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Such techniques are extensively used in biotechnology, e. Probe-based technical systems are obtained by immobilising probes to inorganic substances, i. This is also referred to as solid-phase hybridisation.

DNA chips or micro-arrays are intrinsically miniaturised extensions of conventional tests of nucleic acid hybridisation. Micro-arrays are minia- turised solid supports typically a glass slide or grid of single-stranded DNA fragments that can represent all, or a subpopulation of, the genes of an organism. The great advantage of these systems is that they can only require small amounts of resources.

The term genome is used in the more abstract sense to refer to the sum total of the genetic information or DNA of an organism. A typical genome project seeks to determine the complete DNA structure for a given organ- ism and to identify and map all of the genes.

However, the major event in molecular genetics was the elucidation of the human genome sequence in The Human Genome Project cost nearly 3 billion dollars. While there has been much hype concerning the ethical and commer- cial implications of these discoveries, this is only the beginning of the under- standing of the real functional activity within cells, in tissues and in whole organisms. There still exists a vast gulf between our understanding of individual molecular mechanisms and pathways and how they are integrated into an orderly homeostatic system.

While a cell will have only one genome it can have many proteomes. The DNA alphabet is composed of four bases, while proteins in contrast are constructed from approximately 20 amino acids.

While the genes through transcription determine the sequence of amino acids in a protein, it is not totally clear what the protein does and how it inter- acts with other proteins. The proteome is extremely dynamic, and minor alterations in the external or internal environment can modify proteome function. Understanding proteomics should give a better holistic view of cellular metabolism. The two areas of genomics and proteomics must have a strong synergistic relationship.

Such molecular medicine could well be one of the most remarkable achievements of biotechnology of this century. The ability to clone DNA or manipulate genes and to obtain successful expression in an organism is nowadays a core technology of quite unparal- leled importance in modern bioscience and biotechnology.

The expression and acceptance of genetic engineering in the context of biotechnology, where novel gene pools can be created and expressed in large quantities, will offer outstanding opportunities for the well-being of humanity. An antisense gene can be constructed by reversing the nucleotide sequence of the gene. Antisense technology was used in transgenic plants to control ripening — the FlavrSavr tomato.

The antisense technology can silence genes using double-stranded complementary synthetic oligonu- cleotides. This technology has been extensively practised in transgenic organisms and in gene therapy studies. RNA interference A central feature of modern molecular biology has been the transcription and translation of the RNA molecule.

The molecules were viewed as simple carriers of messages and fetchers of materials i. In the last decade it has become apparent that the genome produces vast numbers of RNAs with functions other than making proteins. These miRNAs have been shown to inhibit mRNA and prevent translation of large numbers of messages at a time, and have been shown to be deregulated in several diseases. The naturally occurring form of post-translational interference of gene activity within a cell is now being extensively studied worldwide and increasingly being viewed as a possible new therapeutic class.

At present, interference RNAs RNAi are a most valuable basic research tool while their therapeutic potential is being extensively explored. How can siRNA compounds be delivered to their cellular targets? Current patent applications with RNAi are almost exclusively related to technical invention, and complex patent applications are now arriving dealing with nucleotide insertion see later.

Systems biology is a new discipline, which examines how these components interact and form networks and, furthermore, how such networks generate whole-cell functions and ulti- mately the organism. Systems biology does not concentrate on individual genes and proteins, one at a time, but encompasses the behaviour and relationships of all components in a particular biological system from a functional perspective.

Biological systems are primarily composed of infor- mation genes, their encoded products and the regulatory components con- trolling the expression of these genes. Systems biology endeavours to interpret complex biological systems by integrating all levels of functional information into a cohesive model.

Consequently, this new approach of systems biology represents a paradigm shift from previous molecular biology thinking. A widely adopted approach to systems biology incorporates bottom-up data collection from all the biological networks Table 3. Systems analysis has been utilised historically in many areas of biol- ogy, including ecology, developmental biology and immunology.

However, the genomics and proteomics revolution has catapulted molecular biology into the exciting realms of systems biology. The impact of systems biology on human disease and other biological areas will be highlighted in later chapters.

In contrast, others considered that newly synthesised organisms with their additional genetic material would not be able to compete with the normal strains present in nature. The present views of gene manipulation studies are becoming more moderate as experiments have shown that this work can proceed within a strict safety code when required, involving physical and biological containment of the organism.

The standards of containment enforced in the early years of recom- binant DNA studies were unnecessarily restrictive, and there has been a steady relaxation of the regulations governing much of the routine genetic engineering activities. However, for many types of study, particularly with pathogenic microorganisms, the standards will remain stringent. Thus, for strict physical containment laboratories involved in this type of study must have highly skilled personnel and correct physical containment equipment, for example negative-pressure laboratories, autoclaves, safety cabinets, etc.

