Medical brain Notes 9

  Introduction to Biotechnology The  Chambers Science and Technology Dictionary  defines biotechnology as ‘the use of organisms or their components in industrial or commercial processes, which can be aided by the techniques of genetic manipulation in developing e.g. novel plants for agriculture or industry.’ Despite the inclusiveness of this definition, the biotechnology sector is still often seen as largely medical or phar-maceutical in nature, particularly amongst the general public. While to some extent the huge research budgets of the drug companies and the widespread familiarity of their products makes this understandable, it does distort the full picture and somewhat unfairly so. However, while therapeutic instruments form, in many respects, the ‘acceptable’ face of biotechnology, elsewhere the science is all too frequently linked with unnatural interference. While the agricultural, industrial and environmental applications of biotechnology are potentially very great, the shadow

  The Role of Environmental Biotechnology While pharmaceutical biotechnology represents the glamorous end of the market, environmental applications are decidedly more in the Cinderella mould. The reasons for this are fairly obvious. The prospect of a cure for the many diseases and conditions currently promised by gene therapy and other biotech-oriented medical miracles can potentially touch us all. Our lives may, quite literally, be changed. Environmental biotechnology, by contrast, deals with far less apparently dramatic topics and, though their importance, albeit different, may be every bit as great, their direct relevance is far less readily appreciated by the bulk of the population. Cleaning up contamination and dealing rationally with wastes is, of course, in everybody’s best interests, but for most people, this is simply addressing a problem which they would rather had not existed in the first place. Even for industry, though the benefits may be noticeable on the balance sheet, t

  The Scope for Use There are three key points for environmental biotechnology interventions, namely in the manufacturing process, waste management or pollution control, as shown in Figure 1.1.  Accordingly, the range of businesses to which environmental biotechnology has potential relevance is almost limitless. One area where this is most apparent is with regard to waste. All commercial operations generate waste of one form or another and for many, a proportion of what is produced is biodegradable. With disposal costs rising steadily across the world, dealing with refuse constitutes an increasingly high contribution to overheads. Thus, there is a clear incentive for all businesses to identify potentially cost-cutting approaches to waste and  employ them where possible.  Changes in legislation throughout Europe, the US and elsewhere, have combined to drive these issues higher up the political agenda and biological methods of waste treatment have gained far greater acceptance as a resul

  The Market for Environmental Biotechnology The UK’s Department of Trade and Industry estimated that 15 – 20% of the global environmental market in 2001 was biotech-based, which amounted to about 250 – 300 billion US dollars and the industry is projected to grow by as much as ten-fold over the following five years. This expected growth is due to greater acceptance of biotechnology for clean manufacturing applications and energy production, together with increased landfill charges and legislative changes in waste management which also alter the UK financial base favourably with respect to bioremediation. Biotechnology-based methods are seen as essential to help meet European Union (EU) targets for biowaste diversion from land-fill and reductions in pollutants. Across the world the existing regulations on environmental pollution are predicted to be more rigorously enforced, with more stringent compliance standards implemented. All of this is expected to stimulate the sales of biotechnol

  Modalities and local influences Another of the key factors affecting the practical uptake of environmental biotechnology is the effect of local circumstances. Contextual sensitivity is almost certainly the single most important factor in technology selection and repre-sents a major influence on the likely penetration of biotech processes into the marketplace. Neither the nature of the biological system, nor of the application method itself, play anything like so relevant a role. This may seem somewhat unexpected at first sight, but the reasons for it are obvious on further inspection. While the character of both the specific organisms and the engineering remain essentially the same irrespective of location, external modalities of economics, legislation and custom vary on exactly this basis. Accordingly, what may make abundant sense as a biotech intervention in one region or country, may be totally unsuited to use in another. In as much as it is impossible to discount the wider global

  Microbes and Metabolism So fundamental are the concepts of cell growth and metabolic capability to the whole of environmental biotechnology and especially to remediation. Metabolic pathways (Michal 1992) are interlinked to produce what can develop into an extraordinarily complicated net-work, involving several levels of control. However, they are fundamentally about the interaction of natural cycles and represent the biological element of the nat-ural geobiological cycles. These impinge on all aspects of the environment, both living and nonliving. Using the carbon cycle as an example, carbon dioxide in the atmosphere is returned by dissolution in rainwater, and also by the process of photosynthesis to produce sugars, which are eventually metabolised to liberate the carbon once more. In addition to constant recycling through metabolic pathways, carbon is also sequestered in living and nonliving components such as in trees in the relatively short term, and deep ocean systems or ancient

  The Immobilisation, Degradation or Monitoring of Pollutants from a Biological Origin Removal of a material from an environment takes one of two routes: it is either degraded or immobilised by a process which renders it biologically unavailable for degradation and so is effectively removed.  Immobilisation can be achieved by chemicals excreted by an organism or by chemicals in the neighbouring environment which trap or chelate a molecule thus making it insoluble. Since virtually all biological processes require the substrate to be dissolved in water, chelation renders the substance unavailable. In some instances this is a desirable end result and may be viewed as a form of  remediation, since it stabilises the contaminant. In other cases it is a nuisance, as digestion would be the preferable option. Such ‘unwanted’ immobilisation can be a major problem in remediation, and is a common state of affairs with aged contamination. Much research effort is being applied to find methods to rev

