Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives

Plants contain a large number of cell types and exhibit complex regulatory mechanisms. Studies at the single-cell level have gradually become more common in plant science. Single-cell transcriptomics, spatial transcriptomics, and spatial metabolomics techniques have been combined to analyze plant development. These techniques have been used to study the transcriptomes and metabolomes of plant tissues at the single-cell level, enabling the systematic investigation of gene expression and metabolism in specific tissues and cell types during defined developmental stages. In this review, we present an overview of significant breakthroughs in spatial multi-omics in plants, and we discuss how these approaches may soon play essential roles in plant research.

Detection, regulation, and functions of RNA N6-methyladenosine modification in plants

N⁶-Methyladenosine (m⁶A) is the most abundant internal chemical modification in eukaryotic mRNA and plays important roles in gene expression regulation, including transcriptional and post-transcriptional regulation. m⁶A is a reversible modification that is installed, removed, and recognized by methyltransferases (writers), demethylases (erasers), and m⁶A-binding proteins (readers), respectively. Recently, the breadth of research on m⁶A in plants has expanded, and the vital roles of m⁶A in plant development, biotic and abiotic stress responses, and crop trait improvement have been investigated. In this review, we discuss recent developments in research on m⁶A and highlight the detection methods, distribution, regulatory proteins, and molecular and biological functions of m⁶A in plants. We also offer some perspectives on future investigations, providing direction for subsequent research on m⁶A in plants.

The Engagement of Cytochrome P450 Enzymes in Tryptophan Metabolism

Tryptophan is metabolized along three main metabolic pathways, namely the kynurenine, serotonin and indole pathways. The majority of tryptophan is transformed via the kynurenine pathway, catalyzed by tryptophan-2,3-dioxygenase or indoleamine-2,3-dioxygenase, leading to neuroprotective kynurenic acid or neurotoxic quinolinic acid. Serotonin synthesized by tryptophan hydroxylase, and aromatic L-amino acid decarboxylase enters the metabolic cycle: serotonin → N-acetylserotonin → melatonin → 5-methoxytryptamine→serotonin. Recent studies indicate that serotonin can also be synthesized by cytochrome P450 (CYP), via the CYP2D6-mediated 5-methoxytryptamine O-demethylation, while melatonin is catabolized by CYP1A2, CYP1A1 and CYP1B1 via aromatic 6-hydroxylation and by CYP2C19 and CYP1A2 via O-demethylation. In gut microbes, tryptophan is metabolized to indole and indole derivatives. Some of those metabolites act as activators or inhibitors of the aryl hydrocarbon receptor, thus regulating the expression of CYP1 family enzymes, xenobiotic metabolism and tumorigenesis. The indole formed in this way is further oxidized to indoxyl and indigoid pigments by CYP2A6, CYP2C19 and CYP2E1. The products of gut-microbial tryptophan metabolism can also inhibit the steroid-hormone-synthesizing CYP11A1. In plants, CYP79B2 and CYP79B3 were found to catalyze N-hydroxylation of tryptophan to form indole-3-acetaldoxime while CYP83B1 was reported to form indole-3-acetaldoxime N-oxide in the biosynthetic pathway of indole glucosinolates, considered to be defense compounds and intermediates in the biosynthesis of phytohormones. Thus, cytochrome P450 is engaged in the metabolism of tryptophan and its indole derivatives in humans, animals, plants and microbes, producing biologically active metabolites which exert positive or negative actions on living organisms. Some tryptophan-derived metabolites may influence cytochrome P450 expression, affecting cellular homeostasis and xenobiotic metabolism.

Characterization of synthetic antigen binding fragments targeting Toc75 for the isolation of TOC in A. thaliana and P. sativum

Roughly 95% of the proteins that make up the chloroplast must be imported from the cytoplasm. The machinery responsible for the translocation of these cargo proteins is called the translocon at the outer membrane of chloroplast (TOC). The TOC core consists of three proteins, Toc34, Toc75, and Toc159; no high-resolution structure has been solved of fully assembled TOC from plants. Efforts toward determining the structure of the TOC have been hindered almost entirely by difficulties in producing sufficient yields for structural studies. In this study, we introduce an innovative method that utilizes synthetic antigen binding fragments (sABs) to isolate TOC directly from wild-type plant biomass including A. thaliana and P. sativum. Binding between the sABs and the POTRA domains was characterized by size-exclusion chromatography coupled with small-angle X-ray scattering (SEC-SAXS), X-ray crystallography, and isothermal titration calorimetry. We also demonstrate the isolation of the TOC from P. sativum, laying the framework for large-scale isolation and purification of TOC for functional and structural studies.

Two Distinct Molecular Types of Phytochrome A in Plants: Evidence of Existence and Implications for Functioning

Phytochrome (phy) system in plants comprising a small number of phytochromes with phyA and phyB as major ones is responsible for acquiring light information in the red-far-red region of the solar spectrum. It provides optimal strategy for plant development under changing light conditions throughout all its life cycle beginning from seed germination and seedling establishment to fruiting and plant senescence. The phyA was shown to participate in the regulation of this cycle which is especially evident at its early stages. It mediates three modes of reactions-the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is the sole light receptor in the far-red spectral region responsible for plant's survival under a dense plant canopy where light is enriched with the far-red component. Its appearance is believed to be one of the main factors of plants' successful evolution. So far, it is widely accepted that one molecular phyA species is responsible for its complex functional manifestations. In this review, the evidence of the existence of two distinct phyA types-major, light-labile and soluble phyA' and minor, relatively light-stable and amphiphilic phyA″-is presented as what may account for the diverse modes of phyA action.

Cross-Kingdom Regulation of Plant-Derived miRNAs in Modulating Insect Development

MicroRNAs (miRNAs), a class of non-coding small RNAs, are crucial regulatory factors in plants and animals at the post-transcriptional level. These tiny molecules suppress gene expression by complementary oligonucleotide binding to sites in the target messenger. Recently, the discovery of plant-derived miRNAs with cross-kingdom abilities to regulate gene expression in insects has promoted exciting discussion, although some controversies exist regarding the modulation of insect development by plant-derived miRNAs. Here, we review current knowledge about the mechanisms of miRNA biogenesis, the roles of miRNAs in coevolution between insects and plants, the regulation of insect development by plant-derived miRNAs, the cross-kingdom transport mechanisms of plant-derived miRNAs, and cross-kingdom regulation. In addition, the controversy regarding the modulation of insect development by plant-derived miRNAs also was discussed. Our review provides new insights for understanding complex plant-insect interactions and discovering new strategies for pest management and even crop genetic improvement.

CircPCBL: Identification of Plant CircRNAs with a CNN-BiGRU-GLT Model

Circular RNAs (circRNAs), which are produced post-splicing of pre-mRNAs, are strongly linked to the emergence of several tumor types. The initial stage in conducting follow-up studies involves identifying circRNAs. Currently, animals are the primary target of most established circRNA recognition technologies. However, the sequence features of plant circRNAs differ from those of animal circRNAs, making it impossible to detect plant circRNAs. For example, there are non-GT/AG splicing signals at circRNA junction sites and few reverse complementary sequences and repetitive elements in the flanking intron sequences of plant circRNAs. In addition, there have been few studies on circRNAs in plants, and thus it is urgent to create a plant-specific method for identifying circRNAs. In this study, we propose CircPCBL, a deep-learning approach that only uses raw sequences to distinguish between circRNAs found in plants and other lncRNAs. CircPCBL comprises two separate detectors: a CNN-BiGRU detector and a GLT detector. The CNN-BiGRU detector takes in the one-hot encoding of the RNA sequence as the input, while the GLT detector uses k-mer (k = 1 - 4) features. The output matrices of the two submodels are then concatenated and ultimately pass through a fully connected layer to produce the final output. To verify the generalization performance of the model, we evaluated CircPCBL using several datasets, and the results revealed that it had an F1 of 85.40% on the validation dataset composed of six different plants species and 85.88%, 75.87%, and 86.83% on the three cross-species independent test sets composed of Cucumis sativus, Populus trichocarpa, and Gossypium raimondii, respectively. With an accuracy of 90.9% and 90%, respectively, CircPCBL successfully predicted ten of the eleven circRNAs of experimentally reported Poncirus trifoliata and nine of the ten lncRNAs of rice on the real set. CircPCBL could potentially contribute to the identification of circRNAs in plants. In addition, it is remarkable that CircPCBL also achieved an average accuracy of 94.08% on the human datasets, which is also an excellent result, implying its potential application in animal datasets. Ultimately, CircPCBL is available as a web server, from which the data and source code can also be downloaded free of charge.

