Open Source Technology in the

ClassroomBy Jesse Kasehagen

Santa Barbara Middle SchoolUCSB MRL RET 2, 2012

RET I: Research

The new sensor platform is sensitive, selective, reusable, andrapid. Both the signal-on and signal-off streptavidin sensors respondsensitively to their target, exhibiting detection limits below 1 nM(Figure 3). Neither architecture responds significantly to nontargetedproteins, such as a mixture of IgG antibodies (Figure S2), and botharchitectures support the detection of their targets directly in

complex sample matrices, such as 50% blood serum, 5% (w/v) soilin buffer, and foodstuffs (Figure 3, bottom and Figure S3). Thesensors are also readily regenerable: a short rinse with deionizedwater to disrupt hybridization and remove the recognition strandbefore the addition of fresh recognition strand allows reuse for morethan five cycles (Figure S4). Finally, both sensors equilibrate

Figure 1. Here we demonstrate a novel electrochemical sensing architecture that retains the selectivity and convenience of E-DNA sensors1-10 whileexpanding its range to the detection of macromolecules that bind to specific small molecules. The new architecture utilizes a largely double-stranded DNAas a rigid-but-dynamic scaffold to support a small-molecule recognition element. One strand of the scaffold, the “anchoring strand”, is attached to theelectrode surface at its thiol-modified 5! terminus and labeled with a redox tag (here methylene blue) at its 3! terminus. The second strand, the “recognitionstrand”, is modified either at its 3! terminus or, as shown, its 5! terminus with a small-molecule recognition element. (Left) In the unbound state, the scaffoldsupports efficient electron transfer between the redox label and the electrode. (Center) The binding of the macromolecular target to this recognition elementreduces the transfer efficiency, thus significantly reducing the observed faradaic current. (Right) Shown here are representative square wave voltammogramsof the free and target-bound sensor (for the detection of 30 nM anti-digoxigenin antibody in 50% blood serum).

Figure 2. Sensor response depends on the flexibility of the DNA scaffold.Using a 27 base anchoring strand and 5! placement of the biotin recognitionelement (distal to the electrode), we achieve optimal signaling with arecognition strand of 19 bases (centered on the middle of the anchoringstrand). In contrast, 3! placement of the recognition element produces asharp transition from signal-off behavior at short lengths to signal-onbehavior for recognition strands of 21 or more bases. Double-strandedscaffolds 17 bases in length lacking the small molecule recognition element(Ctrl) do not respond to target. All data represent addition of saturating (50nM) streptavidin target.

Figure 3. Both the signal-on and signal-off streptavidin sensors achievesubnanomolar detection limits and are able to function in complex samples.Shown on the top are titrations of signal-on (23S17B3) and signal-off (19B5)streptavidin sensors in buffer (the biphasic nature of the curves arises dueto the subnanomolar dissociation constant of the streptavidin-biotininteraction). The sensors function comparably in complex samples such asblood serum, soil suspensions, and beer (bottom), yielding similar signalsupon addition of saturating (30 nM) streptavidin target. The error bars inthis and the following figure represent the standard deviations of measure-ments conducted using three separately fabricated electrodes. The signal-on construct has large electrode-to-electrode variability in gain, althoughdetection limits are similar for each individual electrode. (Figure S7 presentstitration data for individual electrodes.)

6956 J. AM. CHEM. SOC. 9 VOL. 131, NO. 20, 2009

C O M M U N I C A T I O N S

Dow

nloa

ded

by U

OF

CALI

FORN

IA S

AN

TA B

ARB

ARA

on

Nov

embe

r 3, 2

009

| http

://pu

bs.a

cs.o

rg

Pub

licat

ion

Dat

e (W

eb):

May

4, 2

009

| doi

: 10.

