Plant Systems Biology

This volume aims to provide a timely view of the state-of-the-art in systems biology. The editors take the opportunity to define systems biology as they and the contributing authors see it, and this will lay the groundwork for future studies. The volume is well-suited to both students and researchers interested in the methods of systems biology. Although the focus is on plant systems biology, the proposed material could be suitably applied to any organism.

Progress in plant biology relies on the quantification, analysis and mathematical modeling of data over different time and length scales. This book describes common mathematical and computational approaches as well as some carefully chosen case studies that demonstrate the use of these techniques to solve problems at the forefront of plant biology. Each chapter is written by an expert in field with the goal of conveying concepts whilst at the same time providing sufficient background and links to available software for readers to rapidly build their own models and run their own simulations. This book is aimed at postgraduate students and researchers working the field of plant systems biology and synthetic biology, but will also be a useful reference for anyone wanting to get into quantitative plant biology.

This book discusses theoretical approaches to the taxonomy of biological systems and theory and mathematical approaches to the problem of plant diversity, cultivation, and the environment. Particular attention is given to theoretical and practical problems of soil and the environmental sustainability of phytocoenosis, with the goal to enhance the productivity of agricultural crops: cereals, legumes, vegetables, and fruit. Providing valuable information on the distribution of chemical elements in the soil–plant system and on the migration of chemical elements in the food chain, this book looks at the composition of the soil and the distribution of elements in the soil–plant system that are manifested as adaptations of plant organism to environmental conditions. With chapters written by acknowledged scientists in the field of genetics, plant selection, ecology, and agro-economy, the book attempts, in many cases, to find consensus between the need to address ways to decrease the excess load on the environment and the need to provide adequately for the human population in agro-developed countries. This book also presents precision farming techniques, including the introduction of differentiated agrochemicals and considering variability of soil fertility and crop conditions. An important element for the conservation and adaptation of plant organism to environmental conditions is the use of physiologically active compounds.

Recent major advances in the field of comparative genomics and cytogenomics of plants, particularly associated with the completion of ambitious genome projects, have uncovered astonishing facets of the architecture and evolutionary history of plant genomes. The aim of this book was to review these recent developments as well as their implications in our understanding of the mechanisms which drive plant diversity. New insights into the evolution of gene functions, gene families and genome size are presented, with particular emphasis on the evolutionary impact of polyploidization and transposable elements. Knowledge on the structure and evolution of plant sex chromosomes, centromeres and microRNAs is reviewed and updated. Taken together, the contributions by internationally recognized experts present a panoramic overview of the structural features and evolutionary dynamics of plant genomes.This volume of Genome Dynamics will provide researchers, teachers and students in the fields of biology and agronomy with a valuable source of current knowledge on plant genomes.

In this authoritative guide, expert investigators provide cutting-edge chapters dealing with modern plant systems biology approaches. This work provides the kind of detailed description and implementation advice that is crucial for getting optimal results.

This book introduces students to methods that will help them understand behaviour in terms of cellular components and their interactions in non-intuitive ways, which calls for an interdisciplinary approach combining mathematical, chemical, computational and biological strategies. Tibor Ganti was one of the early pioneers who proposed a theoretical framework to understand living principles in terms of chemical transformation cycles and their coupling. The twenty-first century then brought with it a novel ‘systems’ paradigm, which shone new light on all previous work and was accompanied by numerous implications for the way we conceive of chemical and biological complexity today. This book seeks to equip students to take advantage of any field that investigates living systems. Based on a conceptualisation of science-oriented branches, engineering-oriented branches and biology as astoundingly complex fields, those structures laden with biochemical detail encompass a deeper theory unifying our knowledge of designed systems. Readers will be pleasantly surprised at how lucidly the topics are presented. The book offers an indispensable resource for students and professionals working in systems and synthetic biology or any of the various related fields of research.

Recent advances in science have clarified the role of plant specialized metabolites (classically known as plant secondary metabolites), which cannot be considered only bioactive molecules used for human health but also pivotal factors for the global ecosystem. They play major roles in plant life, evolution, and mutualism. To provide the reader a general view of plant specialized metabolites, it is important to consider both the biochemistry and the functional/ecological role of these important compounds. Around 200,000 specialized metabolites are formed by a wide array of plant metabolic pathways from numerous plant taxa and through learning how other species (including human beings) rely on them. Plant Specialized Metabolism: Genomics, Biochemistry, and Biological Functions will provide the reader with special insights into the sophisticated nature of these metabolites and their various and valuable uses based on the most recent findings in science. The field of plant specialized metabolism has witnessed tremendous growth in the past decade. This growth has had a profound impact on multiple disciplines in life science, including biochemistry, metabolism, enzymology, natural product chemistry, medicinal chemistry, chemical ecology, and evolution. It also has yielded valuable knowledge and technology readily applicable in various industries, such as agriculture, horticulture, energy, renewable chemicals, and pharmaceuticals. The book focuses on the molecular background of secondary metabolite biosynthesis, their functional role, and potential applications.

