Rising frequency of ozone-favorable synoptic weather patterns contributes to 2015-2022 ozone increase in Guangzhou

Objective weather classification methods have been extensively applied to identify dominant ozone-favorable synoptic weather patterns (SWPs), however, the consistency of different classification methods is rarely examined. In this study, we apply two widely-used objective methods, the self-organizing map (SOM) and K-means clustering analysis, to derive ozone-favorable SWPs at four Chinese megacities in 2015-2022. We find that the two algorithms are largely consistent in recognizing dominant ozone-favorable SWPs for four Chinese megacities. In the case of classifying six SWPs, the derived circulation fields are highly similar with a spatial correlation of 0.99 between the two methods, and the difference in the mean frequency of each SWP is less than 7%. The six dominant ozone-favorable SWPs in Guangzhou are all characterized by anomaly higher radiation and temperature, lower cloud cover, relative humidity, and wind speed, and stronger subsidence compared to climatology mean. We find that during 2015-2022, the occurrence of ozone-favorable SWPs days increases significantly at a rate of 3.2 day/year, faster than the increases in the ozone exceedance days (3.0 day/year). The interannual variability between the occurrence of ozone-favorable SWPs and ozone exceedance days are generally consistent with a temporal correlation coefficient of 0.6. In particular, the significant increase in ozone-favorable SWPs in 2022, especially the Subtropical High type which typically occurs in September, is consistent with a long-lasting ozone pollution episode in Guangzhou during September 2022. Our results thus reveal that enhanced frequency of ozone-favorable SWPs plays an important role in the observed 2015-2022 ozone increase in Guangzhou.

Arsenic methylation and microbial communities in paddy soils under alternating anoxic and oxic conditions

Arsenic (As) methylation in soils affects the environmental behavior of As, excessive accumulation of dimethylarsenate (DMA) in rice plants leads to straighthead disease and a serious drop in crop yield. Understanding the mobility and transformation of methylated arsenic in redox-changing paddy fields is crucial for food security. Here, soils including un-arsenic contaminated (N-As), low-arsenic (L-As), medium-arsenic (M-As), and high-arsenic (H-As) soils were incubated under continuous anoxic, continuous oxic, and consecutive anoxic/oxic treatments respectively, to profile arsenic methylating process and microbial species involved in the As cycle. Under anoxic-oxic (A-O) treatment, methylated arsenic was significantly increased once oxygen was introduced into the incubation system. The methylated arsenic concentrations were up to 2-24 times higher than those in anoxic (A), oxic (O), and oxic-anoxic (O-A) treatments, under which arsenic was methylated slightly and then decreased in all four As concentration soils. In fact, the most plentiful arsenite S-adenosylmethionine methyltransferase genes (arsM) contributed to the increase in As methylation. Proteobacteria (40.8%-62.4%), Firmicutes (3.5%-15.7%), and Desulfobacterota (5.3%-13.3%) were the major microorganisms related to this process. These microbial increased markedly and played more important roles after oxygen was introduced, indicating that they were potential keystone microbial groups for As methylation in the alternating anoxic (flooding) and oxic (drainage) environment. The novel findings provided new insights into the reoxidation-driven arsenic methylation processes and the model could be used for further risk estimation in periodically flooded paddy fields.

4-Nitrophenol at environmentally relevant concentrations mediates reproductive toxicity in Caenorhabditis elegans via metabolic disorders-induced estrogen signaling pathway

4-Nitrophenol (4-NP), as a toxic and refractory pollutant, has generated significant concern due to its adverse effects. However, the potential toxic effects and mechanism remained unclear. In this study, the reproduction, development, locomotion and reactive oxygen species (ROS) production of Caenorhabditis elegans were investigated to evaluate the 4-NP toxicity. We used metabolomics to assess the potential damage mechanisms. The role of metabolites in mediating the relationship between 4-NP and phenotypes was examined by correlation and mediation analysis. 4-NP (8 ng/L and 8 µg/L) caused significant reduction of brood size, ovulation rate, total germ cells numbers, head thrashes and body bends, and an increase in ROS. However, the oosperm numbers in uterus, body length and body width were decreased in 8 µg/L. Moreover, 36 differential metabolites were enriched in the significant metabolic pathways, including lysine biosynthesis, β-alanine metabolism, tryptophan metabolism, pentose phosphate pathway, pentose and glucuronate interconversions, amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, galactose metabolism, propanoate metabolism, glycerolipid metabolism, and estrogen signaling pathway. The mechanism of 4-NP toxicity was that oxidative stress caused by the perturbation of amino acid, which had effects on energy metabolism through disturbing carbohydrate and lipid metabolism, and finally affected the estrogen signaling pathway to exert toxic effects. Moreover, correlation and mediation analysis showed glycerol-3P, glucosamine-6P, glucosamine-1P, UDP-galactose, L-aspartic acid, and uracil were potential markers for the reproduction and glucose-1,6P2 for developmental toxicity. The results provided insight into the pathways involved in the toxic effects caused by 4-NP and developed potential biomarkers to evaluate 4-NP toxicity.

Metabolic profiling of pea (Pisum sativum) cultivars in changing environments: Implications for nutritional quality in animal feed

Field pea seeds have long been recognized as valuable feed ingredients for animal diets, due to their high-quality protein and starch digestibility. However, the chemical composition of pea cultivars can vary across different growing locations, consequently impacting their nutrient profiles. This study employs untargeted metabolomics in conjunction with the quantification of fatty acids and amino acids to explore the influence of three different growing locations in Spain (namely Andalusia, Aragon and Asturias), on the nutritional characteristics of seeds of various pea cultivars. Significant interactions between cultivar and environment were observed, with 121 metabolites distinguishing pea profiles. Lipids, lipid-like molecules, phenylpropanoids, polyketides, carbohydrates, and amino acids were the most affected metabolites. Fatty acid profiles varied across locations, with higher C16:0, C18:0, and 18:1 n-9 concentration in Aragón, while C18:2 n-6 predominated in Asturias and C18:3 n-3 in Andalusia. Amino acid content was also location-dependent, with higher levels in Asturias. These findings underscore the impact of environmental factors on pea metabolite profiles and emphasize the importance of selecting pea cultivars based on specific locations and animal requirements. Enhanced collaboration between research and industry is crucial for optimizing pea cultivation for animal feed production.

Cytokinin signaling is involved in root hair elongation in response to phosphate starvation

Root hair, single-celled tubular structures originating from the epidermis, plays a vital role in the uptake of nutrients from the soil by increasing the root surface area. Therefore, optimizing root hair growth is crucial for plants to survive in fluctuating environments. Root hair length is determined by the action of various plant hormones, among which the roles of auxin and ethylene have been extensively studied. However, evidence for the involvement of cytokinins has remained elusive. We recently reported that the cytokinin-activated B-type response regulators, ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) and ARR12 directly upregulate the expression of ROOT HAIR DEFECTIVE 6-LIKE 4 (RSL4), which encodes a key transcription factor that controls root hair elongation. However, depending on the nutrient availability, it is unknown whether the ARR1/12-RSL4 pathway controls root hair elongation. This study shows that phosphate deficiency induced the expression of RSL4 and increased the root hair length through ARR1/12, though the transcript and protein levels of ARR1/12 did not change. These results indicate that cytokinins, together with other hormones, regulate root hair growth under phosphate starvation conditions.

