Two Ratiometric Fluorescent Probes Based on the Hydroxyl Coumarin Chalcone Unit with Large Fluorescent Peak Shift for the Detection of Hydrazine in Living Cells.

Hydrazine is widely used in industrial and agricultural production, but excessive hydrazine possesses a serious threat to human health and environment. Here two new ratiometric fluorescence probes, DDP and DDC, with the hydroxyl coumarin chalcone unit as the sensing site are developed, which can achieve colorimetric and ratiometric recognition for hydrazine with good sensitivity, excellent selectivity, and anti-interference. The calculated fluorescence limits of detections are 0.26 µM (DDC) and 0.14 µM (DDP). The ratiometric fluorescence response to hydrazine is realized through the adjustment of donor and receptor units in coumarin conjugate structure terminals, accompanied by fluorescence peak shift about 200 nm (DDC, 188 nm; DDP, 229 nm). Stronger electropositivity in the carbon-carbon double bond is helpful to the first phase addition reaction between the probe and hydrazine. Higher phenol activity in the hydroxyl coumarin moiety will facilitate the following dihydro-pyrazole cyclization reaction. In addition, both of these probes realized the convenient detection of hydrazine vapor. The probes were also successfully applied to detect hydrazine in actual water samples, different soils, and living cells.

Farnesoid X receptor (FXR) activation induces the antioxidant protein metallothionein 1 expression in mouse liver.

Farnesoid X receptor (FXR) is a metabolic nuclear receptor, which protects liver from many endogenous and exogenous injuries. Metallothioneins (MTs) belong to a low-molecular-weight protein family involved in metal homeostasis and the regulation of hepatic oxidative stress. In the present study, we aimed to investigate the effect of FXR on hepatic MT1 expression and the underlying mechanism. C57BL/6 mice or primary cultured mouse hepatocytes were treated with the synthetic FXR ligand GW4064 or natural ligand CDCA. RNA-Sequencing (RNA-seq) analysis was performed to identify gene expression profile in the livers of mice treated with GW4064. Real-time PCR and Western blot were applied to determine the expression of MT1 and other FXR target genes in the livers of mice and primary hepatocytes treated with GW4064 and CDCA. Cellular and subcellular locations of MT1 in the livers of mice treated with GW4064 were examined using immunohistochemistry assay. FXR small interfering RNAs (siRNA) was transfected to silence FXR. Luciferase reporter and chromatin immunoprecipitation (ChIP) assays were utilized to confirm the regulation of MT1 gene promoter activity by FXR. RNA-seq analysis revealed that GW4064 treatment significantly induced MT1 expression in mouse liver. Consistently, MT1 expression in the hepatocytes of mouse livers and cultured hepatocytes was upregulated by GW4064 as well as CDCA. In addition, adenovirus-mediated overexpression of FXR markedly increased, while siRNA-mediated FXR silencing significantly suppressed MT1 expression in cultured hepatocytes. Luciferase reporter and ChIP assays further confirmed that the MT1 gene was under the direct control of FXR. Collectively, our findings demonstrate that MT1 is a novel target gene of FXR and may contribute to antioxidative capacity of FXR in liver diseases.

Farnesoid X receptor is essential for the survival of renal medullary collecting duct cells under hypertonic stress.

Hypertonicity in renal medulla is critical for the kidney to produce concentrated urine. Renal medullary cells have to survive high medullary osmolarity during antidiuresis. Previous study reported that farnesoid X receptor (FXR), a nuclear receptor transcription factor activated by endogenous bile acids, increases urine concentrating ability by up-regulating aquaporin 2 expression in medullary collecting duct cells (MCDs). However, whether FXR is also involved in the maintenance of cell survival of MCDs under dehydration condition and hypertonic stress remains largely unknown. In the present study, we demonstrate that 24-hours water restriction selectively up-regulated renal medullary expression of FXR with little MCD apoptosis in wild-type mice. In contrast, water deprivation caused a massive apoptosis of MCDs in both global FXR gene-deficient mice and collecting duct-specific FXR knockout mice. In vitro studies showed that hypertonicity significantly increased FXR and tonicity response enhancer binding protein (TonEBP) expression in mIMCD3 cell line and primary cultured MCDs. Activation and overexpression of FXR markedly increased cell viability and decreased cell apoptosis under hyperosmotic conditions. In addition, FXR can increase gene expression and nuclear translocation of TonEBP. We conclude that FXR protects MCDs from hypertonicity-induced cell injury very likely via increasing TonEBP expression and nuclear translocation. This study provides insights into the molecular mechanism by which FXR enhances urine concentration via maintaining cell viability of MCDs under hyperosmotic condition.

