Krogh, Activity 1

Klug, Old Activity 7.1, Chromosome Aberrations
Klug, NEW Activity 7.1 Aberrations
* In its revised format include Parts 3.3.1 through 3.3.7. These parts should be separated from
the original tutorial then combined to form this new tutorial, Activity 3.3. It will have it's own
Introduction, Summary, and Post-quiz.
* Remove the screen asking if the user wishes to take the quiz.
New organization:
Activity 7.1, Chromosome Aberrations
Introduction (new 7.1.1)
-This will not be programmed as part of the Flash animation.
-This will be converted into a single html page. It will use the image and text from
the first section of Part 7.1.1.
-The title over the image will read “Chromosome Aberrations”
-Splice together the text on old 7.1.1 and 7.1.2 into a total of three paragraphs: “In
both plants and animals….” stands alone. Join “In most cases these…” and
“Breakage can occur…” into a single paragraph. Then make a third single paragraph
with “The loss or gain….” and “Plants show fewer effects….”
Animation (new 7.1.2) Five Types of Chromosomal Rearrangements (old title was
-Modify the title “Overview of…” to just “Five Different Types of
Rearrangements of Chromosome Segments”
- Join together old 7.1.2 through 7.1.6 beginning with the screen listing the
“major types of chromosome aberrations….” through the animation arrow
showing “Reciprocal translocation”.
- The text listing the major types of chromosome aberrations should scroll
upwards to the middle, followed by a pause BEFORE the sequence of examples
appear. Place a 2-3 second pause between each example’s dissolve-in. The text
narrative will appear in the text narrative space and the dissolves will appear in the
graphic space.
- Place scroll flags at the Deletion, Duplication, Inversion, Nonreciprocal
translocation, and at Reciprocal translocation.
- This is the end of this segment.
Animation (new 7.1.3) Deletions
-This is self-contained and will move (blue (Drosophila?) chromosome image)
and skip the old interactive part ( and merge all the other scenes without a
stop (old and old, ending with
-All scenes (old 7.1.3 should follow each other without a stop but using a pause and
dissolve. The text should scroll upwards and the animation shouldn’t start until the
text reaches the center. Dissolve the text after the animation finishes, waiting a beat
before moving on.
-Finish with the blue loop image and associated text “A deletion has been found in
- overview of deletions (new text)
- scroll in text then dissolve in through with a pause between
- terminal deletion (no text change, flag as Terminal deletion)
- intercalary deletion (no text change, flag as Intercalary deletion)
- deficiency loop deletion (no text change, flag as Deficiency loop)
- karyotype photograph (new text, flag as Terminal deletion example)
- interaction (split out as a separate file, see Exercise 7.1.4 Survival of
Deletion Mutations below)
- tumor suppressor (new text, flag as Tumor suppressor gene region)
- tumor suppressor (no text change)
- tumor suppressor (no text change)
- Drosophila (new text, flag as Tumor suppressor gene region)
-Place scroll flags at “Terminal deletions” animation, “Intercalary deletions”,
“Deficiency loop”, “Terminal deletion example” (karyotype photo with new text),
“Intercalary deletion example” with associated text, breaking of chromosome
animation to show intercalary deletion, and “Deficiency loop example” at the image
indicating a blue loop for the Drosophila example.
Exercise (new 7.1.4) Survival of Deletion Mutants
-This is self-contained and will not be merged with another part.
- This is the old interactive screen from the Deletions segment described
- Retitle the exercise Survival of Deletion Mutants
-Delete the instructions at the bottom of the screen “Make a choice…” and the text at
the right side the screen. Instead have the following instructions appear from a popup Instructions box: “Use your knowledge of the notch deletion to predict whether
the illustrated genotypes will survive. Draw down the choices for each individual by
clicking on the black triangles and clicking on a choice in the list for that individual.”
-Add a “Allele Symbols” button to the bottom of the window. Pressing this button
will open a small pop-up window with the 3 allele descriptions (i.e. N+ = …, N = …,
and Y = …). This text will be removed from the right-hand side of the old tutorial.
Animation (new 7.1.5) Duplications
-Delete all stops between text changes and associated animations
-Put all scenes together as one long animation with pauses between animations
and dissolves between text changes
-In the “Examples of Duplication” screen with the “Ribosomal RNA gene area”
animation, the text scrolling of the 3 paragraphs should synchronize with the 3
zooms of the RNA parts.
-Allow perhaps 5 seconds of pause for “Components in the Prokaryotic” Table
image and “Examples of Duplications” Fly Eye Table image, and “Examples of
Duplications – Summary of Trinucleotide…” Table image before moving on.
- This encompasses old to – all the scenes in this section.
- Set scroll flags at “Duplication of BC” animation, “Components” image,
“Examples of Duplications: Ribosomal RNAa” image, “Examples of
Duplications: Fly Eyes” table image, “Examples of Duplications: Summary of
Trinucleotide-Repeat” table image, and “Duplications in Evolution” animation.
