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<jats:p>Nitrogen is a vital nutrient for agricultural, and a defieciency of it causes stagnate cotton growth and yield penalty. Farmers rely heavily on N over-application to boost cotton output, which can result in decreased lint yield, quality, and N use efficiency (NUE). Therefore, improving NUE in cotton is most crucial for reducing environmental nitrate pollution and increasing farm profitability. Well-defined management practices, such as the type of sources, N-rate, application time, application method, crop growth stages, and genotypes, have a notable impact on NUE. Different N formulations, such as slow and controlled released fertilizers, have been shown to improve N uptake and, NUE. Increasing N rates are said to boost cotton yield, although high rates may potentially impair the yield depending on the soil and environmental conditions. This study comprehensively reviews various factors including agronomic and environmental constraints that influence N uptake, transport, accumulation, and ultimately NUE in cotton. Furthermore, we explore several agronomic and molecular approaches to enhance efficiency for better N uptake and utilization in cotton. Finally, this objective of this review to highlight a comprehensive view on enhancement of NUE in cotton and could be useful for understanding the physiological, biochemical and molecular mechanism of N in cotton.</jats:p>

<jats:p>Salinity has become a major environmental concern of agricultural lands, impairing crop production. The current study aimed to examine the role of zinc oxide nanoparticles (ZnO NPs) in reducing the oxidative stress induced by salinity and the overall improvement in phytochemical properties in barley. A total of nine different barley genotypes were first subjected to salt (NaCl) stress in hydroponic conditions to determine the tolerance among the genotypes. The genotype Annora was found as most sensitive, and the most tolerant genotype was Awaran 02 under salinity stress. In another study, the most sensitive (Annora) and tolerant (Awaran 02) barley genotypes were grown in pots under salinity stress (100 mM). At the same time, half of the pots were provided with the soil application of ZnO NPs (100 mg kg<jats:sup>–1</jats:sup>), and the other half pots were foliar sprayed with ZnO NPs (100 mg L<jats:sup>–1</jats:sup>). Salinity stress reduced barley growth in both genotypes compared to control plants. However, greater reduction in barley growth was found in Annora (sensitive genotype) than in Awaran 02 (tolerant genotype). The exogenous application of ZnO NPs ameliorated salt stress and improved barley biomass, photosynthesis, and antioxidant enzyme activities by reducing oxidative damage caused by salt stress. However, this positive effect by ZnO NPs was observed more in Awaran 02 than in Annora genotype. Furthermore, the foliar application of ZnO NPs was more effective than the soil application of ZnO NPs. Findings of the present study revealed that exogenous application of ZnO NPs could be a promising approach to alleviate salt stress in barley genotypes with different levels of salinity tolerance.</jats:p>

<jats:p>The <jats:italic>Ilex</jats:italic> L. (hollies) genus of Aquifoliaceae shows high species diversity in tropical and subtropical regions of Asia and South America. Throughout the range of the genus, <jats:italic>Ilex</jats:italic> species have been widely used in beverage and medicine production and as ornamentals. Here, we assembled a high-quality, chromosome-level genome of <jats:italic>Ilex latifolia</jats:italic>, which has extremely high economic value because of its useful secondary metabolite production and the high ornamental value of its decorative red berries. The 99.8% genome sequence was anchored to 20 pseudochromosomes, with a total length of 766.02 Mb and a scaffold N50 of 33.45 Mb. Based on the comparative genomic analysis of 14 angiosperm species, we recovered <jats:italic>I. latifolia</jats:italic> as the sister group to all other campanulids. Two whole-genome duplication (WGD) events were identified in hollies: one shared ancient WGD in the ancestor of all eudicots and a recent and independent WGD in hollies. We performed a genome-wide search to screen candidate genes involved in the biosynthesis of pentacyclic triterpenoid saponins in <jats:italic>I. latifolia</jats:italic>. Three subfamilies of CYP450 (CYP71A, CYP72A, and CYP716A) appear to have expanded. The transcriptomic analysis of <jats:italic>I. latifolia</jats:italic> leaves at five developmental stages revealed that two CYP716A genes and one CYP72A gene probably play important roles in this biosynthetic pathway. In addition, we totally identified 12 genes in the biosynthesis pathways of pelargonidin and cyanidin and observed their differential expression in green and red fruit pericarps, suggesting an association between pelargonidin and cyanidin biosynthesis and fruit pericarp color change. The accumulation of pelargonidin and cyanidin is expected to play an important role in the ornamental value of <jats:italic>I. latifolia</jats:italic>. Altogether, this study elucidated the molecular basis of the medicinal and ornamental value of <jats:italic>I. latifolia</jats:italic>, providing a data basis and promising clues for further applications.</jats:p>

