Evolution of Gene Regulatory Networks in Plant Development

Evolution of Gene Regulatory Networks in Plant Development

Author: Federico Valverde

Publisher: Frontiers Media SA

Published: 2018-02-15

Total Pages: 252

ISBN-13: 288945407X

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During their life cycle plants undergo a wide variety of morphological and developmental changes. Impinging these developmental processes there is a layer of gene, protein and metabolic networks that are responsible for the initiation of the correct developmental transitions at the right time of the year to ensure plant life success. New omic technologies are allowing the acquisition of massive amount of data to develop holistic and integrative analysis to understand complex processes. Among them, Microarray, Next-generation Sequencing (NGS) and Proteomics are providing enormous amount of data from different plant species and developmental stages, thus allowing the analysis of gene networks globally. Besides, the comparison of molecular networks from different species is providing information on their evolutionary history, shedding light on the origin of many key genes/proteins. Moreover, developmental processes are not only genetically programed but are also affected by internal and external signals. Metabolism, light, hormone action, temperature, biotic and abiotic stresses, etc. have a deep effect on developmental programs. The interface and interplay between these internal and external circuits with developmental programs can be unraveled through the integration of systematic experimentation with the computational analysis of the generated omics data (Molecular Systems Biology). This Research Topic intends to deepen in the different plant developmental pathways and how the corresponding gene networks evolved from a Molecular Systems Biology perspective. Global approaches for photoperiod, circadian clock and hormone regulated processes; pattern formation, phase-transitions, organ development, etc. will provide new insights on how plant complexity was built during evolution. Understanding the interface and interplay between different regulatory networks will also provide fundamental information on plant biology and focus on those traits that may be important for next-generation agriculture.


Book Synopsis Evolution of Gene Regulatory Networks in Plant Development by : Federico Valverde

Download or read book Evolution of Gene Regulatory Networks in Plant Development written by Federico Valverde and published by Frontiers Media SA. This book was released on 2018-02-15 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt: During their life cycle plants undergo a wide variety of morphological and developmental changes. Impinging these developmental processes there is a layer of gene, protein and metabolic networks that are responsible for the initiation of the correct developmental transitions at the right time of the year to ensure plant life success. New omic technologies are allowing the acquisition of massive amount of data to develop holistic and integrative analysis to understand complex processes. Among them, Microarray, Next-generation Sequencing (NGS) and Proteomics are providing enormous amount of data from different plant species and developmental stages, thus allowing the analysis of gene networks globally. Besides, the comparison of molecular networks from different species is providing information on their evolutionary history, shedding light on the origin of many key genes/proteins. Moreover, developmental processes are not only genetically programed but are also affected by internal and external signals. Metabolism, light, hormone action, temperature, biotic and abiotic stresses, etc. have a deep effect on developmental programs. The interface and interplay between these internal and external circuits with developmental programs can be unraveled through the integration of systematic experimentation with the computational analysis of the generated omics data (Molecular Systems Biology). This Research Topic intends to deepen in the different plant developmental pathways and how the corresponding gene networks evolved from a Molecular Systems Biology perspective. Global approaches for photoperiod, circadian clock and hormone regulated processes; pattern formation, phase-transitions, organ development, etc. will provide new insights on how plant complexity was built during evolution. Understanding the interface and interplay between different regulatory networks will also provide fundamental information on plant biology and focus on those traits that may be important for next-generation agriculture.

