New strategies to address world food security and elimination of malnutrition: future role of coarse cereals in human health.

As we face increasing challenges of world food security and malnutrition, coarse cereals are coming into favor as an important supplement to human staple foods due to their high nutritional value. In addition, their functional components, such as flavonoids and polyphenols, make them an important food source for healthy diets. However, we lack a systematic understanding of the importance of coarse cereals for world food security and nutritional goals. This review summarizes the worldwide cultivation and distribution of coarse cereals, indicating that the global area for coarse cereal cultivation is steadily increasing. This paper also focuses on the special adaptive mechanisms of coarse cereals to drought and discusses the strategies to improve coarse cereal crop yields from the perspective of agricultural production systems. The future possibilities, challenges, and opportunities for coarse cereal production are summarized in the face of food security challenges, and new ideas for world coarse cereal production are suggested.

Transcriptome Sequencing and Metabolome Analysis Reveals the Molecular Mechanism of Drought Stress in Millet.

As one of the oldest agricultural crops in China, millet (Panicum miliaceum) has powerful drought tolerance. In this study, transcriptome and metabolome analyses of 'Hequ Red millet' (HQ) and 'Yanshu No.10' (YS10) millet after 6 h of drought stress were performed. Transcriptome characteristics of drought stress in HQ and YS10 were characterized by Pacbio full-length transcriptome sequencing. The pathway analysis of the differentially expressed genes (DEGs) showed that the highly enriched categories were related to starch and sucrose metabolism, pyruvate metabolism, metabolic pathways, and the biosynthesis of secondary metabolites when the two millet varieties were subjected to drought stress. Under drought stress, 245 genes related to energy metabolism were found to show significant changes between the two strains. Further analysis showed that 219 genes related to plant hormone signal transduction also participated in the drought response. In addition, numerous genes involved in anthocyanin metabolism and photosynthesis were confirmed to be related to drought stress, and these genes showed significant differential expression and played an important role in anthocyanin metabolism and photosynthesis. Moreover, we identified 496 transcription factors related to drought stress, which came from 10 different transcription factor families, such as bHLH, C3H, MYB, and WRKY. Further analysis showed that many key genes related to energy metabolism, such as citrate synthase, isocitrate dehydrogenase, and ATP synthase, showed significant upregulation, and most of the structural genes involved in anthocyanin biosynthesis also showed significant upregulation in both strains. Most genes related to plant hormone signal transduction showed upregulated expression, while many JA and SA signaling pathway-related genes were downregulated. Metabolome analysis was performed on 'Hequ red millet' (HQ) and 'Yanshu 10' (YS10), a total of 2082 differential metabolites (DEMs) were identified. These findings indicate that energy metabolism, anthocyanins, photosynthesis, and plant hormones are closely related to the drought resistance of millet and adapt to adversity by precisely regulating the levels of various molecular pathways.

MiR-224-5p Targeting OCLN Promotes the Proliferation, Migration, and Invasion of Clear Cell Renal Cell Carcinoma Cells.

A number of studies reported that miR-224-5p is involved in a variety of cancer-related cellular processes, yet its physiological role in clear cell renal cell carcinoma (ccRCC) remains unclear. In order to clarify the function of miR-224-5p in ccRCC, real-time quantitative-PCR was conducted to compare the expression of miR-224-5p in human normal renal tubular epithelial cell lines and ccRCC cell lines first, and a strikingly upregulated expression was observed in ccRCC cell lines. Inhibition of miR-224-5p expression by microRNA inhibitors could inhibit the proliferation, migration, and invasion of ccRCC cells. Besides, it was validated by dual-luciferase assay in which miR-224-5p directly targeted OCLN gene. The expression of OCLN was downregulated in ccRCC cells, and overexpression of miR-224-5p could inhibit the mRNA and protein expression levels of OCLN. Overexpression of OCLN could reduce the proliferation, migration, and invasion of ccRCC cells, while overexpressed miR-224-5p could partially reverse that inhibitory effect. Therefore, the promotive effect of miR-224-5p on the proliferation, invasion, and migration of ccRCC cell lines was at least partly due to the inhibition of OCLN expression. These findings highlighted the important function of miR-224-5p, which was promoting cell proliferation, migration, and invasion by downregulating OCLN, in the pathogenesis of ccRCC, and provided a potential treatment strategy.

Delivery of miR-224-5p by Exosomes from Cancer-Associated Fibroblasts Potentiates Progression of Clear Cell Renal Cell Carcinoma.

