recursal/Fanatic-Fandom huggingface dataset:
BiologyBeckonsYou

**Welcome** to the Biology Beckons You!
Hi! This is how we get our science on! Here you will find a growing number of protocols and how-to's for the SRJC Biology lab, which is searchable and editable. I hope this can be a good resource for us, as we grow and become a more integrated department!

We are gathering information, protocols, and any other helpful information that pertains to the lab so that staff and faculty can communicate, contribute and improve the environment of our Life Sciences Department.

Some of the information may have been taken from other sources and some we wrote ourselves. If it works, then keep it and if it doesn't, improve it!

* A full list of existing categories can be found at Special:Categories.
* \*\*\*\* To see this site best, download AdBlocker. It is a really easy widget that will take the ads away.\*\*\*
* Please do not put anything on this site that you wouldn't want anyone to see. Please do not put private information, or anything that the public cannot be privy to. This site is on a public, Wikipedia-like site, which is very common for labs to do. However it can be accessed by anyone.

**BROWSE BELOW FOR CATEGORIES**
I Love You, Brandon

"**I Love You, Brandon**" is the eighteenth episode in the first season of *Punky Brewster*.

## Synopsis

Henry scolds Brandon for eating several valuable stamps. After that, Punky takes him on a walk, where he is hit by a car. He is rushed to the veterinary hospital, where his prognosis is grim.

## Cast

* Soleil Moon Frye as Punky Brewster
* George Gaynes as Henry Warnimont
* Susie Garrett as Betty Johnson
* Cherie Johnson as Cherie Johnson
* Ami Foster as Margaux Kramer
* Casey Ellison as Allen Anderson
* Sandy as Brandon "the Wonder Dog"
MICRO 5 Intro and Lab Safety

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Back to MICRO 5

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## Before the Semester

Prior to class, turn on Bunsen burners to purge lines. For Spring semester, one burner per bench was sufficient. For Fall semester, I like to set up all bunsen burners to purge lines. Apparently, gas concentration in line goes down when not used -- so purging allows students to easily light burners.

Make sure loops are out for students to access.

Make sure Vesphene bottles are out -- 2 or 3 squeeze bottles on side of classroom (across from library) by sink, and 2 or 3 squeeze bottles in back corner near waste cart. Waste baskets nearby for easy use.

Also make sure strikers are distributed and flint is sufficiently long. Flints that are almost worn out can be moved to bench closest to prep lab door, in order for tech to keep an eye on them.

## Intro and Safety:

#### **Materials**

* Edits to manual
* Microscope Log
* Lab Agreement signature sheets
Culturing Paramecia

> **BACK TO CULTURING PROTISTS**
>
>

**Background**

Paramecia are the most common of the protozoans. They occur abundantly in waters containing decaying

vegetable matter, since their food consists mainly of bacteria that decompose dead organic matter. A single Paramecium can consume 2–5 million E.coli in 24 hours. Paramecia are oval in shape and quick moving. They are barely visible to the naked eye, usually white or clear in color (although P. bursaria are green due to a symbiotic relationship with green algae), and can reproduce both sexually and asexually. When conditions are favorable, Paramecia reproduce asexually by transverse division at a rate of up to five times daily. Paramecia and other ciliates are easily found in pond water and provide an excellent study organism for students. Cultures are easily started and maintained. Many culture techniques and media recipes have been tried culture media for Paramecia are described here.

**1x Chalkley****Alfalfa Medium** **\*\* RECOMMENDED\*\***

Alfalfa medium is also excellent for growing ciliates. Add one alfalfa for each liter of boiling 1× Chalkey’s solution. Allow the alfalfa to soak and form a sediment on the bottom of the container. The sediment will be a food source for bacteria.

To culture ciliates, add 10 previously boiled wheat seeds to a jar containing 750 mL of cooled alfalfa medium. Inoculate the jar with 100 mL of ciliate culture. If time allows, wait three weeks for the culture to peak. Subculture by preparing culture dishes with 200 mL of fresh medium and add 5–6 mL of the established ciliate culture as inoculum. (Monitor cultures regularly using a stereoscope.)

**Tips**

* When ciliate numbers are high, they are easier to see with the naked eye. Observe cultures regularly using a stereoscope to monitor population levels. Ciliate cultures will often strike a perfect “balance” and continue to thrive for long periods of time. Thriving cultures can be used in turn to create multiple subcultures.
* Alfalfa pills can be purchased at garden shops, farm supply stores, and health food stores.
* Paramecia and other ciliates are generally fast-moving organisms, which makes them challenging for students in slide

manipulation and focusing. Quieting solutions, such as methyl cellulose, can be helpful in slowing down the organisms for microscopic observation. Use low power (100X) to scan for Paramecia before switching to a higher magnification (400X).

**Disposal**

Paramecium cultures may be disposed of according to Flinn Suggested Biological Waste Disposal Method Type IV. Please consult your current Flinn Scientific Catalog/Reference Manual for proper disposal procedures.
Mealworms

## About

Mealworms are interesting little critters. They are commonly used as food for reptiles, fish, and other small animals. Mealworms grow up in to darkling beetles; they are used as food in their larval stage (the mealworm; which is not actually a worm!). Here at the lab, we have a breeding container for these little bugs. They require very little maintenance and are easy to clean up after!

 Quick Facts

 **Class** | Insecta

* **Diet:** Detrivore
* **Lifespan:** 2-4 weeks or longer (for adult darkling beetles)
* **Temp:** 72-81 Fahrenheit
* **Habitat:** Ground dweller
* **Humidity:** 50-70%

## Feeding

Feed these guys as needed; when they exhaust or almost exhaust their carrot in the container.

1. Open fridge, find carrots.
2. Break off or cut off a piece of carrot for the bugs.
3. Place it somewhere in their home.
4. You are done!

