Download or read book Integration of OMICS Data to Understand Plant Metabolism written by Carlos Alberto Labate and published by Frontiers Media SA. This book was released on 2019-07-10 with total page 153 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Omics and its Integration A Systems Biology Approach to Understanding Plant Physiology written by Kashif Ali and published by Frontiers Media SA. This book was released on 2023-11-27 with total page 155 pages. Available in PDF, EPUB and Kindle. Book excerpt: Due to the complexity and interconnectivity of many biological processes, an integrative systems biology approach is required to better understand them. The integration of various omics data (including genomics, proteomics, transcriptomics, and metabolomics data) will provide a holistic view that highlights the relationship among the various biomolecules and their functions in plant growth, resistance, quality, and many other important traits. Recent advances in analytical power and in the ability to process large data sets has enabled researchers to integrate multi-omics data and have a much deeper knowledge of the cell, tissue, organ, or even an entire organism being studied. The goal of this Research Topic is not only to publish high-quality and reliable omics data but also to answer the bigger question of how to integrate and correlate different data sets from multiple omics studies. Can one omics data set be used as a primary data set for the design and execution of another omics study? If so, then how it can be done? What are its pre-requisites? How can we plan research involving multi-omics approach to reach a meaningful conclusion? These are the questions that need our attention and their answers are critical for the future of omics-based research. For this Research Topic, we welcome contributors to submit manuscripts related to the following themes: • Studies on plant-based genomics, transcriptomics, proteomics, and metabolomics; • Development of new analytical methods for omics utilizing in plants; • Advancements in the current analytical methods for utilizing omics in plants; • Integration of multi-omics data sets; • Development of new statistical methods for data analysis.

Download or read book Plant Omics Trends and Applications written by Khalid Rehman Hakeem and published by Springer. This book was released on 2016-08-23 with total page 522 pages. Available in PDF, EPUB and Kindle. Book excerpt: To comprehend the organizational principle of cellular functions at diff erent levels, an integrative approach with large-scale experiments, the so-called ‘omics’ data including genomics, transcriptomics, proteomics, and metabolomics, is needed. Omics aims at the collective characterization and quantifi cation of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. Currently, omics is an essential tool to understand the molecular systems that underlie various plant functions. Furthermore, in several plant species, the development of omicsresources has progressed to address the particular biological properties of individual species. Integration of knowledge from omics-based research is an emerging issue as researchers seek to identify significance, gain biological insights and promote translational research. From these perspectives, we intend to provide the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances. Th e present book covers a wide range of omics topics, and discusses the latest trends and application area of plant sciences. In this volume, we have highlighted the working solutions as well as open problems and future challenges in plant omics studies. We believe that this book will initiate and introduce readers to state-of-the-art developments and trends in omics-driven research.

Download or read book Omics Applications for Systems Biology written by Wan Mohd Aizat and published by Springer. This book was released on 2018-10-31 with total page 99 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explains omics at the most basic level, including how this new concept can be properly utilized in molecular and systems biology research. Most reviews and books on this topic have mainly focused on the technicalities and complexity of each omics’ platform, impeding readers to wholly understand its fundamentals and applications. This book tackles such gap and will be most beneficial to novice in this area, university students and even researchers. Basic workflow and practical guidance in each omics are also described, such that scientists can properly design their experimentation effectively. Furthermore, how each omics platform has been conducted in our institute (INBIOSIS) is also detailed, a comprehensive example on this topic to further enhance readers’ understanding. The contributors of each chapter have utilized the platforms in various manner within their own research and beyond. The contributors have also been interactively integrated and combined these different omics approaches in their research, being able to systematically write each chapter with the conscious knowledge of other inter-relating topics of omics. The potential readers and audience of this book can come from undergraduate and postgraduate students who wish to extend their comprehension in the topics of molecular biology and big data analysis using omics platforms. Furthermore, researchers and scientists whom may have expertise in basic molecular biology can extend their experimentation using the omics technologies and workflow outlined in this book, benefiting their research in the long run.

