BioStrike

BioStrike from DIYBCN on Vimeo.

Segons la WHO, la resistència als antibiòtics es un problema que afecta a tot el mon i que, sense cap acció coordinada globalment, pot donar lloc a una situació on els antibiòtics actuals no tinguin cap efecte en el tractament d’infeccions.

Moltes bactèries produeixen certs compostos tòxics produïts per a competir contra altres microorganismes. Aquests compostos son emparats com a antibiòtics en la medicina, salvant milers de vides cada any.

Malauradament, l’abús d’aquests compostos i la manca de recerca, ha originat l’aparició de soques resistents. Al no disposar d’eines per combatre-les, suposa tornar a una època pre-antibiòtics.

El tipus de microorganismes ve determinat per l’ecosistema on es troben. Per tal d’assolir el major nombre d’ecosistemes, es convida a ciutadans i centres d’educació a participar en la recerca de nous microorganismes productors d’antibiòtics, per mitja de l’aïllament de soques salvatges. Es important tenir en compte que aquests microorganismes, no comporten cap risc per la salut humana.

Per tal de duu a terme aquesta tasca, s’ensenyarà als diferents participants com aïllar actinomicets, a partir de mostres de terra i enfrontar-les amb E. coli (o similar) per tal de determinar-ne les propietats per a inhibir el creixement.

Tot i semblar complex, es tracta d’un procés que pot dur-se a terme a qualsevol cuina. Tot i així, per tal de promoure el projecte, es repartiran 100 kits per l’aïllament i el cultiu d’aquestes soques. Cada kit contindrà:

  • Protocol per la sembra i l’aïllament d’actinomicets, versió estàndard
  • Protocol per la sembra i l’aïllament d’actinomicets, versió DIY[1]
  • 20 plaques de petri (100 kits * 20 plaques/kit = 2000 plaques petri)
  • 20 nanses de sembra (100 kits * 20 nanses/kit = 2000 nanses)
  • 1 cupó vàlid per a la seqüenciació de l’ ADN de la regió 16/18S de la soca d’interès
  • Glicerol
  • 1 flascó borosilicat 100 ml

Basant-se en la capacitat de cada soca per inhibir el creixement, els participants podran analitzar la regió 16/18S dels microorganismes aïllats. D’aquesta manera, i per mitja d’eines bioinformàtiques, podran identificar la soca a la qual pertany.

S’oferirà la possibilitat de realitzar anàlisis metagenòmics de les regions 16S o 18S als diferents participants amb l’objectiu de generar un mapa metagenòmic del territori. Aquest tipus de test no estarà cobert per l’actual concurs, donat el seu cost (~100€).

Amb l’objectiu d’organitzar totes les dades obtingudes, es crearà una base de dades que contingui tota la informació relativa a l’obtenció de les mostres (localització GPS, temperatura i humitat mostra, seqüencia ADN, fotografies dels cultius, etc…). Les dades seran accessibles de manera gratuïta.

Aquesta base de dades, serà accessible via web o Android.

Per tal de promoure el registre de dades, es proposaran diferents objectius a assolir per part dels participants, per tal d’engrescar-los i realitzar un major nombre d’assajos. Aquests objectius seran considerats com a Insígnies (tasques concretes) o Assoliments (conjunt d’Insígnies).

Aquestes tasques tindran una baixa barrera d’entrada, però la corba d’aprenentatge augmentarà gradualment a mesura que els participants progressen.

Els usuaris podran comprar els seus resultats amb la resta d’usuaris de la xarxa Biostrike.