<jats:p>Selenium (Se) is an essential trace element for human and animal health, and toward an understanding of the uptake and translocation of Se in plants is important from the perspective of Se biofortification. In this study, we conducted hydroponic experiments to investigate the mechanisms of organic Se [selenomethionine (SeMet) and selenomethionine-oxide (SeOMet)] uptake, translocation, and the interactions between SeMet and SeOMet in rice. We also investigated differences in the dynamics of organic and inorganic Se uptake by rice roots. Concentration-dependent kinetic results revealed that SeMet uptake during a 1 h exposure was 3.19–16.0 times higher than that of three other Se chemical forms, with uptake capacity (<jats:italic>V<jats:sub>max</jats:sub></jats:italic>) values ordered as follows: SeMet&amp;gt;SeOMet&amp;gt;selenite&amp;gt;selenate. Furthermore, time-dependent kinetic analysis revealed that SeMet uptake by roots and content in shoots were initially clearly higher than those of SeOMet, although the differences gradually diminished with prolonged exposure time; while no significant difference was found in the transfer factor of Se from rice roots to shoots between SeMet and SeOMet. Root uptake of SeOMet was significantly inhibited by carbonyl cyanide 3-chlorophenylhydrazone (CCCP) (30.4%), AgNO<jats:sub>3</jats:sub> (41.8%), and tetraethylammonium chloride (TEACl) (45.6%), indicating that SeOMet uptake is a metabolically active process, and that it could be mediated <jats:italic>via</jats:italic> aquaporins and K<jats:sup>+</jats:sup> channels. Contrarily, SeMet uptake was insensitive to CCCP, although markedly inhibited by AgNO<jats:sub>3</jats:sub> (93.1%), indicating that rice absorbs SeMet primarily <jats:italic>via</jats:italic> aquaporins. Furthermore, Se uptake and translocation in rice treated simultaneously with both SeMet and SeOMet were considerably lower than those in rice treated with SeMet treatment alone and notably lower than the theoretical quantity, indicating interactions between SeMet and SeOMet. Our findings provide important insights into the mechanisms underlying the uptake and translocation of organic Se within plants.</jats:p>

<jats:p>The concept of “cell type,” though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes. Transcriptomic snapshots of cells at various stages of differentiation, and of cells under different physiological conditions, have shown that in many cases variation is more continuous than discrete, raising questions about the relationship between cell type and cell state. Some researchers have rejected the notion of fixed types altogether. Throughout the history of discussions on cell type, cell biologists have compared the problem of defining cell type with the interminable and often contentious debate over the definition of arguably the most important concept in systematics and evolutionary biology, “species.” In the last decades, systematics, like cell biology, has been transformed by the increasing availability of molecular data, and the fine-grained resolution of genetic relationships have generated new ideas about how that variation should be classified. There are numerous parallels between the two fields that make exploration of the “cell types as species” metaphor timely. These parallels begin with philosophy, with discussion of both cell types and species as being either individuals, groups, or something in between (e.g., homeostatic property clusters). In each field there are various different types of lineages that form trees or networks that can (and in some cases do) provide criteria for grouping. Developing and refining models for evolutionary divergence of species and for cell type differentiation are parallel goals of the two fields. The goal of this essay is to highlight such parallels with the hope of inspiring biologists in both fields to look for new solutions to similar problems outside of their own field.</jats:p>

<jats:p>We propose metabolic models for the haptophyte microalgae <jats:italic>Tisochrysis lutea</jats:italic> with different possible organic carbon excretion mechanisms. These models—based on the DRUM (Dynamic Reduction of Unbalanced Metabolism) methodology—are calibrated with an experiment of nitrogen starvation under day/night cycles, and then validated with nitrogen-limited chemostat culture under continuous light. We show that models including exopolysaccharide excretion offer a better prediction capability. It also gives an alternative mechanistic interpretation to the Droop model for nitrogen limitation, which can be understood as an accumulation of carbon storage during nitrogen stress, rather than the common belief of a nitrogen pool driving growth. Excretion of organic carbon limits its accumulation, which leads to a maximal C/N ratio (corresponding to the minimum Droop N/C quota). Although others phenomena—including metabolic regulations and dissipation of energy—are possibly at stake, excretion appears as a key component in our metabolic model, that we propose to include in the Droop model.</jats:p>