  The players Traditionally, life was placed into two categories – those having a true  nucleus  (eukaryotes) and those that do not (prokaryotes). This view was dramatically disturbed in 1977 when Carl Woese proposed a third domain, the archaebacteria, now described as archaea, arguing that although apparently prokaryote at first glance they contain sufficient similarities with eukaryotes, in addition to unique features of their own, to merit their own classification (Woese and Fox 1977, Woese, Kandler and Wheelis 1990). The arguments raised by this proposal con-tinue (Cavalier-Smith 2002) but throughout this book the classification adopted is that of Woese, namely, that there are three divisions: bacteria, archaea (which together comprise prokaryotes) and eukaryotes. By this definition, then, what are referred to throughout this work simply as ‘bacteria’ are synonymous with the term eubacteria (meaning ‘true’ bacteria).  It is primarily to the archaea, which typically inhabit extreme

  Metabolism The energy required to carry out all cellular processes is obtained from ingested food in the case of chemotrophic cells, additionally from light in the case of phototrophs and from inorganic chemicals in lithotrophic organisms. Since all biological macromolecules contain the element carbon, a dietary source of carbon is a requirement. Ingested food is therefore, at the very least, a source of energy and carbon, the chemical form of which is rearranged by passage through various routes called metabolic pathways. One purpose of this reshuffling is to produce, after addition or removal of other elements such as hydrogen, oxygen, nitrogen, phosphorous and sulphur, all the chemicals necessary for growth. The other is to produce chemical energy in the form of adenosine triphosphate (ATP), also one of the ‘building blocks’ of nucleic acids. Where an organism is unable to synthesise all its dietary requirements, it must ingest them, as they are, by definition, essential nutrients

  The genetic blueprint for metabolic capability Metabolic capability is the ability of an organism or cell to digest available food. Obviously, the first requirement is that the food should be able to enter  the cell which sometimes requires specific carrier proteins to allow penetration across the cell membrane.  Once entered, the enzymes must be present to catalyse all the reactions in the pathway responsible for degradation, or catabolism. The information for this metabolic capability, is encoded in the DNA. The full genetic information is described as the genome and can be a single circular piece of DNA as in bacteria, or may be linear and fragmented into chromosomes as in higher animals and plants.  Additionally, many bacteria carry plasmids, which are much smaller pieces of DNA, also circular and self-replicating. These are vitally important in the context of environmental biotechnology in that they frequently carry the genes for degradative pathways. Many of these plasmids may

  Metabolic Pathways of Particular Relevance to Environmental Biotechnology Having established that the overall strategy of environmental biotechnology is to make use of the metabolic pathways in micro-organisms to break down or metabolise organic material. Metabolic pathways operating in the overall direction of synthesis are termed anabolic while those operating in the direction of breakdown or degradation are described as catabolic: the terms catabolism and anabolism being applied to describe the degradative or synthetic processes respectively.  It has been mentioned already and it will become clear from the forthcoming discussion, that the eventual fate of the carbon skeletons of biological macromolecules is entry into the central metabolic pathways.

  Glycolysis As the name implies, glycolysis is a process describing the splitting of a phosphate derivative of glucose, a sugar containing six carbon atoms, eventually to produce two pyruvate molecules, each having three carbon atoms. There are at least four pathways involved in the catabolism of glucose. These are the Embden – Meyerhof (Figure 2.1), which is the one most typically associated with glycolysis, the Ent-ner – Doudoroff and the phosphoketolase pathways and the pentose phosphate cycle, which allows rearrangement into sugars containing 3, 4, 5, 6 or 7 carbon atoms. The pathways differ from each other in some of the reactions in the first half up to the point of lysis to two three-carbon molecules, after which point the remainder of the pathways are identical. These routes are characterised by the particular enzymes present in the first half of these pathways catalysing the steps between glucose and the production of dihydroxyacetone phosphate in equilib-rium with glyceralde

  Lipids This class of macromolecules (see Figure 2.2) includes the neutral lipids which are triacylglycerols commonly referred to as fats and oils. Triacylglycerols are found in reservoirs in micro-organisms as fat droplets, enclosed within a ‘bag’, called a vesicle, while in higher animals, there is dedicated adipose tissue, comprising mainly cells full of fat. These various fat stores are plundered when energy is required by the organism as the degradation of triacylglycerols is a highly exer-gonic reaction and therefore a ready source of cellular energy. Gram for gram, the catabolism of these fats releases much more energy than the catabolism of sugar which explains in part why energy stores are fat rather than sugar. If this were not the case the equivalent space taken up by a sugar to store the same amount of energy would be much greater. In addition, sugar is osmotically active which could present a problem for water relations within a cell, should sugar be the major energy stor