Ecological Networks Module
Lesson 1 - Cell phone network introduction
Unit: Ecological networks Part 1- Network Interactions
Lesson Title: Lesson 1- Cell phone network introduction
Instructional Activities: (Two 50-min periods, may fit into one 90 min period)
Before beginning lesson: see cell phone advance prep 1.doc for help with lesson flow and advance preparation
INTRODUCTION TO NETWORKS (Power Point)
- Warm-up: see slide 1 in power point (Network intro and cell phone activity.ppt)
a. Pre-assess student understanding using this worksheet. (PreAssessment Ecological Networks.doc)
Once you have collected the student worksheets, lead a class discussion based on the two questions listed below. Goal: connect the idea of networks to previous knowledge. Some things they may come up with: computer networks, etc…b. Describe what you think the word "network" means.
c. Give at least 2 examples of a “network" - Introduce concept of networks: see slides #2 - 7 in power point. Concepts to introduce: what is a network, what is a node, what is an edge, what are some examples of networks in biology?
Key concepts: many things in biology may be represented as networks. A network is made of the individual parts of the system and the interactions between those parts of the system. We will use the word “nodes” to represent the parts of the system, and “edges” to represent the interactions. A food web is used as an example of a network, and students should have previous experience with food webs from middle school.
INTRODUCE CELL PHONE ACTIVITY (Power Point)
- Use slides #8-13 to provide students with an overview of the cell phone activity you will be completing in class.
Diagram should include both the number/letter label for each student as well as names for each student (see slide 9). The names of their classmates don’t get used later on in class, it just makes the activity a little more fun and functions as a get to know your classmates activity.
Direction of arrows in a network is a very important concept. Often interactions work in just one direction. Emphasize this using cell phone examples in slides 10 and 11
Why the "rules for network" (slide 12)? Most kids have experience with cell phones in real life, and they know its easy to add numbers to phone books or to call back someone who called you, so this is a pre-emptive strike against kids who say “Why can’t I just…?” The third rule is an attempt to get kids to talk to each other, avoiding a situation where one student collects all of the information cards and creates the poster by him/herself. This activity should be a lesson in teamwork as well as networks!
Slide 13 is an overview of what will be happening in the class. This is an important slide! There is a lot of moving around and switching groups in this activity, so it is important to give students a preview of what they will be doing.
STUDENTS CREATE PAPER VERSION of CELL PHONE NETWORK
- After reviewing the power point, pass out instructions handout (optional) and cell phone cards. (cell phone student instructions.doc), (Cell Phones.pdf)
You will have already given an overview of the instructions, so you may not need to go over the instructions with them. Inform students that you expect them to refer to their handout first before they ask you for help with “what to do next.” You may want to leave the PowerPoint slide with the instructions posted during the activity (slide #13 of Network intro and cell phone activitiy.ppt).
Another Idea: you may not find it necessary to pass out instructions to the students at all – the PowerPoint may have given your students enough information to complete the task on their own. Whether or not to hand instructions to each student is up to the teacher, it may be necessary for some classes but not necessary for others. You may wish to simply print a class set of 12 instructions, and place one at each of the stations (7 for the numbered stations and 5 for the lettered stations)
Inform students that there is some information on the cell phone student cards that is unnecessary for today’s lesson: the actual phone number (this is just for fun, they do not actually need this piece of information), and the information on the carrier, roaming, etc… This information is what the Cytoscape simulation is based on, but there are no questions written which require the students to use this info in lesson 1.
Extension idea: you may choose to add some challenge questions using that extra info (carriers, etc) and see if they can answer them using their paper network. This might enhance their appreciation of Cytoscape when they get to use it in lesson 2!
Classroom management tip: it is important to have time limits for each of the segments of this activity. Announce time limits beforehand, write them on the board, and/or you may wish to have a signal such as a bell because this activity can get loud!
- Students will fill out names on their cell phone cards.
Allow students to mingle in the classroom, give them 3 minutes to find the names of all of the people in their phone book. Purpose: to get students to mingle and learn each other’s names. Emphasize that on the poster you want to see both number/letter labels and actual student names from their classmates.
Note: if you do not have 35 students, it would be a good idea to come up with fake names for the students who are missing from the network. You can write these names on the white board. If no one was assigned 7A or 6A, for example, write on the white board 7A = Jesse, 6A = Tommy, etc… If you do not do this, each group will come up with different fake names and that gets confusing when you try to compare networks!!
- Students will meet with their numbered groups to begin network drawing.
See cell phone advance prep 1.doc for info on what should be ready at each station. Documents you should have photocopied and ready to go: Information Sheet for A, B, and C.doc, Information Collecting Sheets.doc
Important notes for teacher: make sure that students recognize that their drawing at this point will be incomplete. For example, they may know that 4a can call student 5b but they do not know the name of student 5b. Students will be tempted to “make up” additional information (such as a fake name for person 5b). Therefore, it is important to emphasize that they will obtain this information later, and that the network they draw at this point should ONLY include information that they KNOW.
Each numbered group will be creating one network poster. Remind students to use pens and color so their poster will be easy to read. Students are all expected to participate in the drawing (this is emphasized in the instructions). Students have done this successfully by splitting up portions of the network between group members, or by assigning different tasks: such as reader, node drawer, edge drawer, decorator/color specialist.
Suggested break point if required due to class time
- Students will meet with lettered groups to collect all additional information needed to complete network. Post the instructions from the PowerPoint (slide #13) to guide students.
Use of the "information collecting sheets" should smooth this portion of the lesson, because students will know exactly what information they need to find out. Remind them again that they need information on names as well as number/letters, and they should not be making up any names. Each number/letter is assigned to an actual classmate, and any numbers that are unassigned are named on the white board.
- Students will meet with their numbered groups again to finish network drawing.
STUDENTS ANALYZE CELL PHONE NETWORK
- Using handout (Intro to networks Student Questions.doc), students will analyze the cell phone network they have just created and will answer questions about routes of information flow through the system. See Intro to networks Teacher KEY.doc for answers.
Tell students that when they are completely done with their network, they should raise their hands. The teacher can then check on the poster to see if it looks complete, and then pass out the introduction to networks questions. Keep in mind that the students will need to use their poster to answer the questions, so these questions need to be done in class.
There is a suggested homework assignment which students can work on in class when finished with the intro to networks questions. This HW is to create a challenge question about the cell phone network. Encourage them to write a question which is tricky, inform students that they can use any information given on the cell phone cards (carrier, roaming, email, photo capacity). Inform students that these questions will be shuffled, and given out to another group tomorrow as a challenge (during the Cytoscape activity).
The goal is to have students analyze the creation they just made, and to observe how information can flow through the system from one node (person/cell phone) to another distant node.
A secondary goal is for them to analyze a paper version of the network, so they can compare and contrast this analysis with the analysis that can be completed using a computer program (Cytoscape). They should see, after the next lesson, that you can answer more complex questions about large networks using computers.
Assessment:
How will I know they know……
- Cell phone poster: were students able to successfully create a linked network? (group assignment)
- Cell phone questions: were students able to answer analysis questions about their network? (individual assignment)
- Cell phone homework: were students able to create a thoughtful challenge question about the network? (individual assignment)
- Networks quiz: are students able to create a network, and track the flow of energy through a network? (quiz)
Resources:
PowerPoint- Network intro and cell phone activity.ppt
PreAssessment Ecological Networks.doc
Cell Phones.pdf
cell phone student instructions.doc
cell phone advance prep 1
Information Collecting Sheets.doc
Information Sheet for A, B, and C.doc
Intro to Networks Student Questions
Intro to Networks Teacher Key
Intro to Networks Extention.doc
Accommodations:
The concept of networks can very easily be connected to your students’ daily lives. Think of any needed example, specific to their background, to link the examples given in this lesson.
Extension Activities:
A potential assignment would be for students to create their own network based on something else in their life. A family tree, perhaps, using the relationship “is the child of”, or a tree showing their social group, using the relationship “is friends with”. Challenge students to think about what the nodes in the network would be (people, computers, phones, etc…) and what the relationships, or edges, should be. Keep in mind that in today’s network, the nodes were student cell phones, and the edges were the relationship “can call”. Also view the Extension Activity that also can serve as a further lead in to Lesson 2 (Intro to Networks Extention.doc).
