Introduction to Biotechnology PDF

Introduction I. Introduction I.1. Definitions I.1.1. what is Biotechnology Biotechnology is a multidisciplinary science that combines the potential of a living entity or a part of this entity with different techniques and processes for an economic purpose. Currently, biotechnology is considered...

Introduction I. Introduction I.1. Definitions I.1.1. what is Biotechnology Biotechnology is a multidisciplinary science that combines the potential of a living entity or a part of this entity with different techniques and processes for an economic purpose. Currently, biotechnology is considered among the most emerging technologies, due to the great progress in molecular biology in recent years. I.1.2. Etymological origin of the word Biotechnology The word biotechnology is formed from two terms:  Bio whose Greek origin is Bios which means life. This term evolved to the word Biology at the beginning of the 19th century.  Technology coming from the Greek Technologia. This word appeared in French texts in 1656 to designate "the study of techniques, tools, machines and materials" According to Robert Bud, the term "biotechnology" was used by the Hungarian Károly Ereky in 1919 to describe a technology based on the conversion of organic raw materials into a more useful product in a book entitled "The biotechnology of meat, fat and milk production in large-scale agriculture". Since its appearance, the notion of biotechnology has been defined in various ways. I.1.3. Some Definitions of Biotechnology Giving a definition of biotechnology proves difficult because the field encompasses different scientific and production activities. In addition, biotechnology covers a wide range of biological and technological concepts. However, the absence of a general definition has not slowed the progression of biotechnological development. This is a list of definitions of biotechnology used by organizations from various countries. Most of these definitions encompass both old and new biotechnologies. A. United Nations Definition 1 Introduction  According to Article 2 of the United Nations Convention on Biological Diversity of Rio 1992, biotechnology is defined as: "any technological application using biological systems, living organisms, or their derivatives, to make or modify products or processes for specific use".  According to Article 3 of the Cartagena Protocol, signed in Montreal in January 2000 on the prevention of biotechnological risks, the definition takes into account two distinct aspects: a. Biotechnology as "the application of nucleic acids and in vitro techniques, including recombinant deoxyribonucleic acid (DNA) and direct injection of nucleic acids into cells or organelles, b. The fusion of cells from different taxonomic families, to overcome physiological barriers of reproduction or recombination. These fusions are different from techniques used in traditional selection and breeding. B. FAO Definition (United Nations Food and Agriculture Organization) This organization gives two complementary definitions of biotechnology: "The use of biological processes or living organisms for the production of materials and services beneficial to humanity. Biotechnology involves the use of techniques that increase the economic value of plants and animals and develop microorganisms to act in the environment". "Biotechnology involves the scientifically-based manipulation of living organisms, particularly at the genetic level, to produce new products such as hormones, vaccines, monoclonal antibodies, etc." I.2. The origins of biotechnologies I.2.1. Fermentation It is a natural phenomenon, occurring during the decomposition of organic matter by microorganisms, particularly carbohydrate substrates, without the use of oxygen. During this degradation, there is production of acid, alcohol or gas. These are molecules of interest, which present a benefit for humans. THE FIELDS OF APPLICATION OF FERMENTATION PRODUCTS 2 Introduction  In food industries.  In medical and pharmaceutical applications.  In plastic industries  In mining industries. I.2.2. Genetics Genetics has evolved considerably, it is a branch that brings together several disciplines related to DNA and which contributes to the understanding of the expression of hereditary characters and their regulations. The knowledge of the chemical nature of DNA and then its spatial organization elucidated by Watson and Crick in 1953 opened new perspectives for very fine studies on DNA that fall within the field of molecular biology. I.2.3. Cell culture Cell culture is a process that allows cells to reproduce outside their natural living environment or the organism from which they originate. Scientists have developed the cell culture process to cultivate microorganisms outside their original environment. Several types of cells can be cultured: unicellular microorganisms (bacteria, yeasts, etc.) and cells from multicellular organisms (plants and animals). By cultivating them in the laboratory, we can control their growth and obtain large quantities of microorganisms or useful substances. There are several applications for cell culture, including:  allowing researchers to better understand how cells function;  allowing the testing of medicines, beauty products or even verifying the toxicity of certain chemical products and thus avoiding tests on animals;  allowing the production of certain vaccines whose viruses develop inside cells;  allowing the production of tissues such as new skin for severe burn victims. I.2.4. Recombinant DNA The interest in recombinant DNA began in 1970. It is linked to the discovery of restriction enzymes that cut DNA from any species in a specific manner (at specific sites). From then on, the idea of cutting a DNA molecule and then inserting a fragment from another molecule was conceivable. Thus, fragments of DNA of interest could be cut from a donor organism by restriction enzymes and then inserted directly into the DNA of a host organism in order to 3 Introduction express new characters non-existent in the host through vectors most often represented by bacterial plasmids. In this latter case, the recombinant DNA vectors multiply at the rate of bacterial divisions and we obtain thousands of the recombinant vectors carrying the inserted DNA fragment. We then say that the recombinant vector is cloned. Some recombinant proteins synthesized in yeast cells Saccharomycetes cerevisiae:  Surface protein of hepatitis B virus.  