Non-CG DNA hypomethylation promotes photosynthesis and nitrogen fixation in soybean.

Non-CG DNA methylation, a plant-specific epigenetic mark mainly regulated by chromomethylase (CMT), is known to play important roles in Arabidopsis thaliana. However, whether and to what extent non-CG DNA methylation modulates agronomic traits in crops remain to be explored. Here, we describe the consequences of non-CG DNA hypomethylation on development, seed composition, and yield in soybean (Glycine max). We created a Gmcmt mutant line lacking function of all four CMT genes. This line exhibited substantial hypomethylation of non-CG (CHG and CHH) sites. Non-CG hypomethylation enhanced chromatin accessibility and promoted or repressed the expression of hundreds of functionally relevant genes, including upregulation of GOLDEN-LIKE 10 (GmGLK10), which led to enhanced photosynthesis and, unexpectedly, improved nitrogen fixation efficiency. The Gmcmt line produced larger seeds with increased protein content. This study provides insights into the mechanisms of non-CG methylation-based epigenetic regulation of soybean development and suggests viable epigenetic strategies for improving soybean yield and nutritional value.

Chaperoning shape-shifting tau in disease.

Many neurodegenerative diseases, including Alzheimer's, originate from the conversion of proteins into pathogenic conformations. The microtubule-associated protein tau converts into ß-sheet-rich amyloid conformations, which underlie pathology in over 25 related tauopathies. Structural studies of tau amyloid fibrils isolated from human tauopathy tissues have revealed that tau adopts diverse structural polymorphs, each linked to a different disease. Molecular chaperones play central roles in regulating tau function and amyloid assembly in disease. New data supports the model that chaperones selectively recognize different conformations of tau to limit the accumulation of proteotoxic species. The challenge now is to understand how chaperones influence disease processes across different tauopathies, which will help guide the development of novel conformation-specific diagnostic and therapeutic strategies.

Correlative microscopy: Illuminating the endomembrane system of plant seeds.

The endomembrane system of cereal seed endosperm is a highly plastic and dynamic system reflecting the high degree of specialization of this tissue. It is capable of coping with high levels of protein synthesis and undergoes rapid changes to accommodate these storage proteins in newly formed storage organelles such as ER-derived protein bodies (PBs) or protein storage vacuoles (PSVs). The study of endomembrane morphology in cereal endosperm is challenging due to the amount of starch that cereal seeds accumulate and the progressive desiccation of the tissue. Here we present a comprehensive study of the endomembrane system of developing barley endosperm cells, complemented by CLEM imaging. The use of genetically fused fluorescent protein tags in combination with the high resolution of electron microscopy brings ultrastructural research to a new level and can be used to generate novel insights in cell biology in general and in cereal seed research in particular.

Proteome plasticity during Physcomitrium patens spore germination - from the desiccated phase to heterotrophic growth and reconstitution of photoautotrophy.

The establishment of moss spores is considered a milestone in plant evolution. They harbor protein networks underpinning desiccation tolerance and accumulation of storage compounds that can be found already in algae and that are also utilized in seeds and pollen. Furthermore, germinating spores must produce proteins that drive the transition through heterotrophic growth to the autotrophic plant. To get insight into the plasticity of this proteome, we investigated it at five timepoints of moss (Physcomitrium patens) spore germination and in protonemata and gametophores. The comparison to previously published Arabidopsis proteome data of seedling establishment showed that not only the proteomes of spores and seeds are functionally related, but also the proteomes of germinating spores and young seedlings. We observed similarities with regard to desiccation tolerance, lipid droplet proteome composition, control of dormancy, and ß-oxidation and the glyoxylate cycle. However, there were also striking differences. For example, spores lacked any obvious storage proteins. Furthermore, we did not detect homologs to the main triacylglycerol lipase in Arabidopsis seeds, SUGAR DEPENDENT1. Instead, we discovered a triacylglycerol lipase of the oil body lipase family and a lipoxygenase as being the overall most abundant proteins in spores. This finding indicates an alternative pathway for triacylglycerol degradation via oxylipin intermediates in the moss. The comparison of spores to Nicotiana tabacum pollen indicated similarities for example in regards to resistance to desiccation and hypoxia, but the overall developmental pattern did not align as in the case of seedling establishment and spore germination.

