SATW - Do-it-yourself von Laborgeräten in der Bioanalytik

Publication

The article came out in the SATW magazine "SATW Info 2/15 – Biotechnology for all / DIY in bioanalytics: doing and grasping it yourself"

Download in German: File:SATW_INFO_2-15_DIY-Bio_DE.pdf

Download in English: File:SATW_INFO_2-15_DIY-Bio_EN.pdf

Download in French: File:SATW_INFO_2-15_DIY-Bio_FR.pdf

Overview

Co-Development of a workshop on DIY laboratory instruments for bioanalytics, colorimetry, low-cost microcontrollers and simple DIY electronics, enzymatic assays. With a concept of "teach the teachers", we are looking into DIY lab-tools as means of a pedagogic tool for interdisciplinary thinking at the biomedical/engineering/molecular interface. Coproduced with SATW, Swiss Academy of Technical Sciences, Hackteria and FHNW, School for Lifesciences.

Unsere moderne Gesellschaft ist ohne Technologien nicht denkbar. Viele dieser Technologien werden nicht oder ungenügend verstanden. Eine eigene Urteilsbildung wird dadurch schwierig. Dies gilt auch für bioanalytische Methoden, welche heute in den unterschiedlichsten Bereichen eingesetzt werden. Es können chemische Substanzen, biologische Marker oder Gene in Lebensmitteln, der Umwelt oder in Flüssigkeiten und Geweben des menschlichen Körpers nachgewiesen werden. Die gemessenen Daten und deren Interpretation können für den einzelnen Menschen oder die Gesellschaft wichtig sein. Die Funktionsweise und Anwendungsmöglichkeiten dieser Geräte sind für Nichtspezialisten eine "black box". Wir möchten gerne das Verständnis für bioanalytische Messungen und Auswertungen nach dem Motto "bauen - messen - verstehen - reflektieren - vertrauen" verbessern. Im Rahmen dieses Projektes soll ein Workshop entwickelt und als Pilot mit interessierten Hochschuldozierenden (teach-the-teacher) durchgeführt werden.

Das Projekt wurde gefördert durch SATW, Schweizerische Akademie der Technischen Wissenschaften.

Participants:

A very interesting and interdisciplinary group of participants has already come together, from various schools in Switzerland, from engineering, life science and design.

Goal:

The goal of the workshop is to collaboratively develop further the educational concept of the Do-It-Yourself method for student training, document our experience and reflections as an educational guideline and hopefully co-develop an interesting summer (or winter) school concept to be held in 2015/16 in different universities.

Dissemination:

We will have the opportunity that the output of our workshop will be published in the SATW News online publication and sent to their large network.

Working paper:

A first version of our experience and a "Vademecum" has been written and will be continously developed further during future experiences.

Download here: File:SATW_Vademecum_V1.pdf

Team

Project Plan

Coaches

Daniel Gygax, FHNW
Marc Dusseiller, hackteria
Urs Gaudenz, HSLU / hackteria

Weitere potentielle Teilnehmer

Brian Degger (AU/UK) - confirmed
Laura Suter-Dick, FHNW - confirmed
Sciotti Michelangelo, FHNW - confirmed
Andreas Thommen, FHNW-students - confirmed

Sachiko Hirosue, EPFL - confirmed, joins wed night for 2nd day
Thomas Vetterli, EPFL - almost confirmed, details will follow
Christoph Stamm, FHNW
Eric Kübler, FHNW
EPFL? Renaud? ?
Daniel Sciboz, HEAD - Interaction Design - no reply
LAPASO netzwerk? dresden? oder studi?
someone from the group of van der Meer, UNIL - sebatical
(Alexandre de Spindler, ZHAW - Bioinformatik) - no reply
Shintaro Miyazaki, Design (IXDM), FHNW http://www.shintaro-miyazaki.com/ - no time
Rüdiger Trojok, openbioprojects / synergenen / hackteria - no time
Silvio Dinardo, HLSU - no time
Robin Scheibler - EPFL - no time
2 anderi Marcel Egli und Franziska Heinze - contacted later

Wir sollten noch weitere leute aus anderen Schulen mit dabei haben!