Lipid Droplets from Plants and Microalgae: Characteristics, Extractions, and Applications

Plant and algal LDs are gaining popularity as a promising non-chemical technology for the production of lipids and oils. In general, these organelles are composed of a neutral lipid core surrounded by a phospholipid monolayer and various surface-associated proteins. Many studies have shown that LDs are involved in numerous biological processes such as lipid trafficking and signaling, membrane remodeling, and intercellular organelle communications. To fully exploit the potential of LDs for scientific research and commercial applications, it is important to develop suitable extraction processes that preserve their properties and functions. However, research on LD extraction strategies is limited. This review first describes recent progress in understanding the characteristics of LDs, and then systematically introduces LD extraction strategies. Finally, the potential functions and applications of LDs in various fields are discussed. Overall, this review provides valuable insights into the properties and functions of LDs, as well as potential approaches for their extraction and utilization. It is hoped that these findings will inspire further research and innovation in the field of LD-based technology.

A2TEA: Identifying trait-specific evolutionary adaptations

Background: Plants differ in their ability to cope with external stresses (e.g., drought tolerance). Genome duplications are an important mechanism to enable plant adaptation. This leads to characteristic footprints in the genome, such as protein family expansion. We explore genetic diversity and uncover evolutionary adaptation to stresses by exploiting genome comparisons between stress tolerant and sensitive species and RNA-Seq data sets from stress experiments. Expanded gene families that are stress-responsive based on differential expression analysis could hint at species or clade-specific adaptation, making these gene families exciting candidates for follow-up tolerance studies and crop improvement. Software: Integration of such cross-species omics data is a challenging task, requiring various steps of transformation and filtering. Ultimately, visualization is crucial for quality control and interpretation. To address this, we developed A2TEA: Automated Assessment of Trait-specific Evolutionary Adaptations, a Snakemake workflow for detecting adaptation footprints in silico. It functions as a one-stop processing pipeline, integrating protein family, phylogeny, expression, and protein function analyses. The pipeline is accompanied by an R Shiny web application that allows exploring, highlighting, and exporting the results interactively. This allows the user to formulate hypotheses regarding the genomic adaptations of one or a subset of the investigated species to a given stress. Conclusions: While our research focus is on crops, the pipeline is entirely independent of the underlying species and can be used with any set of species. We demonstrate pipeline efficiency on real-world datasets and discuss the implementation and limits of our analysis workflow as well as planned extensions to its current state. The A2TEA workflow and web application are publicly available at: https://github.com/tgstoecker/A2TEA.Workflow and https://github.com/tgstoecker/A2TEA.WebApp, respectively.

Phytochemistry and Biological Activities of Essential Oils from Six Aromatic Medicinal Plants with Cosmetic Properties

In this work, the chemical composition and antioxidant and antimicrobial activities of the essential oils (EOs) of six species-Laurus nobilis, Chamaemelum nobile, Citrus aurantium, Pistacia lentiscus, Cedrus atlantica, and Rosa damascena-have been studied. Phytochemical screening of these plants revealed the presence of primary metabolites, namely, lipids, proteins, reducing sugars, and polysaccharides, and also secondary metabolites such as tannins, flavonoids, and mucilages. The essential oils were extracted by hydrodistillation in a Clevenger-type apparatus. The yields are between 0.06 and 4.78% (mL/100 g). The analysis of the chemical composition carried out by GC-MS showed the presence of 30 to 35 compounds and represent between 99.97% and 100% of the total composition of EOs, with a variation in the chemical composition detected at the level of the majority compounds between these species. Indeed, in the EO of Laurus nobilis, 1,8-cineole (36.58%) is the major component. In Chamaemelum nobile EO, the most abundant compound is angelylangelate (41.79%). The EO of Citrus aurantium is rich in linalool (29.01%). The EO of Pistacia lentiscus is dominated by 3-methylpentylangelate (27.83%). The main compound of Cedrus atlantica is β-himachalene (40.19%), while the EO of Rosa damascenaa flowers is rich in n-nonadecane (44.89%). The analysis of the similarity between the EOs of the plants studied by ACH and ACP showed that the chemical composition of the EOs makes it possible to separate these plants into three groups: the first represented by Chamaemelum nobile, because it is rich in oxygenated monoterpenes, the second defined Cedrus atlantica and Rosa damascena, which are rich in sesquiterpenes, and the third gathers Pistacia lentiscus, Laurus nobilis and Citrus aurantium, which are composed of oxygenated sesquiterpenes and monoterpenes (these three species are very close). The study of the antioxidant activity showed that all the EOs tested have a high capacity for scavenging free radicals from DPPH. The EOs of Laurus nobilis and Pistacia lentiscus showed the highest activity, 76.84% and 71.53%, respectively, followed by Cedrus atlantica EO (62.38%) and Chamaemelum nobile (47.98%) then Citrus aurantium EO (14.70%). Antimicrobial activity EO was tested against eight bacterial strains and eight fungal strains; the results showed that EOs exhibit significant bactericidal and fungicidal activities against all the microorganisms tested, of which the MICs of the bacterial strains start with 5 mg/mL, while the MICs of the fungal strains are between 0.60 mg/mL and 5 mg/mL. Thus, these EOs rich in antimicrobial and antioxidant components can serve as a natural alternative; this confirms their use as additives in cosmetics.

Biodiversity mitigates trade-offs among species functional traits underpinning multiple ecosystem services

Biodiversity loss and its effects on humanity is of major global concern. While a growing body of literature confirms positive relationships between biodiversity and multiple ecological functions, the links between biodiversity, ecological functions and multiple ecosystem services is yet unclear. Studies of biodiversity-functionality relationships are mainly based on computer simulations or controlled field experiments using only few species. Here, we use a trait-based approach to integrate plant functions into an ecosystem service assessment to address impacts of restoration on species-rich grasslands over time. We found trade-offs among functions and services when analysing contributions from individual species. At the community level, these trade-offs disappeared for almost all services with time since restoration as an effect of increased species diversity and more evenly distributed species. Restoration to enhance biodiversity also in species-rich communities is therefore essential to secure higher functional redundancy towards disturbances and sustainable provision of multiple ecosystem services over time.

