GERO315 Sp2021 lab manual PDF

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GERO-315 Lab Manual Spring 2021

Table of Contents Introduction…………………………………………………………………………………………………………1 Rubric…………………………………………………………………………………………………………………..1 Lab Schedule………………………………………………………………………………………………………..2 Lab 1 – Averages and Standard Deviation….…………………………………………………………3 Lab 2 – Scientific Method and Epidemiology.……………………………………….………………5 Lab 3 – Modeling Ion Movement………………………………………………………………………….7 Lab 4 – HHMI Lab……….………………………………………………………………………………………10 Lab 5 – Cerebellum Lab………….………………………….……………………………………………….14 Lab 6 – Vision and Hearing Lab………………………………………….……………………………….17 Lab 7 – Test My Brain……………………….……….………………………………………………….…….20 Lab 8 – Music and the Brain………………………………………………………………………………..22

Introduction and Rubric Main contacts for lab: Timothy Lu, [email protected] and Maria Ashna, [email protected] Welcome to GERO-315! This lab is designed to teach you the fundamentals of data analysis, how to perform a scientific study, and how to report your findings in paper format. Your training applies to science, but also to any career involving data (like marketing and business)! The labs will also teach you about neuroscience and using neuroscience as a tool to understand data analysis. We will be grading you based on a rubric. The rubric will act as your guide for the components necessary to obtain a good grade but remember that quality work is necessary to receive full credit! We will leave comments on each paper that will help you improve throughout the semester. This manual contains instructions for all the labs. Each lab will be worth 10 points. There will be 8 labs throughout the semester. Each lab will be approximately 3 pages long, with some variation depending on the lab. You will also need to cite your work (not included in page count). The page requirements are as follows: -

1.5-2 pages of written text Separate page for graphics

Papers must be 12 pt font, a standard font (such as Arial, Times, or Calibri), with standard 1” margins. The papers are to be single spaced. Also, .PDF or .DOCX only! No .pages files, they will *not* be graded and you will receive a zero. Your paper will have 4 major sections which are briefly described below. Introduction introduces the lab and your hypothesis. Give pertinent background information as needed that explains what you are doing. Methods talk about what you did for the lab to collect data or information. Results talk about the data you collected without analyzing it. Discussion will analyze the data in your results. The discussion section will also be where you talk about how to improve your research and why this type of study matters. If there are exceptions to this, we will make sure that it is stated in that lab’s instructions. Most of your labs will require outside sources that you must cite using the APA style! Please cite using in-line citations (author, year). You will need 2 outside sources. We’ll usually provide one source. Labs must be submitted by 11:59pm on the due date through TurnItIn. You will lose 1 point per day it is late. Anything submitted after a week will receive a 0. Plagiarism detected by TurnitIn will be punished with a 0. Points Breakdown for Labs: 2 points for reaching page limit for written 1 point for having graphics (properly formatted) 1 point per section (intro, methods, results, discussion), 4 points total 1 points for having 2 sources 2 points for having proper formatting, looking professional, no typos, etc; TOTAL POINTS: 10

If there are clear exceptions to this rubric, we will let you know within the lab instructions. What follows is the lab schedule. This is subject to change as midterm dates are finalized and based on lab timing. We will let you know in class and via announcement of these changes. Otherwise, due dates are here and on Blackboard! Schedule First Day of Class/Intro to Labs Lab 1 Intro

Week 1

20-Jan

2

25-Jan

2 3

27-Jan Lab 1 Due/Lab 2 intro 1-Feb Lab 2 Q & A session

3

3-Feb Lab 2 Due/Lab 3 intro

4 4

8-Feb Lab 3 Q & A session Lab 3 Due 10-Feb Lab 4 Intro

5

15-Feb

President’s Day

5

17-Feb

Lab 4 Q&A Session

6

22-Feb

Lab 4 Due/Lab 5 Intro

6

24-Feb

Lab 5 Q&A

7 7

1-Mar 3-Mar

MT 1 review (tentative) MT 1 (tentative)

