Biochemical analysis techniques WORLD OF MICROBIOLOGY AND IMMUNOLOGY 63 • • loss of the potato crops in Ireland resulted in the death due to starvation of at least one million people, and the mass emigra- tion of people to countries including the United States and Canada. The famine was attributed to many sources, many of which had no basis in scientific reason. Dr. C. Montane, a physician in the army of Napoleon, first described the pres- ence of fungus on potatoes after a prolonged period of rain. He shared this information with Berkeley, who surmised that the fungus was the cause of the disease. Berkeley was alone in this view. Indeed, Dr. John Lindley, a botany professor at University College in London, and a professional rival of Berkeley’s, hotly and publicly disputed the idea. Lindley blamed the famine on the damp weather of Ireland. Their dif- fering opinions were published in The Gardener’s Chronicles. With time, Berkeley’s view was proven to be correct. A committee formed to arbitrate the debate sided with Berkeley. On the basis of the decision, farmers were advised to store their crop in well-ventilated pits, which aided against fungal growth. The discovery that the fungus Phytophthora infestans was the basis of the potato blight represented the first disease known to be caused by a microorganism, and marked the beginning of the scientific discipline of plant pathology. Berkeley also contributed to the battle against poultry mildew, a fungal disease that produced rotting of vines. The disease could e devastating. For example, the appearance of poultry mildew in Madeira in the 1850s destroyed the local wine-based economy, which led to widespread starvation and emigration. Berkeley was one of those who helped established the cause of the infestation. BEVERIDGE , T ERRANCE J. (1945- ) Beveridge, Terrance J. Canadian microbiologist Terrance (Terry) J. Beveridge has fundamentally contributed to the understanding of the structure and function of bacteria. Beveridge was born in Toronto, Ontario, Canada. His early schooling was also in that city. He graduated with a B.Sc. from the University of Toronto in 1968, a Dip. Bact. in 1969, and an M.Sc. in oral microbiology in 1970. Intending to become a dentist, he was drawn to biological research instead. This interest led him to the University of Western Ontario lab- oratory of Dr. Robert Murray, where he completed his Ph.D. dissertation in 1974. His Ph.D. research focused on the use of various tech- niques to probe the structure of bacteria. In particular, he developed an expertise in electron microscopy. His research interest in the molecular structure of bacteria was carried on in his appointment as an Assistant Professor at the University of Guelph in 1975. He became an Associate Professor in 1983 and a tenured Professor in 1986. He has remained at the University of Guelph to the present day. Beveridge’s interest in bacterial ultrastructure had led to many achievements. He and his numerous students and research colleagues pioneered the study of the binding of met- als by bacteria, and showed how these metals function to cement components of the cell wall of Gram-negative and Gram-positive bacteria together. Bacteria were shown to be capable of precipitating metals from solution, producing what he termed microfossils. Indeed, Beveridge and others have discovered similar appearing microfossils in rock that is mil- lions of years old. Such bacteria are now thought to have played a major role in the development of conditions suitable for the explosive diversity of life on Earth. In 1981, Beveridge became Director of a Guelph-based electron microscopy research facility. Using techniques including scanning tunneling microscopy, atomic force microscopy and confocal microscopy, the molecular nature of regularly-structured protein layers on a number of bacterial species have been detailed. Knowledge of the structure is allowing strategies to overcome the layer’s role as a barrier to antibacterial compounds. In another accomplishment, the design and use of metallic probes allowed Beveridge to deduce the actual mechanism of operation of the Gram stain. The mechanism of the stain technique, of bedrock importance to microbiology, had not been known since the development of the stain in the nineteenth century. In the 1980s, in collaboration with Richard Blakemore’s laboratory, used electron microscopy to reveal the structure, arrangement and growth of the magnetically-responsive parti- cles in Aquaspirillum magnetotacticum. In the past decade, Beveridge has discovered how bacterial life manages to sur- vive in a habitat devoid of oxygen, located in the Earth’s crust miles beneath the surface. These discoveries have broadened human knowledge of the diversity of life on the planet. Another accomplishment of note has been the finding that portions of the bacterial cell wall that are spontaneously released can be used to package antibiotics and deliver them to the bacteria. This novel means of killing bacteria shows great potential in the treatment of bacterial infections. These and other accomplishment have earned Beveridge numerous awards. In particular, he received the Steacie Award in 1984, an award given in recognition of out- standing fundamental research by a researcher in Canada, and the Culling Medal from the National Society of Histotechnology in 2001. See also Bacterial ultrastructure; Electron microscope exami- nation of microorganisms; Magnetotactic bacteria BIOCHEMICAL ANALYSIS TECHNIQUES Biochemical analysis techniques Biochemical analysis techniques refer to a set of methods, assays, and procedures that enable scientists to analyze the substances found in living organisms and the chemical reac- tions underlying life processes. The most sophisticated of these techniques are reserved for specialty research and diag- nostic laboratories, although simplified sets of these tech- niques are used in such common events as testing for illegal drug abuse in competitive athletic events and monitoring of blood sugar by diabetic patients. To perform a comprehensive biochemical analysis of a biomolecule in a biological process or system, the biochemist womi_B 5/6/03 1:09 PM Page 63 Biochemical analysis techniques WORLD OF MICROBIOLOGY AND IMMUNOLOGY 64 • • typically needs to design a strategy to detect that biomole- cule, isolate it in pure form from among thousands of mole- cules that can be found in an extracts from a biological sample, characterize it, and analyze its function. An assay, the biochemical test that characterizes a molecule, whether quan- titative or semi-quantitative, is important to determine the presence and quantity of a biomolecule at each step of the study. Detection assays may range from the simple type of assays provided by spectrophotometric measurements and gel staining to determine the concentration and purity of proteins and nucleic acids, to long and tedious bioassays that may take days to perform. The description and characterization of the molecular components of the cell succeeded in successive stages, each one related to the introduction of new technical tools adapted to the particular properties of the studied molecules. The first studied biomolecules were the small building blocks of larger and more complex macromolecules, the amino acids of