ABI transcription factors and PROTEIN L-ISOASPARTYL METHYLTRANSFERASE module mediate seed desiccation tolerance and longevity in Oryza sativa.

In contrast to desiccation-tolerant orthodox seeds, recalcitrant seeds are desiccation sensitive and are unable to survive for a prolonged time. Here, our analyses of Oryza species with contrasting seed desiccation tolerance reveals that PROTEIN L-ISOASPARTYL METHYLTRANSFERASE (PIMT), an enzyme that repairs abnormal isoaspartyl (isoAsp) residues in proteins, acts as a key player that governs seed desiccation tolerance to orthodox seeds but is ineffective in recalcitrant seeds. We observe that, unlike the orthodox seed of Oryza sativa, desiccation intolerance of the recalcitrant seeds of Oryza coarctata are linked to reduced PIMT activity and increased isoAsp accumulation due to the lack of coordinated action of ABA and ABI transcription factors to upregulate PIMT during maturation. We show that suppression of PIMT reduces, and its overexpression increases, seed desiccation tolerance and seed longevity in O. sativa. Our analyses further reveal that the ABI transcription factors undergo isoAsp formation that affect their functional competence; however, PIMT interacts with and repairs isoAsp residues and facilitates their functions. Our results thus illustrate a new insight into the mechanisms of acquisition of seed desiccation tolerance and longevity by ABI transcription factors and the PIMT module.

Integration of transcriptome and metabolome reveals the accumulation of related metabolites and gene regulation networks during quinoa seed development.

Quinoa seeds are gluten- and cholesterol-free, contain all amino acids required by the human body, have a high protein content, provide endocrine regulation, protein supplementation, and cardiovascular protection effects. However, metabolite accumulation and transcriptional regulatory networks in quinoa seed development are not well understood. Four key stages of seed development in Dianli-3260 and Dianli-557 were thus analyzed and 849 metabolites were identified, among which sugars, amino acids, and lipids were key for developmental processes, and their accumulation showed a gradual decrease. Transcriptome analysis identified 40,345 genes, of which 20,917 were differential between the M and F phases, including 8279 and 12,638 up- and down-regulated genes, respectively. Grain development processes were mainly enriched in galactose metabolism, pentose and glucuronate interconversions, the biosynthesis of amino acids, and carbon metabolism pathways, in which raffinose, phosphoenolpyruvate, series and other metabolites are significantly enriched, gene-LOC110689372, Gene-LOC110710556 and gene-LOC110714584 are significantly expressed, and these metabolites and genes play an important role in carbohydrate metabolism, lipid and Amino acid synthesis of quinoa. This study provides a theoretical basis to expand our understanding of the molecular and metabolic development of quinoa grains.

Sex on steroids: how brassinosteroids shape reproductive development in plants.

Since the discovery of brassinolide in the pollen of rapeseed, brassinosteroids (BRs) have consistently been associated with reproductive traits. However, compared to what is known for how BRs shape vegetative development, the understanding of how these hormones regulate reproductive traits is comparatively still lacking. Nevertheless, there is now considerable evidence that BRs regulate almost all aspects of reproduction, from ovule and pollen formation to seed and fruit development. Here, we review the current body of knowledge on how BRs regulate reproductive processes in plants, and what is known about how these pathways are transduced at the molecular level. We then discuss how the manipulation of BR biosynthesis and signaling can be a promising avenue for improving crop traits which rely on efficient reproduction. We thus propose that BR hold an untapped potential for plant breeding, which could contribute to attain food security in the coming years.

Non-targeted GC-MS metabolomics-based differences in Indica rice seeds of different varieties.

