This Volume presents generic protocols for wet experimental and computer-based systems and synthetic biology approaches relevant to the field of hydrocarbon and lipid microbiology. It complements a second Volume that describes protocols for systems and synthetic biology applications. The wet experimental tools presented in this Volume include protocols for the standardisation of transcriptional measurements, application of uracil excision-based DNA editing for, inter alia, multi-gene assembly, the use of fluxomics to optimise "reducing power availability", and the incorporation of non-canonical amino acids into proteins for optimisation of activities. Phenome-ing microbes, using a combination of RNA-seq and bioinformatic algorithms, is presented, as is an illustration, using methylotrophs as an example, of how the different key omics approaches constitute a pipeline for functional analysis, acquisition of a systems overview, and metabolic optimisation. Complementary computational tools that are presented include protocols for probing the genome architecture of regulatory networks, genome-scale metabolic reconstruction, and bioinformatic approaches to guide metabolic engineering. The Volume also includes an overview of how synthetic biology approaches can be used to improve biocontainment. Hydrocarbon and Lipid Microbiology ProtocolsThere are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

The present volume presents essential information on advancements in oilseed production, processing and utilization. Advances in the technology of seed processing to produce oil and oil quality for edible and industrial applications are well presented, followed by hybrid technology, biotechnology, oil technology and meal quality for animal nutrition. The following areas are also covered: the potential for oil in developing biodiesel markets, fatty acid long chains and their derivative, pollination management, and safety of pollinators from harmful effects of pesticides. This volume also includes an economic assessment of oilseed integrated pest management (IPM) programs in different regions of the world. Dr. Surinder Kumar Gupta is Professor/Chief Scientist (Oilseeds) Plant Breeding & Genetics and Nodal officer in School of Biotechnology, S K University of Agricultural Sciences & Technology, Faculty of Agriculture, Chatha, Jammu-India. He holds a distinguished academic and service record and has been devoted primarily to research on oilseed Brassicas for nearly two decades. He has written two books on plant breeding and edited three volumes, one on 'Recent Advances in Oilseed Brassicas', Kalyani Publishers, New Delhi, India, second on 'Rapeseed Breeding-Advances in Botanical Research', Vol. 45, Academic Press, Elsevier Publishers and third on Biology and Breeding of crucifers, CRC Publishers, Taylor and Francis Group.

This volume covers recent developments in both fundamental and applied research in biological nitrogen fixation. It emphasizes the application of biological nitrogen fixation for sustainable agriculture, which should lead to poverty alleviation, environmental protection, and good agricultural practices generally. The roles of, and advances in, plant breeding, plant molecular biology, nodule physiology, and symbiotic and associative interactions between plants and microbes in sustaining agricultural productivity and soil fertility are described. The evolution of symbioses and nitrogen fixation are also covered in this volume. To ensure high agricultural productivity, while protecting the environment (both soil and water resources), requires plant cultivars that also respond to beneficial microbes. The volume, therefore, describes the physiology and genomics of nitrogen-fixing bacteria together with the biochemistry and molecular genetics of the nitrogenase enzyme that actually fixes atmospheric nitrogen to a usable form.

This volume, which covers the most recent data on the role of nitrogen fixation in agriculture and forestry and on the biology of both plants and nitrogen-fixing microbes, is intended to serve as a useful reference for students and researchers, both in the laboratory (academic and commercial) and in the field.

Two of the recent books in the Methods in Molecular Biology series, Yeast Protocols and Pichia Protocols, have been narrowly focused on yeasts and, in the latter case, particular species of yeasts. Food Microbiology Pro- cols, of necessity, covers a very wide range of microorganisms. Our book treats four categories of microorganisms affecting foods: (1) Spoilage organisms; (2) pathogens; (3) microorganisms in fermented foods; and (4) microorganisms p- ducing metabolites that affect the flavor or nutritive value of foods. Detailed information is given on each of these categories. There are several chapters devoted to the microorganisms associated with fermented foods: these are of increasing importance in food microbiology, and include one bacteriophage that kills the lactic acid bacteria involved in the manufacture of different foods-cottage cheese, yogurt, sauerkraut, and many others. The other nine chapters give procedures for the maintenance of lactic acid bacteria, the isolation of plasmid and genomic DNA from species of Lac- bacillus, determination of the proteolytic activity of lactic acid bacteria, det- mination of bacteriocins, and other important topics.