Aurone Derivative Revealing the Metabolism of Lipid Droplets and Monitoring Oxidative Stress in Living Cells.

Lipid droplets (LDs) are closely connected to many physiological processes and abnormal LDs are related to many diseases. Herein, a family of two-photon fluorescence compounds based on the aurone skeleton were developed as efficient LDs imaging probes. They exhibit the obvious solvatochromism effect from blue to orange emission (∼140 nm shift) in various solvents. The robust probes possess low toxicity to living cells, high photobleaching resistance, and superior photostability and can light up LDs with high specificity. Furthermore, the probe DMMB (aurone skeleton with dimethylamino) was carefully applied in real-time monitoring of the morphological changes of LDs and the interactions between LDs and mitochondria under specific physiological conditions (e.g., starvation). We have observed for the first time the dynamic change between mitochondria and LDs when mitochondrial damage is caused by a large excess of H2O2 in a short period of time.

An efficient virus-induced gene silencing (VIGS) system for functional genomics in Brassicas using a cabbage leaf curl virus (CaLCuV)-based vector.

MAIN CONCLUSION: CaLCuV-based VIGS effectively works in cabbage and contributes to efficient functional genomics research in Brassica crop species. Virus-induced gene silencing (VIGS), a posttranscriptional gene silencing method, is an effective technique for analysing the functions of genes in plants. However, no VIGS vectors have been available for Brassica oleracea until now. Here, tobacco rattle virus (TRV), pTYs and cabbage leaf curl virus (CaLCuV) gene-silencing vectors (PCVA/PCVB) were chosen to improve the VIGS system in cabbage using the phytoene desaturase (PDS) gene as an efficient visual indicator of VIGS. We successfully silenced the expression of PDS and observed photobleaching phenomena in cabbage in response to pTYs and CaLCuV, with the latter being more easy to operate and less expensive. The parameters potentially affecting the silencing efficiency of VIGS by CaLCuV in cabbage, including the targeting fragment strategy, inoculation method and incubation temperature, were then compared. The optimized CaLCuV-based VIGS system involves the following: an approximately 500 bp insert sequence, an Agrobacterium OD600 of 1.0, use of the vacuum osmosis method applied at the bud stage, and an incubation temperature of 22 °C. Using these parameters, we achieved a stable silencing efficiency of 65%. To further test the effectiveness of the system, we selected the Mg-chelatase H subunit (ChlH) gene in cabbage and knocked down its expression, and we observed yellow leaves, as expected. We successfully applied the CaLCuV-based VIGS system to two other representative Brassica crop species, B. rapa and B. nigra, and thus expanded the application scope of this system. Our VIGS system described here will contribute to efficient functional genomics research in Brassica crop species.

From reversible to irreversible bistable switches via bifurcations in a gene regulatory network.

The interplay of small, noncoding microRNAs (miRNAs), mRNAs and proteins plays crucial roles in almost all cellular processes. MiR-124, widely known as a memory-related miRNA, can regulate LTM by binding to the mRNA of CREB1 stimulated with 5-HT. In this paper, we establish a regulatory network model of CREB1 and miR-124 stimulated by 5-HT, in which miR-124 inhibits CREB1, which in turn enhances miR-124. Our model validates three protocols based on 5-HT in experiments on the induction of LTM in Aplysia. A steady-state analysis and numerical bifurcations of the abstracted system beyond memory formation, when the fast reaction has been in the equilibrium, can facilitate more abundant dynamical behaviors such as bistability and oscillation. The original system also exhibits bistability under appropriate feedback strengths, which is relevant to the mechanism of LTM formation. Furthermore, we specifically show a change in the transition from a reversible switch to an irreversible switch via bifurcations of the negative regulation of miR-124 on CREB1, which eventually maintains a high phosphorylated CREB1 level after initially elevated by 5-HT. These findings indicate that miR-124 provides an inhibitory constraint on long-term synaptic plasticity through the regulation of CREB1.

Genome-wide analysis of HSP70 family genes in cabbage (Brassica oleracea var. capitata) reveals their involvement in floral development.

BACKGROUND: Heat shock proteins have important functions in regulating plant growth and response to abiotic stress. HSP70 family genes have been described in several plant species, but a comprehensive analysis of the HSP70 family genes in cabbage has not been reported to date, especially their roles in floral development. RESULTS: In this study, we identified 52 BoHSP70 genes in cabbage. The gene structures, motifs, and chromosome locations of the BoHSP70 genes were analyzed. The genes were divided into seven classes using a phylogenetic analysis. An expression analysis showed that the BoHSP70 genes were highly expressed in actively growing tissues, including buds and calluses. In addition, six BoHSP70 genes were highly expressed in the binuclear-pollen-stage buds of a male fertile line compared with its near isogenic sterile line. These results were further verified using qRT-PCR. Subcellular localization analysis of the bud-specific gene BoHSP70-5 showed that it was localized in the cytoplasm. CONCLUSIONS: Our results help to elucidate the involvement of the BoHSP70 family genes in cabbage floral development and establish the groundwork for future research on the functions of these genes.