Protein of the malaria parasite.  Platelet growth factor. I.2.5. Transgenesis and genetic engineering It is the artificial transfer by a vector from one organism to another (the host) of another species, with the possibility of replication and expression. There is therefore direct manipulation comparable to surgery on the DNA of microorganisms, plants or animals. Genetic engineering refers to all techniques and processes related to DNA recombination work in the medical field, pharmaceutical research, agriculture, agri-food and the environment. It has become conceivable to create transgenic microorganisms, plants or animals by introducing a foreign DNA sequence called a transgene into a somatic or gamete cell which, after fertilization, would produce a transgenic organism capable of synthesizing, for example, proteins not synthesized in the normal organism of the same species. I.2.6. Enzymatic Engineering Enzymes are catalysts of specific metabolic reactions in living organisms. They possess two important properties: their specificity and their regulation. In general, enzymes are not very stable and are soluble in aqueous phase. Their use, outside the living organism, for industrial purposes as is the case in biotechnology, is very difficult due to their instability and loss of catalytic activity, hence the interest in their immobilization. The immobilization of enzymes is essential either:  For the realization of bioreactors usable on an industrial scale.  For the realization of biosensors in measurement and detection devices. 4 Introduction I.2.7. Bioremediation It is a waste management technique using organisms to remove or neutralize pollutants or contaminants from a contaminated site. Genetic manipulation has made it possible to obtain microorganisms and enzymes specific for the degradation and metabolization of toxic residual products. The use of microorganisms or enzymes constitutes a less polluting technique and more biodegradable waste. Some examples of bioremediation techniques:  Obtaining methane and gas from urban solid waste.  Digestion of plant waste via bacteria, biological purifiers.  Degradation of hydrocarbons by microorganisms. I.2. Evolution of biotechnologies over time  Ancient biotechnology (before 1800) Long history of fermented foods since people began to settle (9000 BC)  Often discovered by accident!  Improvement of flavor and texture  Deliberate contamination by bacteria or fungi (molds)  1866; Louis Pasteur publishes his conclusions on the direct link between yeast and fermenting sugars 1915  Production of baker's yeast: Saccharomyces cerevisiae  Classical biotechnology  Different types of drinks (beer, wine, cider...)  Vinegar, Glycerin, Acetone, Butanol  Lactic acid, Citric acid  Antibiotics  Etc. Chemical transformations to produce therapeutic products Substrate + Microbial Enzyme Product 5 Introduction  Modern biotechnology In 1953, JD Watson and FHC Crick first lifted the veil on the mysteries surrounding DNA as genetic material; by giving a structural model of DNA known as the "Double Helix Model of DNA". I.3. Definition of green, white, and red biotechnologies, etc. The central concept of this section is that biotechnology is nowadays a very broad field of scientific research and the term "biotechnology" encompasses many processes and applications. Many of these uses do not immediately come to mind when the term "biotechnology" is mentioned. This section covers the spectrum of main applications of biotechnology using the color code green biotechnology related to agriculture, red related to medicine, white to industry, etc. (see Fig. 1) Figure 01: Main applications of biotechnology using the color code I.3.1. Red biotechnology 6 Introduction Encompasses all uses of biotechnology related to medicine. Red biotechnology includes the production of vaccines and antibiotics, the development of new drugs, molecular diagnostic techniques, regeneration therapies and the development of genetic engineering to cure diseases through genetic manipulation. Some relevant examples of red biotechnology are cell therapy and regenerative medicine, gene therapy and drugs based on biological molecules such as therapeutic antibodies. I.3.2. White biotechnology / Industry White biotechnology includes all uses of biotechnology related to industrial processes - which is why it is also called "industrial biotechnology". White biotechnology pays particular attention to the design of low-resource consumption processes and products, making them more energy-efficient and less polluting than traditional ones. There are numerous examples of white biotechnology, such as the use of microorganisms in the production of chemicals, the design and production of new materials for daily use (plastics, textiles...) and the development of new sustainable energy sources such as biofuels. I.3.3. Grey biotechnology / Environment Grey biotechnology includes all applications of biotechnology directly related to the environment. These applications can be divided into two main branches: maintenance of biodiversity and removal of