Els objectius de Biostrike son:

  • Distribuir 100 BioStrike kits a diferents centres d’educació
  • Conscienciar a la ciutadania sobre la importància de l’ús i el desenvolupament de nous antibiòtics
  • Conscienciar a la ciutadania sobre la importància dels ecosistemes i el manteniment de la seva diversitat
  • Desenvolupar protocols oberts per a la recerca de nous antibiòtics
  • Gamificar la ciència ciutadana per tal d’estimular el públic
  • Distribuir horitzontalment el coneixement, per mitja de l’aprenentgate comunitari (o Do it Together)
  • Col·laboració científica mundial basada en el moviment Open Source

[1] DIY: Do it yourself (fes-ho tu mateix)

DIYBio BCN at Novum 2015

Diy Bio BCN and WAAG were invited to participate at Novum 2015 and we decided to join efforts and make one stand together.

Barcelona county is constantly organising activities for society and science divulgation. They decided to include WAAG society and DIY BIO BCN to make a pop-up lab. Pieter Van Boheemen came from WAAG and the whole crew of DBB supported him. We brought equipment built during the BH Academy and some students were showing their work as well. Quick experiments were organized to be carried out by the visitors:

1. Yeast Balloons. Balloons were filled with CO2 produced by fermenting yeasts and then given to the kids.

Yeast balloons

Yeast balloons

2. Chloroplasts chromatography.  To spot DNA in spinach cells and perform Chlorophyll spectroscopy in order to check the health of plants. Could we make chromatography in paper?

Chloroplasts chomathography

Chloroplasts chomathography

3. DNA Jewelry. DNA was extracted using an open protocol and materials found in any local supermarket. DNA was then saved to small eppendorfs and given away to visitors.

4. Cellulose Kombucha. A culture of Kombucha was shown to visitors. They were able to try the drinkable juice made out of it.

Here is a link to one article from Vanguardia and the main link to the event of NOVUM 2015.

Some of the pictures from our own gallery.

The Whole Crew

The Whole Crew

Visitors

Visitors

Visitors

Visitors

BHA01 Practice 08: Injection pump

How can we deliver or extract any substance to our bioreactor, without contamination and if possible, in an automated manner? Well, we could build an injection system using a servo motor and either a syringe or a peristaltic system to pull the liquids from a reservoir and push it to the bioreactor. The WAAG has proposed a good system with both options available.

Peristaltic pump

In this case, a rotating gear system creates an alternating compression and relaxation cycle in the tube, similarly to our gut or throat. This way the system can suck whatever is in the reservoir and push it to the bioreactor. This method has the advantage that the medium to be pumped does not get into contact with any moving part and it is easy to change the source of the medium to be injected.

Syringe pump

In the case of a syringe pump, we need a motor that can push the syringe. To do so, an infinite screw is controlled by the step motor and this way we can push the content of the syringe. In this case, there are movable parts in contact with the medium and you will need to unplug the syringe, then load it, and push the sample again.

 

 

BHA 01 Practice 06: Magnetic Stirrer

Magnetic Stirrer

How to mix the products of your cultures? in a  reproducible manner? Normally, people would shake solutions when trying to mix something. But this is not reproducible and everybody would get different results. So, a magnetic stirrer is a device that will mix your solutions creating a vortex when moving a magnetic piece inside your solution. The design provided by WAAG was good and comply with the our requirements. We needed to control a motor, paste some magnets to the rotor and make a base close enough to it so we can put our bottles with solutions over it. Do you remember the neodymium  magnets we got from the HDD? We can use them in this device. The circuit diagrams and code is uploaded in our forum section.

Fan motor used as magnetic stirrer

Fan motor used as magnetic stirrer

Magnetic Stirrer

Magnetic Stirrer

 

BHA01 Practice 05: Centrifuge

Centrifuge

Cells are made of many different biomolecules. For example, the outer membrane is made of lipid molecules, the nucleus contains DNA, RNA, proteins, etc. Besides that, cells are surrounded by other molecules suspended in their media. Each biomolecule has different characteristics: electric charges (polarization), mass, etc. How could we separate them?

A centrifuge is a device that uses the centrifugal force to separate the different materials suspended in the liquid so at the end, you will have the heavier elements down at the bottom and subsequent lighter molecules staked up. Two factors are of main importance: a motor with torque enough to achieve the required G forces (calculated based in the number or revolutions per minute-rpm-) and the rotor radius.  The torque is proportional to the radius of the rotor and so will be the force.