Lesson 2 - Cytoscape cell phone network
Unit: Ecological Networks Part 1- Network interactions
Lesson Title: Lesson 2- Cytoscape cell phone network
Instructional Activities:
INTRODUCTION/WARM-UP
- Warm Up Idea: list at least 2 ways in which your cell phone network from yesterday could be altered or “messed up”. Hint: think of things that might happen that could change who could call who.
Goal: get students thinking about the cell phone network again, and get the students thinking about how changes in a network will impact how a network will function. The cool thing about Cytoscape is that students will be able to make these big system changes and run simulations to see what the impact is.
Possible student responses: add a phone number to your phone book, cell phone dies so you can’t call your friends, drop your cell phone and break it, can’t get a signal, lose your friends phone numbers, etc…
If you did the homework assignment (create your own challenge question), have students pass in 3x5 cards now which have the questions on them. You can shuffle them and re-pass them out to students to answer while they are in the computer lab.
WHAT IS CYTOSCAPE?
- Show Power Point on Cytoscape and networks to show the program we will be using (Network Examples in Cytoscape.ppt)
Today the class will be using a computer program that is used in real-life biology research labs in order to study the interactions within networks. It will allow us to answer complex questions about complex networks.
Slides 2-4 show how food webs, something students are familiar with, can be written in network format with clear nodes and edges. Slides 3 & 4 show networks that have been created by teachers using the Cytoscape program.
Slide 5 shows the cell phone network which the students made yesterday- it will probably be much more neat and organized and easy to read than what students could come up with on paper.
Slides 6-7 show some applications of this software and how it is used in research labs. Networks can be REALLY complex! We hope to use this software again when we talk about genes and proteins in this class.
- Hook up teacher computer to projector in order to demonstrate how to use Cytoscape.
a. Pass out Cytoscape Instructions.doc and demonstrate the steps involved in opening the program.
Advice for teachers: you will need to test out these instructions beforehand. The program might open in a slightly different way depending on whether you are using a mobile laptop lab, your own personal computer, or the library computer lab. You should be able to follow the Cytoscape instructions step-by-step with the students following along.
b. Demonstrate some of the features of the cytoscape program. The most important features for today’s lesson are under the "simulation" menu.
- It is up to the comfort level of the teacher to decide how much time to spend on the "how-to".
- Selecting nodes: if you click on a node (remember: each node represents a cell phone), it will turn grey. This indicates that you have "selected" that node.
- Knockout and reactivate selected nodes: selecting nodes is useful if you would like to “knock out” that node from your system. In order to do this, select a node (see above) and then under simulation click on knockout selected nodes. The node will still appear on the screen, but all the arrows connecting it to the network will disappear. You have removed the node from the network: it can no longer make or receive phone calls. You can reinstate the node into the network by selecting reactivate selected nodes.
- Knockout & Reactivate nodes based on carrier: Remember from day 1 that the cell phone information cards had a bunch of extra information on them about what cell phone carrier you were using, whether or not the phone had email capability, etc… These properties are programmed into the Cytoscape version of the cell phone network. Therefore, we can use this information to knockout groups of cell phones based on their properties.
- Knockout by carrier: each phone has been assigned to one of seven carriers (note: these correspond to the numbered groups they originally met in while making the network). You can select to knockout a carrier, such as Verizon, and then all of the phones serviced by Verizon will be knocked out of your network.
- Knockout & Reactivate nodes based on property:
- Knockout by property: each phone can be put into a category of either phones with or phones without for each of the three properties email, roaming, picture.
- Phone Tree. You can use this function to answer questions about how information will be passed through the entire system.
- A separate window will show up for the phone tree function (see screenshot), and in this window you can select a start node from a list of all of the phones in the network. This represents the origin of the information flow. After selecting a start node, hit the start button and watch as the info flows through your cell phone network!
- When a person receives a phone call, their node turns red. When 1A is selected as a start node, all everyone except 5C gets a call, so 34 nodes turn red. (see screenshot)
- After all the calls have been made, a statistics window will pop up. This window gives some great information that they might be able to use to answer their questions. (see screenshot).
- Shortest Path. This feature is useful if you would like to determine the shortest path of information flow (ie least number of phone calls) between person A and person B.
- Reset Graph. This is a very important button because it will reset anything you have done; the knockouts, the phone tree, etc… If students think that they messed up, tell them to hit the reset button and try it again. It is also important to reset in between questions.
- Help page. This will link you to the ISB cell phone simulator help page (see screenshot), which has helpful links with instructions similar to those given above. May be helpful for students looking for help while on their computers.
- Pass out assignment for today: Cytoscape Cell Phone Questions.doc (also see Cytoscape Questions Teach KEY.doc). We will be answering more complex network questions using the large 35-node cell phone network.
Important: students should be using the computer tools to answer these questions, rather than just using the screen as a neater paper version of their network. Encourage the students to fool around with the various options in the software. If it seems to get messed up, they can always close the program and re-open it by following the instructions again.
STUDENTS IN COMPUTER LAB
- Walk to computer lab or pass out computers from mobile laptop lab. Students should work in groups of two on this activity, if possible. Students need to bring with them: Cytoscape instructions, Cytoscape cell phone questions, and a pen or pencil.
- LOGGING IN: it is very important that you STAGGER THE LOGIN process for all of the students in your class. There are many ways to accomplish this. One suggestion is to split the partners into 4 groups (have them number off 1-4), then tell them “Ones can log in now, Twos can log in now, etc…” Leave a few minutes lag time between each group.
Whenever you have many students logging on at once, it will slow down the system. In order to avoid this, stagger the timing of students log on… This is VERY IMPORTANT. If the computers freeze or slow down, students will get frustrated with the activity before they even begin!
- Wander the room and monitor student progress.
Things to look for:
a. look for the cell phone network screen to be open on their computer. They should NOT have a blank Cytoscape screen- the network should automatically appear if students follow the directions correctly.
b. If students are using the information flow feature, the nodes in the network should be turning red as information passes from cell phone to cell phone. Looking for the red color is an easy way to determine whether students are actually using the software.
c. If a student seems to have “screwed up” their network, and if you can’t figure out what they’ve done, DON’T PANIC! Simply close the program and then follow the instructions to restart.
Encourage students to play around with the software. Trying different things is the easiest way to learn how to use a program, and they should not be able to “ruin” the network, because they can always close down the program and re-open it from the website!
If students get done early: encourage them to try to create their own network and try to run the simulation on it. (see extension activities)
Assessment: How will I know they know…
Cytoscape Questions: student should be able to answer questions by manipulating cell phone simulation. Monitor student progress in computer lab: if the simulator is working, you should see nodes changing color from white to red as messages are passed through the network.
Resources:
Network Examples in Cytoscape.ppt (power point)
Cytoscape Cell Phone Questions.doc
Cytoscape Questions Teach KEY.doc
Accommodations:
This lesson results in students more thoroughly understanding how and why technology is used to understand complex networks and it also highlights many important aspects of biological networks (importance of redundancy, the variation in node importance, etc.). You can offer biological examples to illustrate this, but you can also encourage students to connect this further to their daily life. The conceptual thinking behind this is what is important, not the specific examples. This may also help when students become confused or intimidated by vocabulary. In this case, the vocabulary words (Cytoscape, simulation, knock out, etc.) are not required to master the needed content and ideas.
Extension Activities:
Have students create their own networks using Cytoscape.
How to make a network in Cytoscape.ppt If more guidance is needed for students to research their own network than given in the above PowerPoint presentation, provide students with possible networks to research, such as the African Savannah, Arctic Tundra, etc.
Also, the Extension Activity document listed in Lesson 1 can be completed after this lesson, instead of after Lesson 1 if more information on Bioinformatics is desired.