contaminants. Regarding the first, it is worth mentioning the application of molecular biology to the genetic analysis of populations and species that are part of ecosystems, their comparison and classification, as well as cloning techniques aimed at preserving species and genome storage technologies. Regarding the removal of pollutants or bioremediation, grey biotechnology uses microorganisms and plants to isolate and eliminate different substances such as heavy metals and hydrocarbons, with the additional possibility of subsequently using these substances or by-products of this activity. I.3.4. Green biotechnology / Agriculture Green biotechnology is focused on agriculture as a field of work. Green biotechnological approaches and applications include the creation of new plant varieties of agricultural interest, the production of bio-fertilizers and bio-pesticides, using in vitro cultures and plant cloning. The first approach is the one that needs to be developed and generate the most interest and social controversy. The production of modified plant varieties is based almost 7 Introduction exclusively on transgenesis, or the introduction of genes of interest from another variety or organism into the plant. Three main objectives are sought using this technology. First, varieties are expected to be resistant to pests and diseases, for example, currently used and commercialized maize varieties resistant to pests such as the European corn borer. Second, the use of transgenic plants aims to develop varieties with improved nutritional properties (for example, higher vitamin content). Finally, transgenesis in plants is also being studied as a means of developing plant varieties that can serve as bio-factories and produce substances of medical, biomedical or industrial interest in quantities that are easy to isolate and purify. I.3.5. Blue biotechnology / Sea Blue biotechnology relies on the exploitation of marine resources to create products and applications of industrial interest. Given the fact that the sea presents the greatest biodiversity, there is potentially a wide range of sectors to benefit from the use of this type of biotechnology. Many blue biotechnology products and applications are still the subject of study and research, although some of them are actually used daily. Undoubtedly, the use of raw materials from the sea represents the most widespread blue biotechnology in many different sectors. These materials, mainly hydrocolloids and gelling agents, are already widely used in food, health, treatment, etc. Medicine and research are other major beneficiaries of the development of blue biotechnology. Some marker molecules from marine organisms are now commonly used in research. Enzymatically active molecules useful in diagnosis and research have also been isolated from marine organisms. Some biomaterials and pharmacological or regenerative agents are produced or studied for their use in these sectors. Finally, sectors such as agriculture and cosmetics are analyzing the potential of blue biotechnology for their future development. I.4. Typical biotechnology products examples I.4.1. Agronomy Sector Numerous transgenic works concern the introduction of genes for resistance to herbicides or insects, and to a lesser extent, to certain viruses and diseases. Associated with a rational use of herbicides and pesticides, these transgenic plants will improve the efficiency of agriculture, while respecting the environment even better. 8 Introduction A. Resistance to insects The bacterium Bacillus thuringiensis constitutes a veritable reservoir of insect resistance genes. Indeed, the different strains of this soil bacterium contain several insecticidal proteins with different modes of action, affecting only certain insects. Each of these proteins is encoded by a single gene, so it is a character easily transferable by genetic engineering. Several teams have obtained tobaccos, potatoes, cottons, tomatoes, and corn resistant to insects’ thanks to this source of genes. In the case of corn, resistance to the European corn borer is conferred by the Cry a gene, commonly called Bt. This gene allows, in corn cells, the production of a protein that transforms into a toxin in the digestive tract of the corn borer. In other animals and humans, this protein is simply digested without any toxic effect. B. Resistance to diseases Viruses, fungi, and bacteria are responsible for significant losses in plant production. However, there is no method for treating diseases caused by viruses in cultivated plants. Through transgenesis, it is possible to obtain plants resistant to viruses. These transgenic plants synthesize proteins that block the multiplication and development of viruses. Thus, it has been possible to obtain zucchini and melons resistant to cucumber mosaic virus. The development of plants resistant to fungi and bacteria is ongoing. C. Resistance to herbicides Glufosinate (Basta or Liberty) and glyphosate (Roundup) are total herbicides that destroy both weeds and cultivated plants. The herbicide resistance genes introduced into a plant prevent the active ingredient from acting on it, transforming the total herbicide into a selective herbicide for this plant. Thus, the herbicide destroys all present weeds while totally respecting the cultivated plant. Moreover, these total herbicides have the property of not being persistent. Many transgenic plants have been developed to obtain tolerance to these herbicides. These include varieties of sugar beet, rapeseed, cotton, corn, potato, and soybean. D. Fruit ripening These are the most advanced results concerning food quality. For melon and tomato, it has been possible to obtain transgenic varieties with delayed ripening. These fruits can be harvested at a more advanced stage of ripening, thus