Article for the “bio/mol/text” competition: A recently published article from Harvard biologists forced many news agencies to release notes: scientists have turned E. coli into a biological analogue of a computer, in which the role of electrical signals is played by short RNA molecules. In my article, I would like to give a short overview of the achievements of modern bioengineers, and then tell the general public about how “biocomputers” work and what we expect from them.
The general sponsor of the competition is the company: the largest supplier of equipment, reagents and consumables for biological research and production.
The sponsor of the audience award and partner of the “Biomedicine Today and Tomorrow” nomination was the Invitro company.
"Book" sponsor of the competition - "Alpina Non-Fiction"
Throughout the existence of mankind, the main way to learn anything has been observation. Aristotle broke chicken eggs at different stages of incubation and sketched what he saw, later trying to explain it. Over time, a slightly more reliable method appeared - an experiment in which we completely control the observation conditions. However, lately scientists have increasingly wanted to intervene in living processes, come up with new genes useful to humanity, or simply break something and see what happens.
In modern biology, issues of intervention in living systems are dealt with by synthetic biologists and bioengineers. They develop rational approaches to control and program cellular functions; are studying methods for creating artificial genetic constructs, circuits and networks. You can either look for inspiration in nature, moving genes between organisms, or come up with completely new systems that have no analogues in the living world.
To better understand the material, let’s quickly refresh your school knowledge.
Genetic apparatus in 30 seconds
Modern basic principles of molecular biology are briefly described by the so-called central dogma(Fig. 1): genetic information encodes the protein sequence and is stored in the cell in the form of DNA, and RNA carries information about amino acids to the molecular machine of protein synthesis - ribosome. You need to enter two terms: transcription- the process of RNA synthesis from a DNA template, - and broadcast- the process of protein synthesis from amino acids using an RNA matrix.
Figure 1. The central dogma of molecular biology. The diagram shows the main processes of transmission and implementation of genetic information in a cell.
To give a detailed overview of modern advances in synthetic biology would require a whole series of articles, so I will limit myself to a select few that are most useful to humans, or simply the most exciting developments.
Let's start with something simple - with a breakdown.
Site-directed mutagenesis offers a relatively simple way to determine the role of a particular gene/protein in cellular processes - the process that stops working due to the breakdown of this gene or protein obviously depends on its function. For example, we turn off a certain gene that interests us in a plant → instead of normal flowers we see only stamens and pistils → conclusion: the gene is involved in the formation of flower parts. It would seem that nature is already full of mutants, so why create new ones? But finding which gene is turned off in a natural mutant is much more difficult than manually breaking it definite us the gene.
Alien genes
Instead of turning off genes, you can try introducing genes from other species into the body. Classical studies in the field genetic modification are aimed at agriculture and livestock breeding, but this does not mean that we cannot solve more interesting problems using the same methods.
Tropical diseases have recently attracted more and more media attention. This includes the Zika virus, Dengue fever, and malaria. And it is the latter infection that causes the most concern. In the last century, Plasmodium falciparum has become resistant to almost all classical drugs. Artemisinin, developed in the 1970s (for its development, by the way, they were awarded Nobel Prize 2015), has become a new hope for doctors and has indeed led to a sharp decrease in mortality from malaria over recent decades. Now artemisinin is commercially produced using an artificial biochemical pathway - the enzymes that carry out the necessary reactions are collected from different bacteria into one modified strain. From the point of view of chemical technologists, this is great solution- we don’t worry about isolating intermediate products, we spend less energy on carrying out reactions, and it’s easy to isolate the product - just filter out the bacteria.
To solve the problem of insect-borne diseases, there is another solution - mutagenic chain reaction , . The name sounds scary, and this is largely true. The essence of the method is to make a change in the genome spread throughout the population, with the potential to ultimately change absolutely all organisms of a given species. Figure 2 shows how the mutant type (labeled in blue) may become dominant in the population. We violate the Mendelian laws of inheritance by introducing enzymes that modify it into the genome.
Using a mutagenic chain reaction, mosquitoes can be made unable to transmit malaria, and all descendants The modified mosquito will also be unable to infect humans.
For many scientists, the mutagenic chain reaction is of great concern. A mutation, once introduced into the genome of a single individual, spreads uncontrollably in the genomes of children, grandchildren, great-grandchildren and all subsequent generations of the population. Because of this, “wild” organisms may disappear from the face of the earth.
A less radical, but very similar method is already being used. In Brazil, factories produce GM mosquitoes, whose offspring are sterile, and release them into the wild. This helps reduce the number of mosquitoes that carry Dengue, Zika, malaria and the like. However, since the method only works on two generations, there is no danger that something will get out of control.
Everything happens according to the laws of population genetics: modified males compete on equal terms with natural ones for reproduction, so the number of viable children in the next generation decreases, which means the number decreases. Profit!
Brain in technicolor
Restriction enzymes, the same enzymes that edited the genomes of mosquitoes and fruit flies, can also help us in neuroscience.
Method Brainbow allowed neuroscientists to paint each neuron in the brain (in this case a rat) an individual color. And the point here is not only that it looks incredibly beautiful, but also that the structure of the brain has become discernible on one more level more accurately: now we can trace the connections of neurons located in the same layer of the cortex, find less obvious paths for conducting signals , bring us a little closer to compiling connectome- maps of all neuron contacts in the brain. It works like this: several fluorescent proteins are inserted into the genome different colors, and when a cell differentiates into a neuron, restriction enzymes randomly turn off some of them. Thus, each neuron has its own color and clearly stands out from the rest (Fig. 3).
Networks, circuits, and loops
But we will not dwell for long on modifications and insertions of single (non-interacting) genes, because all the complexity and intricacy of living systems is mainly due to the huge number and diversity of regulatory systems operating both at the level of transcription and translation. We now know enough about regulation to try to create networks genes that work as and when we need them.
One of important types gene networks - oscillators . These are systems that cycle between multiple states. For example, oscillatory networks regulate circadian rhythms in animals and the daily rhythms of cyanobacteria. Artificial oscillators are one of the first topics of research for bioengineers. Bacteria that cyclically change color as a result of a vicious circle of activation and shutdown of different genes (video) appeared back in 2008. Having such “temporary” control over protein production could be very important, since all of nature lives in cycles.
At the same time, newer articles talk about the possibility of achieving synchronous color changes in an entire colony.
Video. Bacteria that oscillate between fluorescent and colorless states.
Another "colored" example is bacteria, which react to light, resulting in the color they were illuminated with. Such “bacterial TV” (example in Figure 4) opens up for us a new way to control the bacterial genome, which does not require any chemical exposure to the culture. Really, different lengths waves of light irradiating cells - something like buttons on a remote control that turn on the synthesis of different proteins.
Figure 4. Scientists from the Massachusetts Institute of Technology depicted the logo of their university on a Petri dish with modified bacteria ( top left- the image that was projected onto the colony).
RNA
Scientists have not forgotten another type of macromolecule - ribonucleic acids. Let’s not dwell now on the importance of RNA for cells and its role in the processes of the emergence of life and evolution, but let’s talk more about the practical side of its use in synthetic biology.
On the one hand, RNA is much more diverse than DNA and proteins: many conformations (spatial structures) allow RNA to play any role, from a carrier of genetic information, a receptor/sensor, a structural framework, to even enzymatic activity.
On the other hand, RNA is maximally unstable in pure form, does not live in a cage long time, and working with it requires more time and effort.
The reasons for this are a little non-trivial: RNA reacts chemically with itself, and people also secrete a lot of RNases (enzymes that degrade RNA) in their sweat and breath, which acts as the first barrier of defense against viruses.
However, there are beautiful and complex developments in this area as well. Scientists from Harvard University developed RNA biosensors: modified cells produce recognition RNAs, which are then applied to paper in the form of a cell extract. These test strips are dried and can be stored for a long time. When used, water and a sample are applied to them, the RNA receptor recognizes a certain target and triggers the synthesis of a colored protein (Fig. 5).