Evolution of Gene Regulatory Networks in Plant Development

Evolution of Gene Regulatory Networks in Plant Development

Author:

Publisher:

Published: 2018

Total Pages: 0

ISBN-13:

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During their life cycle plants undergo a wide variety of morphological and developmental changes. Impinging these developmental processes there is a layer of gene, protein and metabolic networks that are responsible for the initiation of the correct developmental transitions at the right time of the year to ensure plant life success. New omic technologies are allowing the acquisition of massive amount of data to develop holistic and integrative analysis to understand complex processes. Among them, Microarray, Next-generation Sequencing (NGS) and Proteomics are providing enormous amount of data from different plant species and developmental stages, thus allowing the analysis of gene networks globally. Besides, the comparison of molecular networks from different species is providing information on their evolutionary history, shedding light on the origin of many key genes/proteins. Moreover, developmental processes are not only genetically programed but are also affected by internal and external signals. Metabolism, light, hormone action, temperature, biotic and abiotic stresses, etc. have a deep effect on developmental programs. The interface and interplay between these internal and external circuits with developmental programs can be unraveled through the integration of systematic experimentation with the computational analysis of the generated omics data (Molecular Systems Biology). This Research Topic intends to deepen in the different plant developmental pathways and how the corresponding gene networks evolved from a Molecular Systems Biology perspective. Global approaches for photoperiod, circadian clock and hormone regulated processes; pattern formation, phase-transitions, organ development, etc. will provide new insights on how plant complexity was built during evolution. Understanding the interface and interplay between different regulatory networks will also provide fundamental information on plant biology and focus on those traits that may be important for next-generation agriculture.


Book Synopsis Evolution of Gene Regulatory Networks in Plant Development by :

Download or read book Evolution of Gene Regulatory Networks in Plant Development written by and published by . This book was released on 2018 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: During their life cycle plants undergo a wide variety of morphological and developmental changes. Impinging these developmental processes there is a layer of gene, protein and metabolic networks that are responsible for the initiation of the correct developmental transitions at the right time of the year to ensure plant life success. New omic technologies are allowing the acquisition of massive amount of data to develop holistic and integrative analysis to understand complex processes. Among them, Microarray, Next-generation Sequencing (NGS) and Proteomics are providing enormous amount of data from different plant species and developmental stages, thus allowing the analysis of gene networks globally. Besides, the comparison of molecular networks from different species is providing information on their evolutionary history, shedding light on the origin of many key genes/proteins. Moreover, developmental processes are not only genetically programed but are also affected by internal and external signals. Metabolism, light, hormone action, temperature, biotic and abiotic stresses, etc. have a deep effect on developmental programs. The interface and interplay between these internal and external circuits with developmental programs can be unraveled through the integration of systematic experimentation with the computational analysis of the generated omics data (Molecular Systems Biology). This Research Topic intends to deepen in the different plant developmental pathways and how the corresponding gene networks evolved from a Molecular Systems Biology perspective. Global approaches for photoperiod, circadian clock and hormone regulated processes; pattern formation, phase-transitions, organ development, etc. will provide new insights on how plant complexity was built during evolution. Understanding the interface and interplay between different regulatory networks will also provide fundamental information on plant biology and focus on those traits that may be important for next-generation agriculture.

Genetic Regulatory Mechanisms Underlying Developmental Shifts in Plant Evolution

Genetic Regulatory Mechanisms Underlying Developmental Shifts in Plant Evolution

Author: Verónica S. Di Stilio

Publisher: Frontiers Media SA

Published: 2019-10-09

Total Pages: 261

ISBN-13: 2889630595

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Book Synopsis Genetic Regulatory Mechanisms Underlying Developmental Shifts in Plant Evolution by : Verónica S. Di Stilio

Download or read book Genetic Regulatory Mechanisms Underlying Developmental Shifts in Plant Evolution written by Verónica S. Di Stilio and published by Frontiers Media SA. This book was released on 2019-10-09 with total page 261 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Plant Gene Regulatory Networks

Plant Gene Regulatory Networks

Author: Kerstin Kaufmann

Publisher: Springer Nature

Published:

Total Pages: 380

ISBN-13: 1071633546

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Book Synopsis Plant Gene Regulatory Networks by : Kerstin Kaufmann

Download or read book Plant Gene Regulatory Networks written by Kerstin Kaufmann and published by Springer Nature. This book was released on with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Plant Development: Role of Gene Regulatory Networks

