Understanding life

Using Biotech Tools to Understand Life



Both academic and industrial scientists have come to depend on various biotechnologies to study the workings of biological systems in remarkably precise detail. These biotech research tools have allowed them to answer long-standing scientific questions and have changed the questions they ask, the problems they tackle and the methods they use to get answers.



Research Applications of Biotechnology

Researchers use biotechnology to gain insight into the precise details of cell processes: the specific tasks assigned to various cell types; the mechanics of cell division; the flow of materials in and out of cells; the path by which an undifferentiated cell becomes specialized; and the methods cells use to communicate with each other, coordinate their activities and respond to environmental changes. Once they have teased apart details of a process, researchers must then reassemble the pieces in a way that provides insight into the inner workings of cells and, ultimately, of whole organisms.



Understanding Cell Processes

Researchers have made tremendous progress toward charting the path of a cell from a single, fertilized egg to a whole organism. The development of a multicelled organism from a single cell involves cell proliferation and cell differentiation—groups of cells becoming specialized, or differentiated, to perform specific tasks.

Cell differentiation is the process of turning off certain genes within a group of cells while turning on others. Scientists are optimistic about elucidating the many steps in the differentiation pathway and identifying the external and internal factors regulating the process. Two important breakthroughs have fueled this optimism: the development of a protocol for maintaining human stem cells in culture and the birth of the cloned sheep Dolly. A delicate balance exists between factors that stimulate cell division and those that inhibit it. Any disruption of this balance leads to uncontrolled cell proliferation cancer or cell death.

We have known for decades the basic requirements for keeping small numbers of plant and animal cells in culture. We maintained these cultures primarily to collect products that cells produce naturally. For example, plant-cell culture gives us flavors, colors, thickeners and emulsifiers for food processing.

Researchers now are keeping cells in culture to investigate the molecular basis of many cell processes, especially cell growth, proliferation, differentiation and death.



All cells progress through essentially the same cycle: They increase in size up to a certain point, the genetic material replicates, and the cell divides in two. Understanding what controls the cell cycle is essential to understanding the cause of many human and animal diseases, the basis of increasing crop plant yields, and a means for quickly increasing the cells used to manufacture products as diverse as fermented foods and medicines.



Improvements in cell-culture technology have allowed us to better understand the molecular basis of the cell cycle. The rigorously controlled sequence of steps in the cell cycle depends on both genetic and nutritional factors. A delicate balance exists between factors that stimulate cell division and those that inhibit it. Any disruption of this balance leads to uncontrolled cell proliferation cancer or cell death.



Studying cells in culture has led to a radical revision of our view of cell death. We once thought cells died in an unorganized, passive way, as cell parts and processes gradually deteriorated. But we now know that much cell death is a highly organized, well-planned sequence of events programmed into the genome.



Prolonged cell stress and other factors trigger programmed cell death, or apoptosis, in which the cell dismantles itself in an orderly way, breaks down its genome and sends a signal to the immune system to dispatch white blood cells that will remove it. Programmed cell death eliminates cells with damaged DNA, removes immune system cells that attack healthy cells and shapes tissue formation during development. A better understanding of cell death can also help us figure out why only some cells with environmentally damaged DNA turn cancerous; what breaks down in autoimmune diseases; and how to create better tissues for replacement therapies.



Stem Cell Technology

After animal cells differentiate into tissues and organs, some tissues retain a group of undifferentiated cells to replace that tissue’s damaged cells or replenish its supply of certain cells, such as red and white blood cells. When needed, these adult stem cells (ASCs) divide in two. One cell differentiates into the cell type the tissue needs for replenishment or replacement, and the other remains undifferentiated.



Embryonic stem cells (ESCs) have much greater plasticity than ASCs because they can differentiate into any cell type. Mouse embryonic stem cells were discovered and cultured in the late 1950s. The ESCs came from 12-day-old mouse embryo cells from biotechnology to biology: that were destined to become egg or sperm (germ cells) when the mouse matured. In 1981, researchers found another source of mouse ESCs with total developmental plasticity—cells taken from a 4-day-old mouse embryo. In the late 1990s researchers found that human ESCs could be derived from the same two sources in humans: primordial germ cells and the inner cell mass of 5-day-old embryos. These human embryonic stem cells were found to have the same pluripotent properties. Consequently, scientists believe ESCs have enormous potential to lead to treatments and cures for a variety of diseases.