The link between changing in host carbon allocation and resistance to Magnaporthe oryzae: a possible tactic for mitigating the rice blast fungus

One of the most destructive diseases affecting rice is rice blast, which is brought on by the rice blast fungus Magnaporthe oryzae. The preventive measures, however, are not well established. To effectively reduce the negative effects of rice blasts on crop yields, it is imperative to comprehend the dynamic interactions between pathogen resistance and patterns of host carbon allocation. This review explores the relationship between variations in carbon allocation and rice plants' ability to withstand the damaging effects of M. oryzae. The review highlights potential strategies for altering host carbon allocation including transgenic, selective breeding, crop rotation, and nutrient management practices as a promising avenue for enhancing rice blast resistance. This study advances our knowledge of the interaction between plants' carbon allocation and M. oryzae resistance and provides stakeholders and farmers with practical guidance on mitigating the adverse effects of the rice blast globally. This information may be used in the future to create varieties that are resistant to M. oryzae.

Induced resistance to herbivory and the intelligent plant

Plant induced responses to environmental stressors are increasingly studied in a behavioral ecology context. This is particularly true for plant induced responses to herbivory that mediate direct and indirect defenses, and tolerance. These seemingly adaptive alterations of plant defense phenotypes in the context of other environmental conditions have led to the discussion of such responses as intelligent behavior. Here we consider the concept of plant intelligence and some of its predictions for chemical information transfer in plant interaction with other organisms. Within this framework, the flow, perception, integration, and storage of environmental information are considered tunable dials that allow plants to respond adaptively to attacking herbivores while integrating past experiences and environmental cues that are predictive of future conditions. The predictive value of environmental information and the costs of acting on false information are important drivers of the evolution of plant responses to herbivory. We identify integrative priming of defense responses as a mechanism that allows plants to mitigate potential costs associated with acting on false information. The priming mechanisms provide short- and long-term memory that facilitates the integration of environmental cues without imposing significant costs. Finally, we discuss the ecological and evolutionary prediction of the plant intelligence hypothesis.

Vegetal memory through the lens of transcriptomic changes - recent progress and future practical prospects for exploiting plant transcriptional memory

Plant memory plays an important role in the efficient and rapid acclimation to a swiftly changing environment. In addition, since plant memory can be inherited, it is also of adaptive and evolutionary importance. The ability of a plant to store, retain, retrieve and delete information on acquired experience is based on cellular, biochemical and molecular networks in the plants. This review offers an up-to-date overview on the formation, types, checkpoints of plant memory based on our current knowledge and focusing on its transcriptional aspects, the transcriptional memory. Roles of long and small non-coding RNAs are summarized in the regulation, formation and the cooperation between the different layers of the plant memory, i.e. in the establishment of epigenetic changes associated with memory formation in plants. The RNA interference mechanisms at the RNA and DNA level and the interplays between them are also presented. Furthermore, this review gives an insight of how exploitation of plant transcriptional memory may provide new opportunities for elaborating promising cost-efficient, and effective strategies to cope with the ever-changing environmental perturbations, caused by climate change. The potentials of plant memory-based methods, such as crop priming, cross acclimatization, memory modification by miRNAs and associative use of plant memory, in the future's agriculture are also discussed.

Robotic mechanical wounding is sufficient to induce phenylacetaldoxime accumulation in Tococa quadrialata

This study investigated the accumulation of phenlyacetaldoxime (PAOx) and PAOx-Glc in Tococa quadrialata leaves in response to herbivore infestation and mechanical wounding. Results show that PAOx levels peaked at 24 h post-infestation, while PAOx-Glc remained present for several days. The accumulation of PAOx began as early as 3 h after herbivory, with PAOx-Glc significantly increased after 6 h. Mechanical wounding induced similar responses in PAOx and PAOx-Glc accumulation as herbivory, suggesting that continuous tissue damage triggers the production of these compounds. Interestingly, SpitWorm-treated leaves showed the highest levels of both PAOx and PAOx-Glc, indicating that herbivore-derived oral secretions (OS) play a role in the induction of these compounds. Additionally, JA-independent PAOx production was found to be associated with tissue damage rather than specific known signaling compounds. Emission of benzyl cyanide and 2-phenylethanol, PAOx-derived plant volatiles, was observed in response to herbivory and SpitWorm treatment providing plant-derived OS, further highlighting the role of herbivore cues in plant defense responses.

A library of electrophysiological responses in plants - a model of transversal education and open science

Electrophysiology in plants is understudied, and, moreover, an ideal model for student inclusion at all levels of education. Here, we report on an investigation in open science, whereby scientists worked with high school students, faculty, and undergraduates from Chile, Germany, Serbia, South Korea, and the USA. The students recorded the electrophysiological signals of >15 plant species in response to a flame or tactile stimulus applied to the leaves. We observed that approximately 60% of the plants studied showed an electrophysiological response, with a delay of ~ 3-6 s after stimulus presentation. In preliminary conduction velocity experiments, we verified that observed signals are indeed biological in origin, with information transmission speeds of ~ 2-9 mm/s. Such easily replicable experiments can serve to include more investigators and students in contributing to our understanding of plant electrophysiology.

Nitric oxide and cytokinin cross-talk and their role in plant hypoxia response

Nitric oxide (NO) and cytokinins (CKs) are known for their crucial contributions to plant development, growth, senescence, and stress response. Despite the importance of both signals in stress responses, their interaction remains largely unexplored. The interplay between NO and CKs emerges as particularly significant not only regarding plant growth and development but also in addressing plant stress response, particularly in the context of extreme weather events leading to yield loss. In this review, we summarize NO and CKs metabolism and signaling. Additionally, we emphasize the crosstalk between NO and CKs, underscoring its potential impact on stress response, with a focus on hypoxia tolerance. Finally, we address the most urgent questions that demand answers and offer recommendations for future research endeavors.

Advances in understanding the interaction between Solanaceae NLR resistance proteins and the viral effector Avr

The rising prevalence of viral-induced diseases, particularly those caused by certain strains, poses a substantial risk to the genetic diversity of Solanaceae crops and the overall safety of horticultural produce. According to the "gene-for-gene" hypothesis, resistance proteins are capable of selectively identifying nontoxic effectors produced by pathogens, as they are under purview of the host's immune defenses. The sensitivity and responsiveness of Solanaceae plants to viral attacks play a crucial role in shaping the outcomes of their interactions with viruses. Pathogenic organisms, devise an array of infection tactics aimed at circumventing or neutralizing the host's immune defenses to facilitate effective invasion. The invasion often accomplishes by suppressing or disrupting the host's defensive mechanisms or immune signals, which are integral to the infection strategies of such invading pathogens. This comprehensive review delves into the myriad approaches that pathogenic viruses employ to infiltrate and overcome the sophisticated immune system of tomatoes. Furthermore, the review explores the possibility of utilizing these viral strategies to bolster the resilience of horticultural crops, presenting a hopeful direction for forthcoming progress in plant health and agricultural stability.

Cloning and functional validation of DsWRKY6 gene from Desmodium styracifolium

The purpose of this study was to analyze the role of transcription factor in Desmodium styracifolium, proving that the DsWRKY6 transcription factor was related to the plant phenotypes of Desmodium styracifolium - cv. 'GuangYaoDa1' and it could be used in molecular-assisted breeding. 'GuangYaoDa1' was used as the material and its DNA was the template to clone DsWRKY6, the transgenic Arabidopsis thaliana line was constructed by agrobacterium tumefaciens‑mediated transformation. Transgenic Arabidopsis thaliana was cultivated to study phenotype and physiological and biochemical indexes. Phenotypic observation showed that DsWRKY6 transgenic Arabidopsis thaliana had a faster growth rate while compared with the control group, they had longer lengths of main stem, lateral branches of cauline leaves, and root, but a lower number of cauline leaves and lateral branches of cauline leaves. And it also showed that their flowering and fruiting periods were advanced. The results of physiological and biochemical indexes showed that the relative expressions of DsWRKY6 increased and the abscisic acid content significantly increased in DsWRKY6 transgenic Arabidopsis thaliana compared with the control group. According to the above results, DsWRKY6 could regulate the advancing of flowering and fruiting periods caused by the improvement of abscisic acid content, and expression of the DsWRKY6 transcription factor might be the cause of the upright growth of 'GuangYaoDa1'.