Plant Development: Role of Gene Regulatory Networks

Author: Isabel Nelson

Publisher: States Academic Press

Published: 2021-11-16

Total Pages: 247

ISBN-13: 9781639894208

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Gene regulatory networks are composed of molecular regulators such as transcription factors which bind short, non-coding DNA sequences. These sequences are also called cis-regulatory elements and are located in the promoter region of a gene. Transcription regulators form an interconnected regulatory network which integrates endogenous and environmental signals into changes in gene expression. Gene regulatory networks provide an insight about organization of plant cells and their functions. They consist of thousands of connections between the target genes and transcription factors. Together, they regulate many cellular functions. They also help in understanding the regulation of genes under various conditions. The book studies, analyses and upholds the pillars of gene regulatory networks and its utmost significance in modern times. From theories to research to practical applications, case studies related to all contemporary topics of relevance to this field have been included herein. As this field is emerging at a rapid pace, the contents of this book will help the readers understand the modern concepts and applications of the subject.


Book Synopsis Plant Development: Role of Gene Regulatory Networks by : Isabel Nelson

Download or read book Plant Development: Role of Gene Regulatory Networks written by Isabel Nelson and published by States Academic Press. This book was released on 2021-11-16 with total page 247 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene regulatory networks are composed of molecular regulators such as transcription factors which bind short, non-coding DNA sequences. These sequences are also called cis-regulatory elements and are located in the promoter region of a gene. Transcription regulators form an interconnected regulatory network which integrates endogenous and environmental signals into changes in gene expression. Gene regulatory networks provide an insight about organization of plant cells and their functions. They consist of thousands of connections between the target genes and transcription factors. Together, they regulate many cellular functions. They also help in understanding the regulation of genes under various conditions. The book studies, analyses and upholds the pillars of gene regulatory networks and its utmost significance in modern times. From theories to research to practical applications, case studies related to all contemporary topics of relevance to this field have been included herein. As this field is emerging at a rapid pace, the contents of this book will help the readers understand the modern concepts and applications of the subject.

Gene Regulatory Networks Control Plant Development, Cell Identity, and Responses to the Environment

Gene Regulatory Networks Control Plant Development, Cell Identity, and Responses to the Environment

Author: Joel Rodriguez Medina

Publisher:

Published: 2020

Total Pages: 0

ISBN-13:

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As most plants lack the ability to move, they grow and adapt to different environmental conditions. The phenotype of a plant is determined by both its genetic makeup and the environment. Understanding the key molecular players that drive these responses has the potential to guide breeding programs for climate-resilient crops, and advance food security. In this dissertation, I used a systems biology framework to explore how gene regulatory networks underlie plant development and growth in three different contexts: in response to changes in the environment, between root cell types and tissues, and between species. In Chapter I, I link newly identified transcription factors that control nitrogen-associated metabolism with their underlying regulatory network in Arabidopsis thaliana. I further used mutations in key metabolic genes to describe a phenomenon whereby there is extensive transcriptional feedback upon genetic perturbation of metabolism. In Chapter II, I integrate genomic datasets from two different Solanum species. A major finding from analysis of these datasets is the identification of a group of genes with different translational regulation between tomato species upon exposure to elevated CO2. In Chapter III, I describe cases of innovation, conservation, and repurpose of gene function in regulatory circuits controlling cell-type specification in the root of tomato. In Chapter IV I return to gene regulation of nitrogen from a temporal dynamic perspective. I analyze time series expression data to elucidate how the regulation of the nitrogen response changes over time. I propose a subnetwork of genes that are temporally regulated and identify transcription factors that might be important for this mechanism. This work expands our knowledge not only of gene networks at a cell and tissue-specific resolution, but also sheds light on the evolutionary relationships between equivalent cell types in tomato, rice and Arabidopsis


Book Synopsis Gene Regulatory Networks Control Plant Development, Cell Identity, and Responses to the Environment by : Joel Rodriguez Medina