A comprehensive overview of genotoxicity and mutagenicity associated with outdoor air pollution exposure in Brazil

This review examined the mutagenicity and genotoxicity associated with exposure to outdoor air pollutants in Brazil. A search was performed on the Web of Science database using a combination of keywords that resulted in 134 articles. After applying exclusion criteria, a total of 75 articles were obtained. The articles were classified into three categories: (1) studies with plants and animals, (2) in vitro studies, and (3) human biomonitoring. The investigations were conducted in 11 of 27 Brazilian states with the highest prevalence in the southeast and south regions. Only 5 investigations focused on the effects of burning biomass on the quality of outdoor air. Plants, especially Tradescantia pallida, were the main air pollution biomonitoring tool. When available, a significant association between levels of air pollutants and genetic damage was described. Among the in vitro studies, Salmonella/microsome is the most used test to evaluate mutagenesis of outdoor air in Brazil (n = 26). Human biomonitoring studies were the least frequent category (n = 18). Most of the investigations utilized micronucleus bioassay, in oral mucosa cells (n = 15) and lymphocytes (n = 5), and the comet assay (n = 6). The analysis in this study points to the existence of gaps in genotoxicity studies and our findings indicate that future studies need to address the variety of potential sources of pollution existing in Brazil. In addition to extent of the impacts, consideration should be given to the enormous Brazilian biodiversity, as well as the determination of the role of socioeconomic inequality of the population in the observed outcomes.

Links to rare climates do not translate into distinct traits for island endemics

Current models of island biogeography treat endemic and non-endemic species as if they were functionally equivalent, focussing primarily on species richness. Thus, the functional composition of island biotas in relation to island biogeographical variables remains largely unknown. Using plant trait data (plant height, leaf area and flower length) for 895 native species in the Canary Islands, we related functional trait distinctiveness and climate rarity for endemic and non-endemic species and island ages. Endemics showed a link to climatically rare conditions that is consistent with island geological change through time. However, functional trait distinctiveness did not differ between endemics and non-endemics and remained constant with island age. Thus, there is no obvious link between trait distinctiveness and occupancy of rare climates, at least for the traits measured here, suggesting that treating endemic and non-endemic species as functionally equivalent in island biogeography is not fundamentally wrong.

Jordanian Use of and Beliefs Concerning the Efficacy of Medicinal Plants: A Cross-Sectional Study

Background: Medicinal herbs are incorrectly believed to be free of risks and are commonly used for self-medication without medical supervision. Jordan does not currently have a national policy on traditional medicine (TM) and/or complementary/alternative medicine (CAM). The present study aims to explore the use of and beliefs about the efficacy of medicinal plants among the Jordanian population. Method: A cross-sectional study was conducted using a self-administrated questionnaire for the duration between April and June 2019. Multiple linear regression analysis was used to identify predictors of positive attitudes towards the use of medicinal plants. Results: A total of 1,057 individuals participated in the study. The participants in our study showed a positive attitude towards the use of medicinal plants and herbs (median score of 33.0 (interquartile range (IQR): 26.0-37.0; equals 68.8% of the maximum total score), and believed in alternative therapies other than chemical drugs for disease treatment, mainly using medicinal herbs and plants. The majority of the participants (77.8% (n = 822)) believe in the efficacy of the use of medicinal herbs and plants and are aware (64.6 % (n = 683)) of the correct and proper way of using these plants and herbs. Pharmacists and herbalist are the main sources of information for the proper use of medicinal herbs and plants. Age was the main predictor of positive attitudes towards the use of medicinal plants and herbs (P<0.001). Conclusion: Efforts must be made to regulate the dispensing of these products, to educate health service providers and to raise consumer awareness.

Environmental toxicants and health adversities: A review on interventions of phytochemicals

Toxicity arising from environmental contaminants has attracted global interest in the last few decades, due to the high morbidity and mortality associated with them. Efforts have been made to combat the consequential outcomes of environmental toxicity in humans through traditional remediation techniques and therapeutic measures which have been hampered by one or more limitations. Consequently, this scenario has triggered interest in the medicinal properties of phytochemicals. Thus, this review gives a succinct and in-depth elucidation of the various environmental contaminants and their toxicity effects on humans. It delves into the various classes of phytochemicals and their intervention roles. The study adopted a desk review of existing literatures from scientific reports and peer reviewed articles through triangulation of data sources. "Phytochemicals" are group of secondary metabolites obtained from plants with medicinal properties. These groups of compounds are included but not limited to flavonoids, tannins, saponins, alkaloids, cardenoloids, terpenoids, and phytosteroids. This review corroborates the prophylactic and therapeutics efficacy of these phytochemicals as anti-metastatic, anti-inflammatory, anti-aging, anti-oxidant, anti-microbial and live saving substances with empirical findings from several laboratory, clinical trials and epidemiologic studies. It conclude that given the wide range of medicinal properties of phytochemicals, there is an urgent need for its full optimization in the pharmaceutical industry and future studies should focus on identifying the bioactive molecules in these compounds and its effectiveness against mixer toxicity.

Medicinal terpenoid UDP-glycosyltransferases in plants: recent advances and research strategies

Terpenoid glycosides have significant curative effects on many kinds of diseases. Most of these compounds are derived from medicinal plants. Glycosylation is a key step in the biosynthesis of medicinal terpenoids. In plants, UDP-dependent glycosyltransferases comprise a large family of enzymes that catalyze the transfer of sugars from donor to acceptor to form various bioactive glycosides. In recent years, numerous terpenoid UDP-glycosyltransferases (UGTs) have been cloned and characterized in medicinal plants. We review the typical characteristics and evolution of terpenoid-related UGTs in plants and summarize the advances and research strategies of terpenoid UGTs in medicinal plants over the past 20 years. We provide a reference for the study of glycosylation of terpenoid skeletons and the biosynthetic pathways for medicinal terpenoids in plants.

Electrochemical Characterization of the Antioxidant Properties of Medicinal Plants and Products: A Review

Medicinal plants are an important source of bioactive compounds with a wide spectrum of practically useful properties. Various types of antioxidants synthesized in plants are the reasons for their application in medicine, phytotherapy, and aromatherapy. Therefore, reliable, simple, cost-effective, eco-friendly, and rapid methods for the evaluation of antioxidant properties of medicinal plants and products on their basis are required. Electrochemical methods based on electron transfer reactions are promising tools to solve this problem. Total antioxidant parameters and individual antioxidant quantification can be achieved using suitable electrochemical techniques. The analytical capabilities of constant-current coulometry, potentiometry, various types of voltammetry, and chrono methods in the evaluation of total antioxidant parameters of medicinal plants and plant-derived products are presented. The advantages and limitations of methods in comparison to each other and traditional spectroscopic methods are discussed. The possibility to use electrochemical detection of the antioxidants via reactions with oxidants or radicals (N- and O-centered) in solution, with stable radicals immobilized on the electrode surface, via oxidation of antioxidants on a suitable electrode, allows the study of various mechanisms of antioxidant actions occurring in living systems. Attention is also paid to the individual or simultaneous electrochemical determination of antioxidants in medicinal plants using chemically modified electrodes.

Emerging trends in nitrogen and phosphorus signalling in photosynthetic eukaryotes

Phosphorus (P) and nitrogen (N) are the major nutrients that constrain plant and algal growth in nature. Recent advances in understanding nutrient signalling mechanisms of these organisms have revealed molecular attributes to optimise N and P acquisition. This has illuminated the importance of interplay between N and P regulatory networks, highlighting a need to study synergistic interactions rather than single-nutrient effects. Emerging insights of nutrient signalling in polyphyletic model plants and algae hint that, although core P-starvation signalling components are conserved, distinct mechanisms for P (and N) sensing have arisen. Here, the N and P signalling mechanisms of diverse photosynthetic eukaryotes are examined, drawing parallels and differences between taxa. Future directions to understand their molecular basis, evolution, and ecology are proposed.