*\*\*You can wet the carrot a little bit before putting it in to give them more water. They get water from their vegetables\*\**

## Cleaning

* Try to remove all the shed skins first. This is usually the easiest.
* Gently move any pupae you see to the top dish. This prevents them from getting eaten while they grow. Remove any adult beetles from this dish as soon as possible.
* Remove any dead adult beetles.
* Occasionally, use a sifter to remove debris from their container. Slowly sift through all of their bedding until it looks nice and clean to you.
* Replace their food source (the oatmeal and wheat) as needed.
* Be gentle when picking up live bugs.

## Links & Resources

Here are some extra links on these bugs, if you desire to acquire extra knowledge on them.

* Raising Mealworms
* Darkling Beetle Facts
* In-depth Care Guide
* Care Sheet
* Raising Mealworms
* Care Mealworms
* What are Mealworms
Isolation from Soil

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NOTE\*\*\* Spring 2018 I had WAY too many plates leftover. Talk to Steven about expected #s

### Lab 1

**Per pair of students**

* Soil Sample (provide sterile petri dishes and forceps for collection)
* 4x 4.5 mL (16 x 125?) tubes of NaCl 0.85% (dilution blanks) = 0.85g NaCl /100mL H2O
	+ example\*\*\*\*(12 g NaCl / 100 mL water) = (w/v = g/mL) 12% NaCl solution\*\*\*
* \*\*\*4 x AIA (Actinomycete Isolation Agar) plates
	+ Link to homemade recipe
	+ Link to pre-made at Sigma Aldrich
* weighing paper
* 4 x 1ml sterile pipettes (wrap in foil and autoclave)
* sterile dirt collection vessels (we used petri dishes the first time)
* manual pipettors
* sterile spatulas?
* sharpies

**Other Equipment**

* vortexers
* balances
* alcohol beaker (1 per pair)
* glass spreaders (1 per pair)

### Lab 2

**Per pair of students**

* \*\*\*4x fresh AIA plates
* original incubated AIA plates
* loops
* dissecting microscope
* forceps
* beaker of alcohol
* sharpies

### Lab 3

**Per pair of students**

* Plates of *Streptomyces griseus* controls (incubate 2-3 days on AIA - takes 2-3 days to see colonies)
	+ Get stock plate one week early to have time to grow up plates
* \*\*\*5 x Penassay Agar plates (had 20 leftover in Spring, confirm student #)

* Lab 2 incubated AIA plates
* loops
* forceps (small sharp)
* beaker of alcohol
* dissecting scopes

### Lab 4

**Per Table**

* Broth Cultures (each group gets 3 of the 6 cultures so make 3 of each per class): *Escerichia coli, Pseudomonas aeruginosa, Staphylococcus epidermidis, Enterococcus faecalis, Klesiella pneumoniae, Staphylococcus aureus.* (Can be 24-48 hours. Either is fine)

**Per pair of students**

* Lab 3 incubated Penassay Agar plates
* loops
* sharpies

### Lab 5

**Per pair of students**

* Lab 3 and 4 incubated Penassay Agar streak plates
Enzyme Lab Instructor Notes

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Back to Enzyme Lab

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### **Safety Precautions**

* Students must wear their safety glasses while using the buffers and MUST wash their hands afterward.  Otherwise, we may have safety glasses to give the students.

**Materials Locations: If I am not here**

* The enzyme juice is “fresh squeezed” and is located in the fridge in the prep room. Each lab table gets 1-25mL flask.
* The frozen enzyme test tube (6/section) is located in the ice chest behind your bench.

**Dirty Test Tubes:**

The wash bucket for the dirty test tubes is in the sink. ***MAKE SURE that your students wipe off the writing and remove any remaining bits with the test tube brush and make sure that the tubes fill with water and sink. If they do not do it, I have to do it and that is A LOT of test tubes for one person to wash!!!! (# of test tubes x # of benches x # of sections)***

**Cold Tubes**

The cold tubes are located in the freezer, they have the liver enzyme juice already added for convenience of time. Students need to start at B.

**Petri Dishes:**

Please have each table perform a swab of various areas for the Scopes and Cells lab. There is no exercise but I put the plates with the Bacteria cell boards to observe diversity and have a discussion about the scientific method - positive and negative controls, etc. To avoid pathogens caution students against using any mucus membranes (nose, saliva etc.). There are 2 extra plates for you to use as negative and positive controls and each plate is labeled by section time and table #.

**Boiling Water:**

* Use caution when handling hot test tubes.
* Watch the water levels and refresh when needed**. It evaporates quickly and the beakers will explode if the water runs out**

**End of Class/Before you leave:**

* Please allow time for your students to wash down the tabletops.
* Place enzyme flasks back into the fridge (if no class after)
* Turn off and unplug hot plate
* Please replace 15 clean test tubes on the racks on each bench
* Make sure that all dirty tubes cleaned are sunken and soaking in the sink
* Replace 6 swab tubes for the next class

**PM Folks:**

* Turn off and unplug water bath
* Please instruct your students to return the lab to the way you found it: push in chairs, wipe down benches and return experiments to their original conditions.
How to set up pages

**To set up a protocol page:**

1. Click on Contribute > Add a page
2. Name the page as accurately as you can. Name it whatever you would be searching for, if you could not find the location of the page.
3. Write your protocol. Add videos and pictures to make it the best page ever!
4. Save the page
5. Make sure to add the main category page name(s) on the list of categories at the bottom of your new page. This helps when someone just clicks on the category, then they can find all pages pertaining to that category. Right now, we only have a small list of categories on the front page but if you make one up for your page, please ass it to the bottom of the HOME page also, so we can click through to that category!
6. You can add your page to more than one category. For example, I would put the Gold Fish page in Room 317, Student Employees,and Animal Care categories.

Viola!
Guppies

## About

Our guppies are interesting little creatures. We have several of them; perhaps too many to count. This page will outline the care you must give them for them to be happy!

## Quick Facts

 **Class** | Actinopterygii

* **Diet:** Omnivore (Algal particles and insects in the wild)
* **Lifespan:** 2-5 years
* **Temp:** 74~82 Fahrenheit
* **Habitat:** Freshwater

## Daily Checklist

* Check the water level; should not be all the way up to the top. The yellow square in the photo indicates roughly how much space should be left when filling with water.
* Feed the guppies
* Check overall health of tank

## How to feed

1. Locate the food. It is in a yellow container. There is a photo of what their food container looks like located to the right.
2. Open the food door on their aquarium, and sprinkle the food in for them; as little as possible.
3. Be careful to not over-feed so the tank doesn't get dirty.