1021

/ja90

1159

5

3. You donʼt have to be a “rocket scientist” to actually contribute useful data to a research project.

2. Many experiments involve on-the-spot troubleshooting (much like open-source technology does)

1. Laboratory work is difficult, thought provoking and rewarding.

Objective: To build a point-of-care device for a doctorʼs visit

Research Topic: Biosensors

What 3 things did I learn?

RET II: Curriculum Basis

The Arduino

A CNC

Runs any program whether on a computer, as an integrated sensor or...

Built to run as a milling machine, explorative microscopy and autosampling

Why Open Source?Benefits:

1. If you can IMAGINE IT and have the patience, you can modify any program to fit your unique needs2. Usually free and easily downloadable3. Peer-friendly review and sharing capabilities

Cons:

1. You have to have patience because there is virtually no technical support to call!

Tinker but DONʼT give up!

Lesson Ideas

• Introduction to circuits using a variety of sources (e.g. Little Bits and Manylabs software) to learn about them (Lessons #1).

• Build a simple graphite circuit (Lesson #2).

• Using Graphite Potentiometers (Lesson #3).

• Using a CNC machine as a platform for producing gigapixel images (Lesson #4).

• Using a CNC machine as a platform for an autosampler (Lesson #5).

Introducing Electricity and Circuits

ApplicationUnderstanding

Exploration

Electricity is something students are commonly interested in...

Curiosity

Lesson # 1Little Bits Activities

Students will get to:

Learn how circuits work!

Learn how to assemble a simple circuit- with magnets!

Imagine and create!

Place  a  “Y”  for  each  part  “used”  to  complete  the  circuit  in  the  table  below  after  completing  the  task  on  the  computer  for  each  exercise:

Circuit #

Button Knob Light Tilt And Or Not + <30 >30 <50 >50

1

2 y y

3

4

5

6

7

8

9

Example of ManyLabs interactive activity

ManyLabs Activities

Adding a tabulation step

Lesson #2Students get to create a circuit with graphite and then test its voltage or resistance using a voltmeter or LED.

Leads of Voltmeter are closest to source: Reading=6.15V from a 9V battery.

Leads of Voltmeter are farthest from source: Reading - 167.9mV from a 9V battery.

Hook an LED to resistive layer (graphite) and see what happens...

Building A Graphite Circuit

Lesson #3: Using A Graphite Potentiometer

2 different arduino setups: A) computer using ManyLabs B) simple LED readout without using a computer

Students get to: Perform an experiment to deterine the relationship between conductivity and amount of light perceived through sheets of graphite paint with different dilutions.

Sample ManyLabs Activity: Exploring Graphite Potentiometers

Lesson #3 ManyLabs Results:

Potentiometer measuring conductivity with of a 5V source with input values of 0-5. A higher number means less resistance. Light values of 0-780 were arbitrarily established by program. A higher number means more light detected. This graph shows a best fit line for 3 different thicknesses of shades run through the Sensor Plotting Program using ManyLabs Software. This is an inverse-relationship where the thicker the layer, the more conductive it is but less light penetration; the thinner the layer, the less conductive it is, and more light penetrates.

Sensor Undiluted 1:2 1:3

Conductivity 4.01 3.98 3.52

Light 80 92 110

!"!#$"%"

%#$"&"

&#$"'"

'#$"("

(#$"

!" &!" (!" )!" *!" %!!" %&!"

!"#$

%&'()*+,!-.

#/+0123!

4*15+!.0/&2!!

"#$%&'()*+,!)676!4*15+!!

+,-.,/%"

0.1,2-3+,-.,/%4"

LED POT Readout Test

1:4

Ratio= paint:water

1:2

Undiluted

Lesson #4: Explorable Microscopy!

Explore great details in photographs of fossils, leaves, and cells.

How does it work?1. Focus Stacking: A process taking multiple photos at different focal distances to give a higher depth of field (DOF) than a single photo.

2. Image Mosaicing: “quadrant”-grouping of lots of photos with ~30% overlap that allows stitching together of all photos in a seamless high resolution image.

