Biocompatibility FeOOH QD@ATP-BODIPY nanocomposite for glutathione detection and intracellular imaging.

Monitoring of glutathione has attracted considerable attention owing to its biological and clinical significance. An eco-friendly, economic, simple, biocompatible probe with excellent sensitivity and selectivity is very important. Herein, FeOOH QD@ATP-BODIPY nanocomposite was fabricated from one-step synthesized FeOOH quantum dots (FeOOH QD) and commercial boron-dipyrromethene-conjugated adenosine 5'-triphosphate (ATP-BODIPY) for glutathione (GSH) sensing in solutions and living cells. Three fascinate merits of FeOOH QD were confirmed: (a) as fluorescence quencher for ATP-BODIPY, (b) as selective recognizer of GSH and (c) with carrier effects and membrane permeability. The construction and response mechanism of the nanocomposite was based on the competitive coordination chemistry and redox reaction of FeOOH QD between GSH and phosphate group of ATP-BODIPY. Under the optimal conditions, the detection limit for GSH was as low as 68.8 nM. Excellent linear range of 0.2-400 µM was obtained. Furthermore, the chemical response of the nanocomposite exhibits high selectivity toward GSH over other electrolytes and biomolecules. It was successfully applied for GSH determination in human serum samples. The MTT assay exhibited FeOOH QD@ATP-BODIPY nanocomposite own good biocompatibility. FeOOH QD@ATP-BODIPY respond to GSH in living cells in situ was also proved via fluorescence imaging. These suggested that the FeOOH QD@ATP-BODIPY nanocomposite had potential application in biological and clinical applications.

Decoding the Structural Diversity: A New Horizon in Antimicrobial Prospecting and Mechanistic Investigation.

The escalating crisis of antimicrobial resistance (AMR) underscores the urgent need for novel antimicrobials. One promising strategy is the exploration of structural diversity, as diverse structures can lead to diverse biological activities and mechanisms of action. This review delves into the role of structural diversity in antimicrobial discovery, highlighting its influence on factors such as target selectivity, binding affinity, pharmacokinetic properties, and the ability to overcome resistance mechanisms. We discuss various approaches for exploring structural diversity, including combinatorial chemistry, diversity-oriented synthesis, and natural product screening, and provide an overview of the common mechanisms of action of antimicrobials. We also describe techniques for investigating these mechanisms, such as genomics, proteomics, and structural biology. Despite significant progress, several challenges remain, including the synthesis of diverse compound libraries, the identification of active compounds, the elucidation of complex mechanisms of action, the emergence of AMR, and the translation of laboratory discoveries to clinical applications. However, emerging trends and technologies, such as artificial intelligence, high-throughput screening, next-generation sequencing, and open-source drug discovery, offer new avenues to overcome these challenges. Looking ahead, we envisage an exciting future for structural diversity-oriented antimicrobial discovery, with opportunities for expanding the chemical space, harnessing the power of nature, deepening our understanding of mechanisms of action, and moving toward personalized medicine and collaborative drug discovery. As we face the continued challenge of AMR, the exploration of structural diversity will be crucial in our search for new and effective antimicrobials.

Enhanced humification via lignocellulosic pretreatment in remediation of agricultural solid waste.

Stover and manure are the main solid waste in agricultural industry. The generation of stover and manure could lead to serious environmental pollution if not handled properly. Composting is the potential greener solution to remediate and reduce agricultural solid waste, through which stover and manure could be remediated and converted into organic fertilizer, but the long composting period and low efficiency of humic substance production are the key constraints in such remediation approach. In this study, we explore the effect of lignocellulose selective removal on composting by performing chemical pretreatment on agricultural waste followed by utilization of biochar to assist in the remediation by co-composting treatment and reveal the impacts of different lignocellulose component on organic fertilizer production. Aiming to discover the key factors that influence humification during composting process and improve the composting quality as well as comprehensive utilization of agricultural solid waste. The results demonstrated that the removal of selective lignin or hemicellulose led to the shift of abundances lignocellulose-degrading bacteria, which in turn accelerated the degradation of lignocellulose by almost 51.2%. The process also facilitated the remediation of organic waste via humification and increased the humic acid level and HA/FA ratio in just 22 days. The richness of media relies on their lignocellulose content, which is negatively correlated with total nitrogen content, humic acid (HA) content, germination index (GI), and pH, but positively correlated with fulvic acid (FA) and total organic carbon (TOC). The work provides a potential cost effective and efficient framework for agricultural solid waste remediation and reduction.