Download or read book Plant Metabolomics written by Kazuki Saito and published by Springer Science & Business Media. This book was released on 2006-06-29 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolomics – which deals with all metabolites of an organism – is a rapidly-emerging sector of post-genome research fields. It plays significant roles in a variety of fields from medicine to agriculture and holds a fundamental position in functional genomics studies and their application in plant biotechnology. This volume comprehensively covers plant metabolomics for the first time. The chapters offer cutting-edge information on analytical technology, bioinformatics and applications. They were all written by leading researchers who have been directly involved in plant metabolomics research throughout the world. Up-to-date information and future developments are described, thereby producing a volume which is a landmark of plant metabolomics research and a beneficial guideline to graduate students and researchers in academia, industry, and technology transfer organizations in all plant science fields.

Download or read book Nutrient Use Efficiency in Plants written by Malcolm J. Hawkesford and published by Springer. This book was released on 2014-11-14 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nutrient Use Efficiency in Plants: Concepts and Approaches is the ninth volume in the Plant Ecophysiology series. It presents a broad overview of topics related to improvement of nutrient use efficiency of crops. Nutrient use efficiency (NUE) is a measure of how well plants use the available mineral nutrients. It can be defined as yield (biomass) per unit input (fertilizer, nutrient content). NUE is a complex trait: it depends on the ability to take up the nutrients from the soil, but also on transport, storage, mobilization, usage within the plant, and even on the environment. NUE is of particular interest as a major target for crop improvement. Improvement of NUE is an essential pre-requisite for expansion of crop production into marginal lands with low nutrient availability but also a way to reduce use of inorganic fertilizer.

Download or read book Omics data based identification of plant specialized metabolic genes written by Peipei Wang and published by Frontiers Media SA. This book was released on 2023-06-30 with total page 182 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Advances in Plant Omics and Systems Biology Approaches written by Flavia Vischi Winck and published by Springer Nature. This book was released on 2022-02-03 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the post-genomic era, several plant species have been sequenced and massive genomic information is now available which contributed to expand the development of novel technical strategies for the study of additional levels of biological information of plant species. This book focuses on the “omics” approaches together with systems analysis of several different plant species, which have revealed very interesting variations on the cellular responses at the protein, transcript and metabolite levels in response to changes environmental conditions. The volume covers recent technological advances in the area of “omics” and synthesizes recent findings of the field of plant “omics” and systems biology together along with techniques that can be applied for such studies.

Download or read book PlantOmics The Omics of Plant Science written by Debmalya Barh and published by Springer. This book was released on 2015-03-18 with total page 839 pages. Available in PDF, EPUB and Kindle. Book excerpt: PlantOmics: The Omics of Plant Science provides a comprehensive account of the latest trends and developments of omics technologies or approaches and their applications in plant science. Thirty chapters written by 90 experts from 15 countries are included in this state-of-the-art book. Each chapter describes one topic/omics such as: omics in model plants, spectroscopy for plants, next generation sequencing, functional genomics, cyto-metagenomics, epigenomics, miRNAomics, proteomics, metabolomics, glycomics, lipidomics, secretomics, phenomics, cytomics, physiomics, signalomics, thiolomics, organelle omics, micro morphomics, microbiomics, cryobionomics, nanotechnology, pharmacogenomics, and computational systems biology for plants. It provides up to date information, technologies, and their applications that can be adopted and applied easily for deeper understanding plant biology and therefore will be helpful in developing the strategy for generating cost-effective superior plants for various purposes. In the last chapter, the editors have proposed several new areas in plant omics that may be explored in order to develop an integrated meta-omics strategy to ensure the world and earth’s health and related issues. This book will be a valuable resource to students and researchers in the field of cutting-edge plant omics.

Download or read book Omics in Plant Breeding written by Aluízio Borém and published by John Wiley & Sons. This book was released on 2014-06-03 with total page 253 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational and high-throughput methods, such as genomics, proteomics, and transcriptomics, known collectively as “-omics,” have been used to study plant biology for well over a decade now. As these technologies mature, plant and crop scientists have started using these methods to improve crop varieties. Omics in Plant Breeding provides a timely introduction to key omicsbased methods and their application in plant breeding. Omics in Plant Breeding is a practical and accessible overview of specific omics-based methods ranging from metabolomics to phenomics. Covering a single methodology within each chapter, this book provides thorough coverage that ensures a strong understanding of each methodology both in its application to, and improvement of, plant breeding. Accessible to advanced students, researchers, and professionals, Omics in Plant Breeding will be an essential entry point into this innovative and exciting field. • A valuable overview of high-throughput, genomics-based technologies and their applications to plant breeding • Each chapter explores a single methodology, allowing for detailed and thorough coverage • Coverage ranges from well-established methodologies, such as genomics and proteomics, to emerging technologies, including phenomics and physionomics Aluízio Borém is a Professor of Plant Breeding at the University of Viçosa in Brazil. Roberto Fritsche-Neto is a Professor of Genetics and Plant Breeding at the University of São Paulo in Brazil.

