Bio 123, UZH

Gates can also be built by using integrases.

With our input we control these integrases. They can for example inverte the terminator, or even cut the whole thing out!

This one works when either A or B are present

see picture

In the classic cloning, you have a cDNA library, which you amplify by PCR, etc.

But nowadays, you just go online and order your genes of interest. And they synthesize the DNA for you. There are many advantages (you can delete restriction sites etc.) and its not even that expensive.

But how do they synthesize these genes for you?

Take the DNA, divide it into parts and synthesize Oligonucleotides which have overlappings to each other. Then insert primers with uniques sites.

1.       Many parts are undefined

2.       The circuits are unpredictable

3.       Many parts are incompatible

4.       Variability crashes the system

5.       Safety and ethical challenges

Genetically identical cells which are grown under same circumstances and still show differences

Its logical that individual cells from an organism are different (f.e. From the liver, heart, etc.).

But how about the variability between cells from the same type, that are siblings from the same parent cell and are grown under identical conditions?

And where lies the boundary between differentiation and non-genetic cell-to-cell variability?

(Its to mention that to notice this is only possible with the newest technologies, where we can quantify the cells)

Such variability cannot described with qualitative terms, so we need quantification.

• Fluorescence activated cell sorter/analyzer (flow cytometry)
• Single-cell micro-dissection for further analysis

• Ultrasensitivity
• positive feedback

Intrinsic noise is when you have two gens which are regulated identically, but you get different outputs (even under identical conditions!).

Otherwise, when you get the same output (and maybe sometimes a little darker yellow or lighter, etc.) you only would have extrinsic noise.

Intrinsic noise is when you have two gens which are regulated identically, but you get different outputs (even under identical conditions!).

Otherwise, when you get the same output (and maybe sometimes a little darker yellow or lighter, etc.) you only would have extrinsic noise.

when you cannot explain where it cames from, its stochastic, not regulated or controlled

Active: can measure noise and somehow create an anti-noise signal which cancel the noise out

Passive: prevents noise from entering 

Active: can measure noise and somehow create an anti-noise signal which cancel the noise out

Passive: prevents noise from entering 

Certain controllers, measure something, have an output,

Feed-back/forward motifs

But the problem with this one is that it cost energy!

Builiding a compartiment which shields it off from other compartments(compartimentize the reaction, doesnt cost much energy)

• Highthroughput-sequencing technologies parallelize the sequencing process producing  thousands or millions of sequences at once

• Low cost production of large volumes of sequence data

A collection of DNA fragments with adapters ligated to each end

The stretches of DNA read by the sequencer (the library consists in the end of reads)

Identifier sequence that allows pooling several samples without physical separation

(Barcoding: DNA-Barcoding (englisch DNA barcoding) ist eine taxonomische Methode zur Artenbestimmung anhand der DNA-Sequenz eines Markergens.)

Deutsch: Angleichung/Anpassung

The aligning and merging of reads in order to restruct the original sequence

You can distinguish two types:

1. Mapping= assembling reads against an existing backbone sequence
2. De novo=  assembling short reads to full length sequences

E: Sequenced reads that overlap are reassembled back into longer sequences.

D: Ein Contig ist ein Satz überlappenderDNA- oder Protein-Stücke (reads), die von derselben genetischen Quelle stammen. Ein solches Contig kann dazu genutzt werden, die Original-DNA-Sequenz dieser genetischen Quelle abzuleiten.

A series of linked contig which are in the right order but not necessary connected in one continuous stretch of sequence

Either how many or how long reads we create

The average number of reads representing a given nucleotide in the reconstructed sequence is called depth of coverage

See picture

- High number of reads and low input

- Short read but very high throughput

- clonal amplification

- State-of-the-arts optics used for detection

- At the end of the bridge amplification, you get a cluster. This is what you actually going to sequence!

- SBS (sequencing by synthesis)

- Mid-to-High number of reads and low input

- Short reads and low throughput

- but very quick (usefull during a surgery when quick results are needed)

- beads (Kugel) are used for monoclonal amplifications

- ph-meter is used

- no modified nucleotides

- Low number of reads and high input

- SMRT (single molecule real time sequencing)

- Eavesdropping (lauschen) on the DNA polymerase as it replicates DNA 

- Only to the last phosphore ist fluorescent dye attache, the strand is natural

-> https://www.youtube.com/watch?v=v8p4ph2MAvI