Students get to...

Lesson #5: Autosampler

Students get to : Learn data collection with a complex setup with arduinos running a sensor and CNC to computer for logging data.

Testing #1

Thank you to:Frank Kinnaman - RET Program Coordinator

Adriana Patterson - Research Mentor Peter Sand - ManyLabs and Sensors

Edward Ford - ShapeokoZach Kaplan - Inventables

Professor Kevin Plaxco and Research GroupAki Stankoski - Programmer Extroardinaire

Dotti Pak, Julie Standish and Mary Guan - MRLUCSB and the National Science Foundation

Resource Page

http://www.arduino.cc/

https://www.inventables.com/technologies/cnc-mill-kits-shapeoko

http://www.google.com/imgres?q=researching+electricity&start=204&hl=en&client=safari&sa=X&rls=en&biw=1417&bih=764&tbm=isch&prmd=imvns&tbnid=Q-RQTNB8L6jtfM:&imgrefurl=http://www.darkgovernment.com/news/army-researching-lightning-as-a-weapon/&docid=c3juj8X64zu6NM&imgurl=http://www.darkgovernment.com/news/wp-content/uploads/2012/06/lightning.jpg&w=288&h=252&ei=rykHUP-cJ-jo2gWLibgB&zoom=1&iact=hc&vpx=983&vpy=337&dur=28&hovh=201&hovw=230&tx=117&ty=99&sig=103048663153388835097&page=7&tbnh=139&tbnw=159&ndsp=34&ved=1t:429,r:12,s:204,i:154 (lightning pic)

http://www.google.com/imgres?q=van+de+graaff+generator&start=236&hl=en&client=safari&sa=X&rls=en&biw=1417&bih=764&addh=36&tbm=isch&prmd=imvns&tbnid=B3CsglbWehiGPM:&imgrefurl=http://www.visualphotos.com/image/1x8464929/girl_with_van_de_graaf_generator&docid=MFAbRw4vROxg1M&imgurl=http://www.visualphotos.com/photo/1x8464929/Girl_with_Van_de_Graaf_Generator_2F8928.jpg&w=429&h=670&ei=h1IHULWVPM6A2QWmlMzdBA&zoom=1&iact=hc&vpx=923&vpy=360&dur=1008&hovh=281&hovw=180&tx=104&ty=135&sig=103048663153388835097&page=7&tbnh=138&tbnw=96&ndsp=35&ved=1t:429,r:32,s:236,i:226 (Van de graff pic)

http://www.google.com/imgres?q=little+bits+electronics&hl=en&client=safari&sa=X&rls=en&biw=1417&bih=764&tbm=isch&prmd=imvns&tbnid=_MANPI2s8aKM8M:&imgrefurl=https://community.littlebits.cc/projects/the-beautiful-game&docid=VAhWkX1atGPKoM&imgurl=https://littlebits-production.s3.amazonaws.com/uploads/image/asset/127/large_IMG_2450.JPG&w=600&h=400&ei=TIsHUJaVBInE2gXbsci2BA&zoom=1&iact=hc&vpx=731&vpy=259&dur=5746&hovh=183&hovw=275&tx=138&ty=89&sig=103048663153388835097&page=3&tbnh=140&tbnw=212&start=50&ndsp=30&ved=1t:429,r:27,s:50,i:333 (Fooseball table)

http://www.google.com/imgres?q=little+bits+electronics&hl=en&client=safari&sa=X&rls=en&biw=1417&bih=764&tbm=isch&prmd=imvns&tbnid=LUL9LE_-53x57M:&imgrefurl=http://littlebits.cc/&docid=Bk5HqYVo4iEnrM&imgurl=http://littlebits.cc/wp-content/uploads/2012/01/servo.jpg&w=600&h=400&ei=TIsHUJaVBInE2gXbsci2BA&zoom=1&iact=hc&vpx=1126&vpy=426&dur=613&hovh=168&hovw=254&tx=151&ty=98&sig=103048663153388835097&page=1&tbnh=150&tbnw=228&start=0&ndsp=18&ved=1t:429,r:11,s:0,i:116 (Little bits fan circuit)

