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"Systems Biology" AND plant

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
Hoe-Han Goh
This chapter introduces different aspects of bioinformatics with a brief discussion in the systems biology context. Example applications in network pharmacology of traditional Chinese medicine, systems metabolic engineering, and plant genome-scale modelling are described. Lastly, this chapter concludes on how bioinformatics helps to integrate omics data derived from various studies described in previous chapters for a holistic understanding of secondary metabolite production in P. minus.
2018: Advances in Experimental Medicine and Biology
Syarul Nataqain Baharum, Kamalrul Azlan Azizan
Over the last decade, metabolomics has continued to grow rapidly and is considered a dynamic technology in envisaging and elucidating complex phenotypes in systems biology area. The advantage of metabolomics compared to other omics technologies such as transcriptomics and proteomics is that these later omics only consider the intermediate steps in the central dogma pathway (mRNA and protein expression). Meanwhile, metabolomics reveals the downstream products of gene and expression of proteins. The most frequently used tools are nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS)...
2018: Advances in Experimental Medicine and Biology
Hoe-Han Goh, Chyan Leong Ng, Kok-Keong Loke
Functional genomics encompasses diverse disciplines in molecular biology and bioinformatics to comprehend the blueprint, regulation, and expression of genetic elements that define the physiology of an organism. The deluge of sequencing data in the postgenomics era has demanded the involvement of computer scientists and mathematicians to create algorithms, analytical software, and databases for the storage, curation, and analysis of biological big data. In this chapter, we discuss on the concept of functional genomics in the context of systems biology and provide examples of its application in human genetic disease studies, molecular crop improvement, and metagenomics for antibiotic discovery...
2018: Advances in Experimental Medicine and Biology
Luca Narduzzi, Jan Stanstrup, Fulvio Mattivi, Pietro Franceschi
Compound identification is the main hurdle in LC-HRMS-based metabolomics, given the high number of 'unknown' metabolites. In recent years, numerous in silico fragmentation simulators have been developed to simplify and improve mass spectral interpretation and compound annotation. Nevertheless, expert mass spectrometry users and chemists are still needed to select the correct entry from the numerous candidates proposed by automatic tools, especially in the plant kingdom due to the huge structural diversity of natural compounds occurring in plants...
November 2018: Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment
Georg Basler, Alisdair R Fernie, Zoran Nikoloski
Methodological and technological advances have recently paved the way for metabolic flux profiling in higher organisms, like plants. However, in comparison to omics technologies, flux profiling has yet to provide comprehensive differential flux maps at a genome-scale and in different cell types, tissues, and organs. Here we highlight the recent advances in technologies to gather metabolic labeling patterns and flux profiling approaches. We provide an opinion of how recent local flux profiling approaches can be used in conjunction with the constraint-based modelling framework to arrive at genome-scale flux maps...
October 19, 2018: Bioscience Reports
Emrah Özcan, Tunahan Çakır
Systems-based investigation of diseases requires integrated analysis of cellular networks and high-throughput data of gene products. The use of genome-scale metabolic networks for such integration has led to the elucidation of cellular mechanisms for several cell types from microorganisms to plants. It has become easier and cheaper to generate high-throughput data over years in the form of transcriptome, proteome and metabolome. This has tremendously improved the quality and quantity of information extracted from such data enabling the documentation of active pathways and reactions in cell metabolism...
2018: Advances in Neurobiology
Ebru Alazi, Arthur F J Ram
Filamentous fungi are the most important microorganisms for the industrial production of plant polysaccharide degrading enzymes due to their unique ability to secrete these proteins efficiently. These carbohydrate active enzymes (CAZymes) are utilized industrially for the hydrolysis of plant biomass for the subsequent production of biofuels and high-value biochemicals. The expression of the genes encoding plant biomass degrading enzymes is tightly controlled. Naturally, large amounts of CAZymes are produced and secreted only in the presence of the plant polysaccharide they specifically act on...