Sollen wir uns ausschliesslich auf deutsch sprechende teilnehmer konzentrieren?

SATW-DIY Kit

Electronic Kit

more about DIY turbidity meters

Bauteile Starter Set Basic für FPGA oder Arduino Projekte mit Box P00000178 	1 Fr. 23.50
UV-LED im Transparenten Gehäuse / 5mm           P00000103   1 	Fr. 0.60
UV-LED im Transparenten Gehäuse / 3mm 	         P00000519   1 	Fr. 0.50
Lochraster-Steckplatine / Breadboard / Fullsize P00000473   1 	Fr. 11.90
SparkFun Seitenschneider 	                 TOL-08794   1 	Fr. 3.90
SparkFun Spitzzange 	                         TOL-08793   1 	Fr. 3.90
Krokodil Klemmen - Multicolored 10 Stück 	 P00000096   1 	Fr. 5.90
Adafruit Trinket - 5.0V 			 ada-1501    1 	Fr. 10.90 
Kabel USB 2.0 A -> Mini 5-Pin 30cm Blau 	 P00000527   1 	Fr. 1.90
HiSpeed Kabel USB 2.0 A -> Mini 5-Pin 80cm Schwarz 	P00000205 	5
Digital Multimeter (Voltmeter) mit Backlight / BEST B830L 	P00000132 	3 Fr. 19.90

PLAY-ZONE GmbH Hinterbergstrasse 36 6330 Cham

Web: [1]

Zusätzliches Material aus Lab (Marc):

Coin Cell Batteries
Small Multimeters
Blue Tac 
Heissleimpistolen + Heissleim
paar kleine Schraubenzieher
ruber bands

Bio Kit

Tools:
Cuvettes, Square (12mm x 12mm)
Marker
Dropper
Wastebox
Falcentubes 50ml
Knife
Knoblauchpresse
Filterpapier
Plastikbecher
Raffel

Liquids:
PBS (Phosphate Buffer Solution, Instant)
Standard (p-Nitrophenyl Phosphate)
Potato (to extract the enzyme)

Turbidity Meter

Laser Cut Turbidity Sensor Holder

rigth

SATW-Kit turbidity meter

media:SATW_TURBI_kit.pdf File:SATW_bb.pdf breadboard setup

/*
TrinketKeyboard example
For Trinket by Adafruit Industries
*/
#include <TrinketKeyboard.h>
#define PIN_LED 1
#define PIN_BUTTON    0
const int analogInPin = 1;  // Analog input pin that the potentiometer is attached to
int sensorValue = 0;        // value read from the pot
void setup()
{
 // button pins as inputs
 pinMode(PIN_LED, OUTPUT);
 pinMode(PIN_BUTTON, INPUT);
 // setting input pins to high means turning on internal pull-up resistors
 digitalWrite(PIN_LED, HIGH);
 digitalWrite(PIN_BUTTON, HIGH);
 // remember, the buttons are active-low, they read LOW when they are not pressed
 // start USB stuff
 TrinketKeyboard.begin();
}
void loop()
{
 TrinketKeyboard.poll();
 // the poll function must be called at least once every 10 ms
 // or cause a keystroke
 // if it is not, then the computer may think that the device
 // has stopped working, and give errors
 if (digitalRead(PIN_BUTTON) == LOW)
 {
     sensorValue = analogRead(analogInPin);            
   // type out a string using the Print class
   TrinketKeyboard.print("Sensor value ");
       TrinketKeyboard.println(sensorValue);
 }
}

[/source]

Protein Phosphatase Assay

The p-Nitrophenyl Phosphate phosphatase activity assay is very simple, non-expensive, and routinely used for the unit determination of all NEB protein phosphatases.

The PNPP phosphatase activity is assayed in a reaction mixture (50 μl) containing 50 mM PNPP and a protein phosphatase buffer supplemented with additional components when required (PH Buffer?). The reaction is initiated by addition of enzyme (and quenched after 5-10 minutes by addition of 1 ml of 1 N NaOH). The amount of product, p-nitrophenol, is determined by reading the absorbance at 405 nm and using a molar extinction coefficient of 18,000 M-1 cm-1 (16,000 M-1cm-1 for 0.5 M EDTA) (1, 3).

