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NATIONAL QUALIFICATIONS CURRICULUM SUPPORT

Biotechnology
Unit 3: Biotechnology
Student Materials

[HIGHER]
Margot McKerrell

The Scottish Qualifications Authority regularly reviews the arrangements for National Qualifications. Users of all NQ support materials, whether published by LT Scotland or others, are reminded that it is their responsibility to check that the support materials correspond to the requirements of the current arrangements.

Acknowledgement Learning and Teaching Scotland gratefully acknowledge this contribution to the National Qualifications support programme for Biotechnology. The advice of Jim Stafford is acknowledged with thanks. First published 2004 Learning and Teaching Scotland 2004 This publication may be reproduced in whole or in part for educational purposes by educational establishments in Scotland provided that no profit accrues at any stage.

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Contents
Introduction Section 1: Biotechnological processing Large-scale cell and tissue culture production Comparison of batch and continuous flow processes Downstream processing Enzymes in production Production of transgenic organisms New breeding techniques Biotechnology applications Agriculture and horticulture Clinical and forensic medicine Environment 4 5 7 12 14 23 28 30 33 34 35 42 43 Advice for problem-solving outcomes 46

Section 2:

Bibliography Appendix:

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INTRODUCTION

Introduction
Biotechnology is the use of micro-organisms, cells or cell products (such as proteins) in industrial and commercial processes. It is sometimes thought that biotechnology is a recent technology but, in fact, some biotechnology processes have been in existence for many centuries micro-organisms are used to produce bread, beer and cheese. In this unit, you will find out about some of the modern biotechnology processes used by industry for a wide range of commercial products. You will also learn about some of the current applications of biotechnology in agriculture, horticulture, clinical medicine and forensic medicine, such as crops with built-in pest resistance, genetically engineered vaccines and the use of monoclonal antibodies in home pregnancy kits. While this is a stand-alone unit, it is highly recommended that you complete the other two units comprising Higher Biotechnology ( Microbiology (Higher) and Microbiological Techniques (Higher)) beforehand, as the underpinning knowledge from the other two units is assumed in this one.

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BIOTECHNOLOGICAL PROCESSING

Section 1
Biotechnological processing
This section introduces you to the many different ways in which products are made using biotechnology processes. Some products, such as antibiotics, are made by micro-organisms grown in large culture vessels called fermenters. Other products are made using microbial enzymes that have been immobilised and contained within a fermenter. Another method is to genetically modify an animal, such as a sheep, so that the product is present in its milk. Industrial biotechnology processes are often illustrated as flow diagrams, showing the stages in the process. A generalised flow diagram for a biotechnological process is shown below:

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The topics covered in this section are: Large-scale cell and tissue culture production Comparison of batch and continuous flow processes Downstream processing Enzymes in production Production of transgenic organisms New breeding techniques.

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Large-scale cell and tissue culture production


Laboratory models Many biotechnology products are made by growing micro-organisms in fermenters or bioreactors, for example penicillin (an antibiotic) and beer are produced in large quantities in fermenters containing as much as 100,000 litres of culture medium. However, before a product is made on such a large scale, the optimum conditions for growth of the micro-organism and formation of the product have to be found. To do this, a laboratory model fermenter is used. This type of fermenter is relatively small, containing only a few litres of culture medium. By carrying out experiments in a laboratory model, the costs involved with making culture media and sterilising it, compared to full-scale production, are reduced. An added benefit of these trials is that, if several laboratory model fermenters are available, many different experiments can be run simultaneously, which reduces the time needed to develop the optimal conditions for a new process in an industrial-scale fermenter. Laboratory model fermenters are used to find the optimum conditions that ensure maximum growth of the micro-organism and maximum product formation. Growth conditions that are investigated include: the range of pH required for maximum growth of the micro-organism the range of temperature needed for maximum growth of the microorganism the quantity of oxygen needed by the micro-organism the nutrient supply needed by the micro-organism. Laboratory models can also be used to investigate: the the the the range of substrates that can be used rate at which nutrients are used up stage when useful products are produced volume of gas consumed by cells or tissues as they grow.

The growth rate of the micro-organism is monitored during these investigations by measuring the mean generation time of the microorganism. This is the time taken for the micro-organism to double in numbers. Also, laboratory fermenters are used to find out the growth phase when useful product is formed.

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BIOTECHNOLOGICAL PROCESSING

Scaling up After laboratory-scale fermenters have been used to work out the optimum growth conditions, the process is next scaled up to a pilot plant fermenter , containing several hundred litres of culture medium. The pilot plant fermenter is used to trial the industrial process and production, as described below. It is used to confirm that the growth conditions that were optimal in the laboratory-scale fermenter are the same when the process is scaled up. The control systems in the pilot plant fermenter are fine tuned to ensure that the optimum temperature, pH and volume of the culture medium are maintained. It is used to ensure that aseptic conditions can be maintained (by ensuring both that contaminant micro-organisms are prevented from entering the fermenter, and that the micro-organisms are contained within the fermenter and are not escaping into the surrounding environment). The pilot plant fermenter is used to study the best way of recovering the product from the culture medium (a process known as downstream processing ). Sufficient product is formed to allow initial safety trials to be carried out. This is to ensure that the product is harmless to the production workers and those who will eventually buy and use it. After the pilot plant systems have been developed, the cost of scaling up to an industrial plant fermenter is worked out. Assuming that it is not prohibitive (and large custom-built fermenters are expensive), the process can be further scaled up to full industrial size. Industrial fermenters Industrial fermenters, or bioreactors, are used for large-scale fermentations. They are used for growing bacteria, fungi and for animal and plant cells. Fermenters are used for the production of a wide range of substances such as vaccines, enzymes, organic acids, amino acids and antibiotics. Industrial fermenters range in capacity from about 20 litres up to 1 million litres. In general, fermenters designed for the growth of animal cells tend to be smaller, due to the high cost of the culture medium needed to grow these cells.