Scientists also have been able to isolate stem cells from human placentas donated following normal, full-term pregnancies. Under certain culture conditions, these cells were transformed into cartilage-like and fat-like tissue. Maintaining cultures of ESCs and ASCs can provide answers to critical questions about cell differentiation: What factors determine the ultimate fate of unspecialized stem cells? How plastic are adult stem cells? Could we convert an ASC into an ESC with the right combination of factors? Why do stem cells retain the potential to replicate indefinitely? Is the factor that allows continual proliferation of ESCs the same factor that causes uncontrolled proliferation of cancer cells? If so, will transplanted ESCs cause cancer?



The answers to these and many other questions will determine the limits of the therapeutic potential of ESCs and ASCs. Only when they understand the precise mix of factors controlling proliferation and development will scientists be able to reprogram cells for therapeutic purposes. Using stem cell cultures, researchers have begun to elaborate the intricate and unique combination of environmental factors, molecular signals and internal genetic programming that decides a cell’s fate. Israeli scientists directed ESCs down specific developmental pathways by providing different growth factors. Others discovered that nerve stem cells require a dose of vitamin A to trigger differentiation into one specific type of nerve cell, but not another.



What factors wipe out a differentiated cell’s identity and take it back to its embryonic state of complete plasticity? Before Dolly’s birth, we did not know we could ask that question, much less answer it.



Another type of ASC, mesenchymal stem cells, can differentiate into at least three different cell types (fat cells, bone cells and cartilage cells) depending in part on the mix of nutrients and growth factors. Their destiny also depends on their physical proximity to one another. If mesenchymal stem cells are touching each other, they may become fat cells; if the cell density is too high, they will not differentiate into bone cells even when provided the appropriate nutrients and chemical signals.



Researchers have recently demonstrated that some types of mesenchymal stem cells might have even more developmental flexibility in vivo. When injected into mouse embryos, these cells differentiate into most of the cell types found in mice. In 2005, researchers at Johns Hopkins University began what was believed to be the first clinical trial in the United States of adult mesenchymal stem cells to repair muscle damaged by heart attack. Results of the trial, which used an Osiris Therapeutics experimental technology, were promising, even thought it was only a Phase I study for safety. Forty-two percent of patients who received the therapy experienced improvement in their condition at six months, versus only 11 percent of placebo patients.



Another approach to developing therapies based on cells takes a different tack. Rather than determining the molecular events that turn a stem cell into a specific cell type, scientists are studying the de-differentiation process.



De-differentiation Is Possible

Scientists had assumed a specialized animal cell could not revert to the unspecialized status of an embryonic stem cell. (Interestingly, specialized plant cells retain the potential to de-specialize.) They assumed a gene turned off during the differentiation process could not be activated. The birth of Dolly proved that assumption was incorrect. In a procedure known as somatic cell nuclear transfer (SCNT), a nucleus from a fully differentiated body (somatic) cell was placed in an egg, and its identity—adult sheep mammary gland cell nucleus—was erased. That egg developed into Dolly.



The birth of Dolly via SCNT showed that the genetic programming of a nucleus from a specialized somatic cell can be erased and reprogrammed, in vitro, by placing it in an egg cell. The egg develops into a 5- or 6-day-old embryo that is genetically identical to the animal that provided the nucleus, and cells taken from the embryo can develop into any cell type found in the animal. After SCNT showed we could generate ESCs containing undifferentiated genetic material from adult cells for some animals, it seemed likely we could develop similar techniques for using human patients’ own genetic material to develop replacement cells and tissues for therapeutic purposes. This idea is called therapeutic cloning.



Other possibilities are now emerging for cellular de-differentiation and re-differentiation. For example, differentiated blood cells, when starved, revert to a stem cell-like condition. With the proper coaxing, scientists have converted those cells into nerve and liver cells and even into blood vessels, which consist of two cell types with very different functions: muscle cells for contraction and cells lining the inner surface for movement of substances into and out of the blood. In addition, scientists have established conditions for de-differentiating a highly specialized type of nerve cell into a type of neural stem cell. The neural stem cells were then reprogrammed into many other types of cells found in the nervous system.



