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Evolution of Gene Regulatory Networks in Plant Development

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889454075 Year: Pages: 252 DOI: 10.3389/978-2-88945-407-5 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany
Added to DOAB on : 2018-11-16 17:17:57
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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.

Modulating Prokaryotic Lifestyle by DNA-Binding Proteins

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889451050 Year: Pages: 296 DOI: 10.3389/978-2-88945-105-0 Language: English
Publisher: Frontiers Media SA
Subject: Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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The Overview of the Topic was the following: “One of the most active areas of research in molecular microbiology has been the study of how bacteria modulate their genetic activity and its consequences. The prokaryotic world has received much interest not only because the resulting phenomena are important to cells, but also because many of the effects often can be readily measured. Contributing to the interest of the present topic is the fact that modulation of gene activity involves the sensing of intra- and inter-cellular conditions, DNA binding and DNA dynamics, and interaction with the replication/transcription machinery of the cell. All of these processes are fundamental to the operation of a genetic entity and condition their lifestyle. Further, the discoveries achieved in the bacterial world have been of ample use in eukaryotes. In addition to the fundamental interest of understanding modulation of prokaryotic lifestyle by DNA-binding proteins, there is an added interest from the healthcare point of view. As it is well known the antibiotic-resistance strains of pathogenic bacteria are a major world problem, so that there is an urgent need of innovative technologies to tackle it. Most of the acquired resistances are spread by processes of horizontal gene transfer mediated by mobile elements in which DNA replication and gene expression are of basic interest. There is an imperative of finding new alternatives to the ‘classical’ way of treatment of bacterial infections and these new alternatives include the discovery of new drugs and of new bacterial targets. Nevertheless, these new alternatives will find a dead-end if we are unable to obtain a better understanding of the basic processes modulating bacterial gene expression. Our goal to achieve with this Topic of Frontiers is to accelerate our understanding of protein-DNA interactions. First, the topic will bring together several very active researchers in the study of gene replication, gene regulation, the strategies applied by the different proteins that participate in these processes, and their consequences. We will also acquire an in-depth knowledge of some of the mechanisms of gene regulation, gene transfer and gene replication. Further, the readers of the papers will realize the importance of the topic and will learn the most recent thinking, results, and approaches in the area”. We are fully confident that we have exceeded our expectations. Now we are proud to present the final output of the Topic, which is the eBook. It includes 24 articles contributed by 118 authors. As of today, Monday, 16th, January 2017, the total number of readings has reached 19,284, 14,921 article views, and 2,944 article downloads.

Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450428 Year: Pages: 111 DOI: 10.3389/978-2-88945-042-8 Language: English
Publisher: Frontiers Media SA
Subject: General and Civil Engineering --- Biotechnology --- Science (General) --- Genetics
Added to DOAB on : 2018-02-27 16:16:44
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The complexity of living organisms surpasses our unaided habilities of analysis. Hence, computational and mathematical methods are necessary for increasing our understanding of biological systems. At the same time, there has been a phenomenal recent progress allowing the application of novel formal methods to new domains. This progress has spurred a conspicuous optimism in computational biology. This optimism, in turn, has promoted a rapid increase in collaboration between specialists of biology with specialists of computer science. Through sheer complexity, however, many important biological problems are at present intractable, and it is not clear whether we will ever be able to solve such problems. We are in the process of learning what kind of model and what kind of analysis and synthesis techniques to use for a particular problem. Some existing formalisms have been readily used in biological problems, others have been adapted to biological needs, and still others have been especially developed for biological systems. This Research Topic has examples of cases (1) employing existing methods, (2) adapting methods to biology, and (3) developing new methods. We can also see discrete and Boolean models, and the use of both simulators and model checkers. Synthesis is exemplified by manual and by machine-learning methods. We hope that the articles collected in this Research Topic will stimulate new research.

Molecular and Cellular Plant Reproduction

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452118 Year: Pages: 302 DOI: 10.3389/978-2-88945-211-8 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Science (General)
Added to DOAB on : 2017-10-13 14:57:01
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Plant reproduction is essential not only for producing offspring but also for increasing crop quality and yield. Moreover, plant reproduction entails complex growth and developmental processes, which provide a variety of opportunities for elucidating fundamental principles in biology. The combinational employment of molecular genetic approaches and emerging technologies, such as florescence-based imaging techniques and next generation sequencing, has led to important progresses in plant reproduction using model plants, crops, and trees. This e-book compiles 31 articles, including 1 hypothesis and theory, 4 perspectives, 12 reviews, and 14 original research papers. We hope that this E-book will draw attention of all plant biologists to exciting advances in the field of plant reproduction and help solve remaining challenging questions in the future. We wish to express our appreciation to all the authors, reviewers, and the Frontiers editorial office for their excellent contributions that made the publication of this e-book possible.

Plant Development and Organogenesis: From Basic Principles to Applied Research

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ISBN: 9783039281268 9783039281275 Year: Pages: 246 DOI: 10.3390/books978-3-03928-127-5 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Plant Sciences --- Biology --- Science (General)
Added to DOAB on : 2020-01-30 16:39:46
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The way plants grow and develop organs significantly impacts the overall performance and yield of crop plants. The basic knowledge now available in plant development has the potential to help breeders in generating plants with defined architectural features to improve productivity. Plant translational research effort has steadily increased over the last decade due to the huge increase in the availability of crop genomic resources and Arabidopsis-based sequence annotation systems. However, a consistent gap between fundamental and applied science has yet to be filled. One critical point often brought up is the unreadiness of developmental biologists on one side to foresee agricultural applications for their discoveries, and of the breeders to exploit gene function studies to apply to candidate gene approaches when advantageous on the other. In this book, both developmental biologists and breeders make a special effort to reconcile research on the basic principles of plant development and organogenesis with its applications to crop production and genetic improvement. Fundamental and applied science contributions intertwine and chase each other, giving the reader different but complementary perspectives from only apparently distant corners of the same world.

Keywords

wheat-rye hybrids --- genes of reproductive isolation --- stem apical meristem --- molecular marker --- Rht18 --- reduced height --- wheat --- semi-dwarf --- linkage map --- CLE --- CLV --- WUS --- stem cells --- meristem --- SAM --- signaling --- locule --- Arabidopsis --- auxin --- HD-Zip transcription factors --- light environment --- photoreceptors --- wounding --- root plasticity --- hydrogen peroxide --- protoxylem --- plant development and organogenesis --- proline biosynthesis --- RolD --- rol genes --- Vasculature --- Organogenesis --- Development --- Brassicaceae --- Asteraceae --- flowering time --- photoperiod --- vernalization --- ambient temperature --- gibberellins --- age --- plant breeding --- grass --- ligule --- organogenesis --- boundaries --- shoot meristem --- morphogenesis --- molecular regulation --- cell wall --- cytoskeleton --- Arabidopsis --- root --- stem cells --- root development --- differentiation --- ground tissue --- radial patterning --- proximodistal patterning --- Plant in vitro cultures --- somatic cell selection --- hairy roots --- rol genes --- Agrobacterium rhizogenes --- genetic transformation --- recalcitrant species --- KNOX transcription factors --- plant development --- tree phase change --- transformation --- morphogenic --- embryogenesis --- meristem formation --- organogenesis --- GRETCHEN HAGEN 3 (GH3) IAA-amido synthase group II --- root apical meristem --- auxin --- cytokinin --- lateral root cap --- auxin minimum --- auxin conjugation --- plant development and organogenesis --- translational research --- crop productivity --- genetic improvement --- Arabidopsis thaliana --- regulatory networks --- phytohormones --- rol genes --- plant cell and tissue culture

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