*\*\*Guppies should be fed every day. It's okay if some days are missed.\*\**

## Cleaning

The guppies don't make too much of a mess, but do need to be cleaned out every once and awhile or it could become unhealthy for them. Cleaning them out every few weeks is ideal. Here are some tips:

* UNPLUG EVERYTHING FIRST. The heater and the filter.
* Use a suction tool to clean out the gravel.
* Really focus on the gravel. All the waste tends to get stuck in it, so you must sift it around to get everything out.
* Pull out as much water as you need, without removing over 75% of it. Generally, try to take out about half. If you need to take out more because its really dirty though, it's okay.
* Pull out all their plants, hide-aways, and everything else, and clean those with DI water and a sponge or other cleaning tool. No soap!
* Clean out the filter and, especially, the filter tube. The filter doesn't need to be cleaned every time, but the tube should be. Clean the tube with a brush or the tube cleaner with magnet.
* Clean out the area under the "pots" on top of the tank. Remove the pot try, put it aside, and wash out the entire tray. It usually catches the most grime (besides the filter tube).
* Don't forget to plug the heater back in!

## Links & Resources

Here are some extra links and resources about guppies, just in case you want to learn more!

* Guppy Care
* Very extensive guppy guide
* Guppy Begginer's Guide
Catalase

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## **Lab 1 Materials**

* Broth cultures per table:
* *Staphylococcus epidermidis*
* *Staphylococcus aureus*
* *Enterococcus faecalis*
* NA plate = 1/pair
* Inoculating loop per student

\*\*\* If doing Coagulase 1 on the same day, the students can use their S.a. and S.e. broth cultures for that lab as well.\*\*\*\*

## **Lab 2 Materials**

* Incubated Plates
* Clean glass slides (student tables)
* Clean toothpicks (back counter)
* Hydrogen peroxide (back counter)
Reagent Library

### Barritt's Reagent (V-P Test)

1. Solution A is prepared by dissolving 6 grams of a-naphthol in 100 ml of 95% ethyl alcohol.
2. Solution B is prepared by dissolving 16 grams of potassium hydroxide in 100 ml of water.

### Crystal Violet

#### Ingredients

* 20 g crystal violet
* 200 ml 95% ethyl alcohol
* 8 g ammonium citrate monohydrate
* 800 ml deionized water

#### Prepare Crystal Violet Stain

1. Dissolve 20 g crystal violet in 200 ml of 95% ethyl alcohol.
2. Dissolve 8 g ammonium oxalate monohydrate in 800 ml deionized water.
3. Mix the crystal violet and ammonium oxalate monohydrate solutions to make the crystal violet stain. Filter the stain if necessary.

### Phosphate Buffered Saline (PBS) (10x)

* 40.0gNaCl
* 1.0g KCl
* 7.2g Na 2 HPO 4 (Monobasic potassium phosphate)
* 1.2g KH 2 PO 4 (Sodium phosphate dibasic)
* 500mL media water
Ubiquity of Microorganisms

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Per student pairs:

* 6 NA plates (72/class of 24)

* 5 sterile swabs (60/class of 24) with extras.
	+ Use 20 x 150 TT, plastic or metal cap. Add 1 ml of water to moisten.
	+ Store carefully, as spores are often seen growing on wooden applicators.
	+ Maria added a fifth swab so that each person can swab half of plate C (unwashed, moist body part)

\*\*\*\* Re-plate, parafilm, and store the cultures that will be used for unknowns at the end of the semester. So they are not touched or contaminated.\*\*\*\*\*\*\*\*\*\*\*\*\*\*
Goldfish

## **About**

   Our Goldfish at the Lab are very friendly animals. We currently have 2 of them, and they live in harmony together. They are very friendly and simple fish! These fish will follow you around as you move in front of the tank and will often go right up to your hands when you work on the tank.

 Quick Facts

 **Class** | Actinopterygii

* **Diet:** Omnivore (Plant matter and insects in the wild)
* **Lifespan:** 5-10 years
* **Temp:** 68-74 Fahrenheit, tolerates wide range
* **Habitat:** Freshwater

## Feeding

1. Open the top right drawer right under the goldfish tank. (*The one nearest to the sink*)
2. Locate the food. It is in a petri dish; it is pictured here. It will be sitting inside the drawer.
3. Drop in several pellets. Make sure both fish get some.
*\*\*The Goldfish need to be fed **once every day**. If some days are missed every once and awhile, it's not too big of a deal.\**

## Cleaning

The goldfish can generate quite a mess if left uncleaned for too long. The snails in the tank help out, but that's not enough; they are messy fish and the snails need our help. There is no specific way to clean the tank; do it however you like, but here are some general tips:

* Use a large bucket or trash can to siphon all the dirty water in to. Put it on a cart or a chair.
* Use a siphon tube to clean out the tank. Ask which one to use; we have a nice one that makes cleaning easy.
* The gravel holds the most dirt, so you want to focus on that with your siphon.
* Make sure you don't take out more water than you have to put in. The replacement water is kept in the white containers under the sink.
* You also can scrub the walls with the special white sponge. This is kept in various places; please ask someone where it is. This will get all the algae off the walls and make the aquarium look nice.
* Use a razor or plastic scraper to remove the string-like algae that shows up on the walls. Be careful to not scratch the tank.
* Don't worry too much about scaring the fish. As long as you don't actively chase them with tools or be purposely mean to them, they will be fine.
* Occasionally pull out some of the stringy algae.

## Links & Resources

If you wish to learn more about goldfish care, here are some links for you. This is not necesarry knowledge for the lab, but it's always nice to have some extra knowledge.

