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Belousova DA, Shishov VV, Arzac A, Popkova MI, Babushkina EA, Huang JG, Yang B, Vaganov EA. VS-Cambium-Developer: A New Predictive Model of Cambium Functioning under the Influence of Environmental Factors. PLANTS (BASEL, SWITZERLAND) 2023; 12:3594. [PMID: 37896057 PMCID: PMC10609909 DOI: 10.3390/plants12203594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/01/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023]
Abstract
Climate changes influence seasonal tree-ring formation. The result is a specific cell structure dependent on internal processes and external environmental factors. One way to investigate and analyze these relationships is to apply diverse simulation models of tree-ring growth. Here, we have proposed a new version of the VS-Cambium-Developer model (VS-CD model), which simulates the cambial activity process in conifers. The VS-CD model does not require the manual year-to-year calibration of parameters over a long-term cell production reconstruction or forecast. Instead, it estimates cell production and simulates the dynamics of radial cell development within the growing seasons. Thus, a new software based on R programming technology, able to efficiently adapt to the VS model online platform, has been developed. The model was tested on indirect observations of the cambium functioning in Larix sibirica trees from southern Siberia, namely on the measured annual cell production from 1963 to 2011. The VS-CD model proves to simulate cell production accurately. The results highlighted the efficiency of the presented model and contributed to filling the gap in the simulations of cambial activity, which is critical to predicting the potential impacts of changing environmental conditions on tree growth.
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Affiliation(s)
- Daria A. Belousova
- Research Department, Siberian Federal University, 660041 Krasnoyarsk, Russia;
| | - Vladimir V. Shishov
- Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia;
| | - Alberto Arzac
- Institute of Ecology and Geography, Siberian Federal University, 660041 Krasnoyarsk, Russia; (A.A.); (E.A.V.)
| | | | - Elena A. Babushkina
- Khakass Technical Institute, Siberian Federal University, 655017 Abakan, Russia;
| | - Jian-Guo Huang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Bao Yang
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China;
| | - Eugene A. Vaganov
- Institute of Ecology and Geography, Siberian Federal University, 660041 Krasnoyarsk, Russia; (A.A.); (E.A.V.)
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Chen H, Wu Q, Ni M, Chen C, Han C, Yu F. Transcriptome Analysis of Endogenous Hormone Response Mechanism in Roots of Styrax tonkinensis Under Waterlogging. FRONTIERS IN PLANT SCIENCE 2022; 13:896850. [PMID: 35734248 PMCID: PMC9208659 DOI: 10.3389/fpls.2022.896850] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/29/2022] [Indexed: 06/02/2023]
Abstract
As a promising oil species, Styrax tonkinensis has great potential as a biofuel due to an excellent fatty acid composition. However, frequent flooding caused by global warming and the low tolerance of the species to waterlogging largely halted its expansion in waterlogged areas. To explore endogenous hormones and phytohormone-related molecular response mechanism of S. tonkinensis under waterlogging, we determined 1-aminocyclopropane-1-carboxylic acid (ACC) and three phytohormone content (ABA, abscisic acid; SA, salicylic acid; IAA, indole-3-acetic acid) and analyzed the transcriptome of its seedlings under waterlogged condition of 3-5 cm. The sample collecting time was 0, 9, 24, and 72 h, respectively. It was concluded that ACC presented an upward trend, but other plant hormones showed a downward trend from 0 to 72 h under waterlogging stress. A total of 84,601 unigenes were assembled with a total length of 81,389,823 bp through transcriptome analysis. The GO enrichment analysis of total differentially expressed genes (DEGs) revealed that 4,637 DEGs, 8,238 DEGs, and 7,146 DEGs were assigned into three main GO functional categories in 9 vs. 0 h, 24 vs. 0 h, and 72 vs. 0 h, respectively. We also discovered several DEGs involved in phytohormone synthesis pathway and plant hormone signaling pathway. It was concluded that the decreased transcription of PYL resulted in the weak ABA signal transduction pathway. Moreover, decreased SA content caused by the low-expressed PAL might impact the resistance of S. tonkinensis seedlings under waterlogging stress. Our research may provide a scientific basis for the understanding of the endogenous hormone response mechanism of S. tonkinensis to waterlogging and lay a foundation for further exploration of the waterlogging defect resistance genes of S. tonkinensis and improving its resistance to waterlogging stress.
