bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction and Application of Genomic DNA Libraries
Authors: Kim Hye Ran , Yang Tae Jin , Kudrna David A. , Wing Rod A. 
Published: July 2004

AbstractCrop failures, pathogenic outbreaks and famine are serious problems facing society. Understanding an organism's genome will help provide the genetic tools needed to solve these complex problems in a shorter time and with less effort. To efficiently study an organism's genome, it can be partitioned into a permanent and stable collection of DNA fragments, called a library. Such libraries provide convenient access to a genome for both laboratory and breeding applications. Genomic libraries can be used as substrates to physically map and sequence entire genomes, clone agriculturally important genes and to investigate gene expression patterns. Further, genomic libraries also provide powerful tools and resources for evaluating germplasm conservation stocks and biological diversity. The ongoing explosion of genetic data and molecular clone resources has opened new scientific possibilities to researchers venturing across all avenues of applied science. In this chapter we will present the details for small and large insert library construction and their applications.
Isolation and Analysis of Gene Regulatory Sequences
Authors: Hehl Reinhard , Steffens Nils Ole , Wingender Edgar 
Published: July 2004

AbstractDatabase‐assisted bioinformatic approaches facilitate the analysis of gene regulatory sequences and allow the identification of putative transcription factor binding sites or common regulatory motifs in similarly expressed genes. These approaches complement experiments that identify specific regulatory sites. They may be easily established if the respective transcription factors responsible for gene expression have already been cloned and annotated to the databases.In this chapter we summarise recent results on transcriptional regulation in plants and describe the most abundant transcription factor families ofArabidopsis thaliana. We summarise experimental approaches to delineate gene regulatory sequences that should precede a database‐assisted analysis. The plant cis‐regulatory DNA element database PLACE and the transcription factor databases PlantCARE and TRANSFAC® are described, including connected software tools. PlanCARE is a plant specific database and TRANSFAC® covers transcription factors of all eukaryotes. The content and use of the TRANSFAC® database is presented in detail. Furthermore, we give examples on the identification of putative transcription factor binding sites in previously identified regulatory sequences and compile other databases that are relevant for the identification of regulatory sequences.
Molecular Mapping and Marker‐Assisted Selection of Quantitative Trait Loci in Plants
Authors: Prince James P. , Ogundiwin Ebenezer A. 
Published: July 2004

AbstractSince the dawn of agriculture, mankind has tried to mould crop plants into more useful types. Over the years, experience and intuition led to the development of sophisticated and successful artificial selection (breeding) of many types of plants for human food, fibre, shelter, profit and pleasure. Just compare the cultivated tomato with some of its small‐ and green‐fruited relatives, or cultivated maize to teosinte. Most of this ‘improvement’ was probably through simple field selection and propagation of desirable genotypes. Scientifically based plant breeding, not appearing until the 20th century, has also had great successes in plant improvement, particularly in disease resistance and yield. Breeders have achieved good results for both single‐gene traits and polygenic traits, but the polygenic traits, encoded by multiple genes often referred to as quantitative trait loci (QTL), are much more difficult to work with. Advances in molecular genetics in the last 20 years have enabled the placement of molecular markers on to maps of the chromosomes of most major crop plants and the subsequent tagging of genes of interest by their placement near these markers. A major goal of these efforts is marker‐assisted selection (MAS), the use of molecular markers to track traits in breeding programmes. In this chapter, we will discuss the basics of molecular mapping in crop plants, the identification of the location of QTL and MAS. While not intended as an exhaustive review of the techniques nor of successes in this field, this chapter will provide lists of crops with linkage maps and QTLs identified to serve as entry points into the literature for investigators interested in pursuing this technology in a particular crop.
Gene Expression and Level of Expression
Authors: De Buck Sylvie , Depicker Anna 
Published: July 2004

AbstractGenes encoding heterologous proteins are introduced into the plant genome for several purposes. First, the plant‐made protein can be a tool in fundamental research. Second, the synthesis of heterologous proteins in plants can have biotechnological applications. Plants are capable of producing several types of recombinant proteins. Indeed, for the production of all these proteins, the use of plants is obvious, because they have several important advantages; plants can grow easily and inexpensively in large quantities and they can be harvested and processed with the available agronomic infrastructures and upscaling is very simple. Finally, using processes similar to those used in food and feed industry, specifically desired proteins can be easily purified. However, the stability of accumulation is as important as the accumulation levels themselves. Indeed, the introduced transgenes are not always correctly expressed and are often susceptible to position effects and homology‐dependent gene silencing (HDGS) mechanisms. Although the mechanism that induces silencing is still not completely unravelled, already some factors are defined which influence transgene expression, such as copy number and chromosomal position, methylation pattern in the integration region and properties of the transgene sequence itself.
Engineering of Crops for Improved Agronomic Traits
Authors: Gatehouse A.M.R. 
Published: July 2004

