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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.

The plant microbiome and its importance for plant and human health

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193783 Year: Pages: 189 DOI: 10.3389/978-2-88919-378-3 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Microbiology --- Science (General)
Added to DOAB on : 2015-11-19 16:29:12
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The study of plant-microbe associations by new techniques has significantly improved our understanding of the structure and specificity of the plant microbiome. Yet, microbiome function and the importance of the plant’s microbiome in the context of human and plant health are largely unexplored. Comparable with our human microbiome, millions of microbes inhabit plants, forming complex ecological communities that influence plant growth and health through its collective metabolic activities and host interactions. Viewing the microbiota from an ecological perspective can provide insight into how to promote plant health and stress tolerance of their hosts or how to adapt to a changing climate by targeting this microbial community. Moreover, the plant microbiome has a substantial impact on human health by influencing our gut microbiome by eating raw plants such as lettuce and herbs but also by influencing the microbiome of our environment through airflow. This research topic comprising reviews, original and opinion articles highlights the current knowledge regarding plant microbiomes, their specificity, diversity and function as well as all aspects studying the management of plant microbiomes to enhance plant growth, health quality and stress tolerance.

Novel clinical applications of extracellular vesicles

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889196456 Year: Pages: 66 DOI: 10.3389/978-2-88919-645-6 Language: English
Publisher: Frontiers Media SA
Subject: Medicine (General) --- Allergy and Immunology
Added to DOAB on : 2016-08-16 10:34:25
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During the last years, the research on extracellular vesicles (EVs) has raised giving new insights into pathophysiology of several diseases. EVs are membrane-bound particles secreted by almost all cell types. Depending on their biogenesis and size they include exosomes, microparticles / microvesicles and apoptotic bodies. Characteristically, EVs carry markers from the source cell membrane and contain genetic material, lipids and proteins inside. They are known to play a role in cell-to-cell communication and to produce genotypic and phenotypic modifications in the target cell including: antigen presentation, apoptosis induction, cellular activation, inhibition or differentiation. In particular, increasing concentrations of EVs have been found in many diseases such as cancer, autoimmune and cardiovascular diseases, among others. Most of the studies in EVs are focused on the characterization of EVs compounds, identifying mechanism of action, their potential use as biomarkers, and few of them investigate a therapeutic usage. However, there are some issues to be achieved on the path to their clinical application. This research topic offers a common place to discuss current and novel clinical applications of EVs pointing on future directions. We encouraged the submission of original articles, reviews, hypothesis, controversies, future perspectives and personal viewpoints on the following topics of interest, but not limited to: • Contribution of EVs to better understand the pathology of immunological diseases. • Standardization of isolation and quantification protocols in the daily clinical practice. • Possible applications of EVs as clinical biomarkers (diagnostic, prognostic and evolution marker). • Therapeutic role of EVs being vehicles of specific cargo: current clinical trials? • Novel immunological functions of EVs.

