Methods in enzymology on CD-ROM/Methods in enzymology, Journal Year: 2022, Volume and Issue: unknown, P. 279 - 303
Published: Jan. 1, 2022
Language: Английский
Journal of Agriculture and Food Research, Journal Year: 2025, Volume and Issue: unknown, P. 101814 - 101814
Published: March 1, 2025
Language: Английский
Citations
0
Metabolites, Journal Year: 2021, Volume and Issue: 11(7), P. 445 - 445
Published: July 8, 2021
Plants are constantly challenged by changing environmental conditions that include abiotic stresses. These limiting their development and productivity subsequently threatening our food security, especially when considering the pressure of increasing global population. Thus, there is an urgent need for next generation crops with high resilience to climate change. The dawn a new era characterized emergence fourth industrial revolution (4IR) technologies has redefined ideological boundaries research applications in plant sciences. Recent technological advances machine learning (ML)-based computational tools omics data analysis approaches allowing scientists derive comprehensive metabolic descriptions models target species under specific conditions. Such accurate imperatively essential devising roadmap resilient deterioration. By synthesizing recent literature collating on metabolomics studies responses stresses, context 4IR era, we point out opportunities challenges offered science, analytical intelligence, big analytics. Specifically, highlight advancements (plant) workflows use decipher dynamics chemical space define stress
Language: Английский
Citations
21
Environment International, Journal Year: 2022, Volume and Issue: 167, P. 107423 - 107423
Published: July 21, 2022
Health risks caused by crucial environmental carcinogens N-nitrosamines triggered ubiquitous attention. As the liver exerted vital function through metabolic process, lipid metabolism disorders have been confirmed as potential drivers for toxicological effects, and mechanisms of regulation related to hepatotoxicity induced remained largely unclear. In this study, we comprehensively explored disturbance hepatic homeostasis in mice nitrosamines. The results implied that nitrosamines exposure accompanied injury, inflammatory infiltration, edema. Lipidomics profiling analysis indicated decreased levels phosphatidic acids (PA), phosphatidylcholines (PC), phosphatidylethanolamines (PE), lyso-phosphatidylcholines (LPC), lyso-phosphatidylethanolamines (LPE), diacylglycerols (DAG) triacylglycerols (TAG), elevation ceramides (Cer) decomposition free fatty (FFA) high-dose group. Importantly, promoted acid oxidation (FAO) facilitating uptake decomposition, together with upregulation genes associated FAO activation cytokines TNF-α, IL-1β NLRP3. Furthermore, translocase CD36-mediated was correlated enhancement oxidative stress exposure. Overall, our contributed new strategies interpret early toxic effects
Language: Английский
Citations
16
Plant and Cell Physiology, Journal Year: 2022, Volume and Issue: 63(10), P. 1457 - 1473
Published: July 7, 2022
The identification of transcription factor (TF) target genes is central in biology. A popular approach based on the location by pattern matching potential cis-regulatory elements (CREs). During last few years, tools integrating next-generation sequencing data have been developed to improve performance matching. However, such not yet comprehensively evaluated plants. Hence, we a new streamlined method aiming at predicting CREs and plant TFs specific organs or conditions. Our implements supervised machine learning strategy, which allows decision rule models be learnt using TF ChIP-chip/seq experimental data. Different layers genomic features were integrated predictive models: position gene, DNA sequence conservation, chromatin state various CRE footprints. Among tested features, crucial for improving accuracy method. Furthermore, transferability across TFs, species. Finally, validated our correctly inferring key controlling metabolite biosynthesis organ level Arabidopsis. We tool-Wimtrap-to reproduce species conditions/organs are available. Wimtrap user-friendly R package that supports an Shiny web interface provided with pre-built can used quickly get predictions gene targets different conditions Arabidopsis thaliana, Solanum lycopersicum, Oryza sativa Zea mays.
Language: Английский
Citations
11
The Plant Journal, Journal Year: 2024, Volume and Issue: 118(6), P. 2269 - 2295
Published: April 5, 2024
The mature seed in legumes consists of an embryo and coat. In contrast to knowledge about the embryo, we know relatively little We analyzed gene expression during development using a panel cultivated wild pea genotypes. Gene co-expression analysis identified modules related development, dormancy, domestication. Oxidoreductase genes were found be important components developmental domestication processes. Proteomic metabolomic revealed that favored proteins involved photosynthesis protein metabolism at expense defense. Seed coats peas rich cell wall-bound metabolites protective compounds predominated their coats. Altogether, have shown altered modified (mostly reduced) transcripts along with metabolite composition coat, especially content investigated dynamic profiles selected phenolic flavonoid across development. These usually deteriorated palatability processing seeds. Our findings further provide resources study secondary strategies for improving quality legume seeds which comprise part human diet.
Language: Английский
Citations
1
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: June 6, 2024
Abstract Seeds of Brassicaceae species produce a large diversity specialized metabolites (SMs) that strongly influence their quality, with beneficial or toxic effects on human and animal nutrition, provide resistance to biotic abiotic stresses. While the distribution these compounds has been described in leaves roots tissues, very limited information is available about spatio-temporal accumulation seeds model crop plants. Camelina sativa (camelina) an oilseed cultivated for industrial uses. we previously explored detail SM plasticity, no expression SM-related proteins genes camelina seeds. In this study used untargeted metabolomics (LC-MS/MS), proteomics (DIA) transcriptomics (RNA-Seq) analyse synthesis, transport, modifications degradations SMs are accumulated different seed tissues (i.e. coat, endosperm, embryo) at 6 developmental 2 germination stages. Our results showed specific patterns many SMs, related genes, during coat embryo development. We also that, differently from Arabidopsis thaliana seeds, defence antinutritional glucosinolates were both corresponding degradation products isothiocyanates present high level embryos dry C. . Characterizing spatial dynamics will contribute development crops optimized quality nutrition.
Language: Английский
Citations
0
Methods in molecular biology, Journal Year: 2024, Volume and Issue: unknown, P. 171 - 182
Published: Jan. 1, 2024
Language: Английский
Citations
0
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: June 29, 2024
Abstract Dirigent (DIR) proteins mediate regio- and stereoselectivity of phenoxy radical coupling monolignols for (neo)lignan or lignin synthesis. However, the role DIR lignans in plant development response to environmental stresses remains elusive. Here, we provide a functional characterization cytokinin-responsive DIRIGENT13 ( DIR13 ) Arabidopsis thaliana . was localized root endodermis at margins lateral primordia roots. While not necessary Casparian strip formation, promoted both main growth. Untargeted metabolomics imaging mass spectrometry analyses unveiled facilitating synthesis primary Interestingly, activated production putative oxomatairesinol matairesinol-cysteine which are oxidative derivatives lignan matairesinol. Our data also identified as an enhancer salt drought tolerance. Particularly, attenuated stress-mediated inhibition germination Moreover, reactive oxygen species (ROS) accumulation under control stress conditions, cytokinin further enhanced salt-induced ROS specifically overexpressing line. results uncover DIR13-produced priming accumulation, mediating abiotic tolerance architecture.
Language: Английский
Citations
0
Plant Direct, Journal Year: 2024, Volume and Issue: 8(8)
Published: Aug. 1, 2024
Light/dark (LD) cycles are responsible for oscillations in gene expression, which modulate several aspects of plant physiology. Those can persist under constant conditions due to regulation by the circadian oscillator. The response transcriptome light regimes is dynamic and allows plants adapt rapidly changing environmental conditions. We compared Arabidopsis LD (LL) 3 days identified different co-expression networks two regimes. Our studies yielded unforeseen insights into regulation. Intuitively, we anticipated that clusters regulated oscillator would display cycles. However, found transcripts encoding components flavonoid metabolism pathway were rhythmic LL but not LD. also discovered expressions many stress-related genes significantly increased during dark period relative subjective night LL, whereas expression these was similar. nocturnal pattern suggested a form "skotoprotection." transcriptomics data made available web application named
Language: Английский
Citations
0
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Aug. 30, 2024
Abstract Cadmium (Cd) is a major environmental pollutant with high toxicity potential. Even though reduction of growth, including the primary root, clear consequence Cd exposure, profound understanding impact on root apical meristem (RAM) and elongation/differentiation zone (EDZ) still lacking. In this study, Arabidopsis thaliana roots were subjected to divided into tips (RT) remaining (RR) separately assess effect using transcriptomics, ionomics metabolomics. Elemental profiling revealed lower accumulation in RT differences mineral contents between RR. Transcriptomic analysis demonstrated distinct gene expression patterns RR, having less RT. Functional enrichment genes associated iron sulfur homeostasis as well response light both RR RT-specific responses included several regulated by transcription factor ELONGATED HYPOCOTYL 5 (HY5) notably, hy5 mutant showed increased sensitivity compared wild type. This study provides comprehensive insights inhibitory effects elucidating molecular mechanisms involved, particularly highlighting role HY5 accumulation.
Language: Английский
Citations
0