Formerly the "Center for Desert Agriculture"

Recent Submissions

  • Effect of D-ring C-3’ methylation of strigolactone analogs on their transcription regulating activity in rice

    Jamil, Muhammad; Haider, Imran; Kountche, Boubacar Amadou; Al-Babili, Salim (Plant Signaling & Behavior, Informa UK Limited, 2019-09-25) [Article]
    Strigolactones (SLs) are a well-known class of plant hormones, which are involved in a number of developmental and adaptation processes and mediate different interspecific interactions. In spite of the growing knowledge on SL biosynthesis and signal transduction, effects of structural modifications on the activity and efficiency of SLs and their analogs remain largely elusive. SLs are characterized by the presence of a lactone ring (D-ring) that is connected by an enol ether bridge to a second moiety. In this study, we investigated the effect of additional D-ring methylation of SL analogs on their transcription regulating activity. For this purpose, we compared the SL analogs MP13 and AR8, which differ only by the presence of a methyl group at the C-3ʹ atom in the latter. Transcription regulating activity was determined by quantitative real-time PCR measurement of transcript levels of SL-dependent, feed-back regulated genes in treated wild type and ccd7 mutant rice seedlings. Results obtained indicate that C-3ʹ methylation reduces the transcription regulating activity, as shown by the more pronounced suppression of the SL biosynthesis genes DWARF27 (D27) and CAROTENOID CLEAVAGE DIOXYGENASES (CCD7 and CCD8) and higher induction of the SL signaling repressor gene DWARF53 (D53) in MP13 treated seedlings. These results are consistent with a recent study on the biological activities of MP13 and AR8.
  • Mining biosynthetic gene clusters in Virgibacillus genomes.

    Othoum, Ghofran K.; Bougouffa, Salim; Bokhari, Ameerah; Lafi, Feras Fawzi; Gojobori, Takashi; Hirt, Heribert; Mijakovic, Ivan; Bajic, Vladimir B.; Essack, Magbubah (BMC genomics, Springer Science and Business Media LLC, 2019-09-05) [Article]
    BACKGROUND:Biosynthetic gene clusters produce a wide range of metabolites with activities that are of interest to the pharmaceutical industry. Specific interest is shown towards those metabolites that exhibit antimicrobial activities against multidrug-resistant bacteria that have become a global health threat. Genera of the phylum Firmicutes are frequently identified as sources of such metabolites, but the biosynthetic potential of its Virgibacillus genus is not known. Here, we used comparative genomic analysis to determine whether Virgibacillus strains isolated from the Red Sea mangrove mud in Rabigh Harbor Lagoon, Saudi Arabia, may be an attractive source of such novel antimicrobial agents. RESULTS:A comparative genomics analysis based on Virgibacillus dokdonensis Bac330, Virgibacillus sp. Bac332 and Virgibacillus halodenitrificans Bac324 (isolated from the Red Sea) and six other previously reported Virgibacillus strains was performed. Orthology analysis was used to determine the core genomes as well as the accessory genome of the nine Virgibacillus strains. The analysis shows that the Red Sea strain Virgibacillus sp. Bac332 has the highest number of unique genes and genomic islands compared to other genomes included in this study. Focusing on biosynthetic gene clusters, we show how marine isolates, including those from the Red Sea, are more enriched with nonribosomal peptides compared to the other Virgibacillus species. We also found that most nonribosomal peptide synthases identified in the Virgibacillus strains are part of genomic regions that are potentially horizontally transferred. CONCLUSIONS:The Red Sea Virgibacillus strains have a large number of biosynthetic genes in clusters that are not assigned to known products, indicating significant potential for the discovery of novel bioactive compounds. Also, having more modular synthetase units suggests that these strains are good candidates for experimental characterization of previously identified bioactive compounds as well. Future efforts will be directed towards establishing the properties of the potentially novel compounds encoded by the Red Sea specific trans-AT PKS/NRPS cluster and the type III PKS/NRPS cluster.
  • CRISPR-Based Directed Evolution for Crop Improvement.