Magnetic Properties and Microstructure of FePt(BN, X, C) (X = Ag, Re) Films.

A sputtered FePt(BN, Re, C) film, here boron nitride (BN), was compared to a reference sample FePt(BN, Ag, C). Intrinsically, these films illustrate a high anisotropy field (Hk) and perpendicular magnetocrystalline anisotropy (Ku),although the reference sample shows a higher value (Hk = 69.5 kOe, Ku = 1.74 × 107 erg/cm3) than the FePt(BN, Re, C) film (Hk = 66.9 kOe, Ku = 1.46 × 107 erg/cm3). However, the small difference in the anisotropy constant (K2/K1) ratio presents a close tendency in the angular dependence of the switching field. Extrinsically, the out-of-plane coercivity for the reference sample is 32 kOe, which is also higher than the FePt(BN, Re, C) film (Hc = 27 kOe), and both films present lower remanence (Mr(parallel)/Mr(perpendicular) = 0.08~0.12), that is, the index for perpendicular magnetic anisotropy. The higher perpendicular magnetization for both films was due to highly (001) textured FePt films, which was also evidenced by the tight rocking width of 4.1°/3.0° for (001)/(002) X-ray diffraction peaks, respectively, and high-enough ordering degree. The reference sample was measured to have a higher ordering degree (S = 0.84) than FePt(BN, Re, C) (S = 0.63). As a result, the Ag segregant shows stronger ability to promote the ordering of the FePt film; however, the FePt(BN, Re, C) film still has comparable magnetic properties without Ag doping. From the surface and elemental composition analysis, the metallic Re atoms found in the FePt lattice result in a strong spin-orbital coupling between transition metal Fe (3d electron) and heavy metals (Re, Pt) (5d electron) and we conducted high magnetocrystalline anisotropy (Ku). Above is the explanation that the lower-ordered FePt(BN, Re, C) film still has high-enough Ku and out-of-plane Hc. Regarding the microstructure, both the reference sample and FePt(BN, Re, C) show granular structure and columnar grains, and the respective average grain size and distributions are 6.60 nm (12.5%) and 11.2 nm (15.9%). The average widths of the grain boundaries and the aspect ratio of the columnar grain height are 2.05 nm, 1.00 nm, 2.35 nm, and 1.70 nm, respectively.

Removal of dye pollution by an oxidase derived from mutagenesis of the Deuteromycete Myrothecium with high potential in industrial applications.

It is estimated that over 700,000 tons of synthetic dyes are produced annually, 15% of which are emitted as effluents. These highly stable dyes enter the world water ecosystems and stay in the environment, and eventually cause adverse impacts to the environment. Current wastewater treatment methods, such as filtration, coagulation, and chemical oxidation, have sideeffects, including toxic residue formation, membrane fouling, bioaccumulation, and secondary pollutant formation. Given the issues mentioned, it is necessary to study how to improve the degradation of synthetic dye with a cost-effective and ecofriendly approach. Natural oxidation provides a greener option. Recently, Deuteromycetes fungus Myrothecium verrucaria G-1 (M. verrucaria G-1) has shown great potential in producing high level of dye oxidase. This study aims to generate a dye oxidase hyperproducer, 3H6 from M. verrucaria G-1 by using atmospheric and room temperature plasma (ARTP) coupled with ultraviolet (UV) irradiation. This method increases oxidase production by nearly 106.15%. After a simple precipitation and dialysis, this mutant oxidase increases by 1.97-fold in a specific activity with dye degradation rates at 70% for Mmethylene blue (MB) and 85% for Congo red (CR). It is found that the genetic stability of 3H6 remains active for ten generations. The size of oxidase is 65 kDa, and optimum temperature for reaction is 30 °C with 4.5 pH. This study presents that the first combined mutagenesis approach by ARPT-UV on fungus species generates an impressive increment of acid dye oxidases production. As such, this method presents a cost-effective alternative to mitigate hazardous dye pollution.