being more flavorful. On the other hand, it results in better preservation and improved transport suitability, reducing losses. Melon is 9 Introduction the first genetically modified fruit obtained by a French research laboratory. A gene capable of blocking ethylene synthesis has been introduced, which slows down ripening. Fruit detachment is delayed and the melon, maintained on the plant, continues to accumulate sugars. I.4.2. Industry Sector Biotechnologies open up numerous perspectives in the fields of industry, by producing new molecules (Molecular Farming) and improving industrial processes and product quality. A. Paper pulps Lignins are one of the major constituents of wood, but they hinder the paper industry which cannot valorize them and must eliminate them by costly and polluting methods. Work conducted by French public research has made it possible to identify the genes involved in lignin synthesis and to develop transgenic poplar varieties, in which the lignin content is greatly reduced. This facilitates the bleaching of paper pulp and thus reduces the impact on the environment. The same type of work has been carried out on eucalyptus. B. Industrial oils They are synthesized from fossil raw materials, whose resources are limited. It is therefore necessary to turn to other renewable resources. Among the many research programs, we can mention the one aimed at obtaining transgenic rapeseed with high erucic or ricinoleic acid content for the production of lubricants, plastics, etc. This strategy should promote the development of biodegradable lubricants and plastics. C. Dyes An original example is the obtaining of colored transgenic cottons through the introduction of a bacterial or plant gene coding for a pigment. This will avoid the use of chemical dyes that are difficult to recycle. I.4.3. Health Sector Genetically modified, tobacco, corn, or potato plants can produce therapeutic molecules or vaccines. The great advantage of producing these molecules is the absence of risks of contamination by viruses pathogenic to humans. 10 Introduction A. Blood products Research conducted in France has already made it possible to produce plasma proteins from transgenic tobacco plants, allowing the obtaining of recombined human hemoglobin. Studies show that it is possible to synthesize human albumin, used in trauma treatment, from tobacco or potato. This albumin should be cheaper than that derived from blood plasma. This new source would allow meeting the increasing needs. B. Vaccines American researchers are working on developing a vaccine banana for humans, preventing cases of gastroenteritis caused by the E. coli bacterium. It would then be conceivable to vaccinate populations in developing countries, the most affected by these bacterial diarrheas, at a low cost. C. Human proteins Work is currently underway to produce proteins or glycoproteins for therapeutic use from soybeans, tobacco, potatoes, rice, or rapeseed. I.5. Industrial domains concerned For sustainable development, enzymatic processes constitute the most interesting and most used "clean" industrial applications:  Textile industry, starch and fecula, beer, pastry and bread-making, wines and fruit juices, degradation of starch into sugars for alcohol production as a solvent.  Food industry additives for improving the nutritional qualities of foods, dairy industry for converting lactose into assimilable sugar, cheese flavors, biosynthetic food flavors, synthetic food colorants),  Animal feed (protein hydrolysis for the production of high-yield flours),  Cosmetics industry (production of cream bases and collagens), paper industry (pulp dissolution, bleaching, viscosity control of starches), tanning processes (removal of hair and fats), fat treatment (hydrolysis of fats and lecithins, esterification, production of solubility agents, bio-detergents, soaps and saponification processes), fine chemistry (pharmaceutical products). 11 Introduction  Traditional fermentation processes: alcoholic fermentation, organic acids (citric acid, acetic acid,...),  Production of antibiotics, production of chemical derivatives, biopolymers, etc. using microorganism cultures.  The use of enzymes and biocatalysts: food processes, chemical substances, chemotherapy, biosensors, medical diagnostic equipment.  The industry of fuels and organic products alternative to petroleum: hydrogen photolysis, biomass digesters for methane production, alcohols (from plant sugars).  Molecular biology and genetic engineering of recombinant DNA (donor DNA, vector DNA or host DNA): use for the synthesis of organic products (chemical products; bio-proteins: synthetic hormones, antibodies, blood factors).  Interferon and monoclonal antibody technologies: development of therapeutics, diagnostic equipment.  Plant cell cultures and single-cell proteins: biomass production, chemical products (steroids, alkaloids, etc.)  Bioremediation for waste treatment and use: wastewater treatment, soil depollution or detoxification (metabolization of pollutants by microorganisms), herbicides, treatment and conversion of by-products from the agri-food industry (cellulose waste, whey from cheese and butter production, animal fats, rendering and animal meals, etc.).  Biological nitrogen fixation processes: reduction of nitrogen fertilizer use for agricultural production, production of ammonia from atmospheric gaseous nitrogen.  Other associated industrial processes: wastewater recycling system; collection, pre- treatment and filtration of drinking water catchments, extraction and purification of mining products, development of reactors without fossil fuel and without polluting chemistry, isolation/concentration and recovery or filtration of catalysts and organisms used in the manufacture of by-products. 12