Biology -Virus Modeling

Background

In 1892, a Russian biologist by the name of Dimitri Ivanowsky made a revolutionary discovery. After years of research and experiments on tobacco plants infected with the tobacco mosaic disease, he transmitted the disease to healthy plants by rubbing them with juice extracted from the infected plants. He passed the extract through a fine-porcelain filter, and discovered that the disease causing agent was smaller than any known bacteria. These small disease causing agents were called filterable viruses and later, just simply called viruses. In 1935, a scientist by the name of W. M. Stanley found that viruses are very different than bacteria, in that viruses have a noncellular organization. As research continued, information about the structure of viruses became known and that parts of any virus included a chromosome-like part, surrounded by a protein coat, and all viruses have a capsid, DNA or RNA (inside the head of the virus), and a tail (or tail fiber). Each virus type has a different known shape or structure that allows it to be recognized, as well as a life cycle for which it can reproduce. Since viruses can only be seen by powerful microscopes, this scientific visualization modeling experiment is to acquaint students in recognizing the various shapes and life cycles of viruses through the process of making both a simple physical model and a virtual model of a virus type on the computer. The physical model will be used to demonstrate the major parts of a virus and the computer model will be used to actually model all components of the virus. Animation can later be used to show movement of the virus through its life cycle. Scientists often make these types of models to study possible viral structures, and model ways viruses may bind to host cells.

Data Gathering

The best way to start learning about viruses is to review what is in the North Carolina state adapted curriculum for biology, specifically the topic of viruses. Since many different types of viruses are know, have each student research one virus type to identify its shape, structure, characteristics, and life cycle. Have students start at the library, but the internet has loads of information about this topic. Listed in the reference section of this scientific visualization website are suggested URLs to begin this research and modeling experiment. Once a virus is identified, have students to begin the modeling by first sketching the virus on grid paper and if animating the model, have students make a storyboard. Listed in this website's reference section are URL's that explain modeling and other needed visualization materials to help in the process.  Below are links to  Scientific American's site with the January 1999 issue's article on influenza viruses and a link to  some examples of biochemical modeling  found on the Internet:

http://www.sciam.com/1999/0199issue/0199laver.html

Biochemical Modeling Examples 

You may want to include a written report from the students about their chosen virus to determine that they fully understand the biological component of the experiment. Also, since the model is to be made in 3D, time may be needed to instruct students in the basics of using a 3D graphics software and the common commands associated with that software package.

Modeling

The modeling experiment is in three stages. The first stage is identifying the major parts of a virus through the process of making a simple physical model (prototype). Second, students are to research a particular virus and gather information that is useful for modeling their chosen virus. Finally, each student is to use a computer graphics software and actually develop a 3D representation/model (static) of the virus. Later, if time allows, animating the model would benefit the student by seeing the virus move through one or more stages of its life cycle, as well as develop the students' skills in basic animation.

Stage One: Physical Model

After careful review of viruses from the state curriculum, begin with the following scientific visualization processes that include: prototyping, researching, and modeling.

For this beginning stage, I believe the basics of any visualization can be first taught by association. What that means is that if you can associate one area to another, or better yet, compare a simple idea with a complex task, it makes learning easier. Let's use this way of teaching in this scientific modeling exercise by first, having students make a simple (small) physical model(s) that they can touch, feel, and hold.

Two model types that can teach students to observe, formulate, recognize, and use spatial relationships are as follows:

Problem: Make a model showing the major components of a virus

The Nuts and Bolts Model

Material needs for each student: Have student use these materials, under your supervision, and make a simple model of a virus showing the virus head, chromosome part, and tail area.

AND/OR

The Polystyrene Ball and Colored Pipecleaner Model

Material Needs: Have students use these materials, under your supervision, and place the pipecleaner pieces into the ball to represent a virus shape. You science and biology teachers may want to have each color from the pipecleaners represent a virus stage, chromosome, or structure. Bending the pipecleaners will help give various shapes to the model.

Stage Two: Research

Many different type of viruses are known to scientists and biologist, so have each student pick a different virus and begin the research needed to identify its shape and life cycle. Use the library and internet for the research. Once the information is obtained, have students write a report on the virus identifying it's characteristics, shape description, and life cycle. Begin this research by using the references on this website, or just start the process by using an internet search engine.

Stage Three: Modeling the Virus

Once the research stage is completed, have students sketch their virus on grid paper to identify the various parts they want to show and where each part is to be placed within the model. If you are wanting to have students animate the model, I suggest that you have students do a storyboard for each major move or cycle. After students complete the sketching exercise and have gained your approval to continue, you would want to instruct the students on the software they are to use and show some good examples of virus models (see figures above). To further aid the students in starting the modeling process, have students begin their models by using primitive shapes (3D) that directly reflect the basic structure of the virus they are to model. Each primitive shape can represent a major component in the shape and structure of their virus. The next process is to refine the primitives into the desired shapes needed for properly modeling the virus. Remember, colors and textures are just as important as the 3D representation. Finally, do a simple animation that demonstrates a basic movement the virus may do during one or more stages of it's life cycle. You can make this part as complex or simple as you need to, but this modeling exercise lends itself as being an excellent way to introduce animation to beginners.
Listed below are three examples representing the primitive modeling stages students are to go through in this exercise:

Wireframe representation

Solid 3D representation

Transparent 3D representation


 
 

Additional Resources for Biochemical Modeling and Virus Information

 

http://www.ks.uiuc.edu/Overview/gallery/structure.html

http://ernie.bgsu.edu/~midden/MITBCT/cb/virus/virus.html

http://www.bocklabs.wisc.edu/Welcome.html

http://www.ks.uiuc.edu/Research/vmd/

http://www.ks.uiuc.edu/Research/cell_motility/kinesin/

http://www.bocklabs.wisc.edu/virusviz.html
 
 


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