes.  If the largest size bit is used first, it is probable that the plastic will crack.

Drilling a hole

If the gel box being constructed is like mine, that is to say, small, then I advise attaching the electrode to the jack before attaching the jack to the box.  My gel box required 3” long electrodes.

The jacks I used work like a typical nut bolt comb and the screw portion pinches the whole thing in place (see the image below).

Banana jack

Once the jack is in place the next step is to bend the electrode into an appropriate shape.  In my case, that shape was a sideways “U” shape.  Since there are two electrodes it is important to make sure that they are approximately the same length, shape, and parallel to each other.  If these parameters are not met, then the DNA bands may not migrate straight across the gel. The image below shows how I bent and positioned my electrode.

Gel box, side view showing electrode

It may be necessary to attach the electrodes to the bottom of the box with a bit of glue (I had good results with super glue and hot-glue).  All of the electrode materials I tried using (sterling silver, stranded wire, platinum, steel cable) refused to stay in the position I wanted and in every case adhesive was necessary.

Gel about to be run

There are some safety issues I should point out.  First off, this gel box is more dangerous than commercial gel boxes.  The jacks I used to make the gel box have exposed metal and when a gel is running you could electrocute yourself if you connect the two electrodes.  The next safety issue is the lid.  Most commercial gel boxes integrate their wires into the lid so that when the lid is removed the loop is broken and the electrocution hazard is removed – this gel box does not do that.

There are a number of behavioral things that can be done to avoid this safety issues.  I would recommend fixing the lid to the box with some clear tape whenever the box is being used.  This will help prevent someone from shocking themselves when trying to remove the gel and should reduce the risk of electrocution if the gel box gets tipped over.  Another behavioral tip is to always disconnect the wires from the power supply before manipulating the boxes in any way.

Filled wells

Does the gel box work?  Yup.  Can I reliably follow a simple protocol? Nope.

Gel results

While preparing the molten agarose I forgot about it and the solution boiled for too long and became more concentrated.  I had aimed for a 2% gel and got something much higher.  Nevertheless, the gel turned out awesome!  I ran 5uL of 100bp ladder (Promega) in each well at 70V for 80 minutes.  Deviations in band with are due to the gel comb’s teeth being uneven.  The gel was stained with ethidium bromide for 20minutes and washed with water three times for 5 minutes each.

Bzzzzt

Links to some supplies.

Most of the supplies I used were store bought and I did my best to find the closest online equivalent.  I do not endorse or recommend any of the products below, I link them only to help people locate the supplies they may need.

How to add a double decker to your shaker

Joseph Elsbernd, of the Cheap Ass Science Blog brings us a rather simple but ingenious way to get double the area out of your shaker/rocker using nothing but a bit of pvc tubing and your choice of decking material.

Via Cheap Ass Science

Cheap A** Microscope Incubator

Joseph Elsbernd, a Graduate student out of UC Davis Med Center, has built a rather ingenious tool for keeping his cultures warm while on the microscope. Using some pvc, plastic sheeting, a bit of duck tape and a hair dryer he built a fully encompassing incubator for his microscope.

I especially like the picture below showing how his first version was literally just a cardboard box.

Versions of Microscope Incubator

Versions of Microscope Incubator

You can check out more pictures of the incubator at Josephs blog: Cheep A** Science

Garage Bio Inaugural Podcast

Derick Jacoby and Eri Gentry of BioCurious have launched a podcast dedicated to garage biology with the aim of capturing the expertise of some of the people that pass through BioCurious.

 In this inaugural episode, Eri and Derek discuss the BioCurious opening, safety in synthetic biology, and host a roundtable discussion with George Church on the potential of DIY Bio.

Listen to garage bio