Roles of AGD2a in Plant Development and Microbial Interactions of Lotus japonicus.

Arabidopsis AGD2 (Aberrant Growth and Death2) and its close homolog ALD1 (AGD2-like defense response protein 1) have divergent roles in plant defense. We previously reported that modulation of salicylic acid (SA) contents by ALD1 affects numbers of nodules produced by Lotus japonicus, but AGD2's role in leguminous plants remains unclear. A combination of enzymatic analysis and biological characterization of genetic materials was used to study the function of AGD2 (LjAGD2a and LjAGD2b) in L. japonicus. Both LjAGD2a and LjAGD2b could complement dapD and dapE mutants of Escherichia coli and had aminotransferase activity in vitro. ljagd2 plants, with insertional mutations of LjAGD2, had delayed flowering times and reduced seed weights. In contrast, overexpression of LjAGD2a in L. japonicus induced early flowering, with increases in seed and flower sizes, but reductions in pollen fertility and seed setting rates. Additionally, ljagd2a mutation resulted in increased expression of nodulin genes and corresponding increases in infection threads and nodule numbers following inoculation with Rhizobium. Changes in expression of LjAGD2a in L. japonicus also affected endogenous SA contents and hence resistance to pathogens. Our results indicate that LjAGD2a functions as an LL-DAP aminotransferase and plays important roles in plant development. Moreover, LjAGD2a activates defense signaling via the Lys synthesis pathway, thereby participating in legume-microbe interaction.

Comprehensive Analysis of Tumor Immune Microenvironment Characteristics for the Prognostic Prediction and Immunotherapy of Oral Squamous Cell Carcinoma.

Background: Oral squamous cell carcinoma (OSCC) is the most common cancer of oral and maxillofacial region. A recent clinical research has shown that tumor immune microenvironment (TIME)cells are closely related to immunotherapy sensitivity and OSCC prognosis. Nonetheless, a comprehensive analysis of TIME in OSCC has not been reported. Methods: Bioinformatics and computational algorithms were employed to determine the significance of TIME cells in 257 OSCC patients. TIME scores were measured by three TIME models, and then used to evaluate the prognosis of OSCC patients. Results: High TIME score was characterized by better prognosis in OSCC patients less than 60 years old, overexpression of immunotherapy targets (e.g., PD-1 and CLTA-4), and higher T-cell activity to inhibit tumor growth. Besides, poor prognosis was associated with low time score. Conclusion: TIME score exhibited potential as a prognostic biomarker and an indicator in predict immunotherapeutic outcomes. Through the understanding of TIME model, this study can provide a better scheme for immunotherapy as the effective treatment of OSCC patients in the future.

Switching Field Distribution in BN/FePtCAg/MgTiON and FePtCAg/MgTiOBN Films.