Rice seeds of different varieties exhibited distinct metabolic profiles in our study. We analyzed the metabolites in seeds of six rice varieties (CH, HM, NX, YX, HY, and MX) using non-targeted GC-MS. Our findings revealed that amino acids, sugars, and organic acids were predominant in all varieties, with significant differences observed in CH compared to the others. Specifically phenylalanine and glycine content differed notably in NX and YX, respectively. Additionally, 1,5-anhydroglucitol content in NX, and glutamate, aspartate, and lactulose in NX, YX, HM, HY, and MX were up-regulated. Due to the biological functions of these amino acids and sugars, these indicated that compared to CH, rice of NX were more conducive to metabolism of carbohydrate and fat, and healthy growth maintenance in the human body, but mightThese variations suggest that NX rice may be more beneficial for carbohydrate and fat metabolism and overall health maintenance compared to CH. However, it may not be suitable for diabetic patients. YX rice may not be an ideal glycine supplement, rice ofwhile HM, HY, and MX rice could serve as potential lactulose sources. Furthermore, NX and YX rice exhibited higher levels of main storage proteins compared to CH. This study offers valuable insights into the metabolic differences among various rice varieties.

Integrative phenotyping analyses reveal the relevance of the phyB-PIF4 pathway in Arabidopsis thaliana reproductive organs at high ambient temperature.

BACKGROUND: The increasing ambient temperature significantly impacts plant growth, development, and reproduction. Uncovering the temperature-regulating mechanisms in plants is of high importance, for increasing our fundamental understanding of plant thermomorphogenesis, for its potential in applied science, and for aiding plant breeders in improving plant thermoresilience. Thermomorphogenesis, the developmental response to warm temperatures, has been primarily studied in seedlings and in the regulation of flowering time. PHYTOCHROME B and PHYTOCHROME-INTERACTING FACTORs (PIFs), particularly PIF4, are key components of this response. However, the thermoresponse of other adult vegetative tissues and reproductive structures has not been systematically evaluated, especially concerning the involvement of phyB and PIFs. RESULTS: We screened the temperature responses of the wild type and several phyB-PIF4 pathway Arabidopsis mutant lines in combined and integrative phenotyping platforms for root growth in soil, shoot, inflorescence, and seed. Our findings demonstrate that phyB-PIF4 is generally involved in the relay of temperature signals throughout plant development, including the reproductive stage. Furthermore, we identified correlative responses to high ambient temperature between shoot and root tissues. This integrative and automated phenotyping was complemented by monitoring the changes in transcript levels in reproductive organs. Transcriptomic profiling of the pistils from plants grown under high ambient temperature identified key elements that may provide insight into the molecular mechanisms behind temperature-induced reduced fertilization rate. These include a downregulation of auxin metabolism, upregulation of genes involved auxin signalling, miRNA156 and miRNA160 pathways, and pollen tube attractants. CONCLUSIONS: Our findings demonstrate that phyB-PIF4 involvement in the interpretation of temperature signals is pervasive throughout plant development, including processes directly linked to reproduction.

Upregulated synthesis and production of bioactive compounds in Lotus arabicus L. by in vitro feeding with dried powder of date palm seeds.

BACKGROUND: Plants are considered the primary source of many principal bioactive compounds that have been utilized in a wide range of applications including the pharmaceutical and biotechnological industries. Therefore, there is an imperative need to modulate the production of natural bioactive components. The present study aimed to determine the importance of dried and pulverized date palm seeds (DPS) as a natural elicitor for the synthesis of secondary metabolites in Lotus arabicus L. RESULTS: The presence of various antioxidant compounds, simple sugars, amino acids, fatty acids and reasonable mineral contents was distinct in the phytochemical characterization of DPS. The major components detected in DPS analysis were the 5-(hydroxymethyl) furfural and 2,3-dihydro-3,5-dihydroxy-6-methyl-4H-pyranone. The induced callus of L. arabicus (seven weeks old) was supplemented with DPS at different concentrations (0, 2, 4, 8 and 10 g/l) in culture media. Treatment with 8 g/l DPS induced the highest antioxidant capacity, ascorbic acid content and secondary metabolites (total phenolics and flavonoids) in the produced callus. Stress biomarkers (hydrogen peroxide and malondialdehyde) were found in the control ranges except at 10 g/l DPS. The expression patterns of key genes involoved in secondary metabolism modulation, such as phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), flavonol synthase (FLS) and deoxyxylulose phosphate reductoisomerase (DXR), were triggered after DPS treatments. Moreover, the quantitative profiling of phenolic and flavonoid compounds showed that supplementation with DPS, especially at 8 g/l, led to pronounced increases in most of the measured compounds. CONCLUSION: The marked upregulation of eliciting-responsive genes and overproduction of secondary metabolites provide molecular-based evidence for intensifying the principal pathways of phenylpropanoid, flavonoid and terpenoid biosynthesis. Overall, the present in vitro study highlights the stimulating capacity of DPS utilization to improve the bioactive components of L. arabicus at the physiological and molecular levels, enhancing its potential as a medicinal herb.