Beer-Lambert law

To determine the amount of product of the reaction the absorbance of light at 405 nm is determined (the liquid turn yellow).
The full measurement path look as follows:

Battery - Light emiting Diod - Light beam - Test cuvette with assay - light sensor - Measurement Unit - Read Out - Human Operator

The Absorbance in the test cuvette with assay can be described by the Beer-Lambert law:

http://en.wikipedia.org/wiki/Beer%E2%80%93Lambert_law

Absorbance (I = Intensity of Radiation, ε = Absorption coefficient [M-1cm-1], c = concentration [M] d = Cell length [cm])
A = - log10 (I0 / I)
A = ε * c * d

Absorption coefficient Calculator (Molar extinction coefficient or cross-section):
http://www.calctool.org/CALC/chem/chemspec/epsilon

Error creating thumbnail: File missing

Color and Beer

Color and Alcohol

You all know that there are different colors of beer, dark and light, but you might not know that it is an indicator of something, and an important measurement in q.c. for industrial beer production. The Degrees lovibond scale was invented by brewer Joseph WIlliams Lovibond who developed the first worlds first practical coloromiter Originally a sight only technique, it is now determined by spectroscopy at 430nm (uv/blue) the absorbance of This yellow comes as the result of a number of reactions, notably the Maillard (or browning reaction)

http://www.chemtronic-gmbh.de/images/chemtronic/Apps_d_pdf/EBC%20Bierfarbe%20I.pdf

Teach-the-Teachers Workshop

Fixed Date: 2 days 15-16. October 2014

Schedule:

Arrival and Welcome: 12h
Day 1: 13h - 18h - Building instruments

Dinner / Discussion

Day 2: 9h - 12h - Isolation and use of enzymes
Lunch
Day 2: 13:30 - 15h - Enzymes meet instruments
Day 2: 15:30 - 19h - Discussion outlook

(Voluntary Dinner for reflections)

Location

Raum 229

HLS, Hochschule für Lifescience, Gründenstrasse 40, Muttenz (BL)

Site plan & directions

Overview Pilot Workshop

Was ist Do-it-Yourself und Open Hardware
Einführung in Elektronik, LED, Licht-Sensoren, Messtechnik
Konzepte der Bioanalytik / Photometric Analysis / Spectrophotemetry
Prototyping
Konzepte der Bioanalytik
Isolieren und anwenden eines Enzyms (Phosphatase aus Kartoffeln)
Test des DIY-Colorimeters mit Mikrokontroller - Vergleich mit dem DIY-Prototyp
Diskussion und Feedback zu den Lehrkonzepten
Ausblick

Voluntary Evening Reflection

informal discussion about the educational value of DIY and future summerschool concepts

Presentation

Meeting Minutes

Notes by Urs Gaudenz, please complete or correct if needed

Goals:

Student Centered Learning
Foster Interdisciplinary Collaborations in Nanobiotechnology
Bring Educational Concept of “DIY-Lab” in Institutions
Teaching Creativity

Potential Collaborations

Working with non-Institutional Partners from the Do It You Self (DIY) Community, the biohacking communities (hackteria.org) and open researchers (GaudiLabs)
Student Workshops in dedicated lectures during the Semester
Specific Summer School at different universities.
Creating a Community of Practice across Institutions in Switerland.

Common Language
Go back to basic, start from scratch, explaining concepts of electronics and enzymes in universal language. In the old times most scientists had to build their own lab equipment. In biology there is a big industry that builds sophisticated devices. More and more Scientists just “press buttons” on complex machines.

“If you don’t build your lab you don’t own your lab.”

“If you can’t open it you don’t own it”

Examples for terminology that are discussed differently in different disciplines (e.g. physics, engineering, biotechnology) :

Optical Spectrometer
Absorption
Turbidity
Optical Density
Volts
Substrate
Assay
Design

These are crucial discussions which enable communication across disciplinary boundaries.
Student Centered means involve people.