Animation (new 7.1.6) Inversions
-Delete all stops between text changes and associated animations
-Put all scenes (old through together as one long animation with
pauses between animations and accompanying dissolves of text changes
-Leave off the interactivity page ( Inversion Pairing quiz) from this segment Inversions (new text, flag as Inversions) Inversions animation Paracentric Inversions (new text, flag as Paracentric Inversions) Inversion Effects (new text, flag as Inversion Effects) Evolutionary advantages (new text, flag as Evolutionary Advantages) Inversion Pairing (new text, flag as Inversion Pairing) Inversion Pairing with Crossover (new text, flag as Inversion Pairing
with Crossover) Inversion Pairing Quiz (move this to Inversion Pairing Exercise below) Inversion Pairing Paracentric (new text) Inversion Pairing Paracentric (new text) Evolutionary Advantages of Inversions (new text)
Exercise (new 7.1.7) Inversion Pairing
- Move instructions from text box (“Start with the left…”) to a pop up window
when clicking on the Instructions button found at the lower right of the image.
- This exercise is self-contained.
Exercise (new 7.1.8) Evolutionary Advantages of Inversions Quiz (3 questions)
-Flag the following sections: “Inversions” at the beginning, “Paracentric Inversions”,
“Inversion Effects” for the Mottled eye, “Evolutionary Advantages”, “Inversion Pairing”,
“Inversion Pairing with Crossover”
Animation (new 7.1.9) Translocations
-Delete all stops between text changes and associated animations
-Put all scenes (old through together as one animation with pauses
between animations and accompanying dissolves of text changes
-Do not include the interactive page (old and because they’ll be used
as the new Exercise 7.1.9 below. Translocations (new text, flag as Translocations) Translocations (new art) Translocations (new art and text) Construct Translocation Exercise (move to new Exercise 7.1.9 below) Construct Translocation Exercise (move to new Exercise 7.1.9 below) Balanced Translocations (new text, flag as Balanced Translocations) Balanced Translocations (new art) Robertsonian Translocation (new text, flag as Robertsonian
Translocation) Robertsonian Translocation (new text) Robertsonian Translocation (new text)
-Flag the following sections: “Translocation”, Balanced Translocation”, and
Robertsonian Translocation”
Exercise (new 7.1.10) Constructing a Heterozygote Translocation
-Change the title of the old interactivity page and to Constructing a
Heterozygote Translocation
-Move the instructions for this exercise (“Drag the chromosome selections…”) from
the text box to a pop-up box labeled Instructions
-This exercise is self-contained.
-There appears to be a programming problem that occurs when the upper blue
chromosome #2 is dragged onto the image next to the blue #1 chromosomes or the
yellow chromosome 4s are dragged next to the chromosome 3s--- the whole
animation quits and jumps to the Introduction for the whole module! There appears
to be a brief flash-frame indicating that the answer was correct, but the near
instantaneous jump to the Introduction happens too fast to be sure. This needs to be
-The error box “Heads Up, Sorry this is wrong” can stay.
Summary (Part 7.1.11)
-This will not be programmed as part of the Flash animation.
Post-quiz (Part 7.1.12)
-This will not be programmed as part of the Flash animation.
First Pass Comments from Eric Stavney 10/20/03
1. On the Introductory page, can we give some more white margin on the left side of
the graphic? The photo is crowding the left border. Slide it rightwards a bit and/or
reduce it.
[Andy 10/23: Make this correction. Decrease the size of the image so that it doesn’t crash the
left border. Also, remove the caption from the image and add it as HTML below the JPEG.
It is impossible to read as it is now.]
2. In 7.1.3, the Deletions segment, we need pauses between the dissolves at the scroll
flags Terminal Deletions, Intercalary Deletions, Deficiency Loop, and Terminal
Deletion example. These animation sequences come fast and furious, and we need to
hold the end result (last frame) of each animation sequence at least 3-4 seconds
before dissolving to the start of the next sequence.
[Andy 10/23: Make this correction. Longer pauses are needed between each of the segments
3. Just before the Scroll flag Deficiency Loop Example in 7.1.3 there is a caption that
flashes onscreen for less than a second saying “Loss of cell division control…..” We
need this to stay onscreen for at least 4 seconds before dissolving to the sequence at
the scroll flag.
[Andy 10/23: Make this correction. I was not able to use the scroll control to find this
segment but it would appear if I used the Play button. I suspect that this segment is NOT
under the control of the scroll control. The action of the animation should be under the
control of the scroll control. Don’t embed movies within movies.]
4. In 7.1.5 (Duplications) we need a gentle fade-in of the sequence beginning at the
scroll flag Duplication of BC. The preceding sequence fades out nicely but the
following sequence cuts in abruptly and should fade in. The graphic that comes up
is a big table of ribosome components. This table also needs to dissolve away to
reveal the next sequence, not abruptly disappear.