Genetic manipulation of the genes for clonal seeds results in sterility in cotton.

BACKGROUND: Heterosis is a common phenomenon in plants and has been extensively applied in crop breeding. However, the superior traits in the hybrids can only be maintained in the first generation but segregate in the following generations. Maintaining heterosis in generations has been challenging but highly desirable in crop breeding. Recent study showed that maternally produced diploid seeds could be achieved in rice by knocking out three meiosis related genes, namely REC8, PAIR1, OSD1 to create MiMe in combination with egg cell specific expression of BBM transcription factor, a technology called clonal seeds. Interestingly, there has been very limited reports indicating the feasibility of this approach in other crops. RESULTS: In this study, we aimed to test whether clonal seeds could be created in cotton. We identified the homologs of the three meiosis related genes in cotton and used the multiplex CRISPR/Cas9 gene editing system to simultaneously knock out these three genes in both A and D sub-genomes. More than 50 transgenic cotton plants were generated, and fragment analysis indicated that multiple gene knockouts occurred in the transgenic plants. However, all the transgenic plants were sterile apparently due to the lack of pollen. Pollination of the flowers of the transgenic plants using the wild type pollens could not generate seeds, an indication of defects in the formation of female sexual cells in the transgenic plants. In addition, we generated transgenic cotton plants expressing the cotton BBM gene driven by the Arabidopsis egg cell specific promoter pDD45. Two transgenic plants were obtained, and both showed severely reduced fertility. CONCLUSIONS: Overall, our results indicate that knockout of the clonal seeds related genes in cotton causes sterility and how to manipulate genes to create clonal seeds in cotton requires further research.

Integrated analysis of metabolome, transcriptome, and bioclimatic factors of Acer truncatum seeds reveals key candidate genes related to unsaturated fatty acid biosynthesis, and potentially optimal production area.

BACKGROUND: Lipids found in plant seeds are essential for controlling seed dormancy, dispersal, and defenses against biotic and abiotic stress. Additionally, these lipids provide nutrition and energy and are therefore important to the human diet as edible oils. Acer truncatum, which belongs to the Aceaceae family, is widely cultivated around the world for its ornamental value. Further because its seed oil is rich in unsaturated fatty acids (UFAs)- i.e. α-linolenic acid (ALA) and nervonic acid (NA)- and because it has been validated as a new food resource in China, the importance of A. truncatum has greatly risen. However, it remains unknown how UFAs are biosynthesized during the growth season, to what extent environmental factors impact their content, and what areas are potentially optimal for their production. RESULTS: In this study, transcriptome and metabolome of A. truncatum seeds at three representative developmental stages was used to find the accumulation patterns of all major FAs. Cumulatively, 966 metabolites and 87,343 unigenes were detected; the differential expressed unigenes and metabolites were compared between stages as follows: stage 1 vs. 2, stage 1 vs. 3, and stage 2 vs. 3 seeds, respectively. Moreover, 13 fatty acid desaturases (FADs) and 20 ß-ketoacyl-CoA synthases (KCSs) were identified, among which the expression level of FAD3 (Cluster-7222.41455) and KCS20 (Cluster-7222.40643) were consistent with the metabolic results of ALA and NA, respectively. Upon analysis of the geographical origin-affected diversity from 17 various locations, we found significant variation in phenotypes and UFA content. Notably, in this study we found that 7 bioclimatic variables showed considerable influence on FAs contents in A. truncatum seeds oil, suggesting their significance as critical environmental parameters. Ultimately, we developed a model for potentially ecological suitable regions in China. CONCLUSION: This study provides a comprehensive understanding of the relationship between metabolome and transcriptome in A. truncatum at various developmental stages of seeds and a new strategy to enhance seed FA content, especially ALA and NA. This is particularly significant in meeting the increasing demands for high-quality edible oil for human consumption. The study offers a scientific basis for A. truncatum's novel utilization as a woody vegetable oil rather than an ornamental plant, potentially expanding its cultivation worldwide.