A pharmacological approach to investigating effector translocation in rice-Magnaporthe oryzae interactions

Fungal pathogens deliver effector proteins into living plant cells to suppress plant immunity and control plant processes that are needed for infection. During plant infection, the devastating rice blast fungus, Magnaporthe oryzae, forms the specialized biotrophic interfacial complex (BIC), which is essential for effector translocation. Cytoplasmic effectors are first focally secreted into BICs, and subsequently packaged into dynamic membranous effector compartments (MECs), then translocated via clathrin-mediated endocytosis (CME) into the host cytoplasm. This study demonstrates that clathrin-heavy chain inhibitors endosidin-9 (ES9) and endosidin-9-17 (ES9-17) blocked the internalization of the fluorescently labeled effectors Bas1 and Pwl2 in rice cells, leading to swollen BICs lacking MECs. In contrast, ES9-17 treatment had no impact on the localization pattern of the apoplastic effector Bas4. This study provides further evidence that cytoplasmic effector translocation occurs by CME in BICs, suggesting a potential role for M. oryzae effectors in co-opting plant endocytosis.

Investigation of Arabidopsis root skototropism with different distance settings

Plants can activate protective and defense mechanisms under biotic and abiotic stresses. Their roots naturally grow in the soil, but when they encounter sunlight in the top-soil layers, they may move away from the light source to seek darkness. Here we investigate the skototropic behavior of roots, which promotes their fitness and survival. Glutamate-like receptors (GLRs) of plants play roles in sensing and responding to signals, but their role in root skototropism is not yet understood. Light-induced tropisms are known to be affected by auxin distribution, mainly determined by auxin efflux proteins (PIN proteins) at the root tip. However, the role of PIN proteins in root skototropism has not been investigated yet. To better understand root skototropism and its connection to the distance between roots and light, we established five distance settings between seedlings and darkness to investigate the variations in root bending tendencies. We compared differences in root skototropic behavior across different expression lines of Arabidopsis thaliana seedlings (atglr3.7 ko, AtGLR3.7 OE, and pin2 knockout) to comprehend their functions. Our research shows that as the distance between roots and darkness increases, the root's positive skototropism noticeably weakens. Our findings highlight the involvement of GLR3.7 and PIN2 in root skototropism.

Exploring the complex information processes underlying plant behavior

Newly discovered plant behaviors, linked to historical observations, contemporary technologies, and emerging knowledge of signaling mechanisms, argue that plants utilize complex information processing systems. Plants are goal-oriented in an evolutionary and physiological sense; they demonstrate agency and learning. While most studies on plant plasticity, learning, and memory deal with the responsiveness of individual plants to resource availability and biotic stresses, adaptive information is often perceived from and coordinated with neighboring plants, while competition occurs for limited resources. Based on existing knowledge, technologies, and sustainability principles, climate-smart agricultural practices are now being adopted to enhance crop resilience and productivity. A deeper understanding of the dynamics of plant behavior offers a rich palette of potential amelioration strategies for improving the productivity and health of natural and agricultural ecosystems.

syn-tasiRnas targeting the coat protein of potato virus Y confer antiviral resistance in Nicotiana benthamiana

Trans-acting small interfering RNAs (tasiRNAs) are 21-nt phased (phased siRNAs) resulting from successive DCL-catalyzed processing from the end of a double-stranded RNA substrate originating from the RDR of an AGO-catalyzed cleaved RNA at a micro RNA target site. Plant tasiRNAs have been synthesized to produce synthetic tasiRNAs (syn-tasiRNAs) targeting viral RNAs that confer viral resistance. In this study, we engineered syn-tasiRNAs to target potato virus Y (PVY) infection by replacing five native siRNAs of TAS1c with 210-bp fragments from the coat protein (CP) region of the PVY genome. The results showed that the transient expression of syn-tasiR-CPpvy2 in Nicotiana benthamiana (N. benthamiana) plants conferred antiviral resistance, supported by the absence of PVY infection symptoms and viral accumulation. This indicated that syn-tasiR-CPpvy2 successfully targeted and silenced the PVY CP gene, effectively inhibiting viral infection. syn-tasiR-CPpvy1 displayed attenuated symptoms and decreased viral accumulation in these plants However, severe symptoms of PVY infection and a similar amount of viral accumulation as the control were observed in plants expressing syn-tasiR-CPpvy3. syn-tasiR-CPpvy/pvx, which targets both PVY and potato virus X (PVX), was engineered using a single precursor. After the transient expression of syn-tasiR-CPpvy/pvx3 and syn-tasiR-CPpvy/pvx5 in N. benthamiana, the plants were resistant to both PVY and PVX. These results suggested that engineered syn-tasiRNAs could not only specifically induce antiviral resistance against one target virus but could also be designed for multi-targeted silencing of different viruses, thereby preventing complex virus infection in plants.

Identification of mitogen-activated protein kinases substrates in Arabidopsis using kinase client assay

Mitogen-activated protein kinase (MPK) cascades are essential signal transduction components that control a variety of cellular responses in all eukaryotes. MPKs convert extracellular stimuli into cellular responses by the phosphorylation of downstream substrates. Although MPK cascades are predicted to be very complex, only limited numbers of MPK substrates have been identified in plants. Here, we used the kinase client (KiC) assay to identify novel substrates of MPK3 and MPK6. Recombinant MPK3 or MPK6 were tested against a large synthetic peptide library representing in vivo phosphorylation sites, and phosphorylated peptides were identified by high-resolution tandem mass spectrometry. From this screen, we identified 23 and 21 putative client peptides of MPK3 and MPK6, respectively. To verify the phosphorylation of putative client peptides, we performed in vitro kinase assay with recombinant fusion proteins of isolated client peptides. We found that 13 and 9 recombinant proteins were phosphorylated by MPK3 and MPK6. Among them, 11 proteins were proven to be the novel substrates of two MPKs. This study suggests that the KiC assay is a useful method to identify new substrates of MPKs.

ShF5H1 overexpression increases syringyl lignin and improves saccharification in sugarcane leaves

The agricultural sugarcane residues, bagasse and straws, can be used for second-generation ethanol (2GE) production by the cellulose conversion into glucose (saccharification). However, the lignin content negatively impacts the saccharification process. This polymer is mainly composed of guaiacyl (G), hydroxyphenyl (H), and syringyl (S) units, the latter formed in the ferulate 5-hydroxylase (F5H) branch of the lignin biosynthesis pathway. We have generated transgenic lines overexpressing ShF5H1 under the control of the C4H (cinnamate 4-hydroxylase) rice promoter, which led to a significant increase of up to 160% in the S/G ratio and 63% in the saccharification efficiency in leaves. Nevertheless, the content of lignin was unchanged in this organ. In culms, neither the S/G ratio nor sucrose accumulation was altered, suggesting that ShF5H1 overexpression would not affect first-generation ethanol production. Interestingly, the bagasse showed a significantly higher fiber content. Our results indicate that the tissue-specific manipulation of the biosynthetic branch leading to S unit formation is industrially advantageous and has established a foundation for further studies aiming at refining lignin modifications. Thus, the ShF5H1 overexpression in sugarcane emerges as an efficient strategy to improve 2GE production from straw.