Download or read book Characterizing Complex Phenotypes in Metabolism written by Monica L. Mo and published by . This book was released on 2009 with total page 104 pages. Available in PDF, EPUB and Kindle. Book excerpt: The advent of high-throughput technologies has resulted in an explosion of molecular data. A major challenge is found in interpreting and understanding these different types of data sets at a phenotypic level. Systems biology has capitalized on these technologies by consolidating various types of biological information into structured networks for their analysis and computation. The bottom-up systems biology approach, in particular, has been crucial in providing mechanistic foundations for systems-level modeling in microorganisms, and its extension to eukaryotic metabolism has made it possible to elucidate complex phenotypes in a systematic manner. The work presented in this dissertation describes the integrative use of high-throughput data and genome-scale network reconstructions to characterize complex phenotypes of eukaryotic metabolism. First, the genome-scale reconstructions of yeast and human metabolism are discussed, which provide the contextual basis in which "omics" data is analyzed. Previously developed constraint-based modeling approaches were refined to analyze "omics" data sets, in particular for transcriptomic and metabolomic data. Finally, example applications are presented in the evaluation of physiological and perturbed metabolic states of yeast and human cellular systems. The studies discussed herein are: (1) analyzing drug response phenotypes of human metabolism; (2) evaluating genetic and environmentally perturbed processes in yeast ammonium assimilation; and (3) characterizing the pluripotent phenotype of embryonic stem cell metabolism. The work described in these studies represents advancement towards integrating bottom-up and data-driven approaches to understanding broader "omics"--To-phenotype relationships.

