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Abstract Matrix vesicles (MVs) have shown strong effects in diseases such as vascular ectopic calcification and pathological calcified osteoarthritis and in wound repair of the skeletal system due to their membranous vesicle characteristics and abundant calcium and phosphorus content. However, the role of MVs in the progression of osteoporosis is poorly understood. Here, we report that annexin A5, an important component of the matrix vesicle membrane, plays a vital role in bone matrix homeostasis in the deterioration of osteoporosis. We first identified annexin A5 from adherent MVs but not dissociative MVs of osteoblasts and found that it could be sharply decreased in the bone matrix during the occurrence of osteoporosis based on ovariectomized mice. We then confirmed its potential in mediating the mineralization of the precursor osteoblast lineage via its initial binding with collagen type I to achieve MV adhesion and the subsequent activation of cellular autophagy. Finally, we proved its protective role in resisting bone loss by applying it to osteoporotic mice. Taken together, these data revealed the importance of annexin A5, originating from adherent MVs of osteoblasts, in bone matrix remodeling of osteoporosis and provided a new strategy for the treatment and intervention of bone loss.

Abstract Fibroblast growth factor 19 (FGF19) is recognized to play an essential role in cartilage development and physiology, and has emerged as a potential therapeutic target for skeletal metabolic diseases. However, FGF19-mediated cellular behavior in chondrocytes remains a big challenge. In the current study, we aimed to investigate the role of FGF19 on chondrocytes by characterizing mitochondrial biogenesis and fission–fusion dynamic equilibrium and exploring the underlying mechanism. We first found that FGF19 enhanced mitochondrial biogenesis in chondrocytes with the help of β Klotho (KLB), a vital accessory protein for assisting the binding of FGF19 to its receptor, and the enhanced biogenesis accompanied with a fusion of mitochondria, reflecting in the elongation of individual mitochondria and the up-regulation of mitochondrial fusion proteins. We then revealed that FGF19-mediated mitochondrial biogenesis and fusion required the binding of FGF19 to the membrane receptor, FGFR4, and the activation of AMP-activated protein kinase alpha (AMPKα)/peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC-1α)/sirtuin 1 (SIRT1) axis. Finally, we demonstrated that FGF19-mediated mitochondrial biogenesis and fusion was mainly dependent on the activation of p-p38 signaling. Inhibition of p38 signaling largely reduced the high expression of AMPKα/PGC-1α/SIRT1 axis, decreased the up-regulation of mitochondrial fusion proteins and impaired the enhancement of mitochondrial network morphology in chondrocytes induced by FGF19. Taking together, our results indicate that FGF19 could increase mitochondrial biogenesis and fusion via AMPKα-p38/MAPK signaling, which enlarge the understanding of FGF19 on chondrocyte metabolism. Video Abstract

Gap junctions, which are mainly composed of connexin units, play an indispensable role in cell morphogenesis, proliferation, migration, adhesion and differentiation of osteoblast lineage cells, and thus mediate bone development, homeostasis and disease occurrence. Platelet-derived growth factor-AA (PDGF-AA) is proved to have a great influence on osteoblast cell lines and is widely applied in the field of bone defect and wound healing. However, the role of PDGF-AA on gap junction formation in the osteoblast lineage remains elusive. In the current study, we aimed to investigate the impact of PDGF-AA on gap junction formation and cell-to-cell communication in the osteoblast lineage and explore its underlying biomechanism. We first found that PDGF-AA promoted cell proliferation and thus increased gap junction formations in living primary osteoblasts and MC3T3-E1 cells through scrape loading and dye transfer (SL/DT) assay. We then confirmed that PDGF-AA enhanced gap junction formations through up-regulation of connexin 43 (Cx43). We next detected the activation of p-Akt signaling in primary osteoblasts and MC3T3-E1 cells that were induced by PDGF-AA. Through inhibitory experiments, we further confirmed that PDGF-AA-mediated gap junction formation occurred via the activation of PI3K/Akt signaling. Taking together, our results provided evidences that PDGF-AA promoted gap junction formation in the osteoblast lineage through p-Akt signaling, which helped to understand the role of PDGF-AA in bone regeneration and diseases.