In 2005, Harvard University scientists succeeded in creating cells similar to ESCs by fusing a human skin cell with an ESC. The resulting hybrid cell was de-differentiated and ESC-like. Two years later, researchers at the University of Wisconsin, Madison, and Japan’s Kyoto University succeeded in reprogramming skin cells into cells indistinguishable from embryonic stem cells—without using egg cells or ESCs as starting material. Instead, they used different combinations of genes to trigger de-differentiation. The researchers noted that work with embryonic stem cells remains critical. It is simply too early in this young scientific field to know which techniques will prove most effective in medical applications.



Understanding Gene Function

The cell processes described above—growth, proliferation, differentiation, apoptosis—and many more are carried out and controlled by proteins. Proteins are the molecular players that regulate and drive each minute step of the overall process. Understanding the details of cell processes in health and disease means understanding proteins. Because genes contain the information for making proteins, understanding proteins means understanding gene function. The tools of biotechnology give scientists myriad opportunities to study gene function. Here are only a few of the ways biotechnology allows investigators to probe the genetic basis of cell functions.



Molecular Cloning

If scientists voted for the most essential biotechnology research tool, molecular cloning would likely win. If scientists voted for the most essential biotechnology research tool, molecular cloning would likely win. Either directly or indirectly, molecular cloning has been the primary driving force of the biotechnology revolution and has made remarkable discoveries routine. The research findings made possible through molecular cloning include identifying, localizing and characterizing genes; creating genetic maps and sequencing entire genomes; associating genes with traits and determining the molecular basis of the trait.



Molecular cloning involves inserting a new piece of DNA into a cell in such a way that it can be maintained, replicated and studied. To maintain the new DNA fragment, scientists insert it into a circular piece of DNA called a plasmid that protects the new fragment from the DNA-degrading enzymes found in all cells. Because a piece of DNA is inserted, or recombined with, plasmid DNA, molecular cloning is a type of recombinant DNA technology.



The new DNA, now part of a recombinant molecule, replicates every time the cell divides. In molecular cloning, the word clone can refer to the new piece of DNA, the plasmid containing the new DNA and the collection of cells or organisms, such as bacteria, containing the new piece of DNA. Because cell division increases, or “amplifies,” the amount of available DNA, molecular cloning provides researchers with an unlimited amount of a specific piece of genetic material to manipulate and study. In addition to generating many copies of identical bits of genetic material, molecular cloning also enables scientists to divide genomes into manageable sizes. Even the simplest genome— the total genetic material in an organism—is too cumbersome for investigations of single genes. To create packages of genetic material of sizes that are more amenable to studies such as gene sequencing and mapping, scientists divide genomes into thousands of pieces and insert each piece into different cells. This collection of cells containing an organism’s entire genome is known as a DNA library. Because identifying and mapping genes relies on DNA libraries created with molecular cloning, “to clone” can also mean to identify and map a gene.



One of the primary applications of molecular cloning is to identify the protein product of a particular gene and to associate that protein with the appearance of a certain trait. While this is useful for answering certain questions, genes do not act in isolation from one another. To fully understand gene function, we need to monitor the activity of many genes simultaneously. Microarray technology provides this capability.



Microarray Technology

With microarray technology, researchers can learn about gene function by monitoring the expression of hundreds or thousands of genes at one time. For example, a 12,000-gene microarray allowed researchers to identify the 200 or so genes that, based on their gene expression profiles, distinguish stem cells from differentiated cells. Monitoring simultaneous changes in gene function will shed light on many basic biological functions. For example, scientists are using microarrays to observe the changes in gene activity that occur as normal cells turn cancerous and begin to proliferate. In addition to providing information on possible causes of cancer, this type of information can shed light on the genes that let a cell know that it is time to divide.



Microarrays that display various tissue types allow us to determine the different genes that are active in different tissues. Simply being able to link an active gene to a tissue type can clue researchers in on its function. For example, a plant gene active in leaves but not roots or seeds may be involved in photosynthesis.



Different environmental conditions also affect gene expression. Researchers subject plants to stresses such as cold and drought, and then they use microarray technology to identify the genes that respond by initiating protein production. Researchers are also comparing gene activities of microbes in polluted environments to those of microbes in pristine environments to identify genes that break down environmental contaminants.



Antisense and RNA Interference

Another approach to understanding the relationship of genes, proteins and traits involves blocking gene expression and measuring resulting biochemical or visible changes. Scientists use antisense technology to block genes selectively. Antisense molecules are small pieces of DNA (or, more often, its close relative, RNA) that prevent production of the protein encoded in the blocked DNA.