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Fermenters can be designed to operate under aerobic conditions (where oxygen is added) or anaerobic conditions (where oxygen is excluded from the fermentation process). Fermenters designed to work under anaerobic conditions are known as anaerobic digesters. Many aerobic fermentation processes take place in a stirred tank bioreactor (Figure 1). This is a cylindrical vessel made of stainless steel that has mechanisms for stirring the culture medium, monitoring the conditions within the bioreactor, cooling the culture medium and harvesting the product. Figure 1: A typical stirred tank bioreactor

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Some of the features of a typical bioreactor are described below: Stainless steel container Most industrial fermentations take place under sterile conditions and it is essential that the bioreactor is sterilised before it is inoculated, and that sterile conditions are maintained while the fermentation process is taking place. Many bioreactors are made of stainless steel, as this allows them to be sterilised in situ (this means without dismantling them) using saturated steam produced under high pressure. The pressure is monitored using a pressure gauge situated on the outside of the bioreactor. If the pressure should exceed the safety limit, a safety valve is positioned on top of the bioreactor to allow steam and liquid to escape. The internal surface of a bioreactor is smooth, to help maintain aseptic conditions within the bioreactor. Paddles Within the bioreactor is a motor-driven central shaft that supports the paddles. They turn around and create turbulence so that the microorganism and the nutrients are mixed together. The speed at which the paddles are turned depends on the type of micro-organism being cultivated. In general, the stirring rates are higher for bacteria than that for fungi or for animal cells. This is because high stirring rates may damage the fungal mycelium and animal cells. Baffles These are found in bioreactors used for growing bacteria and fungi. There are normally four baffles projecting into the bioreactor from the inner walls. Their function is to prevent swirling and vortexing of the culture medium. Sparger This introduces air into the bioreactor. The air is sterilised before entering the bioreactor by passing through an air filter . The sparger can have a single hole through which the air is introduced, or it can have multiple perforations. The size of the perforations affects the size of the air bubbles. The smaller the air bubble, the more efficiently air is introduced into the bioreactor. Air that is sparged into the bioreactor is used to provide a source of oxygen for the micro-organisms, so that they grow under aerobic conditions.

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It has been found that the use of spargers damages fragile animal cells, so alternative approaches are used in bioreactors designed for animal-cell culture. Anti-foaming agents Aeration and agitation of the culture medium causes foam to be produced, which can interfere with the production process. To prevent this, antifoaming agents are added to the culture medium. Electrically operated probes The temperature and pH of the culture medium are monitored using electrically operated probes. The pH probe is linked to a control panel and, if it detects any changes in the culture medium, the control panel activates a pump that allows alkali or acid to be added to the bioreactor to restore the optimum pH. Water jacket The temperature probe is also linked to the control panel and, if a change in temperature is detected, a pump is activated that allows cooler or warmer water to flow around the water jacket situated around the outer part of the bioreactor. Therefore, the water jacket is involved in the regulation of the temperature of the bioreactor. Pressure gauge As mentioned previously, the pressure gauge is used when the bioreactor is being sterilised under pressure. It is also used when a fermentation is being carried out, as it can indicate the presence of a blockage in any of the pipelines leading out of the bioreactor. Inoculation/sampling port This is a port that is used to introduce the starter culture to the bioreactor. It is also used to remove samples of the culture medium during the fermentation process, to allow analysis such as monitoring the growth phases and finding out how much product has formed. Harvest pipe This is for the collection of culture media from the bioreactor at the end of the fermentation process. Media collected from the bioreactor will contain cells, as well as substances secreted from the cells.

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Comparison of batch and continuous flow processes


Processes occurring in industrial fermenters can either be batch culture or continuous culture. Bacterial cells, fungi and animal cells can be grown in either type of culture. Batch culture In a batch culture , or closed system , sterile nutrients are added to the fermenter and they are brought to the correct operating conditions (temperature, level of oxygen). The cells are inoculated and the fermentation process is allowed to proceed. Nothing is added to or removed from the closed system during this time, except small samples that are removed for analysis (to measure growth rate, concentrations of nutrients remaining and rate of product forming). Figure 2 shows a typical graph of the growth curve of the cells in the fermenter, and the changes in concentration of nutrients and product over the time period of the batch culture. Figure 2: Batch culture

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The cells in the fermenter show a typical growth curve with a lag phase, a log (or exponential) phase, stationary phase and death phase. The cells are growing at their fastest during the log phase, but as they use up the available nutrients and produce waste, the conditions within the fermenter become unfavourable and the cells enter the stationary phase. Batch cultures are often used for the production of secondary metabolites , such as penicillin . A secondary metabolite is one produced during the stationary phase that is a by-product of metabolism, and is not critical for the functioning of the cells. Other secondary metabolites include vitamins and steroids. Advantages of batch culture include the following: It is useful for the production of secondary metabolites. The fermentation time is short, so product can be made relatively quickly. It is easy to control. All stages of growth of the cells is possible.

Continuous flow culture Continuous flow culture is an open system that involves a continuous feed of nutrients (or substrate) into the fermenter and the continuous removal of product from it. Temperature and pH are monitored and any changes are corrected, so that these conditions remain constant throughout the process. In this type of culture, the continuous replenishment of nutrients and removal of waste allows the cells to reach a higher density than in a batch culture. In some continuous flow culture systems, the cells are removed from the fermenter continuously, whereas in other systems the cells remain within the fermenter. Continuous flow culture is used for the production of metabolites, such as lactic acid (a primary metabolite produced during the log phase) and vitamin C (a secondary metabolite produced during the stationary phase). Figure 3 shows a typical graph of the growth curve of the cells (which have remained within the fermenter), and the concentration of nutrients and product over the time period of the continuous culture.

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Figure 3: Continuous culture

Advantages of continuous culture include: increased productivity continuous supply of product.

Downstream processing
After fermentation, the desired product must be extracted from the culture medium and purified. The extraction and purification of a product is known as downstream processing because, in a flow diagram, it occurs after the fermentation process. The following flow diagram shows some of the downstream processing steps that may follow fermentation.

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Figure 4: Steps involved in downstream processing

The types of products that are extracted from the culture medium and further purified include whole cells, such as yeast; organic acids, such as lactic acid and citric acid; antibiotics, such as penicillin; and alcohol, amino acids, enzymes and vaccines. The final product can either be in liquid or solid form. The way that the products are extracted and purified depends on the chemical nature of the product. Some products (such as proteins) are heat sensitive, and so techniques must be used that will not destroy them. Also, it is important to minimise the number of steps used in downstream processing, as the more steps there are, the higher the chance of losing some of the product (thus getting a poorer yield); and also, the more steps, the more expensive the process.

