Week 5

Updates on my two projects.


Sensor project:

This last week was incredibly productive! So the grad student I am working with, developed an arduino code based off of some code that was already accessible online. However with his good understanding of code writing, he altered and added various functions to the code that made it work specifically for our project.  I did't really contribute much in this part of the project, as the programming was over my head. However, once completed, the grad student explained to me how the code worked as a whole and how each line of the code functioned.

Essentially, all the code does is take the amount of breaths taken in 5 seconds and multiplies that           number by 12 giving amount of breaths per minute (as there are 60 seconds in a minute). So every 5 seconds a new breath rate is spit out. Another part of the code is that the last 5 breath rate readings are always averaged. so every 5 seconds an immediate breath rate as well as an average of the last 25 seconds is given. As of right now this information is just fed into a computer but the goal is to get his information on a tiny screen and then stored on a memory chip. 

Following, we constructed a board on which the circuit, a 9V battery, the arduino and the piezo (breath rate sensor) are attached (later the screen and the memory chip will also be added.) We took this setup along with some wires, cables,  and a wave detector, and tested in a real experiment. * And guess what........ It worked essentially FLAWLESSLY.

We put the piezo underneath a anesthetized rat. The rate had a steady breath rate of 48 (and we knew this how? our code and circuit!) and when the rat would be given a slightly higher dose of the drug the heart rate would increase, again seen through out setup. IT was truly incredible to see our project work so well.

So the goal for this week is to assemble a screen and integrate it along with a memory chip into our setup and code. Once that's done we are incredibly close to the final product.

* As this experiment felt with animals, I wasn't able to actively do anything. I primarily, stood back and watched the experiment take its course, all the while enjoying our product. :D


Electrode project:

This project isn't quite as productive as the other one. This one, to me, is also more difficult. So this Wednesday I am meeting someone in the electron microscopy lab again. This time I am bringing the coated electrodes, though to actually see if the coating has stuck to the platinum electrodes. I am having a hard time coating them, tomorrow however I will receive help form another grad student so hopefully I'll have the electrodes in time.



***As my grad student and I have made far more advancements on the breath rate sensor project, I will be primarily focusing on that project in my presentation at the end of the school year, but I will dedicate a fair amount of time to the other one as well. Just in case you were interested. ***

Weeks 3 and 4

Hello!

I am so sorry for not having posted as frequently these last few weeks. However, this is due to the fact that there have been some setbacks:

In research, many instruments are incredibly expensive so labs tend to share some of these instruments. The potentiostat, an instrument that is integral to my experiments, is a good example. Because it is so expensive, the lab I am working in and another lab in the building are sharing it.  This other lab has been using the instrument quite frequently these last 2 weeks, creating some difficulties for the advancement on the coating of platinum electrodes project.

This week however, we will receive the potentiostat again, and I will be able to finally coat the electrodes. Then, on Tuesday or Wednesday I will take these electrodes to an electron microscopy lab in the Chemical Sciences Building and have some scans taken to double check that the electrodes are actually coated.

In addition, either this week or next week I will be able to watch an experiment in which a mouse brain is exposed and some carbon fiber electrodes are inserted. (This isn't directly part of my project, however I think it would be cool to see this happen.)

Over the last two weeks however, Drew and I have made great progress on our sensor project. Here's an update:

• In the last two weeks we have been working on building a circuit (using resistors, capacitors, diodes, wires, etc.) where we tap a sensor and then we can see a spike in a signal on the screen of a signal detector.  All in all we worked about 20 hours just to build a circuit that works properly. Our next goal is to write an arduino code that can read a signal output from the piezo (the sensor) and can store the information. Our goal is to make this completely independent from a big computer. This project will take much longer than the length of my SRP, yet I am thrilled to be a part of its beginning.

      **** I would like to post a picture but the grad student I'm working with said I should't until                                                   

               we've finished. 

In summary:

For the sensor project: The goal for the rest of the project is to get this sensor up and running with just an arduino and no computer. 