This Volume addresses the pros and cons of oligonucleotide probes, primers and primer combinations, and importantly considers how to design the best tools for the microbial taxa and/or processes being investigated. Individual chapters focus on the design of primers targeting genes that code for enzymes associated with the following functions: degradation of aromatic, aliphatic and chlorinated hydrocarbons under aerobic and anaerobic conditions, methanogenesis, methane oxidation, and the nitrogen cycle. Hydrocarbon and Lipid Microbiology Protocols There are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

This book is the lasting product, a resource of up-to-date information in the scientific literature for the field of animal cell technology, as it was presented during a pleasant and stimulating meeting in TylAsand, Sweden, in June 2001. The title of the meeting, From Target to Market, indicates the usefulness of Animal Cell Technology during all steps in the pharmaceutical development process. Following the biotech products reaching the market, it shows an upward trend in the contribution of biotech products to total New Molecular Entity output in the nineties, which continued until 1996 when biotech represented 25% of the annual output. Since then the proportion has been decreasing. A perceived hurdle from a market perspective is that a protein per definition is biodegradable and thus requires intravenous, or for some drugs subcutaneous administration. New promising administration technologies such as pulmonary delivery were highlighted at this meeting. The emphasis on project selection prior to entry in the development phase has triggered a portfolio management using more extensive preclinical data before a development decision is taken. Animal cells have become a very important tool in the drug discovery process. The next generation of products will evolve from applications such as gene therapy, novel vaccines, cell therapy, and gene regulation. Animal cell technology has a major role to play in the post-sequence era.

Plant protoplasts have proved to be an excellent tool for in vitro manipulation, somatic hybridization, DNA uptake and genetic trans- formation, and for the induction of somac1onal variation. These studies reflect the far-reaching impact of protoplast research in agriculture and forest biotechnology. Taking these aspects into consideration, the series of books on Plant Protoplasts and Genetic Engineering provides a survey of the literature, focusing on recent information and the state of the art in protoplast manipulation and genetic transformation. This book, Plant Protoplasts and Genetic Engineering VII, like the previous six volumes published in 1989, 1993, 1994, and 1995, is unique in its approach. It comprises 27 chapters dealing with the regeneration of plants from protoplasts, and genetic transformation in various species of Agrostis, Allium, Anthriscus, Asparagus, Avena, Boehmeria, Carthamus, Coffea, Funaria, Geranium, Ginkgo, Gladiolus, Helianthus, Hordeum, Lilium, Lithospermum, Mentha, Panax, Papaver, Passiflora, Petunia, Physcomi- trella, Pinus, Poa, Populus, Rubus, Saintpaulia, and Swertia. This book may be of special interest to advanced students, teachers, and research scientists in the field of plant tissue culture, molecular biology, genetic engineering, plant breeding, and general biotechnology. New Delhi, June 1996 Professor y. P. S. BAJAJ Series Editor Contents Section I Regeneration of Plants from Protoplasts 1. 1 Regeneration of Plantlets from Protoplasts of Allium cepa (Onion) E. E. HANSEN, J. F. HUBSTENBERGER, and G. C. PHILLIPS (With 3 Figures) 1 Introduction ...3 2 Protoplast Isolation ...4 3 Protoplast Culture ...8 4 Regeneration of Plantlets ...9 5 Summary...

This volume contains the papers presented at the Sixth International Ion Exchange Conference organised by the SCI and held at Churchill College, Cambridge, UK, in July 1992. As on previous occasions, most recently in 1988, the organising committee did not engage plenary speakers but decided to solicit state-of-the-art contributions from the ion exchange community. This book contains the refereed papers presented at the meeting, whether in poster or oral form. Extra papers were presented at the meeting as posters because they were not available in time for refereeing purposes. The subject matter of the meeting and therefore the contents of the book is subdivided into seven separate topic areas as follows: resin developments; water treatment; fundamentals; biotechnology, food and pharmaceuticals; environmental and pollution control; membranes, inorganic materials and nuclear; and hydrometallurgy. The coverage of the meeting is similar to 1988 although there are fewer subdivisions on this occasion. The more restricted coverage this time reflects the smaller number of papers offered by authors. This is probably due to the world wide industrial recession which has affected commercial development and exploitation of the technology and restricts the ability of practitioners and academics to contribute to and attend international meetings. Nevertheless, the advances in biotechnology, growing concern about the environment and the. need for novel separation processes have provided sufficient impetus to stimulate a sufficient number of workers in the field.