Abstract
Maximum crop productivity in a manner which is both environmentally sustainable and cost effective is a major challenge to agriculture. Since plants routinely encounter sustained periods of stress, sufficient to limit their growth and reproductive capacity, one means of achieving this goal of increased productivity is through a greater understanding of the complex adaptive responses that plants have evolved to combat these various forms of stress. Plant stress is classified as being either biotic (as a result of infestation by pests, pathogens, and/or weeds) or abiotic (as a consequence of unfavourable soils and/or climates, including inadequate or excessive supply of water). Biotechnology not only offers new opportunities and technologies for understanding the underlying mechanisms enabling plants to respond to stress, but also provides a powerful tool in the production of crop species with increased tolerance to biotic and abiotic forms of stress.

The current chapter serves as an introduction to the section on Agronomic Traits where key issues and recent developments in the improvement of crops to respond to stress, are addressed. It thus provides a brief overview both of the current status and future perspectives of transgenic crops with enhanced tolerance to pathogens (chapter

), insect pests (chapter

) and herbicides (chapter

). Furthermore, it considers the molecular bases of plant adaptation to abiotic stress and the use of QTLs and marker‐assisted breeding for the production of crops with increased tolerance to abiotic stress (chapter

).
Introduction
Authors: Kishore Ganesh 
Published: July 2004

Abstract
Plant metabolic engineering as a scientific discipline has come of age. Our understanding of the related microbial metabolic pathways and ability to introduce and express genes in plants, coupled with the rapidly evolving tools of systems biology are at the heart of this development. The scientific and commercial outcomes of plant metabolic engineering are numerous—from a greater and in depth understanding of metabolic reactions in plants to enhance productivity, increase sustainability and quality of the fundamental food, feed, fiber and fuel production systems of this planet.
Lipid Metabolism
Authors: Schmid Katherine M. 
Published: July 2004

AbstractLipids are an immensely diverse group of compounds, technically including all biomolecules that dissolve more readily in non‐polar solvents than in water. This review will emphasisze two prominent groups of lipids: the acyl lipids, whose hydrophobic units are derived from fatty acids, and the isoprenoids, made up of five‐carbon isopentene units. Acyl lipids, in the form of the triacylglycerols stored as energy reserves, underpin the vegetable oil industry. In addition, acyl lipids that dominate the bilayers of plant membranes, are indispensable for the protective layers that prevent plant desiccation and pathogen attack, and include several signalling molecules. Isoprenoids are even more diverse than acyl lipids, with more than 25,000known. Two prominent groups are the sterols, which are important membrane constituents, and the carotenoids, which collect light for photosynthesis, protect plants from excessive light, attract pollinators and fruit dispersal agents, and provide vitamin A precursors for consumers. Biotechnology has provided both a tool for understanding plant lipid metabolism, and a means of altering quality and quantity of these constituents to better serve the needs of industry and human nutrition better.
Storage Proteins and their Metabolism
Authors: Hagan N.D. , Higgins T.J.V. 
Published: July 2004

AbstractThe identification and cloning of storage protein genes over the last 20 years has provided new tools to improve grain and forage crops. To date, storage protein biotechnology has been used to address deficiencies of essential amino acids in important crop species, improve the digestibility of forage crops for ruminant animals and improve quality traits such as the bread making quality of wheat dough. High lysine maize is already available through the breeding of storage protein mutants, whilst transgenic crops containing storage proteins that impart a nutritional benefit are currently undergoing field trials. However, despite recent advances in this area, a number of limitations remain. In some cases, the rate of synthesis of particular amino acids limits protein accumulation. In other cases, the introduction of a new storage protein has altered the expression levels of endogenous proteins, potentially affecting desirable traits. In addition, some of the storage proteins targeted for use in transgenic plants have been identified as allergens.
Amino Acids
Authors: Hoefgen Rainer , Hesse Holger , Galili Gad 
Published: July 2004

Abstract
Amino acids perform essential functions in both primary and secondary plant metabolism besides their obvious role in protein synthesis. They can be categorised on the basis of their function such as serving to assimilate and transport nitrogen from sources to sinks or serving as precursors for secondary products such as hormones, vitamins, co‐factors and compounds in plant defence. Thus, synthesis of amino acids directly or indirectly controls various aspects of plant growth and development. Recent investigations of genes involved in amino acid biosynthesis reveal that this is a dynamic process controlled by metabolic, environmental and developmental factors including mineral nutrients such as nitrate and sulphate. This chapter intends to provide fundamental knowledge on nitrogen and sulphur metabolism as basis for amino acid biosynthesis and to highlight examples in which combined molecular, biochemical and genetic approaches have helped to define the pathways and uncover regulatory mechanisms of amino acid biosynthesis in plants. These studies have implications for both basic and applied research because amino acid biosynthesis is as well a target for herbicide action as an option to improve the nutritional quality of crops by metabolic engineering and plant breeding.
Metabolic Engineering of Plant Secondary Metabolism
Authors: Peters Reuben J. , Croteau Rodney B. 
Published: July 2004