Surface engineering of carbon-coated cobalt-doped nickel phosphides bifunctional electrocatalyst for boosting 5-hydroxymethylfurfural oxidation coupled with hydrogen evolution.

Multiple surface/interface engineering is an effective approach to develop efficient electrocatalysts for promoting the practical application of electrocatalysis and achieving carbon neutrality. Herein, a deep eutectic liquid precursor containing phosphorus was designed. The self-supported three-dimensional (3D) cobalt-doped Ni12P5/Ni3P nanowire networks coated with a thin layer of carbon (Co-NixP@C) were prepared by using an in-situ one-step pyrolysis method. The as-obtained Co-NixP@C hybrid possesses a superaerophobic/superhydrophilic surface, which could promote electrolyte diffusion and enhance bubble release. Density functional theory (DFT) calculations reveal that Co-doping in NixP@C can promote the adsorption and activation of 5-hydroxymethylfurfural (HMF) molecules, and optimize the energy barrier of H* absorption. The self-supported Co-NixP@C was used as an efficient bifunctional electrocatalyst for HMF oxidation coupled with hydrogen evolution reaction (HER) in a 1.0 M KOH solution. A nearly 100 % yield of 2,5-furandicarboxylic acid (FDCA) was achieved. The self-supported Co-NixP@C displayed high activity and stability for both HER and HMF conversion. The HMF oxidation coupled with HER can be efficiently driven by a 1.5 V commercial photovoltaic panel under sunlight. This study lays the foundation for large-scale industrialization in sustainable fine-chemical and energy engineering.

Sensing for hydrazine of a pyrene chalcone derivative with acryloyl terminal group.

Hydrazine, as a toxic substance, seriously endangers human health and the environment. Based on the excellent luminescent properties and low biological toxicity of pyrene derivatives, combing with chalcone derivatives easily attacked by nucleophilic group, a pyrene derivative PCA decorated by acryloyl terminal group as fluorescent probe for hydrazine was developed. The compound shows fluorescent peak red shift and intensity enhancement with increasing solvent polarity from hexane (459 nm) to methanol (561 nm). Based on strong fluorescence emission in methanol, methanol-HEPES mixed solution was used as the solvent in the spectral recognition experiments. The probe exhibits fluorescent change from yellow fluorescence (576 nm) to blue fluorescence (393 nm) with 800-fold ratiometric fluorescence enhancement (I393nm/I576nm) after the reaction with hydrazine. The probe can recognize hydrazine in fast response rate with kinetic constant calculated being 2.7 × 10-3 s-1 and 15 min as response time. The probe also can monitor hydrazine in real water samples and various soils.

Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.).

Cabbage (Brassica oleracea L. var. capitata) accounts for a critical vegetable crop belonging to Brassicaceae family, and it has been extensively planted worldwide. Simple sequence repeats (SSRs), the markers with high polymorphism and co-dominance degrees, offer a crucial genetic research resource. The current work identified totally 64,546 perfect and 93,724 imperfect SSR motifs in the genome of the cabbage 'TO1000.' Then, we divided SSRs based on the respective overall length and repeat number into different linkage groups. Later, we characterized cabbage genomes from the perspectives of motif length, motif-type classified and SSR level, and compared them across cruciferous genomes. Furthermore, a large set of 64,546 primer pairs were successfully identified, which generated altogether 1,113 SSR primers, including 916 (82.3%) exhibiting repeated and stable amplification. In addition, there were 32 informative SSR markers screened, which might decide 32 cabbage genotypes for their genetic diversity, with level of polymorphism information of 0.14-0.88. Cultivars were efficiently identified by the new strategy designating manual diagram for identifying cultivars. Lastly, 32 cabbage accessions were clearly separately by five Bol-SSR markers. Besides, we verified whether such SSRs were available and transferable in 10 Brassicaceae relatives. Based on the above findings, those genomic SSR markers identified in the present work may facilitate cabbage research, which lay a certain foundation for further gene tagging and genetic linkage analyses, like marker-assisted selection, genetic mapping, as well as comparative genomic analysis.