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Extracting cells from liquid culture An example of when cells are removed from liquid medium is during alcohol production, such as in the making of beer. Removal of the yeast causes the beer to become clearer. Alcohol is formed when yeast cells undergo anaerobic respiration, a process known as fermentation. One of the reasons why yeast can be removed from the liquid medium in this fermentation process is because yeast cells naturally flocculate , or clump together. The flocculated cells precipitate out of solution (by becoming a more solid mass) and so they can be separated relatively easily from the liquid culture medium. Yeast cells used to make lagers flocculate and sink to the bottom of the fermentation vessel, whereas yeast cells used to make ales rise to the top of the fermentation vessel after flocculating. Yeast cells that are removed from the liquid medium are used to start another fermentation. By using the same yeast, the brewers are able to maintain the flavour of the beer. In some fermentation processes, flocculating agents are added to the yeast suspension to help them to flocculate. Following flocculation, the yeast cells may be removed from the culture medium by filtration . In this process, a filter retains the flocculated cells, while allowing the liquid culture medium to flow through. The yeast cells are retained by the filter because of their large size in relation to the pores in the filter. Some strains of yeast used in alcohol production do not flocculate and they are centrifuged from the culture medium. In this process, the culture medium and yeast cells are spun round in a centrifuge at very high speed, thus causing high centrifugal forces. This causes the yeast cells, which are more dense, to form a solid pellet. The liquid culture medium is then easily separated from the pellet of yeast cells. Centrifugation is not routinely used to separate yeast cells after alcohol fermentation, due to the high initial cost of the centrifuge and the associated energy and maintenance costs. A method used to remove bacterial cells from liquid culture is to freeze- dry the cells. The bacterial cells are frozen, then the frozen liquid is removed by sublimation (this is the removal of the liquid as a gas). This leaves the cells completely dehydrated. They can then be stored or transported without becoming denatured. When freeze-dried bacteria are required for use, they are re-hydrated by the addition of a sterile aqueous solution.

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Obtaining solvent and solute from liquid medium The previous section described the methods used to obtain whole cells from the fermentation process. However, at the end of a fermentation process, it can be a solvent, or a solute, that has been made and secreted by the microbial cells (such as antibiotics, proteins, organic acids or amino acids), that is the desired end-product, rather than the cells. In the extraction and purification of solvents and solutes, some of the techniques employed are similar to those used to separate whole cells, for example flocculation, precipitation, filtration and centrifugation. Two organic acids that are produced by fermentation are citric acid and lactic acid . Both are used in the food industry as acidifiers. The extraction of both these organic acids involves the addition of chalk or lime, which causes precipitates to form. The precipitates (which are solid) are removed from the liquid solution by filtration. Both acids then undergo further downstream processing. Proteins and polysaccharides can be precipitated out of solution by the addition of several different types of chemicals (such as acetone and ammonium sulphate). The precipitate can be separated from the remaining liquid by filtration or by centrifugation. Ultrafiltration This technique makes use of a semi-permeable membrane (this means that the membrane contains pores). When a solution is passed through the membrane, any molecules that are larger than the pore size are retained by the membrane, while molecules of a smaller size than the pores flow through the membrane. Ultrafiltration is involved in the separation of molecules in the range of 0.001 m to 0.02 m (a mm is 10 6 of a metre).

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Distillation This method is used in the production of consumable alcohol (such as whisky), fuel alcohol (such as gasohol), acetone and acetic acid (vinegar). Different molecules have different boiling points, so they can be separated from each other on this basis. The fermented liquid containing the product is heated. Alcohol is a volatile substance and so has a fairly low boiling point and turns to vapour at lower temperatures. The vapour is collected in a condenser (which is cooled with cold water), cools down, condenses back into a liquid, and is collected as a pure substance. The diagram below shows a distillation in process. Figure 5: Distillation apparatus

Protein purification The first stage in protein purification is often to precipitate the protein from the liquid medium, as described on p18. The precipitate will contain the protein, but it may also contain other contaminating substances. Depending on the end-use of the protein, it may have to be further purified.

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To do this, the precipitate is dissolved in a small volume of liquid. It is then subjected to a technique known as column chromatography . In this technique, a metal or glass column is packed with a resin that separates proteins according to their size, charge or shape . Figure 6: Separation of proteins according to their size

Figure 6 shows proteins being separated by size. The mixture of proteins is loaded into the top of the column. The proteins are washed through the column using a buffer and, as they pass down the column, the large proteins move faster than the small proteins. The proteins in the mixture are thus separated from each other. This separation is followed by measuring the absorbance of the liquid as it elutes from (comes off) the column. When a protein elutes from the column, it causes an increase in absorbance.

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Figure 7 shows a typical graph of absorbance against volume of liquid eluted. Each peak on the graph corresponds to a protein that has eluted from the column shown in Figure 6. This graph shows two peaks, so the two proteins have been separated according to their size. The peak on the left corresponds to the larger protein as it eluted first; the peak on the right represents the smaller protein. Figure 7: Elution profile of proteins

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Figure 8 shows the purification of lysozyme, an enzyme that is positively charged at pH10. It is applied to a column filled with a negatively charged resin. Lysozyme binds to the negatively charged resin, whereas all other proteins flow through the column. Lysozyme is then eluted from the column by changing the buffer running through the column to one that breaks the bond between lysozyme and the resin. Figure 8: Purification of lysozyme, a positively charged protein

Lysozyme is eluted from the column with buffer that breaks the lysozymeresin bond

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Figure 9 shows the purification of interferon (a protein molecule used to fight viral infections). A mixture of substances, containing interferon, is applied to a column filled with antibodies with a complementary shape to interferon. Interferon binds specifically to the antibodies; other substances do not. Interferon is then eluted by changing the buffer flowing through the column to one that breaks the bond between interferon and the antibody. Figure 9: Purification of interferon

Interferon is eluted from the column with buffer that breaks the interferonantibody bond

Solvent extraction Penicillin (an antibiotic) is extracted from the fermentation medium by solvent extraction. The fermentation medium is mixed with a solvent. Penicillin is more soluble in the solvent than in the fermentation medium, so it moves from the fermentation medium into the solvent. The solvent and the fermentation medium do not mix (just as oil and water do not mix), so they can be separated from each other.

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Drying Spray dryers are used for drying large volumes of liquid. The liquid is turned into an aerosol of very small droplets that are passed into a stream of hot air. Water in the droplets evaporates, leaving behind a solid product. Chamber dryers are used to dry smaller volumes of liquid. The liquid is placed on shelves inside the cabinet and water evaporates from it. A solid product is formed.