For the electrode project: I must coast some electrodes, have someone run electron microscopy on them, and if it is revealed that they really are coated, hopefully in a few weeks these electrodes can be inserted in a mouse/rat brain for testing.  

**** This may not occur until after my SRP because it could become a lengthy process.  

Week 2

Hello Again!

Last week was incredibly exiting! Here's an update on my two projects!

1. Update on my Arduino Project: 

Last week was the first week that I was really able to get my hands dirty with the Arduino. Once I installed all the necessary software, I pulled up a website that had various tutorials and mini projects that were intended for beginners to understand the basics of circuits and programming. One mini project I did, for example, was turning an LED light on an off by pressing a button. Although a simple project like this has no real application to the one I intend on pursuing, it allows me to understand the fundamentals and the basics of how Arduinos work and how they are programmed.

Here are two pictures: 

On the left you can see a project I did, in which you would press a button and the corresponding LED light (red, yellow, or green) would get brighter every time you pressed the button. After 4 presses, however, the LED light goes back to dim.  

On the right are the parts I'm going to use in my project. In the middle you can see the Arduino (greenish-blueish colored thing). To the left of it are some wires, above and below some resistors and capacitors, and in the top right, a USB cable that plugs from your Arduino to the computer. 

     2.  Update on my Polymer Coating Project:

Last week on Tuesday, Richard, the graduate student that I'm working with, discovered that a chemical engineer and biomedical engineer at Cornell University already managed to coat Platinum with this PEDOT:Nafion composite polymer. Although I though that this was going to be a major set back, turns out that this allows us to use these platinum coated electrodes to do more interesting experiments. The professors at Cornell coated platinumm electrodes, however, they didn't put them to use and we are going to attempt to do that. 

On Wednesday, I, with the help of Richard, repeated the experiment outlined in the paper, step by step. First, after multiple stoicheometry calculations, I created a .01 M solution of EDOT. I then placed all my electrodes in the solution and ran a current through the electrodes. Around 200 seconds after the initial current was applied we looked at the chronopotentiometric curves ( Potential/V vs Time) they got and they aligned incredibly well with ours. 

Although this was just a repeat of someone else experiment, it was exiting to know that we could coat platinum and that we can move on to further experiments. 

In the next few weeks I will coat the platinum electrodes and then we will perform some further experiments and then put them to the test. I can't wait to see what we'll see.

See you soon!

P.S. I got my own lab notebook this week, and I won't lie, I feel pretty special. 

Week 1

Greetings!

Although this post is a little late, I have much to report. Last week was my first official week, and although I'm only beginning to delve into my projects I have already learned so much.

I am working on two projects, however the polymer synthesis project is the bigger project and I will dedicate this post solely to this project. At the end of this week however I will report on this weeks progress on both projects.

Composite polymer coating for electrodes:

       In the past few months and years, Dr. Heien's lab has been developing a polymer composite known as PEDOT:Nafion for the coating of carbon-fiber electrodes. This composite polymer is created like this. Acetonitrile (ACN), 3,4-Ethylenedioxythiophene (a monomer abbreviated as EDOT), and Nafion are combined in solution in very specific concentrations. The carbon fiber electrode, a chlorodized silver wire (the reference electrode) and a tightly coiled silver wire (the counter electrode) are then all lowered into the solution already created. Each of the the three electrodes are then hooked up to a potentiostat which applies a triangle wave form (1.5 V to -.8 V) for 15 seconds. This voltage causes the EDOT monomers around the electrode to form the polymer PEDOT. In addition under the correct voltage the PEDOT polymer also bonds to Nafion in the solution, forming the PEDOT:Nafion composite polymer (Figure 1). This composite Polymer then settles onto the carbon fiber electrode forming a uniform coat about 100 nm thick (Figure 2). 

      

Figure 1: EDOT (the monomer) is seen in the top left corner.
PEDOT:Nafion (the composite polymer) can be seen on the right side

       Why is it important that the electrodes are coated with the this PEDOT:Nafion composite polymer? This extra coating on the electrode has three purposes...