In this study, we used the modified CRISPR/Cas9 system to produce targeted point mutations in cauliflower. Acetolactate synthase (ALS) and Centromere-specific histone H3 variant (CENH3) genes were selected as the base-editing targets and hypocotyls of cauliflower were used as explants. For ALS gene, a C-to-T conversion in the Pro182 codon (CCT) can alter the encoded amino acid, likely resulting in herbicide resistance, and a C-to-T mutation in the Leu133 codon (CTT) in the CENH3 gene may produce a haploid inducer. Results indicated that the transformation efficiency was 1.8%–4.5% and the mutation efficiencies for the ALS and CENH3 genes were approximately 22% and 87%, respectively. The ALS mutant cauliflower showed strong herbicide resistance, with possible immediate implications for broadleaf weed control in cauliflower fields.

Articular cartilage, composed of collagen type II as a major extracellular matrix and chondrocyte as a unique cell type, is a specialized connective tissue without blood vessels, lymphatic vessels and nerves. This distinctive characteristic of articular cartilage determines its very limited ability to repair when damaged. It is well known that physical microenvironmental signals regulate many cell behaviors such as cell morphology, adhesion, proliferation and cell communication even determine chondrocyte fate. Interestingly, with increasing age or progression of joint diseases such as osteoarthritis (OA), the major collagen fibrils in the extracellular matrix of articular cartilage become larger in diameter, leading to stiffening of articular tissue and reducing its resistance to external tension, which in turn aggravates joint damage or progression of joint diseases. Therefore, designing a physical microenvironment closer to the real tissue and thus obtaining data closer to the real cellular behaviour, and then revealing the biological mechanisms of chondrocytes in pathological states is of crucial importance for the treatment of OA disease. Here we fabricated micropillar substrates with the same topology but different stiffnesses to mimic the matrix stiffening that occurs in the transition from normal to diseased cartilage. It was first found that chondrocytes responded to stiffened micropillar substrates by showing a larger cell spreading area, a stronger enhancement of cytoskeleton rearrangement and more stability of focal adhesion plaques. The activation of Erk/MAPK signalling in chondrocytes was detected in response to the stiffened micropillar substrate. Interestingly, a larger nuclear spreading area of chondrocytes at the interface layer between the cells and top surfaces of micropillars was observed in response to the stiffened micropillar substrate. Finally, it was found that the stiffened micropillar substrate promoted chondrocyte hypertrophy. Taken together, these results revealed the cell responses of chondrocytes in terms of cell morphology, cytoskeleton, focal adhesion, nuclei and cell hypertrophy, and may be beneficial for understanding the cellular functional changes affected by the matrix stiffening that occurs during the transition from a normal state to a state of osteoarthritis.

Due to the lack of accurate labels for the airborne synthetic aperture radar altimeter (SARAL), the use of deep learning methods is limited for estimating the above ground level (AGL) of complicated landforms. In addition, the inherent additive and speckle noise definitely influences the intended delay/Doppler map (DDM); accurate AGL estimation becomes more challenging when using the feature extraction approach. In this paper, a generalized AGL estimation algorithm is proposed, based on a fully supervised altimetry enhancement network (FuSAE-net), where accurate labels are generated by a novel semi-analytical model. In such a case, there is no need to have a fully analytical DDM model, and accurate labels are achieved without additive noises and speckles. Therefore, deep learning supervision is easy and accurate. Next, to further decrease the computational complexity for various landforms on the airborne platform, the network architecture is designed in a lightweight manner. Knowledge distillation has proven to be an effective and intuitive lightweight paradigm. To significantly improve the performance of the compact student network, both the encoder and decoder of the teacher network are utilized during knowledge distillation under the supervision of labels. In the experiments, airborne raw radar altimeter data were applied to examine the performance of the proposed algorithm. Comparisons with conventional methods in terms of both qualitative and quantitative aspects demonstrate the superiority of the proposed algorithm.