Enzymes in production
The majority of industrial enzymes are produced from gram-positive bacteria and from fungi grown in batch culture. Generally, the enzymes are extracellular , which means that, during fermentation, they are secreted from the micro-organisms into the culture medium in large quantities. After fermentation, downstream processing takes place. The enzymes are purified from the culture medium by precipitation and filtration, which removes contaminants. Extracellular enzymes are relatively easy to extract from the medium. However, some enzymes are intracellular , which means that the microbial cells must first be harvested, then broken open and the enzyme released. Detergents or enzymes are often used to break down cell walls and membranes in order to release the desired enzyme. After the enzyme is released, downstream processing using precipitation and filtration continues. Both intracellular and extracellular enzymes may be dried to make them more concentrated. High-value medical and pharmaceutical enzymes that require a high level of purity may be further purified by the use of column chromatography. Enzymes such as those in biological washing powders often have limited downstream processing, as their purity is not as critical. A flow diagram to show the extraction of an intracellular enzyme is shown in Figure 10.

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Figure 10: Obtaining an intracellular enzyme

Uses of enzymes Enzymes have a wide variety of uses, some of which are: in biological washing powders, to degrade protein, starch and lipid-based stains in the baking and brewing industries, to break down starch in flour and barley in the dairy and confectionery industries, to produce sweeteners in the leather industry, to make the leather more pliable in the textile industry, to make cloth softer in the medical/pharmaceutical industry, in diagnostic kits.

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Some specific enzymes and their uses are as follows. Pectinase is an enzyme that breaks down pectin, a component of the cell walls of plants. Pectinase is used to clarify (make clear) fruit juice. It is also used to release juices, oils and colour from fruit. These are then added as flavourings and colourings to soft drinks. Urokinase Heart attacks and strokes can be caused by an obstruction in a blood vessel, or by a blood clot. Normally, a protein called plasmin breaks down blood clots in your body. The enzyme urokinase helps your body to make plasmin . Urokinase can be given therapeutically to help remove blood clots, so is useful in preventive medicine. Cellulase This is an enzyme that breaks down cellulose, the main component of plant cell walls. Cellulase is used to convert plant waste material into edible feedstock for animals. It is also used to treat denim to give the stone-washed effect. Lysozyme This enzyme is used to disrupt the cell walls of bacteria and yeast cells. It can be used in downstream processing to break open cells to release intracellular enzymes. Immobilisation of enzymes As demand has increased for the use of enzymes in industrial and pharmaceutical processes, a technique has been developed called enzyme immobilisation . Briefly, this technique involves attaching an enzyme to an insoluble support. The enzyme makes the product, the product is removed, and the enzyme can be used again and again. There are three main methods of immobilising enzymes. Adsorption The enzyme is attached to the solid support by non-covalent bonds (see Figure 11 overleaf).

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Figure 11: Adsorption of an enzyme onto a solid support

Entrapment The enzyme is trapped in a jelly-like matrix or capsule. Figure 12: Entrapment of an enzyme

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Bonding The enzyme is attached to the solid support by covalent bonding . Figure 13: Bonding of an enzyme

There are many advantages associated with the use of immobilised enzymes: immobilised enzymes can be recycled and used again immobilised enzymes are more stable there is easier and cheaper separation of enzyme and product, so reducing costs they are ideal for use in a continuous flow process.

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Production of transgenic organisms


A transgenic organism is one with DNA (a gene) inserted into it from a different (foreign) organism. A common laboratory exercise to demonstrate this is where bacteria have a fluorescent gene from a jellyfish inserted into them, so that the transgenic bacteria are fluorescent too! Micro-organisms, animals and plants can be made transgenic. The techniques associated with introducing foreign DNA into micro-organisms is covered in Unit 1 ( Microbiology (Higher)). You may find it useful to revise these techniques before proceeding with this section. Any organism that has been genetically modified by the insertion of foreign DNA is known as a genetically modified organism (GMO). Transgenic animals Animals can have foreign DNA inserted into them by microinjection or by viral infection. Microinjection involves injecting foreign DNA into a newly fertilised egg cell using a small glass-needled syringe. Viral infection involves introducing the foreign DNA into a virus, then using the virus to infect a fertilised egg cell. In many cases, the inserted foreign DNA codes for a drug that the animal then makes and secretes. The use of transgenic animals is an alternative to the production of drugs using cell culture and fermenters. Transgenic plants Foreign DNA can be inserted into plants using a plasmid from the bacterium Agrobacterium tumefaciens. The plasmid is genetically modified with the foreign DNA. The following procedure outlines how a transgenic plant can be produced using A. tumefaciens and its plasmid. 1. The plasmid (containing an antibiotic resistance gene) is obtained from A. tumefaciens .

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2.

The plasmid is cut open with a restriction enzyme endonuclease and the foreign DNA is inserted into the plasmid to produce a genetically modified plasmid. A. tumefaciens is transformed with the genetically modified plasmid. Protoplasts are made from plant cells. (A protoplast is a plant cell that has had the cell wall removed, using the enzyme cellulase). Protoplasts are incubated with transformed A. tumefaciens . Protoplasts are plated out onto nutrient medium containing the same antibiotic as the antibiotic-resistant gene in the plasmid. Only those protoplasts that are infected with A. tumefaciens grow in the selective media. Growing plant cells are isolated and grown on to produce transgenic plants.

3. 4.

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There are several reasons as to why biotechnologists want to produce transgenic plants: to to to to to improve crop yields protect against pests and diseases protect against herbicides (weedkillers) protect against harsh environments increase the variety of available plants.