OBJECTIVES: Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma. Cancer-associated fibroblasts (CAFs) as the primary components of cancer stroma can affect tumor progression by secreting exosomes, while exosomes are carriers for proteins, nucleic acids, and other agents that responsible for delivery of biological information. Given this, exosomes derived from CAFs are emerging as promising biomarkers in clinical cancer diagnosis. Nevertheless, their role in clear cell renal cell carcinoma (ccRCC) remains poorly understood. METHODS: Here, we separated fibroblasts from ccRCC tissue, extracted exosomes, observed their morphology, and detected the expression of exosome marker proteins including Hsp70, CD9, and CD63. In the meantime, we labeled exosomes and performed coculture experiment to verify the delivery of miR-224-5p from CAFs to 769-P cells with exosomes as a carrier, so as to clarify the effect of CAF-derived exosomes on ccRCC cell malignant behaviors, as well as to discuss how miR-224-5p involves in above regulation. RESULTS: Transmission electron microscopy was firstly applied, and it was noted that the exosomes we isolated were in normal range. Besides, Western blot also confirmed the presence of exosome marker proteins Hsp70, CD9, and CD63. Furthermore, coculture experiments were performed and the CAF-derived exosomes were observed to be able to facilitate the malignant behaviors of ccRCC cells, and the exosomal miR-224-5p could be internalized by ccRCC cells to participate in regulation of cell proliferation, migration, invasion, and apoptosis. CONCLUSION: To sum up, miR-224-5p can enter ccRCC cells via CAF-derived exosomes, in turn, promoting the malignant behaviors of ccRCC cells, which indicates that miR-224-5p has the potential severing as a therapeutic target for ccRCC.

Cotyledons facilitate the adaptation of early-maturing soybean varieties to high-latitude long-day environments.

Soybean (Glycine max), a typical short-day plant (SDP) domesticated in temperate regions, has expanded to high latitudes where daylengths are long from soybean emergence to bloom, but rapidly decrease from seed filling to maturity. Cotyledons are well known as the major storage organs in seeds, but it is unclear whether developing cotyledons store flowering substances at filling stage in SD for upcoming seedlings, or instead respond to photoperiod for floral induction after emergence of matured seeds in long-day (LD). Here, we report that cotyledons accelerate flowering of early-maturing varieties not resulting from stored floral stimuli but by perceiving photoperiod after emergence. We found that light signal is indispensable to activate cotyledons for floral induction, and flowering promoting gene GmFT2a is required for cotyledon-dependent floral induction via upregulation of floral identity gene GmAP1. Interestingly, cotyledons are competent to support the entire life cycle of a cotyledon-only plant to produce seeds, underlying a new photoperiod study system in soybean and other dicots. Taken together, these results demonstrate a substantial role for cotyledons in flowering process, whereby we propose a 'cotyledon-based self-reliance' model highlighting floral induction from emergence as a key ecological adaptation for rapid flowering of SDPs grown in LD environments at high latitudes.

Characteration and comparative analysis of the whole chloroplast genomes of five common millet (Panicum miliaceum).

Common millet (Panicum miliaceum) is the most valuable and ancient domesticated important crops in the world. We compared five common millet complete chloroplast genomes. A complete map of the variability across the genomes of the five common millet was produced that included single nucleotide variants, InDels, and structural variants, as well as differences in simple sequence repeats and repeat sequences. Molecular phylogeny strongly supported division of the five walnut species into single monophyly with a 100% bootstrap value. The availability of these genomes will provide genetic information for identifying species and hybrids, taxonomy, phylogeny, and evolution in common millet.

Sulforaphane alleviates retinal ganglion cell death and inflammation by suppressing NLRP3 inflammasome activation in a rat model of retinal ischemia/reperfusion injury.

This study aims to study the potentials of sulforaphane (SFN) against retinal ischemia/reperfusion (I/R) injury. A rat retinal I/R injury method was established. Retinal thickness change and retinal ganglion cell (RGC) death were determined using hematoxylin and eosin (H&E) staining and Fluoro-Gold (FG) labeling. The inflammatory cytokines production and microglia activation were evaluated by using quantitative real-time polymerase chain reaction (qRT-PCR), Western blot, and enzyme-linked immunosorbent assay (ELISA). Knockdown NLRP3 was performed, and the according changes of retinal RGCs were assessed. SFN administration significantly inhibited I/R and caused retinal thickness change and prevented RGCs death in retinal I/R model. SFN suppressed inflammatory cytokines production, microglia activation, and inflammasome activation. In accordance, NLRP3 knockdown presented the similar inhibitory effect on I/R rats. This study demonstrates that SFN prevents RGCs death and acts as a potent neuroprotective modulator in retinal I/R injury, which may be associated with inhibition of the NLRP3 inflammasome activation.

