Industrial Biotechnology

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Dec 6, 2012 (4 years and 9 months ago)

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Industrial Biotechnology

Lecturer Dr.
Kamal

E. M.
Elkahlout

Assistant Prof. of
Biotechnology

1

CHAPTER 1

INTRODUCTION

Scope of Biotechnology & Industrial
Biotechnology

2

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


N
ucleic
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).

4


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.


T
he
microorganisms involved or their products
are
very valuable.


T
he
scale is
large.
F
ermentors

as large as 50,000
liters or larger.

5


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.

7


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
.

8


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 carbon
-
containing compounds
or catabolism
.


W
hen
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.


23


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.

25


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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