1. Industrial Biotechnology
Lecturer Dr. Kamal E. M. Elkahlout
Assistant Prof. of Biotechnology

2. Scope of Biotechnology & Industrial Biotechnology
CHAPTER 1 INTRODUCTION
Scope of Biotechnology & Industrial Biotechnology

3. NATURE OF BIOTECHNOLOGY AND INDUSTRIAL MICROBIOLOGY
United Nations Conference on Biological Diversity (the Earth Summit) at the meeting held in Rio de Janeiro, Brazil in 1992 defined Biotechnology as
Any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use.
Some of these include the use of microorganisms to make
the antibiotic, penicillin or the dairy product, yoghurt;
the use of microorganisms to produce amino acids or enzymes are also examples of biotechnology.

4. All aspects of biological manipulations now have molecular biology dimensions.
Traditional biotechnology
Nucleic acid biotechnology or molecular biotech.
Industrial microbiology the study of the large-scale and profit motivated production of microorganisms or their products for direct use, or as inputs in the manufacture of other goods.
E.g., yeast produced for direct consumption (food or , animal feed), bread-making, ethanol production (alcoholic beverages, manufacture of perfumes, pharmaceuticals, etc).

5. Industrial biotechnology is a branch of biotechnology and includes the traditional and nucleic acid aspects.
Characteristics of Industrial Biotechnology:
The immediate motivation is profit and the generation of wealth.
The microorganisms involved or their products are very valuable.
The scale is large. Fermentors as large as 50,000 liters or larger.

6. Industrial Biotechnology has Multi-disciplinary or Team-work Nature.
In a modern industrial biotechnology organization teams may include in addition to microbiologist chemical or production engineers, biochemists, economists, lawyers, marketing experts, and other high-level functionaries.
They all cooperate to achieve the purpose of the firm which is the generation of profit or wealth.

7. In the team work, the microbiologist has a central and key role in his organization.
Some of his functions include:
a. the selection of the organism to be used in the processes;
b. the choice of the medium of growth of the organism;
c. the determination of the environmental conditions for the organism’s optimum productivity i.e., pH, temperature, aeration, etc.
d. during the actual production the microbiologist must monitor the process for the absence of contaminants, and participate in quality control to ensure uniformity of quality in the products;
e. the proper custody of the organisms usually in a culture collection, so that their desirable properties are retained;
f. the improvement of the performance of the microorganisms by genetic manipulation or by medium reconstitution.

8. Obsolescence in Industrial Biotechnology
As profit is the motivating factor in the pursuit of industrial microbiology, less efficient methods are discarded as better ones are discovered.
Indeed a microbiological method may be discarded entirely in favor of a cheaper chemical method.
This was the case with ethanol for example which up till about 1930 was produced by fermentation.
When cheaper chemical methods using petroleum as the substrate became available in about 1930, fermentation ethanol was virtually abandoned.
From the mid-1970s the price of petroleum has climbed steeply. It has once again become profitable to produce ethanol by fermentation.
Several countries notably Brazil, India and the United States have officially announced the production of ethanol by fermentation for blending into gasoline as gasohol.

9. Free Communication of Procedures in Industrial Biotechnology
Many procedures employed in industrial biotechnology do not become public property for a long time because the companies which discover them either keep them secret, or else patent them.
The undisclosed methods are usually blandly described as ‘know-how’.
The reason for the secrecy is obvious and is designed to keep the owner of the secret one step ahead of his/her competitors.
For this reason, industrial microbiology textbooks often lag behind in describing methods employed in industry.

10. Meaning of FERMENTATION word in industrial biotechnology
Fermentation from the Latin verb fevere, which means to boil.
It originated from the fact that early at the start of wine fermentation gas bubbles are released continuously to the surface giving the impression of boiling.
Fermentation has three different meanings.

11. The first meaning relates to microbial physiology.
It is defined as the type of metabolism of a carbon source in which energy is generated by substrate level phosphorylation and in which organic molecules function as the final electron acceptor (or as acceptors of the reducing equivalents) generated during the break-down of carbon-containing compounds or catabolism.
When the final acceptor is an inorganic compound the process is called respiration.
Respiration is referred to as aerobic if the final acceptor is oxygen and anaerobic when it is some other inorganic compound outside oxygen e.g sulphate or nitrate.

12. The second usage is in industrial biotechnology.
It is any process in which micro-organisms are grown on a large scale, even if the final electron acceptor is not an organic compound (i.e. even if the growth is carried out under aerobic conditions).
Thus, the production of penicillin, and the growth of yeast cells which are both highly aerobic, and the production of ethanol or alcoholic beverages which are fermentations in the physiological sense, are all referred to as fermentations.

13. The third usage concerns food.
A fermented food is one, the processing of which microorganisms play a major part.
Microorganisms determine the nature of the food through producing the flavor components as well deciding the general character of the food, but microorganisms form only a small portion of the finished product by weight.
Foods such as cheese, bread, and yoghurt are fermented foods.