A related, but mechanistically different, method of silencing genes is known as RNA interference (RNAi). Antisense technology works by using a single strand of DNA or RNA to physically block protein production from the RNA template. In RNA interference, adding small, double-stranded pieces of RNA to a cell triggers a process that ends with the enzymatic degradation of the RNA template. RNA interference, which was discovered serendipitously in plants in the 1990s, appears to be a natural mechanism that virtually all organisms use to defend their genomes from invasion by viruses. RNAi therapies are now in clinical testing. Precisely blocking the functions of single genes to assess gene function can provide important insights into cell processes.



Most cell processes are structured as pathways that consist of small biochemical steps. Sometimes the pathway resembles a complex chain reaction that starts with one protein causing changes in another protein. At other times, the pathway is a sequence of enzyme-catalyzed reactions in which each enzyme (protein) changes a molecule slightly and then hands it off to the next enzyme. The physical manifestation of a certain trait or disease is the culmination of many or all of these steps.



Gene Knockouts

One of biotech’s most powerful research tools for elucidating gene function is targeted mutations, or gene knockouts. By deleting or disrupting a specific gene, we gain valuable information about that gene’s role in the expression of a certain protein. When gene-knockout technology is combined with our ability to derive genetically identical animals from cultured cells, we can determine how the absence of a protein affects the whole organism. Scientists have created a wide variety of genetically identical colonies of mice with very specific genes knocked out to study the processes of gene regulation, DNA repair and tumor development.



For years scientists have used animal models of disease to understand the pathophysiology of disease in humans. Our research capabilities in disease pathology broadened greatly as we coincidentally learned more about the genetic causes of diseases, developed methods of knocking out specific genes and learned how to maintain cultures of embryonic stem cells. Using this suite of technologies, researchers have created animal disease models for Alzheimer’s disease, aging, cancer, diabetes, obesity, cardiovascular disease and autoimmune diseases. Using nuclear transfer and embryonic stem cell culture, scientists should be able to develop animal disease models for many more species.



Putting the Pieces Together: ‘Omics’ and Related Tools

Biotech’s powerful research tools have set a fast pace for basic scientific discovery. They have enabled researchers to tease apart cellular and genetic processes so thoroughly that we are beginning to understand biological systems at their most fundamental level—the molecular level. But biological organisms do not operate as molecular bits and pieces. The only way to truly understand organisms is to reassemble these bits and pieces into systems and networks that interact with each other. This need to assemble separate findings into a complete picture has given birth to a rash of “omics”: genomics, proteomics, metabolomics, immunomics and transcriptomics. These research avenues attempt to integrate information into whole systems rather than focus on the individual components in isolation from each other. The biotechnologies are important tools in these endeavors, but information technologies are also essential for integrating molecular data into a coherent whole. The fields of research described below bridge scientific discoveries in cellular and molecular biology with their commercial applications.



Genomics

Genomics is the scientific study of the genome and the role genes play, individually and collectively, in determining structure, directing growth and development, and controlling biological functions. It consists of two branches: structural genomics and functional genomics.



Structural Genomics

The field of structural genomics includes the construction and comparison of various types of genome maps and large-scale DNA sequencing. The Human Genome Project and the less well-publicized Plant Genome Research Program are structural genomics research on a grand scale. In addition to genome

mapping and sequencing, the objective of structural genomics research is gene discovery, localization and characterization. Private and public structural genomics projects have generated genome maps and complete DNA sequences for many organisms, including crop plants and their pathogens, disease-causing

bacteria and viruses, yeast essential to the food processing and brewing industries, nitrogen-fixing bacteria, the malaria parasite and the mosquito that transmits it, and the microbes we use to produce a wide variety of industrial products.



In addition, in the spring of 2003, the Human Genome Project was completed (“rough drafts” of the genome were completed in 2000). Because all living organisms share a common heritage and can translate genetic information from many other organisms into biological function, the different genome projects inform each other, and any gene discovered through these projects could have wide applicability in many industrial sectors.



Knowing the complete or partial DNA sequences of certain genes or markers can provide researchers with useful information, even if the precise details of gene function remain unknown.

For example, sequence data alone can:

●●help plant breeders follow specific traits in a breeding program and test for inheritance without having to rear the plants to reproductive maturity.

●● be used to isolate specific recombinant molecules or microbes with unique biochemistry.

●● identify the genes involved in complex traits that are controlled by many genes and those that have an environmental component.