This produces inexpensive, durable and accurate analyzers that can use a drop of saliva or blood to identify a disease or infection in a minute outside the laboratory anywhere in the world.
Biocomputer
From a review of the general achievements of synthetic biology, we can now move on to the promised consideration of the topic of “biocomputers.” Ahead of us lies the most the hard part material, but this does not make it any less interesting and beautiful. First, let's remember what computing devices do: they receive certain signals as input, process them (for example, compare, sum, select one of several), and then produce an output corresponding to the input data.
All living organisms are formally biocomputers: based on external conditions (light, availability of food, population density and many others), they decide which proteins to synthesize, in which direction to move, when to reproduce and make reserves... But only all these actions - not what we want to get. Synthetic biologists want to determine the signals, the “computation” process, and the outcome themselves. Why do we need this? Applications of “living computing” can be found in biotechnology, medicine, and even in scientific activity itself. They will help us achieve significant automation of processes, be it blood testing or monitoring a biotechnological process. And now it is in many ways possible to implement this.
A good example is the lactose operon, the work of which begins only when two conditions are met: THERE IS lactose AND NO glucose. Operation of the operon - output; glucose, lactose - inputs, conditions - processing.
Logics
An important element in calculations are logical gates (the so-called valves), performing basic operations, such as AND, OR, NOT, and so on. They allow you to reduce the number of signals, make it possible to add branching (if... then... etc.) to a future program. Such schemes can be implemented both at the gene level (Fig. 6) and at the translation stage using short synthesized RNA molecules. Chains of activator and repressor proteins may well be considered transistors.
Memory
A computer is unthinkable without memory, and biologists understand this. The first article on artificial biological memory was published back in 2000. Using an external signal, scientists were able to switch the cell between two stable states (for example, between the synthesis of two different proteins), which are formally a single bit of memory (Fig. 7).
Figure 7. Diagram of a gene switch. Inductors 1 And 2 - control signals, repressor genes ensure the simultaneous operation of only one half (one of two states) of the system.
Such basic elements open up enormous scope for imagination - for example, there are schemes that count the number of events that determine the boundary of light and shadow... But still there is more to come long haul research, ideas and breakthroughs.
iGEM
It’s hard to believe, but synthetic biology has a fairly low barrier to entry (of course, only if you have the desire and knowledge). How is this possible? The path lies through competition iGEM (International Genetically Engineered Machine), founded in 2004. Now teams of up to six people from schoolchildren and bachelor's students can participate (there is also a separate section for everyone who is “older”).
iGEM is a real biohackathon: in spirit, the competition is very close to the biohacking movement, which has been gaining popularity over the past 10 years. In the spring, teams register and come up with a project idea. Over the summer they will have to teach bacteria (as the most standard and favorite object) something new and unusual.
This, of course, requires the presence of a laboratory, the ability to think non-trivially, good theoretical training and properly developed laboratory skills.
But with reagents and starting materials, everything is much more interesting: MIT contains a “registry of standard biological spare parts” - a database of simple components such as plasmids, primers, promoters, terminators, proteins, protein domains and much more (Fig. 8), which are stored in DNA molecule format. There are now over 20,000 registered parts, so you can find almost anything from classic fluorescent proteins to heavy metal sensors and the famous CRISPR/Cas. After the organizing committee approves the project of the registered team, they are sent all necessary components from the registry.
The winner is selected by a panel of 120 distinguished scientists at the annual fall conference in Boston.
As an example, I’ll tell you about one of the projects of students at Imperial College London ( Imperial College London), who won the Grand Prize in 2016. The main idea is to regulate the species ratio of bacteria in joint cultures. This may further make it possible to fully realize the potential of entire synthetic ecosystems. Students combined a bacterial system quorum feelings(by which bacteria communicate and coordinate their behavior within a species), computational circuits from RNA that compared quorum signals different types, and growth-inhibiting proteins (the general scheme is shown in Fig. 8). Thus, bacteria are always aware of the number of all species, and due to growth inhibitors they are able to keep its ratio constant. RNA comparators were developed from scratch, and software for recording and analyzing co-culture growth data was also introduced.
This event is quite popular in university circles, the number of participants reaches five thousand people, and even in Russia recently its own
3. Ethical issues
Synthetic biology A term long used to describe approaches in biology that seek to integrate different fields of study in order to create a more holistic approach to understanding the concept of life.
Recently, the term has been used in a different sense, signaling a new field of study that combines science and engineering for the purpose of designing and building new biological functions and systems.
Synthetic biology is a new direction of genetic engineering. Developed by a small galaxy of scientists. The main goals are:
- Learn more about life by building it from atoms and molecules, and not taking it apart, as was done before.
- Make genetic engineering worthy of its name - transform it from an art into a rigorous discipline that continually evolves, standardizing previous artificial creations and recombining them to make new, more complex living systems that did not previously exist in nature.
- Erase the boundary between living things and machines in order to arrive at truly programmable organisms.
More than 100 laboratories around the world are engaged in synthetic biology. Work in this area is fragmented; Biologist Drew Andy from the Massachusetts Institute of Technology is working on their systematization. This will make it possible to design living systems that behave in predictable ways and use interchangeable parts from standard set genes. Scientists are striving to create an extensive genetic bank that allows them to create any desired organism. The bank consists of biobricks - DNA fragments whose function is strictly defined and which can be introduced into the cell genome to synthesize a previously known protein. All selected biobricks are designed to interact well with all others on two levels:
- mechanical so that they can be easily manufactured, stored and included in the genetic chain;
- software so that each brick sends certain chemical signals and interacted with other pieces of code.
Now the Massachusetts Institute of Technology has created and systematized more than 140 biobricks. The difficulty lies in the fact that many engineered DNA fragments, when introduced into the genetic code of the recipient cell, destroy it.
Synthetic biology is capable of creating engineered bacteria that can produce complex and scarce drugs cheaply and in industrial quantities. Engineered genomes could lead to alternative energy sources or bacteria that help remove excess carbon dioxide from the atmosphere.
"The development of technology leads to
that the difference between natural and
man-made, between the body and
the mechanism will start gradually
blur. The person will
rebuild the first ones in any way
and partially grow the second;
the border between them will become
conditional to the point of impossibility
find out the origin of the object"
"In 2010, an American engineer
and biologist Craig Venter
with the group synthesized the first cell with
artificial genome assembled
on a supercomputer"
"In 1975, the world's leading biologists accepted
decision to ban the use
recombinant DNA technology, and then
developed rules for working with them"
""The chemical synthesis of life is one of the tasks
always facing synthetic
organic chemistry» Craig Venter.
"Venter moves towards the role of God: creates
artificial life that never
would not have arisen under natural conditions"
"Synthetic biology is software
roving life. Cells are living
computers, and DNA is a programming language"
Andrew Hessel
Synthetic biology (Synbio) is a rapidly developing theoretical field of biology and practice, a new direction in genetic engineering. More than 100 laboratories around the world are engaged in synthetic biology. Work in this area is fragmented. Biologist Drew Andy from the Massachusetts Institute of Technology is working on their systematization.
The term synthetic biology was coined in 1980. It was used by Barbara Hobom when describing bacteria that had been genetically modified using recombinant DNA. The term was coined again in 2000 by Eric Kohl and a number of other speakers during the American Chemical Society meeting, which takes place every year in San Francisco.
Synthetic biology began with the work of Steven Benner and Peter Schultz. In 1989, Benner from ETH (Eidgenssische Technische Hochschule) in Zurich created DNA containing, in addition to the four known letters of the genetic alphabet, two more. Since then, several variants of similar DNA have been obtained, but so far no one has managed to achieve the functioning of their genes, that is, transcription and translation (protein synthesis).
