1A Lab Tasks - 1A Lab task PDF

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BIMM 121 Fall 2020 Lab Tasks

LAB TASKS DOCUMENT For every lab session, there will be a lab tasks document that contains instructions for what you need to do before and during lab. It will also specify what individual work needs to be in your lab notebook after each lab session. Every lab tasks document will have the same format, with the boxes below summarizing the key tasks, followed by additional information you will need to accomplish those tasks. Make sure you read the lab document at least the day before each lab, so that you have time to do any of the pre-lab tasks. The first box (yellow), will contain directions for what you need to do before lab. The second box (grey), will contain directions for what you need to do during lab. In this section, you will find detailed information about what to do before and during lab. Pay attention for sections that look like this: o

NB1: specific thing to include in your notebook, make sure it’s there before lab

o

NB2: specific thing to include in your notebook, put in during lab

Any time you see the ‘NB’ bullet point, that is something specific you need to put in your google doc notebook: answers to a question, calculations, a graph, etc. This is in addition to the general information that you should have in your notebook for every lab session (see Lab Notebook Guidelines, on canvas). Lab notebooks will be checked weekly (for completion work must show a good-faith effort to earn full credit)

Continue to the next page to see the lab tasks for the first lab.

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BIMM 121 Fall 2020 Lab Tasks

1A - INTRODUCTION, DILUTION ACTIVITY Before lab: • •

Read the “zoom basics” and “online community” guidelines below. (You don’t need to connect to class yet, just read through so you are ready when it is time). Read and complete the “Biofilm disruptor dilutions” pre-lab, making sure to answer the questions in your notebook (NB1 - NB5)

During lab: Introductions • Your IA will provide instructions for introductory activities in break out rooms (under Introductions, below), then you’ll come back together to share your group name with the whole class. Dilution activity • Your IA will provide instructions on group roles (manager, reporter, questioners) and they will tell you which data set to work with for part 5. • In your breakout group, share your biofilm disrupter dilution plans. Discuss any differences you have, and make sure everyone is on the same page with correct way to perform the dilutions. • Still in your breakout group, complete the data analysis tasks for the absorbance data. Make sure to put all of the items (NB6-NB9) in your lab notebook. • Come back together into the main room to share and discuss your analysis. Make sure you answer question NB10 in your notebook after the discussion.

Pre-lab: Zoom basics Many of you may already be used to using Zoom from the Spring quarter, but the basics below will contain helpful information for the best way to set up your Zoom sessions for BIMM 121. 1. If you haven’t already, download zoom for your computer or mobile device and connect your UCSD Zoom Pro account (directions here: https://digitallearning.ucsd.edu/learners/learningremotely/tools.html). If possible, try to sign on with your UCSD sso credentials (this makes it easier to automatically sort you into groups). 2. Before connecting to class, update your profile to include your full name. If possible, get ready to use headphones during the meeting (this prevents audio feedback).

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BIMM 121 Fall 2020 Lab Tasks 3. Find the zoom link for your lab section on Canvas, under ‘Zoom links’ and click on it when you are ready to enter class. Be sure to attend only the lab section you are officially enrolled in. You will be placed in a waiting room, and the IA will take attendance as they let you into the main lab room. 4. We recommend that you set your Zoom window up according to the following guidelines: - Mute yourself when you enter the class (mute, and most other controls can be found at the bottom of the screen) - Click on the ‘chat’ button (may be hidden under ‘more’ button) to display chat, which you can use to ask questions - Click on the ‘participants’ button (may be hidden under ‘more’ button) to bring up a list of your classmates, and also to bring up the response icons (we will sometimes ask for a ‘yes’ or ‘no’, and you can find the ‘raise hands’ button here which you can use when you would like to ask a question out loud - If someone shares their screen, the chat and participants window’s may pop out and get in the way - you can exit full screen by pushing the escape key. - You are not required to turn on your video, but we encourage it to help build community, especially in your small group breakout rooms. Make sure to check your surroundings and what’s visible on your camera, or use a virtual background, to avoid distracting your classmates. If you are unable to use video or prefer not to, please consider putting up a picture of yourself or something you like If you’ve followed the guidelines above, your zoom window should look something like this:

. 5. During lab sessions and in your small break out rooms, you will be expected to share your screen in order to work together or present your results to the class. You can do this by

