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"Systems Biology" AND plant

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
Dinesh Kumar Saini, Sunil Pabbi, Pratyoosh Shukla
Cyanobacteria are the oxygenic photosynthesis performing prokaryotes and show a connecting link between plastids of eukaryotic autotrophs and prokaryotes. A variety of pigments, like chlorophyll, carotenoids and phycobiliproteins which exhibit different colors are present in cyanobacteria. Increasing consciousness about the harmful effects of synthetic or chemical dyes encouraged people to give more preference towards the usage of natural products, such as plant or microbial-derived colors in food and cosmetics...
August 2, 2018: Food and Chemical Toxicology
V F Lima, D B Medeiros, L Dos Anjos, J Gago, A R Fernie, D M Daloso
Plant atmospheric CO2 fixation depends on the aperture of stomatal pores at the leaf epidermis. Stomatal aperture or closure is regulated by changes in the metabolism of the two surrounding guard cells, which respond directly to environmental and internal cues such as mesophyll-derived metabolites. Sucrose has been shown to play a dual role during stomatal movements. The sucrose produced in the mesophyll cells can be transported to the vicinity of the guard cells via the transpiration stream, inducing closure in periods of high photosynthetic rate...
2018: Plant Signaling & Behavior
Cristina López-Hidalgo, Victor M Guerrero-Sánchez, Isabel Gómez-Gálvez, Rosa Sánchez-Lucas, María A Castillejo-Sánchez, Ana M Maldonado-Alconada, Luis Valledor, Jesus V Jorrín-Novo
Holm oak ( Quercus ilex ) is the most important and representative species of the Mediterranean forest and of the Spanish agrosilvo-pastoral "dehesa" ecosystem. Despite its environmental and economic interest, Holm oak is an orphan species whose biology is very little known, especially at the molecular level. In order to increase the knowledge on the chemical composition and metabolism of this tree species, the employment of a holistic and multi-omics approach, in the Systems Biology direction would be necessary...
2018: Frontiers in Plant Science
Marcello Iriti, Sara Vitalini
No abstract text is available yet for this article.
July 19, 2018: International Journal of Molecular Sciences
Muhammad Bilal, Songwei Wang, Hafiz M N Iqbal, Yuping Zhao, Hongbo Hu, Wei Wang, Xuehong Zhang
Shikimic acid is an important intermediate for the manufacture of the antiviral drug oseltamivir (Tamiflu®) and many other pharmaceutical compounds. Much of its existing supply is obtained from the seeds of Chinese star anise (Illicium verum). Nevertheless, plants cannot supply a stable source of affordable shikimate along with laborious and cost-expensive extraction and purification process. Microbial biosynthesis of shikimate through metabolic engineering and synthetic biology approaches represents a sustainable, cost-efficient, and environmentally friendly route than plant-based methods...
September 2018: Applied Microbiology and Biotechnology
Lufei Zhao, Fei Liu, Nigel M Crawford, Yong Wang
Nitrogen is an essential macronutrient that affects plant growth and development. Improving the nitrogen use efficiency of crops is of great importance for the economic and environmental sustainability of agriculture. Nitrate (NO₃- ) is a major form of nitrogen absorbed by most crops and also serves as a vital signaling molecule. Research has identified key molecular components in nitrate signaling mainly by employing forward and reverse genetics as well as systems biology. In this review, we focus on advances in the characterization of genes involved in primary nitrate responses as well as the long-term effects of nitrate, especially in terms of how nitrate regulates root development...
July 13, 2018: International Journal of Molecular Sciences
Ulrich Kutschera
The founders of modern biology (Jean Lamarck, Charles Darwin, August Weismann etc.) were organismic life scientists who attempted to understand the morphology and evolution of living beings as a whole (i.e., the phenotype). However, with the emergence of the study of animal and plant physiology in the nineteenth century, this "holistic view" of the living world changed and was ultimately replaced by a reductionistic perspective. Here, I summarize the history of systems biology, i.e., the modern approach to understand living beings as integrative organisms, from genotype to phenotype...
June 14, 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
Arun Kumar Dangi, Babita Sharma, Ishu Khangwal, Pratyoosh Shukla
Plants are continually facing biotic and abiotic stresses, and hence, they need to respond and adapt to survive. Plant response during multiple and combined biotic and abiotic stresses is highly complex and varied than the individual stress. These stresses resulted alteration of plant behavior through regulating the levels of microRNA, heat shock proteins, epigenetic variations. These variations can cause many adverse effects on the growth and development of the plant. Further, in natural conditions, several abiotic stresses causing factors make the plant more susceptible to pathogens infections and vice-versa...
August 2018: Molecular Biotechnology
Katy Vandereyken, Jelle Van Leene, Barbara De Coninck, Bruno P A Cammue
Plant stress responses involve numerous changes at the molecular and cellular level and are regulated by highly complex signaling pathways. Studying protein-protein interactions (PPIs) and the resulting networks is therefore becoming increasingly important in understanding these responses. Crucial in PPI networks are the so-called hubs or hub proteins, commonly defined as the most highly connected central proteins in scale-free PPI networks. However, despite their importance, a growing amount of confusion and controversy seems to exist regarding hub protein identification, characterization and classification...
2018: Frontiers in Plant Science
Yujia Song, Shoufa Song
Artificial bioretention system consisting of Ophiopogon japonicus infiltration medium was used to simulate an infiltration experiment of rainfall runoff. Continuous extraction method was used to detect contents of inorganic phosphorus (P) under exchangeable state (Ex-P) and aluminium phosphate (Al-P) and iron phosphate (Fe-P) at different depths (0, 5, 15 and 35 cm) of soil infiltration medium in bioretention system. Effluent total P (TP) concentration of the system was also monitored. Results indicated that the adsorption of inorganic P, Al-P and Fe-P by soil infiltration medium was implemented layer by layer from top to bottom and gradually weakened...
June 4, 2018: Environmental Science and Pollution Research International
Julie B Fiévet, Thibault Nidelet, Christine Dillmann, Dominique de Vienne
Heterosis, the superiority of hybrids over their parents for quantitative traits, represents a crucial issue in plant and animal breeding as well as evolutionary biology. Heterosis has given rise to countless genetic, genomic and molecular studies, but has rarely been investigated from the point of view of systems biology. We hypothesized that heterosis is an emergent property of living systems resulting from frequent concave relationships between genotypic variables and phenotypes, or between different phenotypic levels...
2018: Frontiers in Genetics
Dario Di Silvestre, Andrea Bergamaschi, Edoardo Bellini, PierLuigi Mauri
The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification...
June 3, 2018: Proteomes
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