The RNA-binding glycine-rich proteins (RBGs) of the glycine-rich protein family play vital roles in regulating gene expression both at the transcriptional and post-transcriptional levels. However, the members and functions in response to abiotic stresses of the RBG gene family remain unclear in Brassica oleracea. In this study, a total of 19 BoiRBG genes were identified through genome-wide analysis in broccoli. The characteristics of BoiRBG sequences and their evolution were examined. An analysis of synteny indicated that the expansion of the BoiRBG gene family was primarily driven by whole-genome duplication and tandem duplication events. The BoiRBG expression patterns revealed that these genes are involved in reaction to diverse abiotic stress conditions (i.e., simulated drought, salinity, heat, cold, and abscisic acid) and different organs. In the present research, the up-regulation of BoiRBGA13 expression was observed when subjected to both NaCl-induced and cold stress conditions in broccoli. Moreover, the overexpression of BoiRBGA13 resulted in a noteworthy reduction in taproot lengths under NaCl stress, as well as the inhibition of seed germination under cold stress in broccoli, indicating that RBGs play different roles under various stresses. This study provides insights into the evolution and functions of BoiRBG genes in Brassica oleracea and other Brassicaceae family plants.

Abstract Microenvironmental biophysical factors play a fundamental role in controlling cell behaviors including cell morphology, proliferation, adhesion and differentiation, and even determining the cell fate. Cells are able to actively sense the surrounding mechanical microenvironment and change their cellular morphology to adapt to it. Although cell morphological changes have been considered to be the first and most important step in the interaction between cells and their mechanical microenvironment, their regulatory network is not completely clear. In the current study, we generated silicon-based elastomer polydimethylsiloxane (PDMS) substrates with stiff (15:1, PDMS elastomer vs. curing agent) and soft (45:1) stiffnesses, which showed the Young’s moduli of ~450 kPa and 46 kPa, respectively, and elucidated a new path in cytoskeleton re-organization in chondrocytes in response to changed substrate stiffnesses by characterizing the axis shift from the secreted extracellular protein laminin β1, focal adhesion complex protein FAK to microfilament bundling. We first showed the cellular cytoskeleton changes in chondrocytes by characterizing the cell spreading area and cellular synapses. We then found the changes of secreted extracellular linkage protein, laminin β1, and focal adhesion complex protein, FAK, in chondrocytes in response to different substrate stiffnesses. These two proteins were shown to be directly interacted by Co-IP and colocalization. We next showed that impact of FAK on the cytoskeleton organization by showing the changes of microfilament bundles and found the potential intermediate regulators. Taking together, this modulation axis of laminin β1-FAK-microfilament could enlarge our understanding about the interdependence among mechanosensing, mechanotransduction, and cytoskeleton re-organization.

IntroductionNitrogen (N) is essential for plant growth and yield production and can be taken up from soil in the form of nitrate or peptides. The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) genes play important roles in the uptake and transportation of these two forms of N.MethodsBioinformatic analysis was used to identify and characterize the NPF genes in Setaria. RNA-seq was employed to analyze time-series low nitrate stress response of the SiNPF genes. Yeast and Arabidopsis mutant complementation were used to test the nitrate transport ability of SiNRT1.1B1 and SiNRT1.1B2.ResultsWe identified 92 and 88 putative NPF genes from foxtail millet (Setaria italica L.) and its wild ancestor green foxtail (Setaria viridis L.), respectively. These NPF genes were divided into eight groups according to their sequence characteristics and phylogenetic relationship, with similar intron-exon structure and motifs in the same subfamily. Twenty-six tandem duplication and 13 segmental duplication events promoted the expansion of SiNPF gene family. Interestingly, we found that the tandem duplication of the SiNRT1.1B gene might contribute to low nitrogen tolerance of foxtail millet. The gene expression atlas showed that the SiNPFs were divided into two major clusters, which were mainly expressed in root and the above ground tissues, respectively. Time series transcriptomic analysis further revealed the response of these SiNPF genes to short- and long- time low nitrate stress. To provide natural variation of gene information, we carried out a haplotype analysis of these SiNPFs and identified 2,924 SNPs and 400 InDels based on the re-sequence data of 398 foxtail millet accessions. We also predicted the three-dimensional structure of the 92 SiNPFs and found that the conserved proline 492 residues were not in the substrate binding pocket. The interactions of SiNPF proteins with NO3− were analyzed using molecular docking and the pockets were then identified. We found that the SiNPFs NO3− binding energy ranged from-3.4 to -2.1 kcal/mol.DiscussionTaken together, our study provides a comprehensive understanding of the NPF gene family in Setaria and will contribute to function dissection of these genes for crop breeding aimed at improving high nitrogen use efficiency.

