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Marine Metagenomics by Takashi Gojobori,Tokio Wada,Takanori Kobayashi,Katsuhiko Mineta Pdf
This book presents the state-of-art marine metagenome research and explains the method of marine metagenomic analysis in an easy-to-understand manner. Changes in the marine environment due to global warming and pollution have become a major global problem. Maintaining a healthy marine ecosystem requires advanced environmental monitoring and assessment systems. As such, the book presents a novel metagenomic monitoring method, which has been developed for comprehensive analyses of the DNA of microorganisms living in seawater to further our understanding of the dynamics of the marine environment. The book can be used as a primer for new researchers and as a manual on experimental methods.
Metagenomics by Wolfgang R. Streit,Rolf Daniel Pdf
This volume provides up-to-date and novel techniques for various screening technologies currently used in metagenomics and related areas. Starting with DNA/RNA isolation from environmental samples, the book continues by delving into areas such as current methods used to isolate DNA and construct metagenomic libraries, establishment of metagenome libraries in non-E. coli hosts, and topics like function-driven mining of metagenomic DNA, screening and analyzing protocols for a wide array of different genes encoding enzymes, bacterial viruses and much more. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Metagenomics: Methods and Protocols, Third Edition provides a comprehensive collection of up-to-date metagenome protocols and tools for the recovery of many major types of biocatalysts and allows for the easy setup of these screens in microbiology laboratories.
From Genes to Species: Novel Insights from Metagenomics by Eamonn P. Culligan,Roy D. Sleator Pdf
The majority of microbes in many environments are considered “as yet uncultured” and were traditionally considered inaccessible for study through the microbiological gold standard of pure culture. The emergence of metagenomic approaches has allowed researchers to access and study these microbes in a culture-independent manner through DNA sequencing and functional expression of metagenomic DNA in a heterologous host. Metagenomics has revealed an extraordinary degree of diversity and novelty, not only among microbial communities themselves, but also within the genomes of these microbes. This Research Topic aims to showcase the utility of metagenomics to gain insights on the microbial and genomic diversity in different environments by revealing the breadth of novelty that was in the past, largely untapped.
Mining of Microbial Wealth and MetaGenomics by Vipin Chandra Kalia,Yogesh Shouche,Hemant J. Purohit,Praveen Rahi Pdf
The existence of living organisms in diverse ecosystems has been the focus of interest to human beings, primarily to obtain insights into the diversity and dynamics of the communities. This book discusses how the advent of novel molecular biology techniques, the latest being the next-generation sequencing technologies, helps to elucidate the identity of novel organisms, including those that are rare. The book highlights the fact that oceans, marine environments, rivers, mountains and the gut are ecosystems with great potential for obtaining bioactive molecules, which can be used in areas such as agriculture, food, medicine, water supplies and bioremediation. It then describes the latest research in metagenomics, a field that allows elucidation of the maximum biodiversity within an ecosystem, without the need to actually grow and culture the organisms. Further, it describes how human-associated microbes are directly responsible for our health and overall wellbeing.“/p>
Metagenomics: Perspectives, Methods, and Applications provides thorough coverage of the growing field of metagenomics. A diverse range of chapters from international experts offer an introduction to the field and examine methods for metagenomic analysis of microbiota, metagenomic computational tools, and recent metagenomic studies in various environments. The emphasis on application makes this text particularly useful for applied researchers, practitioners, clinicians and students seeking to employ metagenomic approaches to advance knowledge in the biomedical and life sciences. Case-study based application chapters examine topics ranging from viral metagenome profiling, metagenomics in oral disease and health, metagenomic insights into the human gut microbiome and metabolic syndromes, and more. Additionally, perspectives on future potential at the end of each chapter provoke new thought and motivations for continued study in this exciting and fruitful research area. Provides thorough coverage of the rapidly growing field of metagenomics, with an emphasis on applications of relevance to translational researchers, practitioners, clinicians and students Features a diverse range of chapters from international experts that offer an introduction to the field and examine methods for metagenomic analysis of microbiota, metagenomic computational tools and research pipelines Highlights perspectives on future potential at the end of each chapter to provoke new thought and motivations for continued study in this exciting and fruitful research area