Lesson 3 - Introduction to extremophiles
Unit: Ecological Networks Part 1- Network interactions
Lesson Title: Lesson 3- Introduction to extremophiles
In this activity, the students will be introduced to the fascinating world of extremophiles. The students will brainstorm questions and research these unique organisms. In the following lesson, students will be presented with a real life example of an event that affected the Great Salt Lake ecosystem, the building of a causeway. Based on observations of this phenomenon, students will generate hypotheses about factors affecting the growth of one prominent extremophile organism in this ecosystem, Halobacterium. They will then think about how they could design an experiment to test their hypotheses. This will lead to the implementation of an experiment testing the affect of salinity on the growth of Halobacterium. In following lessons, the concept of networks will be expanded to include biological networks. Specifically, the students will be creating a network of the interactions existing in the Great Salt Lake ecosystem.
Instructional Activities:
INTRODUCTION
- Show a video of extreme skateboarding or talk about the man who skateboarded over the Great Wall of China (an extreme skater) this past summer. Discuss and hook about the fact that extreme humans exist. These people are risk takers, and they ultimately are as mortal as the rest of us.
- Tell students that there actually are organisms called extremophiles on Earth.
- As a class, brainstorm what an extremophile could possibly be. Record ideas on the white board. Ask students where they think these “extreme” organisms called extremophiles may live.
- Students may come up with ideas such as organisms that live in extreme temperatures, acidity, and may even suggest something like withstanding extreme pressure (There are no right or wrong answers at this point, all student answers are accepted)
- Students may suggest that extremophiles live in volcanoes, sulfur springs, etc. All answers are accepted and recorded.
- Use the Extreme life.ppt PowerPoint and Extreme life script.doc to show pictures of deep sea vents, sulfur springs, and other examples of extreme environments with living organisms. Characteristics that make the environments harsh such as temperature, pressure, lack of oxygen, lack of light, metabolic toxins, etc. should be discussed. This could be connected to the idea of “extreme” in marketing such as extreme sports, extreme flavor Doritos, etc. Video clips can be used. Teacher avoids discussing salt environments, unless the students suggest it.
STUDENT GENERATED QUESTIONS ON EXTREMOPHILES
- Guide a discussion for students to generate many questions about extremophiles such as: How are extremophiles classified? Where do they live? What is their source of energy? How do they tolerate different abiotic factors? Where did they come from? (see IntrotoExtremSuggQuestions.doc for examples) Record the questions on the board. Prompt if question-generation runs out. NOTE: The focus should not be on salt and Halobacteria in this section. Students will focus on and learn more about Halobacterium in upcoming lesson. Students should not use the Internet as a resource at this point. They will be using the Internet at a later point.
STUDENTS RESEARCH QUESTIONS ABOUT EXTREMOPHILES
- Using the provided Extremophile reading packets (Domain Archaea.doc, Life in Extreme Environments.doc, Rock-eating microbes.doc) students will split into groups of 3-4 and research teacher assigned questions (the ones generated by the class).
- Have students report out the answers to their questions. Depending upon available class time, students can give oral presentations with transparencies, and/or use butcher paper for posters.
Assessment:
Student presentations.
Resources:
Extreme life.ppt
Extreme life script.doc
IntroExtremSuggQuestions.doc
Domain Archaerevised.doc
Life in Extreme Environmentsrevised.doc
Rock-eating microbes.doc
Accommodations:
Provide students with more focused support in finding information within the readings. Break apart readings into smaller articles and read aloud excerpts as a class. Help students orally summarize paragraphs after they read.
Extension Activities:
Have students build a Cytoscape network using the blank template in the cell phone simulation program, from Lesson 2, to map out an extremophile´s environment or interactions. For uploading a network diagram: http://baliga.systemsbiology.net/cytoscape/blank/
Have students make a 'wanted' poster of an extremophile. This would be a good way to address classification and encourage students to become familiar with a variety of organisms. Extremophile Wanted Poster Teacher Tips for this model organism activity can be used for Extremophiles (instead of model organisms). A variation of this activity is found in Lesson 1 of the 'Environmental Influence on Gene Networks' module.
Lesson 4 - GSL case study introduction
Unit: Ecological Networks Part 1- Network interactions
Lesson Title: Lesson 4- GSL case study introduction
The students will be presented with a real life example of an event that affected the Great Salt Lake ecosystem - the building of a causeway. Based on observations of this phenomenon, students will generate hypotheses about factors affecting the growth of one prominent organism in this ecosystem, Halobacterium. They will then think about how they could design an experiment to test their hypotheses. This will lead to the implementation of an experiment testing the effect of salinity on the growth of Halobacterium.
Teacher Background Information
Instructional Activities:
Please note: There are VERY IMPORTANT steps that need to be taken for lab preparation. Please prepare the Halobacterium culture AT LEAST 4 days prior to beginning the lab with students. The directions for this are located in Lesson 6- Conducting halo salinity experiment in the section entitled, “Preparation of the Culture”.
INTRODUCTION
- Warm-up: Does a change in the environment result in a change in the life residing there? Does this include extremophiles? Why or why not? Give examples in your explanation.
If you want to emphasize vocabulary, use the terms abiotic and biotic in the question.With the extremophile research fresh in their minds, students may use examples of extremophile populations changing as a result of change in temperature, oxygen availability, etc. Accept all answers, and do not lead the students into thinking about salinity or Halobacterium.
- Introduce students to their Case Study Mission and the objectives for the lesson using Slide 1 (Link to PowerPoint – GSL Case Study.ppt):
- Analyze how an ecological disturbance could affect an entire ecosystem.
- Analyze the effect of natural events and human activities on the Earth’s capacity to sustain biological diversity.
Tell students they should use all information they know about life while analyzing the case study, including information learned (from this course and in previous years) about both extreme and non-extreme organisms.
- Present PowerPoint on the GSL causeway to introduce the investigative problem.
While keeping the warm-up question in mind and while presenting the entire PowerPoint, instruct students to write down their ideas in their journals. These will be referred to at the end of the presentation. EXPLORATION OF CASE STUDY
- Present slides #2-6. Have students discuss and record the differences they note in the pictures presented in slides 4-6.
- Slide 2: Case Study Details
- Slide 3: Specifics about Case Study
- Slide 4: Picture showing the North (Purple) and South Arms of the Great Salt Lake. Do not reveal it is the Great Salt Lake at this point; only refer to it as a body of water. The color differences in the lake are important for the students to notice. However, this slide, along with slide 6, may be difficult for students to see depending on your classroom and screen. If there is glare or any other obstacle in viewing this, explain the differences in color to the students.
- Slide 5: Picture of the railroad and causeway over the body of water. Students can note differences in the two sides of the causeway.
- Slide 6: 1984-Body of water in non-drought conditions; 2004-Body of water in drought conditions. Be certain to click through all items on the slides to show a comparison of the water levels. Encourage students to carefully observe all of the differences between the two pictures.
- When you get to slide 7, go slowly through the brainstorming questions, one at a time. As students offer suggestions, write them down in order to encourage active participation, inquiring questions and thoughtful ideas.
- Feel free to scroll back to the picture (slide 6) while they’re brainstorming.
- While they’re answering the second and third brainstorming questions, lead them to understanding that a change in the environment often results in a change in life. (Remind them of their warm-up question)
- After probing the students to give many possibilities, ask them what other information would be helpful. These are things that you can come back to at the end of the presentation if needed. After they have requested a variety of information, share slide 8 with them.
- Encourage them to think of as many possibilities as they can for the questions on this slide (i.e. an industrial plant is dumping freshwater into the side of the water they are near, half of the water is in a different weather pattern, one half has a freshwater spring, etc.). The correct answer: only one arm has rivers feeding into it. Without giving the answer, have them try to answer the remaining questions on slide 8. Use the brainstorming questions to guide their thoughts towards aquatic salt ecosystems that can be found on Earth.
- If only one side gets freshwater, then there are only a few options.
- This water ecosystem is a large puddle and will probably dry up eventually. If they assume this, ask if this is a likely situation given that previous information states the body of water has been around since at least 1902.
- This water ecosystem is either a small sea or a saltwater lake that is fed only on one arm by freshwater rivers.
- This water ecosystem was created by the damming of a river. Ask the students if this is likely the case after looking at the previous pictures. (No dams are apparent).
- After going through any possibilities, they should be able to see that option #2 makes the most sense. If students are struggling with identifying this as a saltwater ecosystem, revisit slide 6 and discuss what more or less water may do to any sample of water (dilute solutions).