Transforming growth factor-beta2 (TGF-β2) is recognized as a versatile cytokine that plays a vital role in regulation of joint development, homeostasis, and diseases, but its role as a biological mechanism is understood far less than that of its counterpart, TGF-β1. Cartilage as a load-resisting structure in vertebrates however displays a fragile performance when any tissue disturbance occurs, due to its lack of blood vessels, nerves, and lymphatics. Recent reports have indicated that TGF-β2 is involved in the physiological processes of chondrocytes such as proliferation, differentiation, migration, and apoptosis, and the pathological progress of cartilage such as osteoarthritis (OA) and rheumatoid arthritis (RA). TGF-β2 also shows its potent capacity in the repair of cartilage defects by recruiting autologous mesenchymal stem cells and promoting secretion of other growth factor clusters. In addition, some pioneering studies have already considered it as a potential target in the treatment of OA and RA. This article aims to summarize the current progress of TGF-β2 in cartilage development and diseases, which might provide new cues for remodelling of cartilage defect and intervention of cartilage diseases.

Abstract Background Brassica oleracea includes several morphologically diverse, economically important vegetable crops, such as the cauliflower and cabbage. However, genetic variants, especially large structural variants (SVs), that underlie the extreme morphological diversity of B. oleracea remain largely unexplored. Results Here we present high-quality chromosome-scale genome assemblies for two B. oleracea morphotypes, cauliflower and cabbage. Direct comparison of these two assemblies identifies ~ 120 K high-confidence SVs. Population analysis of 271 B. oleracea accessions using these SVs clearly separates different morphotypes, suggesting the association of SVs with B. oleracea intraspecific divergence. Genes affected by SVs selected between cauliflower and cabbage are enriched with functions related to response to stress and stimulus and meristem and flower development. Furthermore, genes affected by selected SVs and involved in the switch from vegetative to generative growth that defines curd initiation, inflorescence meristem proliferation for curd formation, maintenance and enlargement, are identified, providing insights into the regulatory network of curd development. Conclusions This study reveals the important roles of SVs in diversification of different morphotypes of B. oleracea, and the newly assembled genomes and the SVs provide rich resources for future research and breeding.

Z-DNA refers to the left-handed double-helix DNA that has attracted much attention because of its association with some specific biological functions. However, because of its low content and unstable conformation, Z-DNA is normally difficult to observe or identify. Up to now, there has been a lack of unified or standard analytical methods among diverse techniques for probing Z-DNA and its transformation conveniently. In this work, NaCl, MgCl2, and ethanol were utilized to induce d(GC)8 from B-DNA to Z-DNA in vitro, and Fourier transform infrared (FTIR) spectroscopy was employed to monitor the transformation of Z-DNA under different induction conditions. The structural changes during the transformation process were carefully examined, and the DNA chirality alterations were validated by the circular dichroism (CD) measurements. The Z-DNA characteristic signals in the 1450 cm−1–900 cm−1 region of the d(GC)8 infrared (IR) spectrum were observed, which include the peaks at 1320 cm−1, 1125 cm−1 and 925 cm−1, respectively. The intensity ratios of A1320/A970, A1125/A970, and A925/A970 increased with Z-DNA content in the transition process. Furthermore, compared with the CD spectra, the IR spectra showed higher sensitivity to Z-DNA, providing more information about the molecular structure change of DNA. Therefore, this study has established a more reliable FTIR analytical approach to assess BZ DNA conformational changes in solutions, which may help the understanding of the Z-DNA transition mechanism and promote the study of Z-DNA functions in biological systems.