Harnessing Useful Rhizosphere Microorganisms for Pathogen and Pest Biocontrol

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450596 Year: Pages: 334 DOI: 10.3389/978-2-88945-059-6 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Microbiology --- Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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Growing demographic trends require sustainable technologies to improve quality and yield of future food productions. However, there is uncertainty about plant protection strategies in many agro-ecosystems. Pests, diseases, and weeds are overwhelmingly controlled by chemicals which pose health risks and cause other undesirable effects.Therefore, an increasing concern on control measures emerged in recent years. Many chemicals became questioned with regard to their sustainability and are (or will be) banned. Alternative management tools are studied, relying on biological, and low impact solutions. This ResearchTopic concerns microbial biocontrol agents, root-associated microbiomes, and rhizosphere networks. Understanding how they interact or respond to (a)biotic environmental cues is instrumental for an effective and sustainable impact. The rhizosphere is in this regard a fundamental object of study, because of its role in plant productivity. This e-book provides a polyhedral perspective on many issues in which beneficial microorganisms are involved. Data indeed demonstrate that they represent an as yet poorly-explored resource, whose exploitation may actively sustain plant protection and crop production. Given the huge number of microbial species present on the planet, the microorganisms studied represent just the tip of an iceberg. Data produced are, however, informative enough about their genetic and functional biodiversity, as well as about the ecosystem services they provide to underp in crop production. Challenges for future research work concern not only the biology of these species, but also the practices required to protect their biodiversity and to extend their application in the wide range of agricultural soils and systems present in the world. Agriculture cannot remain successfully and sustainable unless plant germplasm and useful microbial species are integrated, a goal for which new knowledge and information-based approaches are urgently needed.Growing demographic trends require sustainable technologies to improve quality and yield of future food productions. However, there is uncertainty about plant protection strategies in many agro-ecosystems. Pests, diseases, and weeds are overwhelmingly controlled by chemicals which pose health risks and cause other undesirable effects.Therefore, an increasing concern on control measures emerged in recent years. Many chemicals became questioned with regard to their sustainability and are (or will be) banned. Alternative management tools are studied, relying on biological, and low impact solutions. This ResearchTopic concerns microbial biocontrol agents, root-associated microbiomes, and rhizosphere networks. Understanding how they interact or respond to (a)biotic environmental cues is instrumental for an effective and sustainable impact. The rhizosphere is in this regard a fundamental object of study, because of its role in plant productivity. This e-book provides a polyhedral perspective on many issues in which beneficial microorganisms are involved. Data indeed demonstrate that they represent an as yet poorly-explored resource, whose exploitation may actively sustain plant protection and crop production. Given the huge number of microbial species present on the planet, the microorganisms studied represent just the tip of an iceberg. Data produced are, however, informative enough about their genetic and functional biodiversity, as well as about the ecosystem services they provide to underp in crop production. Challenges for future research work concern not only the biology of these species, but also the practices required to protect their biodiversity and to extend their application in the wide range of agricultural soils and systems present in the world. Agriculture cannot remain successfully and sustainable unless plant germplasm and useful microbial species are integrated, a goal for which new knowledge and information-based approaches are urgently needed.

Actinobacteria in Special and Extreme Habitats: Diversity; Function Roles and Environmental Adaptations

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450138 Year: Pages: 229 DOI: 10.3389/978-2-88945-013-8 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Microbiology
Added to DOAB on : 2018-02-27 16:16:44
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Actinobacteria are highly diverse prokaryotes that are ubiquitous in soil, freshwater and marine ecosystems. Although various studies have focused on the ecology of this phylum, data are still scant on the diversity, abundance and ecology of actinobacteria endemic to special and extreme environments, such as gut, plant, alkaline saline soil, deep sea sediments, hot springs and other habitats. Actinobacteria are well-known producers of a vast array of secondary metabolites, many of which have useful applications in medicine and agriculture. Furthermore, actinobacteria also have diverse functions in different environments apart from antibiotic production. For example, actinobacteria are reported to contribute to the break-down and recycling of organic compounds. They play a significant role in fixation of nitrogen, improvement plant growth, biodegradation, bioremediation and environmental protection. Therefore, understanding the actinobacterial diversity and distribution in such special environments is important in deciphering the ecological roles of these microorganisms and for biotechnological bioprospecting. Recent advances in cultivation, DNA sequencing technologies and -omics (metagenomics, metaproteomics etc) methods have greatly contributed to the rapid advancement of our understanding of microbial diversity, function and they interactions with environment. Furthermore, comparative genomic studies can provide overall information about actinobacterial speciation, evolution, metabolism and environment adaptation mechanisms. This research topic comprising reviews and original articles highlights the recent advances regarding the unexpectedly diverse/rare group of actinobacteria with special selective isolation methods or culture-independent methods, as well as their biological activities, ecophysiologica function and mechanisms from diverse special and extreme environments.

Drug Repositioning: Current Advances and Future Perspectives

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889456963 Year: Pages: 153 DOI: 10.3389/978-2-88945-696-3 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Therapeutics
Added to DOAB on : 2019-01-23 14:53:43
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Drug repositioning is the process of identifying new indications for existing drugs. At present, the conventional de novo drug discovery process requires an average of about 14 years and US$2.5 billion to approve and launch a drug. Drug repositioning can reduce the time and cost of this process because it takes advantage of drugs already in clinical use for other indications or drugs that have cleared phase I safety trials but have failed to show efficacy in the intended diseases. Historically, drug repositioning has been realized through serendipitous clinical observations or improved understanding of disease mechanisms. However, recent technological advances have enabled a more systematic approach to drug repositioning. This eBook collects 16 articles from 112 authors, providing readers with current advances and future perspectives of drug repositioning.