1. It makes the electrode more sensitive to Dopamine 
2. It increases the selectivity of the electrode for Dopamine (Figure 2)
3. It reduces the amount of biomaterial amassing on the electrode ( eg. bloodclots, etc.) (Figure 3) 

These three effects that the coating has makes neurotransmitter detection and uptake by an electrode much more accurate. 

Figure 2:
On the left is a picture showing the increase in Dopamine selectivity
On the right is an electron microscopy scan revealing the uniform coating
on the end of an electrode

Figure 3:
Left: Uncoated electrode left in brain
for 30 minutes (Lots of biomass present)
Right: Coated electrode left in brain
for 6 hours (Less biomass present)

Furthering this Research:

In my project I am particularly interested in the last purpose the composite polymer fulfills: it reduces the amount of "gunk" that attaches to the electrode when in the brain. I am interested in this because in Deep Brian Stimulation surgeries electrodes made of platinum are used to send electrical signals to affected parts of the brain. Since this electrode is in the brain for some time, biomaterial will naturally attach to it. Therefore, it would be useful to create a polymer that could coat the platinum electrodes as well. To do this however, I will change the concentration of ACN, EDOT, and Nafion, and I will also have to apply a different voltage range to it.

Last Wednesday, under the supervision of a graduate student I repeated the carbon-fiber electrode coating experiment to become familiar with how the process goes. I pipetted out the correct volumes of the 3 compounds in the solution and combined them in a 20mL vile. I then took the 20mL vile to the potentiostat, hooked up the Counter Electrode, the carbon-fiber Electrode, and the Reference Electrode, and ran the triangle wave form through the electrodes, allowing the reaction to take place around the electrode. This week, I'm taking things a step further and I am going to begin trying to coat the platinum electrodes.

After last week, I have a good grasp on the previous experiments that were conducted and now I have the necessary to knowledge to begin my actual project.

More coming on this project and my other one this weekend!

Thanks for reading!

Gil Wondrak


Sources: I learned most of this information from this article and the people who wrote it.

Michael Heien. "Biocompatible PEDOT:Nafion Composite Electrode Coatings for Selective Detection of Neurotransmitters in Vivo" Analytical Chemistry. Web. 24 February 2015. 

Where am I working?

I have the privilege to work in Dr. Heien's lab which is located in the Department of Chemistry at the University of Arizona.

Dr. Heien's lab is a Neuroanalytical Chemistry lab. Throughout the lab are microscopes, solutions, and wires going all over the place.

This lab is has two aspects or sub components that are intertwined :

1. The Chemical Aspect: There are multiple microscopes throughout to analyze samples and conduct experiments.
2. The Electrical Aspect: The lab has several stations with screw drivers and other tools to build electrical circuits that are used throughout the lab.

Here is a picture of the lab:

Introduction and Background

Hello! My name is Gil Wondrak and I am currently a senior at BASIS Tucson North. At the beginning of the 2014-2015 school year, we seniors we were offered the unique opportunity to pursue an internship, known as an SRP, or Senior Research Project at BASIS, in the last trimester of this school year (February-May). The Purpose of the SRP is to get our hands dirty and receive first hand experience in areas of study or research that interests us or that we intend to pursue as a career later in life.

For my SRP, I will be working approximately 24 hours a week in a lab in the Department of Chemistry at the University of Arizona. My main supervisor/advisor in the lab is Dr. Heien, however I will also be performing experiments and conducting projects under the direct supervision of one of his graduate students.

My Project will be split up into two separate smaller ones....

1. In my first project I will be developing polymer electrodes in the detection of various neurotransmitters (such as dopamine, etc.). I will be making these polymer electrodes from PEDOT (poly-ethylenedioxythiophene). The goal of of research in this area is to develop polymer coatings that detect neurotransmitters for not only carbon fiber electrodes, but for  electrodes of other materials as well. 
2. In my second Project I will be attempting to make a Raspberry Pi (essentially a mini computer) into a portable lab. In other words, my goal will be to program this mini computer into a machine that could run an experiment without using much equipment. 

I look forward to this incredible project and opportunity that lies ahead of me. Feel free to leave any comments or questions on my future posts, and I will happily answer them!