Wheat is among the top 10 and most widely grown crops in the world. However, wheat is often infected with many soil-borne diseases, including sharp eyespot, mainly caused by the necrotrophic fungus Rhizoctonia cerealis, and Fusarium head blight (FHB), caused by Fusarium graminearum, resulting in reduced production. Piriformospora indica is a root endophytic fungus with a wide range of host plants, which increases their growth and tolerance to biotic and abiotic stresses. In this study, the capability of P. indica to protect wheat seedlings against R. cerealis and F. graminearum was investigated at the physiological, biochemical, and molecular levels. Our results showed that P. indica significantly reduced the disease progress on wheat caused by F. graminearum and R. cerealis in vivo, but not showed any antagonistic effect on F. graminearum and R. cerealis in vitro. Additionally, P. indica can induce systemic resistance by elevating H2O2 content, antioxidase activity, relative water content (RWC), and membrane stability index (MSI) compared to the plants only inoculated with F. graminearum or R. cerealis and control. RNA-seq suggested that transcriptome changes caused by F. graminearum were more severe than those caused by R. cerealis. The number of differentially expressed genes (DEGs) in the transcriptome can be reduced by the addition of P. indica: for F. graminearum reduced by 18% and for R. cerealis reduced 58%. The DEGs related to disease resistance, such as WRKY and MAPK, were upregulated by P. indica colonization. The data further revealed that the transcriptional resistance to F. graminearum and R. cerealis mediated by P. indica is quite different.

In vitro fermental behaviors and colonic inflammation of κ-carrageenan oligosaccharides (KO3 and KO6) obtained from simulated gastric digestion were investigated. With the proceeding of fermentation, κ-carrageenan oligosaccharides were readily degraded, exerting a notable impact on production of SCFAs and composition of gut microbiota. Both KO3 and KO6 significantly promoted pro-inflammatory bacteria Prevotella, while inhibited anti-inflammatory bacteria Bacteroides and Parabacteroides. Notably, fermental behavior of KO3 with larger degrees of polymerization (DPs) and KO6 with smaller DPs showed different responsible for fermentation, of which KO3 improved SCFAs production and highly increased the growth of Bifidobacterium and Lactobacillius, while KO6 reduced SCFAs production and enormously enhanced the abundance of mucin-producing bacteria Prevotellaceae. Associated with inflammatory effect on HT29 cells, KO6 fermental supernatants more promoted the secretions of IL-1β, TNF-α, SIgA and mucin2, hinting that smaller κ-carrageenan oligosaccharides might pose stronger inflammation. The results can be helpful for understanding the safety of κ-carrageenan oligosaccharides.

Background Autism spectrum disorder (ASD) and obesity are serious global public health problems. Studies have shown that ASD children are at a higher risk of obesity than the general population. To investigate the gut microbe characteristics of adults ASD and obese adults, we compared the gut microbiota of adults with ASD to obese adults. Methods The fecal samples were collected from 21 adult patients with ASD and 21 obese adults, and V3–V4 regions of 16S rRNA genes were sequenced by high-throughput DNA sequencing. The gut microbiota of adults with ASD and obese adults was compared. Results We observed the proportion of Firmicutes/Bacteroidetes in ASD was significantly increased, with families Lachnospiraceae and Ruminococcaceae significantly enriched in adult ASD. Eighteen genera, including Lachnospiracea incertae sedis, Ruminococcus, Blautia, and Holdemanella were significantly increased in adult ASD, whereas Megamonas and Fusobacterium were significantly increased in obesity. At the species level, we found six species enriched in ASD and three species enriched in obesity, including Phascolarctobacterium succinatuten producing propionate. Dialister succinatiphilus may be as a biomarker for predicting obesity, as well as Prevotella copri may be a common-owned pathogens of ASD and obesity. Conclusions Some conflicting results have been reported in microbiota studies of ASD, which may be related to age and obesity. Thus, the body mass index should be evaluated before analyzing the gut microbiota of patients with ASD, as obesity is prevalent in these individuals and gut microbiota is severally affected by obesity.

