COMPUTER PROJECT INSTRUCTIONS

Part I: DNA Forensics (10 pts)

Analyzing DNA base sequences is useful for many purposes. It can be used to solve criminal cases or to identify unknown people by their personal DNA, for example. In this exercise you will use DNA evidence to solve a real case involving the Romanov family of Russia. You will then use your learned skills for further analysis in Part II.

First, go to this link:

http://vector.cshl.org/bioforms/guide.pl?b_id=1&p_id=1

Read carefully the information about mitochondrial DNA – you will need it later.

Follow every step of the exercise and answer the questions below:

1. What is a "hypervariable" region and why is it valuable for analysis?

2. Describe how mtDNA is inherited.

3. Why is mtDNA useful for genetic analysis?

4. Based on your analysis, what is the average number of SNPs between any two people?

5. Which of the femur bones belongs to the Czar? Support your answer with your data – that is, how many matches were there between the Czar and the femur bones? Use a table and clearly support your answer with at least a paragraph.

6. Which of the femur bones does not belong to the Czarina or her daughters? Support your answer as in #6.

7. Was Anna's claim true? Support your answer as in #6.

Part II: Analyzing DNA Sequences of the Hominid Family

How closely related are different cultures of Homo sapiens? For that matter, what is the evolutionary relationship among present day humans and other primates such as chimps and gorillas, or other mammals such as mice and horses? You will compare DNA sequences from the mtDNA of these groups to answer these questions.

In addition, you will also compare the mtDNA of a 30,000 year old Neandertal that was extracted from fossil remains in 1997 by Dr. Svante Paabo of the University of Munich. Neandertals are a mystery. They coexisted with our ancestors, the CroMagnon, for 60,000 years and then disappeared 30,000 years ago. Are they direct ancestors, or were they just a branch in the evolutionary tree of the human family? You will make your own judgment.

Go to this link (or click on "DNA Learning Center Login" in Favorites):

http://vector.cshl.org/sequences/login.pl?no_auto=1

Username: biology52 Password: protein

Neandertal vs. Human cultures (15 pts)

Click on "CLEAR".

Click on "Manage Groups".

Choose "Ancient DNA" from drop-down box.

Check all the boxes to the left of the groups (except Asian) and click OK at bottom.

Click on "Open" to the right of "Iceman mtDNA," and then click on the Medline link to find information on this specimen.

Now, you will compare sequences among these different groups.

This is a segment of mtDNA within a region called the "D-loop" which is common to most organisms.

To compare the groups:

· Make sure "align: ClustalW" is chosen to the right of "Compare".

· Choose only two groups at a time by checking the boxes at left, then "Compare".

· Calculate the % of base differences (don't count unknown bases).

· Make a table showing the % differences with each comparison.

Conclusions:

Write a conclusion at this point. Keeping in mind that mutations accumulate over time, what can you conclude about the evolutionary history of these organisms? Where does "Iceman" fit in? What do you conclude about Neandertal – that is, should Neandertal be considered closely related to modern humans? Use your data to support your analysis, and give as many reasons as possible. Several paragraphs are expected.

Modern Humans vs. Other organisms (15 pts)

You will extend your analysis.

Click on "Search by Keyword".

Type in your choice of an animal followed by "D-loop" (the D-loop is part of mtDNA that is common to all organisms). Ex: "Gorilla D-loop"

Choose the D-loop sequence (don't use the entire mitochondrial sequence), click OK.

Do the same for other animals (or primates).

Possibilities: chimpanzee, orangutan, monkey, mouse, rat, horse, zebra, chicken, gorilla, fish, elephant, cow, bison, etc.

Also add "human D-loop" and "Neandertal D-loop".

When completely done, click on "CLEAR".

Conclusions:

Make some comparisons among the members of this group, using a table and conclusions, as above. Some questions you might address are: how does the Neandertal or modern human DNA compare to other organisms? How do members of the same Genus compare with each other (ex: zebras and horses, or rats and mice)? Who is the ancestor of who? Demonstrate originality – research your own questions.