proteins, the bases of nucleic acids and sugar monomers of complex carbohydrates. The molecular characterization of these elementary components was carried out thanks to tech- niques used in organic chemistry and developed as early as the nineteenth century. Analysis and characterization of com- plex macromolecules proved more difficult, and the funda- mental techniques in protein and nucleic acid and protein purification and sequencing were only established in the last four decades. Most biomolecules occur in minute amounts in the cell, and their detection and analysis require the biochemist to first assume the major task of purifying them from any contamination. Purification procedures published in the spe- cialist literature are almost as diverse as the diversity of bio- molecules and are usually written in sufficient details that they can be reproduced in different laboratory with similar results. These procedures and protocols, which are reminis- cent of recipes in cookbooks have had major influence on the progress of biomedical sciences and were very highly rated in scientific literature. The methods available for purification of biomolecules range from simple precipitation, centrifugation, and gel elec- trophoresis to sophisticated chromatographic and affinity techniques that are constantly undergoing development and improvement. These diverse but interrelated methods are based on such properties as size and shape, net charge and bio- properties of the biomolecules studied. Centrifugation procedures impose, through rapid spin- ning, high centrifugal forces on biomolecules in solution, and cause their separations based on differences in weight. Electrophoresis techniques take advantage of both the size and charge of biomolecules and refer to the process where bio- molecules are separated because they adopt different rates of migration toward positively (anode) or negatively (cathode) charged poles of an electric field. Gel electrophoresis methods are important steps in many separation and analysis tech- niques in the studies of DNA, proteins and lipids. Both western blotting techniques for the assay of proteins and southern and northern analysis of DNA rely on gel electrophoresis. The completion of DNA sequencing at the different human genome centers is also dependent on gel electrophoresis. A powerful modification of gel electrophoresis called two- dimensional gel electrophoresis is predicted to play a very important role in the accomplishment of the proteome projects that have started in many laboratories. Chromatography techniques are sensitive and effective in separating and concentrating minute components of a mix- ture and are widely used for quantitative and qualitative analy- sis in medicine, industrial processes, and other fields. The method consists of allowing a liquid or gaseous solution of the test mixture to flow through a tube or column packed with a finely divided solid material that may be coated with an active chemical group or an adsorbent liquid. The different compo- nents of the mixture separate because they travel through the tube at different rates, depending on the interactions with the porous stationary material. Various chromatographic separa- tion strategies could be designed by modifying the chemical components and shape of the solid adsorbent material. Some chromatographic columns used in gel chromatography are packed with porous stationary material, such that the small molecules flowing through the column diffuse into the matrix and will be delayed, whereas larger molecules flow through the column more quickly. Along with ultracentrifugation and Technician performing biochemical analysis. womi_B 5/6/03 1:09 PM Page 64 Biochemistry WORLD OF MICROBIOLOGY AND IMMUNOLOGY 65 • • gel electrophoresis, this is one of the methods used to deter- mine the molecular weight of biomolecules. If the stationary material is charged, the chromatography column will allow separation of biomolecules according to their charge, a process known as ion exchange chromatography. This process provides the highest resolution in the purification of native biomolecules and is valuable when both the purity and the activity of a molecule are of importance, as is the case in the preparation of all enzymes used in molecular biology. The bio- logical activity of biomolecules has itself been exploited to design a powerful separation method known as affinity chro- matography. Most biomolecules of interest bind specifically and tightly to natural biological partners called ligands: enzymes bind substrates and cofactors, hormones bind recep- tors, and specific immunoglobulins called antibodies can be made by the immune system that would in principle interact with any possible chemical component large enough to have a specific conformation. The solid material in an affinity chro- matography column is coated with the ligand and only the bio- molecule that specifically interact with this ligand will be retained while the rest of a mixture is washed away by excess solvent running through the column. Once a pure biomolecule is obtained, it may be employed for a specific purpose such as an enzymatic reaction, used as a therapeutic agent, or in an industrial process. However, it is normal in a research laboratory that the biomol- ecule isolated is novel, isolated for the first time and, therefore, warrants full characterization in terms of structure and func- tion. This is the most difficult part in a biochemical analysis of a novel biomolecule or a biochemical process, usually takes years to accomplish, and involves the collaboration of many research laboratories from different parts of the world. Recent progress in biochemical analysis techniques has been dependant upon contributions from both chemistry and biology, especially molecular genetics and molecular biology, as well as engineering and information technology. Tagging of proteins and nucleic acids with chemicals, especially fluores- cent dyes , has been crucial in helping to accomplish the sequencing of the human genome and other organisms, as well as the analysis of proteins by chromatography and mass spec- trometry. Biochemical research is undergoing a change in par- adigm from analysis of the role of one or a few molecules at a time, to an approach aiming at the characterization and func- tional studies of many or even all biomolecules constituting a cell and eventually organs. One of the major challenges of the post-genome era is to assign functions to all of the gene prod- ucts discovered through the genome and cDNA sequencing efforts. The need for functional analysis of proteins has become especially eminent, and this has led to the renovated interest and major technical improvements in some protein separation and analysis techniques. Two-dimensional gel elec- trophoresis, high performance liquid and capillary chromatog- raphy as well as mass spectrometry are proving very effective in separation and analysis of abundant change in highly expressed proteins. The newly developed hardware and soft- ware, and the use of automated systems that allow analysis of a huge number of samples simultaneously, is making it possi- ble to analyze a large number of proteins in a shorter time and with higher accuracy. These approaches are making it possible to study global protein expression