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Project Description

Drug Abuse Research at Chavkin Lab

Student Name
Mackenzie Andrews

Experiential Learning Category

Research

Associated UW Course (if applicable)

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Summarize your proposed experiential learning activity, including the primary focus of your activity, your intended actions, and
the expectations of your supervisor and/or organization/partners.

My primary focus will be on learning/utilizing the lab's current optogenetic tools to examine how optogenetic
stimulation/inhibition both with and without stress a ects reward processing in di erent areas of the brain. In
order to do this, I will also be processing tissue for veri cation of expression.
The techniques I will be learning to complete this research are brain perfusions ( xing cells), brain slicing,
immunochemistry (introduction of a labeled antibody for marking/visualization), and microscopy/imaging of
mounted tissue.
Other tasks will include keeping up on animal care and using MATLAB/Excel for data processing.
My supervisor will help train me in the aforementioned techniques as well as help to guide my research.

Explain how your activity demonstrates the values of the Honors Program Experiential Learning area you selected. Rather than
reiterating our definition, outline how your activity embodies this definition.
I will be helping to extend the current research that has been done in the Chavkin lab through a guided
independent project. I will be assisting my supervisor with his current research as well as learning the techniques
required to take on my own independent project. With the help of my supervisor, I have outlined my
project/research goals for the summer and identi ed the limitations and barriers that I will need to cross in order
to be successful in completing the planned project.
I am planning to take an active role in the iterative process of identifying an area of discovery, designing a project,
conducting the research, processing the results, and evaluating further areas of discovery based on the results
from the previous experiment.

How and why did you select this engagement? What skills or experiences do you hope to gain from it?
I selected this engagement because I am in the bioengineering major and will be developing a research project for
my capstone. I intend to remain in the Chavkin lab through the entirety of my undergraduate career. The project I
am working on this summer will provide preliminary data for the design of my capstone project. By identifying

how di erent reward circuits in the brain respond to stress, I will get a better idea of which areas of the brain to
focus my following research on.
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Apart from my capstone project, I hope to gain general experience in the research process and how to work in a
lab environment. I will also be learning many new techniques that I will be able to apply to future research.

How does this activity connect to your concurrent or past coursework? How does it speak to your broader education goals and
experiences?
As mentioned above, I am in the bioengineering program and plan to use this research as preliminary work for
my research design capstone project. I am using the general knowledge learned in the introductory chemistry,
biology, physics, and organic chemistry series. My bioengineering coursework during this past fall quarter has
taught me the background to many of the methods I will be learning this summer. In BIOEN 315: Biochemical
Molecular Engineering, I learned the chemistry behind tissue perfusions, protein design, and antibody delivery. In
BIOEN 316: Biomedical Signals and Sensors, I learned the tools for signal acquisition, data processing, and
imaging.

How will your activity contribute to the larger goals of the organization/your partners?
The Chavkin lab is focused on drug abuse research. Encompassed in that eld is research in reward processing
and stress e ects. My research this summer will help to further understand how the reward circuits in the brain
respond to stress. I will be both qualifying and quantifying the extent of expression of signalling molecules
involved in reward circuitry. Knowledge of the signalling pathways involved in addiction will help to ultimately
develop a treatment for drug dependence.
This research is aimed to provide the preliminary data needed to develop improved in vivo methods of recording
the activity of neurons. Such methods have the potential to aid all in vivo neuro research in better understanding
how neurons communicate.

Estimated hours per week: 15

Estimated project start: 06/20/2016

Estimated project end: 08/19/2016

May we share excerpts from your application and final reflection to use as examples?

Yes

Supervisor
First name Antony
Last name Abraham
Title/A liation Post-doc
Organization
(if applicable) Charles Chavkin Lab
UW NetID (if
applicable) abrahama
Email abrahama@uw.edu