8

8-Mar

Lab 5 Due

8 9

10-Mar 15-Mar

Lab 6 Intro No Lab

9

17-Mar

Lab 6 Due

10

22-Mar

Lab 7 Intro

10

24-Mar

Lab 7 Q&A

11

29-Mar

Lab 7 Due

11 12

31-Mar 5-Apr

Lab 8 Intro Lab 8 Q&A Session

12

7-Apr

13

12-Apr

Lab 8 Due

13

14-Apr

MT 2 (tentative)

14

19-Apr

TBD

14

21-Apr

TBD

15 15

26-Apr 28-Apr

TBD Last Day of Class

Wellness Day

Lab 1 – Averages and Standard Deviation In Science, we use “statistics” in order to analyze the data we collect. Statistics is basically the usage of math to look at data we’ve collected and see how it compares to a hypothesis. There are a lot of these equations but for this class we will be talking about three components: average, standard deviation, and the t-test. The world of statistics is large but these are the main calculations you will see when we look at quantitative (numerically calculated) data in the science world. Let me briefly discuss what each of the three components are: Average: This is the expected value of a group if I randomly choose someone from the group. For example, if the class is average is 80 then if I randomly choose someone from the class then I would expect their score to be around 80. Standard Deviation: This tells me how much of a variation there is from the average. If the standard deviation of the class test is 5 then I can expect the score to be either 5 more or 5 less than the average. Using the average of 80 we had, that means most people will fall within 75-85 so if I choose a random person I expect them to be in this range. If someone scores a 90, then they are considered two standard deviations above the average. This is because 90-80=10 so the score is 10 higher. Because 5 + 5 = 10 we can say this person is “two standard deviations” above average meaning they are even further from the average which is less likely. T-Test: This is a “test” to compare two groups and see if there is a “statistically significant” difference between them. We will talk more about this in a future lab. In this lab, you will learn how to calculate average and standard deviation using Excel! These equations will help you look at and understand the data you will be collecting in class. Average and standard deviation are also often called “summary statistics” because they summarize the data. We’ll start with a basic overview. Lets get into how to do these things on Excel. I will be using screenshots from Excel but these equations also work in Google Drive so feel free to use whichever you are more comfortable with.

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Each of the white boxes are “cells”. Each cell has a coordinate that is a letter and a number. When we refer to data in Excel, we often refer to the cells. If I have data in column A from rows 1-20, I would say the data is contained in A1:A20. The colon basically means “to”. Each cell in Excel can contain words or numbers and even formulas. Average When we talk about average we are talking about the most expected value from a set of data. It isn’t necessarily the middle, but it is considered “central” in the sense that the data will populate itself around the average. The average is calculated by taking the sum of all numbers in the set and dividing the sum by how many data points there were. For instance, if there were five data points then the average would be calculated as follows: (n1+n2+n3+n4+n5)/5 More generally, the average is represented this way mathematically:

In order to do this in Excel we will be using the formula =AVERAGE(data). First, let’s assume I have data in A1:A20. For simplicity, I want to calculate the Average underneath the last data point just so I can easily find it. I begin by typing = into the cell A21. This tells Excel I’m about to do a math formula I want it to calculate. I then type AVERAGE(. Inside the parentheses is where I would put my data. Since we refer to data as its cells and NOT its numbers, I will type the cells that contain my data. In this case, that’s A1:A20. I can also click and drag on the data to select it. Your excel should now look something like this:

If you hit enter, you will be given your average! Standard Deviation We use standard deviation to measure the spread of data in a set. Standard deviation is related to the variance (which is covered more in statistics courses). To calculate the standard deviation, we take the square root of the variance. The variance is the sum of all the differences (the data minus the average)

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squared. Luckily, we can just use Excel. We will follow the same steps as average except, we will now use the equation =STDEV() instead of =AVERAGE(). So your equation looks like this:

The standard deviation is important for understanding how the data is distributed! Each standard deviation “unit” is called 1 sigma (σ). We can used these “units” in order to tell us what is within an acceptable range and how much the data is spread out around the mean. This lets us more easily compare two groups using the same tests. For example, if the standard deviation is large in either group, that tells us there may be more participants at one extreme or the other skewing the scores. The combination of using the average and standard deviation mathematically to compare two groups is the t-test.

