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Germline stem cell proliferation is necessary to populate the germline with sufficient numbers of cells for gametogenesis and for signaling the soma to control organismal properties such as aging. The Caenorhabditis elegans gene glp-4 was identified by the temperature-sensitive allele bn2 where mutants raised at the restrictive temperature produce adults that are essentially germ cell deficient, containing only a small number of stem cells arrested in the mitotic cycle but otherwise have a morphologically normal soma. We determined that glp-4 encodes a valyl aminoacyl transfer RNA synthetase (VARS-2) and that the probable null phenotype is early larval lethality. Phenotypic analysis indicates glp-4(bn2ts) is partial loss of function in the soma. Structural modeling suggests that bn2 Gly296Asp results in partial loss of function by a novel mechanism: aspartate 296 in the editing pocket induces inappropriate deacylation of correctly charged Val-tRNAval. Intragenic suppressor mutations are predicted to displace aspartate 296 so that it is less able to catalyze inappropriate deacylation. Thus glp-4(bn2ts) likely causes reduced protein translation due to decreased levels of Val-tRNAval. The germline, as a reproductive preservation mechanism during unfavorable conditions, signals the soma for organismal aging, stress and pathogen resistance. glp-4(bn2ts) mutants are widely used to generate germline deficient mutants for organismal studies, under the assumption that the soma is unaffected. As reduced translation has also been demonstrated to alter organismal properties, it is unclear whether changes in aging, stress resistance, etc. observed in glp-4(bn2ts) mutants are the result of germline deficiency or reduced translation.

Genetic defects vary from trivial to life threatening. Although we tend to think of inherited conditions such as cystic fibrosis and muscular dystrophy as diseases, we often refer to cleft palates or color blindness as inherited defects. However, they are all due to mutations in DNA, the genetic material. Not only are some diseases directly caused by mutations, but susceptibility to infectious disease and to factors such as radiation also is influenced by a variety of genes. True human genetic engineering is still in the future. At present, genetic engineering is restricted to nonhumans and has resulted in the creation of transgenic plants and animals. Eugenics refers to deliberate improvement of the human race by selective breeding. Early eugenic proposals were based on choosing superior parents by visual inspection or medical screening and breeding them in much the same way as for prize pigs and pedigreed dogs. Today, we have reached the position where direct alterations of the human genome at the DNA level are technically feasible although still clumsy.

RNA plays a multifaceted role in biology that is adaptable for many different applications in biotechnology. The most widely understood role of RNA is in protein synthesis, which includes messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA) (see Chapter 2 ). However, RNA plays many other roles. Several small RNAs, such as snRNA, snoRNA, and gRNA, take part in RNA processing by removing introns. Some RNA sequences can catalyze enzyme reactions. Ribozymes, as they are called, are found in many organisms, catalyzing cleavage and ligation of various substrates. Between the increased speed and accuracy of sequencing and a heightened awareness of RNA in the cell, an ever-increasing number of roles has been found for RNA in the regulation of gene expression and in cell defense. Entirely new classes of noncoding RNAs (ncRNAs) have been discovered and characterized.

The environment around us has always been a source of new products and stimulated our imagination in developing new technologies. Our species is very successful at harnessing the environment for our benefit. We are also good at destroying or harming the environment for immediate gains. The readily visible world has been charted and mapped, but areas under the ocean and in the deep recesses of jungles are still unknown. In fact, many parts of the visible world still harbor unknown life forms invisible to the naked eye, including bacteria and viruses. These are found in the air, water, and land. Many have unique metabolisms, and some have abilities never seen before. Many can live in extreme environments once thought too hot or too dry for life to exist.

One of the most promising fields within biotechnology is the development of transgenic plants. The ability to transfer genes from any organism into a plant unleashes a nearly boundless capacity to improve crops and other plants of interest. In this chapter, we explore the basis of this powerful and revolutionary technology.

Two essential features of living creatures are the ability to reproduce their own genome and manufacture their own energy. To accomplish these feats, an organism must be able to make proteins using information encoded in its DNA. Proteins are essential for cellular architecture, giving the cell a particular shape and structure. Proteins include enzymes that catalyze reactions used to make energy. Proteins control cellular processes like replication. Proteins provide channels in the membrane for cells to communicate with each other or share metabolites. Making proteins is a key operation for all living organisms.