Download or read book Gene Regulatory Networks Control Plant Development, Cell Identity, and Responses to the Environment written by Joel Rodriguez Medina and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: As most plants lack the ability to move, they grow and adapt to different environmental conditions. The phenotype of a plant is determined by both its genetic makeup and the environment. Understanding the key molecular players that drive these responses has the potential to guide breeding programs for climate-resilient crops, and advance food security. In this dissertation, I used a systems biology framework to explore how gene regulatory networks underlie plant development and growth in three different contexts: in response to changes in the environment, between root cell types and tissues, and between species. In Chapter I, I link newly identified transcription factors that control nitrogen-associated metabolism with their underlying regulatory network in Arabidopsis thaliana. I further used mutations in key metabolic genes to describe a phenomenon whereby there is extensive transcriptional feedback upon genetic perturbation of metabolism. In Chapter II, I integrate genomic datasets from two different Solanum species. A major finding from analysis of these datasets is the identification of a group of genes with different translational regulation between tomato species upon exposure to elevated CO2. In Chapter III, I describe cases of innovation, conservation, and repurpose of gene function in regulatory circuits controlling cell-type specification in the root of tomato. In Chapter IV I return to gene regulation of nitrogen from a temporal dynamic perspective. I analyze time series expression data to elucidate how the regulation of the nitrogen response changes over time. I propose a subnetwork of genes that are temporally regulated and identify transcription factors that might be important for this mechanism. This work expands our knowledge not only of gene networks at a cell and tissue-specific resolution, but also sheds light on the evolutionary relationships between equivalent cell types in tomato, rice and Arabidopsis

Plant Systems Biology

Plant Systems Biology

Author: Sacha Baginsky

Publisher: Springer Science & Business Media

Published: 2007-06-25

Total Pages: 362

ISBN-13: 376437439X

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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.


Book Synopsis Plant Systems Biology by : Sacha Baginsky

Download or read book Plant Systems Biology written by Sacha Baginsky and published by Springer Science & Business Media. This book was released on 2007-06-25 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Plant Developmental Biology

Plant Developmental Biology

Author: Lars Hennig

Publisher: Humana

Published: 2016-08-23

Total Pages: 448

ISBN-13: 9781493957347

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Plants come in myriads of shapes and colors, and the beauty of plants has fascinated mankind for thousands of years. Long before Mendel discovered the laws of heritab- ity and Darwin developed his theory on evolution, the affection for ornamental plants led people to select alleles that establish novel plant forms. Today, plant developmental biology tries to discover the mechanisms that control the establishment of specialized cell types, tissues, and organs from the fertilized egg during a plant’s life. Although the underlying processes of cell proliferation and differentiation are similar in plants and a- mals, plants are different because their development is usually open, and its outcome is not the faithful repetition of a general plan but is strongly in?uenced by environm- tal conditions. In the last few decades, plant developmental biology has pinpointed a large number of developmental regulators and their interactions and the mechanisms that govern plant development start to emerge. In part, this progress was enabled by the advance of powerful molecular tools for a few model species, most importantly Arabidopsis. This volume of the Methods in Molecular Biology series provides a collection of protocols for many of the common experimental approaches in plant developmental bi- ogy. All chapters are written in the same format as that used in the Methods in Molecular TM Biology series. Each chapter opens with a description of the basic theory behind the method being described.