The other thing is the Kit
Allow tinkering, playful approach, use your creativity, Hand’s On. The kit is a starting point to creatively work. It provides materials that are characteristic for a discipline. The materials also embody discipline-specific knowledge. (eg. easy to sterilize, imprinted scales and units, typical smell and color, iconic objects (blue LED, petri dish)

Background of Maker and Biohacker Commmunity Several years of Do It You Self Electronics and Biology Movement.
At the moment the DIY and Makers get big attention, influence on public outreach, artistic practice, engineering, academics.
Radical Transdisciplinary Practice
Hackteria.org approach: Synthetic Biology, Genetics can be approached by making cheese, Build Microscopes
Swiss Mechatronic Art Society (SGMK)
New formats of collaboration: Workshop, Festivals, Hackaton, Sprints, Seances, Hang-Outs
Institute of Making, Prototyping, Library of Materials
Sharing Knowledge, make a new fundament for industries and research.

Examples of DIY devices (little Exibition):

Microscopes
Gel Electrophoresis Box with high voltage supply
Electronic Force Microscope
DIY Nano-Drop
CD player syringe pump

Feedback

Laura (new to electronics, background biotechnology):
Great to be Hand’s On
Very good to see how these machines work.
Good to have people around to ask.
Very well done.
Will I get lost with many people?
It would help:
See a Schaltkreis, draw Schematic -> mix of experimental and theory.
Go through standard formulas.
Good to get the Background of a Measurement.
Playing around I liked very much.
Did like the Kit / not complete + big box / you have your own stuff and can get more from the box.
With no kit, people don’t know where to start.
The integration is the point.

Brian (Bioartist, biotech backround):
I am still new to making.
Good to investigate things with your hands.
I personally worked on different wavelength during the workshop. It is good to understand a little bit more of what you are doing.
I still try to find a nice reaction.
Talking about color of the beer. (Kafi Schnapps detector)

Marc (Biohacker, background material science):

I liked to see some visitors
I missed the biological part.
We all did electronics.
Would like to see that we all do the bio all together.
The thing with the color: Talk about the spectral composition of the light.
Fundamental to understand is to know about absorption of light.
Working longer on the background, creating the learning experience.
Suggestion for the laser kit: bigger bottom layer.
How much time? Available 15 h = 1 credit. In 3 Days (3 x 5h)
Good to have this critical thinking.

Andreas (Student biotechnology):
Favorite part: Basteln, creat your own setup, being creative.
I prefer to work with wires not with breadboard. (Wiggle)
Giving bio part of workshop was special. Was not sure on what to prepare. Point out what you need.

Eric (senior biotechnology):
It is important to show that you can do it at home in your kitchen.
Do it your self (DIY) the electronic part.
You should be able to do it at home.
I suggest to keep the breadboard.
For me being creative does not mean being messy.
I first make a prototype and then I think on how to bring it in a format that fits the application?
Let the approaches open.
Theory: being more aware of biology. How is light converted. You should have a better understanding?

Urs (founder of GaudiLabs, engineer)
I liked to have a common topic and choose different ways of approach it.
Exchange is important, discussions as well as the little things that happen in between.
Do it together, be proactive in creating the learning environment, contribute, Like a common arranged Swedish buffet.
Give and take. Integration is the focus.

Daniel (SATW, background biotechnology):
I like the technical electronic part. Reminds me of youth. Play with kits.
Was curious to see how the two parts (electronics and bio) fit together. With isolated enzyme.
Lot of things to optimize.
Students can learn a lot by doing.