Morphological, transcriptomics and phytohormone analysis shed light on the development of a novel dwarf mutant of cabbage (Brassica oleracea).

Plant dwarf mutants generally exhibit delayed growth, delayed development, short internodes, and abnormal leaves and flowers and are ideal materials to explore the molecular mechanism of plant growth and development. In the current study, we first discovered a spontaneous cabbage (Brassica oleracea) dwarf mutant 99-198dw, which exhibits a dwarf stature, wrinkled leaves, non-heading, and substantially reduced self-fertility compared with the wild-type 99-198; however, the underlying molecular mechanism of its dwarfism is unknown. Here, we performed comparative phenotype, transcriptome and phytohormone analyses between 99-198 and 99-198dw. Cytological analysis showed that an increase in cell size, a reduction in cell layers, chloroplast degradation and a reduction in mitochondria were observed in 99-198dw. RNA-Seq showed that a total of 3801 differentially expressed genes (DEGs) were identified, including 2203 upregulated and 1598 downregulated genes in the dwarf mutant. Key genes in stress-resistant pathways were mostly upregulated, including salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), ethylene (ET), etc., while the DEGs reported to be related to plant height, such as those involved in the gibberellin (GA), brassinolide (BR), indole-3-acetic acid (IAA), and strigolactone (SL) pathways were mostly downregulated. In addition, the DEGs in the cell division pathway were all downregulated, which is consistent with the cytokinesis defects detected by cytological analysis. The changes in the GA4, JA, ET, SA and ABA contents measured by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) absolute quantification were consistent with the transcriptome analysis. Further hormone treatment tests showed that the exogenous application of GA, BR, 6BA, paclobutrazol (PC), etc. did not rescue the phenotype, implying that the change in phytohormones is due to but not the cause of the dwarf trait. It was speculated that mutation of certain DEG related to cell division or participating in signalling pathway of phytohormones like GA, BR, IAA, and SL were the cause of dwarf. These results are informative for the elucidation of the underlying regulatory network in 99-198dw and enrich our understanding of plant dwarf traits at the molecular level.

A coumarin chalcone ratiometric fluorescent probe for hydrazine based on deprotection, addition and subsequent cyclization mechanism.

A ratiometric fluorescent probe for hydrazine based on a coumarin chalcone framework and a levulinic acid terminal group with a low detection limit (0.1 ppb, 0.003 µM), a large ratiometric fluorescence change (I465/I575, 1265-fold enhancement) and a wide pH work range (3.0-12.0) was developed. The mechanism analysis of the isolated hydrazine product characterized by NMR, HRMS and the crystal structure indicates that the levulinic acid group is firstly removed by deprotection and then the dihydropyrazole ring is formed due to the addition and subsequent cyclization reaction in the presence of hydrazine.

Structurally regular arrangement induced fluorescence enhancement and specific recognition for glutathione of a pyrene chalcone derivative.

Glutathione (GSH) is an important antioxygen and free radical scavenger in the organism. Level of GSH in vivo is associated with many diseases and specific recognition for GSH is very important. Here, a pyrene chalcone derivative 1 1-(2-hydroxyphenyl)-3-(1-pyrenyl)-2-propen-1-one as specific probe for GSH was developed. The probe can give rise to rapid blue fluorescence enhancement for GSH based on Michael addition reaction in pure PBS solution with high sensitivity, fast response rate and high specificity. The compound also can be applied for GSH detection in HeLa cell. Simultaneously, the compound exhibits blue fluorescence emission enhancement in methanol-water (1:1, v/v) solution with fluorescence quantum yield being 0.45 due to the competition of water molecules for hydrogen bonds between hydroxyl and carbonyl and the formation of structurally regular rodlike crystals, which allows regulating fluorescence emission by different solvent condition.

Genetic Diversity, Virulence, Race Profiling, and Comparative Genomic Analysis of the Fusarium oxysporum f. sp. conglutinans Strains Infecting Cabbages in China.

