Download Tutorial17_02

Klug, Old Activity 16.1 Recombinant DNA Technology
Klug, NEW Activity 17.2 Recombinant DNA Technology: Vectors
* In its revised format include parts of old 16.1.5 through 16.1.11. This is the second part
of old 16.1 and is being split into two separate tutorials and renamed. These parts should
be separated from the original tutorial then combined to form this new tutorial, Activity
17.2. It will have it's own Introduction, Summary, and Post-quiz.
* Remove the screen that shows on selecting “module quiz” asking if the user wishes to
take the quiz.
New organization:
Activity 17.1, Recombinant DNA Technology: Vectors
Introduction (New 17.2.1)
-This will not be a part of the Flash animation, but an html page.
-Use the photos of bacteriophages and plasmids from old 16.1.5.1, the
captions, and the same title “Types of Vectors”.
-Use only one page of text (“The fragments of DNA produced…”) and delete
the second page (“Press play to see an example…”)
- This is the end of the segment.
Animation (New 17.2.2) Using a phage vector
- Begin with the same image and title as in 16.1.6.1 showing a blue
bacteriophage (lunar lander!) and the title “Chloning Phage Lambda…”
- Scroll the combined text of the two pages (“Lambda is a bacteriophage
widely used…”) and “DNA is extracted from….” , using a paragraph
break between them)from the bottom of the text window to the top,
stopping when the top line reaches the top. Pause 3 seconds and dissolve
to the animation of 17.2.2.2.
- Run the animation of 17.2.2.2 showing the green/purple DNA of the
bacteriophage emerging and enlarging. Pause 2 seconds and continue
with the animation of 17.2.2.3
- Run the animation of 17.2.2.3 that shows the purple Central gene cluster
popping out of the chromosome and dropping down. Pause 3 seconds and
dissolve to the text of 17.2.2.4.
- Pause 3 seconds and dissolve the text to the new text of 17.2.2.3.
- Bring up the new text in 17.2.2.4 that says “Over 100 vectors based on
phage lambda…” Pause 4 seconds and play the animation of 17.2.2.5
- Run the associated animation (17.2.2.5) showing the orange segment
combining with the green pieces to form a Recombinant Chromosome.
Pause 3 seconds and dissolve the text to the new sequence.
- Bring up the text “The recombinant chromosome is then packaged…..”,
pausing for 5 seconds – this is 17.2.2.6.
- Run the animation of 17.2.2.7 showing the chromosome reduce and fit
inside of the bacteriophage head. Pause 3 seconds and dissolve to the new
text of 17.2.2.8.
Scroll the text of 17.2.2.8 from the bottom of the text window to the top of
the window, stopping when the top line reaches the top. Delete the last
line of this text which says “Press “play” to learn more about plasmids.”
- This is the end of the segment.
- Set up scroll flags: “Extraction” at the start of 17.2.2.2, “Ligation” at the
start of 17.2.2.4, “Packaging” at the start of 17.2.6.6, and “Summary” at
the start of 17.2.2.8.
Animation (New 17.2.3) Plasmid design
- Use the same image of the green/purple pUC18 circle as in old 16.1.7.1.
- Scroll the text of 17.2.3.1 (“Plasmids are naturally occurring….” from the
bottom of the text window to the top of the window, stopping when the
top line reaches the top. Pause for 3 seconds and dissolve to the new text
and image of 17.2.3.2.
- In 17.2.3.2 bring up the new image showing the enlargement of the LacZ
section of the plasmid
- Scroll the text of 17.2.3.2 (“Plasmids have been genetically
engineered…”) from the bottom of the text window to the top of the
window, stopping when the top line reaches the top. Delete the last line of
this text which says “To see how plasmids can be used…..:” Pause for 3
seconds and dissolve to the new text 17.2.3.3.
- Scroll the text of 17.2.3.3 (“Here, the plasmid pUC18 carries…”) from the
bottom of the text window to the top of the window, stopping when the
top line reaches the top.
- This is the end of the segment.
- Set up scroll flags: “Polylinker” at the start of 17.2.3.2. and “Lac Z” at the
start of 17.2.3.3.
Animation (New 17.2.4) Using a plasmid vector
- Use the same image of a bacterium with a yellow plasmid and the title
“Cloning with a Plasmid Vector” in 17.2.4.1
- from the bottom of the text window to the top of the window, stopping
when the top line reaches the top. Delete the last line of this text which
says “Press play to see how a plasmid may be used…..:” Pause for 3
seconds and dissolve to the new text 17.2.4.2.
- Bring up the text of 17.2.4.2 (The DNA to be cloned is isolated…”) and
pause for 4 seconds. The animation that follows will be designated
17.2.4.3
- Run the animation of 17.2.4.3 showing the cleavage of the purple DNA
bar by a Restriction Enzyme. Pause 3 seconds at the end of this and
proceed to the next animation segment, 17.2.4.4.
- Run the animation of 17.2.4.4 showing an orange plasmid vector
descending from the bacterium to the bottom of the screen. Pause 3
seconds and proceed with 17.2.4.5
- Run the animation of 17.2.4.5 showing a yellow orange piece of the
Plasmid vector moving out to the right. Pause 3 seconds and dissolve to
the next text element (but don’t start any animation yet).
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The text element, 17.2.4.6 says “Fragments from the DNA are ligated…”.