https://community.littlebits.cc/projects/mini-hammer-game (mini hammer game)

http://www.google.com/search?q=basic+electricity+and+circuits&hl=en&client=safari&rls=en&prmd=imvns&source=lnms&tbm=isch&sa=X&ei=7pMHUIOvCoOY2AWckq3sBA&ved=0CEcQ_AUoAQ&biw=1417&bih=764 (Circuit Diagram)

http://arduino.cc/en/Main/ArduinoBoardUno

http://en.wikipedia.org/wiki/Potentiometer_(measuring_instrument)

http://www.novatech-usa.com/s.nl/it.A/id.202/.f?sc=8&category=47 (can measure salt content of substances)

http://www.indianjournals.com/ijor.aspx?target=ijor:jre&volume=39&issue=4&article=012

http://www.hyfoma.com/en/content/processing-technology/instrumentation/level-switch/conductive/

http://www.instructables.com/id/Make-a-Pencils-Lead-Potentiometer-Experimentatio/

http://en.wikipedia.org/wiki/Potentiometer

http://www.mrl.ucsb.edu/mrl/outreach/educational/workshops/resources/graphite_potentiometer.pdf

http://vimeo.com/10943815

http://www.encyclo.co.uk/define/graphite%20potentiometer

http://www.youtube.com/watch?v=aElHVTv-75M

http://nasdonline.org/document/1891/d001824/electrical-safety-on-the-farm.html (HUMAN HEART)

Extensions:Extensions for Lesson #3

1." If you have some time, you could have students research and test different (nontoxic) spreadable materials that are conductive and they have at home (i.e., ketchup, mayonnaise, different types of mustards)- something ideally with high salt content- and set up the same lab as above to see which substance has the greatest [salt].

2." You could have students measure thickness (density?) of different conductive fabrics by establishing the same method as the procedure for graphite paint squares.

3. Measure the change in conductivity by sliding the sensor clip from one side (ground) to the other side (5V) to better understand what a potentiometer is.

Scope & Sequence?

Standards Addressed6th Grade:

7. Scientific progress is made by asking meaningful questions and conducting careful investigations. As a basis for understanding this concept and addressing the content in the other three strands, students should develop their own questions and perform investigations. Students will:

a. Develop a hypothesis.

1. b.  Select and use appropriate tools and technology (including calculators, comput­ ers, balances, spring scales, microscopes, and binoculars) to perform tests, collect data, and display data.

2. c.  Constructappropriategraphsfromdataanddevelopqualitativestatements about the relationships between variables.

3. d.  Communicate the steps and results from an investigation in written reports and oral presentations.

e. Recognize whether evidence is consistent with a proposed explanation.

7th Grade:Structure and Function in Living Systems

5. The anatomy and physiology of plants and animals illustrate the complementary nature of structure and function. As a basis for understanding this concept:

1. a.  Students know plants and animals have levels of organization for structure and function, including cells, tissues, organs, organ systems, and the whole organism.

6. Physical principles underlie biological structures and functions. As a basis for un­ derstanding this concept:

2. b.  Students know that for an object to be seen, light emitted by or scattered from it must be detected by the eye.

3. c.  Students know light travels in straight lines if the medium it travels through does not change.

4. f.  Students know light can be reflected, refracted, transmitted, and absorbed by matter.

7. Scientific progress is made by asking meaningful questions and conducting careful investigations. As a basis for understanding this concept and addressing the content in the other three strands, students should develop their own questions and perform investigations. Students will:

1. a.  Select and use appropriate tools and technology (including calculators, comput­ ers, balances, spring scales, microscopes, and binoculars) to perform tests, collect data, and display data.