Springer Handbook of Marine Biotechnology by Se-Kwon Kim Pdf
This Springer Handbook provides, for the first time, a complete and consistent overview over the methods, applications, and products in the field of marine biotechnology. A large portion of the surface of the earth (ca. 70%) is covered by the oceans. More than 80% of the living organisms on the earth are found in aquatic ecosystems. The aquatic systems thus constitute a rich reservoir for various chemical materials and (bio-)chemical processes. Edited by a renowned expert with a longstanding experience, and including over 60 contributions from leading international scientists, the Springer Handbook of Marine Biotechnology is a major authoritative desk reference for everyone interested or working in the field of marine biotechnology and bioprocessing - from undergraduate and graduate students, over scientists and teachers, to professionals. Marine biotechnology is concerned with the study of biochemical materials and processes from marine sources, that play a vital role in the isolation of novel drugs, and to bring them to industrial and pharmaceutical development. Today, a multitude of bioprocess techniques is employed to isolate and produce marine natural compounds, novel biomaterials, or proteins and enzymes from marine organisms, and to bring them to applications as pharmaceuticals, cosmeceuticals or nutraceuticals, or for the production of bioenergy from marine sources. All these topics are addressed by the Springer Handbook of Marine Biotechnology. The book is divided into ten parts. Each part is consistently organized, so that the handbook provides a sound introduction to marine biotechnology - from historical backgrounds and the fundamentals, over the description of the methods and technology, to their applications - but it can also be used as a reference work. Key topics include: - Marine flora and fauna - Tools and methods in marine biotechnology - Marine genomics - Marine microbiology - Bioenergy and biofuels - Marine bioproducts in industrial applications - Marine bioproducts in medical and pharmaceutical applications - and many more...
Functional Metagenomics: Microbial Diversity, Interaction, and Application in Bioremediation uses a 20-chapter, easy-to-understand format to centralize the practical application ideas for functional metagenomics. This important resource not only includes chapters on next-generation sequencing technologies to study important biogeochemical cycles, degradation pathways and detoxification, but also gives insight into several tools that have been developed to integrate metadata and sequence data, allowing downstream comparative analyses of different datasets using several ecological indices.Content further explains the newly developed techniques for sequencing DNA; generating shorter fragments than Sanger sequencing techniques to quickly read larger sequences in a shorter amount of time. The content finally explores the role of metagenomics in studying microbial diversity, interaction and application in bioremediation studies and gives the reader overall detailed information regarding metagenomics, its application as well as techniques. Provides comprehensive information to readers on state-of-the-art applications in metagenomics Summarizes our current knowledge of the use of metagenomics and gives a novel and powerful insight into the already existing bioremediation process Gives an overall picture of metagenomics, its application, processes, and future prospects in the field of bioremediation
National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications
Author : National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications Publisher : National Academies Press Page : 170 pages File Size : 54,5 Mb Release : 2007-06-24 Category : Science ISBN : 9780309106764
The New Science of Metagenomics by National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications Pdf
Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.
The Marine Microbiome by Lucas J. Stal,Mariana Silvia Cretoiu Pdf
This book describes the state-of-the-art concerning the ‘marine microbiome’ and its uses in biotechnology. The first part discusses the diversity and ecology of marine microorganisms and viruses, including all three domains of life: Bacteria, Archaea, and Eukarya. It discusses whether marine microorganisms exist and, if so, why they might be unique. The second part presents selected marine habitats, their inhabitants and how they influence biogeochemical cycles, while the third discusses the utilization of marine microbial resources, including legal aspects, dissemination, and public awareness. The marine microbiome is the total of microorganisms and viruses in the ocean and seas and in any connected environment, including the seafloor and marine animals and plants. The diversity of microbial life remains unquantified and largely unknown, and could represent a hidden treasure for human society. Accordingly, this book is also intended to connect academics and industry, providing essential information for microbiologists from both fields.