Plant Stage, Not Drought Stress, Determines the Effect of Cultivars on Bacterial Community Diversity in the Rhizosphere of Broomcorn Millet (Panicum miliaceum L.).

Broomcorn millet (Panicum miliaceum L.) is one of the oldest domesticated crops and has been grown in arid and semiarid areas in China since 10,000 cal. BP. However, limited information is available about how bacterial communities within the rhizosphere of different broomcorn millet cultivars respond to drought stress. Here, we characterized the changes in the rhizobacterial assemblages of two broomcorn millet cultivars, namely, P. miliaceum cv. HeQu Red (HQR) and P. miliaceum YanLi 10 (YL10), from the jointing stage to the grain filling stage after they were exposed to a short-term drought stress treatment at the seedling stage. Drought significantly inhibited the growth of both cultivars, but the effect on YL10 was higher than that on HQR, indicating that the drought tolerance of HQR was greater than that of YL10. Proteobacteria (33.8%), Actinobacteria (21.0%), Acidobacteria (10.7%), Bacteroidetes (8.2%), Chloroflexi (6.3%), Gemmatimonadetes (5.9%), Firmicutes (3.5%), Verrucomicrobia (2.9%), and Planctomycetes (2.7%) were the core bacterial components of broomcorn millet rhizosphere as suggested by 16S rDNA sequencing results. The diversity and composition of bacterial rhizosphere communities substantially varied at different developmental stages of broomcorn millet. As the plants matured, the richness and evenness of the rhizobacterial community significantly decreased. Principal coordinate analysis showed that the structure of the bacterial rhizosphere community changed notably only at the flowering stage between the two cultivars, suggesting a stage-dependent effect. Although drought stress had no significant effect on the diversity and structure of the bacterial rhizosphere community between the two cultivars, differential responses to drought was found in Actinobacteria and Acinetobacter, Lysobacter, Streptomyces, and Cellvibrio. The relative abundance of Actinobacteria and Lysobacter, Streptomyces, and Cellvibrio in the YL10 rhizosphere was stimulated by the drought treatment compared with that in the HQR rhizosphere, whereas the opposite effect was found in Acinetobacter. Our results suggested that the effects of cultivars on bacterial rhizosphere communities were highly dependent on plant developmental stage, reflecting the genetic variations in the two broomcorn millet cultivars.

Soil bacterial diversity changes in different broomcorn millet intercropping systems.

Plants growing in soil and the diverse microorganisms with which they are in direct contact have adapted to exploit their close association for mutual benefit. Various intercropping systems have been used to control plant disease and improve productivity in fields. Although high-throughput sequencing approaches have provided new insights into the soil bacterial community, current knowledge of intercropping of broomcorn millet with different leguminous plants is limited. In this study, characterization of different bacterial communities of monoculture and intercropping systems was achieved by deep sequencing. A total of 4684 operational taxonomic units were classified to the species level with good sampling depth and sequencing coverage. The abundance of Actinobacteria, Bacteroidetes, Proteobacteria, Acidobacteria, and Gemmatimonadetes varied at different growth stages and was related to growth of the intercropped plant. According to diversity analyses, Glycomyces, Aeromicrobium, Adhaeribacter, and Streptomyces were the dominant genera. In addition, we predicted functional gene composition based on bacterial OTUs present. Functional results showed that membrane transport and nutrient metabolism was highly abundant in all samples, although abundance varied at different growth stages, which indicated these pathways might be affected by the dominant categories of bacterial community. The dynamic changes observed during intercropping of broomcorn millet with different leguminous plants suggest that soil bacterial community structure exhibits a crop species-specific pattern. Further, agronomic trait data from different broomcorn millet intercropping systems were consistent with functional results and suggest that agronomic traits may be influenced by soil bacterial communities.

The complete chloroplast genome of Panicum miliaceum.

