I think I'm ready to submit this lesson plan, but I wish I had a few more weeks. Essentially, it's taking the process of using cytochrome b amino acid sequences to form a taxonomic tree for marine invertebrates. The results don't follow the textbook cladograms, so it leads to a lot of questions. I welcome any suggestions.
Leigh
Invertebrate Evolution:
Making a Phylogenetic Tree
Background
This activity is a webquest that guides students through various bioinformatics tools on the internet including the protein database at NCBI, Cn3D protein viewer, and ClustalW. Students will focus on cytochrome b protein sequences. They will compare protein sequences from different marine organisms and use this to investigate evolutionary relationships.
Description of Audience:
This biotechnology/bioinformatics activity is designed for use in a high school Biology, AP Biology, Biotechnology, Marine Biology, or equivalent course.
State Standards:
This biotechnology/bioinformatics activity fulfills the following State of California Science Standards:
Biology: Grades 9-12: 1b, 1d, 1h, 4b, 4e, 4f, 5a, 7c, 8f
Chemistry: Grades 9-12 10a, 10c
Investigation and Experimentation: Grades 9-12: 1d, 1g, 1l
National Science Standards:
This biotechnology/bioinformatics activity fulfills the following National Science Standards:
Content Standard A: Science as Inquiry
Identify questions and concepts that guide scientific investigations
Design and conduct scientific investigations
Use technology and mathematics to improve investigations and communications
Formulate and revise scientific explanations and models using logic and evidence
Recognize and analyze alternative explanations and models
Content Standard C: Life Science
Biological evolution
Energy and organization in living systems
Content Standard E: Science and Technology
Abilities of Technical Design (Propose design and choose between alternative solutions)
Understanding about science and technology.
STEM Connection:
The availability of technological tools to
Technology Integration:
Students will use computers to access three websites online: NCBI, ClustalW and Cn3dProtein viewer.
NCBI: Students will use this database to locate protein sequences for organisms.
ClustalW: Students will use this site to align and compare the relatedness of
multiple organisms. They will use this site to create phylogenetic trees.
Cn3d Protein viewer: Students will be able to visualize and manipulate a three dimensional image of the polypeptide chains from their sequence results.
Goals:
The goals of this lesson are to:
Expose students to bioinformatics tools and technology on the web.
Allow students to visualize and manipulate the 3D structure of a protein.
Show students how phylogenetic trees can be used as a model of evolutionary relationships.
Show students how differences at the molecular level can be used to infer evolutionary relationships.
Learning Objective(s)
Upon completion of this lesson, students will be able to:
Use NCBI to find protein structure files and protein sequences.
Use Cn3D to visualize and manipulate protein files.
Acquire protein sequences from various invertebrates and align them using ClustalW.
Explain how organisms with dissimilar protein sequences are more distantly related than organisms with more similar protein sequences.
Recognize that there are multiple interpretations of scientific data.
Purpose/Rationale
The purpose of this lesson is to provide a process for students to follow in which they generate data and interpret that data. They will be using modern bioinformatics as a research tool. This process allows them to become familiar with modern research techniques and exposes them to extensive online databases. They will compare their results to other taxonomic trees and recognize that many interpretations of data are possible.
Materials/Resources
In order to complete this lesson, the following materials are needed:
Student access to computers with Internet (1 computer per student)
The following websites:http://www.ncbi.nlm.nih.gov/http://align.genome.jp/
The protein viewer software may be downloaded from: http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
A list of the binomial names of the 17 references species (1 per student)
Invertebrate Evolution Process Sheet (lesson worksheet)
Other invertebrate cladograms (for comparisons) are available at:
http://www.palaeos.com/Invertebrates/Lists/Cladogram.html
http://www.biology.ualberta.ca/courses.hp/zool250/Z250.html
and their textbook.
Teacher Preparation
Students should already be familiar with the concepts of taxonomy including cladograms and common ancestry. They should understand the relationship of DNA sequences to amino acid sequences and protein structure. They should know the role of cytochrome b in electron transport.
3-Step Procedure
#1 Introduction
Review the role of cytochrome b in cellular respiration, protein structure and the relationship of structure and function.
Assess student's prior knowledge of taxonomic trees, and taxonomy nomenclature.
Demonstrate the use of the computer to access the relevant websites. Choose one species to walk through the process of protein sequence acquisition (NCBI) and use a group sequences to demonstrate the use of the alignment website (ClustalW)
Remind students of the procedure for saving files on the school computers.
Prior to lab, have students research the organisms on the species list and find their phylum.
#2 Exploration
Students will be working individually following the directions on the Process sheet and answering the two worksheets that accompany the directions.