Alternative Polyadenylation Is a Novel Strategy for the Regulation of Gene Expression in Response to Stresses in Plants

Precursor message RNA requires processing to generate mature RNA. Cleavage and polyadenylation at the 3'-end in the maturation of mRNA is one of key processing steps in eukaryotes. The polyadenylation (poly(A)) tail of mRNA is an essential feature that is required to mediate its nuclear export, stability, translation efficiency, and subcellular localization. Most genes have at least two mRNA isoforms via alternative splicing (AS) or alternative polyadenylation (APA), which increases the diversity of transcriptome and proteome. However, most previous studies have focused on the role of alternative splicing on the regulation of gene expression. In this review, we summarize the recent advances concerning APA in the regulation of gene expression and in response to stresses in plants. We also discuss the mechanisms for the regulation of APA for plants in the adaptation to stress responses, and suggest that APA is a novel strategy for the adaptation to environmental changes and response to stresses in plants.

Quantifying the Root-to-Shoot Transfer of 4,4'-Methylenedianiline Using Pressure Chamber and Intact Plant Methods

The high-production-volume chemical 4,4'-methylenedianiline (4,4'-MDA) is an aromatic amine used to manufacture 4,4'-methylenedianiline diisocyanate for polyurethane production. Based on 4,4'-MDA's octanol/water partition coefficient (K_OW ) and correlations with the transpiration stream concentration factor (TSCF), significant plant uptake and root-to-shoot transfer are predicted. However, most correlations between K_OW and TSCF were developed for neutral organics and may not be applicable for ionizable bases such as 4,4'-MDA. To investigate, TSCF values for 4,4'-MDA were measured using pressure chamber and intact plant approaches for tomato, soybean, and wheat (intact plants only). ¹⁴ C-labeled 4,4'-MDA was used to increase analytical sensitivity and facilitate measurement of distribution within plant tissues. The TSCF of ¹⁴ C-MDA determined using the pressure chamber method was 0.04 ± 0.00 for tomato and 0.17 ± 0.10 for soybean. These values were lower than predicted from log K_OW and within the range of values for ¹⁴ C-pyrene also measured in our study (0.14 ± 0.00 for tomato and 0.16 ± 0.09 for soybean). The TSCF values calculated from measurements made from intact plants grown to maturity were statistically equivalent to those obtained from the pressure chamber method for soybean and tomato. The distributions of ¹⁴ C within the three plants species were similar, with the roots > leaves ≈ stems > fruit. The log root concentration factors for 4,4'-MDA ranged from 3.68 to 4.33 for the three plant species. This finding indicates that the aromatic amine sorption to root materials is much greater than would be predicted based on its log K_OW and may be the reason for the limited root-to-shoot transfer observed in the pressure chamber and intact plant studies. Environ Toxicol Chem 2023;42:655-662. © 2023 SETAC.

Role of Cytochrome P450 Enzyme in Plant Microorganisms' Communication: A Focus on Grapevine

Cytochromes P450 are ancient enzymes diffused in organisms belonging to all kingdoms of life, including viruses, with the largest number of P450 genes found in plants. The functional characterization of cytochromes P450 has been extensively investigated in mammals, where these enzymes are involved in the metabolism of drugs and in the detoxification of pollutants and toxic chemicals. The aim of this work is to present an overview of the often disregarded role of the cytochrome P450 enzymes in mediating the interaction between plants and microorganisms. Quite recently, several research groups have started to investigate the role of P450 enzymes in the interactions between plants and (micro)organisms, focusing on the holobiont Vitis vinifera. Grapevines live in close association with large numbers of microorganisms and interact with each other, regulating several vine physiological functions, from biotic and abiotic stress tolerance to fruit quality at harvest.

Signaling pathways underlying nitrogen transport and metabolism in plants

Nitrogen (N) is an essential macronutrient required for plant growth and crop production. However, N in soil is usually insufficient for plant growth. Thus, chemical N fertilizer has been extensively used to increase crop production. Due to negative effects of N rich fertilizer on the environment, improving N usage has been a major issue in the field of plant science to achieve sustainable production of crops. For that reason, many efforts have been made to elucidate how plants regulate N uptake and utilization according to their surrounding habitat over the last 30 years. Here, we provide recent advances focusing on regulation of N uptake, allocation of N by N transporting system, and signaling pathway controlling N responses in plants. [BMB Reports 2023; 56(2): 56-64].

Impacts of Radio-Frequency Electromagnetic Field (RF-EMF) on Lettuce (Lactuca sativa)-Evidence for RF-EMF Interference with Plant Stress Responses

The increased use of wireless technology causes a significant exposure increase for all living organisms to radio frequency electromagnetic fields (RF-EMF). This comprises bacteria, animals, and also plants. Unfortunately, our understanding of how RF-EMF influences plants and plant physiology remains inadequate. In this study, we examined the effects of RF-EMF radiation on lettuce plants (Lactuca sativa) in both indoor and outdoor environments using the frequency ranges of 1890-1900 MHz (DECT) at 2.4 GHz and 5 GHz (Wi-Fi). Under greenhouse conditions, RF-EMF exposure had only a minor impact on fast chlorophyll fluorescence kinetics and no effect on plant flowering time. In contrast, lettuce plants exposed to RF-EMF in the field showed a significant and systemic decrease in photosynthetic efficiency and accelerated flowering time compared to the control groups. Gene expression analysis revealed significant down-regulation of two stress-related genes in RF-EMF-exposed plants: violaxanthin de-epoxidase (VDE) and zeaxanthin epoxidase (ZEP). RF-EMF-exposed plants had lower Photosystem II's maximal photochemical quantum yield (F_V/F_M) and non-photochemical quenching (NPQ) than control plants under light stress conditions. In summary, our results imply that RF-EMF might interfere with plant stress responses and reduced plant stress tolerance.

The use of medicinal plants in the prevention of COVID-19 using the Health Belief Model: A survey based on the Iranian population

BACKGROUND

Because of the spread of coronavirus disease 2019 (COVID-19), the preventive measures have increased, such as focusing on the use of medicinal plants in most communities, including Iran. The purpose of this study was to identify the knowledge, attitude, and performance of individuals toward the use of medicinal plants and to identify the predictors of the use of medicinal plants in the prevention of COVID-19.

MATERIALS AND METHODS

This descriptive-analytical study (February-April 2021) was performed on 3840 Iranian men and women aged 20-70 years selected as a multi-stage cluster study. At the first stage, all provinces were divided into five regions: North, South, East, West, and Center. In the second stage, a provincial center and a city were randomly selected from each region (North: Sari, Babol; South: Bushehr, Bandar Genaveh; East: Mashhad, Sabzevar; West: Hamedan, Toisarkan; Center: Yazd, Ardakan). Data were collected by a researcher-made scale based on the Health Belief Model (HBM). Data analysis was performed applying Pearson correlation coefficient, logistic regression, and linear regression.

RESULTS

The results showed that people have relatively high knowledge and positive attitude toward the use of medicinal plants in prevention of COVID-19. The most important reason for positive attitude was the perceived benefits with the mean of 75.06%. Also, half of the people had poor performance. Correlation coefficient showed that the use of medicinal plants with perceived sensitivity (p = 0.000, r = 0.3), perceived benefits (p = 0.012, r = 0.126), perceived barriers (p = 0.000, r = 0.179), and perceived self-efficacy (p = 0.000, r = 0.305) had a significant correlation. The strongest correlation between perceived self-efficacy was observed with the use of herbs in prevention of COVID-19. The HBM constructs can predict 26% of the variance for the use of medicinal plants in the prevention of COVID-19, among which perceived self-efficacy (β = 0.230) was the most powerful predictor.

CONCLUSION

Based on the results, the predictive role of self-efficacy constructs for the use of medicinal plants in prevention of COVID-19 has been confirmed according to the HBM. Therefore, methods of increasing self-efficacy such as training programs and providing appropriate intervention models can be used not only as promoters of using medicinal plants in prevention of COVID-19 but also for improving people's performance in the proper use of medicinal plants.

Myrtinols A-F: New Anti-Inflammatory Peltogynoid Flavonoid Derivatives from the Leaves of Australian Indigenous Plant Backhousia myrtifolia

Our in-house ethnopharmacological knowledge directed our anti-inflammatory investigation into the leaves of Backhousia mytifolia. Bioassay guided isolation of the Australian indigenous plant Backhousia myrtifolia led to the isolation of six new rare peltogynoid derivatives named myrtinols A-F (1-6) along with three known compounds 4-O-methylcedrusin (7), 7-O-methylcedrusin (8) and 8-demethylsideroxylin (9). The chemical structures of all the compounds were elucidated by detailed spectroscopic data analysis, and absolute configuration was established using X-ray crystallography analysis. All compounds were evaluated for their anti-inflammatory activity by assessing the inhibition of nitric oxide (NO) production and tumor necrosis factor- α (TNF-α) in lipopolysaccharide (LPS) and interferon (IFN)-γ activated RAW 264.7 macrophages. A structure activity relationship was also established between compounds (1-6), noting promising anti-inflammatory potential by compounds 5 and 9 with an IC₅₀ value of 8.51 ± 0.47 and 8.30 ± 0.96 µg/mL for NO inhibition and 17.21 ± 0.22 and 46.79 ± 5.87 µg/mL for TNF-α inhibition, respectively.

Recent Advances of Polyphenol Oxidases in Plants

Polyphenol oxidase (PPO) is present in most higher plants, but also in animals and fungi. PPO in plants had been summarized several years ago. However, recent advances in studies of PPO in plants are lacking. This review concludes new researches on PPO distribution, structure, molecular weights, optimal temperature, pH, and substrates. And, the transformation of PPO from latent to active state was also discussed. This state shift is a vital reason for elevating PPO activity, but the activation mechanism in plants has not been elucidated. PPO has an important role in plant stress resistance and physiological metabolism. However, the enzymatic browning reaction induced by PPO is a major problem in the production, processing, and storage of fruits and vegetables. Meanwhile, we summarized various new methods that had been invented to decrease enzymatic browning by inhibiting PPO activity. In addition, our manuscript included information on several important biological functions and the transcriptional regulation of PPO in plants. Furthermore, we also prospect some future research areas of PPO and hope they will be useful for future research in plants.

Ralstonia solanacearum - A soil borne hidden enemy of plants: Research development in management strategies, their action mechanism and challenges

Plant pathogens present in soil cause severe losses to plants every year. Among them, Ralstonia solanacearum, because of its destructive nature, is the world's second most damaging bacterial phytopathogen. Over 310 species of plants belonging to 42 plant families are infected by this deadly pathogen. Around the world, the bacterial wilt (BW) disease causes yield losses that range from 20 to 100%. Control measures for managing this pathogen comprises several diverse approaches. Regardless of whether several control methods are developed to manage the BW disease, efficient management strategies with eco-friendly effects and the desired level of effective control is still awaited and there is need to developed effective management methods to eliminate this fetal disease in several crops under field conditions. An analysis of development in the management strategies will provide an effective way to search and develop control methods with desirable level of effectiveness. In this review, we discussed and analyzed the information reported on the development of various management strategies for the management of R. solanacearum along with the comprehensive presentation on action mechanism of these management strategies. We have also made an effort to summarize the challenges that make hurdle in the effective management of this deadly pathogen. The analysis of the information in this review article will assist in future implications of management strategies and help in developing effective control measures with more efficacy.

A Review Concerning the Polysaccharides Found in Edible and Medicinal Plants in Xinjiang

Approximately 110 types of medicinal materials are listed in the Chinese Pharmacopoeia, both for medicinal purposes and for use as food. There are several domestic scholars who have carried out research on edible plant medicine in China and the results are satisfactory. Though these related articles have appeared in domestic magazines and journals, many of them are yet to be translated into English. Most of the research stays in the extraction and quantitative testing stage, and there are a few medicinal and edible plants that are still under in-depth study. A majority of these edible and herbal plants are also highly enriched in polysaccharides, and this has an effect on immune systems for the prevention of cancer, inflammation, and infection. Comparing the polysaccharide composition of medicinal and edible plants, the monosaccharide and polysaccharide species were identified. It is found that different polysaccharides of different sizes have different pharmacological properties, with some polysaccharides containing special monosaccharides. The pharmacological properties of polysaccharides can be summarized as immunomodulatory, antitumor, anti-inflammatory, antihypertensive and anti-hyperlipemic, antioxidant, and antimicrobial properties. There have been no poisonous effects found in studies of plant polysaccharides, probably because the substances have a long history of use and are safe. In this paper, the application potential of polysaccharides in medicinal and edible plants in Xinjiang was reviewed, and the research progress in the extraction, separation, identification, and pharmacology of these plant polysaccharides was reviewed. At present, the research progress of plant polysaccharides in medicines and food in Xinjiang has not been reported. This paper will provide a data summary for the development and utilization of medical and food plant resources in Xinjiang.

Transcriptional Regulatory Network of Plant Cadmium Stress Response

Cadmium (Cd) is a non-essential heavy metal with high toxicity to plants. Plants have acquired specialized mechanisms to sense, transport, and detoxify Cd. Recent studies have identified many transporters involved in Cd uptake, transport, and detoxification. However, the complex transcriptional regulatory networks involved in Cd response remain to be elucidated. Here, we provide an overview of current knowledge regarding transcriptional regulatory networks and post-translational regulation of the transcription factors involved in Cd response. An increasing number of reports indicate that epigenetic regulation and long non-coding and small RNAs are important in Cd-induced transcriptional responses. Several kinases play important roles in Cd signaling that activate transcriptional cascades. We also discuss the perspectives to reduce grain Cd content and improve crop tolerance to Cd stress, which provides a theoretical reference for food safety and the future research of plant varieties with low Cd accumulation.

Environmental and genealogical effects on DNA methylation in a widespread apomictic dandelion lineage

DNA methylation in plant genomes occurs in different sequences and genomic contexts that have very different properties. DNA methylation that occurs in CG (mCG) sequence context shows transgenerational stability and high epimutation rate, and can thus provide genealogical information at short time scales. However, due to meta-stability and because mCG variants may arise due to other factors than epimutation, such as environmental stress exposure, it is not clear how well mCG captures genealogical information at micro-evolutionary time scales. Here, we analysed DNA methylation variation between accessions from a geographically widespread, apomictic common dandelion (Taraxacum officinale) lineage when grown experimentally under different light conditions. Using a reduced-representation bisulphite sequencing approach, we show that the light treatment induced differentially methylated cytosines (DMCs) in all sequence contexts, with a bias towards transposable elements. Accession differences were associated mainly with DMCs in CG context. Hierarchical clustering of samples based on total mCG profiles revealed a perfect clustering of samples by accession identity, irrespective of light conditions. Using microsatellite information as a benchmark of genetic divergence within the clonal lineage, we show that genetic divergence between accessions correlates strongly with overall mCG profiles. However, our results suggest that environmental effects that do occur in CG context may produce a heritable signal that partly dilutes the genealogical signal. Our study shows that methylation information in plants can be used to reconstruct micro-evolutionary genealogy, providing a useful tool in systems that lack genetic variation such as clonal and vegetatively propagated plants.