in cells and tissues, and will allow comparison of protein products from cells under varying conditions like differentiation and activation by various stim- uli such as stress, hormones, or drugs. A more specific assay to analyze protein function in vivo is to use expression systems designed to detect protein-protein and DNA-protein interac- tions such as the yeast and bacterial hybrid systems. Ligand- receptor interactions are also being studied by novel techniques using biosensors that are much faster than the con- ventional immunochemical and colorimetric analyzes. The combination of large scale and automated analysis techniques, bioinformatic tools, and the power of genetic manipulations will enable scientists to eventually analyze processes of cell function to all depths. See also Bioinformatics and computational biology; Biotechnology; Fluorescence in situ hybridization; Immuno- logical analysis techniques; Luminescent bacteria BIOCHEMISTRY Biochemistry Biochemistry seeks to describe the structure, organization, and functions of living matter in molecular terms. Essentially two factors have contributed to the excitement in the field today and have enhanced the impact of research and advances in bio- chemistry on other life sciences. First, it is now generally accepted that the physical elements of living matter obey the same fundamental laws that govern all matter, both living and non-living. Therefore the full potential of modern chemical and physical theory can be brought in to solve certain biolog- ical problems. Secondly, incredibly powerful new research techniques, notably those developing from the fields of bio- physics and molecular biology, are permitting scientists to ask questions about the basic process of life that could not have been imagined even a few years ago. Biochemistry now lies at the heart of a revolution in the biological sciences and it is nowhere better illustrated than in the remarkable number of Nobel Prizes in Chemistry or Medicine and Physiology that have been won by biochemists in recent years. A typical example is the award of the 1988 Nobel Prize for Medicine and Physiology, to Gertrude Elion and George Hitchings of the United States and Sir James Black of Great Britain for their leadership in inventing new drugs. Elion and Hitchings developed chemical analogs of nucleic acids and vitamins which are now being used to treat leukemia, bacterial infections, malaria, gout, herpes virus infections and AIDS. Black developed beta-blockers that are now used to reduce the risk of heart attack and to treat diseases such as asthma. These drugs were designed and not discovered through random organic synthesis. Developments in knowl- edge within certain key areas of biochemistry, such as protein structure and function, nucleic acid synthesis, enzyme mecha- nisms, receptors and metabolic control, vitamins, and coen- zymes all contributed to enable such progress to be made. Two more recent Nobel Prizes give further evidence for the breadth of the impact of biochemistry. In 1997, the womi_B 5/6/03 1:09 PM Page 65 Biodegradable substances WORLD OF MICROBIOLOGY AND IMMUNOLOGY 66 • • Chemistry Prize was shared by three scientists: the American Paul Boyer and the British J. Walker for their discovery of the “rotary engine” that generates the energy-carrying compound ATP, and the Danish J. Skou, for his studies of the “pump” that drives sodium and potassium across membranes. In the same year, the Prize in Medicine and Physiology went to Stanley Prusiner , for his studies on the prion, the agent thought to be responsible for “mad cow disease” and several similar human conditions. Biochemistry draws on its major themes from many disciplines. For example from organic chemistry, which describes the properties of biomolecules; from biophysics, which applies the techniques of physics to study the struc- tures of biomolecules; from medical research, which increas- ingly seeks to understand disease states in molecular terms and also from nutrition, microbiology, physiology, cell biol- ogy and genetics. Biochemistry draws strength from all of these disciplines but is also a distinct discipline, with its own identity. It is distinctive in its emphasis on the structures and relations of biomolecules, particularly enzymes and biologi- cal catalysis, also on the elucidation of metabolic pathways and their control and on the principle that life processes can, at least on the physical level, be understood through the laws of chemistry. It has its origins as a distinct field of study in the early nineteenth century, with the pioneering work of Freidrich Wöhler. Prior to Wöhler’s time it was believed that the substance of living matter was somehow quantitatively different from that of nonliving matter and did not behave according to the known laws of physics and chemistry. In 1828 Wöhler showed that urea, a substance of biological ori- gin excreted by humans and many animals as a product of nitrogen metabolism, could be synthesized in the laboratory from the inorganic compound ammonium cyanate. As Wöhler phrased it in a letter to a colleague, “I must tell you that I can prepare urea without requiring a kidney or an animal, either man or dog.” This was a shocking statement at the time, for it breached the presumed barrier between the living and the nonliving. Later, in 1897, two German brothers, Eduard and Hans Buchner, found that extracts from broken and thor- oughly dead cells from yeast, could nevertheless carry out the entire process of fermentation of sugar into ethanol. This dis- covery opened the door to analysis of biochemical reactions and processes in vitro (Latin “in glass”), meaning in the test tube rather than in vivo, in living matter. In succeeding decades many other metabolic reactions and reaction path- ways were reproduced in vitro, allowing identification of reactants and products and of enzymes, or biological cata- lysts, that promoted each biochemical reaction. Until 1926, the structures of enzymes (or “ferments”) were thought to be far too complex to be described in chemi- cal terms. But in 1926, J.B. Sumner showed that the protein urease, an enzyme from jack beans, could be crystallized like other organic compounds. Although proteins have large and complex structures, they are also organic compounds and their physical structures can be determined by chemical methods. Today, the study of biochemistry can be broadly divided into three principal areas: (1) the structural chemistry of the components of living matter and the relationships of biological function to chemical structure; (2) metabolism, the totality of chemical reactions that occur in living matter; and (3) the chemistry of processes and substances that store and transmit biological information. The third area is also the province of molecular genetics, a field that seeks to under- stand heredity and the expression of genetic information in molecular terms. Biochemistry is having a profound influence in the field of medicine. The molecular mechanisms of many dis- eases, such as sickle cell anemia and numerous errors of metabolism, have been elucidated. Assays of enzyme activity are today indispensable in clinical diagnosis. To cite just one example, liver disease is now routinely diagnosed and moni- tored by measurements of blood levels