RbPbI3 Seed Embedding in PbI2 Substrate Tailors the Facet Orientation and Crystallization Kinetics of Perovskites.

High power conversion efficiencies (PCEs) in perovskite solar cells (PSCs) have always been awe-inspiring, but perovskite films scalability is an exacting precondition for PSCs commercial deployment, generally unachievable through the antisolvent technique. On the contrary, in the two-step sequential method, the perovskite's uncontrolled crystallization and unnecessary PbI2 residue impede the device's performance. These two issues motivated to empower the PbI2 substrate with orthorhombic RbPbI3 crystal seeds, which act as grown nuclei and develop orientated perovskites lattice stacks, improving the perovskite films morphologically and reducing the PbI2 content in eventual perovskite films. Thence, achieving a PCE of 24.17% with suppressed voltage losses and an impressive life span of 1140 h in the open air.

2D BA2PbI4 Regulating PbI2 Crystallization to Induce Perovskite Growth for Efficient Solar Cells.

Using seeds to control the crystallization of perovskite film is an effective strategy for achieving high-efficiency perovskite solar cells (PSCs). Owing to their excellent environmental stability brought by their long alkyl chain, n-butylammonium (BA) cations are widely used for fabricating efficient and stable PSCs. However, BA-based 2D perovskite is seldom been investigated as a seed. Here, BA2PbI4 is employed to regulate the crystallization of PbI2, acting as nucleation centers. As a result, porous PbI2 film with high crystallinity is obtained, which allows the realization of perovskite film with preferential crystal orientations of (001) and large grain size of over 2 µm. The corresponding PSC achieves a high power conversion efficiency (PCE) of 24.30% and exhibits satisfactory stability, retaining 91.70% of the initial PCE after 300 h of thermal aging at 85°C.

ZnS Nanoseeds Sealed in N, P, S Co-Doped Carbon Hollow Rhombic Dodecahedra as a Superlithiophilic Host for Dendrite-Free Lithium Metal Anodes.

Lithium (Li) metal is considered a hopeful anode for next-generation Li-ion batteries thanks to its ultra-high theoretical specific capacity, extra-low theoretical density, and low negative potential. However, the uncontrolled growth of Li dendrites and volume fluctuation during plating/stripping processes severely hamper its commercial application. Herein, ZnS seeds sealed in N, P, S co-doped carbon hollow rhombic dodecahedra (ZnS@NPS-C HRD) is fabricated as a superlithiophilic host for Li metal anodes (LMAs) to solve the above problems. In addition, the Li nucleation and deposition mechanism on ZnS@NPS-C HRD is investigated by in situ optical microscopy, ex-situ X-ray diffraction, scanning electron microscopy, and theoretical calculations. Owing to the synergistic strategy of ZnS seeds-inducing nucleation and Li-limited growth, the as-prepared composite exhibits stability for 300 cycles in asymmetric cells and a long lifespan over 1100 h in symmetric cells. Moreover, the ZnS@NPS-C HRD@Li|LiFePO4 full cell demonstrates a reversible capacity of 100.91 mAh g-1 after 400 cycles at 1 C.

A simple, robust, cost-effective, and low-input ChIP-seq method for profiling histone modifications and Pol II in plants.

