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Biomolecules
Special Issues
In Silico Studies via Big Data for Revealing Plant Signaling
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In Silico Studies via Big Data for Revealing Plant Signaling

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (31 August 2020) | Viewed by 7780

Special Issue Editors

Prof. Dr. Jen-Tsung Chen

E-Mail Website
Guest Editor
Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
Interests: bioactive compounds; chromatography techniques; medicinal plants; phytochemicals; plant biotechnology; plant growth regulators; plant secondary metabolites
Special Issues, Collections and Topics in MDPI journals
Dr. Parviz Heidari

E-Mail Website
Guest Editor
Faculty of Agricultural, Shahrood University of Technology, Shahrood, Iran
Interests: cell signaling; abiotic stresses; functional analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over recent years, large amounts of plant biology data in genomics, transcriptomics, and proteomics have been revealed. In the meantime, novel bioinformatics tools have been developed for analyzing and revealing new aspects of biological mechanisms and networks in plants. In addition, bioinformatics tools can predict novel functions of genes and protein–protein interactions that are very useful to solve biological problems. This Special Issue explores the new aspects of biological signaling in plant based on an in silico study on multi-omics–big data, including, but not limited to, functional analysis, interaction network, regulatory mechanisms, and comparative analysis. We sincerely invite scientists to contribute both original research articles and reviews on this Special Issue.

Dr. Jen-Tsung Chen
Dr. Parviz Heidari
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • big data
  • biological networks
  • bioinformatics
  • functional analysis
  • machine learning
  • multi-omics
  • pathway analysis
  • plant hormones
  • plant signal transduction
  • data mining
  • protein–protein interaction

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Published Papers (2 papers)

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18 pages, 6850 KiB  
Article
Mapping the Salt Stress-Induced Changes in the Root miRNome in Pokkali Rice
by Kavita Goswami, Deepti Mittal, Budhayash Gautam, Sudhir K. Sopory and Neeti Sanan-Mishra
Biomolecules 2020, 10(4), 498; https://doi.org/10.3390/biom10040498 - 25 Mar 2020
Cited by 18 | Viewed by 3635
Abstract
A plant’s response to stress conditions is governed by intricately coordinated gene expression. The microRNAs (miRs) have emerged as relatively new players in the genetic network, regulating gene expression at the transcriptional and post-transcriptional level. In this study, we performed comprehensive profiling of [...] Read more.
A plant’s response to stress conditions is governed by intricately coordinated gene expression. The microRNAs (miRs) have emerged as relatively new players in the genetic network, regulating gene expression at the transcriptional and post-transcriptional level. In this study, we performed comprehensive profiling of miRs in roots of the naturally salt-tolerant Pokkali rice variety to understand their role in regulating plant physiology in the presence of salt. For comparisons, root miR profiles of the salt-sensitive rice variety Pusa Basmati were generated. It was seen that the expression levels of 65 miRs were similar for roots of Pokkali grown in the absence of salt (PKNR) and Pusa Basmati grown in the presence of salt (PBSR). The salt-induced dis-regulations in expression profiles of miRs showed controlled changes in the roots of Pokkali (PKSR) as compared to larger variations seen in the roots of Pusa Basmati. Target analysis of salt-deregulated miRs identified key transcription factors, ion-transporters, and signaling molecules that act to maintain cellular Ca2+ homeostasis and limit ROS production. These miR:mRNA nodes were mapped to the Quantitative trait loci (QTLs) to identify the correlated root traits for understanding their significance in plant physiology. The results obtained indicate that the adaptability of Pokkali to excess salt may be due to the genetic regulation of different cellular components by a variety of miRs. Full article
(This article belongs to the Special Issue In Silico Studies via Big Data for Revealing Plant Signaling)
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21 pages, 8814 KiB  
Article
Metabolic and Proteomic Perspectives of Augmentation of Nutritional Contents and Plant Defense in Vigna unguiculata
by Aqeel Ahmad, Tanveer Alam Khan, Samavia Mubeen, Iqra Shahzadi, Waheed Akram, Taiba Saeed, Zoobia Bashir, Rui Wang, Mufid Alam, Shakeel Ahmed, Du Hu, Guihua Li and Tingquan Wu
Biomolecules 2020, 10(2), 224; https://doi.org/10.3390/biom10020224 - 3 Feb 2020
Cited by 15 | Viewed by 3108
Abstract
The current study enlists metabolites of Alstonia scholaris with bioactivities, and the most active compound, 3-(1-methylpyrrolidin-2-yl) pyridine, was selected against Macrophomina phaseolina. Appraisal of the Alstonia metabolites identified the 3-(1-methylpyrrolidin-2-yl) pyridine as a bioactive compound which elevated vitamins and nutritional contents of [...] Read more.
The current study enlists metabolites of Alstonia scholaris with bioactivities, and the most active compound, 3-(1-methylpyrrolidin-2-yl) pyridine, was selected against Macrophomina phaseolina. Appraisal of the Alstonia metabolites identified the 3-(1-methylpyrrolidin-2-yl) pyridine as a bioactive compound which elevated vitamins and nutritional contents of Vigna unguiculata up to ≥18%, and other physiological parameters up to 28.9%. The bioactive compound (0.1%) upregulated key defense genes, shifted defense metabolism from salicylic acid to jasmonic acid, and induced glucanase enzymes for improved defenses. The structural studies categorized four glucanase-isozymes under beta-glycanases falling in (Trans) glycosidases with TIM beta/alpha-barrel fold. The study determined key-protein factors (Q9SAJ4) for elevated nutritional contents, along with its structural and functional mechanisms, as well as interactions with other loci. The nicotine-docked Q9SAJ4 protein showed a 200% elevated activity and interacted with AT1G79550.2, AT1G12900.1, AT1G13440.1, AT3G04120.1, and AT3G26650.1 loci to ramp up the metabolic processes. Furthermore, the study emphasizes the physiological mechanism involved in the enrichment of the nutritional contents of V. unguiculata. Metabolic studies concluded that increased melibiose and glucose 6-phosphate contents, accompanied by reduced trehalose (-0.9-fold), with sugar drifts to downstream pyruvate biosynthesis and acetyl Co-A metabolism mainly triggered nutritional contents. Hydrogen bonding at residues G.357, G.380, and G.381 docked nicotine with Q9SAJ4 and transformed its bilobed structure for easy exposure toward substrate molecules. The current study augments the nutritional value of edible stuff and supports agriculture-based country economies. Full article
(This article belongs to the Special Issue In Silico Studies via Big Data for Revealing Plant Signaling)
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