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

Industrial Biotechnology
Lecturer Dr. Kamal E. M. Elkahlout
Assistant Prof. of Biotechnology
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CHAPTER 1
INTRODUCTION
Scope of Biotechnology & Industrial
Biotechnology
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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.
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• 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).
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• 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.
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• 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.
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• 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.
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• 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.
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• 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.
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• 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.
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• 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 carboncontaining 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.
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• 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.
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• 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.
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• 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.
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• 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).
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• 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
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• 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.
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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.
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• 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);
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• 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.
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• ‘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.
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• 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.
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• 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.
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• 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.
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• 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.
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• 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.
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• 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.
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• 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,
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• 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.
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• 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).”
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• 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.
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• 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.
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• 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.
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• 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.
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• 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.
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• 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.
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