* General Care
* Myths & More care info
* Species Information
Water Lab Prep Instructions

**Water Lab**

Prepare ahead:

* ~150mL of 15% sugar/water solution for EACH section and 30% solution (1-3 days)

* Dialysis tubing – cut (check 1 month and cut within a week)

* Blue water ice cubes (1-3 days)
* Olive oil ice cubes (1-3 days)
* Cold red water (1-3 days)
* Colored water for dialysis (0-1 day)
* Acquire milk, ammonia, coffee, orange juice, and soda

* Make sure we have all materials: olive oil,

isopropyl,  etc…
**15 and 30% sugar**
water

Each section will receive ~150mL of each solution, make a bit extra for safety.

* 15% = 30G sugar : 200mL Total volume
* 30% = 60g sugar : 200mL total volume

**Food coloring**

Make sure to put ½ as many drops as mL of total volume Ie., 200mL = 100 drops of food coloring
Prep Lab Semester Preparations

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## Duties

**Here is a list of things that need to be done in the prep lab between semesters. This will help us start the next semester fresh and ready to go!**

### Cleaning:

1. Deep cleaning of all glassware:Look through the glassware cupboards and pull any glassware that looks foggy or just not clean enough. This includes all test tubes, including the test tubes in the boxes. Clean them to the best of your ability and return them to the cupboards.
2. Deep clean sinks: You can use a vinegar soaked rag to soak the metal overnight, this removes rust and hard water stains. May need to request a cleaner.
3. Clean all surfaces: remove objects, dust and sanitize all bench tops, inside hood, shelves, etc...
4. Clean out and organize refrigerator(s). Make sure that anything left is needed and not rotted.

### Organization:

1. Organize glassware
2. Deep clean and organize all cupboards and drawers
3. Organize all messes left over from the previous semester: Make sure that all supplies are returned to their place.
4. Organize and take stock of all prepared slides.

### Stock and Refill:

1. Refill any standard media
2. Report any shortages of glassware: If you noticed that you were running short on anything in the past semester, report the need to the Lab Coordinator
3. Take stock, buy, replace, or report any standard supplies in the lab. Like; cleaners, media, etc...
4. Check First Aid Kit Inventory

### Organisms

1. Take this time to deep clean and care for all of the organisms, report the need for new supplies, deep clean the environments, build new sites for organism care.
Current Semester Break Projects

## OUR SUMMER PROJECT LIST 2017

Here's a list of projects that Danielle is adding: some big and some small. Cross them off as they're finished.

### Projects for us

* Reorganize Animal cupboards: Mulloscs, arthropods, echinoderms, verts, etc...
* Clean all of the yucky gunk off of all of our glassware: Tape residue, old marker, etc...
* Clean, organize tops of prep lab cupboards. See what is in boxes, match ice chest tops and discard extras
* Deep clean counters, sinks, inside cupboards
* Clean ~~classroom drawers~~ and scope cupboards
* Check and organize lab cupboards
* Update organism care pages
* Give fish tank a good cleaning, buy plants and snails and other stuff for it.
* Make more mystery tubes: need more than 15 - Check with Scott about that
* Organize all aquarium stuff. Organize Under touch tank, Put some in storage, bins, etc...
* ~~Update all online to-do pages: Lab care, animal care, etc...~~
* Build our online media library from Beth's hard copy. This can be done any old time and the hard copy is hanging in Danielle's office on the board behind her desk
* Research how to grow mushrooms at home... mushrooms: learn how and test
* Make a "How to make a Scientific Poster" Poster Before Fall Semester

### Danielle's Projects

* Update Website for summer semester
* Update Bio 10 set-up instructions to be more simple and easy like Micro
* Update Review Day materials
* Room 313 Printer - Call Marshall and organize new printer with him -D-
* Set-up Dani's Kindle in the Prep Lab ~D~
* Organize Storage Room for better efficiency
* Build a polypeptide chain out of different beads on wire: like the one on Danielle's window sill -D-
* Mushroom hunting -D-
* Mushroom spore prints
* Build SDS sheets and laminate for Micro classes - D-
* Student Employee mastery list, training list, meeting schedule, etc... -D-
* Inventory database???? Work with Class needs -D-
* Update Bio 10 instructor notebook -D-
* Go through all labs for next Fall and look at inventory needs - See inventory database -D-
Micro 5 Enterotube

\*Ask Maria if these unknowns are what she would like

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ENTEROTUBE CODE BOOK

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https://www.youtube.com/watch?v=wWj5LvLSHD8&ab\_channel=bioprofaz

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* 1 x Enterotube II identification system
* MacConkey Plates as unknowns:
* Gram Stain materials

### Lab 2

Per Student

* Incubated Enterotube
* Incubated plates
* Color Key
* Interpretation Guide

## Original (Steven's Class)

### Lab 1

#### **Materials**

**Per Bench**

* 1 x Enterotube II identification system
* Using MacConkey Plates as unknowns
* Gram Stain materials

*Incubate @ 30° or 37° for 18-24 hours*

#### **Extra additions**

1/2 class continues with biochem tests:

* TSI - 13 tubes
* SIM agar deeps ( don't have) - Need Kovac's REagent to go with
* Urea broth - 13 tubes - make from recipe
* Simmon's citrate agar slants
* nitrate reduction broth (don't have)

### STEVEN's EMAILs REGARDING THE CHANGES

From Spring 2017

If
Beth has Urea and can lend us some, that would be great.  We only need 13
or so of each type of media, since half the class will do enterotubes.  We don’t need Nitrate yet.  SIM is a great one to have, but also requires something called Kovac’s reagent to go along with it (in addition to the media).  Nitrate tests also require additional reagents that I hope we can acquire.

From Fall 2016

I just realized that the Enterotube lab calls for one per table.  That makes sense given the
expense.  Unfortunately, I did not think about that as I was planning the
lab and absurdly thought about using one per student.  I think we have
enough for three semesters, but I am wondering about using two per table this
semester and then phasing out the Enterotube in favor of a handful (3 or 4)
biochemical tests per student.  (We could still do one per table next semester when I have done more advance planning.)