There is no specific requirement for the number of organisms or questions answered in this section, but the more extensive your research and analysis, the better the grade. Students who are faster than others will be expected to provide evidence of more work done in this section – sitting around with nothing to do will result in points taken off in this section.

ALIEN PLANET

Introduction

Process

Grading

Re sources

INTRODUCTION

You are from the planet Mkxpgz. In your solar system is another small planet nearby that has no life on it but would be perfect for a travel and recreational destination. Because the small planet has features that are unique to the planet Earth, you have been commissioned as experts to research a complete ecosystem or biotic area (biome)* on Earth. Your report must describe in as much detail as possible the important characteristics of this ecosystem that would be needed to create it on the new planet.

In addition, you will also be required to prepare an attractive, but informative, travel brochure for this new planet in order to get investors interested in financing the project. Since you have extremely advanced technology there will be no problem creating the biome (a collection of DNA samples will do), but you have to be careful that everything is balanced and nothing is missing. Also, you have the ability to gather all the information you need by tapping into the internet system transmitted from earth.

*Ecosystem: The biotic and abiotic parts of the environment, which includes plant and animal communities along with factors such as climate, altitude, temperature, moisture, light, and the chemical cycles

*Biome: A major region of distinctive plant and animal groups well adapted to the physical environment of its distribution area.

THE PROCESS

1. Using the “Resources” list below, research the biomes web sites to find the perfect one for your new planet. Keep in mind there also exist marine ecosystems (does your small planet have water?)

2. Your report (in Word or any program you wish) will be in two parts. Part I will describe the abiotic factors that exist on the planet and the reasons they will support the biotic factors that you will introduce.

a. Climate (temperature, rainfall, etc.)

b. Seasonal information (light, etc.)

c. Altitude

d. Soil profile

3. Part II will describe the biotic factors that you propose should be introduced:

a. Animals and animal communities: their habitats and niches, adaptations for survival, and reproductive strategies.

b. Plants and plant communities: their importance to the animals in the biome and their adaptations for survival.

c. Any symbiotic relationships that may exist between the species above.

d. Food chains/webs, energy systems, and predator/prey relationships.

e. Anything else that may be important in planning the construction of this planet.

Note: You should include graphics and diagrams to aid you, but use text to interprete them.

4. Create a brochure. You may use any medium you wish: Powerpoint, Adobe PageMaker, Publisher, FrontPage. Remember, this is a way to encourage investors to participate in the project by showing what the planet will look like, and how it will be used for recreation, and therefore should be creative and interesting.

RESOURCES

Here are some sites to help find information on specific ecosystems and biomes.

http://www.hewett.norfolk.sch.uk/curric/GEOG/HABITATS/index15.htm

http://redbaron.bishops.ntc.nf.ca/wells/biomes/

http://www.runet.edu/~swoodwar/CLASSES/GEOG235/biomes/intro.html

http://www.marlborough.la.ca.us/depts/science/biomes.html

http://www.ups.edu/biology/museum/worldbiomes.html

http://www.uwsp.edu/acaddept/geog/faculty/ritter/geog101/biomes_toc.html

Biome Food Webs:

http://curriculum.calstatela.edu/courses/builders/lessons/less/biomes/introbiomes.html

Search Engines (use key words to find info on specific topics)
www.google.com
www.hotbot.com
www.yahoo.com
www.altavista.com
www.dogpile.com

Graphics Sources:
www.ditto.com
http://www.altavista.com/cgi-bin/query?mmdo=16&stype=simage
http://multimedia.lycos.com/
http://www.corbis.com/

GRADING

0-10 pts. each 11-20 pts. each 21-30 pts. each

Information	Incomplete or inaccurate. Does not demonstrate very much understanding of the material on the part of the student.	Some information is given on all of the required categories (animal, plant species, food webs, etc.). Student has learned some things about the ecosystem.	Information is processed by the students (not copied and pasted). Demonstrates that the student has exceptional understanding of the ecosystem.
Graphics/Diagrams	Few, poor	Some graphics are used, but not necessarily in an effective way, or are used too much in place of text. A diagram only of the food web has been copied from a web source.	Graphics are used effectively. More than one diagram is created (besides the food web) and has not been copied.
Brochure	Incomplete or sloppy.	The brochure is complete but does not necessarily appear authentic.	Shows creativity. Brochure is obviously the result of a lot of work.

