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Difference between revisions of "Aperio - Genome Elongation Tests"

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Back to [[User:Aperio]]
 
Back to [[User:Aperio]]
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 +
== SUMMARY ==
  
 
I'm eating crow on this... and more importantly, noticing some kind of change in the (G)Grapes phenotype or at least the Starting Grapes Characteristic (flax has some similar variations in starting values).  This rings a bell with T3 testing but I don't recall if any conclusions were made.
 
I'm eating crow on this... and more importantly, noticing some kind of change in the (G)Grapes phenotype or at least the Starting Grapes Characteristic (flax has some similar variations in starting values).  This rings a bell with T3 testing but I don't recall if any conclusions were made.
  
−
Appreciation (QQQ) x Base Appreciation (QQQ)
+
Disregard my subsequent commentary.  Most of it is based upon a faulty premise that has since been straightened out.  The value of this page, however, is in the research data and the techniques.
−
KGYRYYRYYRYYRK x KGYRYYRYYRYYRK
+
 
 +
 
 +
== REFERENCE ==
 +
 
 +
{|{table} border=10 cellpadding="1" cellspacing="3" style="background-color:#EE82EE"
 +
|'''Vine'''
 +
|'''Initial Grapes (I)'''
 +
|'''Genome Length'''
 +
|-
 +
 
 +
| Amusement
 +
|11
 +
|33
 +
|-
 +
 
 +
| Appreciation
 +
|12
 +
|12
 +
|-
 +
 
 +
| Balance
 +
|08
 +
|31
 +
|-
 +
 
 +
| Contemplation
 +
|12
 +
|18
 +
|-
 +
 
 +
| Distraction
 +
|09
 +
|30
 +
|-
 +
 
 +
| Frivolity
 +
|12
 +
|34
 +
|-
 +
 
 +
| Wisdom
 +
|08
 +
|24
 +
|-
 +
|}
  
−
RYYR = Q
+
(I) has been introduced as the nomenclature for Initial Grape Count trait (NOTE: Legacy T3 that was lost or not adopted)
−
OOOR = G
+
 
 +
Appreciation (QQQ) x Base Appreciation (QQQ) [ KGYRYYRYYRYYRK ]
 +
 
 +
[[Aperio_-_Vine_Cross_Data]]
  
 
Initial Grapes
 
Initial Grapes
Line 21: Line 70:
 
  Aperio #10 10
 
  Aperio #10 10
  
−
If there's no shortening or elongation, all of these vines should be uniform.  A weighted average should take 6 genes for each splint and effectively return a vine identical to the starting vine.
+
If there's no shortening or elongation, all of these vines should be uniform regardless of the splice point.  It will effectively return a vine identical to the starting vine.
  
 
These variations indicate that there is now genetic diversity and the resulting variations produces 4 different starting values (including the original).  IIRC, each of the other vines possess unique starting grape values so this detail MUST be contained in the genome length, the gene combination, or some other self-contained mechanism.
 
These variations indicate that there is now genetic diversity and the resulting variations produces 4 different starting values (including the original).  IIRC, each of the other vines possess unique starting grape values so this detail MUST be contained in the genome length, the gene combination, or some other self-contained mechanism.
  
−
For reference: Initial Grapes (I) / Genome Length
+
Expected Variations should be a truth table of Short (25%) | Normal (50%) | Elongation (25%) based upon Ariella's notes.  That should yield 25% reproduction of the original Appreciation Vine (NN). 6.125% of each of the 4 outlier variations (SS, SE, ES, EE), and 12.25% of each of the 4 normalish vines (SN, EN, NS, NE).
−
  Amusement 11 33
+
 
−
  Apreciation 12 12
+
---
−
  Balance        08 31
+
 
−
  Contemplation 12 18
+
We expect K GYR YYR YYR YYR K which should give us this distribution
−
  Distraction 09 30
+
 
−
  Frivolity 12 34
+
KGYR  1
−
  Wisdom 08 24
+
GYRY  1
 +
YRYY  111
 +
RYYR  111
 +
YYRY  11
 +
YYRK  1
 +
 
 +
Aperio #3 Initial Grapes = 8 (50 trials of Clear Solvent [4 genes])
 +
 
 +
(1) KYRY 11
 +
(1) RYRY 111
 +
(2) RYYR 111 111 111 1
 +
(2) YYRY 111 111 111 11
 +
(1) YRYR 111 1
 +
(3) YRYY 111 111 111 111 111 11
 +
(1) YYRK 111
 +
 
