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"Systems Biology" AND plant

Han Li, Quanyu Zhao, He Huang
Natural and human activities lead to soil degradation and soil salinization. The decrease of farmlands threatens food security. There are approximately 1 billion ha salt-affected soils all over of world, which can be made available resources after chemical, physical and biological remediation. Nostoc, Anabaena and other cyanobacterial species have outstanding capabilities, such as the ability to fix nitrogen from the air, produce an extracellular matrix and produce compatible solutes. The remediation of salt-affected soil is a complex and difficult task...
March 8, 2019: Science of the Total Environment
Woo-Jong Hong, Yu-Jin Kim, Anil Kumar Nalini Chandran, Ki-Hong Jung
Rice (Oryza sativa L.) is both a major staple food for the worldwide population and a model crop plant for studying the mode of action of agronomically valuable traits, providing information that can be applied to other crop plants. Due to the development of high-throughput technologies such as next generation sequencing and mass spectrometry, a huge mass of multi-omics data in rice has been accumulated. Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems biology in rice...
March 14, 2019: Rice
Tegan Armarego-Marriott, Łucja Maria Kowalewska, Asdrubal Burgos, Axel Fischer, Wolfram Thiele, Alexander Erban, Deserah D Strand, Sabine Kahlau, Alexander Hertle, Joachim Kopka, Dirk Walther, Ziv Reich, Mark Aurel Schoettler, Ralph Bock
Upon exposure to light, plant cells quickly acquire photosynthetic competence by converting pale etioplasts into green chloroplasts. This developmental transition involves the de novo biogenesis of the thylakoid system, and requires reprogramming of metabolism and gene expression. Etioplast-to-chloroplast differentiation involves massive changes in plastid ultrastructure, but how these changes are connected to specific changes in physiology, metabolism and expression of the plastid and nuclear genomes is poorly understood...
March 12, 2019: Plant Physiology
Martin P Wierzbicki, Victoria Maloney, Eshchar Mizrachi, Alexander A Myburg
Lignocellulosic biomass, encompassing cellulose, lignin and hemicellulose in plant secondary cell walls (SCWs), is the most abundant source of renewable materials on earth. Currently, fast-growing woody dicots such as Eucalyptus and Populus trees are major lignocellulosic (wood fiber) feedstocks for bioproducts such as pulp, paper, cellulose, textiles, bioplastics and other biomaterials. Processing wood for these products entails separating the biomass into its three main components as efficiently as possible without compromising yield...
2019: Frontiers in Plant Science
Ahmad Tahmasebi, Elham Ashrafi-Dehkordi, Amir Ghaffar Shahriari, Seyed Mohammad Mazloomi, Esmaeil Ebrahimie
Abiotic environmental stresses are important factors that limit the growth, fiber yield, and quality of cotton. In this study, an integrative meta-analysis and a system-biology analysis were performed to explore the underlying transcriptomic mechanisms that are critical for response to stresses. From the meta-analysis, it was observed that a total of 1465 differentially expressed genes (DEGs) between normal and stress conditions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that DEGs were significantly enriched in the ubiquitin-dependent process, biosynthesis of secondary metabolites, plant hormone, and signaled transduction...
February 22, 2019: Progress in Biophysics and Molecular Biology
George W Bassel
Organ function is at least partially shaped and constrained by the organization of their constituent cells. Extensive investigation has revealed mechanisms explaining how these patterns are generated, with less being known about their functional relevance. In this paper, a methodology to discretize and quantitatively analyze cellular patterning is described. By performing global organ-scale cellular interaction mapping, the organization of cells can be extracted and analyzed using network science. This provides a means to take the developmental analysis of cellular organization in complex organisms beyond qualitative descriptions, and provides data-driven approaches to inferring cellular function...