Plants maintain climate fidelity in the face of dynamic climate change

Plants will experience considerable changes in climate within their geographic ranges over the next several decades. They may respond by exhibiting niche flexibility and adapting to changing climates. Alternatively, plant taxa may exhibit climate fidelity, shifting their geographic distributions to track their preferred climates. Here, we examine the responses of plant taxa to changing climates over the past 18,000 y to evaluate the extent to which the 16 dominant plant taxa of North America have exhibited climate fidelity. We find that 75% of plant taxa consistently exhibit climate fidelity over the past 18,000 y, even during the times of most extreme climate change. Of the four taxa that do not consistently exhibit climate fidelity, three-elm (Ulmus), beech (Fagus), and ash (Fraxinus)-experience a long-term shift in their realized climatic niche between the early Holocene and present day. Plant taxa that migrate longer distances better maintain consistent climatic niches across transition periods during times of the most extreme climate change. Today, plant communities with the highest climate fidelity are found in regions with high topographic and microclimate heterogeneity that are expected to exhibit high climate resilience, allowing plants to shift distributions locally and adjust to some amount of climate change. However, once the climate change buffering of the region is exceeded, these plant communities will need to track climates across broader landscapes but be challenged to do so because of the low habitat connectivity of the regions.

Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants

With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of native promoters in controlling gene expression, artificial promoter design aims to synthesize short, inducible, and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling pathways. Synthetic promoters are versatile and can drive gene expression accurately with smart responses; they show potential for enhancing desirable traits in crops, thereby improving crop yield, nutritional quality, and food security. This review first illustrates the importance of synthetic promoters, then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter construction. Restrictions to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.

Xanthones: Biosynthesis and Trafficking in Plants, Fungi and Lichens

Xanthones are a class of secondary metabolites produced by plant organisms. They are characterized by a wide structural variety and numerous biological activities that make them valuable metabolites for use in the pharmaceutical field. This review shows the current knowledge of the xanthone biosynthetic pathway with a focus on the precursors and the enzymes involved, as well as on the cellular and organ localization of xanthones in plants. Xanthone biosynthesis in plants involves the shikimate and the acetate pathways which originate in plastids and endoplasmic reticulum, respectively. The pathway continues following three alternative routes, two phenylalanine-dependent and one phenylalanine-independent. All three routes lead to the biosynthesis of 2,3',4,6-tetrahydroxybenzophenone, which is the central intermediate. Unlike plants, the xanthone core in fungi and lichens is wholly derived from polyketide. Although organs and tissues synthesizing and accumulating xanthones are known in plants, no information is yet available on their subcellular and cellular localization in fungi and lichens. This review highlights the studies published to date on xanthone biosynthesis and trafficking in plant organisms, from which it emerges that the mechanisms underlying their synthesis need to be further investigated in order to exploit them for application purposes.

Organellar DNA continues to provide a rich source of information in the genomics era

The genomics revolution continues to change how ecologists and evolutionary biologists study the evolution and maintenance of biodiversity. It is now easier than ever to generate large molecular data sets consisting of hundreds to thousands of independently evolving nuclear loci to estimate a suite of evolutionary and demographic parameters. However, any inferences will be incomplete or inaccurate if incorrect taxonomic identities and perpetuated throughout the analytical pipeline. Due to decades of research and comprehensive online databases, sequencing and analysis of mitochondrial DNA (mtDNA), chloroplast DNA (cpDNA) and select nuclear genes can provide researchers with a cost effective and simple means to verify the species identity of samples prior to subsequent phylogeographic and population genomic analysis. The addition of these sequences to genomic studies can also shed light on other important evolutionary questions such as explanations for gene tree-species tree discordance, species limits, sex-biased dispersal patterns, adaptation, and mtDNA introgression. Although the mtDNA and cpDNA genomes often should not be used exclusively to make historical inferences given their well-known limitations, the addition of these data to modern genomic studies adds little cost and effort while simultaneously providing a wealth of useful data that can have significant implications for both basic and applied research.

Plant phenological dataset collated by the Finnish Society of Sciences and Letters

Long records of phenological observations constitute data for ecological, climate, and global change studies. Here we provide a unique dataset of plant phenological observations made in boreal Europe between 1750 and 1965 from locations situated across historical and modern Finland, mostly between 70° and 60° N and 30° and 20° E. This dataset was generated initially by the efforts of several generations of volunteers representing naturalists whose field observations and notes had initially made the continuous collection of the data possible. In addition, the data were collated by the Finnish Economic Society and the Finnish Society of Sciences and Letters and published irregularly in the form of several monographs and periodicals by contemporary academic enthusiasts. Each phenological observation contains 11 features including: site name, site latitude, site longitude, scientific species name, phenological stage, and (if any) its substage, year, date (month and day) and the day since the summer solstice, the original literature source, and outlier estimate. Species names given originally either in Latin, Finnish, German, and/or Swedish were transformed into scientific species names. Moreover, outdated taxonomic names were updated as appropriate. Phenological stages that had been given originally either in German, Finnish, and/or Swedish were transformed into English and standardized by excluding synonyms. Site names were adopted at the county level, with corresponding latitude and longitude generated herein. The digitized dataset represents 265,478 observations of 985 taxa (assigned to variety/subspecies/species/hybrid/genus) for their 16 different phenological stages made in 371 locations across the region. We provide this dataset to support comparative studies and modeling projects, seeking to improve the understanding of terrestrial ecosystem dynamics and its responses to a changing environment from a local to a global scale. Use of this dataset for academic or educational purposes is encouraged as long as the data source is correctly cited with attribution given to this presentation of the data. Users are free to use and analyze the data; additionally, we would like to hear from other researchers who use this dataset in teaching or for their own research.

Plant base editing and prime editing: The current status and future perspectives

Precise replacement of an allele with an elite allele controlling an important agronomic trait in a predefined manner by gene editing technologies is highly desirable in crop improvement. Base editing and prime editing are two newly developed precision gene editing systems which can introduce the substitution of a single base and install the desired short indels to the target loci in the absence of double-strand breaks and donor repair templates, respectively. Since their discoveries, various strategies have been attempted to optimize both base editor (BE) and prime editor (PE) in order to improve the precise editing efficacy, specificity, and expand the targeting scopes. Here, we summarize the latest development of various BEs and PEs, as well as their applications in plants. Based on these progresses, we recommend the appropriate BEs and PEs for both basic plant research and crop improvement. Moreover, we propose the perspectives for further optimization of these two editors. We envision that both BEs and PEs will become the routine and customized precise gene editing tools for both plant biological research and crop improvement in the near future.

Developing a culturally acceptable peanut nutrition bar with smallholder women farmers in Kaffrine, Senegal using response surface methodology

To increase farm income and food security, a collaboration was made with smallholder women farmers in Kaffrine, Senegal to develop a culturally acceptable peanut nutrition bar using healthy indigenous and local ingredients and feasible manufacturing methods. This study aimed to use response surface methodology to optimize the bar's formulation and characterize the texture, nutrient profile, sensory qualities, and water activity. The bars were made by varying the ratio of cowpea flour to corn flour (w/w, d.b., 0/100, 25/75, 50/50, 75/25, and 100/0) and the percentage of baobab pulp powder in the cowpea-corn flour blend (w/w, d.b., 15%, 20%, 25%, and 30%) with a fixed amount of 13 g of peanut paste added to all formulations. The use of acacia gum as a binder increased the bars' cohesiveness. Increasing the ratio of cowpea flour to corn flour decreased the cohesiveness and increased protein, fiber, calcium, iron, and folate levels of the bars. Increasing the percentage of baobab pulp powder increased the hardness, fiber, and vitamin C levels, and decreased cohesiveness and water activity of the bars. The bar formulation optimized for sensory acceptance had a cowpea to corn ratio of 85.3:14.7, a baobab level of 9.95%, and 13 g of peanut paste. According to the research, the optimum formulation gave 38%, 32%, 36%, 50%, 11%, and 83% of the recommended dietary allowance of protein, fiber, calcium, iron, vitamin C, and folate, respectively, per serving for school-age children and featured culturally acceptable texture and desirable water activity for commercialization. This study provided critical foundations for the subsequent feasibility assessment of a commercial launch, projected to significantly increase the revenue and nutrient intake of the partnering communities. PRACTICAL APPLICATION: The commercialization of the peanut nutrition bar will serve as a source of new income for Senegalese smallholder women farmers, provide essential nutrients for school-age children and potentially reduce post-harvest loss. Response surface methodology used in this study can also be applied to food product development with indigenous communities to develop an accepted and community-feasible product formulation.