14. ORGANIZATIONAL SET-UP IN AN INDUSTRIAL BIOTECHNOLOGY ESTABLISHMENT
The organization of a fermentation industrial establishment will vary from one firm to another and will depend on what is being produced.
Nevertheless the diagram in Fig. 1.1 represents in general terms the set-up in a fermentation industry.
The culture usually comes from the firm’s culture collection but may have been sourced originally from a public culture collection and linked to a patent.
Or itmay have been isolated ab initio by the firm from soil, the air, the sea, or some other natural body.

16. The nutrients formulated in the medium are compounded from various raw materials, sometimes after appropriate preparation or modification including saccharification as in the case of complex carbohydrates such as starch or cellulose.
An inoculum is first prepared usually from a lyophilized vial whose purity must be checked on an agar plate.
The organism is then grown in shake flasks of increasing volumes until about 10% of the volume of the pilot fermentor is attained.
It is then introduced into pilot fermentor(s) before final transfer into the production fermentor(s) (Fig. 1.2).

18. The extraction procedure depends on the nature of the end product.
The methods are obviously different depending on whether the organism itself, or its metabolic product is the desired commodity.
If the product is the required material the procedure will be dictated by its chemical nature.
Quality control must be carried out regularly to ensure that the right material is being produced.
Sterility is important in industrial microbiology processes and is maintained by various means, including the use of steam, filtration or by chemicals.
Air, water, and steam and other services must be supplied and appropriately treated before use.
The wastes generated in the industrial processes must also be disposed

19. Packaging and sales are at the tail end, but are by no means the least important.
Indeed they are about the most important because they are the points of contact with the consumer for whose satisfaction all the trouble was taken in the first instance.

20. PATENTS AND INTELLECTUAL PROPERTY RIGHTS IN INDUSTRIAL MICROBIOLOGY AND BIOTECHNOLOGY
Patent or intellectual property laws, which have two aims.
First, they are intended to induce an inventor to disclose something of his/her invention.
Second, patents ensure that an invention is not exploited without some reward to the inventor for his/her innovation; anyone wishing to use a patented invention would have to pay the patentee for its use.

21. The prerequisite for the patentability of inventions
The claimed invention must be new, useful and unobvious from what is already known in ‘the prior art’ or in the ‘state of the art’.
For most patent laws an invention is patentable:
a. if it is new, results from inventive activity and is capable of industrial application,
b. if it constitutes an improvement upon a patented invention, and is capable of
industrial application.
For the purposes of the above:
a. an invention is new if it does not form part of the state of the art (i.e., it is not part of the existing body of knowledge);

22. b. an invention results from inventive activity if it does not obviously follow from the state of the art, either as to the method, the application, the combination of methods, or the product which is concerns, or as to the industrial result it produces, and
c. an invention is capable of industrial application if it can be manufactured or used in any kind of industry, including agriculture.

23. ‘the art’ means field of knowledge to which an invention relates.
‘the state of the art’ means everything concerning that art or field of knowledge which has been made available to the public anywhere and at any time, by means of a written or oral description, or in any other way, before the date of the filing of the patent application.
Principles and discoveries of a scientific nature are not necessarily inventions for the purposes of patent laws.

24. Patent laws of different countries will show that differ only in minor details.
For example patents are valid in the UK and some other countries for a period of 20 years whereas they are valid in the United States for 17 years.
International laws have helped to bridge some of the differences among the patent practices of various countries.
The Paris Convention for the protection of Industrial Property provides that each country guarantees to the citizens of other countries the same rights in patent matters as their own citizens.
It guarantees the right of priority in case of dispute.

25. Once an applicant has filed a patent in one of the member countries on a particular invention, he may within a certain time period apply for protection in all the other member countries.
The latter application will then be regarded as having been filed on the same day as in the country of the first application.
Another international treaty signed in Washington, DC came into effect on 1 June, 1968.
This latter treaty, the Patent Cooperation Treaty, facilitates the filing of patent applications in different countries by providing standard formats among other things.

26. A wide range of microbiological inventions are generally recognized as patentable.
Vaccines, bacterial insecticides & mycoherbicides.
Micro-organisms by themselves are not patentable, except when they are used as part of a ‘useful’ process.
On 16 June 1980, the United States Court of Customs and Patent Appeals ruled that “a live human-made micro-organism is patentable”.
Dr. Ananda Chakrabarty then an employee of General Electric Company had introduced into a bacterium of the genus Pseudomonas two plasmids which enabled the new bacterium to degrade multiple components of crude oil.
This single bacterium rather than a mixture of several would then be used for cleaning up oil spills.

27. Claims to the invention were on three grounds.
a. Process claims for the method of producing the bacteria
b. Claims for an inoculum comprising an inert carrier and the bacterium
c. Claims to the bacteria themselves.
The first two were easily accepted by the lower court but the third was not accepted on the grounds that
(i) the organisms are products of nature and (ii) that as living things they are not patentable.
As had been said earlier the Appeals Court reversed the earlier judgment of the lower court and established the patentability of organisms imbued with new properties through genetic engineering.