BN is the currently required segregant for perpendicular FePt media. We found that BN can be diffused from the MgTiOBN intermediate layer during a high temperature process. The FePtCAg film sputtered on MgTiOBN layers illustrates higher perpendicular magnetocrystalline anisotropy (Ku) (1.43 × 107 erg/cm3) and coercivity (normal to film surface) (17 kOe) at 350 K compared to BN/FePtCAg/MgTiON film. From the microstructure, the FePtCAg film shows the granular structure on the MgTiOBN intermediate layer, but parts of the irregular FePt grains are agglomerated and partially separated in the matrix, with grains size being, on average, 26.7 nm. Cross-sectional imaging showed that the FePt grains have a truncated pyramid shape with a lower wetting angle, which is influenced by the surface energy of MgTiOBN. BN segregation at FePt grains or boundaries is still not clear. Using the electron energy loss spectrum (EELS), we found that part of the BN atoms were clearly observed in the FePt lattice and iron-boride oxide was indexed in the x-ray photoelectron spectroscopy (XPS) spectra. To determine the effects of BN segregant (from capping layer or intermediate layer) on the magnetic switching behavior of FePtCAg film, the intrinsic-(ΔHint = 6.17 kOe, 6.54 kOe) and extrinsic- (ΔHext = 0.80 kOe, 0.39 kOe) switching field distribution (SFD) were measured by plotting saturated major- and unsaturated minor- hysteresis loops to evaluate the crystal orientation and microstructure (grains volume and distribution) for BN/FePtCAg/MgTiON and FePtCAg/MgTiOBN films, respectively. The main contribution of intrinsic SFD is the c-axis misalignment for the BN/FePt/MgTiON sample; however, the dispersed magnetic anisotropy has a higher input to intrinsic SFD for FePtCAg/MgTiOBN/CrRu film.

Current Studies of the Effects of Drought Stress on Root Exudates and Rhizosphere Microbiomes of Crop Plant Species.

With the warming global climate, drought stress is considered to be the most important abiotic factor limiting plant growth and yield in the world. Drought stress has serious impacts on crop production. Many researchers have studied the influences of drought stress on crop production and plant physiology; however, few researchers have combined root exudates with root-associated microbiomes for their mutual effects under drought conditions. In this review, we systematically illustrate the impact of drought stress on root exudates and root-associated microbiomes, and then we discuss the mutual regulation of root-associated microbiomes and the host plant in helping the plant adapt to drought. Finally, we construct a framework for the mutual connections between the plant, root exudates, and the microbiome. We hope this review can provide some significant guidelines to promote the study of drought resistance in plants in association with the rhizosphere microbiota.

Characteristics of RNA alternative splicing and its potential roles in ginsenoside biosynthesis in a single plant of ginseng, Panax ginseng C.A. Meyer.

RNA alternative splicing (AS) is prevalent in higher organisms and plays a paramount role in biology; therefore, it is crucial to have comprehensive knowledge on AS to understand biology. However, knowledge is limited about how AS activates in a single plant and functions in a biological process. Ginseng is one of the most widely used medicinal herbs that is abundant in a number of medicinal bioactive components, especially ginsenosides. In this study, we sequenced the transcripts of 14 organs from a 4-year-old ginseng plant and quantified their ginsenoside contents. We identified AS genes by analyzing their transcripts with the ginseng genome and verified their AS events by PCR. The plant had a total of 13,863 AS genes subjected to 30,801 AS events with five mechanisms: skipped exon, retained intron, alternative 5'splice site, alternative 3' splice site, and mutually exclusive exon. The genes that were more conserved, had more exons, and/or expressed across organs were more likely to be subjected to AS. AS genes were enriched in over 500 GO terms in the plant even though the number of AS gene-enriched GO terms varied across organs. At least 24 AS genes were found to be involved in ginsenoside biosynthesis. These AS genes were significantly up-enriched and more likely to form a co-expression network, thus suggesting the functions of AS and correlations of the AS genes in the process. This study provides comprehensive insights into the molecular characteristics and biological functions of AS in a single plant; thus, helping better understand biology.

Integrative transcriptome analysis identifies new oxidosqualene cyclase genes involved in ginsenoside biosynthesis in Jilin ginseng.