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Lab 1 Assignment Now that we’ve talked about it, let’s do the lab! Your lab will be simple. Count something in your house. A category of things like fruit, utensils, canned goods, soda, whatever you think your house has a lot of. I’m going to use utensils as an example. 1. Count the number of utensils you have. Let’s say we have 10 forks, 15 spoons, 14 knives. 2. I want to find the average and standard deviation of these utensils using Excel. Yes, you can probably do the math mentally, but the purpose is to get used to using Excel. 3. Put these numbers in a little “table” with labels. That’s it! You will submit your Excel sheet on Blackboard. If you are using Google Sheets, you can save your Google Sheet as an .xlsx file by hitting file -> download as on the top left. If you’re not sure what it looks like, take a look at the example we have on Blackboard.

DO NOT SUBMIT A .NUMBERS FILE. YOU WILL GET A ZERO.

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Lab 2 – Scientific Method and Epidemiology In this lab, we are going to learn about the basic steps of the scientific method. A core concept used in science research is the hypothesis. A hypothesis is a fancy way of describing a possible theory of why something happens or why something can be true/false. Refer to this website for more detailed information on the various aspects involved in creating and testing a hypothesis as part of the scientific method. . https://askabiologist.asu.edu/explore/scientific-method Let’s talk about population sizes and epidemiology. Having a larger population is important for scientific research! There is a property known as “power” in statistics and to over-simplify a somewhat complicated topic, the more data points (larger population) you have the greater your power. That means that there is more weight behind your research study, and the greater likelihood that your hypothesis will be valid. For example, in epidemiology studies an increase in population leads to the epidemiological findings having more weight. We will learn how to formulate a hypothesis about epidemiology using something topical: COVID-19. We want you to visit this database: https://covid.cdc.gov/covid-data-tracker/#demographics and look at some data points such as race, age, and sex and others. Here is an example of how data related to COVID cases by age looks like.

Come up with your own hypothesis regarding something related to COVID-19 and then use the different data points from this website to see if your hypothesis is valid or not. Some examples of possible hypotheses: there are more cases of COVID in the United States than New Zealand, or, males aged 18-29 are more likely to have COVID-19 than females aged 18-29 due to differences in mask wearing habits. (It is okay if your hypothesis is not validated by the data on the website!). We are more interested in your critical thinking skills and thought process. For your write-up: NO SOURCES NEEDED

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PAGE MINIMUM WILL BE 1 – 1.5 PAGES FOR THIS LAB SUBMIT THE RIGHT FORMAT; SUBMITTING A .PAGES FILE WILL GET YOU A ZERO! FOLLOW THE RUBRIC! Introduction: Talk about the COVID-19 pandemic and how it has affected you and people you know. Talk about the various health habits you and people you know have undertaken (or not) (hand washing, mask wearing, social distancing, others) because of COVID. Talk about how you have formed your hypothesis based on everything you have learned and experienced due to the pandemic. Methods: The method for this lab is pretty straightforward in that you can just talk about researching the CDC website to analyze data points that you were interested in looking at. Results: Describe the data points that you looked at and analyzed. For example, you can list demographic data, or the number of vaccinations that a certain state has given out to its population compared to another state, etc. Discussion: Talk about if the data you have researched supports your hypothesis. If so, how? If not, what other information do you think you might need? Analyze the data that you have collected and talk about reasons why or why not your hypothesis is validated by this data. Has the data surprised you? Not surprised you? Reinforced any prior thoughts/beliefs? Graphics: Include a CLEAR screenshot/visual of the data chart that you have used to test your hypothesis.

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Lab 3 – Modeling Ion Movement For this lab, we will be discussing ion movement within the cell. Our goal is to help you solidify the concepts we have learned in class and understand how 1) ion diffusion based on concentration gradients, 2) ion charges & magnetic interactions and 3) ion permeability (the functional opening and closing of ion channels) can affect the resting potential in the neuron and the neuron’s ability to fire action potentials. Please go to: http://www.nernstgoldman.physiology.arizona.edu/ and down to the Download section. The website doesn’t work since it is running Flash! We will be using this program to run our simulations.