DEFINITION
There are several of them. Here are a number of them:
* Synthetic biology is concerned with the design or reconstruction of biological systems or their components and their creation by encoding the DNA of the desired system or component. Synthetic biology provides efficient technologies for reproduction natural organisms and creating “synthetic” biological material that does not exist in nature.
* Synthetic biology is a new direction of genetic engineering. The term SYNTHETIC BIOLOGY ( Synthetic Biology) has long been used to describe approaches in biology that seek to integrate different fields of study in order to create a more holistic approach to understanding the concept of life. Recently, the term "synthetic biology" has been used in a different sense, signaling a new field of study that combines science and engineering to design and build new (non-naturally occurring) biological functions and systems.
* Design and construction of biological devices and biologically[ systems for useful purposes.
* Synthetic biology is an emerging biological field of research that combines science and technology. It covers a range of different approaches, methodologies and disciplines and different definitions. What they have in common, however, is the fact that they are looking at synthetic biology for new biological functions and design and construction systems that do not occur in nature.
*A field of study that combines science and engineering to design and construct new (not naturally occurring) biological functions and systems. Synthetic biology is a new direction of genetic engineering.
* Synthetic biology represents the convergence of advances in chemistry, biology, computer science and engineering. Experts in these fields are working together to create reusable, systematic methods to increase speed, scale, and precision in biological systems engineering. In a sense, synthetic biology can be seen as an evolution of biology based on "toolboxes" that allows for improved products in many industries, including medicine, energy and environment.
* Synthetic biology is the latest direction of industrial technology at the intersection of computer science, electronics, chemistry and biology, which combines advanced areas of research for the purpose of designing, synthesizing and constructing new, including non-existent in nature, biological functions and living systems. Modern synthetic (systems) biology is an engineering toolkit for the design of functional and controllable living systems with specified properties - energy, industrial and production in nature.
* Synbio deals with things like inserting machine-generated DNA sequences into living cells, i.e., creating new organisms altogether.
OBJECTIVES OF SYNTHETIC BIOLOGY
The main goals are the following:
*Learn more about life by building it from atoms and molecules, rather than taking it apart, as was done before.
*To make genetic engineering worthy of its name is to transform it from an art into a rigorous discipline that continually evolves, standardizing previous artificial creations and recombining them to make new, more complex living systems that did not previously exist in nature.
*Erase the boundary between living things and machines in order to arrive at truly programmable organisms.
* Create an extensive genetic bank that allows you to create any desired organism (by analogy with the creation of an electronic circuit from industrial transistors and diodes). The bank consists of biobricks (BioBrick) - DNA fragments whose function is strictly defined and which can be introduced into the cell genome for the synthesis of a previously known protein. All selected biobricks are designed to interact well with all others on two levels:
mechanical - so that they can be easily manufactured, stored and included in the genetic chain; software - so that each brick sends certain chemical signals and interacts with other pieces of code.
* Colonies of bacteria will be able to synthesize countless amounts of food, medicines, and necessary substances. In this case, the costs will be minimal, the person will be well-fed, healthy, and nothing else is needed.
* Synthesize living organisms that will produce a large number of fuel. In such a situation, there will be no need to extract natural oil and gas.
* The immediate goal of the pioneers of this branch of science is to create an organism with a minimal genome, that is, capable of eating, growing and reproducing.
* The goal of synthetic biology is the rational creation biological organisms with the required properties. This, of course, is very similar to genetic engineering, which has been actively developing since the 70s of the last century. But synthetic biology is based on more high level understanding of biological objects obtained through the development of so-called “systems” biology.
CHALLENGES OF SYNTHETIC BIOLOGY
* The study of organisms through their creation, rather than through their decomposition into parts.
* Development of genetic engineering itself so that it lives up to its name and becomes a discipline capable of consistently developing and creating more and more complex biological systems.
* Expanding the boundaries of the living and non-living worlds so that as a result of their intersection, programmable living beings appear.
ACHIEVEMENTS OF SYNTHETIC BIOLOGY
* In 1989, Benner from ETH (Eidgenssische Technische Hochschule) in Zurich created DNA containing, in addition to the four known letters of the genetic alphabet, two more.
* In 2010, American engineer and biologist Craig Venter synthesized the first cell with an artificial genome assembled on a supercomputer.
* In May 2010, famous American geneticist John Craig Venter announced the creation of the world's first partially synthetic living cell capable of reproduction (yeast, in the genome of which one of the chromosomes is replaced by an analogue completely synthesized in the laboratory).
* At the company of one of the fathers of genomics, K. Venter, the genome of a mycoplasma bacterium was synthesized from individual nucleotides, which is not similar to any of the existing mycoplasma genomes. This DNA was enclosed in a “ready” bacterial shell of killed mycoplasma and a working one was obtained, i.e. a living organism with a completely synthetic genome.
* Evolution has “programmed” yeast to process sugar and produce various biochemicals. To this already functioning organism, Berkeley chemical engineer Kisling added a laboratory-developed genetic program, composed of 12 new genes. She changed the metabolism of yeast, and they began to produce artemisinin.
* Craig Venter and George Church create self-sustaining, highly efficient organisms that transform sunlight directly into clean biofuels with minimal environmental damage and zero yield greenhouse gases. These organisms “will replace the petrochemical industry, most food, and will participate in soil bioremediation and the production of clean energy.
* A company called Evolva managed to create a compound called vanillin, which, unlike vanilla, grew not on a vine but on synthetic yeast.
PROSPECTS FOR SYNTHETIC BIOLOGY
* ARTIFICIAL NUCLEIC ACIDS HAVE ALREADY BEEN CREATED THAT CAN SELF-REPLICATE AND EVOLUTE, WHICH OPENES A NEW ERA IN SYNTHETIC BIOLOGY. Replication; tion (from Latin replicatio - renewal, repetition)
* A huge antibiotic crisis is brewing. And if new antibiotics do not appear in the near future, then we will return to the 19th century, when we will die from tuberculosis, cholera and other rubbish. New antibiotics will be produced using synthetic biology approaches.
CONFERENCES ON SYNTHETIC BIOLOGY
* In June 2004, Massachusetts Institute of Technology held the first conference on synthetic biology.
* Synthetic Biology - Gordon Research Conferences (New Gordon) - will be held June 28 - July 3, 2015
The Synthetic Biology Science Conference at New Gordon will present cutting-edge research in this rapidly developing field and provide an in-depth forum of discussion among practitioners from academia and industry in the various fields contributing to synthetic biology.
* School-conference “Synthetic biology and design of bioengineering devices” on July 11, 2012 in the Moscow building of MIPT.
1. Improving engineering biology for the design of living machines
2. Designing the functionality of industrial microorganisms on an automated workstation using a software package from universities in the USA and Europe.
3. High-throughput in silico modeling of industrial biosystem components for proteomic design, configuration development, loading and resource cell organelles and etc.
4. Testing and debugging of the characteristics of the designed code in a virtual environment (virtual bench) based on the characteristics of the proteome, metabolome, transcriptome and epigenome.
5. Synthesis and transfection of the developed genetic code into a model microorganism in vitro.
* 6th International Conference on Synthetic Biology in London - July 2013
Most of the reports and communications were devoted to modifications of the DNA molecule.
CONCLUSION
Over the past hundred years, science, and with it medicine, has developed at a record pace. However, it was not possible to defeat the main enemies of humanity - hunger and disease. Synthetic biology is at the next stage of development and soon it will be difficult to imagine the modern world without it.
Synthetic biology, a “very powerful set of tools,” will lead to the creation of a vaccine against influenza, and possibly against AIDS. And the day is not far off when microorganisms capable of consuming carbon dioxide and releasing energy will create a safe alternative to traditional fossil fuels. Now that synthetic biology is beginning to take root, our challenge is to ensure that future generations see it as a blessing rather than a curse.