Download or read book Integrated Modeling of Phototrophic Metabolism Leveraging Multi Omics Datasets written by Debolina Sarkar and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Rapid progress in high-throughput experimental technologies has enabled generation of large-scale systems biology datasets. These span all biological hierarchies from genomics describing the genetic make-up, transcriptomics and proteomics at the gene and enzyme expression level, metabolomics that helps quantify the amount and nature of resultant biomolecules, to finally phenomics that describes the overall traits of an individual. This veritable data deluge necessitates algorithmic and computational advances that can leverage multi-omics integration, in order to facilitate the analysis of complex systems and extract meaningful insights. Flux balance analysis (FBA) using genome-scale metabolic (GSM) models provide an advantageous platform for doing so as these models are (relatively) parameter-free, can be constructed using the annotated genome alone and simulated in linear time offering scale-up benefits. GSMs model a network view of metabolism, wherein metabolites are cast as nodes in a graph linked via edges representing all possible biochemical conversions occurring within an organism. In Chapter 1, we present an overview of constraints-based analysis of metabolic networks, including the reconstruction of GSM models, their use within an optimization-based scheme such as FBA, and the various applications of such models. Next, we describe the extension of metabolic modeling frameworks, originally designed for microbial systems, to the study of plants. This is accompanied by its own set of challenges, such as accurately capturing the division of roles between the various tissue and organ systems and dealing with systematic biases that are typically associated with poorly annotated non-model systems. Finally, we explore how the incorporation of new data types, modeling schemes, and computational tools have impacted FBA by helping increase its predictive power and scope. FBA has proven to be quite adept at describing aggregated metabolite flows, i.e., providing a snapshot of metabolism as averaged over the entire growth cycle. However, it is also time invariant, and thus does not accommodate temporally varying cell processes such as sequestering different biomass components at various time points in a growth cycle However, we know from experiments that many organisms including cyanobacteria have a lifestyle that is heavily tailored around light availability and thus show metabolic oscillations. In Chapter 2, we present a framework called CycleSyn that augments FBA by accounting for such temporal trends. CycleSyn discretizes a growth cycle into individual time periods (called Time Point Models or TPMs), each described by its own GSM model. The flow of metabolites across TPMs is allowed while inventorying metabolite levels and only allowing for the utilization of currently or previously produced compounds. Additional time-dependent constraints can also be imposed to capture the cyclic nature of cellular processes. CycleSyn was used to develop a diurnal FBA model of Synechocystis sp. PCC 6803 metabolism. Predicted flux and metabolite pools were in line with published studies, paving the way for constructing time-resolved GSM models. Additionally, the metabolic reorganization that would be required to enable Synechocystis PCC 6803 to fix nitrogen by temporally separating it from photosynthesis was also explored. Similar to modeling multiple metabolic models at once in CycleSyn, in Chapter 3 we extend this to modeling multiple organisms together as in a community, so as to discern the underlying interactions. This community comprised a genetically streamlined unicellular cyanobacterium called Candidatus Atelocyanobacterium thalassa (or UCYN-A) living in a symbiosis with a phototrophic microalga. We used metabolic modeling to glean insights into UCYN-A's unique physiology and metabolic processes governing the symbiotic association. To this end, we developed an optimization-based framework that infers all possible trophic scenarios consistent with the observed data. Possible mechanisms employed by UCYN-A to accommodate diazotrophy with daytime carbon fixation by the host (i.e., two mutually incompatible processes) were also elucidated. We found that the metabolic functions of the two constituents, and UCYN-A's streamlined genome is optimized to support maximal nitrogen fixation flux, alluding that this symbiosis is as close to being a functional 'nitroplast' as any observed till date. We envision that the developed framework using UCYN-A and its algal host will be used as a roadmap and motivate the study of similarly unique microbial systems in the future. Understanding how genomic mutations impact the overall phenotype of an organism has been a focus of efforts aimed at improving growth yield, determining genetic markers governing a trait, and understanding adaptive processes. This has been performed conventionally using genome-wide association studies, which seek to identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. In Chapter 4, we propose a complementary tool called SNPeffect that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect was used to explain differential growth rate and metabolite accumulation in Arabidopsis and poplar as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicated that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally-characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino-acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition. Thus far, we have developed computational frameworks that examine how the metabolism of an organism dictates its total phenotype and interactions with other organisms in a community. In Chapter 5, we take the next step by examining ways in which an organism can impact its host, specifically how the infant gut microbiome is shaped. Fecal samples from newborn infants showed that gut bacteria is detectable by 16 h after birth. However, analysis of the microbiome, proteome, and metabolome data did not suggest a single genomic signature for neonatal gut colonization. Using flux balance modeling, we found E. coli to be the most common early colonizer. The appearance of bacteria was associated with decreased levels of free amino acids and an increase in products of bacterial fermentation, primarily acetate and succinate. Among all the microbial species found, these observations were only consistent with E. coli growing under anaerobic conditions using amino acid fermentation to support maximal ATP yield. These results provide a deep characterization of the first microbes in the human gut and show how the biochemical environment is altered by their appearance. Finally, in Chapter 6, we conclude with our efforts to develop computational frameworks enabling the integration of heterogeneous datasets within constraints-based optimization. We discuss current challenges associated with such modeling frameworks and their uses, and finally present future perspectives for augmenting these models with the incorporation of diverse data types, multi-scale modeling, cross-cutting applications.

Download or read book Plant Metabolic Engineering written by Vladimir Shulaev and published by Humana. This book was released on 2022-12-01 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume looks at the latest techniques used by researchers to study various aspects of plant metabolic engineering. The chapters in this book cover topics such as bioinformatics tools used to discover new genes and pathways; heterologous expression of biosynthetic genes in plant and microbial systems; and omics technologies, such as transcriptomics, proteomics, metabolomics, and data analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Plant Metabolic Engineering: Methods and Protocols is a valuable resource for biologists, chemists, biotechnologists, students, and broad cohorts of researchers who works in the fields of plant metabolism and metabolic engineering.

Download or read book Recent Trends and Techniques in Plant Metabolic Engineering written by Sudesh Kumar Yadav and published by Springer. This book was released on 2018-12-05 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Remarkable research has yielded whole genome data in plants, resulting in the documentation of an ever-increasing number of genes, without establishing their functions. The huge data resources available at the genome, transcriptome, proteome and metabolome levels are of enormous value in the field of functional genomics. This book provides insights into interpreting the sea of data in order to understand basic and practical aspects of plant metabolic engineering. It discusses in detail ways to tap into this enormous pool of data to increase productivity, and offers information that is both interesting and necessary for exploring the manipulation of metabolic pathways. The interdisciplinary approaches presented here also serve as a source of ideas for practical applications.