Final Reflection
Project Title
Drug Abuse Research at Chavkin Lab

Reflection
As is the case with most pursuits in upper academia, this summer took a di erent course as originally planned. At
the beginning of the quarter, Antony and I discussed ideas for potential projects for summer term as well as my
continuing research education. The rst project was focused on learning and utilizing the lab's current
optogenetic tools to examine how optogenetic stimulation and inhibition both with and without stress a ects
reward processing in di erent regions of the brain. In order to do this, I would also be processing brain tissue for
veri cation of viral expression. The techniques I would be learning for that project would be brain perfusions
( xing cells), brain slicing, immunochemistry (introduction of a labeled antibody for marking/visualization), and
microscopy/imaging of mounted tissue.
The other project discussed was processing the data generated by the di erential reinforcement of low rate of
responding (DRL) task that Antony had been running. The aim was to develop speci c questions about the data
from the DRL task and answer those questions through the utilization of MATLAB (Matrix Laboratory, a fourth-
generation programming language and multi-paradigm numerical computing environment).
Originally we put more thought into the optogenetics project, as it would lend itself more strongly to my
Bioengineering Capstone project. However, since my capstone was still two years down the line, we decided to
focus on the second project as I already had the programming knowledge necessary to start the task and there
was a high level of need for a time e cient way to answer the questions being asked for the DRL paper. While the
focus was aimed toward the second project, I also had a goal of learning some of the techniques required for
moving forward with the optogenetics experiment in coming quarters.
The DRL system generates a large amount of data per animal, per run. The times of every reinforced nose poke,
reset response, head entry, inactive nose poke, and the interresponse time between each nose poke are
recorded. A given run can generate between 500 and 3000 pieces of data per animal. With approximately 7 runs
per day, with 8 animals per run, over the course of 30 test days, there was approximately 1 million raw data
points generated.
In order to process that data, I wrote a program that could take the .txt le containing all of the data for a single
run (typically 8 animals) and pull out the times of each of the 5 recorded categories as numerical values and
organize them into a matrix format. These matrices were then either copied into a spreadsheet or were utilized
for further calculations to answer the other research questions posed.
Every batch of animals generated slightly di erent speci cations for the data processing program based on the
speci c genotype string header, number of cages per genotype, number of animals ran, and total number of test
days. I wrote a total of 8 programs for the 8 di erent cohorts of animals ran (wild type cohort 3, CKO cohort 1,
GRK3 cohort 1, GRK3 cohort 2, DKT cohort 2, regional nor-BNI cohort 2, female animals, and a nal program to
handle additional data batches). While each program has it's own speci cations, every program shares the same
4 processing methods: le read-in/data location, data matrix storage, totals/percent error computation, and burst
analysis.
Throughout the summer, I was writing programs and processing data as it was generated. Since no one else in my
lab had knowledge of MATLAB or programming in general, my contribution was extremely important for the
completion of the DRL paper. Aside from the contribution to the lab and their goals of publishing the paper, my
project also helped to further my education in a number of areas. First and foremost, the ability to program and
work with MATLAB is becoming more and more important in the engineering world. All of my engineering classes
utilize MATLAB to analyze information and solve speci c problems. Through my programming this summer, I
learned much more about the MATLAB interface and became more familiar and con dent in my coding abilities.
In addition to the aplication to my engineering major, this project also gave me more insight into how to ask and
answer speci c research questions. Part of the project was developing interesting ways to look at and ask
questions about the vast amount of data generated. Working with Antony, we developed a set of research
questions that could be asked about the data, then I developed the best way to answer the questions in an
e cient and usable format.
Finally, as a nice conclusion to my summer project, we were able to nish writing the paper. The paper is currently
in the review process for publication. Due to my contribution, I am listed as an author on the paper. Being
published is an extremely exciting step in my academic career as future employers and graduate schools will take

research ownership into high consideration when reviewing my future applications for acceptance.
In addition to the data processing for the DRL experiment, I had an aim of learning some of the techniques
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required for moving ahead with some of the optogenetic and immunochemistry experiments for future quarters.
I learned a number of procedural techniques such as brain slicing, slice mounting, microscopy and imaging, and
cresyl violet staining. I also observed some additional procedures that I will be learning such as brain perfusions,
optical stimulation during behavioral tests, forced swim stress, tail ick, and electrophysiology.
While learning and observing these procedures, I picked up a number of applicable skills. I learned more about
physical brain anatomy such as how to recognize di erent brain "landmarks" during slicing and identifying
speci c brain regions such as the prefrontal cortex (PFC), ventral tegmental area (VTA), and the dorsal raphe
nucleus (DRN). All of these additional skills will lend themselves to my Bioengineering Capstone project and my
course material in neurobiology.
I am excited to continue my work with the Chavkin lab. Moving forward, I will be adding to my repertoire of lab
techniques to help build a foundation for starting my Capstone project and neurobiology honors thesis. One of
the overarching lessons that I learned this summer is the need to be exible and creative while doing work in
research. I will be applying that lesson to my future work as well as my other upper academic endeavors.

Submitted on
Sep 18, 2016

Final Evaluation

Response
Completed

Submitted on
Oct 17, 2016

Comments

Mackenzie has been a great addition to the lab and is continuing to work with us. Mackenzie is dedicated to her
work, and interested in a broad array of topics that will provide her with a strong training in science and
engineering during her undergraduate career. She is independent, thoughtful, and can rapidly learn any task that
she is given. I am happy to keep working with Mackenzie as she begins to generate her independent thesis
project.

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