Marine Enzymes for Biocatalysis by Antonio Trincone Pdf
Marine bioprospecting is a highly topical subject - in both applied and basic research - but, as yet, the marine ecosystem is a relatively unexplored source of natural bioactive substances with potential therapeutic activity. This book addresses the use of marine enzymes in biocatalysis through a series of chapters from leading scientists within academic and industrial fields. Biocatalytic processes can take advantage of the habitat-related properties of marine enzymes, such as salt tolerance, hyperthermostability, barophilicity, cold adaptivity, and so on, whilst also taking into consideration substrate specificity and affinity. These evolved properties are linked to the metabolic functions of the enzymes and to the ecological aspects of the natural source. New properties can also be discovered at the molecular level of catalysis, particularly concerning the stereochemical characteristics of products. Marine enzymes for biocatalysis initially examines the nature and level of interest in marine biological diversity, and outlines the fundamentals of biocatalysis. It goes on to detail sources of marine enzymes, and to analyse examples from both chemical and stereochemical viewpoints of catalysis, including microbial enzymes and animal or plant sources. The book goes on to explore the future potential of marine bioprospecting in biocatalysis. Compiles studies from leading scientists in a direct and accessible format. Includes practical descriptions of results, adding further details not often covered in formal articles Takes a molecular view which fully explains the enzymatic aspects of reactions, particularly regarding biocatalytic characteristics and descriptions of bioprocesses Selects examples of chemical and stereochemical aspects of enzymatic action with respect to known terrestrial counterparts
Marine Niche: Applications in Pharmaceutical Sciences by Neelam M Nathani,Chandrashekar Mootapally,Indra R. Gadhvi,Bharat Maitreya,Chaitanya G. Joshi Pdf
This book offers a comprehensive study of biological molecules acquired from marine organisms, which have been exploited for drug discovery with the aim to treat human diseases. Biomolecules have potential impacts on a diverse range of fields, including medical and pharmaceutical science, industrial science, biotechnology, basic research, molecular science, environmental science and climate change, etc. To understand and effectively apply medicinally important biomolecules, multidisciplinary approaches are called for. The ocean remains a rich biological resource, and the vast untapped potential of novel molecules from marine bio-resources has caught the interest of more and more researchers. These novel biological compounds have never been found in terrestrial or other ecosystems, but only in this rich niche. Advances in sampling techniques and technologies, along with increased funding for research and nature conservation, have now encouraged scientists to look deeper in the waters. Aquaculture supports both tremendous seafood production and the bulk production of marine-derived drugs. Furthermore, molecular methods are now being extensively employed to explore the untapped marine microbial diversity. With the help of molecular and biotech tools, the ability of marine organisms to produce new biosynthetic drugs can be greatly enhanced. This book provides an extensive compilation of the latest information on marine resources and their undisputedly vital role in the treatment of diverse ailments.
Encyclopedia of Marine Biotechnology by Se-Kwon Kim Pdf
A keystone reference that presents both up-to-date research and the far-reaching applications of marine biotechnology Featuring contributions from 100 international experts in the field, this five-volume encyclopedia provides comprehensive coverage of topics in marine biotechnology. It starts with the history of the field and delivers a complete overview of marine biotechnology. It then offers information on marine organisms, bioprocess techniques, marine natural products, biomaterials, bioenergy, and algal biotechnology. The encyclopedia also covers marine food and biotechnology applications in areas such as pharmaceuticals, cosmeceuticals, and nutraceuticals. Each topic in Encyclopedia of Marine Biotechnology is followed by 10-30 subtopics. The reference looks at algae cosmetics, drugs, and fertilizers; biodiversity; chitins and chitosans; aeroplysinin-1, toluquinol, astaxanthin, and fucoxanthin; and algal and fish genomics. It examines neuro-protective compounds from marine microorganisms; potential uses and medical management of neurotoxic phycotoxins; and the role of metagenomics in exploring marine microbiomes. Other sections fully explore marine microbiology, pharmaceutical development, seafood science, and the new biotechnology tools that are being used in the field today. One of the first encyclopedic books to cater to experts in marine biotechnology Brings together a diverse range of research on marine biotechnology to bridge the gap between scientific research and the industrial arena Offers clear explanations accompanied by color illustrations of the techniques and applications discussed Contains studies of the applications of marine biotechnology in the field of biomedical sciences Edited by an experienced author with contributions from internationally recognized experts from around the globe Encyclopedia of Marine Biotechnology is a must-have resource for researchers, scientists, and marine biologists in the industry, as well as for students at the postgraduate and graduate level. It will also benefit companies focusing on marine biotechnology, pharmaceutical and biotechnology, and bioenergy.