 +
The first thing that leaps out is that the G dropped
 +
 
 +
K YRY
 +
  YRY Y
 +
    RY YR
 +
K YRY YR
 +
 
 +
    Y YRY
 +
      YRY R
 +
        RY RY
 +
        Y RYY
 +
          RYY R
 +
            YY R K
 +
        Y RYY R K
 +
 
 +
We're looking at (K YRY YR) x (Y RYY R K)
 +
K YRY YRY RYY R K (QQ:10)
 +
 
 +
The missing G is the natural candidate for losing the Initial Grapes (I) trait but this suggests how we get 8 & 12 counts and there has to be more granularity to suggest how to arrive at 9 & 10 counts.
 +
 
 +
Aperio #5 Initial Grapes = 9 (8 trials of Clear Solvent [4 genes])
 +
 
 +
KGYR 1
 +
RRYY 1
 +
YYRY 1111
 +
  YYRK 11
 +
 
 +
I discovered that the endpoints are intact and the RRYY suggests an Elongation of the Left Splint, duplicating the R.  The only thing I don't know here is whether the Right Splint Elongated and I can't disprove it by Clear testing except by volume and it's simply not that important, right now.  I could use a better solvent but I'll pass.
 +
 
 +
Aperio #8 Initial Grapes = 9 (2 trials of Clear Solvent [4 genes])
 +
 
 +
KGYR 1
 +
RYYY 1
 +
 
 +
No Shortening of the Left Splint and it looks like an Elongation of the Right Splint.  This vine should have an S phenotype.  The Left could be elongated but same situation as before.
 +
 
 +
In neither case, it isn't clear that I've learned anything more about the Initial Grapes trait.  It appears that any vine starting with Y has I=8. In cases where there was Elongation but no change of the left splint, I=9 (a drop from 12).
 +
 
 +
Aperio #7 Initial Grapes = 10 (8 trials of Clear Solvent [4 genes])
 +
 
 +
KGYR 1
 +
RYYR 1
 +
YRYY 11
 +
YYRY 111
 +
YYYR 1
 +
 
 +
  K GYR
 +
    YR YY
 +
      YYR Y
 +
          YYY R
 +
            YY RY
 +
              RYY R
 +
                    K
 +
  K GYR YYR YYY RYY RK (QQS: 13) is my guess
 +
 
 +
Looks like #8, with a non-shortened left splint and an elongated right splint. I should retest both more rigorously with better solvent to differentiate them.
 +
 
 +
I'm anticipating:
 +
  #7 K GYR YYR YYY RYY RK (13)
 +
          YYR YYY R (diamond trial confirms)
 +
  #8 K GYR YYR RYY YRY YR K (14)
 +
              RYY RYY R (diamond trial on #8 doesn't allow RYYY)
  
−
(I) has been introduced as the nomenclature for Initial Grape Count trait (NOTE: Legacy T3 that was lost or not adopted)
+
Aperio #10 Initial Grapes = 10 (20 trials of Clear Solvent [4 genes])
 +
 
 +
(1) KGYR 1
 +
(1) RYRY 1
 +
(2) RYYR 1111
 +
(1) YRYR 11
 +
(3) YRYY 111 111 111 1
 +
(1) YYYR 1
 +
(1) YYRK 1
 +
 
 +
(1) K GYR
 +
(1)    YR YR - doesn't fit rules
 +
(1)    R YRY - doesn't fit rules
 +
(1)      YRY Y (of 3)
 +
(1)        RY YY
 +
(1)        Y YYR
 +
(0)          YYR Y
 +
(2)            YR YY (of 3)
 +
(1)            R YYR (of 2)
 +
(1)              YYR K
 +
 
 +
[[http://www.atitd.org/wiki/tale4/GOO_Events/Flower_Talk_Lesson_2 Flower Talk Lesson 2]]

Latest revision as of 23:55, 19 July 2011

Back to User:Aperio

SUMMARY

I'm eating crow on this... and more importantly, noticing some kind of change in the (G)Grapes phenotype or at least the Starting Grapes Characteristic (flax has some similar variations in starting values). This rings a bell with T3 testing but I don't recall if any conclusions were made.

Disregard my subsequent commentary. Most of it is based upon a faulty premise that has since been straightened out. The value of this page, however, is in the research data and the techniques.