Effect of pH on growth and Cd accumulation in different rice varieties under hydroponics

Currently, applying lime to cadmium (Cd)-contaminated paddy fields to increase pH and reduce Cd availability is an effective method to control excessive Cd levels in rice grain. However, under hydroponic conditions, the impact of increased pH on Cd accumulation in different rice varieties remains unclear. This study employed three rice varieties (Yuzhenxiang, Shaoxiang 100, Xiangwanxian 12) with different Cd accumulation characteristics under different pH and long-term treatment with 1 μM CdCl2, to study the effect of pH on growth and Cd accumulation in different rice varieties. The result showed that as pH shifted from 5 to 8, the SPAD values, shoot dry weight, and plant height of the three rice varieties significantly decreased. The main root length, root volume, and root dry weight of Yuzhenxiang, and Shaoxiang100 significantly decreased. Conversely, the root architecture indicators of Xiangwanxian 12 did not change significantly. As for element accumulation, increasing the pH significantly increased the content of Mn in both the shoots and roots of all three varieties. Yuzhenxiang significantly reduced Cd content in both the shoots and roots of rice, while Shaoxiang100 significantly increased Cd content in both parts. Xiangwanxian 12 showed a significant increase in Cd content in the shoots but a decrease in the roots. In terms of subcellular distribution, Yuzhenxiang significantly reduced Cd concentrations in the cell wall and organelles of root cells, resulting in lower Cd concentrations in the root tissue. Conversely, Shaoxiang100 significantly increased Cd concentrations in the cell wall, organelles, and soluble fractions of root cells, leading to higher Cd concentrations in the root tissue. Xiangwanxian 12 also exhibited a decrease in Cd concentrations in the cell wall, organelles, and soluble fraction of root cells, resulting in lower Cd concentrations in the root tissue. Additionally, the expression of the OsNRAMP5 and OsHMA3 gene was significantly increased in Shaoxiang 100, while no significantly change in Yuzhenxiang and Xiangwanxian 12. These results provide important guidance on the impact of pH on Cd accumulation during the vegetative growth stage of different rice varieties.

Proteome-wide analysis reveals G protein-coupled receptor-like proteins in rice (Oryza sativa)

G protein-coupled receptors (GPCRs) constitute the largest family of transmembrane proteins in metazoans that mediate the regulation of various physiological responses to discrete ligands through heterotrimeric G protein subunits. The existence of GPCRs in plant is contentious, but their comparable crucial role in various signaling pathways necessitates the identification of novel remote GPCR-like proteins that essentially interact with the plant G protein α subunit and facilitate the transduction of various stimuli. In this study, we identified three putative GPCR-like proteins (OsGPCRLPs) (LOC_Os06g09930.1, LOC_Os04g36630.1, and LOC_Os01g54784.1) in the rice proteome using a stringent bioinformatics workflow. The identified OsGPCRLPs exhibited a canonical GPCR 'type I' 7TM topology, patterns, and biologically significant sites for membrane anchorage and desensitization. Cluster-based interactome mapping revealed that the identified proteins interact with the G protein α subunit which is a characteristic feature of GPCRs. Computational results showing the interaction of identified GPCR-like proteins with G protein α subunit and its further validation by the membrane yeast-two-hybrid assay strongly suggest the presence of GPCR-like 7TM proteins in the rice proteome. The absence of a regulator of G protein signaling (RGS) box in the C- terminal domain, and the presence of signature motifs of canonical GPCR in the identified OsGPCRLPs strongly suggest that the rice proteome contains GPCR-like proteins that might be involved in signal transduction.

Cold priming on pathogen susceptibility in the Arabidopsis eds1 mutant background requires a functional stromal Ascorbate Peroxidase

24 h cold exposure (4°C) is sufficient to reduce pathogen susceptibility in Arabidopsis thaliana against the virulent Pseudomonas syringae pv. tomato (Pst) strain even when the infection occurs five days later. This priming effect is independent of the immune regulator Enhanced Disease Susceptibility 1 (EDS1) and can be observed in the immune-compromised eds1-2 null mutant. In contrast, cold priming-reduced Pst susceptibility is strongly impaired in knock-out lines of the stromal and thylakoid ascorbate peroxidases (sAPX/tAPX) highlighting their relevance for abiotic stress-related increased immune resilience. Here, we extended our analysis by generating an eds1 sapx double mutant. eds1 sapx showed eds1-like resistance and susceptibility phenotypes against Pst strains containing the effectors avrRPM1 and avrRPS4. In comparison to eds1-2, susceptibility against the wildtype Pst strain was constitutively enhanced in eds1 sapx. Although a prior cold priming exposure resulted in reduced Pst titers in eds1-2, it did not alter Pst resistance in eds1 sapx. This demonstrates that the genetic sAPX requirement for cold priming of basal plant immunity applies also to an eds1 null mutant background.

Crosstalk among plant hormone regulates the root development

The plant root absorbs water and nutrients, anchors the plant in the soil, and promotes plant development. Root is developed from root apical meristem (RAM), which is formed during embryo stage and is maintained by dividing stem cells. Plant hormones have a predominant role in RAM maintenance. This review evaluates the functional crosstalk among three major hormones (auxin, cytokinin, and brassinolide) in RAM development in Arabidopsis, integrating a variety of experimental data into a regulatory network and revealing multiple layers of complexity in the crosstalk among these three hormones. We also discuss possible directions for future research on the roles of hormones in regulating RAM development and maintenance.

Views and perspectives on the indoleamines serotonin and melatonin in plants: past, present and future

In the decades since their discovery in plants in the mid-to-late 1900s, melatonin (N-acetyl-5-methoxytryptamine) and serotonin (5-methoxytryptamine) have been established as their own class of phytohormone and have become popular targets for examination and study as stress ameliorating compounds. The indoleamines play roles across the plant life cycle from reproduction to morphogenesis and plant environmental perception. There is growing interest in harnessing the power of these plant neurotransmitters in applied and agricultural settings, particularly as we face increasingly volatile climates for food production; however, there is still a lot to learn about the mechanisms of indoleamine action in plants. A recent explosion of interest in these compounds has led to exponential growth in the field of melatonin research in particular. This concept paper aims to summarize the current status of indoleamine research and highlight some emerging trends.

Investigating the mechanism of chloroplast singlet oxygen signaling in the Arabidopsis thaliana accelerated cell death 2 mutant

As sessile organisms, plants have evolved complex signaling mechanisms to sense stress and acclimate. This includes the use of reactive oxygen species (ROS) generated during dysfunctional photosynthesis to initiate signaling. One such ROS, singlet oxygen (1O2), can trigger retrograde signaling, chloroplast degradation, and programmed cell death. However, the signaling mechanisms are largely unknown. Several proteins (e.g. PUB4, OXI1, EX1) are proposed to play signaling roles across three Arabidopsis thaliana mutants that conditionally accumulate chloroplast 1O2 (fluorescent in blue light (flu), chlorina 1 (ch1), and plastid ferrochelatase 2 (fc2)). We previously demonstrated that these mutants reveal at least two chloroplast 1O2 signaling pathways (represented by flu and fc2/ch1). Here, we test if the 1O2-accumulating lesion mimic mutant, accelerated cell death 2 (acd2), also utilizes these pathways. The pub4-6 allele delayed lesion formation in acd2 and restored photosynthetic efficiency and biomass. Conversely, an oxi1 mutation had no measurable effect on these phenotypes. acd2 mutants were not sensitive to excess light (EL) stress, yet pub4-6 and oxi1 both conferred EL tolerance within the acd2 background, suggesting that EL-induced 1O2 signaling pathways are independent from spontaneous lesion formation. Thus, 1O2 signaling in acd2 may represent a third (partially overlapping) pathway to control cellular degradation.