Pause 4 seconds when this comes up and then start the animation of
17.2.4.7.
Run the animation of 17.2.4.7 showing a purple piece combining with the
yellow circle. Pause 3 seconds at the end of this and dissolve the text to
the next segment.
In 17.2.4.8, the text changes to say “The bacterial cells are heatshocked…” Pause 5 seconds after this comes up and run the animation of
17.2.4.9.
In 17.2.4.9, the yellow/orange plasmid circle reduces and goes into the
bacterial cell. Pause 4 seconds at the end of this and dissolve to the next
screen of new text and an additional image.
Bring up the photo of the Petri plate and colonies (same illustration at
upper left) as in the existing segment – this is 17.2.4.10
Scroll the combined text of the two text pages of 17.2.4.10 as a single unit
with a paragraph break: “The bacteria are incubated and form colonies…”
coupled with “The medium on the Petri dish contains….”.
This is the end of the segment.
Set up scroll flags: “Removal” at the start of 17.2.4.2, “Isolation” at
17.2.4.4, “Ligation” at 17.2.4.6, “Heat-shock” at 17.2.4.8and “Lac Z” at
the start of 17.2.4.3, “Growth” at 17.2.4.10.
DELETE the Quiz:Vectors of old 16.1.9 – this will be incorporated into the post-quiz
Summary (New 17.2.5)
-This will not be programmed as part of the Flash animation.
-Write a title at the top of the screen that says “Conclusion” if this is consistent
with our new criteria.
- Write the following text under that:
1. Recombinant DNA is created by cutting DNA molecules apart
and combining them together with delivery molecules called
vectors.
2. DNA fragments produced by digestion with restriction
enzymes cannot replicate within bacterial cells. If a researcher
wants to clone a DNA sequence, the fragment must first be
inserted into a vector.
3. [Use the existing paragraph of old 16.1.10.1 which begins
“Bacteriophages, such as phage lambda….”
4. [Use the existing paragraph of old 16.1.10.1 beginning with
“Plasmids are naturally occurring double-stranded….”
-This is the end of the segment.
Post-quiz (New 17.2.6)
-This will not be programmed as part of the Flash animation.
- Delete screen asking if user wants to take the quiz.
-
Quiz questions will be drawn from the old 16.1.9 (“Quiz: Vectors”) and
the extant post-quiz.
First Pass Comments from Eric Stavney 10/17/03
1. The captions on the graphics for the Introduction page are dim and small, making
them very difficult to read. Can we replace these captions with the same words
using the more prominent gold color and font that we’ve had in the other
tutorials?
[Andy 10/23: Remove the captions from the graphic and render them as HTML text.]
2. Let’s add a title at the upper left of the Graphics window throughout 17.2.3 called
“Plasmid Design”.
[Andy 10/23: Please make this change.]
3. I would like to see us shrink the final built graphic of 17.2.3 (plasmid circle with
excerpted region at upper right) and give a little more white space between the
scroll bar and the bottom of the graphic. It’s uncomfortably close right now. I
say shrink the graphic because if you simply move it up, the enlarged inset
(Polylinker Region) will be pushed off the top.
[Andy 10/23: Please make this change and enlarge the labels on the lavender arch.]
4. Delete the last sentence in the text of 17.2.3.3 that says “To see how plasmids can
be used as vectors in creating recombinant DNA, press Play.”
[Andy 10/23: Please make this change. Also, the font for the scrolling narrative
appears to be smaller than normal. Please make sure the font size is consistent
throughout.]
5. In 17.2.4 (Using a Plasmid Vector), the fifth Scroll flag (“Heat Shock”) needs a
wider text box to accommodate these words. The words are rubbing the sides of
their box!
[Andy 10/23: This appears to have been made already.]
6. For the first half of 17.2.4 there is a phantom comma, apostrophe, or tiny that sits
just below the bacterial cell drawing in the upper right hand corner. It disappears
about 2/3 of the way through the animation, and it is probably part of the bacterial
cell graphic. Can we remove this annoying speck?
[Andy 10/23: Please make this change.]
7. The enlarged photo of 17.2.4.10 is rather embarrassingly low resolution. Unless
we have a suitable higher res replacement (how about the original artwork in the
textbook?) we should shrink it to about 60-70% of it’s size to regain some clarity.
You’ll have to repoint the label arrows after shrinking the image, of course.
[Andy 10/23: Please make this change.]
8. Can we give an extra line of white space between the title CONCLUSION and the
body of the text on the Conclusion page? – it feels too tight to me.
[Andy 10/23: Use what ever is the standard format. Be consistent.]
Second Pass Comments from Eric Stavney 10/30/03
1. The fifth scroll flag in 17.2.4 (Heat-Shock) doesn’t fit in its frame – it needs to be
widened.
[Andy 10/31: Make this change.]
[Andy 10/31: The caption on the Intro page should be left-aligned under the images.]
[Andy 10/31: At the beginning of “Cloning with a Plasmid Vector” the image should
occupy the majority of the screen then shrink when new material needs to come on
screen. This same technique should be used with “Cloning Phage Lambda as a
Vector.” There is too much white space.]
[Andy 11/10: I had hoped for more but we’ll live with what we have.]
Third Pass Review by Andy 11/10/03
* this is ready for copyediting.