of enzymes called transaminases and of a hemoglobin breakdown product called bilirubin. DNA probes are coming into play in diagnosis of genetic disorders, infectious diseases and cancers. Genetically engineered strains of bacteria containing recom- binant DNA are producing valuable proteins such as insulin and growth hormone. Furthermore, biochemistry is a basis for the rational design of new drugs. Also the rapid development of powerful biochemical concepts and techniques in recent years has enabled investigators to tackle some of the most challenging and fundamental problems in medicine and phys- iology. For example in embryology, the mechanisms by which the fertilized embryo gives rise to cells as different as muscle, brain and liver are being intensively investigated. Also, in anatomy, the question of how cells find each other in order to form a complex organ, such as the liver or brain, are being tackled in biochemical terms. The impact of biochem- istry is being felt in many areas of human life through this kind of research, and the discoveries are fuelling the growth of the life sciences as a whole. See also Antibody-antigen, biochemical and molecular reac- tions; Biochemical analysis techniques; Biogeochemical cycles; Bioremediation; Biotechnology; Immunochemistry; Immunological analysis techniques; Miller-Urey experiment; Nitrogen cycle in microorganisms; Photosynthesis BIODEGRADABLE SUBSTANCES Biodegradable substances The increase in public environmental awareness and the recognition of the urgent need to control and reduce pollution are leading factors in the recent augment of scientific research for new biodegradable compounds. Biodegradable com- pounds could replace others that harm the environment and pose hazards to public health, and animal and plant survival. Biodegradation, i.e., the metabolization of substances by bac- teria, yeast, fungi, from which these organisms obtain nutri- ents and energy, is an important natural resource for the development of new environmental-friendly technologies with immediate impact in the chemical industry and other eco- nomic activities. Research efforts in this field are two-fold: to identify and/or develop transgenic biological agents that digest specific existing compounds in polluted soils and water, womi_B 5/6/03 1:09 PM Page 66 Biofilm formation and dynamic behavior WORLD OF MICROBIOLOGY AND IMMUNOLOGY 67 • • and to develop new biodegradable compounds to replace haz- ardous chemicals in industrial activity. Research is, therefore, aimed at bioremediation, which could identify biological agents that rapidly degrade existing pollutants in the environ- ment, such as heavy metals and toxic chemicals in soil and water, explosive residues, or spilled petroleum. Crude oil however, is naturally biodegradable, and species of hydrocar- bon-degrading bacteria are responsible for an important reduc- tion of petroleum levels in reservoirs, especially at temperatures below 176° F (80° C). The selection, culture, and even genetic manipulation of some of these species may lead to a bioremediation technology that could rapidly degrade oil accidentally spilled in water. The search for a biodegradable substitute for plastic polymers, for instance, is of high environmental relevance, since plastic waste (bags, toys, plastic films, packing material, etc.) is a major problem in garbage disposal and its recycling process is not pollution-free. In the 1980s, research of polyhy- droxybutyrate, a biodegradable thermoplastic derived from bacterial metabolism was started and then stalled due to the high costs involved in fermentation and extraction. Starch is another trend of research in the endeavor to solve this prob- lem, and starch-foamed packing material is currently in use in many countries, as well as molded starch golf tees. However, physical and chemical properties of starch polymers have so far prevented its use for other industrial purposes in replace- ment of plastic. Some scientists suggest that polyhydroxybu- tyrate research should now be increased to benefit from new biotechnologies, such as the development of transgenic corn, with has the ability to synthesize great amounts of the com- pound. This corn may one day provide a cost-effective biodegradable raw material to a new biodegradable plastics industry. Another field for biodegradable substances usage is the pharmaceutical industry, where biomedical research focuses on non-toxic polymers with physicochemical thermo-sensitiv- ity as a matrix for drug delivering. One research group at the University of Utah at Salt Lake City in 1997, for instance, syn- thesized an injectable polymer that forms a non-toxic biodegradable hydro gel that acts as a sustained-release matrix for drugs. Transgenic plants expressing microbial genes whose products are degradative enzymes may constitute a potential solution in the removal of explosive residues from water and soils. A group of University of Cambridge and University of Edinburgh scientists in the United Kingdom developed trans- genic tobacco plants that express an enzyme (pentaerythritol tetranitrate reductase) that degrades nitrate ester and nitro aro- matic explosive residues in contaminated soils. Another environmental problem is the huge amounts of highly stable and non-biodegradable hydrocarbon compounds that are discarded in landfills, and are known as polyacry- lates. Polyacrylates are utilized as absorbent gels in dispos- able diapers, and feminine hygiene absorbents, as well as added to detergents as dispersants, and are discharged through sewage into underwater sheets, rivers, and lakes. A biodegradable substitute, however, known as polyaspartate, already exists, and is presently utilized in farming and oil drilling. Polyaspartate polymers are degradable by bacteria because the molecular backbone is constituted by chains of amino acids; whereas polyacrylates have backbones made of hydrocarbon compounds. The main challenge in the adoption of biodegradable substances as a replacement for existing hazardous chemicals and technologies is cost effectiveness. Only large-scale pro- duction of environmental friendly compounds can decrease costs. Public education and consumer awareness may be a cru- cial factor in the progress and consolidation of “green” tech- nologies in the near future. See also Amino acid chemistry; Biotechnology; Economic uses and benefits of microorganisms; Transgenics; Waste water treatment BIOFILM FORMATION AND DYNAMIC BEHAVIOR Biofilm formation and dynamic behavior Biofilms are populations of microorganisms that form follow- ing the adhesion of bacteria, algae, yeast, or fungi to a surface. These surface growths can be found in natural settings, such as on rocks in streams, and in infections, such as on catheters. Both living and inert surfaces, natural and artificial, can be colonized by microorganisms. Up until the 1980s, the biofilm mode of growth was regarded as more of a scientific curiosity than an area for seri- ous study. Then, evidence accumulated to demonstrate that biofilm formation is the preferred mode of growth for microbes. Virtually every surface that is in contact with microorganisms has been found to be capable of sustaining biofilm formation. The best-studied biofilms are those formed by bacteria. Much of the current knowledge of bacterial