Current Knowledge in Thyroid Cancer — From Bench to Bedside

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ISBN: 9783038424765 9783038424772 Year: Pages: VIII, 212 DOI: 10.3390/books978-3-03842-477-2 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Biology
Added to DOAB on : 2017-08-11 11:32:17
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In recent years, studies in the field of thyroid cancer have been performed in order to identify and verify thyroid specific biomarkers, as well as cancer-specific changes in gene expression patterns and alterations of the protein content. Furthermore, new drugs, small molecules and antibodies were developed and tested in vitro and in vivo. Trials investigated the ratio between therapeutic and adverse effects. Tyrosine kinase inhibitors (TKI) have become a new therapeutic option of both differentiated thyroid cancer and medullary thyroid cancer. In the last few years, new substances for targeted systemic therapy have been approved after their efficacy was demonstrated in Phase III trials. Most of them show a moderate response. However, adverse effects are common. TKI are used in patients with advanced metastatic thyroid cancer that is radioiodine (RAI)-refractory.In this Special Issue, original studies on the pathophysiology, diagnosis, and therapy of thyroid cancer, including genetics, proteomics, metabolomics, molecular and cell biology, will be published. It will also cover reports on patients, providing novel mechanistic insights into the underlying pathogenesis or new aspects that may impact clinical therapy, and recent study results in order to review the current status of new therapy options in thyroid cancer.

Role of Silicon in Plants

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889453528 Year: Pages: 186 DOI: 10.3389/978-2-88945-352-8 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany
Added to DOAB on : 2018-02-27 16:16:45
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Silicon (Si) is gaining increased attention in the farming sector because of its beneficial effects observed in several crop species, particularly under stress conditions. The magnitude of benefits is predominantly observed in plant species that can accumulate Si above a certain threshold. Therefore, deciphering the molecular mechanisms and genetic factors conferring a plant ability to take up silicon is necessary. Along these lines, several efforts have been made to identify the specific genes regulating Si uptake and distribution in plant tissues. This information finds its usefulness in identifying Si-competent species, and could eventually lead to improving this ability in low-accumulating species. The successful exploitation of Si in agriculture depends highly on the understanding of different Si properties including plant-available Si from the soil, transport within tissues, deposition in planta, and Si effect on different metabolic and physiological processes. In addition, a better comprehension of external factors influencing Si uptake and deposition in plant tissue remains important. A plant can take up Si efficiently only in the form of silicic acid and most soils, despite containing high concentrations of Si, are deficient in plant-available Si. Consequently, soil amendment with fertilizers rich in plant-available Si is now viewed as an affordable option to protect plants from the biotic and abiotic stresses and achieve more sustainable cropping management worldwide. Articles compiled in the present research topic touch upon several aspects of Si properties and functionality in plants. The information will be helpful to further our understanding of the role of Si and contribute to exploit the benefits plants derive from it.