#3 Application
Students will compare their taxonomic trees to those published by other authors. They will identify similarities and differences and judge what they think makes a taxonomic tree reliable.
Assessment
Students will complete worksheets as they do the activity. They will produce a copy of their taxonomic tree.
Lesson variations: students needing more support should be given a modified assignment with fewer species. They may given a prewritten list of sequences to which they add one or more that they have acquired and then they can make a tree from the combined data.
This lesson will require the teacher to be checking for understanding with individual students throughout the activity.
Lesson extension: Students who quickly complete the lesson can be given protein sequences that they use to predict the phylum of unknown organisms. Alternatively, they can be challenged to find additional organisms and compare the tree they produce with the class set.
Teachers’ Self Evaluation
[in progress]
Included in accompanying file:
Student directions page (Parts 1 and 2)
Student answer sheets (Parts 1 and 2)
List of invertebrate species
Sample completed taxonomic tree
Reference amino acid sequences
Sunday, March 1, 2009
Saturday, February 7, 2009
Lesson Plan--let me know how to improve this
A lesson plan for
Podcast on Intertidal Organism
Designed by
Ruth Abatzoglou (ruth dot abatzoglou at sausd dot us)
Background
In this activity students will create a podcast on how an organism survives in the intertidal zone and the challenges it meets. Students learn about the complexity of organisms in the inertidal zone and then focus on a specific organism to study. They will research information about this organism, develop a storyboard for their podcast. They will use iMove, moviemaker or Garage band to create a podcast on how their organism adapts to the harsh conditions of the intertidal zone. In learning about the organisms that makeup the intertidal zone, they will have a better understanding of the impacts on invasive species and how these can alter the biodiversity of the intertidal zone.
Description of Audience:
This activity is designed for use in a general high school Biology or middle school, Biology or Life Science class, preferably as a collaborative project.
State Standards:
This podcast activity fulfills the following State of California Science Standards:
Biology: Grades 9-12: 6a, 6b, 6c, 6d, 6e,
Investigation and Experimentation: Grades 9-12: 1a, 1l, 1m
National Science Standards:
This activity fulfills the following National Science Standards:
Content Standard C: Life Science
Content Standard E: Science and Technology
Content Standard F: Science in personal and social perspectives
STEM Connection:
Podcast and multimedia presentations are being used in many areas of science. Tools such as this can be used to learn about new developments and topics as well as a way to present information in all fields of science from marine science to molecular biology and climate issues.
Technology Integration:
Computer technology using iMovie and GarageBand is used as well as digital pictures; video and audio media, which are integrated in this project.
Goals(s):
The goals of this lesson are to:
• Expose students to marine intertidal zone and the organisms found here so they can understand the importance of biodiversity of the intertidal zone.
• Expose students podcast technology and the use of digital media.
• Reinforce the connection between human impact and invasive species on marine environments.
• Clarify the similarities and differences between organisms that make up the intertidal zone
Learning Objective(s)
Upon completion of this lesson, students will be able to:
• Make and present a multimedia project on an intertidal organism.
• Use digital images and import them into project
• Explain how the diversity of organisms are important to the intertidal zone
• Explain how organisms in the intertidal zone are adapted to this areas.
Purpose/Rationale
I am teaching this unit because learning about the diversity of the intertidal zone is necessary for students to understand why it is important to protect and take care of our intertidal area. In learning about the diversity of the intertidal zone, students will understand why it is important to limit invasive species and take care to protect the watershed they live in. Using technology to create a podcast will help engage students and expose them to this from of media as a science and educational tool. This is also a collaborative project where students need to work together and develop their communication skills in creating their project and presenting the project to their classmates.
Materials/Resources
In order to complete this lesson, the following materials are needed:
• Student access to computers with iMovie, GarageBand or movie-make and computers with lots of memory to story video media.
• LCD projector for project sharing time.
• Internet resources, digital file with video or images of intertidal organisms.
• Storyboard template and intertidal field card template.
Teacher Preparation
Before this lesson, the teacher should be familiar with podcast and iMovie or moviemaker and be able to assist students with their projections. Internet resources on intertidal organisms and possible invasive species should be available or teacher should have appropriate digital resource folders with this available for student projects. A field trip visit to the local intertidal area would be helpful, but not essential.
3-Step Procedure
#1 Introduction
• Introduce students to intertidal zone by pictures video or examples from personal experience.
• Ask students what special adaptations or features organisms would need to live their lives partly underwater and partly out of water.
• Ask students what special adaptations an organisms would need to live in the moving water of the intertidal zone.
