From the histogram to see cycles
and dose in radiation
Analysis of relation between radiation-induced chromosome
aberration (cycles) and the dose in Gy
Fang-I Chu
Chromosome aberrations
(mFISH patterns for damaged genomes)
Project goal

Compare the cycle frequency under different dose in
Gy(for 1, 2, and 4) for two aberration model
-breakage-and-reunion (BR model)
-recombinational misrepair (RM model)
and for the experimental data.

Do this for both 2-cycles and n-cycles(n>2).
Why is this important?

Once we gain possible form of function for the BR
model and RM model, we will be able to estimate the
potential cycle frequency under different dose in Gy

Help us to determine how aberration varies at
different dose in Gy.
Introduction of concepts

A cycle of order n, characterized formally by the
cyclic graph with 2n vertices, indicates that n
chromatin breaks take part in a single irreducible
reaction.

Parenthetically grouped elements are arranged in the
most conservative way possible, in order to bring an
exchange to “closure”.

Closure means all the elements involved in the
exchange.
Introduction of concepts

Aberrations result from misrepair of DNA double
strand breaks.(DSBs)

DSBs: where both DNA sugar-phosphate backbones
of a double helix are broken at nearby sites.

Simple exchange, exchange requires 2 breaks. Which
forms a 2-cycle or cycle of order 2 because there are
2 DSBs involved.(Giving 4 DSB ends)

Complex exchange, exchange requires more than 2
breaks. Which forms a n-cycle or cycle of order n
because there are n DSBs involved.(Giving 2n DSB
ends)
Concepts(continue)

One-way exchanges, a simple terminal translocationin which either centric or acentric elements were
missing.

Ex.(1’-X’)(1), and (12’T)(12-21’) both of which had
missing elements that characterize them as so-called
one-way exchange.

Difference between incomplete changes and one way
exchanges; the former is with one piece left alone,
and the later with one piece attached but it is not
visible.
Incomplete exchange

A truly incomplete exchange is identified when a
painted fragment accompanied by a bicolor
chromosome displays telomere signals on only one
end of the fragment.

When the painted fragment in the incomplete
exchange displays telomere signals on both ends, the
exchange is scored as a false incomplete exchange.

An insertion may involve misrejoining of (a) two
DSBs or (b) one DSB on the painted chromosome.
Break- and-reunion
,Recombinational misrepair and Exchange
Response about comment :what is the difference
bewteen RM (simple) and exchange theory

We can think of exchange is an algorithm, that
applied in RM model.

Since simple exchange under RM model just involves
2 DSBs, it can easily be used to explain how
exchange algorithm works.

RM and BR are two ways how chromosomes
rearrange after radiation; exchange theory is just
develop to illustrate the process in between rearrange.
How do we count cycle numbers from
experimental data
Calculation for number of
2-cycle

Number of 2-cycle=total exchange-number of
incomplete exchange-(interstitial deletions- number
of acentric rings)+number observed of obligate 2cycle

Centric rings can be seen, so they are given in
experimental data.

We can compute number of acentric rings by
introducing a relation parameter 1.2, which gives us:

1.2*number of centric rings =number of acentric
rings
Using the table below to compute number of n-cycle(n>2,
3-cycle, 4-cycle,5-cycle.etc)
Data(cycle counts v.s. dose in Gy)
2-cycle
n-cycle(n>2)
400
350
300
250
200
150
100
50
0
100
80
60
40
20
0
Gy 1
Gy 2
Gy 4
Gy 1
Gy 2
Gy 4
How did we get the cycle frequency?

First we can get the number of cycles under the 1
Gy,2 Gy,and 4Gy from the data table in Loucas and
Cornforth paper.

Then we calculate the value of cycle number/number
of cells scored.

The reason we do this is because we want to get the
cycle number of per exposed cell versus dose; since
we will simulate the cycles number under thousands
of cells using CAS. To unitize the data we got from
experiments help us compare on the same basis
Cycle frequency v.s. dose in Gy
2 cycles
n cycles (n>2)
2
0.6
0.5
1.5
0.4
1
0.3
0.2
0.5
0.1
0
0
Gy1
Gy2
Gy4
Gy1
Gy2
Gy4
Expected final histogram
3-cycle
4-cycle
0.118
0.116
0.114
0.112
0.11
0.108
0.106
0.104
0.102
0.1
0.098
0.06
0.05
0.04
0.03
0.02
0.01
0
Gy1
Gy2
Gy4
Gy1
Gy2
Gy4
5-cycle
0.02
0.015
0.01
0.005
0
Gy1
Gy2
Gy4
Problem we havent solved

We failed to reproduce the histogram graph in Levy
et al ‘s paper because CAS didn’t produce number of
cycle during simulation.

Need to run the data we get from CAS in another
Java program to get the cycle number we need.

Once we manage that, we will be able to get the exact
histogram in Levy et al’s paper.
Progress we’ve done this
morning..

We finally manage to transform the file from CAS to
get it run in java this morning.

However, there are still problems about the
simulation, since we got the same number of cycles
when we simulate different number of cells.

Ex. For 20,000 cells at Gy1 we got 23 of 2-cycle and
1 of n-cycle, and we got the same result for 200 cells
at Gy 1.
conclusions

The dosage of radiation doesn’t seem to influence the
number of cycle linearly as the cycle structure
increases.

The patterns of cycle changes response to radiation
dosage give the information about how DNA
damage is. This could be a way of detecting early
formation of tumor.

There should be a more user-friendly software
available to simulate cycle number. Currently
CAS+Java only run in linux environment, and they
require two stages of execution.
Future research

Compute the cycle frequency of 3-cycles,4 cycles, 5
cycles, and n-cycles where n>5, instead of computing ncycles where n>2.

Draw histogram for about 4 group and the simple
exchange group; also after running CAS, we will get
comparison histogram for real data, BR, and RM for
these five groups.

Observe how the relation between cycle frequency and
dose in Gy varies due to different number cycles.

We are also interested in the changes in cycle frequency
for higher dosage of radiation, like 6 Gy.8 Gy, 10 Gy.