However, synthetic biology can create dual-use products, so it should be under strict government control.
Sources
1. Synthetic Biology
Synthetic Biology (synbio) is an emerging field of natural science, which, however, is based on the principles of engineering. At its core, synthetic biology is concerned with the design or reconstruction of biological systems or their components and their creation by encoding the DNA of the desired system or component. Synthetic biology provides efficient technologies for reproducing natural organisms and creating “synthetic” biological material that does not exist in nature. Synthetic biology can be used to revolutionize the natural sciences and their applications in healthcare, energy and many other sectors, but it also raises serious ethical and biosecurity issues.
2. Revolution in the field of synthetic biology: prospects and risks
(http://ria.ru/science/20131126/979860591.html)
John Craig Venter, along with specialists from his company, started with DNA and built a genetic sequence of nucleotides, which contains more than one million bits of information. Seven years ago, Venter became the first scientist in the world to create biological object based on available genetic information.
Venter's team created an artificial bacterial cell by inserting artificially synthesized DNA into it, after which scientists began to observe how the bacterial cells move, feed, and reproduce themselves. Venter called his new technology “synthetic genomics,” which “will first appear in the digital computer world on the basis of digital biology, and then learn to create new modifications of DNA for very specific purposes. ... This may mean that as we learn the laws of existence of various forms of life, a person will be able to create self-learning robotic and computing systems.
Synthetic genomics in combination with another breakthrough direction in biology - the so-called studies of neomorphic mutations (or as they are also called gain-of-function mutations or GOF studies) - not only opens up a huge number of new prospects, but at the same time sets many difficult questions and poses threats to national security.
Some are already calling Venter's work to create new artificial bacteria “4-D printing.” Let me remind you that 2-D printing is the most normal process printing, which begins after pressing the “Print” key on the keyboard, as a result of which the most ordinary printer gives you a printed article, etc. However, industrial companies, design firms and other consumers are already switching to 3-D printing - in this case, a signal is sent to devices containing all sorts of materials such as plastic, graphite and even food, and at the output we get three-dimensional products. In the case of 4-D printing, two important operations are added: self-assembly and self-reproduction. First, the idea is formalized and gets into the computer, then it is sent to a 3-D printer, and at the output we get a final product that can copy and transform itself. Venter and several hundred other synthetic biologists argue that 4D printing is particularly well suited to constructing living objects using the building blocks that make up living objects themselves, i.e. DNA.
Synthetic genomics, combined with another breakthrough in biology—the so-called neomorphic mutation research (or otherwise known as gain-of-function or GOF research)—not only opens up a huge number of new perspectives, but also poses many difficult questions and threats. for national security.
Now the biologist has become an engineer who programs new forms of life as he pleases. Biologists are now increasingly able to control evolution, i.e. We are witnessing the “end of Darwinism.” Once information macromolecules are able to inherit beneficial mutations through self-sustaining Darwinian evolution, they can begin to give rise to new forms of life.”
Synthetic biology will in the near future give rise to an economic and technological boom, as in the very beginning this century The Internet and social media technologies have done this.
Genetic engineering of existing life forms in nature and creating new ones is the cutting edge of biology.
Venter had no doubt that synthetic biology, a “very powerful set of tools,” would lead to a vaccine against influenza and perhaps against AIDS. And the day is not far off when microorganisms capable of consuming carbon dioxide and releasing energy will create a safe alternative to traditional fossil fuels. Now that synthetic biology is beginning to take root, our challenge is to ensure that future generations see it as a blessing rather than a curse.
3. What is synthetic biology?
Synthetic biology is a new direction of genetic engineering. The term SYNTHETIC BIOLOGY has long been used to describe approaches in biology that seek to integrate different fields of study in order to create a more holistic approach to understanding the concept of life. Recently, the term "synthetic biology" has been used in a different sense, signaling a new field of study that combines science and engineering to design and build new (non-naturally occurring) biological functions and systems.
4.Synthetic biology WIKI en.
Synthetic biology is an interdisciplinary branch of biology, combining disciplines such as biotechnology, evolutionary biology, molecular biology, systems biology andbiophysics, and largely related to genetic engineering.
The definition of synthetic biology is highly debated not only among natural scientists, but also in humanities, art and politics. One of the popular definitions is "The design and construction of biological devices and biological systems for useful purposes." However, the functional aspects of this stem define molecular biology and biotechnology.
5.Synteettinen biology
Synthetic biology (Esperanto)
Synthetic biology is a new field of biological research that combines science and technology. Synthetic biology includes several different approaches, methodologies and disciplines, and various definitions exist. What they all share, however, is that they view synthetic biology as the design and construction of new biological functions and systems that do not occur in nature.
The work on restriktonucleases not only makes it possible to easily create recombinado-DNA molecules and analyze individual genes, but also led us to new era synthetic biology, where not only existing genes are described and analyzed, but also new gene mechanisms can be constructed and evaluated.
6.Synthetic biology (from Finnish)
Synthetic biology is an emerging biological field of research that combines science and technology. It covers a range of different approaches, methodologies and disciplines and different definitions. What they have in common, however, is the fact that they are looking at synthetic biology for new biological functions and design and construction systems that do not occur in nature.
7. Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology
Volume 2, Issue 1, Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and to various applications. We will describe the main features of synthetic biology as a new engineering discipline, covering examples from recent literature and reflecting on the features that make it unique among all other existing engineering fields. We will discuss methods for designing and constructing engineered cells with novel functions within an abstract hierarchy of biological devices, modules, cells, and multicellular systems. Classic engineering strategies of standardization, decoupling, and abstraction will have to be extended to accommodate own characteristics biological devices and modules. To achieve predictability and reliability, engineering biology strategies must incorporate the concept of cellular context into functional definition devices and modules, rational use of redesign and directed evolution to optimize systems, and focus on solving problems using cell populations rather than individual cells. The discussion identifies issues at the heart of the design of complex living systems and provides a trajectory for future development.
8. Five hard truths for synthetic biology
Published online 20 January 2010 | Nature 463, 288-290 (2010) | doi:10.1038/463288a
(http://www.nature.com/news/2010/100120/full/463288a.html)
9.Synthetic Biology Science
(http://ru.science.wikia.com/wiki/Synthetic_biology)
Synthetic Biology is a term long used to describe approaches in biology that seek to integrate different fields of study to create a more holistic approach to understanding the concept of life.
Recently, the term has been used in a different sense, signaling a new field of study that combines science and engineering to design and construct new (non-naturally occurring) biological functions and systems.
Synthetic biology is a new direction of genetic engineering. Developed by a small galaxy of scientists. The main goals are:
Learn more about life by building it from atoms and molecules, and not taking it apart, as was done before.
To make genetic engineering worthy of its name is to transform it from an art into a rigorous discipline that continually evolves, standardizing previous artificial creations and recombining them to make new, more complex living systems that did not previously exist in nature.
Erase the boundary between living things and machines in order to arrive at truly programmable organisms.
More than 100 laboratories around the world are engaged in synthetic biology. Work in this area is fragmented; Biologist Drew Andy from the Massachusetts Institute of Technology is working on their systematization. This will make it possible to design living systems that behave in predictable (and at-will) ways and use interchangeable parts from a standard set of genes. Scientists are striving to create an extensive genetic bank that allows them to create any desired organism (by analogy with creating an electronic circuit from industrial transistors and diodes). The bank consists of biobricks (BioBrick) - DNA fragments whose function is strictly defined and which can be introduced into the cell genome for the synthesis of a previously known protein.
All selected biobricks are designed to interact well with all others on two levels:
mechanical - so that they can be easily manufactured, stored and included in the genetic chain;
software - so that each brick sends certain chemical signals and interacts with other pieces of code.
Synthetic biology is capable of creating engineered bacteria that can produce complex and scarce drugs cheaply and in industrial quantities. Engineered genomes could lead to alternative energy sources (biofuel synthesis) or bacteria that help remove excess carbon dioxide from the atmosphere.
