Assignment SevenSaccharomyces cerevisiae Growth Characterization I:

Aseptic Technique, Growth Media, Culturing & Microscopy

Functional Genomics Research Stream • Freshman Research Initiative • by Dr. Patrick J. Killion

Assigned: March 3, 2009

Due: March 10, 2009

Submission: Beginning of Lecture, 2:30 PM

Format: This Printout

General Introduction

IMPORTANT NOTE: Background material and explanation is purposefully omitted from this assignment text. For more background on the subject matter covered in this assignment be sure to see the lecture notes and the online course notebook, each found on the course website (course materials): http://fg.cns.utexas.edu/

Safety Considerations

As each weak progresses you are beginning to work with more equipment and reagents that could pose a danger to you or your research colleagues if not correctly and safely used.

This week we will begin working with the following equipment:

‣ Bunsen Burners

‣ Inoculating Loops

‣ Culture Spreaders

‣ Centrifuges

‣ Autoclaves

Please refer to your course textbook and the online course notebook for more details on how to safely use these devices. Always ask research stream staff if you have questions or concerns.

Specific Textbook Sections: Unit 4.1, 4.2, 5.1, Appendix I. Always check the online course notebook.

Time Considerations

This week we begin Phase II of research stream activities. As we begin to focus on more Biology intensive researching applications the time schedules and day-to-day dependencies get more complicated. Please pay attention to the order of the various sections of this assignment and plan accordingly. This is your responsibility to manage.

Constraint 1: Section C must run overnight.Constraint 2: Section C cannot run over an entire weekend.Constraint 3: Section D must be done the day after Section C.

I recommend considering the following schedule options for completing your laboratory work this week:

Schedule One:‣ Wednesday: Section A, Section B‣ Thursday: Section C (must go overnight)‣ Friday, Monday, Tuesday: Section D (must be ~24hrs after Section C), Notebook, Write-Up

Schedule Two:‣ Wednesday: Section A, Section B, Section C (must go overnight)‣ Thursday, Friday, Monday, Tuesday: Section D (must be ~24hrs after Section C), Notebook, Write-Up

Schedule Three (not recommended, tight timing per due date):‣ Thursday: Section A, Section B‣ Monday: Section C (must go overnight, cannot go over weekend)‣ Tuesday: Section D (must be ~24hrs after Section C), Notebook, Write-Up

Section A - Plate & Media Production Training

Introduction

The production of both solid and liquid media for Saccharomyces cerevisiae growth is an essential beginning to any experimental process. Growth is typically done on solid plates of agar plus growth nutrients or in liquid cultures. The preparation of these growth mediums involves the manipulation of dry stock reagents as you have learned in previous assignment as well as the tenets of aseptic technique.

Training Sessions

Because the process of media preparation is resource and equipment intensive, instruction in this process will be scheduled in sessions. You must attend one of the following sessions in order to learn how to complete these tasks. After each session you will be provided access to a previously made set of liquid and solid media which you will need to complete the rest of this assignment. You will not be provided these resources, however, until you have completed a training session and have a research staff signature above.

Session Options - Each session will last approximately 20 minutes. Please circle the one you attended (next page).

‣ Wednesday, March 4 - 10:00 AM

‣ Wednesday, March 4 - 2:00 PM

‣ Thursday, March 5 - 10:00 AM

‣ Thursday, March 5 - 12:00 PM

‣ Thursday, March 5 - 2:00 PM

In this session you will learn about:

‣ Basic Aseptic Technique

‣ Media Preparation: Liquid & Solid, Pouring Plates

‣ Sterilization by Autoclave: Media, Equipment, Glassware, Liquids

At the end of session get the signature of a research staff member to verify your attendance:

Research Staff:

Signature: ________________________________ Date: ______________________________________

Preparation QuestionsIn order to prepare for this session please read appropriate sections in Unit 4.1 & 4.2 and then answer the questions:

Question 1: What is the average temperature of autoclaving? _______°C or _______ °F.