- Lead them into brainstorming about the last question. This should further bring them to the idea that the concentration of the salt varies in the north and south arm. Ask them: How would the amount of rainfall received affect the life growing in the ecosystem? Is living in a high saline environment friendly or unfriendly? Are we able to live in this environment? Why or why not? Is it healthy for us to drink salt water?
The questions asked should lead them into the idea that a high saline environment is one that most “typical” life cannot live in.
- Show Slides 9–14 and discuss with students how other organisms are affected by living in a salt water ecosystem.
- Slide 9: 3 vials of E. coli, grown at 37°C for 4 days–the cloudy one had no salt lots of growth; high salt no growth
- Slide 10: Radish seeds watered with varying salt only no salt germinated
- Slide 11: Ivy one watered with freshwater the other with highly concentrated salt water (the dead one received salt water)
- Slide 12: Microscope image of a red onion cell
- Slide 13: Image of the same cells with salt added plasmolysis occurs
- Slide 14: same as slide 12
- Bring them back to the original question, Why do the two sides look different?
- Show them Slide 15 which tells them the body of water in question is the Great Salt Lake. This also shows them the food web. Slide 16 provides questions that will help them further brainstorm and explain possibilities as to why the two arms look so different.
- Students should observe that while there is a robust ecosystem in the south arm of the lake, the north arm has very little species diversity. The prominent organism in the north arm is Halobacterium. (The north arm of the lake is a red color.) It may be helpful to have a printed copy of the food web on Slide 15 for them to look at while they work towards answering the questions on Slide 16.
STUDENTS FORM A TESTABLE HYPOTHESIS AND DESIGN INVESTIGATION
- Students Design Experiment: Use slide 17 as a way to lead them into designing an experiment that will test whether or not Halobacterium can grow in a high saline environment.
Ask the students to think about what factors may affect Halobacterium. They should write these down in their lab book or journal. Possible student answers may be the amount of oxygen, sunlight, salinity, pollution, etc. If students only offer the idea of salinity, encourage students to brainstorm other factors that may affect Halobacterium.
*It is very important to record and keep the list of class hypotheses. Students will revisit this list and design experiments to test these hypotheses as an assessment following the investigation.
- Focusing on the idea of salinity, ask the students how they think salinity may affect the growth of Halobacterium. Students will form a testable hypothesis answering the question.
While emphasizing the need for evidence to support their hypotheses, ask the students how they could test the effect of salinity on the growth of Halobacterium. What are the variables? How would they go about testing their hypothesis? What controls would they need? How would they set up the lab?
- The students should generate a detailed procedure on how they would test their hypothesis. Note: In the students’ procedures they can use the term “measure” in a general format when referring to measuring the growth of Halobacterium. At this point they have not been introduced to the spectrophotometer.
Teacher Options: Depending upon student skill level, the teacher may choose to informally assess or not asses the student’s proposed procedures. Teacher may opt to have students design procedures as a whole group, small groups, or individually. This portion of the lesson should not take up too much of the overall lesson time.
Use the experimental design prompt to guide students. The experimental design grader.doc can be used to assess students procedures.
- The actual, optimized lab should be presented on the next class day. Please see Lesson 6- Conducting halo salinity for further information.
Assessment:
How will I know they know….Collect the student journals to view and evaluate their hypotheses and procedures. The experimental design grader.doc can be used as a rubric.
Resources:
PowerPoint: GSL Case Study.ppt
experimental design prompt
experimental design grader.doc
Accommodations:
During the discussion portion, when viewing the PowerPoint slides, be certain students describe all needed observations out loud as a group while you write down these observations on the board. Some students may not be able to notice the intensity of the color difference between the arms of the lake. Spend time discussing all of the observations noticed and even discuss what other observations a person might make if they were able to physically be at the site. Highlight machines, such as spectrophotometers, that can also be used to qualitatively measure the color and concentration of a solution.
Extension Activities:
Lesson 5 - Spectrophotometer and micropipette use
Unit: Ecological Networks Part 1- Network Interactions
Lesson Title: Lesson 5- spectrophotometer and micropipette use
The students will be introduced to two different pieces of equipment, the micropipette and the spectrophotometer. Both of these instruments will be used in a future investigation. First the teacher will introduce how to use both the micropipette and spectrophotometer through a short video clip and through modeling the use of the equipment. The class will then be divided into groups. Half of the class will start by completing the spectrophotometry activity and half of the class will start with the micropipetting activity. After about 20 minutes the groups will switch. Upon completion of the two activities, students will know how to use the equipment properly and efficiently.
Teacher Background Information: This activity is designed to introduce the students to micropipettes and spectrophotometers. Micropipettes are one of the primary tools of the laboratory biologist. These instruments allow you to measure and dispense small and accurate volumes of liquid solutions. Using correct pipeting technique will greatly increase the chance that your student’s experiment will return meaningful data so that their laboratory experience can be both fun and academically enriching. These micropipettes will allow you to accurately measure volumes as small as 2µl and as large as 1000µl. A microliter is 1 millionth of a liter or 10-6 L.
A spectrophotometer is a device used to measure light intensity. A spectrophotometer can measure either absorbance or transmittance of light. A small beam of light with a specific wavelength is emitted from the spectrophotometer which goes through the sample in a small glass container called a cuvette. The spectrophotometer measures how much light is absorbed by the sample or how much of the light passes through the sample which is transmittance. In this activity students will be using the spectrophotometer to measure the amount of light that is absorbed when various dilutions of food coloring are used. The more particles (food coloring) that are present in a given volume of a sample, the more of the light is absorbed and the less light that is transmitted. In the spectrophotometer activity, it is important to use yellow food coloring with the specified wavelength of 540 nm. The reason 540 nm is used with the yellow food coloring is because the wavelength of yellow is ~600 nm. In order to get a reading with the spectrophotometer, you need to set the wavelength at the complementary wavelength to yellow which is blue ranging ~500 nm. Given the specified food coloring concentrations, a wavelength of 540 nm has the best results. Before completing this lab, the teacher will need to check that they have all materials (see MATERIALS.doc) There is also some advanced preparation required (see ADVANCE PREPARATION.doc) in setting up the lab stations. The lesson is designed for 4 groups of 3-4 students to be working with the spectrophotometer and 6 groups of 3 students working with the micropipettes. The number of groups may vary depending on the number of students and the number of spectrophotometers available. INTRODUCTION (As a whole Group) Explain that half of the class will be begin working with the spectrophotometer and half the class will be working with the micropipettes. After about 20 minutes, the students will switch. Tell the students before the can complete the two activities you will be giving an overview of proper technique and procedure for both the micropipetting and spectrophotometer activity. A short video clip can be shown of a scientist using a micropipette in the lab (CSI or forensic science show). The teacher should emphasize that micropipettes are very expensive and need to be used properly to maintain the instrument and for accuracy in the lab. As a class, read the Objectives, Introduction and begin reading through the procedures. Have the students answer the questions on choosing the correct micropipette and setting the volume as you go through the procedures. When you get to Step 2 of Using the Micropipette, demonstrate each step at the front of the class. You may want to project the picture of the micropipette on the projector as well (micropipette.bmp). Be sure to emphasize the following as you demonstrate how to use the micropipette: Briefly go over the steps of the micropipetting activity. Be sure to emphasize the following when going over the micropipetting activity: Explain that the students will be working in groups of three. Each student will be using all three of the micropipettes. Explain that you are now going to go over how to use the spectrophotometer as a class. Read through the introduction to the spectrophotometer activity. Emphasize the picture showing how a spectrophotometer works. Explain that the light goes through a slit that sets the wavelength. The small beam of light with a specific wavelength passes through the sample in a cuvette. Some of the light is absorbed and some of the light passes through. The amount of light that passes through or the amount of light that is absorbed (this depends on the mode the spectrophotometer is set for, either absorbance or transmittance) is detected and a value is given by the spectrophotometer. Have the students read through the entire procedure. Be sure to emphasize that the spectrophotometer should be set to measure absorbance (not transmittance). Also emphasize that the graduations on the Beral pipets go up to 1 mL. Students will need to measure 1 mL four times in order to put the desired amount of liquid into the cuvette. Background Note for the Teacher: Students should observe that as the number of particles (food coloring) present in a given volume of the sample increases, the light absorbance increases too. Ask students why the cuvette with water needs to be inserted into the spectrophotometer between each reading. Emphasize the importance of a blank. Show the PowerPoint of what a blank is. First, ask students to explain how they would find the mass of a substance like salt using an electronic balance, a beaker, and salt. Students may say that you can put the beaker on the balance and then zero the balance or they may say that you can find the mass of the beaker alone and the mass of the beaker with salt. You can then find the mass of the salt by subtracting the mass of the beaker from the mass of the beaker with salt. Explain that determining absorbance of a sample is similar to finding the mass of a substance in a beaker. The substance that serves as the blank may absorb some of the light (not all the light may be transmitted). For example, in the activity the cuvette with water may absorb some light. In order to find the absorbance just the food coloring, you need to subtract the initial absorbance of the water from the new absorbance of the water and food coloring. Just like with an electronic balance, the spectrophotometer can be zeroed after the blank (cuvette with water) is placed in the spectrophotometer. Now when the cuvette with the water and food coloring is added, any change in absorbance is due to the addition of the food coloring not the water. ACTIVITY (Working in Groups). Assign students to work in groups of three. However, during the spectrophotometer activity, students may need to work in larger groups depending on the class size and the number of spectrophotometers available. After 20 minutes, the teacher should have the groups switch. The teacher may either want to collect all student work including the paper towel from micropipetting lab or have students attach filter paper to their lab journal. If you are not going to look at the paper towel right away, you may want students to draw a circle around each of their dried samples from the micropipetting activity. The smaller volumes become hard to see. Help students understand difficult vocabulary by breaking apart and explaining key root words. For example – spectrophotometer: spectro – photo – meter. “Spectro” comes from the Latin, specere, meaning appearance or to look at – it indicates a range or distribution to look at (e.g. What is the spectrum of trees around your school?). Even more simply, spect = look (e.g. spectacles, inspect). “Photo” means “light” and “meter” indicates something used to measure, often with numbers or quantities (quantitatively). When stringing root words back together, do so one step at a time. A photometer describes something that measures light. A spectrophotometer describes something that measures the range of light. Going even more in depth, this is a machine that measures the many wavelengths of light as they move through a liquid sample. You can go as deep as needed by your students. For example, to extend this further, explain that light is made of wavelengths and these wavelengths result in various colors. Since a spectrophotometer measures the amount of light and the range of light, or the wavelengths, it also measures color and intensity. As an extension, students can practice converting metric units. Examples are at the end of the student sheet for the micropipetting activity.