Cabbage Fusarium wilt (CFW) caused by Fusarium oxysporum f. sp. conglutinans (FOC) is known to significantly affect yield and quality of cabbages worldwide. CFW was first detected in New York, NY, United States, and has now spread to almost all cabbage-planting areas, including a recent outbreak of the disease in China. However, it was unknown whether the FOC strains emerged in China differed from the strains in other areas of the world. From 2009 to 2018, we collected Chinese FOC isolates and compared them to the races 1 and 2 strains in other areas to define their characteristics. Race tests indicated that most of the Chinese FOC strains belonged to race 1 and were more virulent than type strain 52557. To evaluate the genome level diversity, we performed next-generation sequencing and genome assembly for the race 2 strain 58385. Based on the assembled genome, we discovered abundant single-nucleotide polymorphisms and 645 insertion-deletions (InDels) compared with the race 1 strain FGL03-6 by comparative genomic analysis and showed that all FOC race 1 strains have a low genetic variability, with a genomic background distinct from 58385. Furthermore, the internal transcribed spacer, elongation factor-1α, and whole-genome InDel variation studies suggested that the last might be a powerful tool in phylogenetic as well as evolution analysis for F. oxysporum Schlechtend.: Fr. The race, virulence, and genome-based variation profiles could contribute to our knowledge of FOC diversity and support the studies of pathogen characterization in genomic era and also provide clues for CFW-resistance breeding. To our knowledge, this is the first extensive survey conducted for FOC strains.

Integrated analysis of transcriptome and proteome changes related to the Ogura cytoplasmic male sterility in cabbage.

Cabbage (Brassica oleracea L. var. capitata), an important vegetable crop in the Brassicaceae family, is economically important worldwide. In the process of hybrid seed production, Ogura cytoplasmic male sterility (OguCMS), controlled by the mitochondrial gene orf138, has been extensively used for cabbage hybrid production with complete and stable male sterility. To identify the critical genes and pathways involved in the sterility and to better understand the underlying molecular mechanisms, the anther of OguCMS line R2P2CMS and the fertile line R2P2 were used for RNA-seq and iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) proteome analysis. RNA-seq analysis generated 13,037,109 to 13,066,594 SE50-clean reads, from the sterile and fertile lines, which were assembled into 36,890 unigenes. Among them, 1,323 differentially expressed genes (DEGs) were identified, consisting of 307 up- and 1016 down-regulated genes. For ITRAQ analysis, a total of 7,147 unique proteins were identified, and 833 were differentially expressed including 538 up- and 295 down-regulated proteins. These were mainly annotated to the ribosome, spliceosome and mRNA surveillance pathways. Combined transcriptomic and proteomic analyses identified 22 and 70 genes with the same and opposite expression profiles, respectively. Using KEGG analysis of DEGs, gibberellin mediated signaling pathways regulating tapetum programmed cell death and four different pathways involved in sporopollenin synthesis were identified. Secretion and translocation of the sporopollenin precursors were identified, and the key genes participating in these pathways were all significantly down-regulated in R2P2CMS. Light and transmission electron (TE) microscopy revealed fat abnormal tapetum rather than vacuolization and degradation at the tetrad and microspore stages of the OguCMS line. This resulted in the failed deposition of sporopollenin on the pollen resulting in sterility. This study provides a comprehensive understanding of the mechanism underlying OguCMS in cabbage.

Transcriptome Profiling of Resistance to Fusarium oxysporum f. sp. conglutinans in Cabbage (Brassica oleracea) Roots.

Fusarium wilt caused by Fusarium oxysporum f. sp. conglutinans (FOC) is a destructive disease of Brassica crops, which results in severe yield losses. There is little information available about the mechanism of disease resistance. To obtain an overview of the transcriptome profiles in roots of R4P1, a Brassica oleracea variety that is highly resistant to fusarium wilt, we compared the transcriptomes of samples inoculated with FOC and samples inoculated with distilled water. RNA-seq analysis generated more than 136 million 100-bp clean reads, which were assembled into 62,506 unigenes (mean size = 741 bp). Among them, 49,959 (79.92%) genes were identified based on sequence similarity searches, including SwissProt (29,050, 46.47%), Gene Ontology (GO) (33,767, 54.02%), Clusters of Orthologous Groups (KOG) (14,721, 23.55%) and Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) (12,974, 20.76%) searches; digital gene expression analysis revealed 885 differentially expressed genes (DEGs) between infected and control samples at 4, 12, 24 and 48 hours after inoculation. The DEGs were assigned to 31 KEGG pathways. Early defense systems, including the MAPK signaling pathway, calcium signaling and salicylic acid-mediated hypersensitive response (SA-mediated HR) were activated after pathogen infection. SA-dependent systemic acquired resistance (SAR), ethylene (ET)- and jasmonic (JA)-mediated pathways and the lignin biosynthesis pathway play important roles in plant resistance. We also analyzed the expression of defense-related genes, such as genes encoding pathogenesis-related (PR) proteins, UDP-glycosyltransferase (UDPG), pleiotropic drug resistance, ATP-binding cassette transporters (PDR-ABC transporters), myrosinase, transcription factors and kinases, which were differentially expressed. The results of this study may contribute to efforts to identify and clone candidate genes associated with disease resistance and to uncover the molecular mechanism underlying FOC resistance in cabbage.