Both inherited diseases and cancers are genetic in origin. Inherited diseases are genetic defects that are passed on from one individual to another via the germline. Mutations must occur in the germline cells, which give rise to the eggs and sperm, to be passed on to the descendants of a multicellular organism. In contrast, each occurrence of cancer is limited to a single multicellular organism and is not passed on to the next generation. If a mutation does occur in somatic cells—those making up the rest of the body—a variety of possibilities may result. A mutation that occurs early on in embryonic development may be highly detrimental, because each cell of the embryo gives rise to many cells during development. If the single precursor cell for a major organ or tissue suffers a serious mutation, the results may be serious or fatal. Most somatic mutations occurring later in development will affect only one or a few cells and will be of little major significance.

Replication copies the entire set of genomic DNA so that the cell can divide in two. During replication, the entire genome must be uncoiled and copied exactly. This elegant process occurs extremely fast in E. coli, where DNA polymerase copies about 1000 nucleotides per second. Although the process is slower in eukaryotes, DNA polymerase still copies 50 nucleotides per second. Many biotechnology applications use the principles and ideas behind replication; therefore, this chapter first introduces the basics of DNA replication as it occurs in the cell. We then review some of the most widely used techniques in genetic engineering and biotechnology, including chemical synthesis of DNA, polymerase chain reaction, and DNA sequencing.

Several areas of biotechnology are advancing more rapidly than others. Perhaps the two most obvious are speedier DNA sequencing technology and emerging novel roles for RNA. This chapter is new to this edition of this book and tackles a third area. Unlike the other two, this area is on the boundary where biotechnology merges with computer science and electronics.

Aging is a process we all start at birth and continue until death. Some people seem to age very gracefully, whereas others show signs of aging very early. Even ignoring the effects of infection or accident, quite a large range of life spans occurs among humans. Interestingly, there is a dramatic difference in the average life span of similar-sized mammalian species. For example, mice live about 2 to 3 years, whereas other rodents of similar size average about 5 to 10 years. Therefore, age is a relative term with differences within and between species.

Stem cells have ignited controversy among groups of politicians, religious leaders, and many people in the public. Whether scientists should study stem cells is hotly debated in the United States, but other parts of the world are also creating rules and regulations as to the use and study of stem cells. Many of the reports seen in the media provide a very negative slant to the use of stem cells in scientific research, but most of the reports do not explain the reason stem cells are so controversial. In addition, most of the accounts do not explain what a stem cell is and why scientists want to study them. One of the key goals for this chapter is to provide the answers to these questions and to describe the importance these cells have in your tissues and organs. Because of the key role stem cells play in our body, the idea of using stem cells to cure diseases and disabilities has evolved. This chapter explains the motive and current state of research for the use of stem cells in some therapies. Most importantly, the chapter distinguishes between the types of stem cells that are the focus of the heated political debates and the other types of stem cells, and the continuum of characteristics that range between these types of cells.

The term biological warfare typically conjures images of medieval warriors tossing dead cattle over city walls or clandestine government agents secretly releasing mysterious microbes into enemy territory. Of course, biological warfare does encompass such activity, but the vast majority of what constitutes biological warfare is far more mundane. Ever since life evolved on earth about 3.8 billion years ago, organisms have constantly devised new ways to kill each other. Any organism that makes use of toxins—from bacteria to snakes—is engaging in a form of biological warfare. Humans who engage in biological warfare do so by taking advantage of these toxin-producing organisms.

DNA technology has many practical uses. Because every individual has a unique DNA sequence, DNA samples can be used for identification. The legal system is now using DNA evidence to determine guilt or innocence. The application of DNA technology began in Britain in the mid-1980s and appeared in America shortly afterward. Today many societies have reached the point of compiling DNA databases of known criminals—especially serious offenders. However, the most frequent use of DNA evidence is actually in cases of unknown or disputed paternity.

From the genetic viewpoint, the production of a small molecule such as ethanol may well be more complex than production of a protein such as somatotropin. Although proteins are macromolecules, single genes encode them, whereas small molecules must be made by biochemical pathways that require several steps, each catalyzed by a separate enzyme. Thus, multiple genes are involved, together with their regulatory systems. Pathway engineering is the assembly of a new or improved biochemical pathway, using genes from one or more organisms. Most efforts to date have consisted of modification and improvement of existing pathways, rather than the assembly of completely new synthetic schemes. However, totally novel pathways will no doubt begin to appear over the next few years. This brings us to the concept of synthetic biology. This emerging area is constantly changing and is impossible to define precisely. The overall idea is the design of novel biological pathways, devices, or systems. It overlaps with pathway engineering but is more fashionable! Perhaps one key difference is that pathway engineering takes an existing pathway and improves it, whereas in synthetic biology the pathway or device is designed first and then assembled from available components.