10.Synthetic theory of evolution
VIKI ru.
Synthetic theory of evolution (also modern evolutionary synthesis) - modern evolutionary theory, which is a synthesis of various disciplines, primarily genetics and Darwinism. STE also relies on paleontology, systematics, molecular biology and others.
Thus, the essence of the synthetic theory is the preferential reproduction of certain genotypes and their transmission to descendants. Regarding the source genetic diversity the synthetic theory recognizes the main role of gene recombination.
For evolution to occur, three processes must be present:
mutational, generating new gene variants with low phenotypic expression;
recombination, creating new phenotypes of individuals;
selection, determining the correspondence of these phenotypes to given living or growing conditions.
The synthetic theory of evolution can be characterized as a theory of organic evolution through natural selection of genetically determined traits.
Evolution is not always divergent in nature.
Evolution is not necessarily gradual. It is possible that in some cases individual macroevolutionary events may also have a sudden nature.
Macroevolution can go both through microevolution and on its own paths.
According to neo-Darwinism, all characteristics of living beings are completely determined by genotype and the nature of selection. Therefore, parallelism (secondary similarity of related creatures) is explained by the fact that organisms inherited a large number of identical genes from their recent ancestor, and the origin of convergent characters is entirely attributed to the action of selection.
The authors of punctualism contrast their view with gradualism - Darwin's idea of gradual evolution through small changes - and believe punctuated equilibrium sufficient reason to reject the entire synthetic theory.
11. Programmable matter VIKI ru.
Synthetic biology (section)
Synthetic biology is a field of research aimed at creating cells with "new biological functions". Such cells are typically used to create large systems (such as biofilms) that can be “programmed” to use synthetic gene networks (such as genetic bistable switches) so that they can change their color, shape, etc.
Links
Programmable matter
Boston University's Programmable Matter Group
Claytronics Project at Carnegie Mellon University
Universally Programmable Intelligent Matter Project
12. Artificial genome VIKI ru.
Artificial genome is a direction in biological research associated with the genetic modification of existing organisms in order to create organisms with new properties. Unlike genetic engineering, an artificial genome consists of genes synthesized chemically.
It is assumed that in the future artificial genomes may be created not based on DNA or using a different set of nucleotides and other coding principles than in natural genomes. Thus, the creation of artificial genomes is one of the areas of synthetic biology.
Biological safety
preventing widespread loss of biological integrity that may occur as a result of:-
introduction of alien life forms into the existing ecosystem;
introduction of foreign viral or transgenic genes or prions;
bacterial contamination of food;
the effects of gene therapy or engineering or viruses on organs and tissues;
pollution natural resources(water, soil);
possible introduction of alien microorganisms from space.
In synthetic biology (referring to the risks associated with this type of laboratory practice)
In synthetic biology (referring to the risks associated with this type of lab practice)
13.Synthetic biology Tradition
http://traditio-ru.org/wiki/
The field of biology that creates/transforms living organisms.
19th century
Heyday, rapid development SB occurred in the middle of the 19th century - the beginning of the 20th century:
Vitalism
The successes of synthesis were accompanied at this time by the experimental successes of the vitalists (see Drish Embryo Encyclopedia)
Modern works[edit]
Modern works are characterized by incredibly large volumes of bio-information being processed (see systems biology) and (super/ultra) subtle physical tools:
three-dimensional (bio)printer of organs Google search.
living cell synthesis living cell synthesis - Google image request
The parallelism of the creation of life and artificial intelligence.
Philosophy/ontology
Philosophical and ontological questions of the Security Council:
Rady's principle - living from living (in DARPA programs - this was manifested by the implantation of electronic systems in insects and rats)
Difference between bio and zoe
is minimized when the "BIOS" dominates. Valentin Tomberg. Major Arcana Tarot
14.Synthetic biology
http://positime.ru/synthetic-biology
As you know, the term synthetic biology was used back in 1980. It was used by Barbara Hobom when describing bacteria that had been genetically modified using recombinant DNA. The term was coined again in 2000 by one Eric Kohl and a number of other speakers during the meeting of the American Chemical Society, which takes place every year in San Francisco.
It is worth noting that this term was used in 2000 to describe the process of synthesizing artificial organic molecules, which play a very important role in living systems.
This area is new in biology. It was created in order to design and create completely new biological systems that do not occur in nature. Synthetic biology adds to existing organisms new properties, such as bacteria, may acquire new properties or undergo a certain stage of modification. It is expected that in the future they will be able to independently exist and reproduce.
Synthetic biology was created in order to learn much more about life without having to disassemble molecules and atoms into parts. To transform genetic engineering into something new, into a rigorous discipline that is constantly evolving. Also, one of the goals is to blur the lines between machines and people, and to achieve the possibility of programming the human body.
In a word, synthetic biology is at the next stage of development and soon it will be difficult to imagine the modern world without it.
15.Synthetic biology is changing the world
http://www.inventor.perm.ru/news_2011/2010_05_02_01.htm
Over the past hundred years, science, and with it medicine, has developed at a record pace. However, it was not possible to defeat the main enemies of humanity - hunger and disease.
Meanwhile, others appeared on the horizon serious problems, for example, the energy crisis associated with a reduction in oil and gas reserves. Adherents of a new direction in science - synthetic biology - are committed to solving all these problems. At the end of 2010, the first bacterium with a completely synthetic genome was created at the American Craig Venter Institute. Now researchers are literally expected to perform miracles. Craig Venter himself, as well as his competitors, declare that humanity needs new approaches to providing itself with food and energy resources. And they are ready to provide these approaches.
The appearance of the first synthetic bacteria literally blew up the scientific world. This is understandable - Venter and his colleagues succeeded in the incredible - creating life from dead matter.
When scientists made just one mistake in a molecule consisting of 1.08 million nucleotide base pairs, the cell did not come to life. But in the end, the work was completed flawlessly, and an artificially created, but completely living cell was born. Its name is Mycoplasma mycoides JCVI-syn 1.0.
Synthetic biology is a very promising direction in genetic engineering. If scientists usually interfere with the already existing DNA of animals and plants, assigning them hitherto unprecedented properties, then synthetic biology is engaged in the creation of fundamentally new living systems. The immediate goal of the pioneers of this branch of science is to create an organism with a minimal genome, that is, capable of eating, growing and reproducing.
A bacterium with a minimal genome will become the basis to which new genome regions with specified qualities can be added. The result will be microbes that, for example, generate alcohol or polymer molecules during their life processes, from which plastic can then be made. Thus, synthetic biology blurs the line between Life and machines programmed for specific activities.
One of Craig Venter's main investors is the US Department of Energy. This department annually in 2008-2010 invested $115 million in Venter’s developments. Interest is based on the expectation of miracles in the field of alternative energy. Experts believe that within 15-20 years, the research findings can be used to create alternative energy sources.
Back in 2009, Craig Venter and his company entered into an agreement with oil and gas giant ExxonMobil to develop cheap and environmentally friendly fuel. The issue price is $600 million. According to the project, the source of biofuel will be algae with a modified genome, which will allow them to produce hydrocarbons similar in composition to the organic substances of oil. All algae need is sunlight and water, their biomass increases very quickly, and they can be grown in unlimited quantities.
employees Yale University developed a direct method for generating electricity using bacteria. Just two living cells can convert energy chemical reactions into electricity with an efficiency of 10%. However, complications arise from the possibility of industrial use of this method. A colony of bacteria will simply destroy itself with the same electricity it emits.
Millions of bacterial colonies will be able to synthesize countless amounts of food, medicines, and necessary substances. There will be that “eternal bread” that chemists dreamed of in the 19th century. In this case, the costs will be minimal, the person will be well-fed, healthy, and nothing else is needed.