If we did two per table this
semester, I am wondering about the possibility of having the other half of the
students (actually 13, to be precise) performing the handful of biochemical
tests.  Triple Sugar Iron for sure and then 2 or 3 others.  If this
is possible, I realize I am asking you to prepare a bunch of media with little
notice (this is for Tuesday).  The other 2 or 3 could be SIM agar deeps,
Urea broths, and perhaps Citrate Agar or Nitrate Reduction Broths.  Even
just the first two would be great.  If we do not yet have these media, I
can try to think of others.  If it is too late for anything, I can figure
something else out.

### Lab 2

#### **Materials**

**Per bench**

* Incubated Enterotube
* Color Key
* Interpretation Guide
Indigenous Flora

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## Period 1

**Materials/Group:**

* 5% Blood Agar plates per/person. Pour day before used for better hemolytic action
	+ Order enough blood for M5 Microflora, M60 Microbiota and M5 CA-MRSA
	+ 1/student + 1 extra for control
* Control cultures: *S. aureus* and *S. epi (Not correct? Ask Scott.)*
	+ 1 each for Maria
* Sterile swabs in test tubes with enough water to cover cotton tips: 2 per/person
* Toothpicks

* Slides
* Gram stain reagents

## Period 2

**Materials:**

* Gram stain reagents
* Slides
Disinfectant Effectiveness

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### Day 1

**Student pairs**

* 4 NA plates
* 4 sterile swabs
* Tiles split into 4 sections (in storage room)
* bacT (ask scott?)

**Solutions - check which we use**

* Vesvine
* Microban
* hand sanitizer
* antibacT soap
* surgical scrub brush
* Septisol
* Providone Iodine
* H2O2
* 10% Vinegar
* 10% bleach (2 squirt bottles)
* 70% ethanol (2 squirt bottles)
* Clorox wipes or Lysol wipes

Note on board to try other classrooms
Bio 16 Cormorant Pellets Lab

## Materials

\*Make sure to handle items with gloves and autoclave after the lab, as pellets can be a source of bacterial contamination such as salmonella\*

* owl pellets
* Hand magnification loops
* Dissection needles
* Forceps (small)
* small finger bowls
* dissection trays (metal)
* Sorting charts
* Latex gloves

## Materials (Steven)

1. dissecting scopes
2. dissecting needles
3. and maybe a few other glassware items
M&Mology

## Bio  100 materials needed

1.  fun size M&Ms (enough for one pack per student ~ 24)

2.  water lab materials (osmometers, adhesion/cohesion stuff, etc.)

3.  “Incredible journey” activity requires: wooden dice (I’ve already brought wood blocks),  large pictures of various water features: glacier, aquifer, wetlands, ocean, rivers, etc.

4.  Know-no games - Don't know

5.  for a water tasting activity:  a brita filter
pitcher,  60 small drinking glasses (not
paper or plastic, must be glass), 1 liter bottle of spring water
Micro 5

## **SPRING 2022**

Full List of Labs (to finish soon)

***Ames Test|***

***Antibiotic Sensitivity***

Aseptic Technique

C.U.R.E.

Catalase

Coagulase

***Coliform***

Colony Morphology

***ELISA***

*Endospore Stain*

Eneterotube

Eukaryotes: Fungi | Pondwater and Termites

*Gram Stain Unknown*

**Hanging Drop**

*Isolation from Soil*

MacConkey

Microscope Calibration\*

MSA

*Streak Plate*

Transformation

TSI

Ubiquity

Unknown Bacteria 1 (Intro)

Unknown Bacteria 2 (streak plate)

Unknown Bacteria 3 (Isolation 1)

Unknown Bacteria 4 (Isolation 2)

Unknown Bacteria 5 (Biochem 1)

Unknown Bacteria 6 (Biochem 2)

Unknown Bacteria 7 (Biochem 3)

Unknown Bacteria 8 - Biochem 4

Unknown Bacteria 9 - Final results

***WBC***
Koch's Postulate Prep

(after page 38)

## Lab 1 Prep:

Purchase 1 quart organic milk, usually Straus, Maria asked me to avoid Clover b/c it had failed in cheesemaking, Yogourmet starter.

1. Autoclave micro-centrifuge tubes, yellow for yogurt, white for milk. Will need one per pair of each in lab 1. If 48 students in two sections, then need ~25 or so of each.
2. Sterilize agar -- pour plates. Beth used a Tryptic Soy Agar Plus -- the plus meaning a recipe booster she uses. I have used for several years now a mixture of Tryptic Soy Agar mixed with Lactose Broth, following amounts called for on bottles -- i.e., if 20g/L for TSA & 5 g/L for LB, I use 20 + 5 for a liter. Make double the plates as they are used in Lab 1 (1 plate per pair) and Lab 3 (1 plate per pair).
3. Autoclave about 25 empty 12x125 test tubes with caps. A dozen extra minimum is good in case students find different types of colonies and they want to inoculate both.
4. Autoclave several beakers with stirring rods, covered with foil. Enough for a couple to be Bio10 yogurt (if Danielle wants it). A 1 liter, 2 125 ml, 1 500 ml, 1 250 ml (no
5. Heat milk in 1 liter

## Lab 1:

* TSA & LB plate (1/pair)

* microtubes of milk (1/pair)

* microtubes of yogurt (1/pair)

* sterile water (making wet mounts)

* pH strips 2-9

* loops

* wood stirrers

* slides & coverglass
Bio 10 Enzyme Lab Prep

* Start Prep 1-2 weeks before lab
* Thaw and pipette 1-2 days before lab

For 2 sections, we prepared 50g liver : 150mL DI H2O

1. Weigh out appropriate amount of liver
2. Cut into small chunks
3. Add water and liver chunks to blender
4. Blend for about 10 minutes in the hood (it stinks)
5. Pour into TALL SKINNY JARS
6. Let sit for a half an hour
7. Freeze until ready to thaw

Day 2:

1. Thaw in refrigerator a day or two before needed
2. use long pipette and remove the lower, more liquid layer. It can be difficult, maybe spoon some of the top fatty layer off first to avoid contamination. See what works best.
3. Pipette into tiny flasks. Don't put out more than needed, if left out longer than the say, it will rot and become less effective.