Impressions from Workshop

Blackboard notes

Pilot experiments

Pictures

Post-Workshop Discussions in Lausanne

References

p-Nitrophenyl Phosphate (PNPP), Ordering, Description, Properties and Usage:
https://www.neb.com/products/p0757-p-nitrophenyl-phosphate-pnpp

p-Nitrophenyl Phosphate (PNPP) Data Card
https://www.neb.com/~/media/Catalog/All-Products/D59C3FAF466C4ED1830E03673FFB1876/Datacards%20or%20Manuals/P0757Datasheet-Lot0071204.pdf

Calculating the molar absorbance coefficient from experimental data:
https://camtools.cam.ac.uk/access/content/group/6041b37a-7fa4-4a47-808b-b20db3a36122/Module%203/Textbook%20pdf_s/3B3printableversion.pdf

Enzymreaktion http://www.biophys.uni-frankfurt.de/~wille/prakt/anleitungen/01_enzymkinetik.pdf

Related products, Colorimeters et al

Diaglobal Photometer

http://www.diaglobal.de/en/produkte/photometer/vet-photometer.html

Diaglobal GmbH has been developing and producing in-vitro diagnostics for clinical chemistry since 1999. Our products are small mobile photometers with the accompanying reagents and controls. The devices and all of their accessories fit into a briefcase, and enable on-site measurement of various parameters directly from capillary blood. The devices have a wide range of uses, for example in emergency diagnostics, on the hospital ward, in GP practices, in sports as part of training management, in veterinary medicine for livestock owner and veterinarians, in equestrian sports and in process management in the manufacture of biodiesel.

Vet Video: http://www.diaglobal.de/de/VetPhotometer_en.mp4

Breakout for hamatsu c12666ma $300 https://www.tindie.com/products/PureEngineering/arduino-c12666ma-micro-spectrometer-/

"The Hamamatsu C12666MA is an ultra-compact(Finger-tip size) spectrometer head developed based on MEMS and image sensor technologies. The adoption of a newly designed optical system has achieved a remarkably small size. In addition, the employment of hermetic packaging has improved humidity resistance. This product is suitable for integration into a variety of devices, such as integration into printers and hand-held color monitoring devices that require color management. It is also suitable for applications that collaborate with portable devices, such as smartphones and tablets."

Spectral response range: 340 to 780 nm Spectral resolution: 15 nm max.

MultiSpeq - Photosynq, fluorometer / colorimeter for photosynthetic activity

http://blog.photosynq.org/

http://photosynq.venturit.net/

Science Buddies - with Multimeter

http://www.sciencebuddies.org/science-fair-projects/project_ideas/Chem_p075.shtml#procedure

NZ nano - similar to ours laser cut setup

NZ Nano Great Links to other sites

Open-source mobile water quality testing platform / 3D printed Colorimeter - from J. Pearce lab

http://www.iwaponline.com/washdev/004/washdev0040532.htm

http://www.mdpi.com/1424-8220/13/4/5338/htm

http://www.thingiverse.com/thing:45443

http://www.appropedia.org/Open-source_colorimeter

IO Rodeo Open Source Colorimeter

Arduino based Open source DIY kit Colorimeter

IO Rodeo Open Source CheapStat

CheapStat Cyclic Voltametry

PASCO scientific

http://www.pasco.com/prodCatalog/PS/PS-2179_water-quality-colorimeter/index.cfm

Vernier Colorimeter

For Colleges and High-School Science classes

Fluorometers

http://www.turnerdesigns.com/products/laboratory-fluorometer/trilogy-laboratory-fluorometer

http://www.ebay.com/itm/Turner-Designs-Laboratory-Trilogy-Fluorometer-7200-000-accessories-New-Surplus-/251524354862?pt=LH_DefaultDomain_0&hash=item3a9005132e

Videos / Interviews

A final Quote

"There is a growing realization that innovation processes do not automatically follow from the results of research, whatever their potential may be. The “linear model,” which foresees that basic research will somehow ﬁnd its way to being transferred or translated into applied research, which will in turn later appear on the market in the form of commercially viable products or processes, appears as an idealized version of what happened in a given historical period, namely, after World War II. Nor can today’s innovation processes be left to entrepreneurs alone, however strong their “restlessness” (in a Schumpeterian sense) may be. The omnipresent quest for innovation, caught up as it has been in a globalized world, is a hybrid of many elements. It includes the availability of venture capital, and the creativity of determined individuals as much as the ﬂexibility of institutions and regulatory processes".

- Helga Nowotny, The Quest for Innovation and Cultures of Technology, 2006

https://www.berghahnbooks.com/books/freepdfs/NowotnyCultures_intro.pdf