The light goes through an instrument that sets the wavelength. The small beam of light with a specific wavelength passes through the sample in a cuvette. Some of the light is absorbed and some of the light passes through. The amount of light that passes through is detected and a value is given by the spectrophotometer.
Instructional Activities:
Assessment:
How will I know they know……
Resources:
ADVANCE PREPARATION.doc
Answer Key and Example Data.doc
MATERIALS.doc
micropipette.bmp
Spec.ppt
Student Text micropipette.doc
Student Text spectrophotometer.doc
Accommodations:
Extension Activities:
Lesson 6 - Conducting halo salinity experiment
Unit: Ecological Networks Part 1- Network interactions
Lesson Title: Lesson 6- Conducting halo salinity experiment
Instructional Activities:
Please note: The Halobacterium culture should have been prepared AT LEAST 4 days prior to beginning the lab with students. The directions for this are located below in the section entitled, “Preparation of the Culture."
- The students should have already been introduced to their Case Study. (See Lesson 4- Introduction to GSL case study).
- Halobacterium Salinity Lab
Using Slide 18 (from the previous day’s GSL Case Study.ppt), introduce students to the concept of producing an optimized procedure. Review the definition of optimize and discuss how scientists design optimized procedures. Ask students, “Why is this of value to scientists?"
- Present students with the optimized Halobacterium lab procedure.
Discuss with the students how this procedure was optimized by scientists to increase the efficiency or effectiveness of a process as much as possible. Discuss the idea with the students that in the perfect setting they would perform their procedure many times until it was optimized. In the interest of time, the class will use a procedure that has been optimized by scientists.
- Students receive the protocol for the Halobacterium lab (Student Halo Protocol.doc).
Please carefully review the teacher document for further laboratory explanation (Teacher Halo Protocol.doc). If you will not be using an incubator, please refer to this student document: Student Halo Protocol for Stir Plates and ISB Handheld Spectrophotometers
TEACHER PREPARATION INSTRUCTIONS FOR THE HALOBACTERIUM SALINITY LAB
PREPARATION OF THE CULTURE – Note: Please read through the entire direction set before preparing your culture. Important and needed instructions are clarified and more specifically stated below the item with bulleted points. For a print out of these instructions click here.
- You must first prepare the Halobacterium culture for the students to use. This is a fairly easy process, but care must be taken in order to prepare a viable sample for the students to use.
- Open the kit at least 4 days prior to when the students are completing the lab.
- Use one of the enclosed, sterile disposable pipets to add 5 mL of 4.3 M growth medium (from the stock solution bottles in the kit) to 1 Falcon tube. Repeat this step again with a second Falcon tube. Since the graduations on the pipet only go to 1 mL, you will have to transfer 1 mL, 5 times. Be sure to avoid contamination. Using this 1 pipet and the 10 mL of 4.3 M will allow your students to have enough media to complete their experiment. However, if you have a glass pipet and bulb or a suitable micropipette, feel free to use that if you prefer. Make sure there is no soap residue in anything you use. Soap will cause the Halobacterium to lyse.
- Do not add more than 5 mL of growth medium to the Falcon tube. The cells need to have a great deal of empty “air" space in the tube so that oxygen can be forced to cycle through this high saline sample without losing water through evaporation.
- Locate the agar stab enclosed in the kit. This is contained in a Falcon tube and is labeled, “Halobacterium Culture." You should see pink colonies growing on the surface of the agar.
- Use the enclosed toothpick to GENTLY remove a single pink colony from the agar. Carefully remove the toothpick (containing the colony) from the Falcon tube and gently drop the entire toothpick and colony into the Falcon tube that has the 5 mL of growth medium in it. The toothpick should remain in the Falcon tube while the culture is incubating. Place the Falcon tube cap TIGHTLY on the tube (to the second stop) by firmly pressing the cap with your thumb. When completing this, pay careful attention to the bulleted points below that further describe this step.
- If red colonies are present, do not use them. The pink colonies have intact gas vesicles and will form a more viable culture for your students to use.
- It is best to only remove 1 colony with your toothpick. This is because it is likely these organisms are identical genetically. If only one colony is used, we will be limiting the variables in this experiment. However, it is okay if you remove more than 1 colony.
- Try not to transfer agar with the colony. A gentle swabbing motion with the toothpick (instead of a gouging motion) should achieve this. If some agar is transferred, your culture will likely still be viable.
- You should have 2 toothpicks in your kit. However, if toothpicks are not available, you may use a similar object (such as a micropipette tip). Be certain that the object is small enough to allow the Falcon tube to tightly close. We are not terribly worried about contamination in this step, because it is unlikely that anything besides Halobacterium will be able to grow in the 4.3 M medium.
- There are 2 “stops" to closing a Falcon tube. Be certain that the cap is closed to the 2nd stop (as tightly as it can be). Due to the high saline solution, evaporation is likely. This cap placement prevents a great deal of evaporation while the shaking motion of the incubator encourages enough oxygen to cycle through the sample.
- Using a new toothpick and your second Falcon tube containing 5 mL of growth media, repeat the above steps listed in step #5.
- Take the two inoculated Falcon tubes and place them in a shaking incubator at 37°C and 220 rpm for 3-4 days.
- Remove the Falcon tubes from the incubator. You now need to test the sample to make sure you have enough cells for your experiment.
- Set the mode of your spectrophotometer to absorbance and to a wavelength of 600 nm. This will allow you to measure the optical density (OD) of your sample.
- Transfer a sample of your inoculum to a clean cuvette. Use the guidelines listed below.
- Be certain to use a sample size that is appropriate for your spectrophotometer. For the “Fisher Visible Spectrophotometer," at least 2.5-3.0 mL must be used.
- In order to clean your cuvette (before and after testing the OD), use copious amounts of deionized water. Do not use soap on the cuvette. If there is soap residue on the cuvette, it will cause the cells to lyse.