Niche width predicts extinction from climate change and vulnerability of tropical species

Climate change may be a major threat to global biodiversity, especially to tropical species. Yet, why tropical species are more vulnerable to climate change remains unclear. Tropical species are thought to have narrower physiological tolerances to temperature, and they have already experienced a higher estimated frequency of climate-related local extinctions. These two patterns suggest that tropical species are more vulnerable to climate change because they have narrower thermal niche widths. However, no studies have tested whether species with narrower climatic niche widths for temperature have experienced more local extinctions, and if these narrower niche widths can explain the higher frequency of tropical local extinctions. Here, we test these ideas using resurvey data from 538 plant and animal species from 10 studies. We found that mean niche widths among species and the extent of climate change (increase in maximum annual temperatures) together explained most variation (>75%) in the frequency of local extinction among studies. Surprisingly, neither latitude nor occurrence in the tropics alone significantly predicted local extinction among studies, but latitude and niche widths were strongly inversely related. Niche width also significantly predicted local extinction among species, as well as among and (sometimes) within studies. Overall, niche width may offer a relatively simple and accessible predictor of the vulnerability of populations to climate change. Intriguingly, niche width has the best predictive power to explain extinction from global warming when it incorporates coldest yearly temperatures.

A data set for pollinator diversity and their interactions with plants in the Pacific Northwest

Pollinator populations have declined substantially in recent years. The resulting loss in pollination services has both ecological and economic consequences, including reductions in plant diversity and crop production and lower food security. Data sets that identify pollinators and their plant hosts are of the utmost importance for the light can shed on the main causes of pollinator declines. Here we present a data set that contains 67,954 individual pollinator records. The data were collected across the Pacific Northwest, primarily focused in British Columbia (Canada), with 182 individual sites over 11 years, between 2005 and 2017. This data set comprises multiple studies that aimed to collect information on pollinator abundance, diversity, and their interactions with plants. Overall, the data set includes 937 morphospecies (of which 482 were identified to the species level) of pollinators across 105 families, including data for bees, wasps, butterflies, moths, and flies. We also present information on the interactions of these species, with 473 species of plants. The data set is being released for noncommercial use only. Credits should be given to this paper (i.e., proper citation).

Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding

Whole-genome sequencing and assembly have revolutionized plant genetics and molecular biology over the last two decades. However, significant shortcomings in first- and second-generation technology resulted in imperfect reference genomes: numerous and large gaps of low quality or undeterminable sequence in areas of highly repetitive DNA along with limited chromosomal phasing restricted the ability of researchers to characterize regulatory noncoding elements and genic regions that underwent recent duplication events. Recently, advances in long-read sequencing have resulted in the first gapless, telomere-to-telomere (T2T) assemblies of plant genomes. This leap forward has the potential to increase the speed and confidence of genomics and molecular experimentation while reducing costs for the research community.

New Insights into rice pyrimidine catabolic enzymes

INTRODUCTION

Rice is a primary global food source, and its production is affected by abiotic stress, caused by climate change and other factors. Recently, the pyrimidine reductive catabolic pathway, catalyzed by dihydropyrimidine dehydrogenase (DHPD), dihydropyrimidinase (DHP) and β-ureidopropionase (β-UP), has emerged as a potential participant in the abiotic stress response of rice.

METHODS

The rice enzymes were produced as recombinant proteins, and two were kinetically characterized. Rice dihydroorotate dehydrogenase (DHODH), an enzyme of pyrimidine biosynthesis often confused with DHPD, was also characterized. Salt-sensitive and salt-resistant rice seedlings were subjected to salt stress (24 h) and metabolites in leaves were determined by mass spectrometry.

RESULTS

The OsDHPD sequence was homologous to the C-terminal half of mammalian DHPD, conserving FMN and uracil binding sites, but lacked sites for Fe/S clusters, FAD, and NADPH. OsDHPD, truncated to eliminate the chloroplast targeting peptide, was soluble, but inactive. Database searches for polypeptides homologous to the N-terminal half of mammalian DHPD, that could act as co-reductants, were unsuccessful. OsDHODH exhibited kinetic parameters similar to those of other plant DHODHs. OsDHP, truncated to remove a signal sequence, exhibited a kcat/Km = 3.6 x 103 s-1M-1. Osb-UP exhibited a kcat/Km = 1.8 x 104 s-1M-1. Short-term salt exposure caused insignificant differences in the levels of the ureide intermediates dihydrouracil and ureidopropionate in leaves of salt-sensitive and salt-resistant plants. Allantoin, a ureide metabolite of purine catabolism, was found to be significantly higher in the resistant cultivar compared to one of the sensitive cultivars.

DISCUSSION

OsDHP, the first plant enzyme to be characterized, showed low kinetic efficiency, but its activity may have been affected by truncation. Osb-UP exhibited kinetic parameters in the range of enzymes of secondary metabolism. Levels of two pathway metabolites were similar in sensitive and resistant cultivars and appeared to be unaffected by short-term salt exposure."

Evidence of Downregulation in Atmospheric Nitrogen-Fixation Associated with Native Hawaiian Sugarcane (Saccharum officinarum L.) Cultivars

The study of nitrogen fixation in sugarcane has a long history that has demonstrated high potential but with substantial variation in results. This 32-month study sought to assess the response of nitrogen fixation associated with sugarcane (Saccharum officinarum L. cvs. 'Akoki, Honua'ula, and 'Ula) to available soil nitrogen. Plants were grown in large pots of perlite along with a fixing and a non-fixing plant control and administered liquid fertigation with varying amounts of isotopically enriched nitrogen. Assessment of nitrogen fixation utilized nitrogen isotope tracing and acetylene reduction assay in the target and control plants. Isotope enrichment and acetylene reduction assay both indicated that nitrogen fixation peaked under low nitrogen application, and declined with higher application rates, with agreement between the two methods. These results suggest that sugarcane engages in a downregulation of nitrogen fixation under high nitrogen availability, potentially explaining the high variation in published experimental results. This suggests that nitrogen management and fertilization strategy can impact the atmospheric inputs of nitrogen in sugarcane cultivation, and the potential to improve nitrogen application efficiency in cropping systems utilizing sugarcane.

Study of the phytoremediation potential of native plant species identified in an area contaminated by volatile organic compounds: a systematic review

Phytoremediation is a process that uses plants in situ to promote remediation of environments contaminated by organic or inorganic compounds. Phytoremediating species develop methods such as phytoextraction, rhizofiltration, phytodegradation, and phytovolatilization, which can manifest themselves individually or together in a single plant. This study aims to evaluate, through a systematic review, the potential phytoremediation techniques of the genera Syagrus (Mart.), Nephrolepis, Cyperus (L.), Mimosa (L.), Schinus (L.), Brachiaria, and Eryngium (L.) found in a humid area of Rio Grande do Sul, Brazil. The genera that presented significant numbers in the databases consulted were Cyperus and Brachiaria, followed by Nephrolepis. The first two are considered the most promising for phytoremediation processes. The other genera mentioned obtained favorable results for organic contaminants. The studies around these genera are still recent. It is necessary, in research, to highlight which phytoremediation processes the plants exert in relation to the contaminant of the place. In addition, priority should be given to native species that can establish themselves in the environment and that would not unbalance and harm the surrounding biota and ecosystem.