    Butt, Haroon; Zaidi, Syed Shan-e-Ali; Hassan, Norhan; Mahfouz, Magdy M. (Trends in biotechnology, Elsevier BV, 2019-09-04) [Article]
    Directed evolution involves generating diverse sequence variants of a gene of interest to produce a desirable trait under selective pressure. CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9) systems can be programmed to target any genomic locus and perform targeted directed evolution. Here, we discuss the opportunities and challenges of this emerging platform for targeted crop improvement.
  • MAP4K4 associates with BIK1 to regulate plant innate immunity.

    Jiang, Yunhe; Han, Baoda; Zhang, Huoming; Mariappan, Kiruthiga; Bigeard, Jean; Colcombet, Jean; Hirt, Heribert (EMBO reports, EMBO, 2019-09-03) [Article]
    To perceive pathogens, plants employ pattern recognition receptor (PRR) complexes, which then transmit these signals via the receptor-like cytoplasmic kinase BIK1 to induce defense responses. How BIK1 activity and stability are controlled is still not completely understood. Here, we show that the Hippo/STE20 homolog MAP4K4 regulates BIK1-mediated immune responses. MAP4K4 associates and phosphorylates BIK1 at Ser233, Ser236, and Thr242 to ensure BIK1 stability and activity. Furthermore, MAP4K4 phosphorylates PP2C38 at Ser77 to enable flg22-induced BIK1 activation. Our results uncover that a Hippo/STE20 homolog, MAP4K4, maintains the homeostasis of the central immune component BIK1.
  • The Polycomb protein LHP1 regulates Arabidopsis thaliana stress responses through the repression of the MYC2-dependent branch of immunity.

    Ramirez-Prado, J S; Latrasse, D; Rodriguez-Granados, N Y; Huang, Y; Manza-Mianza, D; Brik-Chaouche, R; Jaouannet, M; Citerne, S; Bendahmane, A; Hirt, Heribert; Raynaud, C; Benhamed, M (The Plant journal : for cell and molecular biology, Wiley, 2019-08-23) [Article]
    Polycomb repressive complexes (PRCs) have been traditionally associated to the regulation of developmental processes in various organisms, including higher plants. However, similar to other epigenetic regulators, there is accumulating evidence for their role in the regulation of stress and immune-related pathways. In the current study we show that the PRC1 protein LHP1 is required for the repression of the MYC2 branch of jasmonic acid (JA)/ethylene (ET) pathway of immunity. Loss of LHP1 induces the reduction in H3K27me3 levels in the gene bodies of ANAC019 and ANAC055, as well as some of their targets, leading to their transcriptional up-regulation. Consistently, increased expression of these two transcription factors leads to the mis-regulation of several of their genomic targets. The lhp1 mutant mimics the MYC2, ANAC019 and ANAC055 over-expressers in several of their phenotypes, including increased aphid resistance, ABA sensitivity and drought tolerance. In addition, like the MYC2 and ANAC over-expressers, lhp1 displays reduced Salicylic Acid (SA) content caused by a de-regulation of ICS1 and BSMT1, as well as increased susceptibility to the hemibiotrophic pathogen Pseudomonas syringae pv. tomato DC3000. Together, our results indicate that LHP1 regulates the expression of stress responsive genes as well as the homeostasis and responses to the stress hormones SA and ABA. This protein emerges as a key chromatin player fine-tuning the complex balance between developmental and stress-responsive processes. This article is protected by copyright. All rights reserved.
  • Multiplex CRISPR Mutagenesis of the Serine/Arginine-Rich (SR) Gene Family in Rice.

    Butt, Haroon; Piatek, Agnieszka Anna; Li, Lixin; S N Reddy, Anireddy; M Mahfouz, Magdy (Genes, MDPI AG, 2019-08-10) [Article]
    Plant growth responds to various environmental and developmental cues via signaling cascades that influence gene expression at the level of transcription and pre-mRNA splicing. Alternative splicing of pre-mRNA increases the coding potential of the genome from multiexon genes and regulates gene expression through multiple mechanisms. Serine/arginine-rich (SR) proteins, a conserved family of splicing factors, are the key players of alternative splicing and regulate pre-mRNA splicing under stress conditions. The rice (Oryza sativa) genome encodes 22 SR proteins categorized into six subfamilies. Three of the subfamilies are plant-specific with no mammalian orthologues, and the functions of these SR proteins are not well known. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a genome engineering tool that cleaves the target DNA at specific locations directed by a guide RNA (gRNA). Recent advances in CRISPR/Cas9-mediated plant genome engineering make it possible to generate single and multiple functional knockout mutants in diverse plant species. In this study, we targeted each rice SR locus and produced single knockouts. To overcome the functional redundancy within each subfamily of SR genes, we utilized a polycistronic tRNA-gRNA multiplex targeting system and targeted all loci of each subfamily. Sanger sequencing results indicated that most of the targeted loci had knockout mutations. This study provides useful resource materials for understanding the molecular role of SR proteins in plant development and biotic and abiotic stress responses.
  • To color or to decolor that is the question.

    Mi, Jianing; Al-Babili, Salim (Molecular plant, Elsevier BV, 2019-08-06) [Article]
  • Discovery of a Nitric Oxide-Responsive Protein in Arabidopsis thaliana.

    Zarban, Randa Alhassan Yahya; Vogler, Malvina M.; Wong, Aloysius Tze; Eppinger, Jörg; Al-Babili, Salim; Gehring, Christoph A (Molecules (Basel, Switzerland), MDPI AG, 2019-07-27) [Article]
    In plants, much like in animals, nitric oxide (NO) has been established as an important gaseous signaling molecule. However, contrary to animal systems, NO-sensitive or NO-responsive proteins that bind NO in the form of a sensor or participating in redox reactions have remained elusive. Here, we applied a search term constructed based on conserved and functionally annotated amino acids at the centers of Heme Nitric Oxide/Oxygen (H-NOX) domains in annotated and experimentally-tested gas-binding proteins from lower and higher eukaryotes, in order to identify candidate NO-binding proteins in Arabidopsis thaliana. The selection of candidate NO-binding proteins identified from the motif search was supported by structural modeling. This approach identified AtLRB3 (At4g01160), a member of the Light Response Bric-a-Brac/Tramtrack/Broad Complex (BTB) family, as a candidate NO-binding protein. AtLRB3 was heterologously expressed and purified, and then tested for NO-response. Spectroscopic data confirmed that AtLRB3 contains a histidine-ligated heme cofactor and importantly, the addition of NO to AtLRB3 yielded absorption characteristics reminiscent of canonical H-NOX proteins. Furthermore, substitution of the heme iron-coordinating histidine at the H-NOX center with a leucine strongly impaired the NO-response. Our finding therefore established AtLRB3 as a NO-interacting protein and future characterizations will focus on resolving the nature of this response.
  • Phosphorylation regulates the activity of INDETERMINATE-DOMAIN (IDD/BIRD) proteins in response to diverse environmental conditions.

    Volz, Ronny; Rayapuram, Naganand; Hirt, Heribert (Plant signaling & behavior, Informa UK Limited, 2019-07-18) [Article]
    INDETERMINATE-DOMAIN proteins (IDDs) belong to a diverse plant-specific family of transcriptional regulators that coordinate distinct functions during plant growth and development. The functions of several of these IDD members are transcriptionally regulated, but so far nothing is known about the regulation at the post-translational level in spite of the fact that post-translational modifications of these proteins have been reported in several large-scale proteomics studies. Recently, we showed that IDD4 is a repressor of basal immunity and its characteristic traits are predominantly determined by the phosphorylation at two distinct phosphorylation sites. This finding prompted us to comprehensively review phosphorylation of the various IDD members from the plethora of phosphoproteomics studies demonstrating the post-translational modification of IDDs at highly conserved sites under various experimental conditions. We reckon that the phosphorylation of IDDs is an underrated mechanistic aspect in their regulation and we postulate their importance in IDD/BIRD functioning.
  • A Simplified Method to Engineer CRISPR/Cas9-Mediated Geminivirus Resistance in Plants

    Ali, Zahir; Zaidi, Syed Shan-e-Ali; Tashkandi, Manal; Mahfouz, Magdy M. (Springer New York, 2019-06-21) [Book Chapter]
    Throughout the world, geminiviruses cause devastating losses in economically important crops, including tomato, cotton, cassava, potato, chili, and cucumber; however, control mechanisms such as genetic resistance remain expensive and ineffective. CRISPR/Cas9 is an adaptive immunity mechanism used by prokaryotes to defend against invading nucleic acids of phages and plasmids. The CRISPR/Cas9 system has been harnessed for targeted genome editing in a variety of eukaryotic species, and in plants, CRISPR/Cas9 has been used to modify or introduce many traits, including virus resistance. Recently, we demonstrated that the CRISPR/Cas9 system could be used to engineer plant immunity against geminiviruses by directly targeting the viral genome for degradation. In this chapter, we describe a detailed method for engineering CRISPR/Cas9-mediated resistance against geminiviruses. This method may provide broad, durable viral resistance, as it can target conserved regions of the viral genome and can also be customized to emerging viral variants. Moreover, this method can be used in many crop species, as it requires little or no knowledge of the host plant’s genome.
  • Breeding crops to feed 10 billion.

    Hickey, Lee T; N Hafeez, Amber; Robinson, Hannah; Jackson, Scott A; Leal-Bertioli, Soraya C M; Tester, Mark A.; Gao, Caixia; Godwin, Ian D; Hayes, Ben J; Wulff, Brande B H (Nature biotechnology, Springer Science and Business Media LLC, 2019-06-19) [Article]
    Crop improvements can help us to meet the challenge of feeding a population of 10 billion, but can we breed better varieties fast enough? Technologies such as genotyping, marker-assisted selection, high-throughput phenotyping, genome editing, genomic selection and de novo domestication could be galvanized by using speed breeding to enable plant breeders to keep pace with a changing environment and ever-increasing human population.
  • Piriformospora indica alters Na+/K+ homeostasis, antioxidant enzymes and LeNHX1 expression of greenhouse tomato grown under salt stress

    Abdelaziz, Mohamed E.; Abdelsattar, Mohamed; Abdeldaym, Emad A.; Atia, Mohamed A.M.; Mahmoud, Abdel Wahab M.; Saad, Maged; Hirt, Heribert (Scientia Horticulturae, Elsevier B.V., 2019-06-18) [Article]
    The utilization of symbiosis with beneficial microorganisms provides a strategy to alleviate salt stress that reduces existing gaps in crops production. The root endophytic fungus Piriformospora indica has shown to improve plant growth in diverse plant species under biotic stress, while limited reports have discussed the interaction of P. indica with tomato under salt stress. In this study, the impact of P. indica on tomato exposed to 200 mM NaCl for one month in soil-free culture was examined. Growth performance, marker osmolytes, antioxidant enzymes and expression of LeNHX1-4 genes of tomato leaves were measured. Results show that colonization of roots by P. indica improved root branching, fresh and dry weight of salt-stressed plants. Likewise, P. indica colonization increased levels of chlorophyll b, indole acetic acid, catalase and superoxide dismutase in leaves of tomato under salt stress. Meanwhile, P. indica reduced the increase of abscisic acid and proline levels when compared to non-colonized plants. Importantly, Na+/K+ ratios in shoots and roots of colonized plants were lower than in the corresponding non-colonized plants, which may be attributed to the higher K+ concentration observed in leaves and roots of colonized plants under saline water irrigation condition. This change in ion homeostasis was combined with an increase in LeNHX1 transcripts in leaves of colonized plants. Moreover, compared to non-treated plants, colonization with P. indica enhanced fruit yield by 22% and 65% under normal and saline water irrigation, respectively. Our study shows that P. indica enhances the growth and yield of tomato plants under normal and salt stress conditions, opening up a window of opportunity for its application in desert agriculture.
  • Arabidopsis Proteome and the Mass Spectral Assay Library

    Zhang, Huoming; Liu, Peng; Guo, Tiannan; Zhao, Huayan; Bensaddek, Dalila; Aebersold, Ruedi; Xiong, Liming (Cold Spring Harbor Laboratory, 2019-06-11) [Preprint]
    Arabidopsis is an important model organism and the first plant with its genome sequenced. Knowledge from studying this species has either direct or indirect applications to agriculture and human health. Quantitative proteomics by data-independent acquisition (SWATH/DIA-MS) was recently developed and considered as a high-throughput targetedlike approach for accurate proteome quantitation. In this approach, a high-quality and comprehensive library is a prerequisite. Here, we generated a protein expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We subsequently applied DIA-mass spectrometry using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups with 1,787 of them being differentially expressed which includes 65 proteins known to respond to abscisic acid stress. Mass spectrometry data are available via ProteomeXchange with identifier PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.
  • PREDICTING BIOMASS AND YIELD AT HARVEST OF SALT-STRESSED TOMATO PLANTS USING UAV IMAGERY

    Johansen, K.; Morton, M. J. L.; Malbeteau, Yoann; Aragon Solorio, Bruno Jose Luis; Almashharawi, Samir; Ziliani, Matteo; Angel, Yoseline; Fiene, Gabriele; Negrão, Sónia; Mousa, M. A. A.; Tester, Mark A.; McCabe, Matthew (ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Copernicus GmbH, 2019-06-04) [Article]
    Biomass and yield are important variables used for assessing agricultural production. However, these variables are difficult to estimate for individual plants at the farm scale and may be affected by abiotic stressors such as salinity. In this study, the wild tomato species, Solanum pimpinellifolium, was evaluated through field and UAV-based assessment of 600 control and 600 salt-treated plants. The aim of this research was to determine, if UAV-based imagery, collected one, two, four, six, seven and eight weeks before harvest could predict fresh shoot mass, tomato fruit numbers, and yield mass at harvest and if predictions varied for control and salt-treated plants. A Random Forest approach was used to model biomass and yield. The results showed that shape features such as plant area, border length, width and length had the highest importance in the random forest models. A week prior to harvest, the explained variance of fresh shoot mass, number of fruits and yield mass were 86.60%, 59.46% and 61.09%, respectively. The explained variance was reduced as a function of time to harvest. Separate models may be required for predicting yield of salt-stressed plants, whereas the prediction of yield for control plants was less affected if the model included salt-stressed plants. This research demonstrates that it is possible to predict biomass and yield of tomato plants up to four weeks prior to harvest, and potentially earlier in the absence of severe weather events.
  • Emergent Protective Organogenesis in Date Palms: A Morpho-devo-dynamic Adaptive Strategy During Early Development.

    Xiao, Tingting; Raygoza, Alejandro Aragón; Pérez, Juan Caballero; Kirschner, Gwendolyn Kristin; Deng, Yanming; Atkinson, Brian; Sturrock, Craig; Lube, Vinicius; Wang, Jian You; Lubineau, Gilles; Al-Babili, Salim; Ramírez, Luis Alfredo Cruz; Bennett, Malcolm J; Blilou, Ikram (The Plant cell, American Society of Plant Biologists (ASPB), 2019-05-31) [Article]
    Desert plants have developed mechanisms for adapting to hostile desert conditions, yet these mechanisms remain poorly understood. Here, we describe two unique modes used by desert date palms (Phoenix dactylifera L.) to protect their meristematic tissues during early organogenesis. We used X-ray micro-computed tomography combined with high-resolution tissue imaging to reveal that, after germination, development of the embryo pauses while it remains inside a dividing and growing cotyledonary petiole. Transcriptomic and hormone analyses show that this developmental arrest is associated with the low expression of development-related genes and accumulation of hormones that promote dormancy and confer resistance to stress. Furthermore, organ-specific cell type mapping demonstrates that organogenesis occurs inside the cotyledonary petiole, with identifiable root and shoot meristems and their respective stem cells. The plant body emerges from the surrounding tissues with developed leaves and a complex root system that maximizes efficient nutrient and water uptake. We further show that, similar to its role in Arabidopsis thaliana, the SHORT-ROOT (SHR) homologue from date palms functions in maintaining stem cell activity and promoting formative divisions in the root ground tissue. Our findings provide insight into developmental programs that confer adaptive advantages in desert plants that thrive in hostile habitats.
  • OXI1 and DAD regulate light-induced cell death antagonistically through jasmonate and salicylate levels.

    Beaugelin, Inès; Chevalier, Anne; D'Alessandro, Stefano; Ksas, Brigitte; Novák, Ondřej; Strnad, Miroslav; Forzani, Céline; Hirt, Heribert; Havaux, Michel; Monnet, Fabien (Plant physiology, American Society of Plant Biologists (ASPB), 2019-05-25) [Article]
    Singlet oxygen (1O2) produced from triplet excited chlorophylls in photosynthesis is a signal molecule that can induce programmed cell death (PCD) through the action of the OXIDATIVE STRESS INDUCIBLE 1 (OXI1) kinase. Here, we identify two negative regulators of light-induced PCD which modulate OXI1 expression: DAD1 and DAD2, homologs of the human anti-apoptotic protein DEFENDER AGAINST CELL DEATH. Overexpressing OXI1 in Arabidopsis (Arabidopsis thaliana) increased plant sensitivity to high light and induced early senescence of mature leaves. Both phenomena rely on a marked accumulation of jasmonate and salicylate. DAD1 or DAD2 overexpression decreased OXI1 expression, jasmonate levels and sensitivity to photooxidative stress. Knock-out mutants of DAD1 or DAD2 exhibited the opposite responses. Exogenous applications of jasmonate upregulated salicylate biosynthesis genes and caused leaf damage in wild-type plants but not in the salicylate biosynthesis mutant sid2, indicating that salicylate plays a crucial role in PCD downstream of jasmonate. Treating plants with salicylate upregulated the DAD genes and downregulated OXI1. We conclude that OXI1 and DAD are antagonistic regulators of cell death through modulating jasmonate and salicylate levels. High light-induced PCD thus results from a tight control of the relative activities of these regulating proteins with DAD exerting a negative feedback control on OXI1 expression.
  • β-Cyclocitral is a conserved root growth regulator

    Dickinson, Alexandra J; Lehner, Kevin; Mi, Jianing; Jia, Kunpeng; Mijar, Medhavinee; Dinneny, José; Al-Babili, Salim; Benfey, Philip N (Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2019-05-08) [Article]
    Natural compounds capable of increasing root depth and branching are desirable tools for enhancing stress tolerance in crops. We devised a sensitized screen to identify natural metabolites capable of regulating root traits in Arabidopsis β-Cyclocitral, an endogenous root compound, was found to promote cell divisions in root meristems and stimulate lateral root branching. β-Cyclocitral rescued meristematic cell divisions in ccd1ccd4 biosynthesis mutants, and β-cyclocitral-driven root growth was found to be independent of auxin, brassinosteroid, and reactive oxygen species signaling pathways. β-Cyclocitral had a conserved effect on root growth in tomato and rice and generated significantly more compact crown root systems in rice. Moreover, β-cyclocitral treatment enhanced plant vigor in rice plants exposed to salt-contaminated soil. These results indicate that β-cyclocitral is a broadly effective root growth promoter in both monocots and eudicots and could be a valuable tool to enhance crop vigor under environmental stress.
  • MVApp - Multivariate analysis application for streamlined data analysis and curation

    Julkowska, Magdalena; Saade, Stephanie; Agarwal, Gaurav; Gao, Ge; Pailles, Yveline; Morton, Mitchell J L; Awlia, Mariam Sahal Abdulaziz; Tester, Mark A. (Plant Physiology, American Society of Plant Biologists (ASPB), 2019-05-07) [Article]
    Modern phenotyping techniques yield vast amounts of data that are challenging to manage and analyze. When thoroughly examined, this type of data can reveal genotype-to-phenotype relationships and meaningful connections among individual traits. However, efficient data mining is challenging for experimental biologists with limited training in curating, integrating and exploring complex datasets. Additionally, data transparency, accessibility and reproducibility are important considerations for scientific publication. The need for a streamlined, user-friendly pipeline for advanced phenotypic data analysis is pressing. In this manuscript we present an open-source, online platform for multivariate analysis (MVApp), which serves as an interactive pipeline for data curation, in-depth analysis and customized visualization. MVApp builds on the available R-packages and adds extra functionalities to enhance the interpretability of the results. The modular design of the MVApp allows for flexible analysis of various data structures and includes tools underexplored in phenotypic data analysis, such as clustering and quantile regression. MVApp aims to enhance findable, accessible, interoperable and reproducible data transparency, streamline data curation and analysis, and increase statistical literacy among the scientific community.
  • A Highly Sensitive SPE-Derivatization-UHPLC-MS Approach for Quantitative Profiling of Carotenoid-derived Dialdehydes from Vegetables

    Mi, Jianing; Jia, Kunpeng; Balakrishna, Aparna; Feng, Qitong; Al-Babili, Salim (Journal of Agricultural and Food Chemistry, American Chemical Society (ACS), 2019-05-06) [Article]
    Oxidative cleavage of carotenoids leads to dialdehydes (diapocarotenoids, DIALs), besides the widely known apocarotenoids. DIALs are biologically active compounds that presumably impact human health and play different roles in plant development and carotenoid-metabolism. However, detection of DIALs in plants is challenging due to their instability, low-abundance and poor ionization efficiency in mass spectrometry. Here, we developed a solid phase extraction (SPE) and derivatization protocol coupled with ultra-high performance liquid chromatography−mass spectrometry (UHPLC-MS) for quantitative profiling of DIALs. Our method significantly enhances the sensitivity of DIALs detection with detection limit of 0.05 pg/mg dried food materials, allowing unambiguous profiling of 30 endogenous DIALs with C5 to C24 from vegetables. Our work provides a new and efficient approach for determining the content of DIALs from various complex matrices, paving the way for uncovering the functions of DIALs in human health and plant growth and development.
  • Overexpression of the NAC transcription factor JUNGBRUNNEN1 (JUB1) increases salinity tolerance in tomato

    Alshareef, Nouf Owdah Hameed; Wang, Jian You; Ali, Shawkat; Al-Babili, Salim; Tester, Mark A.; Schmöckel, Sandra M. (Plant Physiology and Biochemistry, Elsevier BV, 2019-05-01) [Article]
    Soil salinity is a major abiotic stress affecting plant growth and yield, due to both osmotic and ionic stresses. JUBGBRUNNEN1 (JUB1) is a NAC family transcription factor that has been shown to be involved in responses to abiotic stresses, such as water deficit, osmotic, salinity, heat and oxidative stress. In Arabidopsis thaliana (Arabidopsis), JUB1 has been shown to improve plant stress tolerance by regulating H2O2 levels. In the horticultural crop, Solanum lycopersicum cv. Moneymaker (tomato), overexpression of AtJUB1 has been shown to partially alleviate water deficit stress at the vegetative stage. In this study, we investigated the effect of Arabidopsis JUB1 overexpression in salinity tolerance in tomato. In hydroponically grown tomato seedlings, AtJUB1 overexpression results in higher prolines levels and improves the maintenance of water content in the plant under salinity stress. The transgenic tomato plants are more tolerant to salinity stress compared to control lines based on plant biomass. However, at the reproductive stage, we found that overexpression of AtJUB1 only provided marginal improvements in yield-related parameters, in the conditions used for the current work. The combination of improved water deficit and salinity stress tolerance conferred by AtJUB1 overexpression may be beneficial when tomato plants are grown in the field under marginal environments.

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