### Nutrient Agar Plates

These plates will be set out for the students to swab during the Enzyme Lab, but they will incubate and be saved for S&C Lab.

Prepare 8 plates per section = 1 - control / 1 + control / 6 plates (1 per bench)

Prepare them the week before:

1. Mix agar to the instructions on the agar jar. Agar is located in the media cupboard.
2. Autoclave
3. We usually use about 15-18mL agar/plate. SO... 8 plates x # of sections x 18mL per plate = XmL agar total
4. Maybe split the agar into smaller flasks before pouring plates. DO THIS AS ASEPTICALLY AS POSSIBLE!
5. Let the agar cool a little but not too much, it solidifies pretty fast. Don't lollygag!
6. Pour plates near a bunsen burner, leave to set with lids on.
7. Clearly split each plate into four sections (not controls) and clearly label each plate!!!
8. Refrigerate in labelled bags until use.
9. If there is agar left over, pour into a media bottle with an orange top, re-autoclave, label and put in the glass cupboard with the other media.
10. If you have too many plates, bag them up tightly with tape, label and date the bag and put into the fridge.

After Enzyme Lab:

1. Have the students swab the plates
2. Incubate the plates 2-3 days
3. Group and put into Bacterial Fridge in Room 317 until s&C Lab

### Cotton Swabs

These will be used to swab the nutrient agar plates

1. Take used but not dirty swabs
2. Put 4 in each "20" test tube: (6 tubes x # of sections = x # of tubes needed (plus a few for good measure) x 4 = # of swabs needed)
3. autoclave the tubes
4. Remove and separate for each class section
5. Cover with cling wrap and refrigerate

PLEASE MAKE SURE THE TUBES DO NOT BECOME MOLDY!

### Buffers

You will need pH 2, 4, 7, 10, and 13 buffers in squeeze bottles. Just make sure that there is enough prepared in the reagent cupboard. Check the acid and base cupboards for extra. If one is out, make more per instructions on the capsule bottles.

### Day-Of Set-up Instructions

* Make sure to add calculator to each student station
* Put up pH board at buffer station
* Only fill student station waters half way
* Do not turn on Hot plates
* Boiling chips
* Put out extra tube rack with clean tubes in the back of the room
* Remember cold tubes with 1 drop Enzyme in freezer x6
* Eyewear!
Bio 16 Microgreens Lab

## Planting Labs

### Materials Per Group

* mizuna or garnet giant seeds (Each group can choose 1)
* potting mix/soil (no fertilizer)
* vermiculite (Not using)
* flat trays to catch water under the sprout trays
* Sprout trays
* seed shakers
* buckets
* trowels
* cups for scooping soil
* trays to minimize mess
* sharpies
* Wood stirrers for tray labels or lab tape
* Balances (If we can have all 6, please provide)
* Weight boats

## Harvest Labs

### Materials

* scissors
* scales (If we can have all 6, please provide)
* trays
* weigh boats
* Buckets for disposal
* Spatulas for digging
M5 Koch's Postulates

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### **Methods**

\*Purchase 1 quart organic milk, usually Straus, Maria asked me to avoid Clover b/c it had failed in cheesemaking, Yogourmet starter.

1. Autoclave microtubes, yellow for yogurt, white for milk. Will need one per pair of each in lab 1. If 48 students in two sections, then need ~25 or so of each.
2. Autoclave extra beakers with stir bars to pour milk in for sterile transfer to microtubes, extra for Bio 10
3. Sterilize agar -- pour plates. Beth used a Tryptic Soy Agar Plus -- see recipe link
4. Autoclave about 25 empty 12x125 test tubes with caps. A dozen extra minimum is good in case students find different types of colonies and they want to inoculate broth.
5. Autoclave several beakers with stirring rods, covered with foil. Enough for a couple to be Bio10 yogurt (if Danielle wants it). A 1 liter, 2 125 ml, 1 500 ml, 1 250 ml
6. Heat milk in 1 liter

### Day 2:

* 5mL tubes of sterile milk (1/pair + extras)
* loops
* simple stain materials

### Day 3:

per pair of students

* TSA+ plate
* loops
* pH strips
* wood stirrers
* H2O Droppers

### Day 4:

* Incubated plates
* Sterile H2O
* loops
* simple stain materials
Bio 10 Scopes & Cells Lab Set Up

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**Here is the information needed for the Bio 10 Scopes & Cells Lab Set-Up.**

## Instructor Notes

### **Reminders**

* ·        Please have the students assigned to a microscope in the Microscope Log
* ·        Used cover slips need to go in the “used cover slips” finger bowls by the sinks.
* ·        The students need to rinse, wipe and return their slides to their drawers after use. PLEASE remind them that they do not belong in the cover slip disposal containers.

* ·        The students can find their slides in their drawers but I left some extras on your bench just in case.
* ·        Each bench only has one Archaea slide so students need to share.

### **Exercise 7:**

* The yogurt may be in the fridge. Please return it to the fridge after your class.
* After class, please have students return the lab to its original condition: push in chairs, wipe down benches, and neaten all exercise set-ups.

Thanks!

### More Detail

* Ex 1-4: Scopes and prepared slides. Some instructors skip Ex 4 to save time (since you will look at those next week as well)
* Ex 5: Just got a new culture of vinegar eels. Hopefully they will be happy on Monday
* Ex 6: We have toothpicks and methyl blue for cheek cells
* Ex 7: I have home made yogurt that I mix with water, the students just use a dropper to put on the slide. Students are almost never able to find the bacteria, usually need help identifying.
* Ex 8: We have 1 prepared slide of Archaea for each bench. The slides are pink stained and very difficult for students to find. You usually need to help them.
* Ex 9: We have elodea and salt solution, pretty fun.
* Ex 11-14: Poster boards on back bench with cell information and a plant and animal cell model.
* Also on the back bench will be those plates that the student swabbed. Instructors of the past usually just had them there for an example of diversity and an introduction to prokaryotes. And to look at because they are fun.