An Introduction to Environmental Biotechnology provides an introduction to the subject of environmental biotechnology. Environmental biotechnology refers to the use of micro-organisms and other living systems to solve current environmental problems such as the detoxification of pollutants and clean-up of oil tanker spills. Additionally, it refers to the biotechnology of the agricultural environment, as well as the use of biopesticides and the application of microorganisms to the mining, metal recovery and paper industries. This is the only comprehensive introductory account of this subject matter. Beginning with an introduction to microbial growth, An Introduction to Environmental Biotechnology aims to provide the non-specialist with a complete overview of environmental biotechnology. It is presented in an easy to read style with illustrations and includes frequent references to the use of higher plants as well as micro-organisms in environmental biotechnology. An Introduction to Environmental Biotechnology is geared toward a non-specialist audience, including engineers and environmental chemists, and environmental scientists who have limited knowledge of microbiology and biotechnology.

Attention has recently turned to using plants as hosts for the production of commercially important proteins. The twelve case studies in this volume present successful strategies for using plants to produce industrial and pharmaceutical proteins and vaccine antigens. They examine in detail projects that have commercial potential or products that have already been commercialized, illustrating the advantages that plants offer over bacterial, fungal or animal cell-culture hosts. There are many indications that plant protein production marks the beginning of a new paradigm for the commercial production of proteins that, over the next decade, will expand dramatically.

Computational intelligence techniques are gaining momentum in the medical prognosis and diagnosis. This volume presents advanced applications of machine intelligence in medicine and bio-medical engineering. Applied methods include knowledge bases, expert systems, neural networks, neuro-fuzzy systems, evolvable systems, wavelet transforms, and specific internet applications. The volume is written in view of explaining to the practitioner the fundamental issues related to computational intelligence paradigms and to offer a fast and friendly-managed introduction to the most recent methods based on computer intelligence in medicine.

New data on animal cell technology are brought together in this volume, with emphasis given to the basic characterization of cell lines. The merits of different cell culture systems are examined and investigations into the factors influencing cell growth and productivity are presented. A special section deals with the biological properties of proteins produced by engineered animal cells. All those involved in the culture of animal cells will find this volume invaluable.

Heavy metals always pose serious ecological risks when released into the environment due to their elemental non-degradable nature, regardless of their chemical form. This calls for the development of efficient and low-cost effluent treatment and metal recuperation technologies for contaminated waste water, not only because regulatory limits need to be met but also because the waste itself can be a resource for certain precious metals.

Biosorption is a general property of living and dead biomass to rapidly bind and abiotically concentrate inorganic or organic compounds from even very diluted aqueous solutions. As a specific term, biosorption is a method that utilizes materials of biological origin - biosorbents formulated from non-living biomass - for the removal of target substances from aqueous solutions. Recent research on biosorption provides a solid understanding of the mechanism underlying microbial biosorption of heavy metals and related elements.

This book gathers review articles analyzing current views on the mechanism and (bio)chemistry of biosorption, the performance of bacterial, fungal and algal biomass, and the practical aspects of biosorbent preparation and engineering. It also reviews the physico-chemical evaluations of biosorbents and modelling of the process as well as the importance of biosorption during heavy metal removal using living cells. It is a reference work for scientists, environmental safety engineers and R&D specialists who wish to further promote biosorption research and use the accumulated knowledge to develop and build industrial applications of biosorption in heavy metal separation technologies.