Chromatin immunoprecipitation and sequencing (vs ChIP-seq) is an essential tool for epigenetic and molecular genetic studies. Although being routinely used, ChIP-seq is expensive, requires grams of plant materials, and is challenging for samples that enrich fatty acids such as seeds. Here, we developed an Ultrasensitive Plant ChIP-seq (UP-ChIP) method based on native ChIP-seq combined with Tn5 tagmentation-based library construction strategy. UP-ChIP is generally applicable for profiling both histone modification and Pol II in a wide range of plant samples, such as a single Arabidopsis seedling, a few Arabidopsis seeds, and sorted nuclei. Compared with conventional ChIP-seq, UP-ChIP is much less labor intensive and only consumes 1 µg of antibody and 10 µl of Protein-A/G conjugated beads for each IP and can work effectively with the amount of starting material down to a few milligrams. By performing UP-ChIP in various conditions and genotypes, we showed that UP-ChIP is highly reliable, sensitive, and quantitative for studying histone modifications. Detailed UP-ChIP protocol is provided. We recommend UP-ChIP as an alternative to traditional ChIP-seq for profiling histone modifications and Pol II, offering the advantages of reduced labor intensity, decreased costs, and low-sample input.

Intravitreal Topotecan for Vitreous Seeds in Retinoblastoma: A Long-term Review of 91 Eyes.

PURPOSE: To study the long-term efficacy of intravitreal topotecan (IVT) for vitreous seeds in eyes with retinoblastoma and risk factors for their recurrence. DESIGN: Retrospective, non-comparative, interventional study. PARTICIPANTS: Ninety-one eyes of 90 patients with retinoblastoma treated between January 2013 and April 2019. METHODS: Patients with recurrent or refractory vitreous seeds after completion of intravenous or intra-arterial chemotherapy were treated with IVT (30 µg/0.15 ml) by the safety-enhanced technique. The injection was repeated every 4 weeks until the regression of seeds. Patients with a minimum follow-up of 12 months were included in the analysis. MAIN OUTCOME MEASURES: Primary outcome measures were vitreous seed regression and eye salvage. Secondary outcomes were risk factors for vitreous seed recurrence after treatment with IVT, vision salvage, and complications of IVT. RESULTS: The median age of the patients was 18 months, with most having group D (n = 58 [64%]) and group E (n = 26 [29%]) retinoblastoma. Vitreous seeds were refractory in 46 eyes (51%) and recurrent in 45 eyes (49%). A total of 317 IVT injections were administered, with the median being 3 injections. The median number of IVT injections required was 2.5 injections for dust, 3 injections for sphere, and 5 injections for cloud morphologic features. Recurrence of vitreous seeds after IVT was seen in 17 eyes (19%) at a mean follow-up of 7.9 months. At a mean follow-up 34 months, vitreous seed regression was achieved in 88 eyes (97%) and eye salvage was achieved in 77 eyes (85%). Older age (P = 0.018) and recurrence of retinal tumor (15/17 eyes; P < 0.01) significantly increased the risk of vitreous seed recurrence. Cataract was the most common complication seen in 17 eyes (9%). CONCLUSIONS: Intravitreal topotecan at an every 3- to 4-week regimen is effective against both refractory and recurrent vitreous seeds. The vitreous seed morphologic features correspond to the number of injections required for regression. Increasing age and recurrence of retinal tumor increase the risk of vitreous seed recurrence after treatment with IVT. FINANCIAL DISCLOSURE(S): The author(s) have no proprietary or commercial interest in any materials discussed in this article.

Combined image-guided radiofrequency and iodine-125 seeds implantation in the treatment of recurrent hepatocellular carcinoma after hepatectomy.

BACKGROUND: Currently, there is no consensus on the treatment of recurrent hepatocellular carcinoma (HCC) after hepatectomy. It is necessary to assess the efficacy and safety of radiofrequency ablation (RFA) combined with iodine-125 seeds implantation (RFA-125I) in the treatment of recurrent HCC. METHODS: This study retrospectively analyzed the clinical data of patients with postoperative recurrence of HCC receiving RFA-125I or RFA treatment from January 2013 to January 2023. Both RFA and 125I seeds implantation were performed under dual guidance of ultrasound and CT. Overall survival (OS), progression-free survival (PFS), recurrence, and complications were compared between the two groups. RESULTS: A total of 210 patients with recurrent HCC were enrolled in this study, including 125 patients in the RFA-125I group and 85 patients in the RFA group. The RFA-125I group showed a significantly better survival benefit than RFA group (median OS: 37 months vs. 16 months, P < 0.001; median PFS: 15 months vs. 10 months, P = 0.001). The uni- and multivariate analysis showed that RFA-125I was a protective factor for OS and PFS. There were no procedure-related deaths and no grade 3 or higher adverse events in both groups. CONCLUSIONS: RFA combined with 125I seeds implantation under dual guidance of ultrasound and CT is effective and safe for the treatment of HCC patients with recurrence after hepatectomy.