biofilm comes from laboratory studies of pure cultures of bacteria. However, biofilm can also be comprised of a variety of bacteria. Dental plaque is a good example. Many species of bacteria can be present in the exceedingly complex biofilm that form on the surface of the teeth and gums. The formation of a biofilm begins with a clean, bacte- ria-free surface. Bacteria that are growing in solution ( plank- tonic bacteria ) encounter the surface. Attachment to the surface can occur specifically, via the recognition of a surface receptor by a component of the bacterial surface, or non- specifically. The attachment can be mediated by bacterial appendages , such as flagella, cilia, or the holdfast of Caulobacter crescentus. If the attachment is not transient, the bacterium can undergo a change in its character. Genes are stimulated to become expressed by some as yet unclear aspect of the sur- face association. This process is referred to as auto-induction. A common manifestation of the genetic change is the produc- tion and excretion of a large amount of a sugary material. This material covers the bacterium and, as more bacteria accumulate from the fluid layer and from division of the sur- face-adherent bacteria, the entire mass can become buried in womi_B 5/6/03 1:09 PM Page 67 Biogeochemical cycles WORLD OF MICROBIOLOGY AND IMMUNOLOGY 68 • • the sugary network. This mass represents the biofilm. The sugar constituent is known as glycocalyx, exopolysaccharide, or slime. As the biofilm thickens and multiple layers of bacteria build up, the behavior of the bacteria becomes even more complex. Studies using instruments such as the confocal microscope combined with specific fluorescent probes of var- ious bacterial structures and functional activities have demon- strated that the bacteria located deeper in the biofilm cease production of the slime and adopt an almost dormant state. In contrast, bacteria at the biofilm’s periphery are faster-growing and still produce large quantities of the slime. These activities are coordinated. The bacteria can communicate with one another by virtue of released chemical compounds. This so- called quorum sensing enables a biofilm to grow and sense when bacteria should be released so as to colonize more dis- tant surfaces. The technique of confocal microscopy allows biofilms to be examined without disrupting them. Prior to the use of the technique, biofilms were regarded as being a homogeneous distribution of bacteria. Now it is known that this view is incorrect. In fact, bacteria are clustered together in “micro- colonies” inside the biofilm, with surrounding regions of bac- teria-free slime or even channels of water snaking through the entire structure. The visual effect is of clouds of bacteria ris- ing up through the biofilm. The water channels allow nutrients and waste to pass in and out of the biofilm, while the bacteria still remain protected within the slime coat. Bacterial biofilms have become important clinically because of the marked resistance to antimicrobial agents that the biofilm bacteria display, relative to both their planktonic counterparts and from bacteria released from the confines of the biofilm. Antibiotics that swiftly kill the naked bacteria do not arm the biofilm bacteria, and may even promote the devel- opment of antibiotic resistance. Contributors to this resistance are likely the bacteria and the cocooning slime network. Antibiotic resistant biofilms occur on artificial heart valves, urinary catheters, gallstones, and in the lungs of those afflicted with cystic fibrosis, as only a few examples. In the example of cystic fibrosis, the biofilm also acts to shield the Pseudomonas aeruginosa bacteria from the antibacterial responses of the host’s immune system. The immune response may remain in place for a long time, which irritates and dam- ages the lung tissue. This damage and the resulting loss of function can be lethal. See also Anti-adhesion methods; Antibiotic resistance, tests for; Bacterial adaptation BIOGEOCHEMICAL CYCLES Biogeochemical cycles The term biogeochemical cycle refers to any set of changes that occur as a particular element passes back and forth between the living and non-living worlds. For example, car- bon occurs sometimes in the form of an atmospheric gas (car- bon dioxide), sometimes in rocks and minerals (limestone and marble), and sometimes as the key element of which all living organisms are made. Over time, chemical changes occur that convert one form of carbon to another form. At various points in the carbon cycle, the element occurs in living organisms and at other points it occurs in the Earth’s atmosphere, litho- sphere, or hydrosphere. The universe contains about ninety different naturally occurring elements. Six elements, carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus, make up over 95% of the mass of all living organisms on Earth. Because the total amount of each element is essentially constant, some cycling process must take place. When an organism dies, for example, the elements of which it is composed continue to move through a cycle, returning to the Earth, to the air, to the ocean, or to another organism. All biogeochemical cycles are complex. A variety of pathways are available by which an element can move among hydrosphere, lithosphere, atmosphere, and biosphere. For instance, nitrogen can move from the lithosphere to the atmosphere by the direct decomposition of dead organisms or by the reduction of nitrates and nitrites in the soil. Most changes in the nitrogen cycle occur as the result of bacterial action on one compound or another. Other cycles do not require the intervention of bacteria. In the sulfur cycle, for example, sulfur dioxide in the atmosphere can react directly with compounds in the earth to make new sulfur compounds that become part of the lithosphere. Those compounds can then be transferred directly to the biosphere by plants grow- ing in the earth. Most cycles involve the transport of an element through all four parts of the planet—hydrosphere, atmo- sphere, lithosphere, and biosphere. The phosphorous cycle is an exception since phosphorus is essentially absent from the atmos- phere. It does move from biosphere to the lithosphere (when organisms die and decay) to the hydrosphere (when phospho- rous-containing compounds dissolve in water) and back to the biosphere (when plants incorporate phosphorus from water). Hydrogen and oxygen tend to move together through the planet in the hydrologic cycle. Precipitation carries water from the atmosphere to the hydrosphere and lithosphere. It then becomes part of living organisms (the biosphere) before being returned to the atmosphere through respiration, transpi- ration, and evaporation. All biogeochemical cycles are affected by human activ- ities. As fossil fuels are burned, for example, the transfer of carbon from a very old reserve (decayed plants and animals buried in the earth) to a new one (the atmosphere, as carbon dioxide) is accelerated. The long-term impact of this form of human activity on the global environment, as well as that of other forms, is not yet known. Some scientists assert, however, that those affects can be profound, resulting in significant cli- mate changes far into the future. See also Biodegradable substances; Carbon cycle in