BACTERIAL DISEASES / MUSICAL CHAIRS

PROCEDURES::

Pick a disease from the list below. If you find a bacterial disease that is not on the list, that’s OK.
Use the "Resources" list to search for information on the internet.
When you find a site with information, record on your worksheet list:

-the computer number
-the URL (address)
-the name of the disease
-some brief information that is unique to the disease

When you complete that trade places with someone else in the computer lab that has found information on their computer.
Repeat #4 as many times as possible.

RESOURCES:

Sexually transmitted diseases: http://www.mic.ki.se/Diseases/c1.252.810.html

Bacterial diseases: http://www.achoo.com/directory/humanhealthanddisease/category.asp?c=BacFun&r=_a_f

Diseases index: http://gopher1.bu.edu/COHIS/help/find/knowdis.htm

Diseases, general: http://www.mic.ki.se/Diseases/alphalist.html

Diseases index: http://www.yahoo.com/Health/Diseases_and_Conditions/

Diseases index: http://www.jeffersonhealth.org/diseases/inf_diseases/

Try specific searches from these search engines:
    www.google.com
    www.hotbot.com
    www.infoseek.com

DISEASE LIST:
Diphtheria
Leprosy
Tuberculosis
Anthrax
Botulism
Food Poisoning
Gangrene
Tetanus
Impetigo
Toxic Shock Syndrome
Meningitis
Rheumatic fever
Bubonic plague
Cholera
Typhoid fever
Typhus
Rocky Mountain Spotted Fever
Syphilis
Pneumonia
Scarlet Fever

GALACTIC TRAVEL AGENCY, INC.

INTRODUCTION:
It is the year 2050. You are an advertising agency hired by the Galactic Travel Agency to produce an advertising campaign to entice people to sign up for space travel cruises to the planets (using a new suspended animation technique that allows people to "sleep" during the journey). Your ad presentation will be produced in PowerPoint and will contain photos, graph charts, and information about each of the planets.

PROCESS:
1. Prepare to gather information for your ad presentation. You may NOT print any information from the printers. Instead, copy or produce any information on the Zip disk given to you, by downloading files directly on the disk or copying and pasting text into Microsoft Word. The Zip disk will be handed to your teacher at the end of every period for safekeeping.

2. Visit the web sites listed in the Resources section below and gather information about each of the planets (other than Earth). Consider interesting planetary facts that would be an attraction to prospective travelers.

3. Visit the image gallery web site and download photos of the planets for your ad presentation.

4. Create a PowerPoint ad presentation as a brochure for the Galactic Travel Agency. Your teacher will give a lesson in using PowerPoint. Use your imagination. Review the Rubric below to see how the presentation will be graded.

5. The ad presentation should include at least one graph chart comparing planetary statistics (for example, size, composition, annual and rotational cycles, etc.).

RESOURCES:
For information about the planets:

Windows to the Universe

The Nine Planets

Views of the Solar System

Welcome to the Planets

For copyright free photos of the planets:

Lycos Image Gallery

RUBRIC:

0 - 5 pts. 6 - 10 pts. 11 - 15 pts.

PHOTOS	Few or no photos.	At least one photo per planet; no attached text.	Photos are attractively used in the brochure; explanatory subtext is used.
INFORMATION	Incomplete or no information.	Some information for each planet.	Lots of information, well organized and attractive; presents good case to visit.
CHART	Incomplete or no graph.	Includes one accurate graph; graph is used well in brochure.	More than one graph is included; placed attractively with explanatory subtext.

