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A CG CG CG CTTAA AATGC GAATT TTACG GC

A CG CG CG CTTAA AATGC GAATT TTACG GC GC GC T. A CG CG CG CTTAA AATGC GAATT TTACG GC GC GC T. A

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A CG CG CG CTTAA AATGC GAATT TTACG GC

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  1. A CG CG CG CTTAA AATGC GAATT TTACG GC GC GC T A CG CG CG CTTAA AATGC GAATT TTACG GC GC GC T A CG CG CG CTTAA AATGC GAATT TTACG GC GC GC T cell division creates gap at telomere which disrupts DNA secondary structure A CG CG CG CTTAA AATGC GAATT TTACG GC GC GC T A CG CG CG CTTAA AATGC GAATT TTACG GC GC GC T CTTAACGCGCGAAATGC – 5’ GAATTGCGCGCT TTACG – 3’ exonuclease removes everything from end up to resistant DNA secondary structure (including whole genes and part of immortal template strand) A CG CG CG CTTAA AATGC GAATT TTACG GC GC GC T A CG CG CG CTTAA AATGC GAATT TTACG GC GC GC T

  2. Requirements • A DNA plasmid molecule that regulates gene expression after a time delay • Determines sequential gene expression and dictates how long each stages lasts • Linear DNA molecule will be destroyed after its use – i) by wasting away or ii) by destroying the cell (kill switch) • Functionality is (preferably) induced

  3. /* • * Program which simulates the shortening of one end of a DNA molecule of • * starting length 10 units. The DNA has a functional telomere repair • * mechanism for one end of the DNA, but not the other. This repair mechanism • * is present on the 5' end of the 5' to 3' strand. Thus when copying • * a 5' to 3' strand, the resulting 3' to 5' strand is always the same length • * as the template strand. However, when replicating a 3' to 5' strand, • * the resulting 5' to 3' strand is one unit shorter than the template. The • * missing unit is removed from the 3' end of this resulting strand. • * • * It is assumed genes are only encoded meaningfully on the 3' to 5' stand. • * Therefore although the 5' to 3' strand will be eaten away, the loss will • * consist of complementary base sequences which do not meaningfully encode • * genes. Therefore, all we are interested in is the 3' to 5' stand being eaten • * away from its 5' end. When this shorter molecule is copied, it will • * indirectly result in a shorter 5' to 3' strand. • */ • package lineardna; • import java.util.ArrayList; • import java.util.Iterator; • public class ListEnd { • intunitLength; // current length of dna sequence in units • String type; // whether the dna molecule is 5'3' or 3'5' • static intstartLength = 11; // length of dna sequence before shortening • static int[] lengthArray = new int[12]; // array of dna length frequencies (one more than startLength and same as last for loop) • public ListEnd(intunitLength, String type) { • this.unitLength = unitLength; • this.type = type; • } • public static void main(String[] args) { • ArrayListdnas = new ArrayList(); // to hold dna molecule objects • // create original double-sttrandeddna • dnas.add(new ListEnd(startLength, "5'3'")); • dnas.add(new ListEnd(startLength, "3'5'")); • // simulate cell division • for (int divisions = 1; divisions < 21; divisions++) { • ArrayListdnasTemp = new ArrayList(); // holds newly created dnas • Iteratoritr = dnas.iterator(); • while (itr.hasNext()) { • ListEndobj = (ListEnd) itr.next(); • if (obj.type.equals("3'5'")) { // if 3' to 5' • // create a copy 5' to 3' copy that is one unit shorter • if (obj.unitLength - 1 >= 0) { • dnasTemp.add(new ListEnd(obj.unitLength - 1, "5'3'")); • } else { • dnasTemp.add(new ListEnd(0, "5'3'")); • } • } else { // if 5'to3', complementary copy will be same length • if (obj.unitLength - 1 >= 0) { • dnasTemp.add(new ListEnd(obj.unitLength, "3'5'")); • } else { • dnasTemp.add(new ListEnd(0, "3'5'")); • } • } • } • // add newly-created dnas to array • dnas.addAll(dnasTemp); • Iterator itr2 = dnas.iterator(); • // iterate through sequences and record length frequencies • while (itr2.hasNext()) { • ListEnd obj2 = (ListEnd) itr2.next(); • if (obj2.type.equals("5'3'")) { • lengthArray[obj2.unitLength]++; • } • } • intcumSum = 0; • // print length frequencies • for (inti = 0; i < 12; i++) { • System.out.printf("%8s", lengthArray[i] + " "); • cumSum = cumSum + lengthArray[i]; • } • System.out.println(" " + cumSum); • System.out.println(" "); • } // end of for divisions loop • } • }

  4. do something (extracellular) 9 rep 9 on 9 off weak inhibition (extracellular) strong inhibition

  5. do something (extracellular) 9 rep 9 on 9 off weak inhibition (extracellular) strong inhibition do something (extracellular) strong inhibition 9 rep 8 rep 8 on 8 off 9 on 9 off weak inhibition (extracellular) strong inhibition do something (extracellular)

  6. 0 9 weak inhibition strong inhibition Thus when 9 hasn’t been eaten away, it dominates over 0 and lots of 9 is transcribed

  7. strong indirect inhibition intra-cellular signals 0 9 weak direct inhibition (extracellular) (extracellular signal a mass function (do 9) Thus when 9 hasn’t been eaten away, it dominates over 0 and lots of 9 is transcribed. 9 inhibits 0 indirectly by activating an inhibitor protein (left). 9, as an activator, also activates another gene, which can be any cellular function (variable part).

  8. strong indirect inhibition 0 9 weak direct inhibition signal a mass function (extra-cellular signal) When 9 has been eaten away, it cant dominate over 0 because the signal between 9 and 0 is intracellular. However, since 0 is no longer repressed, its extracellular signal can shut down any “immortal 9’s” in other cells through an extracellular message! Could also involve direct binding to existing product of 9’s as well as transcriptional inhibition.

  9. strong indirect inhibition intra-cellular signals 0 9 on 9 off weak direct inhibition (extracellular) do something (possibly extracellular signal for greater coordination) intra-cellular signals 9 rep 9 on 9 off weak inhibition (extracellular) strong inhibition

  10. do something (possibly extracellular signal for greater coordination) intra-cellular signals 9 rep 9 on 9 off weak inhibition (extracellular) strong inhibition do something (extracellular) 9 rep 9 on 9 off weak inhibition (extracellular) strong inhibition

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