microor- ganisms; Composting, microbiological aspects; Economic uses and benefits of microorganisms; Evolution and evolu- tionary mechanisms; Evolutionary origin of bacteria and viruses; Nitrogen cycle in microorganisms; Oxygen cycle in microorganisms womi_B 5/6/03 1:09 PM Page 68 Bioinformatics and computational biology WORLD OF MICROBIOLOGY AND IMMUNOLOGY 69 • • BIOINFORMATICS AND COMPUTATIONAL BIOLOGY Bioinformatics and computational biology Bioinformatics, or computational biology, refers to the devel- opment of new database methods to store genomic informa- tion, computational software programs, and methods to extract, process, and evaluate this information; it also refers to the refinement of existing techniques to acquire the genomic data. Finding genes and determining their function, predicting the structure of proteins and RNA sequences from the avail- able DNA sequence, and determining the evolutionary rela- tionship of proteins and DNA sequences are also part of bioinformatics. The genome sequences of some bacteria, yeast, a nem- atode, the fruit fly Drosophila and several plants have been obtained during the past decade, with many more sequences nearing completion. During the year 2000, the sequencing of the human genome was completed. In addition to this accu- mulation of nucleotide sequence data, elucidation of the three-dimensional structure of proteins coded for by the genes has been accelerating. The result is a vast ever-increas- ing amount of databases and genetic information The effi- cient and productive use of this information requires the specialized computational techniques and software. Bioinformatics has developed and grown from the need to extract and analyze the reams of information pertaining to genomic information like nucleotide sequences and protein structure. Bioinformatics utilizes statistical analysis, stepwise computational analysis and database management tools in order to search databases of DNA or protein sequences to fil- ter out background from useful data and enable comparison of data from diverse databases. This sort of analysis is on-going. The exploding number of databases, and the various experi- mental methods used to acquire the data, can make compar- isons tedious to achieve. However, the benefits can be enormous. The immense size and network of biological data- bases provides a resource to answer biological questions about mapping, gene expression patterns, molecular modeling, molecular evolution, and to assist in the structural-based design of therapeutic drugs. Obtaining information is a multi-step process. Databases are examined, or browsed, by posing complex com- putational questions. Researchers who have derived a DNA or protein sequence can submit the sequence to public reposito- ries of such information to see if there is a match or similarity with their sequence. If so, further analysis may reveal a puta- tive structure for the protein coded for by the sequence as well as a putative function for that protein. Four primary databases, those containing one type of information (only DNA sequence Under the proper conditions, physical phenomena such as lightning are capable of providing the energy needed for atoms and molecules to assemble into the fundamental building blocks of life. womi_B 5/6/03 1:09 PM Page 69 Biological warfare WORLD OF MICROBIOLOGY AND IMMUNOLOGY 70 • • data or only protein sequence data), currently available for these purposes are the European Molecular Biology DNA Sequence Database (EMBL), GenBank, SwissProt and the Protein Identification Resource (PIR). Secondary databases contain information derived from other databases. Specialist databases, or knowledge databases, are collections of sequence information, expert commentary and reference liter- ature. Finally, integrated databases are collections (amalgama- tions) of primary and secondary databases. The area of bioinformatics concerned with the deriva- tion of protein sequences makes it conceivable to predict three-dimensional structures of the protein molecules, by use of computer graphics and by comparison with similar pro- teins, which have been obtained as a crystal. Knowledge of structure allows the site(s) critical for the function of the pro- tein to be determined. Subsequently, drugs active against the site can be designed, or the protein can be utilized to enhanced commercial production processes, such as in phar- maceutical bioinformatics. Bioinformatics also encompasses the field of compara- tive genomics. This is the comparison of functionally equiva- lent genes across species. A yeast gene is likely to have the same function as a worm protein with the same amino acid. Alternately, genes having similar sequence may have diver- gent functions. Such similarities and differences will be revealed by the sequence information. Practically, such knowledge aids in the selection and design of genes to instill a specific function in a product to enhance its commercial appeal. The most widely known example of a bioinformatics driven endeavor is the Human Genome Project. It was initi- ated in 1990 under the direction of the National Center for Human Genome Research with the goal of sequencing the entire human genome. While this has now been accomplished, the larger aim of determining the function of each of the approximately 50,000 genes in the human genome will require much further time and effort. Work related to the Human Genome Project has allowed dramatic improvements in molecular biological techniques and improved computational tools for studying genomic function. See also Hazard Analysis and Critical Point Program (HAACP); Immunological analysis techniques; The Institute for Genomic Research (TIGR); Medical training and careers in microbiology; Transplantation genetics and immunology BIOLOGICAL WARFARE Biological warfare Biological warfare, as defined by The United Nations, is the use of any living organism (e.g. bacterium, virus) or an infec- tive component (e.g., toxin), to cause disease or death in humans, animals, or plants. In contrast to bioterrorism, bio- logical warfare is defined as the “state-sanctioned” use of bio- logical weapons on an opposing military force or civilian population. Biological weapons include viruses, bacteria, rickettsia, and biological toxins. Of particular concern are genetically altered microorganisms, whose effect can be made to be group-specific. In other words, persons with particular traits are susceptible to these microorganisms. The use of biological weapons by armies has been a reality for centuries. For example, in ancient records of battles exist the documented use of diseased bodies and cattle that had died of microbial diseases to poison wells. There are even records that infected bodies or carcasses were catapulted into cities under siege. In the earliest years of the twentieth century, however, weapons of biological warfare were specifically developed by modern methods, refined, and stockpiled by various govern- ments. During World War I, Germany developed a biological warfare program based on the anthrax bacillus (Bacillus anthracis) and a strain of Pseudomonas known as Burkholderia mallei. The latter is also the cause of Glanders disease in cattle. Allied efforts in Canada, the United States, and Britain to develop anthrax-based weapons were