Team:EPF Lausanne/Project/Background
Synthetic Biological Circuits Textbook case
Synthetic biological circuits are an application of synthetic biology where biological parts inside a cell are designed to perform logical functions mimicking those observed in electronic circuits. These circuits can be used to modify cellular functions, change the reaction of the cells to their environment. By implementing rational, controllable logic elements in cellular systems, researchers can use living systems as engineered "machines" to perform a vast range of useful functions.
Development in understanding cellular circuitry can lead to exciting new modifications, such as cells which can respond to environmental stimuli. For example cells could be developed that signal toxic surroundings and react by activating pathways used to degrade the perceived toxin.
Such a gate is promising but cells are not that easy and everything interacts with everything, sometimes it will even interact with something that it shouldn't. Such "rules" make it hard to build robust systems that will act as we want it.
Boolean Logic
To process those bits, digital circuits resort to logic gates. Logic gates performs an elementary logic operation on a given set of bits. There are 3 simple gates (depending on how you want to build them). By combining these simple gates, implementing any digital component is possible. But note that the two universal gates are the NOR and NAND gate, with just the two of them can be used to make all the others.
NOT gate
The NOT gate is the logic gate that implements the logical negation.
| Input | Output |
|---|---|
| A | NOT A |
| 1 | 0 |
| 0 | 1 |
AND gate
The AND gate is the logic gate that implements logical conjugation.
| Input 1 | Input 2 | Output |
|---|---|---|
| A | B | A AND B |
| 0 | 0 | 0 |
| 1 | 0 | 0 |
| 0 | 1 | 0 |
| 1 | 1 | 1 |
OR gate
The OR gate is the logic gate that implements logical disjunction.
| Input 1 | Input 2 | Output |
|---|---|---|
| A | B | A OR B |
| 0 | 0 | 0 |
| 1 | 0 | 1 |
| 0 | 1 | 1 |
| 1 | 1 | 1 |
NOR gate
The NOR gate is the logic gate that implements logical NOR, it is the result of the negation of the OR gate. NOR is a functionally complete operation - NOR gates can be combined to generate any other logical function.
| Input 1 | Input 2 | Output |
|---|---|---|
| A | B | A NOR B |
| 0 | 0 | 1 |
| 1 | 0 | 0 |
| 0 | 1 | 0 |
| 1 | 1 | 0 |
NAND gate
The NAND gate is the logic gate that implements the logical NAND, it is the result of the negation of the AND gate.NAND is a functionally complete operation - NAND gates can be combined to generate any other logical function.
| Input 1 | Input 2 | Output |
|---|---|---|
| A | B | A NAND B |
| 0 | 0 | 1 |
| 1 | 0 | 1 |
| 0 | 1 | 1 |
| 1 | 1 | 0 |
Digital Circuits & Transistors
A digital circuit is often constructed from small electronic circuits called logic gates that can be used to create combinational logic. These logic gates are an arrangement of transistors.
Transisors work just like electrically driven switches that controls electric current. It consists of three layers of a semiconductor material, each capable of carrying a current. A semiconductor is a material such as germanium and silicon that conducts electricity in a "semi-enthusiastic" way.
The semiconductor is given special properties by a chemical process called doping. The doping results in a material that either adds extra electrons to the material (which is then called N-type for the extra negative charge carriers) or creates "holes" in the material's crystal structure (which is then called P-type because it results in more positive charge carriers). The transistor's three-layer structure contains an N-type semiconductor layer sandwiched between P-type layers (a PNP configuration) or a P-type layer between N-type layers (an NPN configuration).
Bits and Bytes
Computers use a base 2 number system to represent information, also known as the binary number system. Computers use this system because it is easier to implement with current electronic technologies.
The word bit is a shortening of the word "Binary digIT". Decimal digits have 10 possible values ranging from 0 to 9, whereas bits have only two possible values : 0 and 1.
In decimal value 6357 is (6 x 10^3) + (3 x 10^2) + (5 x 10^1) + (7 x 10^0) = 6000 + 300 + 50 + 7
In binary you apply the same logic but using powers of 2 instead of powers of 10. In binary 1011 is (1 x 2^3) + (0 x 2^2) + (1 x 2^1) + (1 x 2^0) = 8 + 0 + 2 + 1 = 11
Bits are rarely seen alone in computers. They are almost always bundled together into 8-bit collections, called bytes. With 8 bits in a byte, you can represent 2^8 = 256 values ranging from 0 to 255. For example, a CD uses 2 bytes which gives 2^16 = 65536 possible values!
CRISPR/Cas9 and dCas9
Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease that targets and cleaves any DNA sequence complementary to its guide RNA (gRNA). A derivative of this technology is a catalytically “dead” Cas9 (dCas9) that lacks the ability to cleave DNA. When fused to a RNA polymerase (RNAp) recruiting element (e.g. the omega subunit of RNAp in E. Coli or VP64 in eukaryotes), chimeric dCas9 can act as a programmable transcription activator. In addition, activating dCas9 may also act as a DNA transcription inhibitor: depending on its gRNA-determined binding site, it has been shown in yeasts to sterically hinder RNAP recruitment to promoter sequences.