"

The first Interfaces Conference was held at Swansea in April 1988 and represented the then state of the art of the science of implant surgery. The motivation for the initial venture was a supposed need for a closer interaction and dialogue between the clinician and scientist working in this area. As expressed in the Preface to the first Conference, we felt that the interface was represented graphically, scientifically and psychologically by the drawings of Edgar Rubins (1915), again widely used in the literature to the present Proceedings. The first Conference, we believe, achieved the aims of the organisers in bringing together scientists and clinicians towards an exchange of ideas by logically pursuing the sequence of events in clinical implant surgery. The present Conference, in collaboration with our Italian colleagues, has also attempted to achieve the same aims by examining the behaviour of implants constructed of a variety of materials in both hard and soft tissue. Many contributions in the conference employed the technique of finite element analysis, both for design and optimisation purposes, particularly in relation to bone remodelling. Indeed, this particular aspect of the Conference led to much debate and will require a major examination of the many levels of physical, chemical and biomechanical interactive behaviour of the implant and its environment. All this natural behaviour was presented and discussed, but difficulties and failures remain with such procedures and we feel it is only by continuing such meetings that we progress in this difficult area of clinical science.

The peptide hormones are small proteins that regulate cellular metabolism through their specific interactions with tissues of the endocrine, nervous, and immune systems, as well as in embry onic development. During the past ten years, refinements in the techniques of recombinant DNA technology have resulted in the cloning of genes encoding approximately 50 different hormonal and regulatory peptides, including those in which the peptides themselves and the mRNAs encoding the peptides are present in only trace amounts in the tissues of origin. In addition to provid ing the coding sequences of recognized hormonal and regulatory peptides, gene sequencing has uncovered new bioactive peptides encoded in the precursor pro hormones that are then liberated along with the hormonal peptides during cellular cleavages of the precursors. The encoding of multiple peptides in a single mono cistronic mRNA appears to be a genetic mechanism for the gener ation of biologic diversification without requiring amplification of gene sequences. Two of the objectives in the assembly of this book are to pre sent, in one volume, the known primary structures of the genes encoding several of the polypeptide hormones and related regulatory peptides, and to provide an account of the various ap proaches that have been used to identify and select the cloned genes encoding these polypeptides. The contents of the two in troductory chapters are intended to provide the reader with a brief background of the approaches to gene cloning and the struc ture and expression of hormone-encoding genes."

Bioinformatics is an integrative field of computer science, genetics, genomics, proteomics, and statistics, which has undoubtedly revolutionized the study of biology and medicine in past decades. It mainly assists in modeling, predicting and interpreting large multidimensional biological data by utilizing advanced computational methods. Despite its enormous potential, bioinformatics is not widely integrated into the academic curriculum as most life science students and researchers are still not equipped with the necessary knowledge to take advantage of this powerful tool. Hence, the primary purpose of our book is to supplement this unmet need by providing an easily accessible platform for students and researchers starting their career in life sciences. This book aims to avoid sophisticated computational algorithms and programming. Instead, it will mostly focus on simple DIY analysis and interpretation of biological data with personal computers. Our belief is that once the beginners acquire these basic skillsets, they will be able to handle most of the bioinformatics tools for their research work and to better understand their experimental outcomes. The third volume is titled In Silico Life Sciences: Agriculture. It focuses on plant genetic, genomic, transcriptomic, proteomic and metabolomics data. Using examples of new crop diseases-emergence, crop productivity and biotic/abiotic stress tolerance, this book illustrates how bioinformatics can be an integral components of modern day plant science research.

This book gives a state-of-the-art view by recognized researchers of the nanotechnologies required for future integrated systems leading to innovations in energy, the environment, and biotechnologies. Nanostructures that would be difficult to form using the current semiconductor technology will be realized using a combination of bottom-up and top-down processes, including hybrid nanostructures made of inorganic and organic/biological materials. Bio-sensing, imaging, and cell or molecular manipulation are discussed in Chapters 2-7. The acquisition of basic knowledge on the cellular level will lead to curing serious diseases. Also, nanofabrication technologies, discussed in Chapters 8-15, will lead to next-generation solar cells, secondary batteries, and advanced electronic circuits using nanostructured materials, thus providing solutions for serious energy and environment issues. Prospective readers of this book include graduate students as well as researchers and engineers working in this field.

Genetic engineering is a powerful tool for crop improvement. Crop biotechnology before 2001 was reviewed in Transgenic Crops I-III, but recent advances in plant cell and molecular biology have prompted the need for new volumes.