• Review the watershed of your area and ask students where do things flow when it rains.
• Review appropriate content vocabulary on intertidal organisms structures as needed for your student population.
#2 Exploration
• Students will be working in groups creating their intertidal field cards on different organisms so they develop a background.
• In groups assign organisms for students to create their podcast projects on and complete any addition research needed for their organism.
• Students will develop their storyboards on their organisms and submit it before working with iMove.
#3 Application
The final part of this project, students will create their video project. With a solid storyboard completed students will use iMovie or movie-maker and video or images from the digital resource folder created by the teacher or student field trips to build their project. Narratives and digital music can be overlaid to enhance the final projects.
Assessment
• Student groups will present their projects to the class and share what they learned.
• A quiz can be used by the teacher at the end of all the presentations to see if students learned about the different organisms
• Student groups can also develop their own short quizzes to evaluate how their presentation helped others learn
• Student absent on the day of the presentations or those who didn’t fully participate in the group activities can use their student created field card to review the different organism or they can view the final project on individually to learn about the diversity of the intertidal zone.
• An extension of this lesson would be to have students predict what would happen if a new species was introduced to the intertidal zone and how that would affect the other balance of the biodiversity of the area.
Teachers’ Self Evaluation
• Students had a lot of trouble creating their storyboards and need help making a creative script. More example could have been developed in advance.
• Most of the student had a very limited background on the different intertidal organisms, aside from the sea star and needed more background and information.
• This was the first time for the students to use iMovie and GarageBand and final project took more time than anticipated.
• Students needed access to more video and pictures of their projects. A Second field trip, after the writing of the storyboard would have been helpful so more videos and pictures could be obtained.
Podcast on Intertidal Organism
Designed by
Ruth Abatzoglou (ruth dot abatzoglou at sausd dot us)
Background
In this activity students will create a podcast on how an organism survives in the intertidal zone and the challenges it meets. Students learn about the complexity of organisms in the inertidal zone and then focus on a specific organism to study. They will research information about this organism, develop a storyboard for their podcast. They will use iMove, moviemaker or Garage band to create a podcast on how their organism adapts to the harsh conditions of the intertidal zone. In learning about the organisms that makeup the intertidal zone, they will have a better understanding of the impacts on invasive species and how these can alter the biodiversity of the intertidal zone.
Description of Audience:
This activity is designed for use in a general high school Biology or middle school, Biology or Life Science class, preferably as a collaborative project.
State Standards:
This podcast activity fulfills the following State of California Science Standards:
Biology: Grades 9-12: 6a, 6b, 6c, 6d, 6e,
Investigation and Experimentation: Grades 9-12: 1a, 1l, 1m
National Science Standards:
This activity fulfills the following National Science Standards:
Content Standard C: Life Science
Content Standard E: Science and Technology
Content Standard F: Science in personal and social perspectives
STEM Connection:
Podcast and multimedia presentations are being used in many areas of science. Tools such as this can be used to learn about new developments and topics as well as a way to present information in all fields of science from marine science to molecular biology and climate issues.
Technology Integration:
Computer technology using iMovie and GarageBand is used as well as digital pictures; video and audio media, which are integrated in this project.
Goals(s):
The goals of this lesson are to:
• Expose students to marine intertidal zone and the organisms found here so they can understand the importance of biodiversity of the intertidal zone.
• Expose students podcast technology and the use of digital media.
• Reinforce the connection between human impact and invasive species on marine environments.
• Clarify the similarities and differences between organisms that make up the intertidal zone
Learning Objective(s)
Upon completion of this lesson, students will be able to:
• Make and present a multimedia project on an intertidal organism.
• Use digital images and import them into project
• Explain how the diversity of organisms are important to the intertidal zone
• Explain how organisms in the intertidal zone are adapted to this areas.
Purpose/Rationale
I am teaching this unit because learning about the diversity of the intertidal zone is necessary for students to understand why it is important to protect and take care of our intertidal area. In learning about the diversity of the intertidal zone, students will understand why it is important to limit invasive species and take care to protect the watershed they live in. Using technology to create a podcast will help engage students and expose them to this from of media as a science and educational tool. This is also a collaborative project where students need to work together and develop their communication skills in creating their project and presenting the project to their classmates.
Materials/Resources
In order to complete this lesson, the following materials are needed:
• Student access to computers with iMovie, GarageBand or movie-make and computers with lots of memory to story video media.
• LCD projector for project sharing time.
• Internet resources, digital file with video or images of intertidal organisms.
• Storyboard template and intertidal field card template.
Teacher Preparation
Before this lesson, the teacher should be familiar with podcast and iMovie or moviemaker and be able to assist students with their projections. Internet resources on intertidal organisms and possible invasive species should be available or teacher should have appropriate digital resource folders with this available for student projects. A field trip visit to the local intertidal area would be helpful, but not essential.
3-Step Procedure
#1 Introduction
• Introduce students to intertidal zone by pictures video or examples from personal experience.
• Ask students what special adaptations or features organisms would need to live their lives partly underwater and partly out of water.
• Ask students what special adaptations an organisms would need to live in the moving water of the intertidal zone.
• Review the watershed of your area and ask students where do things flow when it rains.
• Review appropriate content vocabulary on intertidal organisms structures as needed for your student population.
#2 Exploration
• Students will be working in groups creating their intertidal field cards on different organisms so they develop a background.
• In groups assign organisms for students to create their podcast projects on and complete any addition research needed for their organism.
• Students will develop their storyboards on their organisms and submit it before working with iMove.
#3 Application
The final part of this project, students will create their video project. With a solid storyboard completed students will use iMovie or movie-maker and video or images from the digital resource folder created by the teacher or student field trips to build their project. Narratives and digital music can be overlaid to enhance the final projects.
Assessment
• Student groups will present their projects to the class and share what they learned.
• A quiz can be used by the teacher at the end of all the presentations to see if students learned about the different organisms
• Student groups can also develop their own short quizzes to evaluate how their presentation helped others learn
• Student absent on the day of the presentations or those who didn’t fully participate in the group activities can use their student created field card to review the different organism or they can view the final project on individually to learn about the diversity of the intertidal zone.
• An extension of this lesson would be to have students predict what would happen if a new species was introduced to the intertidal zone and how that would affect the other balance of the biodiversity of the area.
Teachers’ Self Evaluation
• Students had a lot of trouble creating their storyboards and need help making a creative script. More example could have been developed in advance.
• Most of the student had a very limited background on the different intertidal organisms, aside from the sea star and needed more background and information.
• This was the first time for the students to use iMovie and GarageBand and final project took more time than anticipated.
• Students needed access to more video and pictures of their projects. A Second field trip, after the writing of the storyboard would have been helpful so more videos and pictures could be obtained.
Our Draft "CSI" activity
It's kind of funny, we started this exercise as a "Fish Market Murder" but in the end it was only possible to find real variable sequence regions that are homologous and short enough by using mammals...
In this case we are using a short portion of the D-loop region of the Mitochondrial Genome.
http://marinebiotech.net/workshop/bioinformatics/Saturdays/CSI_wSeqs.doc
http://marinebiotech.net/workshop/bioinformatics/Saturdays/CSI_wSeqs_answers.doc
In this case we are using a short portion of the D-loop region of the Mitochondrial Genome.
http://marinebiotech.net/workshop/bioinformatics/Saturdays/CSI_wSeqs.doc
http://marinebiotech.net/workshop/bioinformatics/Saturdays/CSI_wSeqs_answers.doc
Saturday, January 10, 2009
Inserting video into Powerpoint
I wanted to insert a video clip into a powerpoint I just made. I had done this in the past, but with my new computer I must have changed the way the clip was saved. I setup saving into quicktime, but my pp will not recognize it. How do I change the video clip format?With so many different ways to save video, what do your recomend? I started using quicktime, because it is easy to transport using fewer mb, but now I found I can't insert it into pp.
I was thinking of doing my lessonplan on the podcast project I did this fall with my students and I was wondering if I should include the video example I made for this project in the powerpoint, or if it would just be easier to include some still pictures.
Hope the colors are not too distracting. I just wanted to try out some of the features of this blog. Ruth
Lesson Plan Files
These files are also located on our MBB Web site
[http://marinebiotech.net/workshop/bioinformatics/2008_AY_sessions.html]
[http://marinebiotech.net/workshop/bioinformatics/2008_AY_sessions.html]
Friday, January 9, 2009
By the way, I forgot to respond to the question from Steve about curriculum standards. It is extremely important in my district that lessons reflect the state standards. I don't have to formally turn lesson plans in but I must teach according to the standards and our science department is always sharing ideas for labs that reflect the standards. Marianne
marinebiotech
Hey Steve,
I am having fun with my students helping them to create their "Powerpoint Notebooks" Feedback from them told me that they really like finding cool pictures to go with their invertebrate notes!
Talk to you tomorrow. Marianne
I am having fun with my students helping them to create their "Powerpoint Notebooks" Feedback from them told me that they really like finding cool pictures to go with their invertebrate notes!
Talk to you tomorrow. Marianne
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