also active in World War II During World War II, Britain actually produced five million anthrax cakes at the U.K. Chemical and Biological Defense Establishment at Porton Down facility that were intended to be dropped on Germany to infect the food chain. The weapons were never used. Against their will, prisoners in German Nazi concentration camps were maliciously infected with pathogens, such as hepatitis A, Plasmodia spp., and two types of Rickettsia bacteria, during studies allegedly designed to develop vaccines and antibacterial drugs. Japan also con- ducted extensive biological weapon research during World War II in occupied Manchuria, China. Unwilling prisoners were infected with a variety of pathogens, including Neisseria meningitis, Bacillus anthracis, Shigella spp, and Yersinia pestis. It has been estimated that over 10,000 prisoners died as a result of either infection or execution following infection. In addition, biological agents contaminated the water supply and some food items, and an estimated 15 million potentially plague-infected fleas were released from aircraft, affecting many Chinese cities. However, as the Japanese military found out, biological weapons have fundamental disadvantages: they are unpredictable and difficult to control. After infectious agents were let loose in China by the Japanese, approximately 10,000 illnesses and 1,700 deaths were estimated to have occurred among Japanese troops. A particularly relevant example of a microorganism used in biological warfare is Bacillus anthracis. This bac- terium causes anthrax. Bacillus anthracis can live as a vegeta- tive cell, growing and dividing as bacteria normally do. The organism has also evolved the ability to withstand potentially lethal environmental conditions by forming a near-dormant, highly resistant form known as a spore. The spore is designed to hibernate until conditions are conducive for growth and reproduction. Then, the spore resuscitates and active meta- bolic life resumes. The spore form can be easily inhaled to produce a highly lethal inhalation anthrax. The spores quickly and easily resuscitate in the warm and humid conditions of the lung. Contact with spores can also produce a less lethal but dangerous cutaneous anthrax infection. womi_B 5/6/03 1:09 PM Page 70 Biological Weapons Convention (BWC) WORLD OF MICROBIOLOGY AND IMMUNOLOGY 71 • • One of the “attractive” aspects of anthrax as a weapon of biological warfare is its ability to be dispersed over the enemy by air. Other biological weapons also have this capacity. The dangers of an airborne release of bioweapons are well documented. British open-air testing of anthrax weapons in 1941 on Gruinard Island in Scotland rendered the island inhabitable for five decades. The US Army con- ducted a study in 1951-52 called “Operation Sea Spray” to study wind currents that might carry biological weapons. As part of the project design, balloons were filled with Serratia marcescens (then thought to be harmless) and exploded over San Francisco. Shortly thereafter, there was a corresponding dramatic increase in reported pneumonia and urinary tract infections. And, in 1979, an accidental release of anthrax spores, a gram at most and only for several minutes, occurred at a bioweapons facility near the Russian city of Sverdlovsk. At least 77 people were sickened and 66 died. All the affected were some 4 kilometers downwind of the facility. Sheep and cattle up to 50 kilometers downwind became ill. The first diplomatic effort to limit biological warfare was the Geneva Protocol for the Prohibition of the Use in War of Asphyxiating, Poisonous or Other Gases, and of Bacteriological Methods of Warfare. This treaty, ratified in 1925, prohibited the use of biological weapons. The treaty has not been effective. For example, during the “Cold War” between the United States and the then Soviet Union in the 1950s and 1960s, the United States constructed research facilities to develop antisera, vaccines, and equipment for protection against a possible biological attack. As well, the use of microorganisms as offensive weapons was actively investigated. Since then, other initiatives to ban the use of biological warfare and to destroy the stockpiles of biological weapons have been attempted. For example, in 1972 more than 100 countries, including the United States, signed the Convention on the Prohibition of the Development Production, and the Stockpiling of Bacteriological (Biological) and Toxin Weapons and on Their Destruction. Although the United States formally stopped biological weapons research in 1969 (by executive order of then President Richard M. Nixon), the Soviet Union carried on biological weapons research until its demise. Despite the international prohibitions, the existence of biological weapons remains dangerous reality. See also Anthrax, terrorist use of as a biological weapon; Bacteria and bacterial infection; Bioterrorism, protective measures; Bioterrorism; Infection and resistance; Viruses and response to viral infection BIOLOGICAL WEAPONS CONVENTION (BWC) Biological Weapons Convention (BWC) The Biological Weapons Convention (more properly but less widely known as The Biological and Toxin Weapons Convention) is an international agreement that prohibits the development and stockpiling of biological weapons. The lan- guage of the Biological Weapons Convention (BWC) describes biological weapons as “repugnant to the conscience of mankind.” Formulated in 1972, the treaty has been signed (as of June 2002) by more than 159 countries; 141 countries have formally ratified the BWC. The BWC broadly prohibits the development of pathogens—disease-causing microorganisms such as viruses and bacteria—and biological toxins that do not have estab- lished prophylactic merit (i.e., no ability to serve a protective immunological role), beneficial industrial use, or use in med- ical treatment. The United States renounced the first-use of biological weapons and restricted future weapons research programs to issues concerning defensive responses (e.g., immunization, detection, etc.), by executive order in 1969. Although the BWC disarmament provisions stipulated that biological weapons stockpiles were to have been destroyed by 1975, most Western intelligence agencies openly question whether all stockpiles have been destroyed. Despite the fact that it was a signatory party to the 1972 Biological and Toxin Weapons Convention, the former Soviet Union maintained a well-funded and high-intensity biological weapons program throughout the 1970s and 1980s, producing and stockpiling biological weapons including anthrax and smallpox agents. US intelligence agencies openly raise doubt as to whether successor Russian biological weapons pro- grams have been completely dismantled. In June 2002, traces of biological and chemical weapon agents were found in Uzbekistan on a military base used by U.S. troops fighting in Afghanistan. Early analysis dates and attributes the source of the contamination to former Soviet Union or successor Russian biological and chemical weapons programs that uti- lized the base. As of 2002, intelligence estimates compiled from vari- ous agencies provide indications that more than two dozen countries are actively involved in the development of biologi- cal weapons. The US Office of Technology