Biological containment can be achieved or enhanced by selecting non- pathogenic organisms as the cloning agents of foreign DNA, or by the deliberate genetic manipulation of a microorganism to reduce the proba- bility of survival and propagation in the environment. Escherichia coli, a bac- terium that is extremely prevalent in the intestinal tracts of warm-blooded and cold-blooded animals as well as in humans, is the most widely used cloning agent.

To offset the risk of this cloning agent becoming a danger in the environment a special strain of E. This strain can only grow under special laboratory conditions and there is no possibility that it can constitute a biohazard if it escapes out of the laboratory. The deliberate releasing of genetically manipulated organisms to the environment is discussed in a later chapter.

Biochemical engineering covers the design of vessels and apparatus suitable for performing such biochemical reactions or transformations. The very beginnings of fermentation technology, or as it is now bet- ter recognised, bioprocess technology, were derived in part from the use of microorganisms for the production of foods such as cheeses, yoghurts, sauerkraut, fermented pickles and sausages, soya sauce and other Oriental products, and beverages such as beers, wines and derived spirits Table 4.

In many cases, the present-day production processes for such products are still remarkably similar. These forms of bioprocessing were long viewed as arts or crafts, but are now increasingly subjected to the full array of mod- ern science and technology. Successful bioprocessing will only occur when all the essential factors are brought together.

The desired product will usually be present in a Bioconversions give higher yields. Biological systems operate at lower Need to provide, handle and dispose of large temperatures, near neutral pH, etc. Much greater specificity of catalytic reaction. Bioprocesses are usually extremely slow when Can achieve exclusive production of an compared with conventional chemical processes. All of these products now command large industrial markets and are essential to modern society Table 4.

More recently, bioprocess technology is increasingly using cells derived from higher plants and animals to produce many important products. The future market growth of these bioproducts is largely assured because, with limited exceptions, most cannot be produced economi- cally by other chemical processes. It will also be possible to make further economies in production by genetically engineering organisms to higher or unique productivities and utilising new technological advances in process- ing.

The advantages of producing organic products by biological as opposed to purely chemical methods are listed in Table 4. The product formation stages in bioprocess technology are essentially very similar no matter what organism is selected, what medium is used or what product formed. Bioprocessing in its many forms is catalysed within each respective cel- lular system by a large number of intracellular biochemical reactions.

Sub- strates derived from the medium are converted into primary and secondary products, intra- and extracellular macromolecules, and into biomass com- ponents such as DNA, RNA, proteins and carbohydrates Fig. These reactions will be dependent on the physical and chemical param- eters that exist in their immediate environments.

In its simplest form, the bioprocess can be seen as just the mixing of microorganisms with a nutrient broth and allowing the components to react, e. All biotechnological processes are essentially performed within contain- ment systems or bioreactors. Large numbers of cells are invariably involved in these processes and the bioreactor ensures their close involvement with the correct medium and conditions for growth and product formation. It also should restrict the release of the cells into the environment.

A main function of a bioreactor is to minimise the cost of producing a product or service. Examples of the diverse product categories produced industrially in bioreactors are given in Table 4.

Growth will be dependent on the availability and transport of necessary nutrients to the cell and subsequent uptake, and on environmental param- eters such as temperature, pH and aeration being optimally maintained.

Dou- bling time td refers to the period of time required for the doubling in the weight of biomass while generation g time relates to the period nec- essary for the doubling of cell numbers. Average doubling times increase with increasing cell size Table 4. It is now possible to develop mathematical equations to describe the essential features of organism growth in bioreactors.

A simple relation- ship exists between growth and utilisation of substrate. In normal practice an organism will seldom have totally ideal condi- tions for unlimited growth; rather, growth will be dependent on a limiting factor, for example, an essential nutrient.

As the concentration of this factor drops, so also will the growth potential of the organism decrease. In biotechnological processes there are three main ways of growing microorganisms in the bioreactor: batch, fed-batch or continuous. Within the bioreactor reactions can occur with static or agitated cultures, in the presence or absence of oxygen, and in liquid or low-moisture conditions e. The microorganisms can be free or can be attached to surfaces by immobilisation or by natural adherence.

The nutrient envi- ronment within the bioreactor is continuously changing and, thus, in turn, enforcing changes to cell metabolism. Eventually, cell multiplication ceases because of exhaustion or limitation of nutrient s and accumulation of toxic excreted waste products.