Transgenic Crops IV deals with cereals, vegetables, root crops, herbs and spices. Section I is an introductory chapter on the impact of plant biotechnology in agriculture. Section II focuses on cereals (rice, wheat, maize, rye, pearl millet, barley, oats), while Section III is directed to vegetable crops (tomato, cucumber, eggplant, lettuce, chickpea, common beans and cowpeas, carrot, radish). Root crops (potato, cassava, sweet potato, sugar beet) are included in Section IV, with herbs and spices (sweet and hot peppers, onion, garlic and related species, mint) in Section V.

This volume is an invaluable reference for plant breeders, researchers and graduate students in the fields of plant biotechnology, agronomy, horticulture, genetics and both plant cell and molecular biology.

The book deepens the understanding of the solid substrate culture technique in order to widen the engineering base needed to encourage its practical use. Theories of practical relevance are explained in detail.

Nanobiotechnology is the convergence of existing and new biotechnology with the 1 ability to manipulate matter at or near the molecular level. This ability to manipulate matter on a scale of 100 nanometers (nm) or less is what constitutes the nanotechnology revolution occurring today, the potentially vast economic and social implications of which are yet to be fully understood (Royal Society, 2004). The most immediate way to understand the implications of nanobiotechnology for ethics is to consider the real life concerns of communities that are mobilizing within civil society. The conflicts and ethical debates surrounding nanotechnology will, almost by definition, emerge on the fault lines between different civil society actors, researchers and financial interests associated with nanobiotechnology, as well as (potentially) government regulators. These fault lines are all reflected within the concerns (as expressed d- cursively) of the communities mobilizing. This chapter will explore converging d- courses regarding converging technologies. Converging Technologies (CT) are already a familiar theme in the next gene- tion of biotechnology, nanotechnology, pharmacogenomics and proteomics research 2 and development. Nanobiotechnology means that previously separate disciplines (IT, physics, chemistry, and biology) are merging and converging to create new applications and even new life forms through converged technological platforms. Schummer (2004), and Glimell and Fogelberg (2003, p. 43), note the predominance of interdisciplinarity as a core theme of nano-discourse.

Algae are important organisms that include seaweeds and a number of single-celled and multicellular microscopic forms. Algae are ubiquitous; they inhabit almost everywhere including oceans, freshwater bodies, rocks, soils, and trees. Man's uses of algae may date back to ancient times. In recent decades, there has been renewed interest in the utilization of algae as sources of health food and high-value chemicals and pharmaceuticals, and for aquaculture, agriculture, and wastewater treatment. Nevertheless, the biotechnological potential of algae is still far from fully exploited, due to a lack of understanding of algal characteristics and culture systems, as well as of advanced research techniques. This book contains selected papers presented at the Fourth Asia-Pacific Conference on Algal Biotechnology held in Hong Kong, on 3-6 July, 2000. Written by experts in the field, this book provides a state-of-the-art account of algal biotechnology research. Topics range from use of algae in agriculture to environmental monitoring and protection, from algal culture systems to production of high-value chemicals and pharmaceuticals by algae, and from algal product purification to gene transformation and regulations. This book is intended for use by researchers and industrialists in the field of algal biotechnology. It will also be an important reference for undergraduate and postgraduate students in biotechnology and food science, as well as in biology in general.

Currently, nanotechnology is exposing the properties of DNA in unprecedented detail leading to new insights on the biological behavior and function of DNA. With the structural perfection of a self-assembling DNA nano-object, such as a DNA origami, it is clear how complex DNA is as a molecule, leading researchers to wonder how many different constructs could be designed and realized. "DNA Nanotechnology: Methods and Protocols" shows the procedures to follow in order to repeat methods that lead to such constructs or to the mastering of the characterization techniques used to study them. The chapters of this book are roughly divided into two parts: some cover the methods for preparing the nanostructures, from the rationale of the operations to the techniques for their handling, while other chapters deal more directly with advanced instrumental techniques that can manipulate and characterize molecules and nanostructures. Written in the highly successful "Methods in Molecular Biology " series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and accessible, "DNA Nanotechnology: Methods and Protocols "serves as an ideal guide to scientists of all backgrounds and aims to ignite interest and spur activity in this young and rapidly growing research field.

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts"