ORCID Profile
0000-0003-4270-7461
Current Organisation
University of Sydney
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Publisher: Cold Spring Harbor Laboratory
Date: 28-08-2021
DOI: 10.1101/2021.08.27.457898
Abstract: Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian heat-tolerant cotton ( Gossypium robinsonii ) was exposed to heat events during pollen development, then mature pollen was subjected to deep proteomic analysis using 57,023 predicted genes from a genomic database we assembled for the same species. Three stages of pollen development, including tetrads, uninucleate and binucleate microspores were exposed to 36°C or 40°C for 5 d and the resulting mature pollen was collected at anthesis (p-TE, p-UN and p-BN, respectively). Using SWATH-MS proteomic analysis, 2,704 proteins were identified and quantified across all pollen s les analyzed. Proteins predominantly decreased in abundance at all stages in response to heat, particularly after exposure of tetrads to 40°C. Functional enrichment analyses demonstrated that extreme heat increased the abundance of proteins that contributed to increased mRNA splicing via spliceosome, initiation of cytoplasmic translation and protein refolding in p-TE40. However, other functional categories that contributed to intercellular transport were inhibited in p-TE40, linked potentially to Rab proteins. We ascribe the resilience of reproductive processes in G. robinsonii at temperatures up to 40°C, relative to commercial cotton, to a targeted reduction in protein transport.
Publisher: Wiley
Date: 21-08-2022
Abstract: Drought is responsible for major losses in rice production. Root tips contain meristematic and elongation zones that play major roles in determination of root traits and adaptive strategies to drought. In this study we analysed two contrasting genotypes of rice: IR64, a lowland, drought‐susceptible, and shallow‐rooting genotype and Azucena, an upland, drought‐tolerant, and deep‐rooting genotype. S les were collected of root tips of plants grown under control and water deficit stress conditions. Quantitative proteomics analysis resulted in the identification of 7294 proteins from the root tips of IR64 and 6307 proteins from Azucena. Data are available via ProteomeXchange with identifier PXD033343. Using a Partial Least Square Discriminant Analysis on 4170 differentially abundant proteins, 1138 statistically significant proteins across genotypes and conditions were detected. Twenty two enriched biological processes showing contrasting patterns between two genotypes in response to stress were detected through gene ontology enrichment analysis. This included identification of novel proteins involved in root elongation with specific expression patterns in Azucena, including four Expansins and seven Class III Peroxidases. We also detected an antioxidant network and a metallo‐sulfur cluster assembly machinery in Azucena, with roles in reactive oxygen species and iron homeostasis, and positive effects on root cell cycle, growth and elongation.
Publisher: Wiley
Date: 17-12-2021
DOI: 10.1111/TPJ.15608
Abstract: Reproductive performance in plants is impaired as maximum temperatures consistently approach 40°C. However, the timing of heatwaves critically affects their impact. We studied the molecular responses during pollen maturation in cotton to investigate the vulnerability to high temperature. Tetrads (TEs), uninucleate and binucleate microspores, and mature pollen were subjected to SWATH‐MS and RNA‐seq analyses after exposure to 38/28°C (day/night) for 5 days. The results indicated that molecular signatures were downregulated progressively in response to heat during pollen development. This was even more evident in leaves, where three‐quarters of differentially changed proteins decreased in abundance during heat. Functional analysis showed that translation of genes increased in TEs after exposure to heat however, the reverse pattern was observed in mature pollen and leaves. For ex le, proteins involved in transport were highly abundant in TEs whereas in later stages of pollen formation and leaves, heat suppressed synthesis of proteins involved in cell‐to‐cell communication. Moreover, a large number of heat shock proteins were identified in heat‐affected TEs, but these proteins were less abundant in mature pollen and leaves. We speculate that the sensitivity of TE cells to heat is related to high rates of translation targeted to pathways that might not be essential for thermotolerance. Molecular signatures during stages of pollen development after heatwaves could provide markers for future genetic improvement.
Publisher: Wiley
Date: 17-02-2022
DOI: 10.1111/PCE.14268
Abstract: Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian arid‐zone cotton ( Gossypium robinsonii ) was exposed to heat events during pollen development then mature pollen was subjected to deep proteomic analysis using 57 023 predicted genes from a genomic database we assembled for the same species. Three stages of pollen development, including tetrads (TEs), uninucleate microspores (UNs) and binucleate microspores (BNs) were exposed to 36°C or 40°C for 5 days and the resulting mature pollen was collected at anthesis (p‐TE, p‐UN and p‐BN, respectively). Using the sequential windowed acquisition of all theoretical mass spectra proteomic analysis, 2704 proteins were identified and quantified across all pollen s les analysed. Proteins predominantly decreased in abundance at all stages in response to heat, particularly after exposure of TEs to 40°C. Functional enrichment analyses demonstrated that extreme heat increased the abundance of proteins that contributed to increased messenger RNA splicing via spliceosome, initiation of cytoplasmic translation and protein refolding in p‐TE40. However, other functional categories that contributed to intercellular transport were inhibited in p‐TE40, linked potentially to Rab proteins. We ascribe the resilience of reproductive processes in G. robinsonii at temperatures up to 40°C, relative to commercial cotton, to a targeted reduction in protein transport.
Publisher: MDPI AG
Date: 20-10-2023
DOI: 10.3390/BIOM13101554
Publisher: MDPI AG
Date: 06-2023
DOI: 10.3390/IJMS24119628
Abstract: Multiple abiotic stress is known as a type of environmental unfavourable condition maximizing the yield and growth gap of crops compared with the optimal condition in both natural and cultivated environments. Rice is the world’s most important staple food, and its production is limited the most by environmental unfavourable conditions. In this study, we investigated the pre-treatment of abscisic acid (ABA) on the tolerance of the IAC1131 rice genotype to multiple abiotic stress after a 4-day exposure to combined drought, salt and extreme temperature treatments. A total of 3285 proteins were identified and quantified across the four treatment groups, consisting of control and stressed plants with and without pre-treatment with ABA, with 1633 of those proteins found to be differentially abundant between groups. Compared with the control condition, pre-treatment with the ABA hormone significantly mitigated the leaf damage against combined abiotic stress at the proteome level. Furthermore, the application of exogenous ABA did not affect the proteome profile of the control plants remarkably, while the results were different in stress-exposed plants by a greater number of proteins changed in abundance, especially those which were increased. Taken together, these results suggest that exogenous ABA has a potential priming effect for enhancing the rice seedlings’ tolerance against combined abiotic stress, mainly by affecting stress-responsive mechanisms dependent on ABA signalling pathways in plants.
Publisher: Springer Science and Business Media LLC
Date: 19-06-2020
Publisher: MDPI AG
Date: 19-08-2020
DOI: 10.3390/IJMS21175980
Abstract: Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species (Oryza sativa cv. Nipponbare and Oryza glaberrima cv. CG14) and an endemic, perennial Australian wild species (Oryza australiensis) were grown in soil at 40% field capacity for 7 d (drought). The hypothesis was that the natural tolerance of O. australiensis to erratic water supply would be reflected in a unique proteomic profile. Leaves from droughted plants and well-watered controls were harvested for label-free quantitative shotgun proteomics. Physiological and gene ontology analysis confirmed that O. australiensis responded uniquely to drought, with superior leaf water status and enhanced levels of photosynthetic proteins. Distinctive patterns of protein accumulation in drought were observed across the O. australiensis proteome. Photosynthetic and stress-response proteins were more abundant in drought-affected O. glaberrima than O. sativa, and were further enriched in O. australiensis. In contrast, the level of accumulation of photosynthetic proteins decreased when O. sativa underwent drought, while a narrower range of stress-responsive proteins showed increased levels of accumulation. Distinctive proteomic profiles and the accumulated levels of in idual proteins with specific functions in response to drought in O. australiensis indicate the importance of this species as a source of stress tolerance genes.
Publisher: ZappyLab, Inc.