[Andy 10/23: Murray and Eric—After some thought, I want a hard fade between major
segments and a soft fade between minor segments. The hard fade is intended to “remind” the
reader that something big has happened—a change of topic—while a soft fade is intended to
suggest the continuity of an idea (e.g. between objects within a phase of mitosis). In general,
if there is a scroll flag then a hard fade is acceptable but transitions within a segment should
be soft.]
5. I’m tempted to ask for more screen time for the Examples of Duplications sequences
towards the end of 7.1.5 – I have trouble taking in everything in only 5 seconds.
Can we extend these sections to 7-8 seconds? Andy?
[Andy 10/23: Make this correction. Extend the pause and scroll the text for these last
6. We need a dissolve, meaning fade out and fade in at the head of the Paracentric
Inversions Scroll flag section of 7.1.6.
[Andy 10/23: No, it is appropriate to have a hard fade to make the user aware of a significant
change in the point of discussion.]
[Andy 10/23: The screen titles should be above the graphic and not above the narration.
Change this throughout.]
7. In 7.1.6, the Evolutionary Advantages Section (marked by scroll flag), the title
“Evolutionary Advantages of Inversions” looks screwy way over in the corner. I
realize we’re trying to keep all our titles over the text area in this tutorial, but I
think we should center this title because it looks odd over in the corner.
[Andy 10/23: The screen titles should be above the graphic and not above the narration.
Change this throughout.]
8. In 7.1.6 (Inversions) within the Inversion Pairing sequence, there is an image of four
blue DNA strands with black genes (A-E) and the title :Resultant gametes” over
them. There’s some kind of flash frames of slightly thicker chromosome lines that
cause the chromosome to pulse twice. Even though this is a cool effect, it isn’t
meaningful, and we should try to cut out the flash frames.
[Andy 10/23: Make this correction. Also, increase the pause between each transition in this
segment. This is an example of where a soft fade is appropriate.]
[Andy 10/23: Increase the font size for the labels on the last screen of Inversion Pairing.]
9. The last sequence of 7.1.6 (Inversion Pairing with Crossover Scroll Flag section), the
very last screen, has a somewhat distorted graphic of the Southwestern USA and a
bunch of graphs whose axes are unreadable. Clearly we have a space problem in
enlarging this graph, but I don’t think it’s worth showing if the user can’t read it.
Any way we can move the map to the far left center and redo the pointer lines so
they extend rightwards to the graphs stacked vertically to the right, instead of
under, the map? Currently there appear to be pointer lines that go nowhere on the
map – they probably were connected in the previous edition. Bottom line: we got to
fix this, possibly by going for a horizontal, rather than a vertical layout.
[Andy 10/23: Eric’s correct. It’s useless if it can’t be read but it’s also a significant change to
render a new horizontal version. Delete this part of the segment--map and narrative.]
10. The title in the very last screen of 7.1.6 (discussed above) looks strange to be rightjustified over the text. At least left-justify the word “Inversions” under
[Andy 10/23: The screen titles should be above the graphic and not above the narration.
Change this throughout.]
11. The Evolutionary Advantages of Inversion Exercise (7.1.8) begins with an animation
that goes way too fast for me. The first image isn’t even on screen for a second
before it’s gone. Please slow down the rate of change between consecutive graphics
by adding perhaps a 4 second pause between them.
[Andy 10/23: Make this change. Slower is better.]
Second Pass Comments from Eric Stavney 10/30/03
1. Center the title under the photo on the Introduction page, and consider using a different
color for it. Tuck the caption more up under the photo.
[Andy 10/31: Make this change. It’s a relatively easy table tag to do center the caption under
the graphic.]
2. I like the work on 7.1.2. Nice job.
3. Let’s keep the graphic and text onscreen to the very end of 7.1.5 instead of fading out to a
white screen.
[Andy 10/23: Make this change.]
[Andy 10/23: The screen titles for “Inversions” and “Inversion Pairing” should be centered
over the graphic window. For the first segment, the label “Inversion of BCD” should appear
when the brown arrow appears and beside the brown arrow. This will allow room for the
centering of the “Inversions” screen title. For the “Paracentric Inversions” segment, the
whole graphic can be moved down so that the title will center without crashing. There is no
reason why the screen title on the “Inversions Effects” segment can’t be centered. ]
[Andy 10/23: For the last segment if “Inversion Pairing,” change the screen title to
“Paracentric Inversion Pairing” and delete the black label “Paracentric inversion
heterozygote” and add “Heterozygote” to the left of the 2 chromosomes. The
“Heterozygote” label should have the same font treatment as the label “Inversion loop, no
crossing over”. Also, all of the brown labels should be moved to the left of the associated
structure instead of above it. This will provide room so that the 3 chromosome structures can
be moved closer together, providing more room at the top for the screen title, without
reducing the image.]
[Andy 10/23: Add a scroll flag titled “Inversion with Crossover” where the second part of the
animations starts. (when the text “If crossing over occurs within the looped region...”