As biotechnology continues its march forward, it will inevitably raise new moral and legal questions. Our expanding knowledge and capabilities—instead of resolving bioethical issues—will most likely create new challenges, and the line between ethical and unethical behavior will only become murkier. There are few “black and white” issues in bioethics, but instead varying shades of gray. Indeed, the complexity of bioethics is such that a student can now obtain a graduate-level degree in the field.

Proteomics has opened the door to identify more and more clinically relevant proteins. Once identified, these proteins need to be studied in detail, including expression of the protein in model organisms by using recombinant DNA techniques. Some proteins will become therapeutic agents, and large amounts of purified protein will be required.

A variety of enzymes have been in industrial use since before genetic engineering appeared. However, a mere couple of dozen enzymes account for over 90% of total industrial enzyme use. Some common examples are listed in this chapter. These proteins are used under relatively harsh conditions and are exposed to oxidizing conditions not found inside living cells. Consequently, these particular proteins are unusually robust and stable and are not at all representative of typical enzymes in this respect. It is notable that most of them are hydrolases that degrade either carbohydrate polymers or proteins.

Many human diseases are due to viruses. These agents consist of genomes of either DNA or RNA inside a protein shell. Despite this deceptive simplicity, virus infections are less well understood than bacterial diseases, largely because viruses cannot be grown alone in culture but depend on a host cell. Until recently, protection against virus diseases relied on public health measures and vaccination. Only since the late 1980s have a significant number of specific antiviral agents become available.

Today we have the genome sequences for humans as well as many other animals, plants, fungi, and bacteria. All these data have given scientists a global view of the various genes in humans and others. However, genes are only the first step to understanding how an organism works. Genes are transcribed into mRNA and then translated into protein. So if we are to truly understand gene function, the gene product or protein must be characterized also—hence, the advent of proteomics. Proteomics refers to the global analysis of proteins, and the proteome refers to the entire protein complement of an organism. The translatome, or the complement of proteins expressed under specific circumstances, also falls into this field of study. Note that the translatome is dynamic and changes when environmental conditions change.

Basic to all biotechnology research is the ability to manipulate DNA. First and foremost for recombinant DNA work, researchers need a method to isolate DNA from different organisms. Isolating DNA from bacteria is the easiest procedure because bacterial cells have little structure beyond the cell wall and cell membrane. Bacteria such as E. coli are the preferred organisms for manipulating any type of gene because of the ease at which DNA can be isolated. E. coli maintain both genomic and plasmid DNA within the cell. Genomic DNA is much larger than plasmid DNA, allowing the two different forms to be separated.

Biotechnology involves the use of living organisms in industrial processes—particularly in agriculture, food processing, and medicine. Biotechnology has been around ever since humans began manipulating the natural environment to improve their food supply, housing, and health. Biotechnology is not limited to humankind. Beavers cut up trees to build homes. Elephants deliberately drink fermented fruit to get an alcohol buzz. People have been making wine, beer, cheese, and bread for centuries. For wine, the earliest evidence of wine production has been dated to c. 6000 BC. All these processes rely on microorganisms to modify the original ingredients. Ever since the beginning of human civilization, farmers have chosen higher yielding crops by trial and error, so that many modern crop plants have much larger fruit or seeds than their ancestors.

For thousands of years people have improved crop plants and domestic animals by selective breeding, mostly at a trial-and-error level. Woollier sheep and smarter sheep dogs have both been improved through many generations of selective breeding. Obviously, the more we know about genetics, the faster and more effectively we can improve our crops and livestock. Today it is possible to alter plants, animals, and even humans by genetic engineering. Most early experiments in animal transgenics were done with mice, but many larger animals have now been engineered, including livestock such as sheep and goats, pets such as cats and dogs, and even monkeys. In a transgenic animal, every cell carries new genetic information. In other words, novel genetic information is introduced into the germline, not merely into some somatic cells as in gene therapy. Consequently, the novel genes in a transgenic animal are passed on to its descendants.

The main practical objectives of nanobiotechnology are using biological components to achieve nanoscale tasks. Some of these tasks are nonbiological and have applications in such areas as electronics and computing, whereas others are applicable to biology or medicine. The purpose of this chapter is to show, by selected examples, how biological approaches can contribute to nanoscience.