Book Synopsis Plant Developmental Biology by : Lars Hennig

Download or read book Plant Developmental Biology written by Lars Hennig and published by Humana. This book was released on 2016-08-23 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plants come in myriads of shapes and colors, and the beauty of plants has fascinated mankind for thousands of years. Long before Mendel discovered the laws of heritab- ity and Darwin developed his theory on evolution, the affection for ornamental plants led people to select alleles that establish novel plant forms. Today, plant developmental biology tries to discover the mechanisms that control the establishment of specialized cell types, tissues, and organs from the fertilized egg during a plant’s life. Although the underlying processes of cell proliferation and differentiation are similar in plants and a- mals, plants are different because their development is usually open, and its outcome is not the faithful repetition of a general plan but is strongly in?uenced by environm- tal conditions. In the last few decades, plant developmental biology has pinpointed a large number of developmental regulators and their interactions and the mechanisms that govern plant development start to emerge. In part, this progress was enabled by the advance of powerful molecular tools for a few model species, most importantly Arabidopsis. This volume of the Methods in Molecular Biology series provides a collection of protocols for many of the common experimental approaches in plant developmental bi- ogy. All chapters are written in the same format as that used in the Methods in Molecular TM Biology series. Each chapter opens with a description of the basic theory behind the method being described.

Plant Development and Evolution

Plant Development and Evolution

Author:

Publisher: Academic Press

Published: 2019-01-04

Total Pages: 660

ISBN-13: 0128098058

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Plant Development and Evolution, the latest release in the Current Topics in Developmental Biology series, highlights new advances in the field, with this new volume presenting interesting chapters on the Evolution of the plant body plan, Lateral root development and its role in evolutionary adaptation, the Development of the vascular system, the Development of the shoot apical meristem and phyllotaxis, the Evolution of leaf diversity, the Evolution of regulatory networks in land plants, The role of programed cell death in plant development, the Development and evolution of inflorescence architecture, the Molecular regulation of flower development, the Pre-meiotic another development, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Current Topics in Developmental Biology series Updated release includes the latest information on Plant Development and Evolution


Book Synopsis Plant Development and Evolution by :

Download or read book Plant Development and Evolution written by and published by Academic Press. This book was released on 2019-01-04 with total page 660 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant Development and Evolution, the latest release in the Current Topics in Developmental Biology series, highlights new advances in the field, with this new volume presenting interesting chapters on the Evolution of the plant body plan, Lateral root development and its role in evolutionary adaptation, the Development of the vascular system, the Development of the shoot apical meristem and phyllotaxis, the Evolution of leaf diversity, the Evolution of regulatory networks in land plants, The role of programed cell death in plant development, the Development and evolution of inflorescence architecture, the Molecular regulation of flower development, the Pre-meiotic another development, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Current Topics in Developmental Biology series Updated release includes the latest information on Plant Development and Evolution

Plant Gene Regulatory Networks

Plant Gene Regulatory Networks

Author: Kerstin Kaufmann

Publisher: Humana

Published: 2017-06-17

Total Pages: 0

ISBN-13: 9781493971244

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This volume presents protocols that analyze and explore gene regulatory networks (GRNs) at different levels in plants. This book is divided into two parts: Part I introduces different experimental techniques used to study genes and their regulatory interactions in plants. Part II highlights different computational approaches used for the integration of experimental data and bioinformatics-based predictions of regulatory interactions. This part of the book also provides information on essential database resources that grant access to gene-regulatory and molecular interactions in different plant genomes, with a specific focus on Arabidopsis thaliana. 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. Thorough and cutting-edge, Plant Gene Regulatory Networks: Methods and Protocols is a valuable resource for scientists and researchers interested in expanding their knowledge of GRNs.


Book Synopsis Plant Gene Regulatory Networks by : Kerstin Kaufmann

Download or read book Plant Gene Regulatory Networks written by Kerstin Kaufmann and published by Humana. This book was released on 2017-06-17 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents protocols that analyze and explore gene regulatory networks (GRNs) at different levels in plants. This book is divided into two parts: Part I introduces different experimental techniques used to study genes and their regulatory interactions in plants. Part II highlights different computational approaches used for the integration of experimental data and bioinformatics-based predictions of regulatory interactions. This part of the book also provides information on essential database resources that grant access to gene-regulatory and molecular interactions in different plant genomes, with a specific focus on Arabidopsis thaliana. 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. Thorough and cutting-edge, Plant Gene Regulatory Networks: Methods and Protocols is a valuable resource for scientists and researchers interested in expanding their knowledge of GRNs.