About 2 million people die every year from malaria in Africa. An effective remedy against malaria - artemisinin. It is made from the root of sweet wormwood. Such production costs a pretty penny, and the people of Africa cannot afford it. In 2004, University of California chemist Jay Keasling conducted a series of experiments that showed that there was a way to make the drug cheaper. The scientist came up with the idea of producing artemisinin using yeast.
One of the areas of synthetic biology that we are involved in is the construction of artificial molecules that have the properties of DNA, but consist of 6 molecules. Developments that are used in medicine bring us $100 million a year,” says Stephen Benner, a professor of chemistry at the University of Florida. According to the scientist, this approach is more ambitious than the work of Craig Venter, who uses sections of natural DNA.
Christopher Voigt and Christina Smolke went even further. They create symbiont bacteria that can live in the human body, while looking for cancer cells in it. There are plans to obtain killer bacteria that could destroy cancer cells.
In December 2010, NASA astrobiologists managed to obtain bacteria that function without phosphorus - one of the standard elements on which earth form life. Arsenic was used as a replacement. The statement that the cellular structure must contain phosphorus, and without it life is impossible, was a dogma for biologists all over the world. This experiment is disruptive traditional biology, makes people realize that their knowledge about this world is insignificant. Steen Rasmussen is trying to move away from DNA altogether, replacing it with peptide nucleic acid (PNA). This molecule will not be located inside the cell, but outside. This will make it easier for the cell to eat and breathe, scientists say.
16.synthetic biology
(http://ru.knowledgr.com/00519961/synthetic biology)
Synthetic biology - new area biological research and technology, which integrates science and engineering. It covers many different approaches, methodologies, and disciplines with many definitions. common goal- design and construction of new biological functions and systems not found in nature.
Biological systems are physical systems that are made up of chemicals. Around the beginning of the 20th century, the science of chemistry went through a transition from the study of natural chemicals to attempts to design and build new chemicals. This transition led to the field of synthetic chemistry. In the same tradition, some aspects of synthetic biology can be seen as an extension and application of synthetic chemistry to biology, and include work ranging from the creation of useful new biochemicals to the study of the origin of life.
Research in synthetic biology can be divided into broad classifications according to the approach they take to the problem at hand: solar cell design, biomolecular engineering, genome engineering, and biomolecular design. The solar cell approach includes projects to make self-multiplying systems from entirely synthetic components. Biomolecular engineering includes approaches that seek to create a set of tools functional units, which can be introduced to introduce new orthogonal functions in living cells. Genome engineering includes approaches to construct synthetic chromosomes for entire or minimal organisms. The biomolecular design approach refers to the general idea of de novo design and combination of biomolecular components. The goal of each of these approaches is similar: create a more synthetic input at a higher level of difficulty by manipulating part of the ongoing level.
17.Synthetic biology
(http://www.sci-lib.net/index.php?showtopic=3905)
20.08.2007, 13:16
Biologists intend to create the first living organism within the next decade
Scientists around the world are currently actively engaged in new, but extremely promising direction science - synthetic biology, the main task of which is the artificial creation of living organisms. According to experts, the first synthetic, but nevertheless living, organisms will be created in 3 to 10 years, AP reports.
"This will be a very big achievement and everyone needs to know about it. We are talking about technology that can fundamentally change our world, in fact it is even difficult to predict exactly how it will change," says Marc Bedow, chief operating officer of the Italian company ProtoLife, which also works in synthetic biology.
Naturally, the first artificially created living organisms will be the most primitive - bacteria created on the basis of genetically modeled DNA and all organic components, without which the existence of a living organism is impossible. The main task facing today in these studies is to create so-called protocells, that is, " building materials"from which future living organisms will be created.
“The creation of protocells is important not only from the point of view of obtaining artificial bacteria, but also for understanding how life arose in natural conditions in the Universe,” he says.
Scientists note that for several years now they have been struggling with the riddle of how minimal and at the same time universal a set of genes should be to ensure the survival of an organism. Knowing this will allow geneticists to literally become “creators of life.”
However, opinions regarding these studies, even in scientific community diverge. Some scientists believe that synthetic biology is a source of solutions to many problems modern world such as air pollution, fuel creation, combating various diseases and other areas. Others say that if these developments fall into the hands of attackers, the consequences could be truly terrible, as it will become possible to create bacteria, viruses and other microorganisms that can cause terrible epidemics and mutations.
And yet, research is ongoing today. According to Bedow, before synthesized living organisms are created, world science still has to solve a number of problems:
18.About synthetic biology
(http://novostinauki.ru/news/61245/)
Genetic engineering opens its arms to dimensions called synthetic biology. This is not at all a formal union of geneticists, botanists and physicists with chemists. This genetic engineering, which does not transfer individual genes back and forth, but studies the structure of entire genomes, the principles of their functioning and comes close to riveting completely new organisms at its discretion.
Issues of synthetic biology are dealt with primarily by fundamental biochemistry, molecular science, chemistry, physics, computer science, and the applied sphere is limited to microbiology, and possibly also pharmacology. Plant synthetic biology is still in its infancy, and in food technology and agriculture it is only a first approximation.
19.Prospects for synthetic biology
(http://novostinauki.ru/news/49977/)
ARTIFICIAL NUCLEIC ACIDS WHICH CAN SELF-REPLICATE AND EVOLUTE ARE CREATED, WHICH OPENES A NEW ERA IN SYNTHETIC BIOLOGY –
Synthetic nucleic acids, called xenonucleic acids, behave in the same way as their natural counterparts, the genetic polymers DNA and RNA. That is, these are spiral molecules that are capable of doubling and also evolving, i.e. replace individual elements in your chain. The creation of such nucleic acids was reported by researchers from the Medical Research Council Laboratory of Molecular Biology (MRC Laboratory of Molecular Biology) in Cambridge, UK, publishing an article in Science (April 20, 2012). This achievement will be used not only in biotechnology and the design of new drugs, but also in studying the origin of life - on Earth and beyond, writes The Scientist. According to publication expert Eric Kool (Stanford University, California), the production of xenonucleic acids suggests that “you do not need to be attached to the ribose or deoxyribose backbone of RNA or DNA in order to have transmitted, inherited and evolving information.” Scientists have been trying to create all sorts of xenonucleic acids for the past 20 years by manipulating various sugars as replacements for ribose and deoxyribose residues. In particular, threose was used to create a DNA resemblance called TNA, and anhydrohexitol gave its name to the artificial biopolymer HNA. These molecules have been studied for applications in biotechnology and medicine. However, they were not analogues of DNA and RNA in the biological sense - they did not self-replicate and did not evolve.
20.Synthetic biology will change our world
(http://oagb.ru/info.php?txt_id=17&nid=15667&page=0)
Thirty years ago, geologist Dougal Dixon rose to prominence with his book After Man: The Zoology of the Future. In it, the author fantasizes about how the animal world of distant times will be transformed, where there will no longer be people.
21. Mine detector mice
In 2012, a group of scientists from Hunter College of the City University of New York bred mice that were hypersensitive to the smell of explosives.
In the mouse MouSensor, with the help of genetic engineering, it was possible to significantly increase (up to 1 million) the number of neurons in the olfactory bulb that respond to molecules of a specific substance - 2,4-dinitrotoluene (DNT, its smell is similar to the smell of TNT - TNT).
Mosquitoes against malaria
For example, a group of scientists from the University of California at Irvine and the French Pasteur Center have already created transgenic mosquitoes that have increased resistance to Plasmodium falciparum (the causative agent of the deadliest type of malaria). Technical capabilities today make it possible to spread large populations of modified insects in the main foci of infection and thereby contain the reproduction of wild individuals carrying the infection.