Question 2: Extremely high temperatures for the sterilization of both solids and liquids can be achieved in an autoclave through the manipulative use of _______________________.

Question 3: Do the conditions of autoclaving kill all forms of life? (Circle one: yes no)

Question 4: Liquids should be sterilized in a bottle with __________ the needed volume to avoid boil-overs and spills.

Question 5: The caps of liquids must be left ___________ in order to prevent explosions.

Question 6: Cycles that are titled “gravity” are typically for _________________________________________.

Question 7: Cycles that are titled “liquid” are typically for __________________________________________.

Question 8: The term “slow exhaust” is a synonym for _____________________________________________.

Question 9: The term “fast exhaust” is a synonym for ______________________________________________.

Question 10: Microwave heating is as effective as autoclave sterilization? (Circle one: true false)

Question 11: Yeast solid media is made of the following components (for plates, online course notebook):__________________________________________________________________________________________

Question 12: Yeast liquid media is made of the following components (for cultures, online course notebook):__________________________________________________________________________________________

Section B - Aseptic Technique

Introduction

Unit 4.1 of your course textbook has excellent perspective and details on the use of laboratory aseptic technique.

Read it now!

Read it.Read it.

Seriously, borrow a book, read it.

This introduction is taken from that section of the textbook and is presented as an attempt to define the term:

Aseptic technique is a set of routine measures that are taken to prevent cultures, sterile media stocks, and other solutions from contamination by unwanted microorganisms (i.e., sepsis). While such actions are sometimes called “sterile technique,” that terminology is appropriate only in reference to preventing introduction of any organisms to laboratory or medical equipment and reagents (such those as used for surgery). Since the goal of a biologist is to grow microorganisms or eukaryotic cells without introduction of extraneous organisms, aseptic techniques are crucial for accurate and meaningful experimentation.

One should keep in mind that a completely sterile working environment does not exist. However, there are a number of simple, common sense procedures that will reduce the risk of culture contaminations. Examples of aseptic technique are cleaning and disinfecting laboratory surfaces prior to use, limiting the duration that cultures or media are uncapped and exposed to the air, keeping petri dishes closed whenever possible, effectively sterilizing inoculating loops and other equipment that comes into contact with cultures or media, and avoiding breathing on cultures or sterile instruments. These precautions will become second nature after practical laboratory experience.

Method of Learning & Evaluation

As you can see, aseptic technique is critical in all of the research we will be doing from here forward.

What will you be doing to learn and demonstrate knowledge of aseptic technique?

We have a few options that could be exercised:

‣ A schedule series of lectures; boring and not likely really learned from.

‣ A writing assignment; boring and not effective - writing about techniques is not the same as doing them.

For these reasons we are going to utilize a new approach with respect to the understanding and use of aseptic technique.

You will be doing an oral presentation on aseptic technique. It is encouraged that you do this in groups of two, three, or four (no more than four). How will you be doing this presentation? Physically - in the lab, at your bench!

This is not a PowerPoint in a lecture hall kind of thing. You will be physically at your bench and you will step-by-step demonstrate various tenets and techniques of aseptic technique. No PowerPoint or computer is desired or needed.

Topics Presented

How will you know what to present?

It is easy - read Units 4.1 and 4.2 in your course textbook and you will be set.

I will go ahead and give some hints. I expect to see coverage of the following topics:

‣ General cleanliness; cleaning of bench space.

‣ Required equipment: Bunsen burner, gloves, anything else?

‣ Bunsen burner lighting, components, general use.

‣ Bench-top aseptic work using a Bunsen burner. Flaming of bottles, technique and rationale.

‣ Manipulating vessels, liquids using aseptic technique.

‣ Sterilizing and using an inoculating loop to transfer from one liquid culture to another.

‣ Making a culture spreader from a Pasteur pipet.

‣ Handling of alcohol fires in beakers (occasionally incurred during use of culture spreader).

‣ Each of the following (you will use just one test plate on which you will do all three):

‣ 1: Use of inoculating loop to streak a culture on a plate.