●● detect microbial contaminants in cell cultures.



Functional Genomics

While sequencing entire genomes and discovering and mapping genes are truly remarkable achievements, they represent only the first milestone in the genomics revolution. Gene sequence and mapping data mean little until we determine what those genes do, how they are regulated, and how the activity of one affects others. This field of study, known as functional genomics, enables researchers to navigate the complex structure of the human genome and to make sense of its content. Studies show that mammalian genomes have roughly the same number of genes and, in some cases, species less complex than mammals have a higher number of genes. It is not, however, the number of genes that is important to our understanding of the various species; rather, it is the compositional, functional, chemical and structural differences that dictate differentiation.Evolutionary analysis is emerging as a critical tool for elucidating the function and interactions of genes within a genome.



Molecular evolutionists use comparative genomics techniques and bioinformatics technologies to analyze the number of changes that DNA sequences undergo through the course of evolution. Using this data, researchers can recognize functionally important regions within genes and even construct a molecular timescale of species evolution.



The fruit fly (Drosophila melanogaster) has proven to be an invaluable model in the study of inherited genes. The humble fly’s desirable attributes include hardiness, availability and short generation time. As a result, a wealth of research and data produced from the study of the fruit fly are publicly available. Researchers at the Center for Evolutionary Functional Genomics at the Arizona Biodesign Institute have developed “FlyExpress,” a web-based informatics tool that uses advanced image processing and database techniques. Using this system, researchers can rapidly analyze gene expression patterns in embryonic image data.



Proteomics

Genes exert their effects through proteins; gene expression is protein production. And there’s an incredible amount of it going on, around the clock, in living cells. A cell may produce thousands of proteins, each with a specific function. This collection of proteins in a cell is known as its proteome, and proteomics is the study of the structure, function, location and interaction of proteins within and between cells. The collection of proteins in an entire organism is also referred as its proteome (e.g., the human proteome).



The structure of a protein molecule is much more complicated than that of DNA, which is a linear molecule composed of only four nucleotides. DNA’s nucleotides—in sequences of three called codons—code for 20 amino acids, which are the building blocks of proteins. Like DNA, proteins are built in a linear chain, but the amino acids form complex bonds that make the chain fold into complicated, intricate shapes. Those shapes are essential to each protein’s function.



We know that the sequence of amino acids affects the shape a protein assumes, but we do not yet understand all the rules that govern the folding process. This means that protein shape or function generally can’t be predicted from the amino acid sequence. Adding to the complexity, proteins undergo modifications after they are built (called post-translational modifications). These affect a protein’s form and function as well, helping to explain how the 25,000 human genes in the genome can make the hundreds of

thousands of proteins that comprise the human proteome.



Unlike the unvarying genome, an organism’s proteome is so dynamic that an almost infinite variety of protein combinations exists. The proteome varies from one cell type to the next, from one year to the next, and even from moment to moment. The cellular proteome changes in response to other cells in the body and external environmental conditions. A single gene can code for different versions of a protein, each with a different function.

When the Human Genome Project began, the first task researchers took on was developing the necessary tools for completing the project’s goals and objectives. Proteomics researchers likewise are developing tools to address many proteomics objectives, such as:

●●cataloging all of the proteins produced by different cell types.

●● determining how age, environmental conditions and disease affect the proteins a cell produces.

●● discovering the functions of these proteins.

●● charting the progression of a process—such as disease development, the steps in the infection process or the biochemical response of a crop plant to insect feeding—by measuring changes in protein production.

●● discovering how a protein interacts with other proteins within the cell and from outside the cell.



Bioinformatics and systems biology

Biotechnology as we know it today would be impossible without computers and the Internet. The common language of computers allows researchers all over the world to contribute and access biological data; the universal language of life enables collaborations among scientists studying any plant, animal or microbe.



One of the most formidable challenges facing researchers today remains in informatics: how to make sense of the massive amount of data provided by biotechnology’s powerful research tools and techniques. The primary problems are how to collect, store and retrieve information; manage data so that access is unhindered by location or compatibility; provide an integrated form of data analysis; and develop methods for visually representing molecular and cellular data.



Bioinformatics technology uses the computational tools of the information technology revolution—such as statistical software, graphics simulation, algorithms and database management—for consistently organizing, accessing, processing and integrating data from different sources.