Cut to the quick
More recently, biologists have developed a new genome editing technology - CRISPR, which allows you to cut and paste DNA fragments with the highest precision. This opens up completely new perspectives in genetic engineering. We are no longer surprised by sheep with a high meat content fatty acids Omega-3, created by Chinese scientists from the Institute of Genetics and Developmental Biology in Beijing, or modernized by biologists from the University of Wyoming from goats whose milk contains spider silk protein. Currently, molecular geneticist Scott Fahrenkrug from the University of Minnesota is implementing his idea - raising hornless cows. To do this, he cut out ten genetic letters from the genome of a dairy cow and inserted 212 from another breed. And yet, genetic engineers are still busy with minor tweaks that boil down to obtaining the right substance or reducing the risk of disease in an animal. If we look into tomorrow, we will see a completely different picture.
The principles of synthetic biology allow us to gain significantly greater control over the design process, opening up new opportunities for scientists to quickly operate with the desired properties of organisms at a fundamentally new – genetic – level.”
Now, the development of technology is leading to the fact that the distinction between natural and man-made, between an organism and a mechanism will gradually begin to blur. A person will rebuild the first in every way and partially grow the second; the boundary between them will become arbitrary to the point of making it impossible to know the origin of the object.
22. Interview with microbiologist Konstantin
(http://postnauka.ru/talks/27769)
What is synthetic biology?
- In a broad sense, the goal of synthetic biology is the rational creation of biological organisms with desired properties. This, of course, is very similar to genetic engineering, which has been actively developing since the 70s of the last century. But synthetic biology is based on a higher level of understanding of biological entities, gained through the development of so-called “systems” biology.
Systems biology arose in connection with the development of a number of high-throughput analytical technologies. Based on these technologies, new areas of knowledge have emerged; they are often collectively called “omics.” This is genomics, which allows us to identify all the genes of an organism; transcriptomics, which allows you to quantify the level of activity of all genes operating in a specific cell type in a given tissue at a given time; proteomics, which allows you to determine all the proteins present in a particular type of cell, tissue, etc. There is also metabolomics - this is the determination of all small molecules, metabolites that are in a cell, tissue or some other natural sample .
From the point of view of synthetic biology, microbiology is ahead of the rest, since microbes are ideal model objects. They are very simple compared to us, so doing many things with them is much more convenient and easier. Formally, the first (and so far only) completely synthetic organism is a microbe made several years ago by Craig Venter's group. This is the same person who first determined the human genome (his own)
New antibiotics will be obtained through the use of synthetic biology methods. We have a huge antibiotic crisis brewing. And if new antibiotics do not appear in the near future, then we will return to the 19th century, when we will die from tuberculosis, cholera and other rubbish.
New antibiotics will be produced using synthetic biology approaches.
23. What is synthetic biology?
(http://www.synberc.org/what-is-synbio)
Synthetic biology represents the convergence of advances in chemistry, biology, computer science and engineering. Experts in these fields are working together to create reusable, systematic methods to increase speed, scale, and precision in biological systems engineering. In some ways, synthetic biology can be seen as an evolution of biology through a "toolkit" that allows for improved products in many industries, including medicine, energy and the environment.
Progress towards synthetic biology has only been practically achieved with the advent of two fundamental technologies, DNA sequencing and synthesis. With sequencing, our understanding of the components and organization of natural biological systems has increased, and synthesis has provided the opportunity to begin testing designs for new, synthetic biological parts and systems.
24. Synthetic Biology - Gordon Research Conferences (New Gordon Conference)
(http://www.grc.org/programs.aspx?id=15842)
June 28 - July 3, 2015
The 2015 Gordon Research Conference on Synthetic Biology will present cutting-edge research from this rapidly evolving field and provide in-depth forum discussions among practitioners from academia and industry in the various fields contributing to synthetic biology.
Synthetic biology - the design of more complex biological systems according to principles drawn from classical engineering disciplines - is experiencing fast growth since its founding areas - such as the development of biological circuits - in the broad field of scientific and industrial biotechnology.
The collegial atmosphere, with scheduled discussion sessions, as well as opportunities for informal meetings in the afternoon and evening, provides the opportunity for brainstorming and promotes interdisciplinary collaboration in various areas of research.
25. School-conference “Synthetic biology and design of bioengineering devices” on July 11, 2012 in the Moscow building of MIPT.
(http://synbio2012.ru/)
Synthetic biology is the latest direction of industrial technology at the intersection of computer science, electronics, chemistry and biology, which combines advanced areas of research for the purpose of designing, synthesizing and constructing new, including non-existent in nature, biological functions and living systems. Modern synthetic (systems) biology is an engineering toolkit for the design of functional and controllable living systems with specified properties - energy, industrial and production in nature.
The achievements of the last decade in the field of genomic and cellular technologies, in terms of their importance for the industry and economy of the countries of the world, are comparable to the discovery of semiconductors in the middle of the last century and the development of the radio-electronic industry in Silicon Valley.
In 2010, American engineer and biologist Craig Venter synthesized the first cell with an artificial genome assembled on a supercomputer. Since then, the largest customers for research in this area have been the US Department of Defense, the US Department of Energy, and companies in the military-industrial complex (Raytheon, Lockheed-Martin, etc.).
26. W: Xeno-nucleic acids - synthetic competitors of DNA
At the 6th International Conference on Synthetic Biology held in London, the overwhelming majority of reports and messages were devoted to one or another modification of the DNA molecule.
27. Waite Gibbs Synthetic Life
(http://wsyachina.narod.ru/biology/handmade_life_2.html)
A new direction in genetic engineering - synthetic biology.
The three main goals of synthetic biology are:
First, it is the study of organisms through their creation, and not through their decomposition into parts. Secondly, the development of genetic engineering itself so that it lives up to its name and becomes a discipline capable of consistently developing and creating increasingly complex biological systems. Thirdly, expanding the boundaries of the living and non-living worlds, so that as a result of their intersection, programmable living beings appear.
Synthetic biology began with the work of Steven Benner and Peter Schultz. In 1989, Benner from ETH (Eidgenssische Technische Hochschule) in Zurich created DNA containing, in addition to the four known letters of the genetic alphabet, two more. Since then, several variants of similar DNA have been obtained, but so far no one has managed to achieve the functioning of their genes, that is, transcription and translation (protein synthesis).
All organisms are based on the same molecules: five nucleotides, the monomers that make up DNA and RNA, and 20 amino acids, the building blocks of protein molecules. (A small number of species have at least two additional amino acids.)
Davis is thinking about creating white blood cells that synthesize unusual proteins that instantly destroy pathogenic microorganisms or cancer cells.
The priority area for the use of artificial living systems will be work where one has to deal with life-threatening chemicals.
By slightly modifying the bacterium, it will be possible to obtain expensive chemical compounds used in the cosmetics industry, and most importantly, the anti-cancer drug Taxol.
In 1975, the world's leading biologists decided to ban the use of recombinant DNA technology, and then developed rules for working with it.
28. Landmark Achievement: Scientists Achieve Success in Yeast Synthesis
In May 2010, the famous American geneticist John Craig Venter announced the creation of the world's first partially synthetic living cell capable of reproduction.
Unlike bacteria, yeast are eukaryotes, that is, their cells contain nuclei, and it is in them that chromosomes, which are carriers of hereditary information, are located.
In the journal Science, researchers presented what can be considered a landmark achievement on this path: yeast, in the genome of which one of the chromosomes is replaced by an analogue completely synthesized in the laboratory.
There are a total of 16 chromosomes in a yeast cell, and chromosome number 3 is one of the smallest: it accounts for only 2.5 percent of the hereditary material, consisting of 12 million nucleotide base pairs.
First, they designed the entire chromosome in a computer, and then, in strict accordance with this plan, synthesized it in a chemical laboratory.
Of particular importance to this work is the fact that the artificial chromosome is not completely identical to the natural one.
The leader of the Synthetic Yeast 2.0 project is Jef Boeke, a professor of molecular biology and genetics at Johns Hopkins University and director of the Systems Genomics Institute at New York University Langone Medical Center.