‣ 2: Use of toothpick to streak a clone on a plate.

‣ 3: Use of a culture spreader to spread a culture on a plate.

Preparation

Are you expected to read and know how to do all of this? No, of course not.

A lot can be learned from reading - the text is very good and quite clear. It is expected that you do read all of Units 4.1 and 4.2 before seeking assistance. You will clearly need to seek research staff assistance to clarify issues, perhaps see demonstrations, and locate equipment. Do this - seek help, ask questions. Interact with other students who have had

questions clarified. Most of these topics were discussed in lecture this week as well and as such should not be foreign. Some notes below will help (adapted from the course textbook).

What is an Inoculating Loop? The inoculating loop is used for the transfer of liquid or solid bacterial cultures. It consists, simply, of a handle with a thin protruding wire that is molded into a circle at the end. Many varieties of loops, made of nickel-chromium or platinum wire, are available from many suppliers. The wire may be permanently attached to a handle or replaceable, and may be obtained as either a straight wire or a twisted loop. The loop shape allows efficient transfer of liquids, which form a film over the loop. Standardized, volumetric loops are commercially available for reproducible transfers of specific volumes of liquid. Both looped and straight wires are suitable for transferring bacteria from solid media.

The inoculating loop must be sterilized immediately before and immediately after use. To sterilize, first place the end of the wire closest to the handle in the blue (hottest) part of a burner flame, until the wire glows red. Then slowly draw the wire through the flame, ensuring that the entire length of the wire glows red. The loop can be cooled quickly by gently touching it to an unused part of an agar plate or in liquid medium. Do not blow on a hot loop or wave it in the air to cool it off.

How are toothpicks used?Autoclaved toothpicks can be used for transfer of cultures as an inexpensive and quick alternative, since they do not need to be flamed like a loop. Toothpicks should be placed into a 100-ml beaker with the narrowest end at the bottom of the beaker, covered with aluminum foil, and autoclaved. The sterile container should be turned on its side during removal of individual toothpicks, to prevent contaminants from falling into the open beaker.

What is a Culture Spreader (besides a predictably questionable band name)?A spreader is used to evenly distribute bacterial cells from a liquid suspension over the surface of a plate. This will yield either a “lawn” of bacteria on nonselective medium, or isolated colonies on selective medium. A spreader can be easily made by heating and bending a piece of a 4- to 5-mm diameter glass rod, as illustrated in Figure 4.2.2 (course textbook). In a pinch, a much less durable spreader can be quickly made from a Pasteur pipet. For safety in handling, melt away sharp ends of rod as a first step. A pair of needle-nose pliers or similar tool is useful for forming bends in glass. Before each use, sterilize the spreader by immersing the triangular end in a beaker of 95% ethanol, passing the spreader quickly through a flame, then allowing the flame to burn out. Be careful not to let the burning ethanol drip into the beaker or onto flammable objects. Sterilize after use by immersing in the ethanol.

Expectations

What expectations are there for your presentation? Just a few but take them seriously.

‣ Completeness: You will cover the material that is stated above.

‣ Participation: All members of a group must participate and/or have a defined section.

‣ Preparation: It should not appear that you read the material once and just rambled through some sub-part of it that you could remember. You should take notes (in your laboratory notebook), come up with a plan, and then present it when you are sure of what you wish to say. It is allowed, even encouraged, that you have your lab notebook open to reference during your talk. Do not spend an inordinate amount of time preparing. This is just one section of the work to be done this week. That said - spend an appropriate amount of time preparing.

‣ Professionalism: We have lots of fun and conversation in the lab. This is not one of those times. This should be considered a serious topic and presented as such. Research staff and students around will be both active and passive audience. You should pretend that these are researchers you do not know but wish to impress.

‣ Duration: The total presentation should last approximately 10 minutes.