First, to gain some “real world perspective” on why maintaining ion balance in your blood and cells is important read this journal paper entitled “The Agony of Ecstasy MDMA and the Kidney” (http://cjasn.asnjournals.org/content/3/6/1852.full). Look up words you do not understand in Google. The key takeaway from the paper is the following photo. The ecstasy leads to an increase in sweating and loss of water which leads to a bunch of issues and ultimately lead to death.

OK now GERO 315, let’s now study the principles of ion movement in and out of excitable cells.

LAB 3 – PART 1: 7

Grab 2 clear plastic cups, 2 paper cups and a pin. Put an inch of water in the clear plastic cup, fill the paper cup with water. Put the paper cup inside the clear plastic cup. Add 5-10 drops of food coloring the water inside the paper cup. Now, lift the paper cup up, take the pin and puncture the side of the paper cup. Now put it back into the clear plastic cup. DESCRIBE what happens. Answer these questions: 1) what does the water inside the paper cup represent based on our lectures? What kind of channel does pin hole represent (be specific!!)? What ion does the food coloring represent? LAB 3 – PART 2: The knowledge you gained from the food coloring should help build your hypothesis about how a cell’s membrane potential is controlled by changes in the ion concentration. Form a hypothesis about what will happen as you decrease Na+ concentrations outside the cell. Remember this hypothesis as you will need it for the lab! Make sure you are in the Goldman tab of the simulator (found on the upper right). You will see that there is PK, PNa, and PCl. The “P” stands for permeability. Permeability represents the openness of the ion channel. The small “o” means we are talking about the outside of the cell and the “i” means we are talking about the inside of the cell. For example [K+]o means outside concentration of Potassium and [K+]i means internal cell concentration. Run through the following. You will be keeping track of numbers so either write them down somewhere. a. Write down the cell resting membrane potential and note the resting [K+]o b. Write down the permeability of potassium (PK+) vs sodium (PNa+) at resting. c. Increase PNa+ to 10x and write down what happens to the membrane potential, this should simulate an action potential if you do it quickly.

We are now going to simulate hyponatremia (too much water, too little salt) like the journal paper. 8

d. Make sure to reset the simulator by selecting the “Default” on the bottom right. e. We are going to take the outside Na+ concentration [Na+]o and decrease it in steps. f. Start at 100 and decrease it in steps to 1. Make sure you have at least 10 concentrations, including 100 and 1. As you decrease, keep track of the potential at each concentration. g. Make a scatter plot of your concentration vs potential chart. Add a trendline to this graph. h. The JAMA article about ““The Agony of Ecstasy MDMA …” describes the many problems that happen with Ecstasy – Answer these questions: How does reducing [Na+]o in your simulator exercise explain what happens with Ecstasy? Why does taking ecstasy sometimes result in this? What does this Ecstasy/simulator change do to the ability to fire action potentials & how might this affect consciousness? What does this Ecstasy/simulator change do to the ability to fire action potentials & how might this affect your heart’s ability to beat? For your write-up: 2 SOURCES REQUIRED! Provided paper is one, find another paper that talks about ion channels. PAGE REQUIREMENT IS 1.5-2 PAGES SUBMIT THE RIGHT FORMAT; SUBMITTING A .PAGES FILE WILL GET YOU A ZERO! FOLLOW THE RUBRIC! For your introduction talk about ion channels and why they are so important in a neuron. Briefly cover their function and what they do. Talk about hyponatremia and ecstasy. End with your hypotheses posited about each manipulation as it relates to neuron function. For your methods talk about the exercises you performed (LAB 1 – PARTS 1, 2 &3). Talk about the website and what you had to do to change the simulator, the food coloring exercise and the magnets. For your results: Describe outcomes from (LAB 1 – PARTS 1, 2 &3). What did the colored water do? How about the magnets with paper placed between them? Using the Nernst/Goldman Simulator talk about your numbers! You do not need to give a number by number breakdown, you can simply explain the trend. Make sure you include these two graphics on a separate page: a. A table with the data from changing the Na+ concentration from 100 to 0 b. Scatter plot with trendline of the data from changing the Na+ concentration from 100 to 0 For your discussion explain your results. Answer all the questions outlined in the lab in red above, with a biological explanation for each results outcome. Talk about whether they prove your hypothesis and how you can improve your study. Talk about why ...