Synthetic biology is moving from theory to practice. Other groups of researchers are already working on the synthesis of other chromosomes, and therefore Professor Buka is confident that yeast with a completely synthesized genome will be available in four years.
29. Ten biggest achievements of the decade in biology and medicine
(http://sciencefirsthand.ru/pdf/sfh_43_48-51.pdf)
Synthetic biology and synthetic genomics- how easy it is to become God Information accumulated over half a century of development of molecular biology today allows scientists to create living systems that have never existed in nature. As it turns out, this is not at all difficult to do, especially if you start with something already known and limit your claims to such simple organisms as bacteria. These days, the United States even hosts a special competition, iGEM (International Genetically Engineered Machine), in which student teams compete to see who can come up with the most interesting modification of common bacterial strains using a set of standard genes. For example, by transplanting a set of eleven specific genes into the well-known E. coli (Escherichia coli), it is possible to force colonies of these bacteria, growing in an even layer on a Petri dish, to consistently change color where the light falls on them. As a result, it is possible to obtain their unique “photographs” with a resolution equal to the size of the bacterium, i.e., about 1 micron. The creators of this system gave it the name “Koliroid”, crossing the species name of the bacterium and the name of the famous company “Polaroid”. This area also has its own megaprojects. Thus, in the company of one of the fathers of genomics, K. Venter, the genome of a mycoplasma bacterium was synthesized from individual nucleotides, which is not similar to any of the existing mycoplasma genomes. This DNA was enclosed in a “ready” bacterial shell of killed mycoplasma and a working one was obtained, i.e. a living organism with a completely synthetic genome.
30. For the first time, a living cell appeared, completely controlled by an artificially synthesized chromosome
Venter opened the most important door in human history slightly. He doesn't just make artificial copies of living beings or expose them to genetic modification, he moves towards the role of God: he creates artificial life that would never arise in natural conditions.
American Craig Venter made a name for himself by deciphering human genome faster and cheaper than anyone in the world.
The guiding principle of synthetic biology is the representation of living cells as complex computer mechanisms capable of self-reproduction.
“The chemical synthesis of life is one of the challenges that has always faced synthetic organic chemistry,” says SynBio's most famous adept, Craig Venter.
Since June 2004, when MIT held its first synthetic biology conference, researchers have developed and produced thousands of programmable biodevices—pieces of genetic machinery that, when assembled, can perform more complex tasks.
These living devices are expected to have enormous benefits. They will be able to produce any pharmaceutical drug imaginable, including those that cannot be created using traditional chemistry, or are too expensive at the moment. In the same way, they can create any other chemical or polymer for the production of plastics, natural wood or silk - and all this will cost several times cheaper than now.
A project by Bill Gates and Jay Keesling to create an organism that would produce a powerful anti-malarial drug.
In 2004, Kiesling, a chemical engineer at Berkeley, convinced the Bill and Melinda Gates Foundation to give $42 million to his project. Kisling started with ordinary baker's yeast. Evolution has “programmed” yeast to process sugar and produce various biochemicals. To this already functioning organism, Kisling added a genetic program developed in the laboratory, composed of 12 new genes. She changed the metabolism of yeast, and they began to produce artemisinin.
The medical aspect of SynBio also fascinated Californian scientists Christopher Voight and Christina Smolke. Now they are on early stages development of microbes that, circulating along with the bloodstream throughout the human body, would find cancerous tumors. These microbes could be equipped with biodevices, one of which would detect low levels oxygen characteristic of a tumor, another would penetrate the cells, a third would produce a toxin that kills these cells, and a fourth would remain “on duty” in case the cancer returns. Over time, these sentinel cells could monitor and regulate blood levels of various vital substances, including glucose and cholesterol.
the loudest projects should be those of the same Craig Venter and George Church. They set out to create a self-sustaining, highly efficient organism that converts sunlight directly into clean biofuel. “The most sustainable source of energy is sunlight, and the most affordable products are petroleum products that can be transported by pipeline,” Church says. “So I will strive to create a long-lasting system of plants that synthesize pure chemicals - octane, diesel, etc. - and can deliver them directly to the pipes without additional purification.”
his “brainchildren” will have to convert sunlight directly into biofuel with minimal damage to the environment and zero greenhouse gas emissions. These organisms, he says, “will replace the petrochemical industry, most food, and will participate in soil bioremediation and the generation of clean energy.”
Andy has already constructed his first synthetic virus, modeled after the well-studied natural T7 virus. Unlike T7, the new virus, called T7.1, was freed from unnecessary complexity. Although its code is only a rough copy of nature's creation, T7.1 nevertheless behaves like a virus, infecting bacterial cells and reproducing within them.
31. Viruses for the brain and "addiction" to antiviruses - our bright future?
(http://specnazspn.livejournal.com/221640.html)
In the near future, hackers will be able to hack not only our computers, but also our brains. Malicious programs that are affecting computer owners today mobile devices, in the near future will become real biological weapons. This opinion is shared by experts in the field of synthetic biology, the newest trend in modern genetics.
Synthetic biology is the programming of life. Cells are living computers, and DNA is a programming language.” Andrew Hessel
Biocybernetics will make it possible to program viruses and bacteria in such a way that, once they enter the human brain, they will become conductors of someone else’s will.
32. Synthetic biology is sneaking into food
Synthetic biology, or synbio for short, is science fiction brought to life. While conventional biotechnology deals with inserting a gene from one organism into another (resulting in GMOs), synbio deals with things like inserting machine-generated DNA sequences into living cells, i.e., creating new organisms altogether. This technology made a significant breakthrough: a company called Evolva managed to create a compound called vanillin, which, unlike vanilla, grew not on a vine but on synthetic yeast.
So Evolva and its magical vanillin “will be the first major synthetic biology nutritional supplement to hit supermarkets,” Nature reports. And we should expect more:
“This product will be a shift for an industry that has typically focused on synthesizing drugs and commodities such as biofuels and rubber. Now, synthetic biology companies are turning to "clean reagents": food and flavor ingredients that command high prices for small quantities. These products will take less time and money to obtain and will be much less dangerous, says Goldsmith."
The term "synthetic biology" was first used in 1980 by Barbara Hobom to describe a bacterium that had been genetically modified using recombinant DNA technology. The term was then coined again in 2000 by Eric Kool and other speakers at the annual meeting of the American Chemical Society in San Francisco. It has been used to describe the synthesis of artificial organic molecules that play a specific role in living systems.
Synthetic biology is an emerging field of biology that aims to design and create new biological systems not found in nature. It deals with adding new properties to existing properties of an organism, for example, bacteria, or modifying existing ones. In the future, it is planned to create individual organisms capable of independent existence and reproduction with strictly specified properties.
There are three main goals of synthetic biology:
- Learn more about life by building it from atoms and molecules, rather than taking it apart, as was done before.
- To make genetic engineering worthy of its name is to transform it from an art into a rigorous discipline that continually evolves, standardizing previous artificial creations and recombining them to make new, more complex living systems that did not previously exist in nature.
- Erase the boundary between living things and machines in order to arrive at truly programmable organisms.
Let's consider the possibilities of synthetic biology for various disciplines. First, biologists will be able to better understand natural biological systems (it is worth remembering the words of Richard Feynman: “What I cannot create, I do not understand”).
Secondly, for chemists, synthetic biology can be thought of as logically: necessary step in synthetic chemistry (synthesis of drugs, new materials, development of more advanced methods of analysis).
Synthetic biology begins its history in 1989, when a team of biologists from Zurich (led by Steven Benner) synthesized DNA containing two artificial nucleotide pairs, in addition to the four known, used by all living organisms on Earth (adenine, guanine, cytosine, thymine - In DNA, in RNA, cytosine is replaced by uracil (Fig. 1).