Background Obesity is the cause of cardiovascular diseases and other diseases, leading to increased medical costs, and causing a great burden to individuals, families and society. The prevalence of obesity is increasing and has become a global health problem. There is growing evidence that gut microbiota plays an important role in obesity. In this article, we revealed the differences in the gut microbiota between 21 people with obesity and 21 control subjects, and predicted the functional potential changes by 16S rRNA sequencing of the fecal bacteria of the subjects. Methods The raw sequencing data of 21 healthy Beijing volunteers was downloaded from Microbial Genome Database System. Microbial 16S rRNA genes of 21 adults with obesity were sequenced on an Illumina MiSeq instrument and analyzed by using bioinformatics and statistical methods. Results The diversity of gut microbiota in people with obesity decreased significantly. There were significant differences in gut microbiota between the Obesity and Control group at different levels. At the phylum level, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria are significantly different between the Obesity and Control group. In people with obesity, the ratio of Firmicutes/Bacteroidetes decreased significantly. At the genus level, there were significant differences among the 16 major genera, of which four genera Prevotella, Megamonas, Fusobacterium and Blautia increased significantly in people with obesity, while the remaining 12 genera, Faecalibacterium, Lachnospiracea_incertae_sedis, Gemmiger and Clostridium XlVa, etc. decreased significantly. At the species level, nine species including Bacteroides uniformis and Prevotella copri had significant differences. Compared with the control group, subjects with obesity were abnormalities in 57 pathways, mainly in Carbohydrate metabolism and Lipid metabolism. Conclusions Overall, our study revealed differences in the gut microbiota between people with obesity and control subjects, providing novel target for the treatment of individuals with obesity.

Abstract Background The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the most important plant tissue in which the cell fate and organ meristems have been determined. In this study, a series of whole-genome small RNA, degradome and transcriptome analyses were performed on cucumber shoot apical tissues treated with high vs. low temperature and long vs. short photoperiod. Results A total of 164 known miRNAs derived from 68 families and 203 novel miRNAs from 182 families were identified. Their 4611 targets were predicted using psRobot and TargetFinder, amongst which 349 were validated by degradome sequencing. Fourteen targets of six miRNAs were differentially expressed between the treatments. A total of eight known and 16 novel miRNAs were affected by temperature and photoperiod. Functional annotations revealed that “Plant hormone signal transduction” pathway was significantly over-represented in the miRNA targets. The miR156/157/SBP-Boxes and novel-mir153/ethylene-responsive transcription factor/senescence-related protein/aminotransferase/acyl-CoA thioesterase are the two most credible miRNA/targets combinations modulating the plant’s responsive processes to the temperature-photoperiod changes. Moreover, the newly evolved, cucumber-specific novel miRNA (novel-mir153) was found to target 2087 mRNAs by prediction and has 232 targets proven by degradome analysis, accounting for 45.26–58.88% of the total miRNA targets in this plant. This is the largest sum of genes targeted by a single miRNA to the best of our knowledge. Conclusions These results contribute to a better understanding of the miRNAs mediating plant adaptation to combinations of temperature and photoperiod and sheds light on the recent evolution of new miRNAs in cucumber.

Sulfated polysaccharides from abalone (Haliotis discus hannai Ino) gonad (AGSP) is shown to have various bioactivities, but it remains unknown whether AGSP produces any effect on high fat diet (HFD)-induced obesity. This study indicated that AGSP inhibited weight gain and improved body composition in HFD-fed mice without reducing food consumption. Moreover, AGSP reduced fat accumulation in the liver and epididymal fat tissues of HFD-fed mice via the modulation of lipid metabolism. Such effects could be associated with the improvement of the gut microbiota as indicated by a decreased ratio of Firmicutes/Bacteroidetes and overall structure changes of the gut microbiota. Butyrate as the end product of bacterial fermentation was significantly increased in AGSP-fed mice, and thus may inhibit lipid-related gene expressions via G protein-coupled receptors-dependent pathways. In short, it suggested that AGSP can be used as beneficial polysaccharides to improve obesity and its associated disorders.

Some polysaccharides from Gracilaria lemaneiformis (GLPs) are shown to have various activities, but the effects of GLPs on diet-induced obesity and the underlying mechanisms are unclear. This study indicated that dietary supplementation with GLPs reduced weight gain and improved body composition in high fat diet (HFD)-fed mice without reduced food consumption. Fat accumulation in the liver and adipose tissues was reduced by GLPs, and the damages of HFD on the intestine were repaired. These effects could be associated with the modulation of the gut microbiota, resulting in a specific microbiota that similar to normal microbiota. Changes in the gut microbiota may affect the expression of lipid-related genes via short chain fatty acids-dependent pathways. It revealed that GLPs can alleviate HFD-induced obesity by improving the gut microbiota dysbiosis, suggesting that G. lemaneiformis can be developed as food supplement to improve metabolic syndrome and intestinal diseases.