A brushless motor was selected due to the advantages they have: they are designed to last, they have a powerful torque and they can have a decent control of rpms. We ordered some of them and started to build the centrifuge design proposed by WAAG. However, we wanted to test our hack abilities and another design was made using a HDD motor. Old HDDs have brushless motors and because they break quite often, they are easy to find for free. So we made the two designs.

HDD motor

One of the students took this project on his own. When dismantling  the HDD you could save some powerful neodymium magnets, the silica dishes and the brushless motor. Do not take the motor apart of the case because this case can work as the base of your device.

Brushless motors can be DC or AC motors. In the case of HDDs, they are AC. They do not have any positive and negative poles to connect. Instead, they have three (or more) different electromagnets (inductors on the stator) inside. Each electromagnet can be activated when passing a digital pulse through it. The idea is to activate each one of them in a sequential way: turn on inductor one and the rotor will move 120 degrees, then activate inductor two while turning off all others and the motor will move 120 degrees more, finally activate inductor number three to complete a full cycle and then repeat. The idea is to send three pulses sequentially and if you regulate the duty cycle you can control the spin velocity of the motor: the shorter the space between pulses the faster the motor will rotate. How can we find the electromagnets terminals? and how to activate them?  The next image shows the connections of the HDD motor:

 

The idea is to measure the resistance between each terminal. There are three inductors sharing a common node. So, if we measure the resistance between each terminal while keeping one terminal as reference, there will be a combination that will give us the same value to each terminal. That will be the right combination and that means you have found the common node and the three terminals. Connect the common node to ground and all other nodes to arduino analog outputs. The electronic circuit and the code is available in our forum section.

Imported Brushless Motors

We bought some brushless motors from China and started building our centrifuge using the WAAG design. We made some improvements to the original design and added code to start, to increase the velocity and to stop the motor. The code and circuits are uploaded in our forum section.

 

3D printed rotor head to hold the eppendorfs

3D printed rotor head to hold the eppendorfs

Brushless motors imported from China

Brushless motors imported from China

Assembled centrifuge

Assembled centrifuge

BHA01 Practice 07: Spectrometer

Spectrometer

How could we control the amount of cells suspended in our solution? You could take a sample with a known volume, look through it in the microscope and count cells manually. This is a time consuming process and there must be a more efficient way to do so.

Three things can occur when light hits an object: it can be reflected, it can be refracted or it can be absorbed. Each atom will absorb a particular wavelength and transmit or reflect others. Each biomolecule will absorb a given set of wavelengths and transmit others. This can be considered as the footprint of the biomolecule. Imagine if we can send light with multiple wavelengths and then monitor which ones are absorbed and the amount of energy that was absorbed. This way we could extrapolate the information and then we will know the amount of cells suspended in our solution. This is the main idea behind a spectrometer.

So, we will need a source with a good spectral emission (it includes as many wavelengths as possible): Xenon lamps are known as the source with the spectral emission more similar to the sun spectra, but they are expensive. An halogen lamp has a smaller emission spectra. An LED has even smaller spectra. A laser has a unique wavelength (~630 nm for red, ~530 nm for green, ~400 nm for blue, etc). Choose your source according to your needs.

And then we need to work in the detection part. How do we read the amount and wavelength of the light that has passed through the sample? In electronics we have two devices that can do so: a photodiode and a CCD or CMOS sensor. You can find cheap CCDs or CMOS sensors in your webcam, your phone, even in your optical mouse! This is a cheap way to build your spectrometer. The easiest way will be to get a webcam, dismantle it and plug it to your computer. Then use software to read the intensity of light per area and plot the results. A photodiode is a device that changes the current that flows through it depending in the intensity of light that hits its surface. Reading the current flowing through the photodiode we could know the amount of light hitting its surface.