Plant hormone profiling of scion and rootstock incision sites and intra- and inter-family graft junctions in Nicotiana benthamiana

Many previous studies have suggested that various plant hormones play essential roles in the grafting process. In this study, to understand the plant hormones that accumulate in the graft junctions, whether these are supplied from the scion or rootstock, and how these hormones play a role in the grafting process, we performed a hormonome analysis that accumulated in the incision site of the upper plants from the incision as "ungrafted scion" and lower plants from the incision as "ungrafted rootstock" in Nicotiana benthamiana. The results revealed that indole-3-acetic acid (IAA) and gibberellic acid (GA), which regulate cell division; abscisic acid (ABA) and jasmonic acid (JA), which regulate xylem formation; cytokinin (CK), which regulates callus formation, show different accumulation patterns in the incision sites of the ungrafted scion and rootstock. In addition, to try discussing the differences in the degree and speed of each event during the grafting process between intra- and inter-family grafting by determining the concentration and accumulation timing of plant hormones in the graft junctions, we performed hormonome analysis of graft junctions of intra-family grafted plants with N. benthamiana as scion and Solanum lycopersicum as rootstock (Nb/Sl) and inter-family grafted plants with N. benthamiana as scion and Arabidopsis thaliana as rootstock (Nb/At), using the ability of Nicotiana species to graft with many plant species. The results revealed that ABA and CK showed different accumulation timings; IAA, JA, and salicylic acid (SA) showed similar accumulation timings, while different accumulated concentrations in the graft junctions of Nb/Sl and Nb/At. This information is important for understanding the molecular mechanisms of plant hormones in the grafting process and the differences in molecular mechanisms between intra- and inter-family grafting.

Biotechnology executive order opens door for regulatory reform and social acceptance of genetically engineered microbes in agriculture

In the United States, regulatory review of genetically engineered microbes for agriculture falls under the Coordinated Framework for the Regulation of Biotechnology (CFRB). However, the lack of a centralized regulatory pathway and multiple oversight authorities can lead to uncertainty in regulatory review. Using three microbial-based technologies for agriculture as illustrative examples, this commentary identifies the weaknesses and challenges associated with the CFRB by assessing the current system and proposed changes to the system under a multi criteria decision analysis framework. In addition, it discusses opportunities for regulatory reform to improve clarity, efficiency, and public acceptance of genetically engineered microbes in agriculture under the CHIPS and Science Act and the 2022 Executive Order on the Bioeconomy.

Unveiling molecular mechanisms of pigment synthesis in gardenia (Gardenia jasminoides) fruits through integrative transcriptomics and metabolomics analysis

This study conducted a combined transcriptomics and metabolomics analysis in premature and mature developmental stages of Gardenia jasminoides Ellis fruits to identify the molecular mechanisms of pigment synthesis. The transcriptomics data produced high-quality clean data amounting to 46.98 gigabytes, exhibiting a mapping ratio of 86.36% to 91.43%. Transcriptomics analysis successfully identified about 3,914 differentially expressed genes which are associated with pivotal biological processes, including photosynthesis, chlorophyll, biosynthetic processes, and protein-chromophore linkage pathways. Functional diversity was clarified by the Clusters of Orthologous Groups (COG) classification, which focused mainly on pigment synthesis functions. Pathways analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) revealed critical pathways affecting pigment development. Metabolomics studies were carried out utilizing Ultra Performance Liquid Chromatography and mass spectrometry (UPLC-MS). About 480 metabolites were detected via metabolomics investigation, the majority of that were significantly involved in pigment synthesis. Cluster and pathway analyses revealed the importance of pathways such as plant secondary metabolite biosynthesis, biosynthesis of phenylpropanoids and plant hormone signal transduction in pigment synthesis. Current research advances our comprehension of the underlying mechanisms at the molecular level governing pigment synthesis in gardenia fruits, furnishing valuable insights for subsequent investigations.

Mapping taste and flavour traits to genetic markers in lettuce Lactuca sativa

Lettuce is the most highly consumed raw leafy vegetable crop eaten worldwide, making it nutritionally important in spite of its comparatively low nutrient density in relation to other vegetables. However, the perception of bitterness caused by high levels of sesquiterpenoid lactones and comparatively low levels of sweet tasting sugars limits palatability. To assess variation in nutritional and taste-related metabolites we assessed 104 members of a Lactuca sativa cv. Salinas x L. serriola (accession UC96US23) mapping population. Plants were grown in three distinct environments, and untargeted NMR and HPLC were used as a rapid chemotyping method, from which 63 unique Quantitative Trait Loci (QTL) were identified. We were able to identify putative regulatory candidate genes underlying the QTL for fructose on linkage group 9, which accounted for up to 36 % of our population variation, and which was stable across all three growing environments; and for 15-p-hydroxyyphenylacetyllactucin-8-sulfate on linkage group 5 which has previously been identified for its low bitterness, while retaining anti-herbivory field effects. We also identified a candidate gene for flavonoid 3',5'- hydroxylase underlying a polyphenol QTL on linkage group 5, and two further candidate genes in sugar biosynthesis on linkage groups 2 and 5. Collectively these candidate genes and their associated markers can inform a route for plant breeders to improve the palatability and nutritional value of lettuce in their breeding programmes.

Unveiling the nutritional spectrum: A comprehensive analysis of protein quality and antinutritional factors in three varieties of quinoa (Chenopodium quinoa Wild)

Quinoa (Chenopodium quinoa) is renowned for its high protein content and balanced amino acid profile. Despite promising protein characteristics, plant-based sources usually possess antinutritional factors (ANFs). This study aimed to analyze the nutritional and ANFs composition of three quinoa varieties (Black, Yellow, and Red), and assessed the protein quality. Among these varieties, Black quinoa showed the highest protein content (20.90 g/100 g) and total dietary fiber (TDF) (22.97 g/100 g). In contrast, Red quinoa exhibited the highest concentration of phenolic compounds (338.9 mg/100 g). The predominant ANFs identified included oxalates (ranging from 396.9 to 715.2 mg/100 g), saponins (83.27-96.82 g/100 g), and trypsin inhibitors (0.35-0.46 TUI/100 g). All three varieties showed similar in vitro protein digestibility (IVPD) (> 76.9 %), while Black quinoa exhibited the highest protein quality. In conclusion to ensure reduction of ANFs, processing methods are necessary in order to fully benefit from the high protein and nutritional value of quinoa.

Aluminum and UV-C light on seed germination and initial growth of white oats

Aluminum (Al) may be beneficial to crops, but in excess becomes detrimental to the germination and initial development of seedlings. The main determining indicators are the type of crop and exposure duration. The aim of this study was to examine the influence of Al and of UV-C light on the germination and initial growth of white oats. Seeds were sown on germitest paper in a solution of 100, 200, 300, 400, or 500 mg/L of aluminum chloride and kept in a germination chamber at 20°C for a 12-hr photoperiod. Germination and seedling growth parameters were determined after 5 and 10 days. The seeds were also exposed to two doses of UV-C (0.85 and 3.42 kJ m-2) under aluminum chloride stress (200 mg/L). Data demonstrated that treatment with aluminum chloride significantly decrease in germination at 200 mg/L and total seedling length at 100 mg/L. Exposure of seeds to UV-C light under excess Al (200 mg/L) did not show a significant effect on germination and growth compared to control (non-irradiated). Results indicated that exposure to high concentration of Al in the medium adversely altered germination and initial growth of white oat seedlings. Although UV-C light alone was not detrimental to the germination process, treatment with UV-C light also failed to mitigate the toxic effects of Al.

