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Synthetic Biology is an emerging field. Much work still is to be done, but the progress already made points out to an exciting sci pathway.

Whether the applications of the Synth-Bio are conducted towards the production of new pharmaceutical products, or to the manufacturing of specialized biocomponents – that might help to reduce the contamination – it really, really has possibilities.

In a  research conducted by Dr. Pamela Silver at the Harvard Medical School (HMS) a  milestone was reached.

As every engineer knows, the design must be strongly tested before going on to the manufacturing issues. That makes it very close to the Maths models. In fact, if a new structure is to be built, an engineer would test the design FIRST, against some complex mathematical models that would output the resistance to pressure, tangential effort and aome other physical factors. After that, the process of building – let’s say a bridge – would include some considerations.

Silver et al, achieved successfully at inducing a memory loop in yeast cells and producing a new mathematical model that predicted – with a certain degree of accuracy – the behaviour of the cells.

The experiment was about including a pair of genes – synthetic – with the ability to produce transcription factors.

Transcription Factors are capable of regulating the activity of specific genes, forcing them to synthetize (or otherwise disable) a specific protein.

The first gene reacted to the presence of Galactose, producing a transcription factor, which in turn, activated the second gene. Then, the second gene reacted by producing a transcription factor, which at the end reactivated itself (the second gene). This caused a feedback loop, that was maintained by the presence of Galactose.

But, when the Galactose was extracted from the medium, then the first gene stopped producing its transcription factor, but the second gene continued producing its own.

The new cells – as expected – kept producing the second gene transcription factor and the experiment was successful.

“Essentially what happened is that the cell remembered that it had been
exposed to galactose, and continued to pass this memory on to its descendents,” says Ajo-Franklin, a co-worker of Dr. Silver. “So after many cell divisions, the feedback loop remained intact without galactose or any other sort of molecular trigger.”

Most important is that the construction phase was guided by the mathematical model. That has profound implications in the future of the Synthetic Biology.

If “black boxes” are to be constructed then it’s positively compulsory to be backed-up on the Mathematical models. Accuracy is needed as to foresee a future when black boxes would be plugged into living cells, knowing exactly what the results will be. The same way a Computer Technician plugs a memory chip into the appropriate mainboard slot of the PC.

http://www.technofender.com/blog/biotechnology/synthetic-biology-inducing-memory-in-yeast-cells/

Structure of DNA

Legend:
Illustration of the double helical structure of the DNA molecule.

The structure of DNA is illustrated by a right handed double helix, with about 10 nucleotide pairs per helical turn. Each spiral strand, composed of a sugar phosphate backbone and attached bases, is connected to a complementary strand by hydrogen bonding (non- covalent) between paired bases, adenine (A) with thymine (T) and guanine (G) with cytosine (C).

Adenine and thymine are connected by two hydrogen bonds (non-covalent) while guanine and cytosine are connected by three.

This structure was first described by James Watson and Francis Crick in 1953.

Protein Synthesis

 

Legend:
Process whereby DNA encodes for the production of amino acids and proteins.

This process can be divided into two parts:

1. Transcription
Before the synthesis of a protein begins, the corresponding RNA molecule is produced by RNA transcription. One strand of the DNA double helix is used as a template by the RNA polymerase to synthesize a messenger RNA (mRNA). This mRNA migrates from the nucleus to the cytoplasm. During this step, mRNA goes through different types of maturation including one called splicing when the non-coding sequences are eliminated. The coding mRNA sequence can be described as a unit of three nucleotides called a codon.

2. Translation
The ribosome binds to the mRNA at the start codon (AUG) that is recognized only by the initiator tRNA. The ribosome proceeds to the elongation phase of protein synthesis. During this stage, complexes, composed of an amino acid linked to tRNA, sequentially bind to the appropriate codon in mRNA by forming complementary base pairs with the tRNA anticodon. The ribosome moves from codon to codon along the mRNA. Amino acids are added one by one, translated into polypeptidic sequences dictated by DNA and represented by mRNA. At the end, a release factor binds to the stop codon, terminating translation and releasing the complete polypeptide from the ribosome.

One specific amino acid can correspond to more than one codon. The genetic code is said to be degenerate.

Simplified Diagram of Cellular Metabolism

The three stages of cellular metabolism lead from food to waste products in animal cells. This series of reactions produces ATP, which is then used to drive biosynthetic reactions and other energy-requiring processes in the cell. Stage 1 mostly occurs outside cells––although special organelles called lysosomes can digest large molecules in the cell interior. Stage 2 occurs mainly in the cytosol, except for the final step of conversion of pyruvate to acetyl groups on acetyl CoA, which occurs in mitochondria. Stage 3 occurs in mitochondria.  

Biotechnology: Present and Future

Legend:

Areas of applied biotechnology:

In 1885, a scientist named Roux demonstrated embryonic chick cells could be kept alive outside an animal’s body. For the next hundred years, advances in cell tissue culture have provided fascinating glimpses into many different areas such as biological clocks and cancer therapy.

Monoclonal antibodies are new tools to detect and localize specific biological molecules. In principle, monoclonal antibodies can be made against any macromolecule and used to locate, purify or even potentially destroy a molecule as for example with anticancer drugs.

Molecular biology is useful in many fields. DNA technology is utilized in solving crimes. It also allows searchers to produce banks of DNA, RNA and proteins, while mapping the human genome. Tracers are used to synthesize specific DNA or RNA probes, essential to localizing sequences involved in genetic disorders.

With genetic engineering, new proteins are synthesized. They can be introduced into plants or animal genomes, producing a new type of disease resistant plants, capable of living in inhospitable environments (i.e. temperature and water extremes,…). When introduced into bacteria, these proteins have also produced new antibiotics and useful drugs.

Techniques of cloning generate  large quantities of pure human proteins, which are used to treat diseases like diabetes. In the future, a resource bank for rare human proteins or other molecules is a possibility. For instance, DNA sequences which are modified to correct a mutation, to increase the production of a specific protein or to produce a new type of protein can be stored . This technique will be probably play a key role in gene therapy.

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