Abstract
In this chapter, we focus on the promise inherent in current efforts to manipulate plant secondary metabolism to improve the yield and/or quality of domestic crop plants. While there is yet no commercial production of any crops engineered in this fashion, a number of crops are in development based on successful research demonstrating the potential of such alteration for improving agriculture and human health. However, as in the deployment of any new technology, there are cautionary notes regarding the possibility of unforeseen and undesirable side effects of such manipulation.
Phytochromes – Biotechnological Prospects
Authors: Reid Robert , Jones Huw D. , Smith Harry 
Published: July 2004

AbstractAt all stages of the life‐cycle plant growth and development processes are exceptionally responsive to signals in the light environment. Light signals can, and often do, determine when a seed germinates, when a plant flowers, the direction in which its stems grow, the balance between stem, leaf and root growth, and the interactions between a plant and it neighbours. All of these processes can be crucial to crop plant performance. More than 50 years of fundamental research has been devoted to discovering the mechanisms through which plants detect and respond to the natural light environment, and this research is now reaching the stage where the finding can be exploited in ways that will enhance crop productivity. This chapter outlines the work that has been done on phytochrome genes and their transgenic expression with a view to identifying promising approaches for the future.
Flowering Time
Authors: Laurie David A. 
Published: July 2004

AbstractFlowering involves profound developmental changes that switch vegetative growth (the production of stems and leaves) to reproductive growth (the production of flowers and seeds). Flowering requires a considerable investment of a plant's resources and elegant mechanisms have evolved to ensure that flowering occurs when conditions are most favourable for pollination, seed development and seed dispersal. Plants commonly use day length (photoperiod) or periods of low temperature (vernalisation) as environmental cues to regulate the timing of flowering. The dramatic developmental changes involved in flowering and the importance of flowering time to adaptation and crop yield have interested researchers for long, and the control of flowering is an area of biology where fundamental and applied aspects are closely interwoven. This chapter briefly discusses research in model plants but is primarily concerned with what is known about the genetic control of flowering time in crop species and the ways in which this affects adaptation and performance.
Seed Germination
Authors: Kermode Allison R. 
Published: July 2004

AbstractSeeds control the survival and reproductive capacity of plants and therefore occupy a critical position in the life history of higher plants. The successful establishment of the new plant both temporally and spatially, as well as the vigour of the young seedling, is largely determined by physiological and biochemical processes that occurred earlier, i.e. during seed development. At dispersal, the quiescent mature seed upon encountering favourable environmental conditions (that can include light of a given wavelength, sufficient water, optimal temperatures and adequate oxygen) commences germination. However, as will be discussed, under conditions that are not optimal for a transition from germination to seedling growth, seeds express genes that impose a transient ‘quiescence’ until those conditions become optimal. The agricultural and forest industries rely upon seeds that exhibit high germinability and vigorous, synchronous growth after germination; hence dormancy is generally considered an undesirable trait. Some of the problems unique to the forest industry in relation to the deep dormancy of conifer species will be discussed. Functional genomic approaches hold promise for elucidating genes and proteins that control seed dormancy and germination. The understanding of molecular and physiological mechanisms underlying seed dormancy, particularly of angiosperms, has been accelerated through the analysis of mutants that are disrupted in their development (including dormancy inception and maintenance) as a result of a deficiency in hormone biosynthesis or response. These and other biotechnological approaches for manipulating germination will be discussed.
Applications of Plant Biotechnology to Ornamental Crops
Authors: Clark David G. 
Published: July 2004

AbstractIn many cases of ornamental crops, biotechnology applications are proving to be very difficult, but there have been several advances made with engineering a wide variety of genetic traits in floriculture crops and turfgrass. Significant gains have also been made in cloning important genes that are proving to be involved with biological processes that scientists hope to manipulate in ornamental crops in the future. The purpose of the rest of this chapter is to provide a status report on the progress that has been made in applying biotechnology to plants grown for the ornamental characteristics, and to project where research efforts will be focused over the next few years.
Plants as Enzyme Factories
Authors: Hood Elizabeth E. 
Published: July 2004

Abstract
In this chapter, we focus on the production of enzymes and other commercially valuable proteins in transgenic plants. Enzymes are ideal for use as catalysts in industrial processes because they can function in aqueous solutions at ambient temperatures and neutral or physiologic pH levels. Furthermore, enzymes have a high specificity, low toxicity, and catalyse reactions relatively quickly at low concentrations. However, temperature and pH extremes can limit enzymatic activity, and certain ions, organic molecules and solvents can inactivate enzymes. Such conditions are often present in large‐scale industrial processes so significant changes are required when moving from chemical to enzymatic catalysts. Nevertheless, the large market opportunity for industrial enzymes and the environmental benefits they provide offer the incentive to invest in the development of efficient production systems and to make the necessary changes in industrial processes.
Production of Pharmaceutical Proteins Using Viral Vectors
Authors: Grill Laurence K. 
Published: July 2004