Glycogen metabolism and structure: A review

Glycogen is a glucose polymer that plays a crucial role in glucose homeostasis by functioning as a short-term energy storage reservoir in animals and bacteria. Abnormalities in its metabolism and structure can cause several problems, including diabetes, glycogen storage diseases (GSDs) and muscular disorders. Defects in the enzymes involved in glycogen synthesis or breakdown, resulting in either excessive accumulation or insufficient availability of glycogen in cells seem to account for the most common pathogenesis. This review discusses glycogen metabolism and structure, including molecular architecture, branching dynamics, and the role of associated components within the granules. The review also discusses GSD type XV and Lafora disease, illustrating the broader implications of aberrant glycogen metabolism and structure. These conditions also impart information on important regulatory mechanisms of glycogen, which hint at potential therapeutic targets. Knowledge gaps and potential future research directions are identified.

Green plastics: Direct production from grocery wastes to bioplastics and structural characterization by using synchrotron FTIR

Lignocellulosic bioplastics were produced using four different green wastes: hemp, parsley stem, pineapple leaves and walnut shell. Two different solutions were used to dissolve the green wastes: trifluoroacetic acid (TFA) and pure water. The changes in their natural structures and the solvent effect during the regeneration in biofilm formation were investigated by using Synchrotron FTIR Microspectroscopy (SR-µFTIR). The presence of cellulose, hemicellulose and lignin components in the water-based biofilms was confirmed. After dissolving in TFA, the spectra demonstrated some additional bands especially in the hemicellulose region. This is due to the hydrolysis of ester bonds and conversion to carboxylic acids. Principal component analysis showed grouping due to different solvents and polymer addition. Hemp-PVA (Polyvinyl Alcohol) composite biofilms were obtained by adding polyvinyl alcohol to the hemp solution to give extra strength to the hemp biofilms. It has been shown that water-based hemp-PVA biofilms do not cause any significant spectral changes, comparing with pure hemp and PVA spectra. However, after dissolving in TFA, unlike water-based biofilms, it appears that TFA molecules are retained by PVA through hydrogen bonds of TFA's carboxylic acid and hydroxyl groups and distinct spectral regions belong to TFA bands are clearly identified.

Research on terahertz image analysis of thin-shell seeds based on semantic segmentation

Assessing crop seed phenotypic traits is essential for breeding innovations and germplasm enhancement. However, the tough outer layers of thin-shelled seeds present significant challenges for traditional methods aimed at the rapid assessment of their internal structures and quality attributes. This study explores the potential of combining terahertz (THz) time-domain spectroscopy and imaging with semantic segmentation models for the rapid and non-destructive examination of these traits. A total of 120 watermelon seed samples from three distinct varieties, were curated in this study, facilitating a comprehensive analysis of both their outer layers and inner kernels. Utilizing a transmission imaging modality, THz spectral images were acquired and subsequently reconstructed employing a correlation coefficient method. Deep learning-based SegNet and DeepLab V3+ models were employed for automatic tissue segmentation. Our research revealed that DeepLab V3+ significantly surpassed SegNet in both speed and accuracy. Specifically, DeepLab V3+ achieved a pixel accuracy of 96.69 % and an intersection over the union of 91.3 % for the outer layer, with the inner kernel results closely following. These results underscore the proficiency of DeepLab V3+ in distinguishing between the seed coat and kernel, thereby furnishing precise phenotypic trait analyses for seeds with thin shells. Moreover, this study accentuates the instrumental role of deep learning technologies in advancing agricultural research and practices.

Understanding starch biosynthesis in potatoes for metabolic engineering to improve starch quality: A detailed review

Potato tubers accumulate substantial quantities of starch, which serves as their primary energy reserve. As the predominant component of potato tubers, starch strongly influences tuber yield, processing quality, and nutritional attributes. Potato starch is distinguished from other food starches by its unique granule morphology and compositional attributes. It possesses large, oval granules with amylose content ranging from 20 to 33 % and high phosphorus levels, which collectively determine the unique physicochemical characteristics. These physicochemical properties direct the utility of potato starch across diverse food and industrial applications. This review synthesizes current knowledge on the molecular factors controlling potato starch biosynthesis and structure-function relationships. Key topics covered are starch granule morphology, the roles and regulation of major biosynthetic enzymes, transcriptional and hormonal control, genetic engineering strategies, and opportunities to tailor starch functionality. Elucidating the contributions of different enzymes in starch biosynthesis has enabled targeted modification of potato starch composition and properties. However, realizing the full potential of this knowledge faces challenges in optimizing starch quality without compromising plant vigor and yield. Overall, integrating multi-omics datasets with advanced genetic and metabolic engineering tools can facilitate the development of elite cultivars with enhanced starch yield and tailored functionalities.

Regulation of sucrose metabolism, sugar transport and pentose phosphate pathway by PacC in apple fruit colonized by Penicillium expansum

A critical transcription factor, PacC, modulates the expression of fungal pH signaling. Although PacC-mediated environmental pH has been reported to regulate the growth and pathogenicity of postharvest pathogens, the involvement of PacC in sucrose metabolism, sugar transport, and the pentose phosphate pathway (PPP) in different zones of decayed fruit remains unclear. Our work showed that the inoculation with a PePacC deletion strain of Penicillium expansum (ΔPePacC) accelerated sucrose catabolism and glucose and fructose accumulation in different zones of apple fruit. This was attributed to an increase in sucrose metabolism enzyme activities and up-regulation of the sugar transporter protein-related gene expression. Moreover, ΔPePacC inoculation increased the PPP-related enzyme activities and the levels of nicotinamide adenine dinucleotide phosphate (NADPH) and NADP+. In conclusion, PacC modulates sucrose metabolism, sugar transport, and the PPP in apple fruit by mediating dynamic changes in environmental pH, thereby enhancing fruit disease resistance.

Regulation of a novel DsGATA1 from Dunaliella salina on the synthesis of carotenoids under red light

Dunaliella salina is a high-quality industrial effector for carotenoid production. The mechanism by which red light regulates carotenoid synthesis is still unclear. In this study, a transcription factor of DsGATA1 with a distinct structure was discovered in D. salina. The recognition motif of DsGATA1 was comparable to that of plant and fungal GATA, despite its evolutionary proximity to animal-derived GATA. The expression of DsGATA1 in D. salina was still noticeably decreased when exposed to red light. Analysis of physiological and biochemical transcriptomic data from overexpressed, interfering, and wild-type strains of DsGATA1 revealed that DsGATA1 acts as a global regulator of D. salina carotenoid synthesis. The upregulated genes in the CBP pathway by DsGATA1 were involved in its regulation of the synthesis of carotenoids. DsGATA1 also enhanced carotenoid accumulation under red light by affecting N metabolism. DsGATA1 was found to directly bind to the promoter of nitrate reductase to activate its expression, promoting D. salina nitrate uptake and accelerating biomass accumulation. DsGATA1 affected the expression of the genes encoding GOGAT, GDH, and ammonia transporter proteins. Moreover, our study revealed that the regulation of N metabolism by DsGATA1 led to the production of NO molecules that inhibited carotenoid synthesis. However, DsGATA1 significantly enhanced carotenoid synthesis by NO scavenger removal of NO. The D. salina carotenoid accumulation under red light was elevated by 46% in the presence of overexpression of DsGATA1 and NO scavenger. Nevertheless, our results indicated that DsGATA1 could be an important target for engineering carotenoid production. KEY POINTS: • DsGATA1 with a distinct structure and recognition motif was found in D. salina • DsGATA1 enhanced carotenoid production and biomass in D. salina under red light • DsGATA1 is involved in the regulation of N metabolism and carotenoid synthesis.

Angelica keiskei water extract Mitigates Age-Associated Physiological Decline in Mice

OBJECTIVE

Angelica keiskei is a medicinal and edible plant that has been reported to possess potent antioxidant properties in several in vitro models, but its effectiveness on naturally aging organisms is still lacking. This study explores the antioxidant and health-promoting effects of Angelica keiskei in naturally aging mice.