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Affiliation(s)
- Hong Chen
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University (NJFU), Nanjing, China
| | - Qikui Wu
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University (NJFU), Nanjing, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Ming Ni
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University (NJFU), Nanjing, China
| | - Chen Chen
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University (NJFU), Nanjing, China
| | - Chao Han
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University (NJFU), Nanjing, China
| | - Fangyuan Yu
- Collaborative Innovation Centre of Sustainable Forestry in Southern China, College of Forest Science, Nanjing Forestry University (NJFU), Nanjing, China
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Ethylene adsorption on chitosan/zeolite composite films for packaging applications. Food Packag Shelf Life 2020. [DOI: 10.1016/j.fpsl.2020.100584] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Liang C, Cheng S, Zhang Y, Sun Y, Fernie AR, Kang K, Panagiotou G, Lo C, Lim BL. Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination. BMC PLANT BIOLOGY 2016; 16:43. [PMID: 26865323 PMCID: PMC4750186 DOI: 10.1186/s12870-016-0726-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 01/28/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Light plays an important role in plant growth and development. In this study, the impact of light on physiology of 20-d-old Arabidopsis leaves was examined through transcriptomic, proteomic and metabolomic analysis. Since the energy-generating electron transport chains in chloroplasts and mitochondria are encoded by both nuclear and organellar genomes, sequencing total RNA after removal of ribosomal RNAs provides essential information on transcription of organellar genomes. The changes in the levels of ADP, ATP, NADP(+), NADPH and 41 metabolites upon illumination were also quantified. RESULTS Upon illumination, while the transcription of the genes encoded by the plastid genome did not change significantly, the transcription of nuclear genes encoding different functional complexes in the photosystem are differentially regulated whereas members of the same complex are co-regulated with each other. The abundance of mRNAs and proteins encoded by all three genomes are, however, not always positively correlated. One such example is the negative correlation between mRNA and protein abundances of the photosystem components, which reflects the importance of post-transcriptional regulation in plant physiology. CONCLUSION This study provides systems-wide datasets which allow plant researchers to examine the changes in leaf transcriptomes, proteomes and key metabolites upon illumination and to determine whether there are any correlations between changes in transcript and protein abundances of a particular gene or pathway upon illumination. The integration of data of the organelles and the photosystems, Calvin-Benson cycle, carbohydrate metabolism, glycolysis, the tricarboxylic acid cycle and respiratory chain, thereby provides a more complete picture to the changes in plant physiology upon illumination than has been attained to date.
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Affiliation(s)
- Chao Liang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Shifeng Cheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Youjun Zhang
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Yuzhe Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Kang Kang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Gianni Panagiotou
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Boon Leong Lim
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Floss DS, Lévesque-Tremblay V, Park HJ, Harrison MJ. DELLA proteins regulate expression of a subset of AM symbiosis-induced genes in Medicago truncatula. PLANT SIGNALING & BEHAVIOR 2016; 11:e1162369. [PMID: 26984507 PMCID: PMC4883957 DOI: 10.1080/15592324.2016.1162369] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 02/26/2016] [Accepted: 03/01/2016] [Indexed: 05/26/2023]
Abstract
The majority of the vascular flowering plants form symbiotic associations with fungi from the phylum Glomeromycota through which both partners gain access to nutrients, either mineral nutrients in the case of the plant, or carbon, in the case of the fungus. (1) The association develops in the roots and requires substantial remodeling of the root cortical cells where branched fungal hyphae, called arbuscules, are housed in a new membrane-bound apoplastic compartment. (2) Nutrient exchange between the symbionts occurs over this interface and its development and maintenance is critical for symbiosis. Previously, we showed that DELLA proteins, which are well known as repressors of gibberellic acid signaling, also regulate development of AM symbiosis and are necessary to enable arbuscule development. (3) Furthermore, constitutive overexpression of a dominant DELLA protein (della1-Δ18) is sufficient to induce transcripts of several AM symbiosis-induced genes, even in the absence of the fungal symbiont. (4) Here we further extend this approach and identify AM symbiosis genes that respond transcriptionally to constitutive expression of a dominant DELLA protein and also genes that do respond to this treatment. Additionally, we demonstrate that DELLAs interact with REQUIRED FOR ARBUSCULE DEVELOPMENT 1 (RAD1) which further extends our knowledge of GRAS factor complexes that have the potential to regulate gene expression during AM symbiosis.
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Affiliation(s)
- Daniela S Floss
- a Boyce Thompson Institute for Plant Research , Tower Road, Ithaca , NY , USA
| | | | - Hee-Jin Park
- a Boyce Thompson Institute for Plant Research , Tower Road, Ithaca , NY , USA
| | - Maria J Harrison
- a Boyce Thompson Institute for Plant Research , Tower Road, Ithaca , NY , USA
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Jiang X, Chen L, Wang X, Long L, Xiao Z, Liu X. Photoinduced Carbon Monoxide Release from Half-Sandwich Iron(II) Carbonyl Complexes by Visible Irradiation: Kinetic Analysis and Mechanistic Investigation. Chemistry 2015. [PMID: 26216203 DOI: 10.1002/chem.201501348] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Three half-sandwich iron(II) complexes, [Fe(η(5) -Cp)(cis-CO)2 X] (X(-) =Cl(-) , Br(-) , I(-) ), were synthesized and characterized. The kinetics of the CO-releasing behaviour of these complexes upon illumination by visible irradiation in various media was investigated. Our results indicated that the CO release was significantly affected by the auxiliary ligands. Of the three light sources used (blue, green, and red), blue light exhibited the highest efficiency. In the photoinduced CO release, the solvents and exogenous nucleophiles in the media were involved, which allowed their CO-releasing reaction to comply with pseudo first-order model rather than the characteristic zero-order model for a photochemical reaction. In aqueous media (D2 O), an intermediate bearing the core of {Fe(II) (cis-CO)2 } involving cleavage of cyclopentadiene was detected. Despite the non-absorption of the red light, its illumination combined with nucleophilic substitution did cause considerable CO release. Assessment of the cytotoxicity of the three complexes indicated that they showed good biocompatibility.
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Affiliation(s)
- Xiujuan Jiang
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing (P. R. China), Fax: (+86) 573-8364-3937
| | - Limei Chen
- School of Metallurgy and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou (P. R. China)
| | - Xiu Wang
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing (P. R. China), Fax: (+86) 573-8364-3937
| | - Li Long
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing (P. R. China), Fax: (+86) 573-8364-3937
| | - Zhiyin Xiao
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing (P. R. China), Fax: (+86) 573-8364-3937
| | - Xiaoming Liu
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing (P. R. China), Fax: (+86) 573-8364-3937. .,School of Metallurgy and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou (P. R. China).
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