Bioinformatics consists, in general, of two branches. The first concerns data gathering, storing, accessing and visualization; the second branch focuses more on data integration, analysis and modeling and is often referred to as computational biology.

Systems biology is the branch of biology that attempts to use biological data to create predictive models of cell processes, biochemical pathways and, ultimately, whole organisms. Systems biology is the branch of biology that attempts to use biological data to create predictive models of cell processes, biochemical pathways and, ultimately, whole organisms. Systems biologists develop a series of mathematical models to elucidate the full complexity of interactions in biological systems. Only with iterative computer biosimulations will we be able to develop a complete picture of the system we are studying. As an indicator of how essential computers have become to biotechnology labs, the phrase in silico has joined in vivo and in vitro as a descriptor of experimental conditions.



Over time, biotechnology products will increasingly focus on systems and pathways, not single molecules or single genes. Bioinformatics technology will be essential to every step in product research, development and commercialization.



Synthetic Biology

Now that scientists have broken genomes apart, can they put them together? Synthetic biology, sometimes described as the inverse of systems biology, seeks to do just that and assemble genomes and whole organisms.

Synthetic biologists are working to:

●●develop a set of “standard parts” that can be used (and re-used) to build biological systems.

●● reverse engineer and redesign biological parts.

●● reverse engineer and redesign a “simple” natural bacterium.



The research is advancing fast. In 2002, researchers at Stony Brook University in New York synthesized the polio virus. Three years later, the 1918 pandemic flu virus was synthesized at the Armed Forces Institute of Pathology. Synthetic biologists also are seeking to build organisms that can create energy and medicines. A project to develop a bacterial strain that can produce a malaria drug precursor attracted more than $40 million in funding from the Gates Foundation. Early in 2006, Dr. Jay Keasling, director of the Berkeley Center for Synthetic Biology, engineered a yeast containing bacterial and wormwood genes into a chemical factory to produce a precursor to artemisinin, the most effective and expensive antimalarial drug.



Researchers at the Howard Hughes Medical Institute and Yale University have used synthetic biology techniques to build proteins that don’t exist in the natural world. They’ve constructed these proteins from beta-amino acids, which are distinct from the alpha-amino acids that compose natural proteins. Their synthetic proteins are as stable as natural ones, but provide a distinct advantage: As they will not be degraded by enzymes or targeted by the immune system as natural ones are, these beta-proteins could be used as the basis for future drugs that would be more effective than natural protein drugs.



The Next Step: Using New Knowledge to Develop Products

Merely understanding biological systems is not enough, and this is especially true in medicine. Companies must turn the information gleaned from basic research, genomics and proteomics into useful products. The tools and techniques of biotechnology are helpful not only in product discovery but also are useful throughout the development process.



Product Discovery

A fundamental challenge facing many sectors of the biotechnology industry is how to improve the rate of product discovery. Many believe that current technology can vastly reduce the time it takes to discover a drug. Moreover, biotechnology is creating the tools to pinpoint the winning compounds far earlier in the process. For example, because scientists had long known the amino acid sequences of insulin and growth hormone, it was possible to commercially produce recombinant versions relatively soon after the advent of the technology. Discovering endogenous proteins that stimulate the immune system and red blood cell production led rapidly to their use as therapeutics. Other basic research has led to new products such as enzymes for food processing or industrial manufacturing and microbes with novel biochemistry for breaking down or synthesizing molecules. In addition, knowing only portions of the DNA sequence of certain genes can provide useful products, even without knowing about the gene’s function or the protein it encodes. For example, new product discoveries based solely on DNA sequence data acquired through structural genomics include:



●● diagnostics for plant, animal and human diseases.

●● tests to identify the presence of genetically modified food products.

●● antisense molecules to block gene expression.

●● tests to identify genetic susceptibilities to certain diseases.

●● tests for microbial contaminants in food products or donated blood.

●● tests for drug-resistant strains of HIV and other pathogens.

●● gene-based therapeutics, such as DNA vaccines and gene therapies.



In general, however, the information accumulating from studies of structural and functional genomics, proteomics and basic biology bolsters new product discovery by helping us understand the basic biology of the process we want to control or change. Understanding the process leads to new and better products, and sometimes

provides new uses for old products. For example, understanding the molecular bases of high blood cholesterol and diabetes, as well as the molecular mechanism of action of statin drugs, leads many researchers to believe that statins (designed to reduce cholesterol levels) might also help people with diabetes. The benefits of this deeper understanding to new product discovery apply to all industrial sectors that use biotechnology: pharmaceuticals, diagnostics, agriculture, food processing, forestry and industrial manufacturing. Medical applications of biotechnology illustrate how understanding molecular details encourages product discovery.



