Stepwise and Blockwise Biochemical Network Laboratory Breadboard Systems and Techniques for Signaling, Disease Research, Drug Discovery, Cell Biology, and Other Applications
A “breadboard” approach by which a biochemical pathway under study is separated or segmented into smaller portions, at least one of which can to a degree of approximation be accurately emulated with a replica microscale and/or nanoscale fluidic implementation whose constituent species, inhibitor(s), catalyst(s) and other reaction agent(s) can be closely controlled and at least one aspect of whose behavior can be measured. Control and measurement information interfaces with a computer that executes algorithms comprising one or more of a control process, control event-script, experiment, data recording, and mathematical model. A model can be used to simulate the actions, behavior, or other aspects of another portion of the biochemical signaling process, pathway, or network. Replica constituents can include enzymes, other proteins, lipids, ions, peptides, and other materials provided under controlled conditions and timing, as well as varying degrees of competitive species, drugs, environmental influences, and substitute or representative molecular crowding.
1 . A method for implementing a “breadboard” approach for the study of a biochemical pathway, the method comprising:
separating a naturally occurring multiple-stage biochemical process into a plurality of smaller portions, at least one of which can to a degree of approximation be accurately emulated with a fluidic implementation replica;
implementing a fluidic implementation replica of at least one of the smaller portions, the replica comprising inputs for reactants, a reaction environment, and provisions for measurement;
providing the controlled introduction of a plurality of biochemical materials into the replica, and
making at least one consuming measurement relating to a resulting biochemical reaction within the replica,
wherein the biochemical reaction are controlled by a computer executing an algorithm, and
wherein the fluidic implementation replica emulates the at least one the smaller portions of the biochemical pathway.
2 . The method of claim 1 wherein the replica is configured to provide outlets for removing the reaction products.
3 . The method of claim 1 wherein the reaction environment is configured to comprise a membrane.
4 . The method of claim 1 wherein the replica configured to comprise at least one sensor.
5 . The method of claim 4 wherein the sensor comprises an antibody.
6 . The method of claim 1 wherein the replica configured for the measurement is made with an external sensor.
7 . The method of claim 1 wherein the replica configured for the measurement is made with an external instrument.
8 . The method of claim 1 wherein the replica configured to provide molecular crowding.
9 . The method of claim 1 wherein the replica configured to provide at least one confined reaction environment.
10 . The method of claim 1 wherein the replica configured to provide at least one constrained reaction environment.
11 . The method of claim 1 wherein a second fluidic implementation replica is used to emulate another smaller portion.
12 . The method of claim 1 wherein the replica configured to provide the introduction of a competitive species.
13 . The method of claim 1 wherein the replica configured to provide the introduction of a drug.
14 . The method of claim 1 wherein the replica configured to provide the introduction of an environmental influence.
15 . The method of claim 1 wherein the algorithm comprises a mathematical model.
16 . The method of claim 14 wherein the algorithm models a gene transcription process.
17 . The method of claim 1 wherein the computer also is executing a mathematical model in communication with the algorithm.
18 . The method of claim 1 wherein the naturally-occurring signaling pathway is not entirely understood.
19 . The method of claim 1 wherein the consuming measurement involves an antibody.
20 . The method of claim 1 wherein the consuming measurement involves a fluorophore.