Computational Systems Biology of Pathogen-Host Interactions

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889198214 Year: Pages: 198 DOI: 10.3389/978-2-88919-821-4 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2016-01-19 14:05:46
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A thorough understanding of pathogenic microorganisms and their interactions with host organisms is crucial to prevent infectious threats due to the fact that Pathogen-Host Interactions (PHIs) have critical roles in initiating and sustaining infections. Therefore, the analysis of infection mechanisms through PHIs is indispensable to identify diagnostic biomarkers and next-generation drug targets and then to develop strategic novel solutions against drug-resistance and for personalized therapy. Traditional approaches are limited in capturing mechanisms of infection since they investigate hosts or pathogens individually. On the other hand, the systems biology approach focuses on the whole PHI system, and is more promising in capturing infection mechanisms. Here, we bring together studies on the below listed sections to present the current picture of the research on Computational Systems Biology of Pathogen-Host Interactions:- Computational Inference of PHI Networks using Omics Data- Computational Prediction of PHIs- Text Mining of PHI Data from the Literature- Mathematical Modeling and Bioinformatic Analysis of PHIs Computational Inference of PHI Networks using Omics Data Gene regulatory, metabolic and protein-protein networks of PHI systems are crucial for a thorough understanding of infection mechanisms. Great advances in molecular biology and biotechnology have allowed the production of related omics data experimentally. Many computational methods are emerging to infer molecular interaction networks of PHI systems from the corresponding omics data. Computational Prediction of PHIs Due to the lack of experimentally-found PHI data, many computational methods have been developed for the prediction of pathogen-host protein-protein interactions. Despite being emerging, currently available experimental PHI data are far from complete for a systems view of infection mechanisms through PHIs. Therefore, computational methods are the main tools to predict new PHIs. To this end, the development of new computational methods is of great interest. Text Mining of PHI Data from Literature Despite the recent development of many PHI-specific databases, most data relevant to PHIs are still buried in the biomedical literature, which demands for the use of text mining techniques to unravel PHIs hidden in the literature. Only some rare efforts have been performed to achieve this aim. Therefore, the development of novel text mining methods specific for PHI data retrieval is of key importance for efficient use of the available literature. Mathematical Modeling and Bioinformatic Analysis of PHIs After the reconstruction of PHI networks experimentally and/or computationally, their mathematical modeling and detailed computational analysis is required using bioinformatics tools to get insights on infection mechanisms. Bioinformatics methods are increasingly applied to analyze the increasing amount of experimentally-found and computationally-predicted PHI data. Acknowledgements: We, editors of this e-book, acknowledge Emrah Nikerel (Yeditepe University, Turkey) and Arzucan Özgür (Bogaaziçi University, Turkey) for their contributions during the initiation of the Research Topic.

Aquaporins: Dynamic Role and Regulation

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452897 Year: Pages: 183 DOI: 10.3389/978-2-88945-289-7 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany --- Physiology
Added to DOAB on : 2018-02-27 16:16:44
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Aquaporins (AQPs), a class of integral membrane proteins, form channels facilitating movement of water and many other solutes. In solute transport systems of all living organisms including plants, animals and fungi, AQPs play a vital role. Plants contain a much higher number of AQP genes compared to animals, the likely consequence of genome duplication events and higher ploidy levels. As a result of duplication and subsequent diversification, plant AQPs have evolved several subfamilies with very diverse functions. Plant AQPs are highly selective for specific solutes because of their unique structural features. For instance, ar/R selectivity filters and NPA domains have been found to be key elements in governing solute permeability through the AQP channels. Combination of conserved motifs and specific amino acids influencing pore morphology appears to regulate the permeability of specific solutes such as water, urea, CO2, H2O2, boric acid, silicic acid and many more. The discovery of novel AQPs has been accelerated over the last few years with the increasing availability of genomic and transcriptomic data. The expanding number of well characterised AQPs provides opportunities to understand factors influencing water transport, nutritional uptake, and elemental balance. Homology-based search tools and phylogenetic analyses offer efficient strategies for AQP identification. Subsequent characterization can be based on different approaches involving proteomics, genomics, and transcriptomic tools. The combination of these technological advances make it possible to efficiently study the inter-dependency of AQPs, regulation through phosphorylation and reversible phosphorylation, networking with other transporters, structural features, pH gating systems, trafficking and degradation. Several studies have supported the role of AQPs in differential phenotypic responses to abiotic and biotic stress in plants. Crop improvement programs aiming for the development of cultivars with higher tolerance against stresses like drought, flooding, salinity and many biotic diseases, can explore and exploit the finely tuned AQP-regulated transport system. For instance, a promising approach in crop breeding programs is the utilization of genetic variation in AQPs for the development of stress tolerant cultivars. Similarly, transgenic and mutagenesis approaches provide an opportunity to better understand the AQP transport system with subsequent applications for the development of climate-smart drought-tolerant cultivars. The contributions to this Frontiers in Plant Science Research Topic have highlighted the evolution and phylogenetic distribution of AQPs in several plant species. Numerous aspects of regulation that seek to explain AQP-mediated transport system have been addressed. These contributions will help to improve our understanding of AQPs and their role in important physiological aspects and will bring AQP research closer to practical applications.

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