28. A study of the transcript of the decision of the Appeals Court and other patents highlights a number of points about the patentability of microorganisms.
First, microorganisms by themselves are not patentable, being ‘products of nature’ and ‘living things’.
However they are patentable as part of a useful ‘process’ i.e. when they are included along with a chemical or an inert material with which jointly they fulfill a useful purpose.
In other words it is the organism-inert material complex which is patented, not the organism itself.

29. An example is a US patent dealing with a bacterium which kills mosquito larva granted to Dr L J Goldberg in 1979, and which reads thus in part:
What is claimed is:
A bacterial larvicide active against mosquito-like larvae comprising:
a. an effective larva-killing concentration of spores of the pure biological strain of Bacillus thuringiensis var. WHO/CCBC 1897 as an active agent; and
b. a carrier.

30. It is the combination of the bacterial larvicide and the carrier which produced a unique patentable material, not the larvicide by itself.
In this regard, when for example, a new antibiotic is patented, the organism producing it forms part of the useful process by which the antibiotic is produced.
Second, a new organism produced by genetic engineering constitutes a ‘manufacture’ or ‘composition of matter’.
The Appeals Court made it quite clear that such an organism was different from a newly discovered mineral, and from Einstein’s law, or Newton’s law which are not patentable since they already existed in nature.
Today most countries including those of the European Economic Community accept that the following are patentable:
the creation of new plasmid vectors,

31. isolation of new DNA restriction enzymes, isolation of new DNA-joining enzymes or ligases,
creation of new recombinant DNA,
creation of new genetically modified cells,
means of introducing recombinant DNA into a host cell,
creation of new transformed host cells containing recombinant DNA,
a process for preparing new or known useful products with the aid of transformed cells, and
novel cloning processes.
Patents resulting from the above were in general regarded as process, not substance, patents.

32. The current US law specifically defines biotechnological inventions and their patentability as follows:
“For purposes of (this) paragraph …. the term ‘biotechnological process’ means:
(A) a process of genetically altering or otherwise inducing a single- or multi-celled organism to-
(i) express an exogenous nucleotide sequence,
(ii) inhibit, eliminate, augment, or alter expression of an endogenous nucleotide sequence, or
(iii) express a specific physiological characteristic not naturally associated with said organism;
(B) cell fusion procedures yielding a cell line that expresses a specific protein, such as a monoclonal antibody; and
(C) a method of using a product produced by a process defined by subparagraph (A) or
(B), or a combination of subparagraphs (A) and (B).”

33. Third, the patenting of a microbiological process places on the patentee the obligation of depositing the culture in a recognized culture collection.
The larvicidal bacterium, Bacillus thuringiensis, just mentioned, is deposited at the World Health Organization (WHO) International Culture depository at the Ohio State University Columbus Ohio, USA.
The motivation for the deposition of culture in a recognized culture collection is to provide permanence of the culture and ready availability to users of the patent.
The cultures must be pure and are usually deposited in lyophilized vials.

34. The deposition of culture solves the problems of satisfying patent laws created by the nature of microbiology.
In chemical patents the chemicals have to be described fully and no need exists to provide the actual chemical.
In microbiological patents, it is not very helpful to describe on paper how to isolate an organism even assuming that the isolate can be readily obtained, or indeed how the organism looks.
More importantly, it is difficult to readily and accurately recognize a particular organism based on patent descriptions alone.
Finally, since the organism is a part of the input of microbiological processes it must be available to a user of the patent information.

35. Culture collections where patent-related cultures have been deposited include the
American Type Culture Collection, (ATCC), Maryland, USA,
National Collection of Industrial Bacteria (NCIB), Aberdeen, Scotland, UK,
Agricultural Research Service Culture Collection, Northern Regional Research Laboratory (NRRL), Peoria, Illinois, USA.
A fuller list is available in the World Directory of Cultures of Micro-organisms.

36. Fourth, where a microbiologist-inventor is an employee, the patent is usually assigned to the employer, unless some agreement is reached between them to the contrary.
The patent for the oil-consuming Pseudomonas discussed earlier went to General Electric Company, not to its employee.
Fifth, in certain circumstances it may be prudent not to patent the invention at all, but to maintain the discovery as a trade secret.
In cases where the patent can be circumvented by a minor change in the process without an obvious violation of the patent law it would not be wise to patent, but to maintain the procedure as a trade secret.

37. Even if the nature of the compound produced by the microorganisms were not disclosed, it may be possible to discover its composition during the processes of certification which it must undergo in the hands of government analysts.
The decision whether to patent or not must therefore be considered seriously, consulting legal opinion as necessary.
It is for this reason that some patents sometimes leave out minor but vital details.
As much further detail as the patentee is willing to give must therefore be obtained when a patent is being considered seriously for use.

38. In conclusion when all necessary considerations have been taken into account and it is decided to patent an invention, the decision must be pursued with vigor and with adequate degree of secrecy because as one patent law states:
The right to patent in respect of an invention is vested in the statutory inventor, that is to say that person who whether or not he is the true inventor, is the first to file…(the) patent application.