- It is okay to simply pour your sample into your cuvette if it holds 5 mL.
- Use Kim wipes to remove any fingerprints, etc. from the exterior of the cuvette.
- Use a sample of your 4.3 M growth medium to blank your spectrophotometer. Again, use an appropriate amount for your spectrophotometer.
- Insert your sample. Record your optical density. Repeat with your second culture.
- Ideally, the OD should read between 0.6 and 0.8 for a great sample. If your OD is lower than 0.6, place your samples back in the incubator for another 24 hours and run the OD again. The sample can be used if the OD is as high as 1.2 or 1.5, but this is not ideal.
- Return your samples to the Falcon tubes.
- Leave your culture at room temperature. Be certain the cap is tightly on the Falcon tube and keep the sample out of direct sunlight. The cells will continue to grow very slowly. If your sample’s OD is extremely high, you may choose to dilute it. However, remember to use 4.3 M medium, not water.
- Before using the culture in the lab, gently swirl the solution to thoroughly mix the cells.
- The original stab can remain at room temperature and will remain a viable culture source for many months.
*Media Prep See this document for directions to make your own media and dilutions.
If you do not have a shaking incubator, you can put the tubes in a non-shaking incubator at 37 degrees and then allow for more incubation time. Or you can have students use flasks with stir bars and stir plates to run the experiment. See this protocol for more information: Student Halo Protocol for Stir Plates and ISB Handheld Spectrophotometers
Assessment:
How will I know they know……
Students conduct the laboratory investigation successfully and safely. The assessment of the laboratory write-up is in the following lesson.
Resources:
PowerPoint: GSL Case Study.ppt
Halobacterium Salinity Lab (Student Handout): Student Halo Protocol.doc
Halobacterium Salinity Lab (Teacher Document): Teacher Halo Protocol.doc
Alternate Lab with stir plates and handheld spectrophotometer: Student Halo Protocol for Stir Plates and ISB Handheld Spectrophotometers
Accommodations:
Choose student lab groups appropriately to strengthen lab skills and promote equal participation. Use verbal and written cues while students are in the lab. Write key items on the board to remind students how to properly use equipment. Use verbal cues throughout the lab to help students stay focused on both making predictions and on the purpose of the lab. Feel free to use other appropriate materials as needed to physically help students with new techniques such as pipetting. If the lab procedure needs to be broken down further, have individual students build a checklist within the pipetting procedure to ensure each tube receives what is needed (growth media + halo versus just growth media).
Extension Activities:
Students learn in this lab that Halobacterium are extremophiles thriving in high saline environments. However, they do not learn why they thrive in this environment, yet die in others. The reason is due to their internal composition (see the Teacher Background Information in Lesson 4- GSL Case study introduction ). As an extension, the students could research and learn more about osmosis in order to thoroughly explain why Halobacterium will lyse when placed in low salt concentrations.
Lesson 7 - Data analysis halo salinity experiment
Unit: Ecological Networks Part 1- Network interactions
Lesson Title: Lesson 7- Data analysis halo salinity
Instructional Activities:
INTRODUCTION
- Warm-up:
- Are all 3 data points within a relatively close range?
- What are some initial reactions/comments that you have?
ANALYSIS OF THE DATA
- Use tab 1 (data-class) of the HalodataTemplate.xls to review the individual data points to begin a discussion on range of data, outliers, and any difficulties or variances they may have encountered while collecting the data from the spectrophotometer.
- Students will have had some exposure to the concept of an outlier in middle school-but will still benefit from a more detailed discussion on this concept and how to recognize data that are out of an acceptable range.
- This period of discussion is also a time to refer back to “why" a particular procedural step was carried out in a specific manner—i.e-saving the sample even after the spectrophotometer data has been collected. If a particular sample gave an unusually high or low absorbance reading-the student/group could return to the station and measure again. This is how professionals in the field proceed and this connection to “real" science can improve students lab procedures/habits.
- Use tab 2 (graph-class) to show the molarity/concentration averages plotted graphically.
- Based on the previous conversation about data reliability, variation, and outliers-examine the class data
- Use tab 3 (graph-class with SD bars) to introduce the standard deviation/range of the data points.
- Students may have heard the term standard deviation (depending on their math level), however, a definition of the term is not necessary at this point-rather a simplified description that these bars are like the range and represent the amount of variation in the data points (Formally, standard deviation is an average of the difference between each data point and the average of the sample)
- Elicit student responses on their confidence in the data and what could be done to increase their confidence in the data (repeat/multiple trials)
- Use tab 4 (data-district) and tab 6 (graph-district) to show the “district" data set.
- Use this larger data set to compare with the class data—are the curves relatively the same? Are the data points within the same range?
- Enter the class averages into tab 5 (data-district + class) and view tab 7 (graph-district + class)
- Elicit student responses on what the graph tells us in regard to the investigative question.
- Elicit student responses on what the graph tells us in regard to physical elements of the lake-especially the north arm that allowed for the increase in halobacteria.
- Graph the data and write a conclusion to the lab
- Students should graph the class data in their logbook/lab book or on their own paper-paying attention to correct graphing procedures (T.A.I.L.S.)
- Students write a conclusion to the original investigative question—citing high and low data points and using appropriate explanatory language to make sense of the data. The student instructions (GraphandConclusionStudentInstructions.doc) give the full prompt.
Assessment—Grading the Graph and Conclusion
- The PowerPoint HaloDataAnalysis-Grader.ppt which contains the rubric for grading the graph and conclusion should be projected.
- It may be beneficial to reinforce the idea that this grading exercise is on an assessment-which will count for a grade and that the class should stay together-so that the teacher can answer any questions or make any necessary clarifications about each point/criterion.
- The PowerPoint is formatted to reveal the criteria for each value point line by line
- The final slide has a suggested method for calculating the graph and conclusion grade-if a teacher chooses to follow a WASL-style- standards-based grading scheme.
- The grading of the graph and conclusion will generally take no more than approximately 20 minutes-which should allow a teacher to proceed to the next step of the assessment—students plan an investigation.
Assessment--Planning an investigation This lesson is an assessment of students’ investigation planning skills. Return to the potential hypothesis list (generated at outset of Halo activities) and have students plan an investigation from one of these potential hypotheses. Students would plan up to “procedure". Use Halobacterium Investigation Plan for student instructions.
***This plan can be graded/assessed in class by using the document “Halo Investigation Plan Grader" ***
- Begin reposting/reprojecting the list of potential hypotheses that were generated during the class discussion on Halo growth and Observations of the north arm of the Great Salt Lake.
- Students will have suggested topics such as pollution, temperature, light intensity, etc—they are free to choose any one of these topics-and plan an appropriate investigation (Question/Hypothesis-Procedure)
- It may be beneficial to allow students to briefly review/look at the materials list/procedure for the salinity to help them get started with their plan.
- Give the investigation plan prompt (Halobacterium Investigation Plan.doc) and have students plan an appropriate investigation
- It may be beneficial to inform students that this exercise is an assessment and should be taken seriously
- This assessment should also be completed be EACH student-some other investigation plans may be done in groups/pairs-but being that this experience happens early in the year, it is important to assess each student’s ability in planning an investigation.
Assessment—Grading the Investigation Plan
- Begin by having students staple or attach a copy of the HaloDataAnalysis-Grader.ppt to their investigation plan and turn it in. (a copy of the rubric for each student will need to be printed ahead of time)
- To ensure objectivity by the student grader-it may be helpful to use an assigned number rather than a name on the student writer’s paper.
- Pass out the papers/plans according to your in-class grading procedure (ensuring that students don’t have their own paper)
- So that students will be more familiar with what is written in the plan they are grading-they should be given 3-4 minutes to read the plan-without using the rubric or assessing points—just to get an idea of what they’ll be assessing
- It will be important to stress to students that the grading proceed together as a class and that any one student no rush ahead on the rubric as the class will assess each criterion-and clarify any questions they may have.
