Difference between revisions of "SATW - Do-it-yourself von Laborgeräten in der Bioanalytik"
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== References == | == References == | ||
− | p-Nitrophenyl Phosphate (PNPP), Description, Properties and Usage:<br> | + | p-Nitrophenyl Phosphate (PNPP), Ordering, Description, Properties and Usage:<br> |
https://www.neb.com/products/p0757-p-nitrophenyl-phosphate-pnpp | https://www.neb.com/products/p0757-p-nitrophenyl-phosphate-pnpp | ||
+ | <br> | ||
+ | p-Nitrophenyl Phosphate (PNPP) Data Card<br> | ||
+ | https://www.neb.com/~/media/Catalog/All-Products/D59C3FAF466C4ED1830E03673FFB1876/Datacards%20or%20Manuals/P0757Datasheet-Lot0071204.pdf | ||
<br> | <br> | ||
Calculating the molar absorbance coefficient from experimental data:<br> | Calculating the molar absorbance coefficient from experimental data:<br> | ||
https://camtools.cam.ac.uk/access/content/group/6041b37a-7fa4-4a47-808b-b20db3a36122/Module%203/Textbook%20pdf_s/3B3printableversion.pdf | https://camtools.cam.ac.uk/access/content/group/6041b37a-7fa4-4a47-808b-b20db3a36122/Module%203/Textbook%20pdf_s/3B3printableversion.pdf | ||
− | |||
== Recommended reading == | == Recommended reading == |
Revision as of 13:53, 17 October 2014
Contents
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.
Team
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?
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)
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
Impressions from Workshop
Project Plan
SATW-DIY 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 Kabel USB 2.0 A -> Mini 5-Pin 30cm Blau P00000527 1 Fr. 1.90 Platinenschalter 12 x 12 X 7 mm mit LED / Blau P00000632 1 Fr. 1.90 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
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 DrBrian
Turbidity Meter
Laser Cut Turbidity Sensor Holder
SATW-Kit turbidity meter
media:SATW_TURBI_kit.pdf File:SATW_bb.pdf breadboard setup <syntaxhighlight lang="c">
/* 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);
} }
</syntaxhighlight>
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
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)
Pilot experiments
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
Recommended reading
can we even make our own DIY Atomic Force Microscope?
http://www.appropedia.org/Open-source_Lab
http://piratepad.net/LinksOnOpenSourceHardware
http://openlabtools.eng.cam.ac.uk/
http://opensource.com/education/14/2/teach-hacking-schools-open-education
http://opensource.com/education/14/9/back-school-open-education-week
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0023783
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