Date: 10-08-2023
DOI: 10.17504/PROTOCOLS.IO.8EPV5XJ86G1B/V1
Abstract: Next-generation sequencing demands high-quality nucleic acid, yet isolating DNA and RNA from plant tissues is often challenging. Despite advancements in the development of a variety of kits and reagents, these products are only limited to isolating nucleic acid from model plant species. In this study, a universal lysis buffer is introduced to isolate nucleic acid from a wide range of plant species to facilitate molecular studies, such as quantitative PCR (qPCR), transcriptomics, whole-genome sequencing, etc. The lysis buffer consists of hexadecyltrimethylammonium bromide (CTAB), sodium chloride (NaCl), tris base, ethylenediaminetetraacetic acid (EDTA) and β-mercaptoethanol (βME). The appropriate concentration of these components enables high-quality DNA and RNA isolation from plant tissues simultaneously. Slight alterations in the methodology lead to the isolation of pure DNA or RNA from the same tissue, enabling high-throughput sequencing. This protocol is fast and enables the isolation of nucleic acid from erse plant species in less than an hour.
Publisher: Springer Science and Business Media LLC
Date: 22-04-2015
DOI: 10.1007/S12010-015-1629-8
Abstract: Low temperature as one of the most important environmental factors limits the productivity of plants across the world. Aegilops, as a wild species of Poaceae, contains low temperature-responsive genes. In this study, we analyzed morphological (wilting, chlorosis, and recovery) and physiological (ion leakage) characteristics to identification of a cold-tolerant genotype. In this experiment, we introduced two transcription factors (TFs) in Aegilops species for the first time. Bioinformatics analysis demonstrated that our nucleotide sequences have high similarity with CBF14 (C-repeat-binding factor) and NAC2 (NAM, ATAF, and CUC) in Triticum aestivum. Based on the physiological and morphological data, one genotype (Aladizgeh) was identified as the most resistant genotype which was selected for further gene expression analysis. The real-time PCR results indicated that the CBF14 gene was not expressed 3 h following cold treatment, but the highest expression was observed after 6, 12, and 24 h of cold treatment however, a sudden decrease was observed in its expression after 30 h. The NAC2 gene also was not expressed 3 h after cold stress, but the highest expression was at 24 h and similar to the CBF14 gene its expression suddenly decreased after 30 h. Our results indicated that this genotype can tolerate -4 °C for 3 h, but the CBF14 and NAC2 genes were activated when treated for longer durations. Expression of TFs studied in this experiment had decreased after 30 h, in which cell death seems to be the important reason.
Publisher: Cold Spring Harbor Laboratory
Date: 07-06-2021
DOI: 10.1101/2021.06.06.447035
Abstract: Reproductive performance in plants is impaired as maximum temperatures consistently approach 40°C. However, the timing of heatwaves critically affects their impact. We studied the molecular responses of cotton male reproductive stages, to investigate the vulnerability of maturing pollen to high temperature. Tetrads, uninucleate and binucleate microspores, and mature pollen were subjected to SWATH-MS and RNA-seq analyses after exposure to 38/28°C (day/night) for 5 days. The results indicated that molecular signatures were down-regulated over developmental stages in response to heat. This was more evident in leaves where three-quarters of differentially changed proteins were decreased in abundance. Functional analysis showed that translation of genes increased in tetrads after exposure to heat however, the reverse pattern was observed in mature pollen and leaves. Proteins involved in transport were highly abundant in tetrads, whereas in later stages of development and leaves, heat suppressed cell-to-cell communication. Moreover, a large number of heat shock proteins (HSPs) were identified in heat-affected tetrads, but these proteins were less abundant in mature pollen and leaves. We speculate that the sensitivity of tetrad cells to heat is related to increased activity of translation involved in non-essential pathways. Molecular signatures during pollen development after heatwaves provide markers for future genetic improvement.