AbstractExtracts and extracted products from plants have probably been used as therapeutics since the beginning of humankind. In the more recent history, it has been a hope of many to improve on nature and genetically manipulate plants to produce better, cheaper, and more specific therapeutics and pharmaceuticals. Viral vector technology has several attributes that allow foreign gene expression to be very effective in specific applications for the production of pharmaceuticals and therapeutics. These attributes include rapid ‘turn‐around’ time, high yield and good measures of safety as far as containment of the gene. The viral vector system will be described in this chapter.
Emerging Production Systems for Antibodies in Plants
Authors: Schillberg Stefan , Twyman Richard M. 
Published: July 2004

AbstractIn this chapter, we discuss the advantages and disadvantages of different production crops that have been used to produce antibodies and their derivatives, including leafy crops, cereals, legumes, fruits and vegetables. We also discuss alternative plant‐based production systems that do not involve stable gene transfer, which shorten the development time and eliminate many of the biosafety concerns, which surround the use of genetically ‐modified organisms as bioreactors.
Risk Assessment and Public Policy Issues
Authors: Newell‐McGloughlin Martina 
Published: July 2004

AbstractWhile exploitation of the fundamental biological phenomenon of genetic change has been the principal well spring of agrarian evolution and, in no small way, has assisted the advancement of civilisation, it did not emerge as an issue of social concern until scientists attained the means to manipulate life at the molecular level. In essence, commercialisation of the products of recombinant DNA technology is just another facet in a long history of human intervention in nature for agricultural and food production. And, as such, the same parameters of risk‐based assessment should apply. Commercialisation of all types of organisms must be undertaken within a regulatory framework that insures adequate protection of the consumer and the environment while not stymieing innovation. The latter may slow the entry of new products into the marketplace and such a delay can sustain reliance on less efficient, less precise, less predictable and sometimes more hazardous alternative technologies and products.
Economic Impact Analysis of Genetically Modified Crops
Authors: Naseem Anwar , Pray Carl 
Published: July 2004

AbstractThis chapter documents, evaluates and synthesises the actual impact of GM crops to date by reviewing previous surveys and empirical studies. We also review the ex‐ante studies and studies based on experimental trials. For the most part we limit our analysis to the impact at the farm level, as this is where the bulk of the evidence lies and where impacts are most direct and measurable. Given that widespread adoption of GM crops will have implications for the whole economy, we also review studies that estimate impacts at the national and global level, with an emphasis on who captures the benefits from the adoption of GM crops. Furthermore, since most of the current set of GM crops affects input use, we review the data on how adoption has affected pesticide/herbicide use.
Intellectual Property Rights and Patent Regimes in Biotechnology and their Impact on Agriculture Development in the Developing World
Authors: Henson‐Apollonio Victoria 
Published: July 2004

Abstract
Modern biotechnology has produced a revolution in agriculture, both in the developing and industrial world. Along with the scientific innovation, a transformation has occurred in the ways that information and knowledge is being transferred, as well. Intellectual property protection schemes have had a variable influence on both the rights associated with actual and perceived control of, and, use of, innovations in agricultural development. This perception has been particularly volatile in the developing world. This chapter discusses technical aspects of intellectual property and then reviews the role of IP regimes in the diffusion of transgenic/genetically engineered plant biotechnology (transgenic cotton) in two selected emergent countries, India and Argentina.
Safe or Unsafe? 15 Years of EU Risk Assessment Research on GMOs
Authors: Economidis Ioannis , Kessler Charles 
Published: July 2004

Abstract
The European Union has been active in supporting research on the safety of GMOs for over 15 years through the funding mechanism of the European Commission. This chapter examines what has been achieved. Although no particular safety or environmental problems have been revealed areas of concern remain. Communication of safety research results appears to be a particular bottleneck, especially from the perspective of public perception.
Factors Influencing Public Policy Development in Agricultural Biotechnology
Authors: Ammann Klaus , Ammann Biljana Papazova 
Published: July 2004

Abstract
It is obvious, that agricultural biotechnology is one of the centreer points of the recent debate. If we focus on the most neuralgic point, it is genetic engineering as a tool for modern plant breeding. It is clear that lay people are anxious regarding the new developments, and it is not only ignorance which makes them fearful. There is a big divide between lay people and scientists and between politicians and citizens, to name just two major divides. The important question is, how can we overcome divides of this dimension and what do we want to set as new policy goals in the appropriate time scales?