Web Quest: Earthquakes and Volcanoes

EARTHQUAKES: WHERE TO BUILD?

Introduction:

Everyone is aware of California’s reputation as an earthquake state. However, a recent earthquake here in Incline Village, as well as past earthquakes in the Reno/Carson City area, have alerted local citizens to the fact that this area is very seismically active as well. There have been reports that a very large earthquake could hit this area in the near future. Your team has been hired as part of an investigative mission for a developer who is considering building a large high-rise structure either in the Reno area, or in the Bay Area of California. You are asked to prepare a recommendation based on information that you will gather from the internet.

Process:

Choose your team of 3 investigators carefully. Each member will have to contribute both to the research for information, as well as preparing the report.

Decide who will take on one of the suggested tasks below.

Several web sites that will help with your investigation are listed below. If you are doing this from a web site you can just click on the links to go to that site. Otherwise, type in the URL (address) from the instruction sheet.

Search and read through the sites carefully. This may take a while – there is a lot of information available at these sites.

Feel free to visit other appropriate sites on the subject. Search engine sites that are good are:

www.google.com
www.hotbot.com
www.infoseek.com

The internet investigation may take a couple of days. After that, your team will have to work together to prepare the report.

A rubric (a description of how something will be evaluated) has been prepared to give you an idea how your report will be graded. Be sure to look over the rubric before you begin.

Resources

http://www.seismo.unr.edu
This is the central site for information about Nevada. Here you will find maps of recent earthquakes, as well as information about past earthquakes.

http://www-geology.ucdavis.edu/~GEL161/earthquake1.html
This will give a description of the type of damage each magnitude can produce. You will have to do an internet search for more detailed information.

http://crustal.ucsb.edu/scec/outreach/
This will give you information about California earthquakes.

http://www.seismo.unr.edu/htdocs/WGB/InclineVillage98/
This covers a recent earthquake here in Incline Village. It also discusses the possibility of future earthquakes.

http://www.abag.ca.gov/bayarea/eqmaps/mapsba.html
This is a good source of maps of recent and historical earthquakes in the Bay Area.

Tasks

Included in your report must be the following:

A comparison of faults to earthquake locations. Describe (with a hand-drawn map) where faults are located for both a California region and a Nevada region. Include a description of where most of the past earthquakes have been located along these faults.

Someone will visit the site: http://www.scecdc.scec.org/Module/ Complete the following activities: (A.) Section 2, Activity 1; (B.) Section 2, Activity 2 – play the "animation of earthquakes…". Report on what you learned.

Someone must visit the site on the type of damage each magnitude will cause in order to report on the expected damage of future earthquakes.

There should be a discussion of past large earthquakes – when and where they occurred and the type of damage they caused, as well as any other important information.

Someone will be expected to take the quiz and include in the report information that was learned from the quiz, particularly question #3 (put this information in #4 of "Final Report" below): http://www.crustal.ucsb.edu/ics/understanding/

Final Report

For any information you got from the internet that wasn’t listed in "Resources", include the URL (address) in the report.

Give a comparison of recent earthquakes that have occurred in the Bay Area and in the Reno/Carson City area. Include a map with this information, as well as magnitudes and faults.

Give a comparison of historical large earthquakes from these two areas. Describe the damage that must have been caused, considering the magnitudes.

Give a prediction of future seismic activity. Would it be wise to build a tall structure in either area? Why or why not? What kind of damage would you expect?

Rubric
You will be graded on the following:

1-3 pts. 4-6 pts. 7-9 pts.

Use of Web sites	A few or none of the sites listed were used. No URL's listed.	Many of the sites were used. URL's listed.	Besides those sites listed, new sites were found and used.
Comparison of earthquakes	Some comparison was given of either recent or historical earthquakes.	A clear comparison was given of both recent and historical earthquakes.	A very detailed comparison was given of both recent and historical quakes