New Targets

The deconstruction of disease pathways and processes into their molecular and genetic components illuminates the exact point of malfunction and, therefore, the point in need of therapeutic intervention. Often, the biotechnology-derived therapeutic compound will not be a gene, protein or any type of biological molecule, but the therapeutic target will always be a gene or protein. Having structure and function information about genes and proteins involved in diseases makes finding useful molecules more rational than trial and error—hence the phrase rational drug design.



Having the complete roster of the molecular players gives us multiple targets to monitor, modulate or block; every step in a complex sequential process is a possible point of intervention. For example, we have elaborated the cascade of events that typifies programmed cell death (apoptosis), and we now know chemotherapy and radiation induce apoptosis. Therefore, tumors that resist chemotherapy and radiation treatments have changes in their apoptosis mechanism. Targeting the molecules involved in apoptosis should lead to new therapies for resistant tumors. With this knowledge of genomics and proteomics, scientists can identify not only the molecular target, but also the location of its bull’s-eye, which is usually one or a few locations within a protein molecule. The new field of chemical genomics allows us to identify small inorganic molecules that bind to those sites. These small molecules may be drawn from a collection of molecules built painstakingly by chemists over decades, or they might be the products of a relatively new technology that uses robotics to generate millions of chemical compounds in parallel processes, combinatorial chemistry.



Product Development

Genomics, proteomics, microarray technology, cell culture, monoclonal antibody technology and protein engineering are just a few of the biotechnologies that are being brought to bear at various stages of product development. Understanding the molecular basis of a process of interest allows many products to be tested in cells, which can save companies time and money and lead to better products. For example, agricultural biotechnology companies developing insectresistant plants can measure the amount of protective protein that a plant cell produces and avoid having to raise plants to maturity. Pharmaceutical companies can use cell-culture and microarray technology to test the safety and efficacy of drugs and observe adverse side effects early in the drug development process.



In addition, by genetically modifying animals to produce therapeutic protein targets or developing advanced transgenic animal models of human diseases, we can learn more about drug candidates’ in vivo effects before they enter human clinical trials. These technologies can help companies identify the best potential drug compounds quickly. Often, a single technology can be used at many steps in the development process. For example, a small piece of DNA that the research lab uses to locate a gene in the genome of a plant pathogen may eventually become a component of a diagnostic test for that pathogen. A monoclonal antibody developed to dentify therapeutic leads might be used to recover and purify a therapeutic compound during scale-up.



Targeted Products

Knowing molecular biology intimately leads to development of highly targeted products. For example, because we now understand the cell cycle and apoptosis, we are better able to develop products to treat diseases rooted in these processes. All cancers stem from uncontrolled cell multiplication and autoimmune diseases from a failure of apoptosis. Drugs for these ailments can be targeted to any of the molecules or cell structures involved in awry cell processes. Functional genomics has provided information on the molecular changes that occur in precancerous cells. Knowing this, we can develop detection tests for molecular markers that indicate the onset of cancer before visible cell changes or symptoms appear. Many chemotherapeutic agents target proteins active during cell division, making no distinction between healthy cells that divide frequently (such as those that produce hair or blood cells) and cancerous cells. To protect those healthy cells, some companies are developing medicines that would stop the cell cycle of healthy cells before delivering a dose of a chemotherapeutic agent.



Products Tailored to Individuals

We are entering the age of personalized medicine in which genetic differences among patients are acknowledged and used to design more effective treatments. A medicine’s effectiveness and safety often varies from one person to the next. Using data acquired in functional genomics, we will be able to identify genetic differences that predispose patients to adverse reactions to certain drugs or make them good subjects for other drugs. This tailoring of therapeutics to the genetic makeup of the patient is known as pharmacogenomics.



Just as people do not respond to a drug the same way, not all stages or types of a disease are the same. Medicines targeted to earlier stages of a disease may not affect a disease that has moved beyond that stage. Some diseases leave molecular footprints as they go from one stage to the next. Others vary in aggressiveness from patient to patient. Knowing the molecular profile allows physicians to diagnose how far the disease has progressed, or how aggressive it is, and choose the most appropriate therapy.