Publisher: Springer Science and Business Media LLC
Date: 08-10-2015
DOI: 10.1007/S00299-015-1878-6
Abstract: The BnSERK1 and BnSERK2 are involved in the process of microspore embryogenesis induction, development, and plantlet regeneration. Little is known about regulatory role of somatic embryogenesis-related kinase (SERK) genes family in the induction of microspore embryogenesis, development and plant regeneration. In this study, the expression of two SERK genes (SERK1 and SERK2) was assessed during the microspore embryogenesis and plantlet regeneration in Brassica napus L. The BnSERK1 was severely up-regulated 1-5 days following microspore culture and its expression drastically decreased in the globular-heart and also torpedo staged microspore-derived embryos (MDEs). In addition, high levels of BnSERK1 transcript were detected in the MDE maturation phase and in the roots and shoots of the regenerated plantlets which indicates a broader role(s) of BnSERK1 in the organ formation, rather than being specific to the embryogenesis. Results of partial sequencing indicated that the BnSERK1 shares a conserved serine-threonine kinase catalytic domain and exhibited 95 % similarity with AtSERK1, CsSERK1, BrSERK1, NaSERK1, and NbSERK1. A steady increase in the expression of BnSERK2 was observed during the MDE initiation and development so that, the highest expression was noted in the MDE maturation phase i.e., late cotyledonary MDEs. Our results also indicated low amounts of BnSERK2 transcript at the onset of rhyzogenesis but significantly higher expression in the developing roots. In contrast, the BnSERK2 strongly up-regulated during the both initially and developed shoots. The BnSERK2 shares highly conserved LRR-RLK domain when compared with different species tested so that, high homology (100 %) was noticed with BrSERK2. Based on our findings, MDE formation and plantlet regeneration seem to be correlated with both BnSERK1 and BnSERK2 expression.
Publisher: MDPI AG
Date: 03-02-2022
DOI: 10.3390/IJMS23031739
Abstract: Rice crops are often subject to multiple abiotic stresses simultaneously in both natural and cultivated environments, resulting in yield reductions beyond those expected from single stress. We report physiological changes after a 4 day exposure to combined drought, salt and extreme temperature treatments, following a 2 day salinity pre-treatment in two rice genotypes—Nipponbare (a paddy rice) and IAC1131 (an upland landrace). Stomata closed after two days of combined stresses, causing intercellular CO2 concentrations and assimilation rates to diminish rapidly. Abscisic acid (ABA) levels increased at least five-fold but did not differ significantly between the genotypes. Tandem Mass Tag isotopic labelling quantitative proteomics revealed 6215 reproducibly identified proteins in mature leaves across the two genotypes and three time points (0, 2 and 4 days of stress). Of these, 987 were differentially expressed due to stress (cf. control plants), including 41 proteins that changed significantly in abundance in all stressed plants. Heat shock proteins, late embryogenesis abundant proteins and photosynthesis-related proteins were consistently responsive to stress in both Nipponbare and IAC1131. Remarkably, even after 2 days of stress there were almost six times fewer proteins differentially expressed in IAC1131 than Nipponbare. This contrast in the translational response to multiple stresses is consistent with the known tolerance of IAC1131 to dryland conditions.
Publisher: Wiley
Date: 03-11-2020
DOI: 10.1111/PCE.13908
Abstract: The development of gametes in plants is acutely susceptible to heatwaves as brief as a few days, adversely affecting pollen maturation and reproductive success. Pollen in cotton ( Gossypium hirsutum ) was differentially affected when tetrad and binucleate stages were exposed to heat, revealing new insights into the interaction between heat and pollen development. Squares were tagged and exposed to 36/25°C (day/night, moderate heat) or 40/30°C (day/night, extreme heat) for 5 days. Mature pollen grains and leaves were collected for physiological and proteomic responses. While photosynthetic competence was not compromised even at 40°C, leaf tissues became leakier. In contrast, pollen grains were markedly smaller after the tetrad stage was exposed to 40°C and boll production was reduced by 65%. Sugar levels in pollen grains were elevated after exposure to heat, eliminating carbohydrate deficits as a likely cause of poor reproductive capacity. Proteomic analysis of pure pollen s les revealed a particularly high abundance of 70‐kDa heat shock (Hsp70s) and cytoskeletal proteins. While short‐term bursts of heat had a minor impact on leaves, male gametophyte development was profoundly damaged. Cotton acclimates to maxima of 36°C at both the vegetative and reproductive stages but 5‐days exposure to 40°C significantly impairs reproductive development.
Location: Iran (Islamic Republic of)
Location: Iran (Islamic Republic of)
No related grants have been discovered for Farhad Masoomi-Aladizgeh.