## Prep Instructions

### **Bacterial Plates**

* 2 weeks before: Make Plates: 1 per bench for every class
* 1 week before: Have students streak the plates with autoclaved used swabs.
* Incubate for 1-3 days
* Refrigerate until class
* Make sure to organize and pre-label ALL plates so there is no poblem with mix-ups\*\*\*

### **Swabs**

* Put 4 used but pretty clean swabs into the 20 metal top tubes.
* Put 1 mL of DI H2O
* Autoclave
* Store the tubes in the fridge and cover with plastic wrap to reduce contamination.

\*\*\*Make sure swabs are well covered while in storage, they mold easily\*\*\*

### **Yogurt**

* Prep some yogurt in a media bottle a week before. Store in the fridge fore use. Not a lot needed.
* Follow instructions on the packet. Incubate.
* For the lab, dilute to a hazy water solution, check under scope to make sure that the bacteria can clearly be seen between fat cells.

### **Pre-check:**

* Vinegar Eels
* Methyl Blue - quantity and dilution
* The yogurt culture - good bacterial presence
* Elodea - quantity
Survivor Wonderland

**Survivor Wonderland** is the 11th chapter of the Survivor Storybook series. This is the first Fans vs. Favorites season in the series.

## Production

The blog for this season is Survivor Wonderland and the tag for the season is we're all mad here.

## Twists

**The Rabbit Hole -** Basically Exile Island, you have chance to win advantages and/or Immunity Idols there.

**Tribe Swap** - After the first 3 tribal councils, we had a tribe swap in which Jordan Pines was left without a tribe and was exiled to the Rabbit Hole until the losing tribe votes someone out at their next tribal council. This made Jordan Pines immune for the round.

**TBA**
Microbiology Laboratory Information

This section of our Wiki includes a lot of information pertinent to a microbiology laboratory, the theory and information behind the cultures, tests, and protocols.

### Bacteria Information

Overview of Bacterial species. Click on the name of the Bacteria to see full description: Overview, Cell structure, metabolism, pathogenicity, ecological roles, genome structure, research, and references.

### Media Information

Overview and information about media used in the lab, including nutrient and chemical selectivity and differentiation information.

### Biochemical Test Information

These tests indicate the presence of certain enzymes that catalyze all the various chemical reactions of which the organism is capable. This in turn means that different species of bacteria must carry out different and unique sets of biochemical reactions. Biochemical tests are used to differentiate species via biochemical reactions.

### Other Protocols and Test Information

Other lab protocols and the theories behind them

## Tests used to identify Gram Positive Bacteria

* Catalase Test
* Mannitol Salt Agar (MSA)
* Blood Agar Plates (BAP)
* Streak-stab technique
* Taxos P (optochin sensitivity testing)
* Taxos A (bacitracin sensitivity testing)
* CAMP Test
* Bile Esculin Agar
* Nitrate Broth
* Spirit Blue agar
* Starch hydrolysis test
* Motility Agar
* Coagulase Test

## Tests used to identify Gram Negative Bacteria

* Oxidase Test
* Sugar (eg glucose) broth with Durham tubes
* Methyl Red / Voges-Proskauer (MR/VP)
* Kliger’s Iron Agar (KIA)
* Nitrate Broth
* Motility Agar
* MacConkey agar
* Simmon’s Citrate Agar
* Urease test
* Sulfur Indole Motility Media (SIM)
Bio 16 Compost Lab

### Materials

#### Lab 1

* Gallon sized plastic jars (we have 24)
* Plastic lids with clear tops – can poke holes if you’d like for air
* Cheese cloth
* Rubber bands
* Compost bags
* gloves
* Pond water and cups for poring about 2-5 table spoons
* spatulas
* Soil (ask instructor - some like some do not want)

### Lab 2:

Compost Jars

Compost lab is a part of the Microscopes lab in the manual

Link to Lab:

https://docs.google.com/document/d/1KkiYmuxwA21YRaWw7-NFZsjcZxC1TXAQ/edit
Fungi Lab Set-Ups

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## Instructor Notes

There is a Fungi video for you to show in class: 5 modules: run time 20 minutes

## Images

Click here to see the lab set-ups

1. Prepare about 75mL of potato (Dextrose) Agar as instructed on the jar. Pour plates and inoculate the plates after cooling with old cultures that are located in the rhizopus drawer.
2. You may make a couple extra to keep a fresh culture.
3. Parafilm the edges of the plates and put in the incubator at 25 degrees for 1-2 days.
4. You can see when the culture is matured by visualization of the spores on the sporangium and it turns "hairy and black". Keep the Parafilm on the plates for increased humidity and reduction of contamination.
5. Store in Rhizopus drawer until used.

**Lichen - 1 day**

1. Collect Fresh Lichen from creak
2. place in blender with a bit of water, maybe 20mL
3. Blend until well pureed

**Sourdough Starter - 3-5 days**

1. 1 cup flour
2. 1/2 cup water
3. 1 T yeast
4. 1 T sugar
5. Mix, cover with parafilm and put in fridge overnight
6. Add more of whatever is needed in the next few days to make a good dough that has lots of bubbles

**Wine - 2 days**

1. 300mL grape juice in a 500mL flask
2. 1 tsp sugar
3. 1/2 pack of yeast
4. use flask top with curved tube to run the CO2 bubbles to a 500mL flask with water
5. Add yeast or sugar as needed

**Cracker Demo - 1 month**

1. Find unsalted and all natural saltine crackers
2. cut two holes in the lids of 4 glass jars
3. hang the crackers in a layer of cheese cloth under the lids of the jars
4. Place certain percentage of salt water in each jar
5. label jar according to humidity
6. May have to use stir bar and a slight amount of heat for the jars with more salt. Allow to dissolve.

