This is an idea that just spawned on me yesterday. The lines between the non-living and living have been blurred and there are some many ways that computers will assist us in many aspects of our lives. Right now, there are chip implants that have been testes in rats to improve memory and cereballar function and have been succesfully tested in Israel. It may be soon before new brain inferfaces will come out the market to help people with speaking disabilities or quadraplegic individuals.
Imaging having the ability to design new viruses to seek and destroy infectious bacteria that are resistant to antibiotics or design multiple viruses that can be used for gene therapy?
There are many viruses called phages that have the ability to infect and destroy bacteria including infectious bacteria (Staphylococcus and Streptococcus). The genomes of bacteriophages are relatively small compared to bacteria. Hence, designing viruses from scratch is not a far-fetched idea and the commercial software to create new synthetic viruses from scratch using synthetic genomics and modular gene design applications may all be possible with the click of an iPad or notebook within a few years.
Currently, scientists and clinicians can design and order small pieces of DNA called oligonucleotides or primers (20 to 30 base pairs ) that can be used to amplify DNA through PCR. These small and large biotech companies take orders over the Internet and synthesize DNA of up to 100- 150 bases (DNA has four bases) within two days.
DNA is the information that encodes for life and can be designed and stored as analog data in computers. On the other hand, what about synthesizing complete artificial genomes of viruses and bacteria? Is that even possible?
Nowadays, a few companies in the world such as Blue Heron can be contracted to design the genomes of not just new viruses, but bacteria and even mitochondrial genomes. Dr. Craig Venter and his team from Synthetic Genomics have generated and synthesized the genomes of different bacteria (Mycobacterium) from scratch and this process involves putting together many pieces of 1000 base pairs at a time to produce an artificial bacterial genome that was successfully transplanted onto another bacteria. Moreover, Dr Venter is on the verge of sequencing the genomes of thousands of marine algae and bacteria from across different parts of the world. When all this DNA information from all these microorganisms becomes available with the next two years, this information will give the necessary insight to the scientific community to fully understand genes and other pieces that were once unknown. For instance, many new antibiotics or even classes of anti-fungals may be discovered during Dr. Venter's acquatic quest around the world that can be used to destroy multi-drug resistant bacteria such as multi-drug resistant tuberculosis or MRSA.
Dr. Venter's accomplishment proves that the boundaries of biotechnology can be pushed significantly to the extent that viruses and bacteria can be synthesized de novo using a simple computers, software and robotic paltforms that are used to design and assemble viruses from scratch. Cloning pieces of DNA is not required to do this as synthesizing new DNA will be much faster than cutting and pasting different DNA coding regions as conventionally done in the research lab.
There are many commercially and freely available software such as Vector NTI that can analyze , organize, label DNA regions from thousands of base pairs belonging to a variety of organisms including that of viruses, mice, rat, worms, and humans. Moreover, all these genomes are available for free and can be downloaded from NCBI.
Moreover, bioinformatics software can be used to find genes of interests, non-coding regions or promoters which can give any researcher the necessary tools to design new genomes from scratch. However simplistic this may sound, synthesizing DNA using a DNA sequence that contains millions of base pair that was originally designed using computer software is very significant in that the fields of computer science and biology have given rise to cyber-genomics.
A brave new DNA world
The genomes of many bacteriophages are known and many of these bacteriophages have the ability to infect bacteria such as lambda X174 which infects E. coli. Viruses/bacteriphages can be found in the millions in the ocean. The problem is being able to isolate these bacteriophages for mass production is tedious and time consuming. For instance, right now there is a bacteriophage that infects Listeria monocytogenes is currently available for treating and protecting cheeses. However, the process of generating bacteriphages from scratch is possible using a synthetic genomics approach and the cost to do that will be feasible within a few years. Moreover, there is only a few companies that have proprietary software to do that.
Hence, it is possible that commercially available software to design new viruses from scratch through modular genetics may be soon available and can may be used by common computer processors and even iPads which lend the possibility of creating this type of software for genetic engineers, clinicians, scientists and even public health officials. Once a virus is designed that specifically attacks only one type of infectious bacterial strain, then the DNA code can be securely uploaded over the Internet to companies dedicated to synthesizing DNA and ship the viral genome back to client. The new synthetic viral DNA can be used to produce mass quantities of bacteria-chopping viruses in the lab by infecting human epithelial cells and concentrate the virus in extremely small volumes.
What about producing new antibiotics?
Moreover, these new viruses can be used to not only produce more viruses that infect infectious bacteria but also produce new classes of antibiotics if such type of antibiotics in the ocean. Phages may have the ability to destroy biofilms that are hard to remove by mechanical debridement and reach the center of the thick biofilm.
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