Completion

In order to do the presentation you simply need to ask one or more of the research staff to come over and witness it. Any students that are in the laboratory are allowed and encouraged to listen in. Give the research staff member the evaluation form at the end of this packet (remove it). They will fill it out and privately submit it for evaluation.

Section C - Saccharomyces cerevisiae Growth

Introduction

Let us get something out of the way when it comes to writing about working with Saccharomyces cerivisiae.

Question 1: How do you spell Saccharomyces cerevisiae? ____________________________________________

Consumable Materials

In Section A of this assignment you attended a training session on plate and media production. At the the end of that session you were given access to stocks of both liquid media and plates for the purpose of yeast growth. Both of these media types will generally be available as laboratory stocks. Thus, you will rarely need to make your own media or plates; it is important that you know how to safely make these items and thus the training provided by Section A.

Contamination Issues & Caution

Laboratory stocks are a major source of productivity gain in the lab. As you have learned in Assignments Five and Six, the production of reagents and buffers can be laborious, time consuming, and error prone. The controlled creation and use of common stocks allows an entire lab to benefit from a centralized effort to keep them available. This is a good thing. Everyone benefits, productivity is increased, experiments experience far less reagent-induced variance, and time in the lab is generally spent more on real work and less on preparatory work.

All of this effort can be undone and worse by contamination of these common laboratory stocks. Contamination is generally undetectable and only shows itself when experiments start to fail or cultures show signs of contamination.

You must be extremely rigorous when working with any laboratory stock and use all parts of aseptic technique.

Getting It Done

You will not be making YPD liquid media or plates for this assignment. The protocols for each, however, are in the online course notebook should you ever need to do so.

Please refer to Time Considerations at the beginning of this assignment for time constraints that you must consider before you engage Section C & D. Once you begin Section C you are committed to performing Section D approximately 24 hours later (in general the next day).

In Section C you will begin plate and liquid media growth from various laboratory stocks of a specific Saccharomyces cerevisiae strain (S288C). These stocks are located in the clear-door 4°C refrigerator on the west side of the laboratory.

This procedure (both steps) will likely take less than 1 hour to perform.

Step 1: Overnight Culture Creation

You will be creating a small overnight culture in liquid media. Only one culture should be created per group.

Note goal: The entire goal of this step of Section C is to get an overnight small-scale culture of yeast growing so that you can use it the next day for Section D.

Note constraint: Section D must be done the day after this portion of Section C.

Adapted notes from course textbook on starting an overnight culture (small scale):

1. Prepare 10 mL of YPD (from lab stock) in a sterile test tube.

2. Follow the instructions for proper sterilization of the inoculating loop.

3. With a cooled loop or sterile toothpick, scoop a small portion of a single isolated colony (solid stock).

4. Insert the loop/toothpick into the liquid medium and shake lightly to dislodge the material.

5. Alternatively, touch the material on the loop to the glass just above the liquid.

6. The inoculum will enter the liquid once it is put on a shaker. It is not necessary to see the yeast in the liquid medium, because even a few cells will grow to a high density after incubation.

7. Cover culture with cap or loose foil. Place the culture in a 30°C shaking ( ∼200 rpm) dry incubator and grow overnight. Note that there are two racks which tightly hold the test tubes in place in the shaking incubator.

Step 2: Plate Creation

You are producing three plates (please note: only one set of three plates per group):

‣ Plate 1: Use a sterile toothpick to streak a plate of S288C (source is solid stock).

‣ Plate 2: Use an inoculating loop to streak a plate of S288C (source is solid or liquid stock).

‣ Plate 3: Use a culture spreader to spread a plate of S288C (source must be ~100 µL liquid stock).

Label all plates completely:

‣ Your Name(s) or Group Name (if you have one), Time & Date

‣ Telephone Number or Email (often helpful if disaster strikes incubator)

‣ Strain Plated (S288C), Method Used to Plate (Loop, Pick, Spread)

Adapted notes from course textbook on using a Culture Spreader:

1. Place a small volume of culture (50 to 500 µl) in the middle of the agar surface.

2. Sterilize the spreader by immersing the hooked end into 95% ethanol in a small beaker, then

3. Burn off the ethanol by passing through a Bunsen burner flame.CAUTION: Be careful not to let the burning ethanol drip into the beaker or onto flammable objects.