- Grade the plans according to the provided rubric
- The rubric follows a WASL-style value points system for grading
- A suggested method for calculating a student grade based on a WASL-style value points to standard is:
10, 9 value points= Exceeds Standard
8, 7 value points= Meets Standard
6, 5 value points= Approaches Standard
4 and below= Below Standard
***Tips for clarifying Investigation Plan Rubric Attributes are listed below*** Tips for in-class grading of the investigation plan:
Scoring Rubric for Awarding Value Points for Investigation Attributes Notes: - If the response does not plan an appropriate procedure for this investigative question, the response cannot earn any of the eight possible procedure value points (e.g. the response repeats the procedure from the salinity lab).
- If there is no manipulated variable present, no points shall be awarded for either manipulated or controlled variables.
- If the response simply names the bulleted attributes listed after “Procedure that includes:" without writing a procedure, no procedure points may be awarded.
- The ‘right’ amount of ingredients (i.e. ‘x’ mL or ‘y’ grams) needed to carry out the procedure does not need to be given in the material list.
- Vague materials used in the procedure (i.e. 1mL) may be credited if the vagueness is clarified in the materials list (i.e. 1mL of insecticide)
- If pre-measured amounts of materials are listed in the materials list, a measuring device may not be needed in the materials list.
- Measuring a vague parameter (e.g. amount of halo instead of O.D/population size) may be credited as a responding variable but is too vague to repeat, so no point can be awarded for ‘logical steps.’
- The word “repeat" at the end of a step, refers to that step only. If “repeat" is listed as a separate step or in a new paragraph, it refers to go back to the beginning.
- If the response correctly implies the controlled, manipulated, or responding variables but identifies them incorrectly, the appropriate value points may not be awarded.
Assessment:
How will I know they know…Grading of graph and conclusion using WASL-style rubric (HaloDataAnalysis-Grader.ppt)
Grading of investigation plan using WASL-style rubric (HaloInvestPlanGrader.doc)
Resources:
GraphandConclusionStudentInstructions.doc
Halobacterium Investigation Plan.doc
HaloDataAnalysis-Grader.ppt
HalodataTemplate.xls
HaloInvestPlanGrader.doc
Accommodations:
This lesson can easily be adapted for various levels of students. Leaving out or adding data can be easily achieved with the Excel template. For more data, see the Baliga Lab website or contact Claudia at cludwig@systemsbiology.org. Remind students that viewing the data as a graph helps to visualize this seemingly complex data set. Use the printouts as ways to keep students on task and organized with their analysis.
Extension Activities:
Lesson 8 - Revisiting the GSL network
Unit: Ecological networks Part 1- Network Interactions
Lesson Title: Lesson 8- Revisiting the GSL network
Instructional Activities:
Important Note: Activity 2 is very important to link the data from the halobacteria investigation back to the GSL ecosystem and network concepts from the entire unit. Depending upon how foodwebs, matter cycles, and ecosystem concepts were taught, teachers may choose to do the entire activities or only activity 2 and certain parts of Activity 1.
ACTIVITY 1 (OPTIONAL): Creating a Food Web Network of the Great Salt Lake Ecosystem
Say to the students “Now that we have explored extremophiles and specifically investigated the effect of salinity on the growth of Halobacterium we will now focus on the entire Great Salt Lake ecosystem. We will focus on the abiotic and biotic factors within the network and exploring how humans have impacted the entire system."
- For a class of 30, divide students into 6 groups with 5 students each.
- The teacher should ask students to recall the cell phone activity and review what a network is, what the components of a network are, and why networks are useful visualization tools. Explain networks are really important to visualizing systems in Biology and today they will be creating a biological network, a food web!
- Review with students about food webs. Distribute the student activity sheet (GSLfoodwebworksheet.doc) and read through the introduction as a class. Have the students complete the pre-activity questions individually of with a small group.
- Read through the first two procedure steps as a class (below).
- You will be working with your assigned group to learn about some of the organisms that live in the Great Salt Lake.
- As a group you will need to answer the following four questions about each of your assigned organisms. Each group member must write down the answers to the questions in the table provided below.
- On the Smartboard or overhead using the table from student sheet 2b, model one organism with which students are familiar such as a fox.
Ask the students what the fox eats. The students can use the food web in the example to determine that a fox eats snakes, raccoons, mice, etc. Ask the students what waste is produced? The students should determine that carbon dioxide is one of the waste products. Ask the students what abiotic or environmental factors the fox needs to survive. Possible student responses may include oxygen, water, sunlight, etc. Finally, ask the students to explain the process by which the fox obtains its energy and whether the fox is a heterotroph or an autotroph? Students should say the fox is a heterotroph because it consumes food and obtains its energy from consuming other organisms.
- Explain that each group will be responsible for researching 2-3 organisms living in the Great Salt Lake. Give the students time (15- 20 minutes) in their groups to research their organism and complete the table provided on the student sheet.
Assign each group 3-4 of the following organisms (you may assign more than one group the same organism):
- Halobacterium
- Migrating Birds
- Marsh Hawk
- Algae
- Brine Shrimp
- Brine Flies
- Meadow Vole
- Salt Grasses
- Cyanobacteria
- Phytoplankton
- After students have gathered their information, have them number off 1-5. Go over the remainder of the procedures with the class (below).
- Next, you will be assigned to a different group in which you will share your information. Together you will create a food web network showing the relationships existing in this ecosystem. Use circles (nodes) to represent the organisms and any abiotic factors and arrows (edges) to represent the relationship between the organisms. Remember the arrow always points toward the consumer!
- Use your food web to answer the following questions.
Alternative approach to step 7:
- Rather than hand drawing the network you could have students create a network using Cytoscape. Show the students how to use Cytoscape using the prepared PowerPoint.
- Have the students create a sif file and then use this to create a network in Cytoscape.
- Have all the 1’s meet together, all the 2’s meet together, etc to create a food web network and answer the associated questions.
ACTIVITY 2: Salinity Effect on Halobacterium PowerPoint
- Say to students: Now that we have explored the effect of salinity on the growth of Halobacterium and designed a food web network with our Great Salt Lake organisms, we will now use all of this knowledge to explore a detailed PowerPoint simulation of the Great Salt Lake Ecological Network. In this network we will consider how an ecological disturbance could affect an entire ecosystem (both abiotic and biotic factors).
- Start PowerPoint (salinity_effect_on_halobacterium.ppt) Description slides below to conduct a class discussion. Do not rush through the slides, encourage all students to participate. You may want to have printed copies of the effect of salinity on the growth of Halobacterium graphs for students to refer to.
- Slide 1: This is the static network of the GSL. You have discovered a relationship between salinity and Halobacterium growth. We will now see how that relationship will be visualized in the network. Please note: students have data only for effect of salinity on Halobacterium growth and they do not have knowledge about other quantitative relationships. Please be sure to distinguish hypothesis from fact.
- Slide 2: First you started with a salinity of 2.5M –what was the effect on growth of halo?
- Slide 3: Students should observe that Halo did not grow at all
- Slide 4: At a salinity of 3.0M –what was the effect on growth of halo?
- Slide 5: Students should observe that Halo showed moderate growth
- Slide 6: At a salinity of 3.5M –what was the effect on growth of halo?
- Slide 7: Students should observe that Halo grew even better
- Slide 8: At a salinity of 4.0M –what was the effect on growth of halo?
- Slide 9: Students should observe that Halo grew extremely well
- Slide 10: At a salinity of 4.5M –what was the effect on growth of halo?
- Slide 11: As a reminder form lab activities ask the students: What overall observation about Halobacterium growth can we make regarding the different salinities? Observation: Halo growth was less relative to growth at 4.0M; 4.5M is approximately the salinity of the North arm of the lake.
- Slide 12: Great Salt Lake Food networks in North and South Arms
Students Hypothesize about the Great Salt Lake Network in the North arm
- Slide 13: Observation: Halo growth was less relative to growth at 4.0M; 4.5M is approximately the salinity of the North arm of the lake.
Students should HYPOTHESIZE what will happen to rest of the network in the North arm of the lake (remind them of salinity-4.5M). Students can write their hypotheses in journals, or they can be discussed in small groups and then shared with the whole class. Students should draw a sketch of how salinity affects the network.
- Before going to slide 14, ask students which nodes are directly affected by salinity. Students should respond by saying that the algae, brine shrimp, and salt grasses nodes will decrease in size. This hypothesis should be based on the information learned about in the PowerPoint before the Halobacterium lab about how most organisms can not thrive/live in a salt environment.