But how to know the wavelength of the incident light? We can use a diffraction grating to split the light into its different wavelength components. As you know, white light is comprised of the sum of all different colours (wavelengths).  Using a prism you can separate the light in all the components (the rainbow colours you observe in nature). You can use a diffraction grating instead of the prism to do the same. Diffraction gratins are found in CDs and DVDs. We choose to use a DVD grating. Get a blank DVD, if you observe the edge you will note that there are two discs pasted each other. Use a razor to split the DVD. Take the transparent part, then cut a small piece and use it to diffract the light. Each wavelength will go through a different path and you will get a nice “rainbow” pattern at the output of the diffraction grating. You can calibrate your photodiode array to indicate that a given side corresponds to the red colour and the other side to the blue colour.

The device needs to be calibrated by doing a “dark” measurement (with your light source OFF), then a “white” measurement (with your source ON) and finally a measure with your sample. By comparing this data you can get an approximation of the amount of  absorbed light and then relate it to the concentration of your sample. You could use a control solution without your sample and repeat the measurement.

 

BHA01 Practice 04: Sterile hood

Sterile hood

We are surrounded by life. Viruses, bacteria, fungi are all around and they are trying to survive. If we want to grow a particular bacteria or yeast or any organism of our interest, it is necessary to ensure that only our organism grows and there is no contamination. Our first approach was to use Bunsen burner improvised with a camping stove and gas cylinder. However, if we want to do longer experiments or more complicated cultures, a wider sterile working area will be required. The design provided by WAAG society comply with all the requirements so we decided to build it.

There were problems with the air pumps shipment so we had to assemble the hood and leave the air pump installation pending. We decided to build the hood using acrilyc due to is transparent. Pictures are showed below.

 

 

BHA01 Practice 01: incubator

So… the D-day just arrived, and we were a bit nervous about what could happen with this first workshop.

Friday night, we met at MADE to be sure that things worked as expected. But, as usually, unexpected problems arise that we could not fix just before the begin of the class. We were awake until late, trying to fix all the issues and we didn’t slept too much, but on Saturday morning we started the first BHA01 practice with 10 people with different backgrounds.

We started with a class about electronics, just to make sure that every participant had the basic skills to understand what we were going to build. After a theory class of 2 hours, we started building the electronic part of the incubator with a protoboard. The idea was to teach students how to build a circuit from scratch in order to give the the tools to build simply electronic circuits.

After that, we started with the Arduino. All the students had the software already installed. There were teams spontaneously integrated: in one side we could observe a team of people with experience in electronics and programming who were actually rebuilding the incubator design and improving it and adapting it to our actual necessities. There was another team soldering and wiring the electronics part with support of everybody. There was another group of BHs testing protocols for Agar and some others cutting the acrylic, wood and other pieces.

Finally, we assemble the incubator boxes. With a bit of patience and a hammer, we build the boxes. After that, we added some porex in the interior to keep the heat inside the box. The acrylic window was glued, the door assembled and the porex placed on site.

It was was a great practice. I was really impressed to find a group of very orderly, quiet and focused people hacking at various projects at the same time: some hacking on electronics, some gluing together stuff laser cut, some others just being very busy at the tables with the arduino code,… just fucking amazing. You rock guys, please keep like this in next weeks.

We want to thank to Valldaura guys to help us cutting the woods, because the designs were quite big for our laser. Thank you Jonathan!!!
Also want to thank to MADE, for allowing us to run the BHA01 in their space. And thanks to FAB Cafe and MOB for allowing us to run the classes during Tuesdays!

BioHack Academy news

We are about to close the BioHack Academy inscriptions!

If you have not filled the registration form yet, you can find it here.

More info: BHA details.


Estem a punt de tancar les inscripcions a la BioHack Academy!

Si encara no has emplenat la teva inscripció, pots fer-ho aquí.

Més informació: BHA details.


Estamos a punto de cerrar las inscripciones a la BioHack Academy!

Si aún no has llenado el registro de inscripción, puedes encontrarlo aquí.

Más información: BHA details.

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