Download or read book Integration of a Constraint based Metabolic Model of Brassica Napus Developing Seeds with 13C metabolic Flux Analysis written by and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The use of large-scale or genome-scale metabolic reconstructions for modeling and simulation of plant metabolism and integration of those models with large-scale omics and experimental flux data is becoming increasingly important in plant metabolic research. Here we report an updated version of bna572, a bottom-up reconstruction of oilseed rape (Brassica napus L.; Brassicaceae) developing seeds with emphasis on representation of biomass-component biosynthesis. New features include additional seed-relevant pathways for isoprenoid, sterol, phenylpropanoid, flavonoid, and choline biosynthesis. Being now based on standardized data formats and procedures for model reconstruction, bna572+ is available as a COBRA-compliant Systems Biology Markup Language (SBML) model and conforms to the Minimum Information Requested in the Annotation of Biochemical Models (MIRIAM) standards for annotation of external data resources. Bna572+ contains 966 genes, 671 reactions, and 666 metabolites distributed among 11 subcellular compartments. It is referenced to the Arabidopsis thaliana genome, with gene-protein-reaction (GPR) associations resolving subcellular localization. Detailed mass and charge balancing and confidence scoring were applied to all reactions. Using B. napus seed specific transcriptome data, expression was verified for 78% of bna572+ genes and 97% of reactions. Alongside bna572+ we also present a revised carbon centric model for 13C-Metabolic Flux Analysis (13C-MFA) with all its reactions being referenced to bna572+ based on linear projections. By integration of flux ratio constraints obtained from 13C-MFA and by elimination of infinite flux bounds around thermodynamically infeasible loops based on COBRA loopless methods, we demonstrate improvements in predictive power of Flux Variability Analysis (FVA). In conclusion, using this combined approach we characterize the difference in metabolic flux of developing seeds of two B. napus genotypes contrasting in starch and oil content.

Download or read book Characterizing Plant Specialized Metabolism Through Computational Tools and Omics Approaches written by Elizabeth Mahood and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Two of the major bottlenecks that currently hinder the study of plant specialized metabolism are the structural elucidation of metabolites and the functional characterization of their associated genes. Although modern analytical instruments (typically mass spectrometers (MS) coupled with liquid chromatography (LC), or LC-MS) are capable of detecting up to thousands of metabolites in plant extracts, no comparable methods exist for the high-throughput structural elucidation of these metabolites. Similarly, the functions of specialized metabolic genes can be difficult to elucidate as they often belong to large gene families that undergo frequent gene duplication. While the most common method of gene function prediction - the transfer of known gene functions through related species - is easily implementable, it may yield inaccurate conclusions for metabolic genes. The goal of this dissertation is to contribute to the alleviation of both bottlenecks. Chapter 1 reviews current methodologies and algorithms for the elucidation of metabolite structure and gene function - especially in relation to plant specialized metabolism. Chapter 2 describes the development of machine learning algorithms to structurally annotate metabolites based on LC-MS data, and the evaluation of their performance with plant metabolites. Chapters 3 and 4 detail the analysis of an integrative transcriptomics and metabolomics experiment undertaken in the model grass species Brachypodium distachyon, designed to both elucidate metabolic functions of genes and characterize stress-induced shifts in metabolism. Chapter 3 explores the utilization of emerging algorithms for i) partial elucidation of the structures of plant metabolites, ii) quantification of the impacts of different environmental conditions on the plant metabolome. Chapter 4 implements integrative-omics analyses to characterize B. distachyon genes involved in facilitating arbuscular mycorrhizal symbiosis, and investigates the activity of one functionally unknown gene. Collectively, these studies find that structural annotation of plant metabolites facilitates the understanding of i) how plants adapt to changing environments, and ii) metabolic activities of plant genes. Such knowledge is essential for alleviation of major bottlenecks in the study of plant specialized metabolism.

Download or read book Metabolomics From Fundamentals to Clinical Applications written by Alessandra Sussulini and published by Springer. This book was released on 2017-01-28 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive view of metabolomics, from the basic concepts, through sample preparation and analytical methodologies, to data interpretation and applications in medicine. It is the first volume to cover metabolomics clinical applications while also emphasizing analytical and statistical features. Moreover, future trends and perspectives in clinical metabolomics are also presented. For researches already experienced in metabolomics, the book will be useful as an updated definitive reference. For beginners in the field and graduate students, the book will provide detailed information about concepts and experimental aspects in metabolomics, as well as examples and perspectives of applications of this strategy to clinical questions.