2018: Frontiers in Bioengineering and Biotechnology
Muhammad Amjad Nawaz, Xiao Lin, Ting-Fung Chan, Muhammad Imtiaz, Hafiz Mamoon Rehman, Muhammad Amjad Ali, Faheem Shehzad Baloch, Rana Muhammad Atif, Seung Hwan Yang, Gyuhwa Chung
Cellulose synthase A (CESA) is a key enzyme involved in the complex process of plant cell wall biosynthesis, and it remains a productive subject for research. We employed systems biology approaches to explore structural diversity of eudicot CESAs by exon-intron organization, mode of duplication, synteny, and splice site analyses. Using a combined phylogenetics and comparative genomics approach coupled with co-expression networks we reconciled the evolution of cellulose synthase gene family in eudicots and found that the basic forms of CESA proteins are retained in angiosperms...
September 28, 2018: Biochemical Genetics
Elaina M Maldonado, Ciarán P Fisher, Dawn J Mazzatti, Amy L Barber, Marcus J Tindall, Nicholas J Plant, Andrzej M Kierzek, J Bernadette Moore
Non-alcoholic fatty liver disease (NAFLD) is a serious public health issue associated with high fat, high sugar diets. However, the molecular mechanisms mediating NAFLD pathogenesis are only partially understood. Here we adopt an iterative multi-scale, systems biology approach coupled to in vitro experimentation to investigate the roles of sugar and fat metabolism in NAFLD pathogenesis. The use of fructose as a sweetening agent is controversial; to explore this, we developed a predictive model of human monosaccharide transport, signalling and metabolism...
2018: NPJ Systems Biology and Applications
Shabir H Wani, Prateek Tripathi, Abbu Zaid, Ghana S Challa, Anuj Kumar, Vinay Kumar, Jyoti Upadhyay, Rohit Joshi, Manoj Bhatt
The current review provides an updated, new insights into the regulation of transcription mediated underlying mechanisms of wheat plants to osmotic stress perturbations. Osmotic stress tolerance mechanisms being complex are governed by multiple factors at physiological, biochemical and at the molecular level, hence approaches like "OMICS" that can underpin mechanisms behind osmotic tolerance in wheat is of paramount importance. The transcription factors (TFs) are a class of molecular proteins, which are involved in regulation, modulation and orchestrating the responses of plants to a variety of environmental stresses...
August 2018: Plant Molecular Biology
Laetitia Virlouvet, Thomas J Avenson, Qian Du, Chi Zhang, Ning Liu, Michael Fromm, Zoya Avramova, Sabrina E Russo
Stress memory refers to the observation that an initial, sub-lethal stress alters plants' responses to subsequent stresses. Previous transcriptome analyses of maize seedlings exposed to a repeated dehydration stress has revealed the existence of transcriptional stress memory in Zea mays . Whether drought-related physiological responses also display memory and how transcriptional memory translates into physiological memory are fundamental questions that are still unanswered. Using a systems-biology approach we investigate whether/how transcription memory responses established in the genome-wide analysis of Z...
2018: Frontiers in Plant Science
Degao Liu, Kaitlin J Palla, Rongbin Hu, Robert C Moseley, Christopher Mendoza, Mei Chen, Paul E Abraham, Jessy L Labbé, Udaya C Kalluri, Timothy J Tschaplinski, John C Cushman, Anne M Borland, Gerald A Tuskan, Xiaohan Yang
Due to public concerns about the decreasing supply of blue water and increasing heat and drought stress on plant growth caused by urbanization, increasing human population and climate change, interest in crassulacean acid metabolism (CAM), a specialized type of photosynthesis enhancing water-use efficiency (WUE) and drought tolerance, has increased markedly. Significant progress has been achieved in both basic and applied research in CAM plants since the beginning of this century. Here we provide a brief overview of the current status of CAM research, and discuss future needs and opportunities in a wide range of areas including systems biology, synthetic biology, and utilization of CAM crops for human benefit, with a focus on the following aspects: 1) application of genome-editing technology and high-throughput phenotyping to functional genomics research in model CAM species and genetic improvement of CAM crops, 2) challenges for multi-scale metabolic modeling of CAM systems, 3) opportunities and new strategies for CAM pathway engineering to enhance WUE and drought tolerance in C3 (and C4 ) photosynthesis crops, 4) potential of CAM species as resources for food, feed, natural products, pharmaceuticals and biofuels, and 5) development of CAM crops for ecological and aesthetic benefits...
September 2018: Plant Science: An International Journal of Experimental Plant Biology
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