Math 297/Biol 497

Biomolecular Computing in Nature

General decryption steps

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1. Polytenization: Macronuclear development begins with the replication of the micronuclear chromosomes to form polytene chromosomes.
2. DNA excision: Selective, precise excision of internal DNA segments occurs, and flanking segments are joined, resulting in chromosomes of lower sequence complexity.
3. Chromosome fragmentation: These lower complexity chromosomes are then transected by vesicle like structures and fragmented. Some fragments are eliminated, and some retained.
4. Telomere addition: The retained fragments are encased in vesicles and telomeric repeats are added to their ends.
5. DNA amplification: The vesicles then break down, the telomerized DNA molecules undergo additional rounds of replication to form the highly amplified macronuclear genome, and the remaining micronuclear limited DNA molecules are degraded.

In the interest of clarity the developing new macronucleus is, while in the development stage, called the macronuclear anlage.

Notes:

1. These steps are according to: L.A. Klobutcher, Characterization of in vivo developmental chromosome fragmentation intermediates in E. Crassus, Molecular Cell 4 (1999), 695 - 704.
2. Degrading the ancestral macronuclei and micronuclei is presumably also part of the decryption protocol.
3. At one point in time there are several genetic units present in the same cytoplasm:
   • The pre-conjugation versions of micronuclei and macronuclei;
   • The post-conjugation new micronuclei;
   • The post-conjugation developing macronuclei.
4. Timelines for the steps of the decryption process are typically given in terms of the number of hours since conjugation-capable cells were mixed. 
5. We will assume that the objective of the decryption process is the creation of a complete set of functional genes for the organism. It is necessary to be somewhat precise about the notions of a gene and a chromosome.
   • Wikipedia description of a gene
   • Wikipedia description of a chromosome.

Units: The length of single-stranded DNA molecule is measure in number of bases, and the length of a double stranded DNA molecule is measure in number of base pairs. The abbreviation for this unit of measurement is bp. 1,000bp is abbreviated Kbp, and 1,000,000bp is abbreviated Mbp.