2. b.  Use a variety of print and electronic resources (including the World Wide Web) to collect information and evidence as part of a research project.

3. c.  Communicatethelogicalconnectionamonghypotheses,scienceconcepts,tests conducted, data collected, and conclusions drawn from the scientific evidence.

4. d.  Construct scale models, maps, and appropriately labeled diagrams to communi­ cate scientific knowledge (e.g., motion of Earthʼs plates and cell structure).

5. e.  Communicate the steps and results from an investigation in written reports and oral presentations.

9th-12th Grade:

5. Electric and magnetic phenomena are related and have many practical applications. As a basis for understanding this concept:

a. Students know how to predict the voltage or current in simple direct current (DC) electric circuits constructed from batteries, wires, resistors, and capacitors.

b. Students know how to solve problems involving Ohmʼs law.

c. Students know any resistive element in a DC circuit dissipates energy, which heats the resistor. Students can calculate the power (rate of energy dissipation) in any resistive circuit element by using the formula Power = IR (potential difference) × I (current) = I2R.

1. d.  Students know the properties of transistors and the role of transistors in electric circuits.

7. Each element on Earth moves among reservoirs, which exist in the solid earth, in oceans, in the atmosphere, and within and among organisms as part of biogeochemi­ cal cycles. As a basis for understanding this concept:

Cal5ifo0rnia Department of Education Reposted June 11, 2009

1. a.  Students know the carbon cycle of photosynthesis and respiration and the nitro­ gen cycle.

2. b.  Students know the global carbon cycle: the different physical and chemical forms of carbon in the atmosphere, oceans, biomass, fossil fuels, and the movement of carbon among these reservoirs.

3. c.  Students know the movement of matter among reservoirs is driven by Earthʼs internal and external sources of energy.

d.* Students know the relative residence times and flow characteristics of carbon in and out of its different reservoirs.

1. Scientific progress is made by asking meaningful questions and conducting careful investigations. As a basis for understanding this concept and addressing the content in the other four strands, students should develop their own questions and perform investigations. Students will:

a. Select and use appropriate tools and technology (such as computer-linked probes, spreadsheets, and graphing calculators) to perform tests, collect data, analyze relationships, and display data.

b. Identify and communicate sources of unavoidable experimental error.

c. Identify possible reasons for inconsistent results, such as sources of error or uncontrolled conditions.

d. Formulate explanations by using logic and evidence.

e. Solve scientific problems by using quadratic equations and simple trigonometric, exponential, and logarithmic functions.

f. Distinguish between hypothesis and theory as scientific terms.

g. Recognize the usefulness and limitations of models and theories as scientific representations of reality.

d. Recognize the issues of statistical variability and the need for controlled tests.

e. Recognize the cumulative nature of scientific evidence.

l. Analyze situations and solve problems that require combining and applying concepts from more than one area of science.

m. Investigate a science-based societal issue by researching the literature, analyzing data, and communicating the findings. Examples of issues include irradiation of food, cloning of animals by somatic cell nuclear transfer, choice of energy sources, and land and water use decisions in California.

n. Know that when an observation does not agree with an accepted scientific theory, the observation is sometimes mistaken or fraudulent (e.g., the Piltdown Man fossil or unidentified flying objects) and that the theory is sometimes wrong (e.g., the Ptolemaic model of the movement of the Sun, Moon, and planets).

8th Grade:9. Scientific progress is made by asking meaningful questions and conducting careful investigations. As a basis for understanding this concept and addressing the content in the other three strands, students should develop their own questions and perform investigations. Students will:

a. Plan and conduct a scientific investigation to test a hypothesis.

b. Evaluate the accuracy and reproducibility of data.

c. Distinguish between variable and controlled parameters in a test.

d. Recognize the slope of the linear graph as the constant in the relationship y=kx and apply this principle in interpreting graphs constructed from data.

GRADE EIGHT