<jats:p>Flax is an important fiber crop that is subject to lodging. In order to gain more information about the potential role of the bast fiber cell wall in the return to the vertical position, 6-week-old flax plants were subjected to a long-term (6 week) gravitropic stress by stem tilting in an experimental set-up that excluded autotropism. Stress induced significant morphometric changes (lumen surface, lumen diameter, and cell wall thickness and lumen surface/total fiber surface ratio) in pulling- and opposite-side fibers compared to control fibers. Changes in the relative amounts and spatial distribution of cell wall polymers in flax bast fibers were determined by Raman vibrational spectroscopy. Following spectra acquisition, datasets (control, pulling- and opposite sides) were analyzed by principal component analysis, PC score imaging, and Raman chemical cartography of significant chemical bonds. Our results show that gravitropic stress induces discrete but significant changes in the composition and/or spatial organization of cellulose, hemicelluloses and lignin within the cell walls of both pulling side and opposite side fibers.</jats:p>

<jats:p>Four P4-ATPase flippase genes, <jats:italic>VdDrs2, VdNeo1, VdP4-4</jats:italic>, and <jats:italic>VdDnf1</jats:italic> were identified in <jats:italic>Verticillium dahliae</jats:italic>, one of the most devastating phytopathogenic fungi in the world. Knock out of <jats:italic>VdDrs2, VdNeo1</jats:italic>, and <jats:italic>VdP4-4</jats:italic>, or knock down of <jats:italic>VdDnf1</jats:italic> significantly decreased the pathogenicity of the mutants in cotton. Among the mutants, the greatest decrease in pathogenicity was observed in Δ<jats:italic>VdDrs2</jats:italic>. VdDrs2 was localized to plasma membrane, vacuoles, and <jats:italic>trans</jats:italic>-Golgi network (TGN). In vivo observation showed that the infection of the cotton by Δ<jats:italic>VdDrs2</jats:italic> was significantly delayed. The amount of two known Verticillium toxins, sulfacetamide, and fumonisin B1 in the fermentation broth produced by the Δ<jats:italic>VdDrs2</jats:italic> strain was significantly reduced, and the toxicity of the crude Verticillium wilt toxins to cotton cells was attenuated. In addition, the defect of VdDrs2 impaired the synthesis of melanin and the formation of microsclerotia, and decreased the sporulation of <jats:italic>V. dahliae</jats:italic>. Our data indicate a key role of P4 ATPases-associated vesicle transport in toxin secretion of disease fungi and support the importance of mycotoxins in the pathogenicity of <jats:italic>V. dahliae</jats:italic>.</jats:p>

<jats:p>Reactive oxygen species (ROS) act as secondary messengers that can be sensed by specific redox-sensitive proteins responsible for the activation of signal transduction culminating in altered gene expression. The subcellular site, in which modifications in the ROS/oxidation state occur, can also act as a specific cellular redox network signal. The chemical identity of ROS and their subcellular origin is actually a specific imprint on the transcriptome response. In recent years, a number of transcriptomic studies related to altered ROS metabolism in plant peroxisomes have been carried out. In this study, we conducted a meta-analysis of these transcriptomic findings to identify common transcriptional footprints for plant peroxisomal-dependent signaling at early and later time points. These footprints highlight the regulation of various metabolic pathways and gene families, which are also found in plant responses to several abiotic stresses. Major peroxisomal-dependent genes are associated with protein and endoplasmic reticulum (ER) protection at later stages of stress while, at earlier stages, these genes are related to hormone biosynthesis and signaling regulation. Furthermore, in silico analyses allowed us to assign human orthologs to some of the peroxisomal-dependent proteins, which are mainly associated with different cancer pathologies. Peroxisomal footprints provide a valuable resource for assessing and supporting key peroxisomal functions in cellular metabolism under control and stress conditions across species.</jats:p>

<jats:p>Common bean seeds are an excellent source of protein as well as of carbohydrates, minerals, vitamins, and bioactive compounds reducing, when in the diet, the risks of diseases. The presence of bioactive compounds with antinutritional properties (e.g., phytic acid, lectins, raffinosaccharides, protease inhibitors) limits, however, the bean’s nutritional value and its wider use in food preparations. In the last decades, concerted efforts have been, therefore, made to develop new common bean genotypes with reduced antinutritional compounds by exploiting the natural genetic variability of common bean and also applying induced mutagenesis. However, possible negative, or positive, pleiotropic effects due to these modifications, in terms of plant performance in response to stresses or in the resulting technological properties of the developed mutant genotypes, have yet not been thoroughly investigated. The purpose of the perspective paper is to first highlight the current advances, which have been already made in mutant bean characterization. A view will be further provided on future research directions to specifically explore further advantages and disadvantages of these bean mutants, their potential use in innovative foods and representing a valuable genetic reservoir of combinations to assess the true functional role of specific seed bioactive components directly in the food matrix.</jats:p>