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BIMM 121 Fall 2020 Lab Tasks pushing the ‘Share Screen’ button at the bottom of the screen. ***Be careful - if you share your screen, we will be able to see your entire screen, including any desktop photos, emails, etc. you may have open on your computer. Even if you share an individual app, like a browser, others may be able to the names of all the tabs you have open. Please be sure you only share what you mean to and that content is appropriate.***

Pre-lab: Community guidelines We want to make sure this class is a welcoming, inclusive community that supports everyone. Please read and adhere to the following community guidelines. - Keep yourself (and your background noise) muted if you are in a large class setting, unless called on - Use chat or the ‘raise-hands’ feature to ask questions in a large class setting - In smaller class settings (lab sections and small groups), it is OK to just speak up during discussion time, but be graceful about accidental interruptions — it is much harder to tell when someone is about to speak (or is done speaking) on Zoom. As long as we are apologetic/forgiving about it, these little interruptions should be no big deal. - Be prepared to engage in discussion thoughtfully and with full attention — do your pre-lab ahead of time - In breakouts, make sure everyone has a chance to participate. You will rotate roles from day to day. Manager - keeps group on track to complete tasks on time and make sure everyone has a chance to participate Reporter - synthesizes ideas and takes note from discussion, is prepared to share out to the larger group Questioner - critique ideas, and question the group as to whether they have thought about the material from different perspectives Member(s) - no special role, but you are expected to contribute to completing the tasks - Be respectful of the ideas of your classmates and the IA, even if they are different from your own - If someone is having a hard time with a task or concept, offer to help — teaching someone else is a great way to enhance your own learning - Be excellent to each other. Everyone may be stressed, so be kind; everyone is learning new things, so be patient

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BIMM 121 Fall 2020 Lab Tasks

Pre-lab: Biofilm disruptor dilutions. Later this week, you will be designing an experiment to test the effect of different concentrations of biofilm inhibitors. Different inhibitors may require different concentrations to work, so you will need to know how to prepare solutions at a specific concentration. You may already be familiar with how to calculate and carry out dilutions; the following questions will serve as a good review. Even though we aren’t in the lab, the hard part of dilutions is the part on paper; mastering these calculations will help prepare for any future lab work you do. Imagine you are in the lab to test a novel chemical compound developed by UCSD researchers called ‘compound X’. The researchers want you to find out what concentrations of compound X inhibit biofilm formation. In the lab, you have micropipettors (used to measure and dispense small volumes), test tubes, and growth media to make your dilutions, and a spectrophotometer to measure the absorbance of the solutions you make. The atomic weight of compound X is 300 g/mole, and when it is dissolved in media, the solution has a deep orange color. The researchers gave you a 100 mM stock solution. Based on studies of a related chemical compound, compound W, the researchers think that a concentration of 50 µM in growth media should be sufficient to prevent biofilm formation, but they want you to find the precise range of concentrations that work. Use the information above to answer the following questions. o

NB1: How would you make a 10 mLs of 1 mM solution of compound X using the stock solution? What is the dilution factor of the 1 mM solution compared to the stock solution? If you need a refresher on scientific prefixes & units, or on dilution factors, see the reference on the next page.

o

NB2: How would you use the 1 mM solution you just made to prepare 3 different test tubes with various concentrations of compound X at 25 µM, 50 µM, and 100 µM. The final volume of each test tube should be 10 mL. Use a table like the one below to make your plans. Concentration (µM)

Volume Compound X

Volume Media

o

NB3: What is the dilution factor of the 50 µM solution relative to the 1 mM solution? Relative to the 100 mM solution?

o

NB4: Why do you think you first had to make the 1 mM solution instead of working directly from the stock solution?

o

NB5: Oh no! You ran out of the 100 mM stock solution, but want to run more tests. The researchers don’t have time to make you more stock solution, but they give you a vial containing pure compound X powder. How would you use this to make 10 mLs of fresh, 100 mM stock solution?

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BIMM 121 Fall 2020 Lab Tasks

Common scientific units review: L = liter, for measuring volumes M = molar (moles/L), for measuring molar concentration (there are also other ways to specify concentration) m = meters, for measuring length g = grams, for measuring mass mole = 6.02 x 1023 molecules Common scientific prefixes: prefix (abbreviation)

meaning

scientific notation

giga (G)

1,000,000,000

109

mega (M)

1,000,000

106

kilo (k)

1000

103

milli (m)

0.001

10-3

micro (µ)

0.000 001

10-6

nano (n)

0.000 000 001

10-9

pico (p)

0.000 000 000 001

10-12

conversion examples: There are 1000 mL in a L. There are 1000 µL in a mL.