February 19, 2019: Molecular Plant
María-Dolores Rey, María Ángeles Castillejo, Rosa Sánchez-Lucas, Victor M Guerrero-Sanchez, Cristina López-Hidalgo, Cristina Romero-Rodríguez, José Valero-Galván, Besma Sghaier-Hammami, Lyudmila Simova-Stoilova, Sira Echevarría-Zomeño, Inmaculada Jorge, Isabel Gómez-Gálvez, María Eugenia Papa, Kamilla Carvalho, Luis E Rodríguez de Francisco, Ana María Maldonado-Alconada, Luis Valledor, Jesús V Jorrín-Novo
Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus , Pines , Poplars , and Eucalyptus . This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus ...
February 6, 2019: International Journal of Molecular Sciences
Lei Zhang, Li-Na Qin, Zi-Rui Zeng, Chang-Zheng Wu, Yuan-Yong Gong, Lai-Hua Liu, Feng-Qiu Cao
Background: Plant root apex is the major part to direct the root growth and development by responding to various signals/cues from internal and soil environments. To study and understand root system biology particularly at a molecular and cellular level, an Arabidopsis T-DNA insertional enhancer trap line J3411 expressing reporters (GFP) only in the root tip was adopted in this study to isolate a DNA fragment. Results: Using nested PCR, DNA sequencing and sequence homology search, the T-DNA insertion site(s) and its flanking genes were characterised in J3411 line...
2019: Plant Methods
Ahmad Tahmasebi, Esmaeil Ebrahimie, Hassan Pakniyat, Mansour Ebrahimi, Manijeh Mohammadi-Dehcheshmeh
Biosynthesis of secondary metabolites in plant is a complex process, regulate by many genes and influence by several factors. In recent years, the next-generation sequencing (NGS) technology and advanced statistical analysis such as meta-analysis and computational systems biology have provided novel opportunities to overcome biological complexity. Here, we performed a meta-analysis and multi-step integrated approach of publicly available transcriptome datasets of twelve economically significant medicinal plants to identify differentially expressed genes (DEGs) between shoot and root tissues to identify the key molecular features which may be effective in the biosynthesis of secondary metabolites...
January 5, 2019: Gene
Andrew J Millar, J Uriel Urquiza, Peter L Freeman, Alastair Hume, Gordon D Plotkin, Oxana Sorokina, Argyris Zardilis, Tomasz Zielinski
A recent initiative named 'Crops in silico' proposes that multi-scale models 'have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts' in plant science, particularly directed to crop species. To that end, the group called for 'a paradigm shift in plant modelling, from largely isolated efforts to a connected community'. 'Wet' (experimental) research has been especially productive in plant science, since the adoption of Arabidopsis thaliana as a laboratory model species allowed the emergence of an Arabidopsis research community...
January 5, 2019: Journal of Experimental Botany
Khader Shameer, Mahantesha B N Naika, K Mohamed Shafi, Ramanathan Sowdhamini
Plants are essential facilitators of human life on planet earth. Plants play a critical functional role in mediating the quality of air, availability of food and the sustainability of agricultural resources. However, plants are in constant interaction with its environment and often hampered by various types of stresses like biotic and abiotic ones. Biotic stress is a significant reason for crop-loss and causes yield loss in the range of 31-42%, post-harvest loss due to biotic stress is in the range of 6-20%, and abiotic stress causes 6-20% of the crop damage...
December 15, 2018: Progress in Biophysics and Molecular Biology
Elena V Zemlyanskaya, Nadya A Omelyanchuk, Elena V Ubogoeva, Victoria V Mironova
The auxin and ethylene pathways cooperatively regulate a variety of developmental processes in plants. Growth responses to ethylene are largely dependent on auxin, the key regulator of plant morphogenesis. Auxin, in turn, is capable of inducing ethylene biosynthesis and signaling, making the interaction of these hormones reciprocal. Recent studies discovered a number of molecular events underlying auxin-ethylene crosstalk. In this review, we summarize the results of fine-scale and large-scale experiments on the interactions between the auxin and ethylene pathways in Arabidopsis...