 95
 90
 85

**Mushroom Boxes**

1. Purchase 2
2. Start first on 10 days before 1st lab
3. Start second 8 days before

**\*\*Add spore prints to the set-up\*\***
The Eukaryotes: Fungi, Termites, Pondwater

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## The Eukaryotes

### **Materials**

* **\*\*The Class Before\*\*\*** Pondwater collection jars
* Pondwater transfer pipettes
* Dichotomous Keys (in drawer of 313 instructor bench)
* microscope supplies
* gram's iodine droppers

#### Live Cultures

* Termites
	+ Forceps and razors
	+ Water droppers
* Saccharomyces
	+ Make simple sugar-water Yeast Stew and let sit for about a day
	+ transfer pipette
* Rhizopus
	+ See Bio 10 Prep instructions for Rhizopus
	+ Forceps and tools

#### Prepared Slides

Fungi

* Aspergillus (Have 14)
* Penicillium (Have 15)

* Coccidiodes (Have 0?)

Protists

* Trypanosoma (Have 12)
* Plasmodium (Have 0?)
* Trichomonas (Have 12)

Helminths

* Echinococcus (Have 8)
* Clonorchis (Have 0 worms / Only eggs)
* Trichinella (Found 1 randomly)
The Bacteria

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* \*\*\**We will use our plates form Ubiquity lab for simple staining.*
* clean microscope slides / cover slips
* Sterile TT of H2O
* bibulous paper
* crystal violet stain
* lens paper and lens cleaner
* Stain trays
* Squeeze DI Water
* clothespins

* Ubiquity Plates or plate cultures of *Bacillus subtilis* and *Staphylococcus aureus* = 1/ bench
* Sterile H2O tubes

### Hanging Drop p. 48

**Hanging drop slide to determine Bacterial Motility**

Materials per table:

**1 x per table**
* 24- to 48-hour **nutrient broth** cultures of *Staphylococcus aureus* and *Pseudomonas aeruginosa,*
* toothpicks
* Lens paper and lens cleaner
* Immersion oil
* Clean depression slides and cover slips
* Petroleum jelly (Vaseline)
* Tub of Microban on the cart for used slides

###
Bio 16 Enzyme Lab

## Lab Manual Setup

* OBS 1 and 2 = 6 test tubes
* OBS 3 - Specificity = 3 test tubes
	+ U - Unknown Enzyme Labeled "U"
* OBS 4 - Temperature = 3 test tubes

\*New manual has no pH

IMAGES AND SETUP

See Bio 10 for full setup

## Steven's Setup

Setup the same as Bio 10 with the following changes:

1. OBS 1 and 2 = 6 test tubes | OBS 3 = 3 test tubes | OBS 4 = 5 test tubes | obs 5 = 3 test tubes
2. Add 2 additional temp baths @ 50 and 70 degrees (Enzyme 2?)

Bio 10 Enzyme Setup
Unknowns

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## Lab 1

Per student:

* Make sure to pre - G stain the plates that we are pulling from, to check for contamination
* 1 x NA plate
* 1 x Unknown = Numbered tube with a bacterial culture
	+ Make 6 Test tubes of each culture: E.f. / E.c. / S.f. / S. a. / E.a. / P.v. / S.e. / P.a.
	+ Number the tops and write out a key for which number corresponds to each culture

## Lab 2

Prepare any of the metabolic or id tests that the students order from the previous class:

They will generally be:

* Gm+ = catalase + --> MSA + --> Coagulase
* Gm- = Lactose Broth --> Brilliant green bile OR TSI --> (BGBB+) --> EMB

## Lab 3

Prepare any of the metabolic or id tests that the students order from the previous class:

They will generally be:

* Gm+ = catalase + --> MSA + --> Coagulase
* Gm- = Lactose Broth --> Brilliant green bile OR TSI --> (BGBB+) --> EMB
Coagulase

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* Ice buckets with....
	+ 2 microtubes of sterile rabbit plasma
		- Reconstitute with 3.5mL sterile water (can store in fridge for up to 5 days)
		- aliquot 350uL/microtube of prepared plasma (can store in freezer for up to 30 days)
		- Put on ice immediately
		- If any left over put in freezer asap
* Streak plates of *Staphylococcus aureus* and *Staphylococcus epidermidis.* \*\*\* If doing Catalase1 on the same day, the students can use their *S.a*. and *S.e*. broth cultures from that lab to use with this lab as well.\*\*\*\*

*\*Incubate microtubes for 24 hours*

## OTHER / QUESTIONS

When you add 6ml to the bottle, how do you mix it? How readily does it dissolve? Then, when students add their bacteria, do you then incubate at 37 overnight?

* I pop the rubber top so that I can easily access the interior of the coagulase bottle with one hand.  I add the sterile water using a sterile 5mL pipet (will do 6mL).   With coagulase bottle secure in the palm of my hand I lift the lid with my fingers, transfer the 6mL and you will see it dissolve instantly.  I do vortex it to make sure it is uniformly distributed throughout the added water.

* Yes it should be incubated overnight in the microtubes.  You want the bacteria to grow and eat the plasma so that they produce their byproducts that cause the reaction/or lack of in the plasma.

When should I mix up the coagulase? Can I make it on Friday, or should I do it Monday morning (day of lab)?

* Day of lab and just before they use it.  It should also be kept on ice until they add the BacT….

Like put the microcentrifuge tubes into a beaker of ice?

* Initially I thought of putting the rack on ice, but that wouldn’t really chill it – thick plastic block type.

* Yes you want the tubes with the plasma to be cold until they are used.  So a beaker of ice would work well.
Introduction to Aseptic Technique

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### Other

Make sure Microban bottles are out -- 2 or 3 squeeze bottles on side of classroom (across from library) by sink, and 2 or 3 squeeze bottles in back corner near waste cart. Waste baskets nearby for easy use.

Also make sure strikers are distributed and flint is sufficiently long. Flints that are almost worn out can be moved to bench closest to prep lab door, in order for tech to keep an eye on them.

\*\*\*\* Re-plate, parafilm, and store the cultures that will be used for unknowns at the end of the semester. So they are not touched or contaminated.\*\*\*\*\*\*\*\*\*\*\*\*\*\*