4. Cool the spreader by touching it lightly to the agar surface, then spread the culture uniformly around the plate.

5. Return spreader to ethanol.

6. Allow liquid to dry such that there are no drops visible on the surface.

7. Incubate plate with agar facing down at appropriate temperature.

Adapted notes from course textbook on using an inoculating loop or sterilized toothpick:

Protocol Note: the online course notebook has an excellent plate streaking and growth protocol for added reference.

Clonal populations (a cluster of cells derived from one single cell) can be derived by streak plating. Each successive streak dilutes the previous streak, such that isolated colonies (clones) can be obtained (Fig. 4.2.3).

Note that this same procedure applies to the use of a sterilized toothpick. A new toothpick is needed each time the instructions say to flame and sterilize the loop. For further clarification see the figure below and your course textbook.

1. First, streak a loopful of liquid or solid culture across a small (∼3-cm long) area near one side of an agar plate.

2. Flame the loop to sterilize.

3. Touch the loop to an unoccupied area of the plate to cool.

4. Lightly drag the loop once through the first streak, then continue to drag in a zigzag manner over a section of the agar surface. Be careful not to cross previous lines.

5. Flame the loop again, and cool by touching agar surface.

6. Again, drag the loop once through the previous streak, then continue to make a second streak.

7. Repeat for a total of four to five streaks.

8. Incubate plate with agar facing down at appropriate temperature.

These plates will be allowed to grow for one day (maximum) in an incubator that is set to 30°C. After one day of growth the plate is stored at 4°C where growth is slowed such that the plate can be kept for an extended period of time. After 24 hours of plate growth show your plates to a research staff member who will sign below to indicate you completed this portion of the assignment successfully. Store your plates in the 4°C refrigerator (agar facing down).

Research Staff:

Have a research staff member evaluate your plates and sign below.

Plate 1: ______ Plate 2: ______ Plate 3: ______ Signature: __________________________ Date:_____________

Section D - Cell Culture Quantitation by Microscopy

We are going to keep this section of the assignment nice and straightforward. You will be using the overnight culture you began in Section C. Have it ready?

Step 1: Serial Dilution of Culture

Recall the principles from serial dilution. You can reference Assignment Five, the course website, or lecture notes to recall how to make serial dilutions.

You will make the following dilutions:

1. 1/12. 1/103. 1/1004. 1/1000

You will make these dilutions in 1.5 mL microcentrifuge tubes. Be sure to mix the cell culture thoroughly before pipetting. You want the cell culture to be fully homogeneous. Be very careful to accurately make the dilution series.

Step 2: Estimating Cell Density by Hemacytometer & Microscopy

A hemacytometer is device that can be used to estimate cell density (count) in cell culture. It is used quite frequently in human cell culture - not so frequently for bacterial and yeast growth (there is a better way that you will learn next week). It is an opportunity, however, for you to use microscopy to see and study yeast cells. It will also exercise your ability to accurately pipette and make serial dilutions.

The hemacytometer is a device designed for counting different cell types and microscopic particles. The procedure is posted in the online course notebook (Protocol: Using a Hemacytometer). An abridged version is presented here for clarity. Please note that you should check the online notebook for updates or clarifications to this protocol that may have been deemed necessary during the week.

For each of the serial dilutions you prepared:

1. Clean the slide carefully with 70% ethanol and a KimWipe. Place the cover slip onto the slide.

2. The volume that fits between the cover slip and slide is fixed, but it is important that the entire counting area be filled with liquid. Place the tip of the pipette in the triangular indention of the slide and expel ~18µl of the culture. As the liquid is added, capillary action will draw the liquid across the entire counting area.