Assessment and the United States Department of State have identified a list of potential enemy states developing biological weapons. Such potentially hostile nations include Iran, Iraq, Libya, Syria, North Korea, and China. The BWC prohibits the offensive weaponization of bio- logical agents (e.g., anthrax spores). The BWC also prohibits the transformation of biological agents with established legit- imate and sanctioned purposes into agents of a nature and quality that could be used to effectively induce illness or death. In addition to offensive weaponization of microorgan- isms or toxins, prohibited research procedures include con- centrating a strain of bacterium or virus, altering the size of aggregations of potentially harmful biologic agents (e.g., refining anthrax spore sizes to spore sizes small enough to be effectively and widely carried in air currents), producing strains capable of withstanding normally adverse environmen- tal conditions (e.g., disbursement weapons blast), and the manipulation of a number of other factors that make biologic agents effective weapons. womi_B 5/6/03 1:09 PM Page 71 Bioluminescence WORLD OF MICROBIOLOGY AND IMMUNOLOGY 72 • • Although there have been several international meet- ings designed to strengthen the implementation and monitor- ing of BWC provisions, BWC verification procedures are currently the responsibility of an ad hoc commission of scien- tists. Broad international efforts to coordinate and strengthen enforcement of BWC provisions remains elusive. See also Anthrax, terrorist use of as a biological weapon; Bacteria and bacterial infection; Biological warfare; Epidemics and pandemics; Vaccine BIOLOGY, CENTRAL DOGMA OF • see M OLECULAR BIOLOGY AND MOLECULAR GENETICS B IOLUMINESCENCE Bioluminescence Bioluminescence is the production of light by living organ- isms. Some single-celled organisms ( bacteria and protista) as well as many multicellular animals and fungi demonstrate bio- luminescence. Light is produced by most bioluminescent organisms when a chemical called luciferin reacts with oxygen to pro- duce light and oxyluciferin. The reaction between luciferin and oxygen is catalyzed by the enzyme luciferase. Luciferases, like luciferins, usually have different chemical structures in different organisms. In addition to luciferin, oxy- gen, and luciferase, other molecules (called cofactors) must be present for the bioluminescent reaction to proceed. Cofactors are molecules required by an enzyme (in this case luciferase) Bioluminescent bacteria. womi_B 5/6/03 1:10 PM Page 72 [...]... he became the first head of the Bacteriology Department in 19 10 He remained head until his retirement in 19 48 He was also the first dean of Industrial Science, first dean of the Graduate College (19 19 19 48), and was Director of the Agriculture Experiment Station from 19 33 until 19 48 In his research life, Buchanan was a microbial taxonomist, concerned with the classification of microorganisms This interest... the Board of Trustees of the Bergey’s Manual of Determinative Bacteriology, and to assume the responsibilities of co-editor of the eighth edition of the manual in 19 74 The Manual is the definitive reference volume on bacterial classification Buchanan was also one of the founders of the International Bulletin of Bacterial Nomenclature and Taxonomy in 19 51 He served on the first editorial board of the journal... and microbiology departments at this company Since 19 83, Borel has been Vice-President of the Pharma division of Novartis Since 19 81, Borel has also been a professor of immunopharmacology in the medical faculty at the University of Bern In 19 71, Borel isolated a compound (subsequently called cyclosporin) from a sample of the fungus Beauvaria nivea that was obtained during a hike by a Sandoz employee who... also BSE and CJD disease, advances in research; BSE and CJD disease, ethical issues and socio-economic impact; Latent viruses and diseases BSE AND CJD: ETHICAL ISSUES AND SOCIO-ECONOMIC IMPACT BSE and CJD: Ethical issues and socio-economic impact 90 • The outbreak of bovine spongiform encephalopathy (BSE) or “mad cow disease” in the United Kingdom and continental Europe continues to concern beef and dairy... in Brussels in 19 61 See also Antibody and antigen; B cells or B lymphocytes; Bacteria and bacterial infection; Bacteriophage and bacteriophage typing; Blood agar, hemolysis, and hemolytic reactions; Immune system; Immunity; Immunization; T cells or T lymphocytes BOREL, JEAN-FRANÇOIS Borel, Jean François (19 3 3- ) Belgian immunologist 84 • Jean-François Borel is one of the discoverers of cyclosporin... of syph teria in the human blood Already famous by the age of thirty-one, accepted the directorship of the newly created Anti-rab Bacteriological Institute in Brussels in 19 01; two yea the organization was renamed the Pasteur Institute of B From 19 01, Bordet was obliged to divide his time betw research and the administration of the Institute In 1 also began teaching following his appointment as prof... International Journal of Systematic and Evolutionary Bacteriology In 19 34 , the Society of American Bacteriologists began the process of expansion by adding a branch that represented bacteriologists in Iowa, Minnesota, North Dakota, South Dakota, and Wisconsin Buchanan became the first President of the Northwest Branch of the Society in 19 35 Buchanan also founded the Iowa State Journal of Science in 19 26 The journal... Genentech, Inc and a member National Academy of Sciences His many honors include the Albert and Mary Lasker Basic Medical Research Award in 19 80, the National Medal of Technology in 19 89, and the National Medal of Science in 19 90 See also Molecular biology and molecular genetics BRENNER, SYDNEY (19 2 7- ) South African–English molecular biologist Brenner, Sydney 86 • Sydney Brenner is a geneticist and molecular... the Pasteur Institute, and from 18 94 to 19 01, Bordet stayed in Paris at the laboratory of the Ukrainian-born scientist Élie Metchnikoff In 18 99, Bordet married Marthe Levoz; they eventually had two daughters, and a son who also became a medical scientist During his seven years at the Pasteur Institute, Bordet made most of the basic discoveries that led to his Nobel Prize of 19 19 Soon after his arrival... with prions and that Creutzfeldt-Jakob disease (CJD) w hepatitis and AIDS in the public and medical conscious the next infectious disease epidemic which may be con through donated blood and tissue In view of the the risk of blood-borne transmission of CJD, some experts mend that the following groups of people not donate bl people with CJD; first-degree relatives of CJD patien • optometrists and opthamologists—hard . electron micrograph of Ebola virus. womi_B 5/6/ 03 1: 10 PM Page 81 Blue-green algae WORLD OF MICROBIOLOGY AND IMMUNOLOGY 82 • • Another group particularly at risk of blood borne infec- tions are hemophiliacs indigenous microorganisms also capable of utilizing hydrocarbons as metabolic substrates. Consequently, seeding of microorgan- womi_B 5/6/ 03 1: 10 PM Page 73 Biotechnology WORLD OF MICROBIOLOGY AND IMMUNOLOGY 74 • • isms. techniques WORLD OF MICROBIOLOGY AND IMMUNOLOGY 63 • • loss of the potato crops in Ireland resulted in the death due to starvation of at least one million people, and the mass emigra- tion of people