REFERENCE

Vine Initial Grapes (I) Genome Length
Amusement 11 33
Appreciation 12 12
Balance 08 31
Contemplation 12 18
Distraction 09 30
Frivolity 12 34
Wisdom 08 24

(I) has been introduced as the nomenclature for Initial Grape Count trait (NOTE: Legacy T3 that was lost or not adopted)

Appreciation (QQQ) x Base Appreciation (QQQ) [ KGYRYYRYYRYYRK ]

Aperio_-_Vine_Cross_Data

Initial Grapes 

Aperio #01	12
Aperio #02	12
Aperio #03	08
Aperio #04	12
Aperio #05	09
Aperio #06	12
Aperio #07	10
Aperio #08	09
Aperio #09	12
Aperio #10	10

If there's no shortening or elongation, all of these vines should be uniform regardless of the splice point. It will effectively return a vine identical to the starting vine.

These variations indicate that there is now genetic diversity and the resulting variations produces 4 different starting values (including the original). IIRC, each of the other vines possess unique starting grape values so this detail MUST be contained in the genome length, the gene combination, or some other self-contained mechanism.

Expected Variations should be a truth table of Short (25%) | Normal (50%) | Elongation (25%) based upon Ariella's notes. That should yield 25% reproduction of the original Appreciation Vine (NN). 6.125% of each of the 4 outlier variations (SS, SE, ES, EE), and 12.25% of each of the 4 normalish vines (SN, EN, NS, NE).

---

We expect K GYR YYR YYR YYR K which should give us this distribution 

KGYR   1
GYRY   1
YRYY   111
RYYR   111
YYRY   11
YYRK   1

Aperio #3 Initial Grapes = 8 (50 trials of Clear Solvent [4 genes]) 

(1) KYRY	11
(1) RYRY	111
(2) RYYR	111 111 111 1
(2) YYRY	111 111 111 11
(1) YRYR	111 1
(3) YRYY	111 111 111 111 111 11
(1) YYRK	111

The first thing that leaps out is that the G dropped 

K YRY
  YRY Y
   RY YR
K YRY YR

    Y YRY
      YRY R
       RY RY
        Y RYY
          RYY R
           YY R K
        Y RYY R K

We're looking at (K YRY YR) x (Y RYY R K) 

K YRY YRY RYY R K (QQ:10)

The missing G is the natural candidate for losing the Initial Grapes (I) trait but this suggests how we get 8 & 12 counts and there has to be more granularity to suggest how to arrive at 9 & 10 counts.

Aperio #5 Initial Grapes = 9 (8 trials of Clear Solvent [4 genes]) 

KGYR	1
RRYY	1
YYRY	1111
YYRK	11

I discovered that the endpoints are intact and the RRYY suggests an Elongation of the Left Splint, duplicating the R. The only thing I don't know here is whether the Right Splint Elongated and I can't disprove it by Clear testing except by volume and it's simply not that important, right now. I could use a better solvent but I'll pass.

Aperio #8 Initial Grapes = 9 (2 trials of Clear Solvent [4 genes]) 

KGYR	1
RYYY	1

No Shortening of the Left Splint and it looks like an Elongation of the Right Splint. This vine should have an S phenotype. The Left could be elongated but same situation as before.

In neither case, it isn't clear that I've learned anything more about the Initial Grapes trait. It appears that any vine starting with Y has I=8. In cases where there was Elongation but no change of the left splint, I=9 (a drop from 12).

Aperio #7 Initial Grapes = 10 (8 trials of Clear Solvent [4 genes]) 

KGYR	1
RYYR	1
YRYY	11
YYRY	111
YYYR	1

K GYR
   YR YY
      YYR Y
          YYY R
           YY RY
              RYY R
                   K
K GYR YYR YYY RYY RK (QQS: 13) is my guess

Looks like #8, with a non-shortened left splint and an elongated right splint. I should retest both more rigorously with better solvent to differentiate them.

I'm anticipating: 

#7 K GYR YYR YYY RYY RK (13)
         YYR YYY R (diamond trial confirms)
#8 K GYR YYR RYY YRY YR K (14)
             RYY RYY R (diamond trial on #8 doesn't allow RYYY)

Aperio #10 Initial Grapes = 10 (20 trials of Clear Solvent [4 genes]) 

(1) KGYR	1
(1) RYRY	1
(2) RYYR	1111
(1) YRYR	11
(3) YRYY	111 111 111 1
(1) YYYR	1
(1) YYRK	1

(1) K GYR
(1)    YR YR - doesn't fit rules
(1)     R YRY - doesn't fit rules
(1)       YRY Y (of 3)
(1)        RY YY
(1)         Y YYR
(0)           YYR Y
(2)            YR YY (of 3)
(1)             R YYR (of 2)
(1)               YYR K

[Flower Talk Lesson 2]

Retrieved from "http://www.atitd.org/wiki/t5w/index.php?title=Aperio_-_Genome_Elongation_Tests&oldid=106277"