Population Genomics: Marine Organisms by Marjorie F. Oleksiak,Om P. Rajora Pdf
Population genomics has provided unprecedented opportunities to unravel the mysteries of marine organisms in the oceans' depths. The world's oceans, which make up 70% of our planet, encompass diverse habitats and host numerous unexplored populations and species. Population genomics studies of marine organisms are rapidly emerging and have the potential to transform our understanding of marine populations, species, and ecosystems, providing insights into how these organisms are evolving and how they respond to different stimuli and environments. This knowledge is critical for understanding the fundamental aspects of marine life, how marine organisms will respond to environmental changes, and how we can better protect and preserve marine biodiversity and resources. This book brings together leading experts in the field to address critical aspects of fundamental and applied research in marine species and share their research and insights crucial for understanding marine ecosystem diversity and function. It also discusses the challenges, opportunities and future perspectives of marine population genomics.
Introduction to Marine Genomics by J. Mark Cock,Kristin Tessmar-Raible,Catherine Boyen,Frédérique Viard Pdf
Marine biology has always played an important role in biological research, being at the origin of many key advances. To a certain extent, the influence of marine biology on the biological sciences was overshadowed over a period of several years by the remarkable advances that were made using powerful model organisms from terrestrial environments. This situation is now changing again, however, due primarily to spectacular developments in genomic methodologies that have significantly accelerated research in a broad spectrum of marine biology disciplines ranging from biodiversity to developmental biology to biotechnology. The data generated by marine genomics projects have had an impact on questions as diverse as understanding planetary geochemical cycles, the impact of climate change on marine fauna and flora, the functioning of marine ecosystems, the discovery of new organisms and novel biomolecules, and investigation of the evolution of animal developmental complexity. This book represents the first attempt to document how genomic technologies are revolutionising these diverse domains of marine biology. Each chapter of this book looks at how these technologies are being employed in a specific domain of marine research and provides a summary of the major results obtained to date. The book as a whole provides an overview of marine genomics as a discipline and represents an ideal starting point for exploring this rapidly developing domain.
The field of marine ecological genomics is evolving at an unprecedented pace. The increasingly cheaper and faster sequencing technologies present new posibilities but also new challegnes. The sheer amound of sequencing data requires elegant solutions for storing, querying and exchanging it. Additonally. sequences alone are not enough to understand the complex interactions between microorganism and the marine environment. Comprehensive environmental and contextual metadata are needed to put the sequences into context. However, the integration of sequence and metadata is not a trivial task. The aim of this thesis was to enhance the field of marine ecological genomics by fulfilling two tasks. Firstly, the technology necessary for data integration, visualization and analysis was set up. Secondly, this technological platform was used to support three ecological analysis of marine microbes. The first task was addressed by improving the existing portal for marine ecological genomics (http://www.megx.net). The main goal of megx.net is to integrate sequences and their metadata based on geographic location. The focus lies on environmental parameters such as temperature, salinity and nutrients. As a result of this thesis, megx.net pofits from a new data model, a net web interface, improved and analysis tools. For the second task, the integrated resources offered by megx.net were used. The effect of environmental stability on the transcription factors content of microbial comunities was quantified using interpolated environmental data. In a second study, interpolations were used to give environmental context to new hypothesis for domains of unknown function in the marine metagenomes. Last but not least, a study of the community structures of high and low DNA content marine microbes was complemented with integrated metadata. The extended technological platform megx.net was sucessfully used to gain new insights into the ecology of marine microbes.