How Do Plants Cope with DNA Damage? A Concise Review on the DDR Pathway in Plants

DNA damage is induced by many factors, some of which naturally occur in the environment. Because of their sessile nature, plants are especially exposed to unfavorable conditions causing DNA damage. In response to this damage, the DDR (DNA damage response) pathway is activated. This pathway is highly conserved between eukaryotes; however, there are some plant-specific DDR elements, such as SOG1-a transcription factor that is a central DDR regulator in plants. In general, DDR signaling activates transcriptional and epigenetic regulators that orchestrate the cell cycle arrest and DNA repair mechanisms upon DNA damage. The cell cycle halts to give the cell time to repair damaged DNA before replication. If the repair is successful, the cell cycle is reactivated. However, if the DNA repair mechanisms fail and DNA lesions accumulate, the cell enters the apoptotic pathway. Thereby the proper maintenance of DDR is crucial for plants to survive. It is particularly important for agronomically important species because exposure to environmental stresses causing DNA damage leads to growth inhibition and yield reduction. Thereby, gaining knowledge regarding the DDR pathway in crops may have a huge agronomic impact-it may be useful in breeding new cultivars more tolerant to such stresses. In this review, we characterize different genotoxic agents and their mode of action, describe DDR activation and signaling and summarize DNA repair mechanisms in plants.

Enhancement of Lipid Stability and Acceptability of Canned Seafood by Addition of Natural Antioxidant Compounds to the Packing Medium-A Review

Seafoods are known to include high contents of valuable constituents. However, they are reported to be highly perishable products, whose quality rapidly declines post-mortem, thus demanding efficient processing and storage. Among the traditional technologies, canning represents one of the most important means of marine species preservation. However, owing to the thermal sensitivity of the chemical constituents of marine species, remarkable degradative mechanisms can be produced and lead to important quality losses. The demand for better quality food makes the need for advanced preservation techniques a topic to be addressed continually in the case of seafood. One such strategy is the employment of preservative compounds obtained from natural resources. The current review provides an overview of the research carried out concerning the effect of the addition of bioactive compounds to the packing medium on the thermal stability of canned seafood. This review addresses the preservative effect of polyphenol-rich oils (i.e., extra virgin olive oil) and different kinds of products or extracts obtained from plants, algae and seafood by-products. In agreement with the great incidence of lipid damage on the nutritional and acceptability values during high-temperature seafood processing, this work is especially focussed on the inhibitory effect of lipid oxidation development.

Trends in the direction of global plant invasion biology research over the past two decades

Invasive plants are a growing ecological problem worldwide, but biases and patterns within invasive plant research may affect our understanding of invasive plant ecology. In this study, we analyzed 458 invasive plant papers sampled from the two journals dedicated entirely to the field of invasion biology, i.e., Biological Invasions and Neobiota. From these papers, we collected information on geographic coverage, climate, habitat, taxonomic coverage, plant functional type, and research topic to examine trends across a 21-year time period from 1999 to 2020. Our analysis found that invasive plant research was consistently biased toward temperate grassland and forest ecosystems particularly within the Americas, Europe, and Australia, and toward smaller, herbaceous invasive plant species (i.e., forbs, grasses, and shrubs), with an increase in interest in invasive nitrogen-fixing legumes over time. Our analysis also identified "hot" research topics in invasive plant research at specific time periods, such as a peak in the use of genetic analysis methods in 2014-2015 and a more recent focus on plant physiological and functional traits. While current models, concepts, and understanding of plant invasion ecology are still driven by such biases, this has been partially offset by recent increased research in understudied systems, as well as increasing awareness that plant invasion is heavily affected by their growth types, physiological traits, and soil interactions. As the field of invasion biology becomes ever increasingly important over time, focusing invasive plant research on understudied ecosystems and plant groups will allow us to develop a more holistic understanding of the ecology of invasive plants. In particular, given the outsized importance of the tropics to global biodiversity, the threats they face, and the dearth of studies, it is of critical importance that more invasive plant research is conducted within the tropics to develop a more globally representative understanding of invasive plant ecology.

Exploring cryptic amyloidogenic regions in prion-like proteins from plants

Prion-like domains (PrLDs) are intrinsically disordered regions (IDRs) of low sequence complexity with a similar composition to yeast prion domains. PrLDs-containing proteins have been involved in different organisms' regulatory processes. Regions of moderate amyloid propensity within IDRs have been shown to assemble autonomously into amyloid fibrils. These sequences tend to be rich in polar amino acids and often escape from the detection of classical bioinformatics screenings that look for highly aggregation-prone hydrophobic sequence stretches. We defined them as cryptic amyloidogenic regions (CARs) and recently developed an integrated database that collects thousands of predicted CARs in IDRs. CARs seem to be evolutionary conserved among disordered regions because of their potential to stablish functional contacts with other biomolecules. Here we have focused on identifying and characterizing CARs in prion-like proteins (pCARs) from plants, a lineage that has been poorly studied in comparison with other prionomes. We confirmed the intrinsic amyloid potential for a selected pCAR from Arabidopsis thaliana and explored functional enrichments and compositional bias of pCARs in plant prion-like proteins.

Interaction between nanomaterials and the innate immune system across evolution

Interaction of engineered nanomaterials (ENMs) with the immune system mainly occurs with cells and molecules of innate immunity, which are present in interface tissues of living organisms. Immuno-nanotoxicological studies aim at understanding if and when such interaction is inconsequential or may cause irreparable damage. Since innate immunity is the first line of immune reactivity towards exogenous agents and is highly conserved throughout evolution, this review focuses on the major effector cells of innate immunity, the phagocytes, and their major sensing receptors, Toll-like receptors (TLRs), for assessing the modes of successful versus pathological interaction between ENMs and host defences. By comparing the phagocyte- and TLR-dependent responses to ENMs in plants, molluscs, annelids, crustaceans, echinoderms and mammals, we aim to highlight common recognition and elimination mechanisms and the general sufficiency of innate immunity for maintaining tissue integrity and homeostasis.

Terminalia arjuna, a Cardioprotective Herbal Medicine-Relevancy in the Modern Era of Pharmaceuticals and Green Nanomedicine-A Review

Herbal medicines were the main source of therapeutic agents in the ancestral era. Terminalia arjuna (TA) is one such medicinal plant widely known for its several medicinal properties, especially its cardiovascular properties. They have several phytochemicals, such as flavonoids, polyphenols, triterpenoids, tannins, glycosides, and several minerals, proteins, and others that are responsible for the above-mentioned medicinal properties. In this review, we have first elaborated on the various processes and their parameters for the efficient extraction of relevant phytochemicals from TA extracts. Secondly, the mechanisms behind the various medicinal properties of TA extracts are explained. We have also highlighted the role of TA extracts on the green synthesis of metallic nanoparticles, especially silver and gold nanoparticles, with an elucidation on the mechanisms behind the synthesis of nanoparticles. Finally, TA extracts-based polymeric formulations are discussed with limitations and future perspectives. We believe that this review could help researchers understand the importance of a well-known cardioprotective medicinal plant, TA, and its biomedical properties, as well as their role in green nanotechnology and various formulations explored for encapsulating them. This review will help researchers design better and greener nanomedicines as well as better formulations to improve the stability and bioavailability of TA extracts.