METHODS

We treated 48-week-old mice with Angelica keiskei water extract (AKWE) 30 days, and measured indicators related to aging and antioxidants. In addition, we conducted network pharmacology analysis, component-target molecular docking, real-time PCR, and MTS assays to investigate relevant factors.

RESULTS

The results indicated that administration of AKWE to mice led to decrease blood glucose levels, improve muscle fiber structure, muscle strength, gait stability, and increase levels of glutathione and superoxide dismutase in serum. Additionally, it decreased pigmentation of the heart tissues. Angelica keiskei combats oxidative stress by regulating multiple redox signaling pathways, and its ingredients Coumarin and Flavonoids have the potential to bind to SIRT3 and SIRT5.

CONCLUSIONS

Our findings indicated the potential of Angelica keiskei as a safe and effective dietary supplement to combat aging and revealed the broad prospects of medicinal and edible plants for addressing aging and age-related chronic diseases.

Heterochromatin in plant meiosis

Heterochromatin is an organizational property of eukaryotic chromosomes, characterized by extensive DNA and histone modifications, that is associated with the silencing of transposable elements and repetitive sequences. Maintaining heterochromatin is crucial for ensuring genomic integrity and stability during the cell cycle. During meiosis, heterochromatin is important for homologous chromosome synapsis, recombination, and segregation, but our understanding of meiotic heterochromatin formation and condensation is limited. In this review, we focus on the dynamics and features of heterochromatin and how it condenses during meiosis in plants. We also discuss how meiotic heterochromatin influences the interaction and recombination of homologous chromosomes during prophase I.

Enhanced growth and metabolite production from a novel strain of Porphyridium sp

Microalgae are capable of generating numerous metabolites that possess notable biological activities and hold substantial promise for various industrial applications. Nevertheless, the taxonomic diversity of these photosynthetic microorganisms has not received thorough investigation. Using the 18S rRNA encoding gene, a recently discovered strain originating from the Tunisian coast (the governorate of Mahdia) was identified as a member of the Porphyridium genus. The growth response as well as the metabolite accumulation of Porphyridium sp. to different culture media (Pm, F/2, and Hemerick) was investigated over a period of 52 days. The highest biomass production was recorded with Pm medium (2 × 107 cell/mL). The apparent growth rates (µ) and the doubling time (Dt) were about 0.081 day-1 and 12.34 days, respectively. The highest chlorophyll a (0.678 ± 0.005 pg/cell), total carotenoids (0.18 ± 0.003 pg/cell), phycoerythrin (3.88 ± 0.003 pg/cell), and proteins (14.58 ± 0.35 pg/cell) contents were observed with F/2 medium. Cultivating Porphyridium sp. in both F/2 and Hemerick media yielded similar levels of starch accumulation. The Hemerick medium has proven to be the most suitable for the production of lipids (2.23% DW) and exopolysaccharides (5.41 ± 0.56 pg/cell).

The impact of Cas9-mediated mutagenesis of genes encoding potato starch-branching enzymes on starch structural properties and in vitro digestibility

The digestibility of starch is affected by amylose content, and increasing amylopectin chain length which can be manipulated by alterations to genes encoding starch-branching enzymes (SBEs). We investigated the impact of Cas9-mediated mutagenesis of SBEs in potato on starch structural properties and digestibility. Four potato starches with edited SBE genes were tested. One lacked SBE1 and SBE2, two lacked SBE2 and had reduced SBE1, and one had reduced SBE2 only. Starch structure and thermal properties were characterised by DSC and XRD. The impact of different thermal treatments on digestibility was studied using an in vitro digestion protocol. All native potato starches were resistant to digestion, and all gelatinised starches were highly digestible. SBE modified starches had higher gelatinisation temperatures than wild type potatoes and retrograded more rapidly. Gelatinisation and 18 h of retrogradation, increased gelatinisation enthalpy, but this did not translate to differences in digestion. Following 7 days of retrogradation, starch from three modified SBE starch lines was less digestible than starch from wild-type potatoes, likely due to the recrystallisation of the long amylopectin chains. Our results indicate that reductions in SBE in potato may be beneficial to health by increasing the amount of fibre reaching the colon after retrogradation.

Citric acid treatment inhibits fading of sorghum (Sorghum bicolor) by modulating the accumulation of flavonoids

Sorghum seeds can discolor during storage. Treatment of seeds with citric acid improves sensory quality and antioxidant activity. This study compared the differences in phenotypic and antioxidant activity between citric acid-treated and water-treated sorghum seeds. The study used transcriptomics and metabolomics approaches to investigate the regulatory mechanisms. The ∆a, ∆b and ∆l values of citric acid-treated sorghum seeds significantly increased after 6 months of storage. The SOD, POD and CAT enzyme activities of the citric acid-treated group were 1.94, 1.91 and 2.45 times higher than those of the control, respectively. The joint transcriptome and metabolome analysis showed that the citric acid-induced changes were mainly focused on the flavonoid biosynthetic pathway. Citric acid treatment up-regulated CHS, ANR, MYB and bHLH genes and promoted flavonoid accumulation. In conclusion, citric acid treatment promotes flavonoid accumulation, delays sorghum seed discoloration, and enhances antioxidant activity and storage life.

Advances of traditional Chinese medicine preclinical mechanisms and clinical studies on diabetic peripheral neuropathy

CONTEXT

Diabetic peripheral neuropathy (DPN) results in an enormous burden and reduces the quality of life for patients. Considering there is no specific drug for the management of DPN, traditional Chinese medicine (TCM) has increasingly drawn attention of clinicians and researchers around the world due to its characteristics of multiple targets, active components, and exemplary safety.

OBJECTIVE

To summarize the current status of TCM in the treatment of DPN and provide directions for novel drug development, the clinical effects and potential mechanisms of TCM used in treating DPN were comprehensively reviewed.

METHODS

Existing evidence on TCM interventions for DPN was screened from databases such as PubMed, the Cochrane Neuromuscular Disease Group Specialized Register (CENTRAL), and the Chinese National Knowledge Infrastructure Database (CNKI). The focus was on summarizing and analyzing representative preclinical and clinical TCM studies published before 2023.

RESULTS

This review identified the ameliorative effects of about 22 single herbal extracts, more than 30 herbal compound prescriptions, and four Chinese patent medicines on DPN in preclinical and clinical research. The latest advances in the mechanism highlight that TCM exerts its beneficial effects on DPN by inhibiting inflammation, oxidative stress and apoptosis, endoplasmic reticulum stress and improving mitochondrial function.

CONCLUSIONS

TCM has shown the power latent capacity in treating DPN. It is proposed that more large-scale and multi-center randomized controlled clinical trials and fundamental experiments should be conducted to further verify these findings.

GhLCYε-3 characterized as a lycopene cyclase gene responding to drought stress in cotton

Drought stress significantly affects crop productivity. Carotenoids are essential photosynthetic pigment for plants, bacteria, and algae, with signaling and antioxidant functions. Lutein is a crucial branch product in the carotenoid synthesis pathway, which effectively improves the stress tolerance of higher plants. lycopene cyclase, a central enzyme for lutein synthesis, holds great significance in regulating lutein production. This research establishes a correlation between lutein content and stress resistance by measuring the drought resistance and lutein content of various cotton materials. To identify which crucial genes are associated with lutein, the lycopene cyclase family (LCYs) was analyzed. The research found that LCYs form a highly conserved family divided into two subfamilies, LCY-ε (lycopene ε-cyclase) and LCY-β (lycopene β-cyclase). Most members of the LCY family contain photoresponsive elements and abscisic acid elements. qRT-PCR demonstrates showed that most genes responded positively to drought stress, and GhLCYε-3 was expressed significantly differently under drought stress. Virus-induced gene silencing (VIGS) assay showed that the content of GhLCYε-3 was significantly increased with MDA and PRO, and the contents of chlorophyll and lutein were significantly decreased in pYL156 plants. The decrease in GhLCYε-3 expression is speculated to lead to reduced lutein content in vivo, resulting in the accumulation of reactive oxygen species (ROS) and decreased drought tolerance. This research enriched the understanding of LCY gene family and lutein function, and provided a new reference for cotton planting in arid areas.