The complex nature of batch growth of microorganisms is shown in Fig. The initial lag phase is a time of no apparent growth, but actual biochemical analyses show metabolic turnover indicating that the cells are in the process of adapting to the environmental conditions and that new growth will eventually begin.

There is then a transient acceleration phase as the inoculum begins to grow to be quickly followed by the exponential phase. In the exponential phase, microbial growth proceeds at the maxi- mum possible rate for that organism with nutrients in excess, ideal envi- ronmental parameters and growth inhibitors absent.

However, in batch cultivations exponential growth is of limited duration and as nutrient conditions change growth rate decreases entering the deceleration phase to Fig. Most biotechnological batch processes are stopped before this stage because of decreasing metabolism and cell lysis.

Many important products such as antibiotics are optimally formed during the stationary phase of the growth cycle in batch cultivation.

However, there are means of prolonging the life of a batch culture and thus increasing the yield by various substrate feed methods: 1 by the gradual addition of concentrated components of the nutrient, e.

This practice depends on fresh medium entering a batch system at the exponential phase of growth with a corresponding with- drawal of medium plus cells. Continuous methods of cultivation will permit organisms to grow under steady state unchanging conditions, in which growth occurs at a constant rate and in a constant environment. In a com- pletely mixed continuous culture system sterile medium is passed into the bioreactor Fig. Factors such as pH and the concentrations of nutrients and metabolic products, which inevitably change during batch cultivation, can be held near constant in continu- ous cultivations.

Products may be required only in relatively small quantities at any given time. Market needs may be intermittent. Shelf-life of certain products is short. High product concentration is required in broth to optimise downstream processing operations. Some metabolic products are produced only during the stationary phase of the growth cycle. Instability of some production strains requires their regular renewal. Continuous processes can offer many technical difficulties.

Table 4. Film Various types of bioreactors; trickling Waste-water treatment, monolayer filter, rotating disc, packed bed, culture animal cells ; bacterial sponge reactor, rotating tube. Continuous Proper control of reaction; excellent Few cases of application in industrial one-stage role for kinetic and regulatory scale; production of single-cell protein; homogeneous studies; higher costs for waste-water treatment.

However, for many reasons Table 4. The full range of cultivation methods for microorganisms is shown in Table 4. Applied microbial genetics An essential aspect of microbial biotechnology is concerned with deriving new and improved strains of producer microorganisms. Selection and screening activities remain a major part of biotechnological programmes. Screening is the use of procedures to allow the detection and isolation of only those microorganisms or metabolites of interest among a large population.

Producer microorganisms require to be preserved with minimum degeneration of genetic qualities, and are normally preserved on agar medium, by reduced metabolism, drying, freeze-drying or by ultra-low tem- peratures. Mutational programmes are primarily aimed at strain improvement, and mutagens available include ultraviolet and ionising radiation and a wide range of chemical mutagens.

Hybridisation between microorganisms is essentially a procedure that facilitates the recombina- tion of genetic material between microorganisms and can be expressed by sexual and parasexual mechanisms.

Protoplast fusion techniques have been used with many microbial cells as well as with plant and animal cells. Fusion rates can be greatly increased by means of the fusogen polyethylene glycol. The basic technology is described else- where.

Recombinant bacteria and fungi are used extensively in certain industrial enzyme productions, while mammalian cell lines are increas- ingly used for recombinant protein production. Gene manipulations are now widely used to a improve yield and quality of existing biomolecules e. For each biotechnology process the most suitable containment system must be designed to give the cor- rect environment for optimising the growth and metabolic activity of the biocatalyst. Bioreactors range from simple stirred or non-stirred open con- tainers to complex aseptic integrated systems involving varying levels of advanced computer control Fig.

Bioreactors occur in two distinct types Fig. This type of process involves considerable chal- lenges on the part of engineering construction and operation. Source: a and b reproduced by permission from Kristiansen and Chamberlain, In all forms of fermentation the ultimate aim is to ensure that all parts of the system are subject to the same conditions.

Within the bioreactor the microorganisms are suspended in the aqueous nutrient medium con- taining the necessary substrates for growth of the organism and required product formation. All nutrients, including oxygen, must be provided to diffuse into each cell and waste products such as heat, carbon dioxide and waste metabolites removed.

All materials coming into contact with the solutions entering the bioreactor or the actual organism culture must be corrosion resistant to prevent trace metal contamination of the process. The materials must be non-toxic so that slight dissolution of the material or components does not inhibit culture growth.

The materials of the bioreactor must withstand repeated sterilisation with high-pressure steam. The bioreactor stirrer system, entry ports and end plates must be easily machinable and sufficiently rigid not to be deformed or broken under mechanical stress. Visual inspection of the medium and culture is advantageous, transparent materials should be used wherever possible.