Abstract Background Radish (Raphanus sativus L.) belongs to the family Brassicaceae, and is an economically important root crop grown worldwide. Flowering is necessary for plant propagation, but it is also an important agronomic trait influencing R. sativus fleshy taproot yield and quality in the case of an imbalance between vegetative and reproductive growth. There is currently a lack of detailed information regarding the pathways regulating the flowering genes or their evolution in R. sativus. The release of the R. sativus genome sequence provides an opportunity to identify and characterize the flowering genes using a comparative genomics approach. Results We identified 254 R. sativus flowering genes based on sequence similarities and analyses of syntenic regions. The genes were unevenly distributed on the various chromosomes. Furthermore, we discovered the existence of R. sativus core function genes in the flowering regulatory network, which revealed that basic flowering pathways are relatively conserved between Arabidopsis thaliana and R. sativus. Additional comparisons with Brassica oleracea and Brassica rapa indicated that the retained flowering genes differed among species after genome triplication events. The R. sativus flowering genes were preferentially retained, especially those associated with gibberellin signaling and metabolism. Moreover, analyses of selection pressures suggested that the genes in vernalization and autonomous pathways were more variable than the genes in other R. sativus flowering pathways. Conclusions Our results revealed that the core flowering genes are conserved between R. sativus and A. thaliana to a certain extent. Moreover, the copy number variation and functional differentiation of the homologous genes in R. sativus increased the complexity of the flowering regulatory networks after genome polyploidization. Our study provides an integrated framework for the R. sativus flowering pathways and insights into the evolutionary relationships between R. sativus flowering genes and the genes from A. thaliana and close relatives.

Various bioactivities of sulfated polysaccharides have been demonstrated, but the exact mechanisms involved are still unclear, which can be mainly attributed to a lack of recognition of polysaccharides metabolism in vivo. To define action mechanisms of sulfated polysaccharide from pacific abalone (AGSP), its metabolic characteristics were first evaluated in a mice model. The result showed that AGSP was hard to be absorbed into plasma, and most might be excreted from the body via feces. The in vitro models showed that human digestive juices had no effects on AGSP, and AGSP could exert its bioactivities by modulating the gut microbiota composition. It was noteworthy that small AGSP fragment was also hard to be absorbed by the body. In summary, this study demonstrated that various bioactivities of AGSP could be mainly attributed to the modulation of the gut microbiota rather than direct action on body organs far away from the digestive tract.

Radish (Raphanus sativus) is an important cruciferous root crop with a close relationship to Chinese cabbage (Brassica rapa). RT-qPCR is used extensively to evaluate the expression levels of target genes, and accurate measurement of target gene expression with this method is determined by the valid reference genes used for data nomalization in different experimental conditions. Screening for appropriate reference genes with stable expression based on RT-qPCR data is important for gene expression and functional analysis research in radish and its relatives. However, many researches have thought that almost no single reference gene is widely suitable for all experimental conditions, and few researchers have paid attention to the validation of reference genes in radish gene expression analysis. In the present study, 12 candidate reference genes were selected for analysis. Their expression in 28 samples, including 20 radish samples from different organs and conditions, four Chinese cabbage organs and four organs of their distant hybrid, was assessed by RT-qPCR and then five software tools—ΔCt, geNorm, NormFinder, BestKeeper and RefFinder—were used to compare their expression stability. The results showed that the most suitable reference genes were different in different organs and conditions. GAPDH, DSS1, and UP2 were optimal reference genes for gene expression analysis in all organs and conditions in radish. UPR, GSNOR1, and ACTIN2/7 were the most stable reference genes in different radish organs. UP2 and GAPDH were suitable reference genes for radish pistil development studies. RPII, UBC9, and GAPDH had the most stable expression in radish under various stresses. DSS1, UP2, and TEF2 were the optimal reference genes for Chinese cabbage organs, whereas TUA was optimal for the distant hybrid. UP2, and TEF2 were appropriate reference genes for all of the samples together. The optimal reference genes we identified, UP2, GAPDH, UPR, and GSNOR1 were verified by normalizing the expression patterns of YAB3, RPL, and FUL. These results will provide important information for selecting target reference genes in different research contexts and improve the accuracy and precision of gene expression analysis for radish, Chinese cabbage and their distant hybrid.