- Slide 14: Observation: Halo growth was less relative to growth at 4.0M; 4.5M is approximately the salinity of the North arm of the lake. Salt grasses, algae, and brine shrimp population nodes have decreased in size due to the increase in salinity.
- Before going to slide 15 ask students which nodes are indirectly affected by salinity. Students should respond with the migrating bird, meadow vole, and marsh hawk nodes (populations) will decrease because their energy source (brine shrimp and salt grasses) is depleted.
- Slide 15: Observation: Halo growth was less relative to growth at 4.0M; 4.5M is approximately the salinity of the North arm of the lake. Migrating birds and meadow vole populations have decreased because their food source populations have decreased.
- Slide 16: Observation: Halo growth was less relative to growth at 4.0M; 4.5M is approximately the salinity of the North arm of the lake. The Marsh Hawk node has decreased in size because its energy source (meadow voles and migrating birds) is depleted.
Students draw conclusions about how ecological disturbance affected the Great Salt Lake Network in its entirety.
- Show slide 17 and ask students to think about the Great Salt Lake network in its entirety. Thinking back to the lesson objectives ask students what is the ecological disturbance that we are referring to here? (Human impact by building the causeway in the 1952) Ask students to summarize how this ecological disturbance affected the entire ecosystem. Students should either draw the GSL showing how the causeway resulted in different ecological networks for the north and the south arm, or they can write about it in paragraph form.
Ask for students to share their conclusions with the entire class.
- Use slide 18 to support student conclusions about how the building of the causeway resulted in an ecological network in the north arm that is different than the network in the south arm.
Assessment:
- Students’ summary conclusions of how the building of the causeway affected the entire Great Salt Lake Network.
- Oral responses by students during discussion.
Resources:
GSLfoodwebworksheet.doc
salinity_effect_on_halobacterium.ppt
Accommodations:
Move slowly through the slides and take time to go back and forth between slides for students who may have a difficult time processing the numerous changes within the network diagram.
Extensions:
Have students discuss the benefits and risks for trying to undo this alteration to the Great Salt Lake. Are there any solutions? Should there be a solution?
Have the students explore a problem or situation in their local environment, such as the removal of a dam, in order to describe the process as well as the advantages and disadvantages of using a systems approach to solving the problem.
Teacher Background Information
Unit: Ecological Networks Part 1- Network interactions
Introduction to extremophiles
Teacher Background information: The Great Salt Lake is an interesting ecosystem to study due to the organisms that inhabit this saline environment and due to the impact humans have had on this ecosystem. In 1952, a causeway was built to replace an existing railroad trestle. Unlike, the previous trestle, the new causeway does not allow circulation of water between the two sides of the Great Salt Lake. The causeway splits the lake into a north and south arm. Because of this and the fact there is no fresh water source into the north part of the lake, the salinity concentration drastically varies between the two sides. The north arm of the lake can be nearly 30% saline while the south may only be 5%. The ecosystem in the south part of the lake is more diverse than the north because of the lower salt concentration. Fewer species of organisms are able to survive in the hypersaline environment in the north end. However, one prominent organism in the north arm of the Lake is Halobacterium of the archaea domain. These organisms are salt loving organisms.
In this lab, the students will be working with Halobacterium sp. NRC-1. Halobacterium is an excellent model organism to use in the classroom because of its unique characteristics. They are easy to culture and are a relatively harmless organism. These archaea are prokaryotes meaning they do not have a nucleus or other membrane bound organelles. Also, these archaea have both a cell wall and membrane that have a notably different composition when compared to their bacterial counterparts. Specifically, their cell wall is composed of different amino acids and sugars. Organisms in this domain inhabit some of the most extreme environments on Earth. There are some species of archaea that can survive in deep sea thermal vents where the heat is more than 300 times that which humans can endure. Some species live in high sulfur and high pressure (7,000 lbs/in2) environments, uninhabitable to most other organisms. 
Halobacterium thrives in salty environments in which most other organisms cannot survive. The optimal salt concentration for Halobacterium is ~4.3 M which is about ten times the salinity of sea water. At more dilute concentrations of salt, the shape of the Halobacterium will become distorted. The cells will lyse at approximately 1 M NaCl. Halobacterium has evolved over millions of years in a high salt environment, and as a result, its physiology is best suited to function in this environment. For example, their proteins have optimal activity in high salt. Also, their cytoplasm contains at least 3M K+ and 1M Na+. This molarity is essentially isotonic to the high saline environment in which they live. At low salt concentrations, water will move into their hypertonic cell causing it to expand. When the concentration difference is great enough (as it is in a 1 M solution) the cell will rupture due to the large intake of water. Halobacterium are found all over the world in hypersaline environments such as the Great Salt Lake and the Dead Sea. Large blooms of Halobacterium appear reddish purple due to the production of the pigment bacteriorhodopsin (Fig. 1). This pigment absorbs light energy to create ATP, which can be used by the organism when oxygen levels are low. Halobacterium can also absorb and digest nutrients (amino acids) from the environment, making them heterotrophs (specifically, aerobic chemoorganotrophs). Halobacterium are limited microaerobic phototrophs, but live optimally as aerobic chemoorganotrophs and are therefore classified as such. Because they live in a harsh environment and process energy is unique ways, they are an even more interesting organism for scientific inquiry.
Figure 1. Solar evaporation ponds at the abandoned chemical plant of the Pittsburgh Plate Glass Company at Bartlett (at northwest end of Owens Lake) are colored vivid red by salt-loving organisms. From http://www.desertusa.com/mag98/april/owens/owenslake.html
Advance Preparation
Unit 1 Ecological networks - Part 1 Network interactions
Laboratory Equipment Requirement: 
| Safety Equipment |
Materials per Group | Equipment per Group | Class Equipment |
|---|---|---|---|
| gloves * | Deionized water | Spectrophotomer | Shaker incubator**** |
| goggles* | 2.3M, 2.8M, 3.3M, 3.8M, 4.3M Growth Medium (GM) | 4 cuvettes | |
| apron* | Live Halobacterium culture | Large rack for Falcon tubes | |
| Falcon tube labels | Kim wipes | ||
| Beral pipet | |||
| P200 micropipet w/tips ** | |||
| 400-1000mL beaker for waste | |||
| 4 Falcon tubes, 17x100mm*** |
* no harmful materials - these materials are recommended but not required.
**Beral pipet may be used. 100μL only fills the first 2 segments (about 4 drops). Discussion of error/precision will be necessary.
***Falcon tubes are provided in the kit for use if you have a shaker incubator. If not, these tubes may be set inside an incubator and periodically shaken (gently). Add an additional 24 hours before checking the OD.
****If you do not have a shaker incubator, you may use small flasks and stir plates. See stir plate protocol within this module - Lesson 6.
To make your own Growth Media - please follow this recipe for optimal results.
Advance preparation and materials required for each lesson:
| Lesson | Description | Preparation and materials |
| Lesson 1 | Building cell phone network manually on paper | Lesson 1 Prep.doc |
| Lesson 2 | Cytoscape analysis of cell phone network | Lesson 2 Prep.doc |
| Lesson 3 | Researching background on extremophiles | Lesson 3 Prep.doc |
| Lesson 4 | Introduction to the GSL case study; hypothesis generation and experimental design | Lesson 4 Prep.doc |
| Lesson 5 | Practicing use of spectrophotometer and micropipettes | Lesson 5 Prep.doc |
| Lesson 6 | Conducting halobacteria salinity investigation | Lesson 6 Prep.doc |
| Lesson 7 | Analysis of halobacteria salinity data: *Assessment- writing a conclusion *Assessment- designing an investigation |
Lesson 7 Prep.doc |
| Lesson 8 | Incorporating laboratory data into GSL context to explain observed phenomena | Lesson 8 Prep.doc |
Standards Addressed
These modules are created based on National and WA State Standards.
For more information on which standards are addressed please see the approprate link AND please also see the sections on "What Students Learn" and "What Students Do" within each module page.
Ecological Networks - Overview of WA State Standards Addressed
Environmental Influence on Gene Networks - Detailed View of WA State Science Standards Addressed