Faster progress in plant biology research could benefit agriculture, the environment, medicine, and our understanding of basic biological processes. This book clearly and directly describes the impediments to greater achievements in plant science and suggests solutions. It presents an innovative plan that would create a comprehensive federal system of management and financial support for plant biology research and training.

The genomic revolution has opened up systematic investigations and engineering designs for various life forms. Systems biology and synthetic biology are emerging as two complementary approaches, which embody the breakthrough in biology and invite application of engineering principles. Systems Biology and Synthetic Biology emphasizes the similarity between biology and engineering at the system level, which is important for applying systems and engineering theories to biology problems. This book demonstrates to students, researchers, and industry that systems biology relies on synthetic biology technologies to study biological systems, while synthetic biology depends on knowledge obtained from systems biology approaches.

Plant Systems Biology is an excellent new addition to theincreasingly well-known and respected Annual Plant Reviews.Split into two parts, this title offers the reader: A fundamental conceptual framework for Systems Biologyincluding Network Theory The progress achieved for diverse model organisms: Prokaryotes, C. elegans and Arabidopsis The diverse sources of “omic” information necessaryfor a systems understanding of plants Insights into the software tools developed for systemsbiology Interesting case studies regarding applications includingnitrogen-use, flowering-time and root development Ecological and evolutionary considerations regarding livingsystems This volume captures the cutting edge of systems biologyresearch and aims to be an introductory material for undergraduateand graduate students as well as plant and agricultural scientists,molecular biologists, geneticists and microbiologists. It alsoserves as a foundation in the biological aspects of the field forinterested computer scientists. Libraries in all universities andresearch establishments where biological and agricultural sciencesare studied and taught and integrated with Computer Sciences shouldhave copies of this important volume on their shelves.

New Opportunities in Metabolomics and Biochemical Phenotyping for Plant Systems Biology.

This is the first book to present a comprehensive and advanced discussion on the latest insights into plant stress biology. Starting with general aspects of biotic as well as abiotic stresses, this handbook and ready reference moves on to focus on topics of stress hormones, technical approaches such as proteomics, transcriptomics and genomics, and their integration into systemic modeling. This book is a valuable resource for researchers as well as professionals not just in plant sciences but also in cell and molecular biology as well as biotechnology.

Plants provide a source of survival for all life on this planet. They are able to capture solar energy and convert it into food, feed, wood and medicines. Though sessile in nature, over many millions of years, plants have diversified and evolved from lower to higher life forms, spreading from sea level to mountains, and adapting to different ecozones. They have learnt to cope with challenging environmental conditions and various abiotic and biotic factors. Plants have also developed systems for monitoring the changing environment and efficiently utilizing resources for growth, flowering and reproduction, as well as mechanisms to counter the impact of pests and diseases and to communicate with other biological systems, like microbes and insects. This book discusses the “awareness” of plants and their ability to gather information through the perception of environmental cues, such as light, gravity, water, nutrients, touch and sound, and stresses. It also explores plants’ biochemical and molecular “computing” of the information to adjust their physiology and development to the advantage of the species. Further, it examines how plants communicate between their different organs and with other organisms, as well as the concepts of plant cognition, experience and memory, from both scientific and philosophical perspectives. Lastly, it addresses the phenomenon of death in plants. The epilogue presents an artist’s view of the beauty of the natural world, especially plant “architecture”. The book provides historical perspectives, comparisons with animal systems where needed, and general biochemical and molecular concepts and themes. Each chapter is selfcontained, but also includes cross talk with other chapters to offer an integrated view of plant life and allow readers to appreciate and admire the functioning of plant life from within and without. The book is a tribute by the Editor to his students, colleagues and co-workers and to those in whose labs he has worked.

This volume provides methods on different aspects and applications on plants, algae, photosynthetic bacteria, synthetic construct design, and multiplex cloning. Chapters cover multiple aspects of synthetic metabolic, photosynthetic systems, metabolic and signaling pathways, advanced engineering of metabolic networks, isolation of organelles and co-culture of microorganisms, and methods for the on command manipulation of the relative stability of proteins. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Plant Synthetic Biology: Methods and Protocols aims to be a useful resource for both researchers starting to explore novel experimental avenues as well as for experts willing to expand their portfolio of tools and strategies.