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New breeding techniques


Gardeners have been cloning their favourite plants for many years, using plant tissue culture techniques. (These were discussed in Unit 2 Microbiological Techniques (Higher)). These techniques can be used on transgenic plants too, so that large numbers of a particular transgenic plant can be obtained. Until recently, cloning was restricted mainly to plants, but now it has been extended to animals. The reason why animal cloning has been developed is to produce a number of identical animals with desired characteristics. For example, if a transgenic sheep has been produced that can secrete a drug in its milk, then it makes sense to clone this animal so that a flock of identical sheep are produced, all making the same drug in their milk. Before moving on to the different types of new breeding techniques, lets find out a bit about embryo developmental biology, because some of that subjects terms are used when describing the new breeding techniques. When an egg cell and a sperm cell fuse, a new cell is produced (called a fertilised egg cell , or a zygote) that contains all the necessary genetic information in its nucleus to produce a new individual. The fertilised egg cell divides into two (this is known as the two-cell stage ) and each new cell is identical to the fertilised egg cell, with the same genetic information inside their nucleus. The two cells are clones of each other. Both of these cells now divide into two and the four cells produced also contain identical genetic information. Cell division continues until a ball of cells is produced, which is called a blastocyst. Again, each cell is identical genetically to the original fertilised egg cell. The cells in the blastocyst are said to be undifferentiated , because they have the capability of becoming any type of cell in the organism and have not yet followed a developmental pathway to become a particular type of cell. After many, many further cell divisions, a multicellular organism is produced. The majority of the cells of this organism (the somatic cells) have the same genetic information in their nucleus as the original fertilised egg cell. However, these cells are now called differentiated cells , because they have followed a developmental pathway and become a particular type of cell (such as a muscle or nerve cell) and cannot become any other type of cell.

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Embryo manipulation This technique has been used by sheep and cattle breeders to increase the numbers of animals in a herd. An egg is fertilised and grown to the two-cell stage. At this point, the two cells are separated and each cell is transplanted into the uterus of the mother. Each transplanted cell now behaves like a fertilised egg cell and continues to divide to produce a new individual. This results in twins being born which are genetically identical (or clones). This process mimics the naturally occurring process where identical twins are produced. The advantage of this technique is that it doubles the reproductive rate of the animal. Embryo cloning The main purpose of this technique is to conserve desired features within an animal for future generations. Embryo cloning has been used to produce many genetically identical mice. These mice are useful in experiments fewer mice are required and the results are more reliable. In addition to this, the embryos of mice have been frozen, so they can be stored for long periods of time. Thus scientists will be able to repeat the experiments in the future. The stages used in embryo cloning in mice are as follows: 1. 2. 3. An egg is taken from a donor mouse and fertilised. The fertilised egg is grown to the blastocyst stage. The undifferentiated cells from the blastocyst are separated from each other. More egg cells are taken from the donor mouse and the nuclei are removed from these cells and discarded. The cells are now said to be enucleated .

4.

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5.

The nuclei are removed from the separated blastocyst cells and each nucleus is transferred into an enucleated egg cell. This has the effect of creating lots of new fertilised egg cells, each one genetically identical and each capable of dividing into a new individual mouse.

6. 7. 8.

Each newly formed cell is grown to the blastocyst stage. Blastocysts are transferred into surrogate mother mice. The surrogate mice give birth to many genetically identical mice (a clone of mice).

Somatic cell cloning This new breeding technique is used to create clones from an animal, using a nucleus from one of its mature differentiated cells. The most famous animal associated with somatic cell cloning was Dolly the Sheep, who was born in July 1996 at the Roslin Institute outside Edinburgh. She was the first animal to be cloned successfully from a cell taken from an adult animal. Since Dolly, many animals have been cloned in this way, including cattle, goats, pigs and mice. However, cloning animals in this way is not problemfree, for example many cloned offspring die during pregnancy or shortly after birth. Some have health problems, such as respiratory and cardiovascular dysfunction. However, as the technology advances, these problems may be overcome. The procedure for somatic cell cloning is very similar to that for embryo cloning. A nucleus is removed from a differentiated cell from an adult (in the case of Dolly, the nucleus was removed from a cell from the udder of a female sheep). The nucleus is transferred into an enucleated egg cell. The new nucleated egg cell is grown for five or six days, and assuming it appears to be developing normally, it is transplanted into a surrogate mother. The animal that is born is identical genetically to the animal from which the nucleus came. If the original animal was a transgenic animal producing a drug in its milk, then the cloned animal will also produce the drug in its milk. In this way, a flock of identical animals producing the desired product can be produced.

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Section 2
Biotechnology applications
You have now completed the first section on biotechnological processing and should now have an understanding of how many of the products of biotechnology are made by using micro-organisms, plants and animals. In this section, you will be introduced to the applications (or uses) of some of these products. You will look at the following areas: agriculture and horticulture clinical and forensic medicine environment.

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Agriculture and horticulture


Crop protection Resistance to pests Insects are pests that cause billions of pounds of damage to crops every year. One way to remove insects is to introduce micro-organisms that kill them. Bacillus thuringiensis is a bacterium that infects the caterpillars of the Gypsy Moth. When this bacterium produces an endospore (a resistant form of the bacteria), it makes a crystalline protein toxin called Bt toxin . Gypsy Moth caterpillars are specifically killed by Bt toxin. It has no harmful effect on humans or other vertebrates. B. thuringiensis and Bt toxin have been sprayed over crops that have been infected with Gypsy Moth and the numbers of the insect have decreased. As an alternative to spraying the crops with B. thuringiensis and Bt toxin, transgenic tobacco and tomato plants have been produced with the gene for Bt toxin inserted into them (using a technique similar to that described on p30). The transgenic tobacco and tomato plants produce the crystalline protein toxin themselves (without spraying), which kills the Gypsy Moth caterpillars. Resistance to herbicides Weeds are a major problem in cultivated crops, as they compete with the crop plants for available light, water and nutrients. When a farmer sprays his crops with herbicide (such as glyphosate ) to kill the weeds, the crops sometimes die too. However, transgenic wheat and maize plants have been produced that have had a herbicide-resistant gene inserted into them. The gene codes for a protein that degrades and detoxifies glyphosate. These transgenic wheat and maize plants can then be sprayed with glyphosate to kill the weeds growing among the crops, leaving the crop plants unaffected. Plant production Tissue culture is a technique used to grow a large number of identical plants with desired characteristics, such as pest or herbicide resistance. An additional benefit of producing large numbers of plants using tissue culture is that it is relatively cheap. The procedures used to produce plants in this way are described in detail in Unit 2 ( Microbiological Techniques (Higher)) .