December 14, 2018: International Journal of Molecular Sciences
Melissa Van Overtveldt, Lukas Braem, Sylwia Struk, Anna M Kaczmarek, François-Didier Boyer, Rik Van Deun, Kris Gevaert, Sofie Goormachtig, Thomas S A Heugebaert, Christian V Stevens
Strigolactones (SLs) are a family of terpenoid allelochemicals that were recognized as plant hormones only a decade ago. They influence a myriad of both above- and belowground developmental processes, and are an important survival strategy for plants in nutrient-deprived soils. A rapidly emerging approach to gain knowledge on hormone signaling is the use of traceable analogs. A unique class of labeled SL analogs was constructed, where the original tricyclic lactone moiety of natural SLs is replaced by a fluorescent cyanoisoindole ring system...
December 15, 2018: Plant Journal: for Cell and Molecular Biology
Marco Grzegorczyk, Andrej Aderhold, Dirk Husmeier
A challenging problem in systems biology is the reconstruction of gene regulatory networks from postgenomic data. A variety of reverse engineering methods from machine learning and computational statistics have been proposed in the literature. However, deciding on the best method to adopt for a particular application or data set might be a confusing task. The present chapter provides a broad overview of state-of-the-art methods with an emphasis on conceptual understanding rather than a deluge of mathematical details, and the pros and cons of the various approaches are discussed...
2019: Methods in Molecular Biology
Alexander Panossian, Ean-Jeong Seo, Thomas Efferth
INTRODUCTION: Adaptogens are natural compounds or plant extracts that increase adaptability and survival of organisms under stress. Adaptogens stimulate cellular and organismal defense systems by activating intracellular and extracellular signaling pathways and expression of stress-activated proteins and neuropeptides. The effects adaptogens on mediators of adaptive stress response and longevity signaling pathways have been reported, but their stress-protective mechanisms are still not fully understood...
November 15, 2018: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
Biswapriya B Misra, Suzie M Reichman, Sixue Chen
The plant ionome is critical for growth, productivity, defense, and it eventually affects food quantity and quality. Located on the leaf surface, stomatal guard cells are critical gatekeepers for water, gas, and pathogens. Insights form ionomics (metallomics) is imperative as we enter an omics-driven systems biology era where an understanding of guard cell function and physiology is advanced through efforts in genomics, transcriptomics, proteomics, and metabolomics. While the roles of major cations (K, Ca) and anions (Cl) are well known in guard cell function, the related physiology, movement and regulation of trace elements, metal ions, and heavy metals are poorly understood...
November 17, 2018: Progress in Biophysics and Molecular Biology
Iain G Johnston
Mitochondria and plastids form dynamic, evolving populations physically embedded in the fluctuating environment of the plant cell. Their evolutionary heritage has shaped how the cell controls the genetic structure and the physical behaviour of its organelle populations. While the specific genes involved in these processes are gradually being revealed, the governing principles underlying this controlled behaviour remain poorly understood. As the genetic and physical dynamics of these organelles are central to bioenergetic performance and plant physiology, this challenges both fundamental biology and strategies to engineer better-performing plants...
November 13, 2018: Molecular Plant
Maricris Zaidem, Simon C Groen, Michael D Purugganan
Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the least few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve...
November 16, 2018: Plant Journal: for Cell and Molecular Biology
Bharat Mishra, Nilesh Kumar, M Shahid Mukhtar
Systems biology is an inclusive approach to study the static and dynamic emergent properties on a global scale by integrating multiomics datasets to establish qualitative and quantitative associations among multiple biological components. With an abundance of improved high throughput -omics datasets, network-based analyses and machine learning technologies are playing a pivotal role in comprehensive understanding of biological systems. Network topological features reveal most important nodes within a network as well as prioritize significant molecular components for diverse biological networks, including coexpression, protein-protein interaction, and gene regulatory networks...
November 12, 2018: Molecular Plant-microbe Interactions: MPMI
Teva Vernoux
Teva Vernoux is a plant developmental biologist and holds positions as the Director of the Institute for Reproduction and Development of Plants at ENS de Lyon, and as a Research Director at Centre National de la Recherche Scientifique. Teva spoke to us about the need for multidisciplinary approaches to tackle multi-scale problems, how to go beyond a list of genes, and the importance of constructive reviews.
November 1, 2018: BMC Biology
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