Outline for AACR fellowship

Based on the sections they request and what we want to say.

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I. Introductory Statement, Background, and Rationale

1.Introduction

• Cancer is a disease that develop over time. As cells replicate their DNA, grow and divide, their genetic instability increases.
• Currenlty we are limited in the ways we are able to track cells throughout multiple rounds of cell division and growth.
• If we get better in tracking cells throughout cells division we would get valuable insights into cancer set up and progression while possibly opening new therapeutic avenues.

2.Tools people use to study Cancer are insufficient today

• the tools people use to study aging, in particular in terms of sorting differentially aged populations are insufficient today: describe the methods

, which results (biological findings) people had using them, and comment. Mechanical, dyes, markers.

3. Natural system store information

From phage lambda to somatic cells, natural living systems are able to encode signals from internal and environemental imputs and store information, allowing the maintain of different cells fates, the heritability of some gene expression patterns and much more. It is indeed clear that the living medium support the encoding of information but we don't know how to control it. Th encoding information into living systems seems to be an approachable but challenging task, and we don't know yet how to do it.

Put past engineering attempts here?

usefull engineering Programmable counting of cell division

4. Challenges associated with genetically encoded memory construction and implementation

Encoding memory will certainely not be a trivial task. To ensure success we will have a well structured approach that can be summarized as follow:

1/ We will carefully explore and choose how to write and store memory. Then we will quantitatively characterize all the parts we will use to build the memory device. 2/ We will design which device architectures are the more suited to respond to different requirements. 3/ In a similar manner, we will design which System architecture would allow the best reliability

5.Some expected outcomes of engineered memory devices

A lot of exciting discovery just waiting to be made, if we have high precision tools.

• A device allowing cells too report their own age would be great tool.

II.Specific Aims

• The overall goal of our project is to establish a rationnal engineering framework supporting the engineering of a cell division counter.
• The implementation of this counter into living cells.
• The specific goal for the year covered by the fellowship to construct the first working bit of memory.

III.Research Design and Methods

Rationnale engineering framework

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This implies: the use different levels of abstraction, the quantitative characterization of all parts and devices we will use, .We have already specified some performance requirements and chosen some working direction that we think has the best potential of success. specific concerns are:Modularity, reuseability, scalability Our design will be done following these requirements.

• System architecture description

Describe the cell cycle counter in abstract (coupled gated oscillators)

• Device architecture description

Practical system Design

• DNA as a storing medium

We choose to store information inside DNA for the following reasons:

DNA is a stable molecule. (even relatively

The natural mechanims of DNA replication allows easy transmission of the information stored inside DNA from one cell to another.

Once a change in DNA sequence is done no Energy is required to maintain the state. Thus we expect this storage to be more stable in front of environemental variation.

DNA modifying enzymes with exquisite specificity are found in nature. They are extensively studied, and also artificialones have been engineered.

• how to store information into DNA sequence?

A/ random: mutation (we don't want that)

B/Directed:

• • Sequence abscence or presence: Integration or excision
  • Sequence orientation: inversion
  • Sequence accessibility: DNA topology

• Using recombinases as memory writers.

We propose to use Site specific recombination as a DNA writing mechanism for the following reasons: 1/ Recombinases are efficient and very specifics for a given sequence, and each different enzyme. 2/ Lot of enzyme nature gave us, which perform a great number of different recombination reaction that we can take advantage. 3/ We have well studied (lambda...), some of them already used in engineering memory (Ham); cite IGEM 2004 project also. 4/ Even if they have different function they share some common catalytic domains. 5/ some attempts have succesfully changed specificity of some of them.

project, methods

• During the first year of the project, We will build the first bit of memory

• Encoding into DNA sequence

• We will have different strategies to ensure succes.

different directions (not putting all the eggs in the same basket)

Question: how many propositions to work on on parallel? 2, maybe maximum 3?

describe precisely what kind of DNA manipulations we' ll perform to write memory.

• we will use DNA sequences inversion

• • Integrases/excisionase

potentially flip DNA? can also be used without flipping (and is efficient!)

• Directed evolution for enhanced Invertases

• Can we use "directed DNA transposition"? I am afraid we still lack specificity but this could also be optimized and some work has already been done. ( add ref)

controlled retrotransposition via an RNA intermediate could also be usefull for combining lineage and counting...see latter for this.

and need to read more

descibed which problems can happen and what you'll do.