New horizon to the world of gut microbiome: seeds germination.

The second brain of humans has been known as the microbiome. The microbiome is a dynamic network composed of commensal bacteria, archaea, viruses, and fungi colonized in the human gastrointestinal tract. They play a vital role in human health by metabolizing components, maturation of the immune system, and taking part in the treatment of various diseases. Two important factors that can affect the gut microbiome's composition and/or function are the food matrix and methods of food processing. Based on scientific research, the consumption of whole grains can make positive changes in the gut microbiota. Seeds contain different microbiota-accessible substrates that can resist digestion in the upper gastrointestinal tract. Seed germination is one of the simplest and newest food processing approaches to improve seeds' bioavailability and overall nutritional value. During germination, the dormant hydrolytic seed's enzymes have been activated and then metabolize the macromolecules. The quality and quantity of bioactive compounds like prebiotics, fiber, phenolic compounds (PC), total free amino acids, and γ-aminobutyric acid (GABA) can increase even up to 4-10 folds in some cases. These components stimulate the survival and growth of healthful bacteria like probiotics and boost their activity. This effect depends on several parameters, e.g., germination environmental conditions. This review aims to provide up-to-date and latest research about promoting bioactive components during seed germination and investigating their impacts on gut microbiota to understand the possible direct and indirect effects of seed germination on the microbiome and human health.

Gut microbiome plays a vital role in human health.Promoting gut beneficial bacteria can treat some human diseases.Beneficial gut bacteria can improve by seed's bioactive compoundsSeed's bioactive compounds can increase during germination.Germination is a low-in-cost process that can make an indirect positive effect on the gut.

Chia (Salvia hispanica L.), a functional 'superfood': new insights into its botanical, genetic and nutraceutical characteristics.

BACKGROUND: Chia (Salvia hispanica L.) seeds have become increasingly popular among health-conscious consumers due to their high content of ω-3 fatty acids, which provide various health benefits. Comprehensive chemical analyses of chia seeds' fatty acids and proteins have been conducted, revealing their functional properties. Recent studies have confirmed the high ω-3 content of chia seed oil and have hinted at additional functional characteristics. SCOPE: This review article aims to provide an overview of the botanical, morphological, and biochemical features of chia plants, seeds, and seed mucilage. Additionally, we discuss the recent developments in genetic and molecular research on chia, including the latest transcriptomic and functional studies that examine the genes responsible for chia fatty acid biosynthesis. In recent years, research on chia seeds has shifted its focus from studying the physicochemical characteristics and chemical composition of seeds to understanding the metabolic pathways and molecular mechanisms that contribute to their nutritional benefits. This has led to a growing interest in various pharmaceutical, nutraceutical, and agricultural applications of chia. In this context, we discuss the latest research on chia, as well as the questions that remain unanswered, and identify areas that require further exploration. CONCLUSIONS: Nutraceutical compounds associated with significant health benefits including ω-3 PUFAs, proteins, and phenolic compounds with antioxidant activity have been measured in high quantities in chia seeds. However, comprehensive investigations through both in vitro experiments and in vivo animal and controlled human trials are expected to provide greater clarity on the medicinal, antimicrobial, and antifungal effects of chia seeds. The recently published genome of chia and gene editing technologies, such as CRISPR, facilitate functional studies deciphering molecular mechanisms of biosynthesis and metabolic pathways in this crop. This necessitates development of stable transformation protocols and creation of a publicly available lipid database, mutant collection, and large-scale transcriptomic datasets for chia.