Synopsis

Lycopene cyclase plays an important role in enhancing the ability of scavenging ROS and drought resistance of plants.

Embryonic exposure to flubendiamide induces hepatotoxicity in domestic chicks by altering drug-metabolizing enzymes, antioxidant status, and liver function

Pesticides have increased crop yield but severely impacted ecosystems and non-target organisms. Flubendiamide, a new generation pesticide, targets insect larvae but also affects non-target organisms. This study examines the effects of lowest observed effect concentration of technical grade flubendiamide (0.5 µg/µL) flubendiamide on chick liver, focusing on cytochrome P450 (CYP) enzyme expression, oxidative stress, and liver damage. Chick embryos treated with flubendiamide showed significant alterations in CYP mRNA and protein levels, indicating increased toxicant accumulation. Elevated CYP3A4, CYP1A1, CYP1A2, and CYP2C19 levels were noted, suggesting enhanced biotransformation and detoxification processes. However, increased oxidative byproducts led to oxidative stress, as evidenced by decreased glutathione (GSH) levels and elevated superoxide dismutase (SOD) and catalase activities. DCFDA staining confirmed increased hydrogen peroxide (H2O2) levels, indicating heightened reactive oxygen species (ROS). Liver function tests revealed significant increases in serum ALP, ALT, and AST levels, indicating acute liver damage. Histopathological analysis showed structural liver damage, including expanded sinusoidal spaces, impaired portal veins, and compromised hepatocyte architecture. These findings underscore flubendiamide's potential hepatotoxicity in non-target organisms, emphasizing the need for cautious pesticide use to minimize environmental impacts.

Enhanced quantification of chlorophyll a and its degradation products in olive oil using time-resolved laser-induced fluorescence fingerprint analysis

Potential errors in the fluorescence analysis of chlorophylls and their degradation products, primarily due to spectral overlap and inner filter, are widely acknowledged. This study aimed to devise a sensitivity-enhanced technique for the concurrent quantification of chlorophyll a and its degradation products while minimizing effects from type-B chlorophylls. Initially, a time-resolved laser-induced fluorescence spectroscopic system was designed and tested on stardard chlorophyll samples. The origins, implications, and mitigation strategies of spectral overlap and the inner filter effect on the measured fluorescence intensity were thoroughly examined. Then, this methodology was proved to be efficacious within complex liquid matrices derived from olive oil. The experimental outcomes not only shed additional light on the mechanisms of chlorophyll fluorescence overlap and the inner filter effect, but also establish a general framework for developing spectrally and timely resolved fluorescence fingerprint analysis for the simultaneous quantification of chlorophylls and their degradation products at high concentrations.

Exploration of a multifunctional biocontrol agent Streptomyces sp. JCK-8055 for the management of apple fire blight

Apple fire blight, caused by the bacterium Erwinia amylovora, is a devastating disease of apple and pear trees. Biological control methods have attracted much attention from researchers to manage plant diseases as they are eco-friendly and viable alternatives to synthetic pesticides. Herein, we isolated Streptomyces sp. JCK-8055 from the root of pepper and investigated its mechanisms of action against E. amylovora. Streptomyces sp. JCK-8055 produced aureothricin and thiolutin, which antagonistically affect E. amylovora. JCK-8055 and its two active metabolites have a broad-spectrum in vitro activity against various phytopathogenic bacteria and fungi. They also effectively suppressed tomato bacterial wilt and apple fire blight in in vivo experiments. Interestingly, JCK-8055 colonizes roots as a tomato seed coating and induces apple leaf shedding at the abscission zone, ultimately halting the growth of pathogenic bacteria. Additionally, JCK-8055 can produce the plant growth regulation hormone indole-3-acetic acid (IAA) and hydrolytic enzymes, including protease, gelatinase, and cellulase. JCK-8055 treatment also triggered the expression of salicylate (SA) and jasmonate (JA) signaling pathway marker genes, such as PR1, PR2, and PR3. Overall, our findings demonstrate that Streptomyces sp. JCK-8055 can control a wide range of plant diseases, particularly apple fire blight, through a combination of mechanisms such as antibiosis and induced resistance, highlighting its excellent potential as a biocontrol agent. KEY POINTS: • JCK-8055 produces the systemic antimicrobial metabolites, aureothricin, and thiolutin. • JCK-8055 treatment upregulates PR gene expression in apple plants against E. amylovora. • JCK-8055 controls plant diseases with antibiotics and induced resistance.

Confronting the data deluge: How artificial intelligence can be used in the study of plant stress

The advent of the genomics era enabled the generation of high-throughput data and computational methods that serve as powerful hypothesis-generating tools to understand the genomic and gene functional basis of plant stress resilience. The proliferation of experimental and analytical methods used in biology has resulted in a situation where plentiful data exists, but the volume and heterogeneity of this data has made analysis a significant challenge. Current advanced deep-learning models have displayed an unprecedented level of comprehension and problem-solving ability, and have been used to predict gene structure, function and expression based on DNA or protein sequence, and prominently also their use in high-throughput phenomics in agriculture. However, the application of deep-learning models to understand gene regulatory and signalling behaviour is still in its infancy. We discuss in this review the availability of data resources and bioinformatic tools, and several applications of these advanced ML/AI models in the context of plant stress response, and demonstrate the use of a publicly available LLM (ChatGPT) to derive a knowledge graph of various experimental and computational methods used in the study of plant stress. We hope this will stimulate further interest in collaboration between computer scientists, computational biologists and plant scientists to distil the deluge of genomic, transcriptomic, proteomic, metabolomic and phenomic data into meaningful knowledge that can be used for the benefit of humanity.

Research progress on carotenoid production by Rhodosporidium toruloides

Carotenoids are natural lipophilic pigments, which have been proven to provide significant health benefits to humans, relying on their capacity to efficiently scavenge singlet oxygen and peroxyl radicals as antioxidants. Strains belonging to the genus Rhodosporidium represent a heterogeneous group known for a number of phenotypic traits including accumulation of carotenoids and lipids and tolerance to heavy metals and oxidative stress. As a representative of these yeasts, Rhodosporidium toruloides naturally produces carotenoids with high antioxidant activity and grows on a wide variety of carbon sources. As a result, R. toruloides is a promising host for the efficient production of more value-added lipophilic compound carotenoids, e.g., torulene and torularhodin. This review provides a comprehensive summary of the research progress on carotenoid biosynthesis in R. toruloides, focusing on the understanding of biosynthetic pathways and the regulation of key enzymes and genes involved in the process. Moreover, the relationship between the accumulation of carotenoids and lipid biosynthesis, as well as the stress from diverse abiotic factors, has also been discussed for the first time. Finally, several feasible strategies have been proposed to promote carotenoid production by R. toruloides. It is possible that R. toruloides may become a critical strain in the production of carotenoids or high-value terpenoids by genetic technologies and optimal fermentation processes. KEY POINTS: • Biosynthetic pathway and its regulation of carotenoids in Rhodosporidium toruloides were concluded • Stimulation of abiotic factors for carotenoid biosynthesis in R. toruloides was summarized • Feasible strategies for increasing carotenoid production by R. toruloides were proposed.