Dilution Factor Review: A 1:10 dilution (aka, a 10% dilution) has a dilution factor of 10. Sometimes you see people call this a ‘ten-fold’ dilution. A common way to calculate dilutions is the equation (V1) (C1) = (V2) (C2), where V1 and C1 are the volume and concentration of the initial solution, and V2 and C2 are the volume and concentration of the final solution. Typically, one of the quantities is unknown; you can fill in the other variables and solve for the unknown one, as long as your units are the same.

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BIMM 121 Fall 2020 Lab Tasks

During lab: Introductions 1. Introduce yourself to your groupmates. When it’s your turn, share your major, your favorite class so far at UCSD, something you’ve enjoyed reading/watching/playing/doing lately, and your goal for BIMM 121. At the end of your turn, call on someone else in the group who hasn’t gone yet. 2. When everyone has gone, work together to come up with a name for your group, based on a common goals for the class or a common interest shared by everyone in the group. We’ll use this name to label results and assign data, so don’t make it too long! o

NB6: record your group name and explain how it relates to something the group has in common.

3. When everyone has gone, come up with a plan for keeping in touch with your group if you have questions about assignments or for studying. Your IA may have suggestions for the best way to do this. You should also use this to let people know if won’t be able to make it to lab. o

NB7: record contact information and/or plan for keeping in touch w. groupmates

During lab: Biofilm disruptor dilutions 4. Share your answers to the dilution pre-lab questions (completed ahead of time) with your group. If you don’t all have the same answers, work together to locate any errors and figure out the correct way to do the dilutions. You should approach this with a spirit of a group study session - work together to help each other understand and make sure everyone is on the same page before moving on. If you get stuck or something doesn’t make sense, remember you can use the ‘ask for help’ button to request an IA or instructor visit to your breakout room. 5. Because compound X is deep orange in solution, you can use readings from the spectrophotometer to measure how much light is absorbed by each solution. More concentrated solutions will absorb more light, and less concentrated solutions will absorb less light. Solutions that are prepared at the same concentration should have the same absorbance. Since you plan to be doing lots of experiments with compound X (we’re pretending here, use your imagination), you’ve asked your lab assistants to prepare several replicates of each dilution. You have 4 lab assistants, and they each prepared 10 tubes for each concentration, then measured the absorbance of each tube. Access the absorbance readings here: https://docs.google.com/spreadsheets/d/1EOWaWsArG_NqgA8nr4P8EzYdKEpQg3s0FPky7mMIeU/edit?usp=sharing (Note: if you cannot access the file, please make sure you are using the google account associated with your UCSD active directory).

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BIMM 121 Fall 2020 Lab Tasks Each lab group will analyze a different lab assistant’s data to check their work. Copy and paste the data for your lab assistant into a new excel file or google sheet. (Everyone should do this on their own computer, you will check your result against your groupmates) 6. Make a chart to visualize the variation between the replicates. A good chart to try is a dotplot, which you can get by modifying a scatter plot (you may have to use the ‘swap’ x/y axis options - you want the y axis to be the absorbance values, and the x axis to be the 3 different concentrations). Be sure to ask for help from your group if you get stuck. Everyone should show their chart to the group to make sure you are all getting similar results. o

NB8: put the chart in your lab notebook with a proper figure caption

7. Next you will calculate descriptive statistics for your lab assistant’s data. For each concentration calculate the mean and the standard deviation. This can be done in excel or google sheets by clicking in an empty cell and using the formulas: Mean: =AVERAGE(array) Standard deviation: =STDEV(array) where the array is the data points, e.g. the 10 cells with absorbance data for a given dilution (you can highlight these to select them). 8. Make a bar graph of the means. Add data labels so that the mean values can be seen. Add custom error bars to select the standard deviation values you calculated (google sheets does not have custom error bars, so just put the standard deviations in a separate table). As always, if you are not sure how to do these things, ask your group for help - you are all in this together. When you are done, show your chart to the group. NB9: put the chart (and table, if needed) in your notebook, along with a proper figure caption. 9. As a group, you will be sharing your results with the bigger section. As a group, help the reporter select representative charts to share. The reporter should be prepared to share their screen with the group, and briefly (< 1 min) discuss their results. 10. When you are called back to the main group, pay attention to the other groups’ data - you will need it to answer the following questions in your notebook, and you will discuss the answers as a class. NB10: Which lab assistant was the most accurate at making their dilutions, and why? What do you think are possible sources of error for the other lab assistants?

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