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Clinical and forensic medicine


Producing vaccines by genetic engineering Vaccination is used to give immunity against specific diseases. In developed countries, such as the UK, there are vaccination programmes in place that have managed to completely eradicate some diseases, such as smallpox. The principles of vaccination are outlined in Unit 1 ( Microbiology (Higher)). Briefly, an antigen (a micro-organism or part of a micro-organism) is artificially introduced into your body. Your immune system makes antibodies against the antigen to destroy and remove it. After the antigen has been removed from your body, memory cells (B lymphocytes) are produced that help you to fight the micro-organism, should it enter your body again. Thus you have acquired immunity against that particular disease. There are a number of ways in which conventional vaccines are made. Vaccines normally contain inactivated (killed) micro-organism or live, attenuated micro-organism (this means that the micro-organism has been artificially mutated so that it does not cause disease) or it can contain part of a micro-organism, such as surface proteins or toxins. There are a number of problems associated with conventional vaccines: Use of inactivated micro-organisms can lead to disease in recipients of the vaccine, as the inactivation process is not always 100% successful. Any surviving micro-organisms can potentially cause disease. Some attenuated micro-organisms become pathogenic again, so can cause disease in recipients of the vaccine. Attenuated vaccines must be monitored carefully. Many vaccines rely on tissue culture, which is expensive and can have low production rates. Some micro-organisms cannot be grown in tissue culture, for example Hepatitis B virus. Producing vaccines using genetic engineering techniques allows some of these problems to be overcome, for example: Genes in a micro-organism that are known to cause disease have been deleted by genetic engineering. This type of attenuated micro-organism cannot become pathogenic again.

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For micro-organisms that cannot be grown in tissue culture, the genes coding for antigenic proteins have been isolated and introduced into E.coli , or other eukaryotic cell systems. These cells are then grown in large scale in a fermenter, the antigenic proteins produced, isolated and used in vaccines. Large quantities of vaccine can be produced. Production of Hepatitis B vaccine Hepatitis B is caused by a virus that infects the liver and may cause liver cancer. Figure 14: Hepatitis B virus

Patients who have been infected with Hepatitis B have a surface protein from the virus present in their blood, which acts as an antigen. This surface protein is called Hepatitis B surface antigen (HBsAg). The gene coding for HBsAg was isolated and cloned by inserting the gene into the nucleus of a yeast cell. The genetically modified yeast cell produces HBsAg protein, which is secreted into the culture medium. The secreted HBsAg protein is extracted from the culture medium, purified and used as a vaccine. Use of plants to produce vaccines Some research has been carried out, whereby plants have been genetically engineered to produce a vaccine. Instead of injecting the vaccine into the patient, it is intended that the plant is eaten and the patient will acquire immunity in this way. An added advantage is that it is cheaper to mass produce plants using tissue-culture techniques than it is to run fermenters, so producing vaccines in plants may be cheaper. Also, plants can be dried and stored, which overcomes the problem of refrigeration that is needed to store many conventional vaccines.

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Research has been carried out on producing Hepatitis B vaccine in bananas and tomatoes. Monoclonal antibodies Antibodies are proteins that are secreted by B lymphocytes in response to an antigen. Although different antibodies are produced by different B lymphocytes, all antibodies produced by a single B lymphocyte are identical, and all bind to the same part of the antigen. Antibodies produced by a single type of B lymphocyte are known as monoclonal antibodies . Biotechnologists want to produce monoclonal antibodies, because they can be used as a reliable analytical reagent to identify and quantify specific antigens. In order to produce monoclonal antibodies, individual B lymphocytes must be isolated and each individual B lymphocyte grown in culture, so that all the antibodies produced are identical. However, a problem in culturing B lymphocytes is that they last only for a few days before dying. This problem has been overcome by fusing (joining) the B lymphocytes with cancer cells that live indefinitely (they are said to be immortal, assuming they are looked after properly!). The fused B lymphocyte and cancer cell are called hybrid cells and can live for a long time and produce identical antibody molecules. After the hybrid cells have been produced, the ones that are making and secreting the desired antibody are selected and these hybrid cells are further cultured to produce hybrid cell clones. Uses of monoclonal antibodies There are many uses of monoclonal antibodies in scientific research, biotechnology and medicine, some of which are outlined below. Research tool There are times when a researcher may want to know whether an antigen is present in a body tissue. To find this out, a monoclonal antibody complementary to the antigen is labelled with radioactivity or fluorescence so that it can be tracked. The monoclonal antibody is incubated with the tissue and, if the antigen is present, the monoclonal antibody binds to it. The tissue will become radioactive or fluorescent at the exact location where the monoclonal antibody has bound. Tissue typing before an organ transplant Monoclonal antibodies have been used to ensure that an organ that is to be transplanted into a patient will not be rejected. This is known as tissue typing. The better the match between the surface proteins on the organ to be transplanted and those found in the patient, the less chance there is of

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rejection. Monoclonal antibodies are used to check the compatibility of these surface proteins. Pregnancy testing The urine of a pregnant woman contains the hormone human chorionic gonadotrophin (hCG). One type of home pregnancy kit consists of a dipstick that contains coloured monoclonal antibodies that bind to hCG. The dipstick is dipped into the urine of the person doing the test. If hCG is present in the urine, it binds to the coloured monoclonal antibodies and together they move up the dipstick. They are stopped about one third of the way up by a row of immobilised monoclonal antibodies that also bind to hCG. A coloured band appearing here indicates that the woman is pregnant. If hCG is not present in the urine, the coloured monoclonal antibodies continue to move further up the dipstick until they are stopped by a second set of immobilised monoclonal antibodies that bind to the coloured monoclonal antibodies. The appearance of a coloured band further up the dipstick indicates the woman is not pregnant. Identifying infective agents Monoclonal antibodies are routinely used in clinical labs to find out if a patient has been exposed to infectious micro-organisms, such as human immunodeficiency virus (HIV) , or if they are suffering from infectious diseases such as glandular fever . A sample of the patients blood is mixed with a labelled monoclonal antibody if the sample changes colour, then the patient has been exposed to the micro-organism. Anti-cancer medicines Monoclonal antibodies are used as therapeutic agents in the fight against cancer. Anti-cancer drugs are attached to monoclonal antibodies that bind specifically to cancer cells. The patient is given the monoclonal antibody drug complex and the monoclonal antibody finds and binds only to cancer cells in the patient. The drug is delivered straight to the cancer cells and not to healthy cells. Transgenic animals As mentioned in the Section 1 of this pack, a transgenic animal is one that has had its genome altered by the insertion of a gene using recombinant DNA technology (another name for genetic engineering). In many cases, the gene codes for a drug that the animal then makes and secretes in its milk. Successful transgenic animals have included sheep and cattle.

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Drugs that have been produced using transgenic animals include interferon (used to fight viral infections), blood clotting factors and alpha-1antitrypsin (AAT) (used to treat emphysema and cystic fibrosis). Production of medical products by transgenic animals Firstly, the gene coding for the medical product, such as AAT, is isolated. This gene is then attached to another gene that is involved in milk production. In this way, the inserted gene becomes part of the sequence of genes involved in milk production. These are inserted into a vector and the vector is introduced into a fertilised egg cell of the animal, such as a sheep. The vector, containing the gene for AAT and the milk-producing gene, becomes incorporated into the sheeps DNA. The egg is placed in the uterus of a surrogate mother sheep. The lamb that is born contains the DNA needed to produce AAT. However, as the AAT gene was attached to the milk-producing gene, AAT is produced and secreted only when the lamb becomes an adult and starts to produce milk. The AAT protein is present in the sheeps milk. Advantages of using transgenic animals It is considered to be cost effective because: there is no need for expensive large-scale fermentation vessels there is no need to continuously monitor or maintain equipment. Animals modify proteins after they have been made, for instance sugar groups are added to proteins as they pass through the Golgi apparatus before being secreted from a cell. Such modifications are sometimes needed to activate a protein. The ability to make and secrete the drug is passed from one generation to the next. The animal does not need to be sacrificed to harvest the drug. Disadvantages of using transgenic animals It is relatively difficult to make a transgenic animal (it took 276 attempts before Dolly was created) and the gene does not always insert into the sheep DNA. The transgenic animal may die before it reaches adulthood. The transgenic animal may die before it produces offspring. Only female transgenic animals produce milk. There are ethical, social and moral issues. Is it right to artificially change the genetic make-up of an animal? Stem cell culture Stem cells are cells that are produced early in embryo development (generally between the two-cell stage and the blastocyst stage see p32 to remind you of these terms). Stem cells obtained during this time are undifferentiated cells

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they have the potential of developing into any of about 200 different types of cells found in the adult organism. Stem cells can also be obtained from the blood in the umbilical cord, which can be obtained after a baby is born. Stem cell culture is still in the very early days of research and development, but it is an area that has generated a lot of interest, both among the scientific community and the general public. Stem cell research could eventually lead to cells and tissues being formed that may be used in the treatment of diabetes, Parkinsons disease and many other disorders and diseases. It is thought that it may even lead to whole organs being cultured to be used in transplants. Stem cell culture may also be used to test new drugs without using animal or humans. However, there are a lot of social, moral and ethical issues surrounding stem cell research. Some of these issues surround the source of the stem cells. Human embryonic stem cells can be obtained from in vitro fertilisation programmes where more embryos are created than are needed. They can also be obtained from an aborted foetus. Both sources are highly emotive and have given rise to much debate. Some people believe that it is better for embryos to be used in stem cell research than to be destroyed. Others believe that using human cells is totally unacceptable, as the cells constitute a person and have the right to life. Many people fear that there will be a black market in the sale of human embryos. What are your views on stem cell culture? DNA profiling Everyone, except identical twins, has a different genetic make-up. These differences in DNA can be used to uniquely identify an individual using a technique known as DNA profiling . Firstly, DNA from an individual is isolated (generally from a blood sample), then digested into smaller fragments using specific restriction endonucleases. The sizes of the fragments from this digestion are unique to each individual. These fragments are then separated according to their size by gel electrophoresis. The DNA fragments are then transferred onto a membrane filter (which is much more robust than a gel). A special labelled probe that binds to certain regions of the DNA is incubated with the membrane. After an appropriate length of time, the membrane is washed and the probe that has bound to the DNA demonstrates a pattern of bands, rather similar to a bar code. Each individual has their own unique bar code, or DNA profile. (The techniques used in DNA profiling are described in more detail in Unit 1: Microbiology (Higher).)

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Figure 15 shows simplified DNA profiles of a mother, father and one of their children. Figure 15: DNA profiles

1 Mother

2 Child

3 Father

Half of our DNA is inherited from our mother; the other half from our father. If you look at the childs profile in Figure 15, you will see which bands were inherited from the mother and which from the father. Some bands, you will observe, are common to all three individuals, so they could have been inherited from either parent. These are non-informative bands. DNA profiling can be used to work out the parentage of a child in paternity disputes. It can also be used to compare, for example, the DNA profile from a sample of blood, semen or tissue at the scene of a crime, to a sample from a suspect. DNA profiling is also used to detect genetic disorders. In this case, a probe is used that binds to a particular band in the DNA profile and it is used as a marker for that particular genetic disorder.

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Environment
Biosensors as detectors of pollution Biosensors have been developed that allow the monitoring and measurement of pollution in the field (as opposed to collecting samples and taking them back to lab for analysis). A biosensor consists of a transducer that is linked to an enzyme, antibody or cell which specifically recognises a particular contaminant, such as a heavy metal. When the biosensor is exposed to this contaminant, the enzyme, antibody or cell cause a change in the transducer so that a signal is produced. This signal can be electrical, or a coloured dye, or light can be emitted as luminescence. The higher the level of contamination, the greater the signal emitted. Bioremediation Bioremediation is the use of micro-organisms to clean up pollution from the environment. The micro-organisms can degrade the pollutant, detoxify it to a less harmful substance, or remove it by accumulation, so reducing the levels of the pollutant. The most common pollutants are hydrocarbons, heavy metals, polychlorobiphenyls (PCBs) and chlorinated solvents. Bioremediation of contaminated soil involves one of two processes: naturally occurring micro-organisms in the soil can be activated so that they increase in number and remove the contamination where the soil is contaminated with a specialised compound, genetically engineered micro-organisms can be released into the soil to specifically target the contamination. Oil spillages are treated in a similar manner to soil contamination. For example, during the Exxon Valdez oil spill in Alaska in 1989, naturally occurring micro-organisms were stimulated by the addition of nutrients. Genetically modified micro-organisms have also been used to clean up oil spills.

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BIBLIOGRAPHY

Bibliography
Some suggested reading materials for teachers/lecturers
The following is a commentary on some published reading materials that may be useful when delivering Higher Biotechnology. This list is in no way exhaustive and is meant only as a starting point for any tutor delivering the units for Higher Biotechnology for the first time. Foundations in Microbiology (3rd edition) by Kathleen Park Talaro and Arthur Talaro Published by WCB/McGraw-Hill ISBN: 0-697-35452-0 This is a general introductory microbiology book that is a good teachers resource, especially if you do not have a microbiology background. The book is aimed at undergraduates, so it is too detailed and advanced to be used as a student resource, but it is easy to read and has lots of good illustrations and diagrams. There is an interactive CD-ROM that can be purchased to accompany the book. It provides lots of detailed background knowledge on many of the topics in all of the three units that comprise Higher Biotechnology. Fundamentals of Microbiology (5th edition) by I Edward Alcamo Published by Benjamin/Cummings Publishing Company ISBN: 0-8053-0532-7 This is another general microbiology book that is a good teachers resource. Again, it is easy to read with lots of diagrams and anecdotes (although they are all American). This book is a good source of graphs that could be the basis for problem-solving questions. It also provides lots of detailed background information for all three units of Higher Biotechnology.

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BIBLIOGRAPHY

Micro-organisms and Biotechnology (1st and 2nd editions) by Jane Taylor Published by Nelson Thornes ISBN: 0-17-448255-8 (second edition) This book is now into its second edition and may be used as a teacher and student resource. Both the first and second edition provide background knowledge for all three units comprising Higher Biotechnology and the book is especially good for the Enumerating Micro-organisms section in Unit 2 (Microbiological Techniques). The second edition also covers some ethical issues surrounding some biotechnology processes. Basic Biotechnology (2nd edition) Edited by Colin Ratledge and Bjorn Kristiansen Published by Cambridge University Press ISBN: 0-521-77917-0 This is a book for teachers who are enthusiasts and want to have a detailed knowledge of biotechnology. It provides all the background knowledge (and more!) required for delivering Unit 3 (Biotechnology).

Some suggested websites


Remember that web addresses are constantly being upgraded and changed. The following web information is correct at the time of publication (February 2005). www.biotechinstitute.org This is an American website that has lots of biotechnology information. It has links to biotechnology-related news stories from a range of sources, e.g. Nature , Yahoo and the BBC. There are teachers resources and links to other websites. Also, you can download back copies of the magazine Your World ; this is aimed at post-16 students. Each issue covers one particular biotechnology topic and so can be used as a classroom resource. www.biowise.org.uk This website provides downloadable case studies on industrial biotechnology which may be useful for Unit 3 (Biotechnology). The case studies highlight companies in the UK that actively use biotechnology; they are a good way to show students the practical relevance of what they are studying.

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www.sgm.ac.uk This is the Society for General Microbiology website, which has links to current hot topics and news items, so it is a good way of keeping up to date with issues in microbiology. It also has educational resources and links to online microbiology resources. www.ncbe.reading.ac.uk This website provides downloadable protocols for practical exercises, as well as online learning materials. It has a good section on safety issues to be taken into consideration when carrying out biotechnology practical exercises. It also provides information about the Scottish Centre for Biotechnology Education. www-saps.plantsci.cam.ac.uk This website has protocol information, details on how to purchase kits that can be used as learning activities, and details of biotechnology workshops for teachers and the annual biotechnology summer school. www.scottishbiotech.org This is the website of the Scottish Colleges Biotechnology Consortium, who deliver technical training to industry and schools. Online courses are available. www.sserc.org.uk This website provides information about the Scottish Institute of Biotechnology Education (SIBE), which runs workshops for teachers and pupils. Members can access an interactive manual on microbiological techniques for schools and colleges. It includes a code of practice on safety in microbiology and notes on micro-organisms for investigations. www.scottish-enterprise.com This is the website of Scottish Enterprise. Information about the Scottish biotechnology industry can be obtained here by clicking on services to industry group, then clicking on life sciences. It is very useful for keeping up to date with the activities of biotechnology companies in Scotland.

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APPENDIX

Appendix
Advice for problem-solving outcomes
Unit 1: Microbiology, Outcome 3 Unit 3: Biotechnology, Outcome 2 Candidates are required to produce one report on a problem-solving activity as part of the evidence for the achievement of Higher Biotechnology. The report can be used as evidence for Outcome 3 to achieve the Unit Microbiology and for Outcome 2 in the Unit Biotechnology. The report must be the individual work of the candidate. One way that a problem can be solved is to carry out a practical investigation, either as an individual or as part of a group. This enables candidates to fulfil the five required performance criteria (PC):

(a) (b) (c) (d) (e)

The problem to be solved is identified. Resources required to solve the problem are identified and obtained. Procedures appropriate to solving the problem are planned and designed. The planned procedures are carried out. The problem-solving procedure is evaluated.

Alternatively, candidates can undertake a paper-based investigation by identifying a particular problem, obtaining data from other sources (for example, biotechnology journals or the internet), then analysing, presenting and evaluating this data. Whichever method is used to solve the problem, it is essential to ensure that candidates produce sufficient evidence to fulfil all the required performance criteria. Suggestions to aid professional judgement in ensuring that performance criteria are covered are given in the support notes of both unit specifications.

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APPENDIX

A case study of a practical investigation that was used by candidates in a presenting centre to solve problems is described below. Title Immobilisation of enzymes Introduction As a learning activity to demonstrate immobilisation, candidates entrapped yeast invertase within alginate beads, then assayed the immobilised enzyme by quantitatively measuring product formed using a standard curve. ( Many experiments used as learning activities can form the basis of problem-solving exercises.) The problem Following this activity, several candidates started to identify potential problems associated with immobilisation. Some wanted to know if immobilisation changed the pH and temperature optima of the enzyme; others wanted to know how often the immobilised enzyme could be used before it stopped making product. Both groups realised that these problems may be genuine in the biotechnology industry if an enzyme is to be immobilised for commercial purposes. ( Note that these problems have a real practical application that can help in the evaluation of the exercise.) The procedure These candidates used the knowledge and practical skills they had previously gained from immobilising enzymes to identify the resources and to plan and design their problem-solving activities. The evaluation The candidates found out that the pH optimum changed, the temperature optimum stayed the same and the immobilised enzyme could be used three times before the quantity of product decreased.

Other learning activities that can be used as the basis of problem-solving activities are given in the support notes of each unit specification. They are as outlined below. Set up a small-scale laboratory fermenter and monitor and control various conditions, such as pH and temperature. Autolyse yeast and test viability at different stages in a downstream process. Investigate the effect of pectinase, amylase, cellulose and RGase on the production and clarity of fruit juice.

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APPENDIX

Investigate the action of cellulase on cellulose. Investigate methods of removing immobilised enzyme beads from the substrate. Analyse data on DNA profiling.

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