BACKGROUND: Jilin ginseng, Panax ginseng, is a valuable medicinal herb whose ginsenosides are its major bioactive components. The ginseng oxidosqualene cyclase (PgOSC) gene family is known to play important roles in ginsenoside biosynthesis, but few members of the gene family have been functionally studied. METHODS: The PgOSC gene family has been studied by an integrated analysis of gene expression-ginsenoside content correlation, gene mutation-ginsenoside content association and gene co-expression network, followed by functional analysis through gene regulation. RESULTS: We found that five of the genes in the PgOSC gene family, including two published ginsenoside biosynthesis genes and three new genes, were involved in ginsenoside biosynthesis. Not only were the expressions of these genes significantly correlated with ginsenoside contents, but also their nucleotide mutations significantly influenced ginsenoside contents. These results were further verified by regulation analysis of the genes by methyl jasmonate (MeJA) in ginseng hairy roots. Four of these five PgOSC genes were mapped to the ginsenoside biosynthesis pathway. These PgOSC genes expressed differently across tissues, but relatively consistent across developmental stages. These PgOSC genes formed a single co-expression network with those published ginsenoside biosynthesis genes, further confirming their roles in ginsenoside biosynthesis. When the network varied, ginsenoside biosynthesis was significantly influenced, thus revealing the molecular mechanism of ginsenoside biosynthesis. CONCLUSION: At least five of the PgOSC genes, including the three newly identified and two published PgOSC genes, are involved in ginsenoside biosynthesis. These results provide gene resources and knowledge essential for enhanced research and applications of ginsenoside biosynthesis in ginseng.

Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer.

BACKGROUND: Ginseng is an important medicinal herb in Asia and Northern America. The basic leucine zipper (bZIP) transcription factor genes play important roles in many biological processes and plant responses to abiotic and biotic stresses, such as drought stress. Nevertheless, the genes remain unknown in ginseng. RESULTS: Here, we report 91 bZIP genes identified from ginseng, designated PgbZIP genes. These PgbZIP genes were alternatively spliced into 273 transcripts. Phylogenetic analysis grouped the PgbZIP genes into ten groups, including A, B, C, D, E, F, G, H, I and S. Gene Ontology (GO) categorized the PgbZIP genes into five functional subcategories, suggesting that they have diversified in functionality, even though their putative proteins share a number of conserved motifs. These 273 PgbZIP transcripts expressed differentially across 14 tissues, the roots of different ages and the roots of different genotypes. However, the transcripts of the genes expressed coordinately and were more likely to form a co-expression network. Furthermore, we studied the responses of the PgbZIP genes to drought stress in ginseng using a random selection of five PgbZIP genes, including PgbZIP25, PgbZIP38, PgbZIP39, PgbZIP53 and PgbZIP54. The results showed that all five PgbZIP genes responded to drought stress in ginseng, indicating that the PgbZIP genes play important roles in ginseng responses to drought stress. CONCLUSIONS: These results provide knowledge and gene resources for deeper functional analysis of the PgbZIP genes and molecular tools for enhanced drought tolerance breeding in ginseng.

Innovative hydrolysis of corn stover biowaste by modified magnetite laccase immobilized nanoparticles.

Intensive studies have been performed on the improvement of bioethanol production by transformation of lignocellulose biomass. In this study, the digestibility of corn stover was dramatically improved by using laccase immobilized on Cu2+ modified recyclable magnetite nanoparticles, Fe3O4-NH2. After digestion, the laccase was efficiently separated from slurry. The degradation rate of lignin reached 40.76%, and the subsequent cellulose conversion rate 38.37% for 72 h at 35 °C with cellulase at 50 U g-1 of corn stover. Compared to those of free and inactivated mode, the immobilized laccase pre-treatment increased subsequent cellulose conversion rates by 23.98% and 23.34%, respectively. Moreover, the reusability of immobilized laccase activity remained 50% after 6 cycles. The storage and thermal stability of the fixed laccase enhanced by 70% and 24.1% compared to those of free laccase at 65 °C, pH 4.5, respectively. At pH 10.5, it exhibited 16.3% more activities than its free mode at 35 °C. Our study provides a new avenue for improving the production of bioethanol with immobilized laccase for delignification using corn stover as the starting material.