Panicum miliaceum is the most important and ancient domesticated crops in the world. The complete chloroplast genome of P. miliaceum was sequenced using the Illumina Hiseq platform (Illumina Inc., San Diego, CA). The chloroplast genome of P. miliaceum was 139,929 bp in length, with 38.60% GC content. It contains a pair of inverted repeats (IRs) (22,723 bp) which were separated by a large single copy (LSC) (81,918 bp) and a small single copy region (SSC) (12,565 bp). A total of 132 genes were annotated, which included 84 protein coding genes, 40 tRNA genes and eight rRNA genes. The neighbour-joining (NJ) phylogenetic analysis with the reported chloroplast genomes showed that P. miliaceum chloroplasts are most closely related to those of the Gramineae family.

Transcriptomic analysis reveals key early events of narciclasine signaling in Arabidopsis root apex.

KEY MESSAGE: Histochemical staining and RNA-seq data demonstrated that the ROS- and plant hormone-regulated stress responses are the key early events of narciclasine signaling in Arabidopsis root cells. Narciclasine, an amaryllidaceae alkaloid isolated from Narcissus tazetta bulbs, employs a broad range of functions on plant development and growth. However, its molecular interactions that modulate these roles in plants are not fully understood. To elucidate the global responses of Arabidopsis roots to short-term narciclasine exposure, we first measured the accumulation of H2O2 and O2- with histochemical staining, and then profiled the gene expression pattern in Arabidopsis root tips treated with 0.5 µM narciclasine across different exposure times by RNA-seq. Physiological measurements showed a significant increase in H2O2 began at 30-60 min of narciclasine treatment and O2- accumulated by 120 min. Compared with controls, 236 genes were upregulated and 54 genes were downregulated with 2 h of narciclasine treatment, while 968 genes were upregulated and 835 genes were downregulated with 12 h of treatment. The Gene Ontology analysis revealed that the differentially expressed genes were highly enriched during oxidative stress, including those involved in the "regulation of transcription", "response to oxidative stress", "plant-pathogen interaction", "ribonucleotide binding", "plant cell wall organization", and "ribosome biogenesis". Moreover, Kyoto Encyclopedia of Genes and Genomes pathway enrichment statistics suggested that carbohydrate metabolism, amino acid metabolism, amino sugar and nucleotide sugar metabolism, and biosynthesis of phenylpropanoid and secondary metabolites were significantly inhibited by 12 h of narciclasine exposure. Hence, our results demonstrate that hormones and H2O2 are important regulators of narciclasine signaling and help to uncover the factors involved in the molecular interplay between narciclasine and phytohormones in Arabidopsis root cells.

Molecular dynamic simulations give insight into the mechanism of binding between 2-aminothiazole inhibitors and CDK5.

Molecular docking, molecular dynamics (MD) simulations, and binding free energy analysis were performed to reveal differences in the binding affinities between five 2-aminothiazole inhibitors and CDK5. The hydrogen bonding and hydrophobic interactions between inhibitors and adjacent residues are analyzed and discussed. The rank of calculated binding free energies using the MM-PBSA method is consistent with experimental result. The results illustrate that hydrogen bonds with Cys83 favor inhibitor binding. The van der Waals interactions, especially the important contact with Ile10, dominate in the binding free energy and play a crucial role in distinguishing the different bioactivity of the five inhibitors.

Exploration of the binding of proton pump inhibitors to human P450 2C9 based on docking and molecular dynamics simulation.

Human P450 protein CYP2C9 is one of the major drug-metabolizing isomers, contributing to the oxidation of 16% of the drugs currently in clinical use. To examine the interaction mechanisms between CYP2C9 and proton pump inhibitions (PPIs), we used molecular docking and molecular dynamics (MD) simulation methods to investigate the conformations and interactions around the binding sites of PPIs/CYPP2C9. Results from molecular docking and MD simulations demonstrate that nine PPIs adopt two different conformations (extended and U-bend structures) at the binding sites and position themselves far above the heme of 2C9. The presence of PPIs changes the secondary structures and residue flexibilities of 2C9. Interestingly, at the binding sites of all PPI-CYP2C9 complexes except for Lan/CYP2C9, there are hydrogen-bonding networks made of PPIs, water molecules, and some residues of 2C9. Moreover, there are strong hydrophobic interactions at all binding sites for PPIs/2C9, which indicate that electrostatic interactions and hydrophobic interactions appear to be important for stabilizing the binding sites of most PPIs/2C9. However, in the case of Lan/2C9, the hydrophobic interactions are more important than the electrostatic interactions for stabilizing the binding site. In addition, an interesting conformational conversion from extended to U-bend structures was observed for pantoprazole, which is attributed to an H-bond interaction in the binding pocket, an internal π-π stacking interaction, and an internal electrostatic interaction of pantoprazole.