It is here that the skills of the process or biochemical engineer and the micro- biologist must come together. Fermentation reactions are multiphase, involving a gas phase contain- ing N2 , O2 and CO2 , one or more liquid phases aqueous medium and liquid substrate and solid microphase the microorganisms and possibly solid substrates. All phases must be kept in close contact to achieve rapid mass and heat transfer.

In a perfectly mixed bioreactor all reactants enter- ing the system must be immediately mixed and uniformly distributed to ensure homogeneity inside the reactor. To achieve optimisation of the bioreactor system, the following operat- ing guidelines must be closely adhered to: 1 the bioreactor should be designed to exclude entrance of contaminating organisms as well as containing the desired organisms 2 the culture volume should remain constant, i.

The standard of materials used in the construction of sophisticated fermenters is important Table 4. Fermentation technologists seek to achieve a maximisation of culture potential by accurate control of the bioreactor environment.

But still there is a great lack of true understanding of just what environmental conditions will produce an optimal yield of organism or product. On the other hand their ability to produce complicated proteins is increased. For successful commercial operation of these bioprocesses quantitative description of the cellular processes is an essential prerequisite: the two most relevant aspects, yield and produc- tivity, are quantitative measures that will indicate how the cells convert the substrate into the product.

To understand and control a fermentation process it is necessary to know the state of the process over a small time increment and, further, to know how the organism responds to a set of measurable environmental conditions. Process optimisation requires accurate and rapid feedback con- trol.

In the future, the computer will be an integral part of most bioreactor systems. However, there is a lack of good sensor probes that will allow on- line analysis to be made on the chemical components of the fermentation process.

A large worldwide market exists for the development of new rapid methods monitoring the many reactions within a bioreactor. In particular, the greatest need is for innovatory microelectronic designs. When endeavouring to improve existing process operations or design it is often advisable to set up mathematical models of the overall system.

A model is a set of relationships between the variables in the system being studied. The actual variables involved can be extensive but will include any parameter that is of importance for the process and can include: pH, temperature, substrate concentration, agitation, feed rate, etc.

The original fermentation system was a shallow tank agitated or stirred by manpower. From this has developed the basic aeration tower system, which now dominates industrial usage. As fermentation systems were further developed, two design solutions to the problems of aeration and agitation have been implemented. The vertical shaft of the CSTR will carry one or more impellers depend- ing on size of the bioreactor Fig. A broad range of impellers have been investigated for stirring and creating homogeneous conditions within the bioreactor.

The impellers are usually spaced at intervals equivalent to one tank diameter along the shaft to avoid a swirling type of liquid movement. The function of the impellers is to create agitation or mixing within the bioreactor and to facilitate aera- tion.

The primary function of agitation is to suspend the cells and nutrient evenly throughout the medium, to ensure that the nutrients, including oxygen, are available to the cells and to allow heat transfer.

Most indus- trial organisms are aerobic and, in most fermentations, the organisms will exhibit a high oxygen demand. Since oxygen is sparingly soluble in aqueous solutions solubility of CO2 in water is about 30 times higher than that of O2 aerobic fermentations can only be supported by vigorous and constant aeration of the medium. Thus stirring has been replaced by pumping, which may be mechanical or pneumatic, as in the case of the airlift bioreactor.

The centrally stirred tank reactor consists of a cylindrical vessel with a motor-driven central shaft that supports one or several agitators with the shaft entering either through the top or the bottom of the vessels. The aspect ratio i. Sterile air is sparged into the bioreactor liquid below the bottom impeller by way of a perforated ring sparger.

The speed of the impellors will be related to the degree of fragility of the cells. Mam- malian cells are extremely fragile when compared to most microorganisms.

In a great many of the high-value processes the bioreactors will be operated in a batch manner under aseptic monoculture. The bioreactors can range from c. Throughout such operations it is imperative to maintain aseptic conditions to ensure the success of the process.

Bioreactors are normally sterilised prior to inocula- tion and contamination must be avoided during all subsequent operations. If contamination occurs during the cultivation this will invariably lead to process failure since more often than not the contaminant can outgrow the participating monoculture. The number of distinct types of bioreactor is quite limited when mea- sured against the wide range of production processes and the varied biolog- ical systems involved.

Large amounts of organic waste waters from domestic and industrial sources are routinely treated in aerobic and anaerobic systems. Activated sludge processes are widely used for the oxidative treatment of sewage and other liquid wastes Fig. Such processes use batch or continuous agitated bioreactor systems to increase the entrainment of air to optimise oxidative breakdown of the organic material.

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