3. Look through the microscope and position the 5×5 grid in the center of the plane of focus. You will likely need to start at the lowest magnification (getting it in focus) and step-wise work up to the highest magnification. Note that the cells can likely only be seen clearly enough to be counted at the highest magnification.

4. All 25 large squares can be counted, or a counting pattern using fewer squares can be used (you will choose 5).

5. The hemacytometer and cover slip should be cleaned with the 70% ethanol and dried with a KimWipe after use.

To determine the number of cells per mL of cell culture:

Compute a mean number of cells counted for each chamber. The purpose of the mean is to determine a reliable number across five samplings. Your final cell number calculation is then: Number cells (mean) × dilution factor × 10,000.

After dilution factor is taken into account your computed cells per mL should match (across dilutions). Do they? ____

Figures of Hemacytometer1:

Figure 1: One of five chosen counting areas:

Figure 2: Zoom In - Two ways to pick five fields to count (and then compute a mean).

Step 3: Quantitation

Complete this table to quantify your hemacytometer readings and calculations.

Dilution Count 1 Count 2 Count 3 Count 4 Count 5 MEAN across 5

STDEV across 5

Computed Cells / mL

Total Cells in Culture

1/1

1/10 N/A

1/100 N/A

1/1000 N/A

[1] = http://arbl.cvmbs.colostate.edu/hbooks/pathphys/reprod/semeneval/hemacytometer.html

Assignment Submission

Sign Off

When you believe you have the assignment completed ask a staff member (Dr. Killion, any Functional Genomics Research Stream Undergraduate Mentor) look over your work and sign below.

You should be able to present the staff member:‣ Complete laboratory notebook with all tables called for in this assignment.

What to do with your materials:‣ Store all plates in the 4°C refrigerator. You will need them for Assignment Eight.

Date: ______________________________________________

Time: ______________________________________________

Staff Name: __________________________________

Staff Signature: __________________________________

Submission

This assignment is due on March 10, 2009 - 2:30 PM.

This printed document is the only component that is needed for final submission.

Please answer the following questions:

I worked a total of _____ hours on this assignment. (please be honest, not graded for hours)

I worked with a group of the following people:

_____________________________________ _______________________________________

_____________________________________ _______________________________________

I adhered to the group work policy of the research stream:

Signature: _______________________________________ Date: ________________________________

Aseptic Technique Evaluation Form

Instructions:

Please fill in each box on a 1 to 10 point subjective scale using your best judgement.

Topics:______ General cleanliness; cleaning of bench space.______ Required equipment: Bunsen burner, gloves, anything else?______ Bunsen burner lighting, components, general use.______ Bench-top aseptic work using a Bunsen burner. Flaming of bottles, technique and rationale.______ Manipulating vessels, liquids using aseptic technique.______ Sterilizing and using an inoculating loop to transfer from one liquid culture to another.______ Making a culture spreader from a Pasteur pipet.______ Handling of alcohol fires in beakers (occasionally incurred during use of culture spreader).

Each of the following:______ 1: Use of inoculating loop to streak a culture on a plate.______ 2: Use of toothpick to streak a clone on a plate.______ 3: Use of a culture spreader to spread a culture on a plate.

______Participation: All members of a group must participate and/or have a defined section.

______Preparation:It should not appear that you read the material once and just rambled through some sub-part of it that you could remember. You should take notes (in your laboratory notebook), come up with a plan, and then present it when you are sure of what you wish to say. It is allowed, even encouraged, that you have your lab notebook open to reference during your talk. Do not spend an inordinate amount of time preparing. This is just one section of the work to be done this week. That said - spend an appropriate amount of time preparing.

______Professionalism:We have lots of fun and conversation in the lab. This is not one of those times. This should be considered a serious topic and presented as such. Research staff and students around will be both active and passive audience. You should pretend that these are researchers you do not know but wish to impress.

______Duration:The total presentation should last approximately 10 minutes.

Students Presenting

____________________________________________ ____________________________________________

____________________________________________ ____________________________________________

Research Staff

Signature: ________________________________ Date: ______________________________________