Identification, characterization and functional differentiation of the NAC gene family and its roles in response to cold stress in ginseng, Panax ginseng C.A. Meyer.

The NAC gene family is one of the important plant-specific transcription factor families involved in variety of physiological processes. It has been found in several plant species; however, little is known about the gene family in ginseng, Panax ginseng C.A. Meyer. Here we report identification and systematic analysis of this gene family in ginseng. A total of 89 NAC genes, designated PgNAC01 to PgNAC89, are identified. These genes are alternatively spliced into 251 transcripts at fruiting stage of a four-year-old ginseng plant. The genes of this gene family have five conserved motifs and are clustered into 11 subfamilies, all of which are shared with the genes of the NAC gene families identified in the dicot and monocot model plant species, Arabidopsis and rice. This result indicates that the PgNAC gene family is an ancient and evolutionarily inactive gene family. Gene ontology (GO) analysis shows that the functions of the PgNAC gene family have been substantially differentiated; nevertheless, over 86% the PgNAC transcripts remain functionally correlated. Finally, five of the PgNAC genes, PgNAC05-2, PgNAC41-2, PgNAC48, PgNAC56-1, and PgNAC59, are identified to be involved in plant response to cold stress, suggesting that this gene family plays roles in response to cold stress in ginseng. These results, therefore, provide new insights into functional differentiation and evolution of a gene family in plants and gene resources necessary to comprehensively determine the functions of the PgNAC gene family in response to cold and other abiotic stresses in ginseng.

The bHLH gene family and its response to saline stress in Jilin ginseng, Panax ginseng C.A. Meyer.

Basic helix-loop-helix (bHLH) gene family is a gene family of transcription factors that plays essential roles in plant growth and development, secondary metabolism and response to biotic and abiotic stresses. Therefore, a comprehensive knowledge of the bHLH gene family is paramount to understand the molecular mechanisms underlying these processes and develop advanced technologies to manipulate the processes efficiently. Ginseng, Panax ginseng C.A. Meyer, is a well-known medicinal herb; however, little is known  about the bHLH genes (PgbHLH) in the species. Here, we identified 137 PgbHLH genes from Jilin ginseng cultivar, Damaya, widely cultivated in Jilin, China, of which 50 are newly identified by pan-genome analysis. These 137 PgbHLH genes were phylogenetically classified into 26 subfamilies, suggesting their sequence diversification. They are alternatively spliced into 366 transcripts in a 4-year-old plant and involved in 11 functional subcategories of the gene ontology, indicating their functional differentiation in ginseng. The expressions of the PgbHLH genes dramatically vary spatio-temporally and across 42 genotypes, but they are still somehow functionally correlated. Moreover, the PgbHLH gene family, at least some of its genes, is shown to have roles in plant response to the abiotic stress of saline. These results provide a new insight into the evolution and functional differentiation of the bHLH gene family in plants, new bHLH genes to the PgbHLH gene family, and saline stress-responsive genes for genetic improvement in ginseng and other plant species.

Structural variation, functional differentiation and expression characteristics of the AP2/ERF gene family and its response to cold stress and methyl jasmonate in Panax ginseng C.A. Meyer.

The APETALA2/Ethylene Responsive Factor (AP2/ERF) gene family has been shown to play a crucial role in plant growth and development, stress responses and secondary metabolite biosynthesis. Nevertheless, little is known about the gene family in ginseng (Panax ginseng C.A. Meyer), an important medicinal herb in Asia and North America. Here, we report the systematic analysis of the gene family in ginseng using several transcriptomic databases. A total of 189 putative AP2/ERF genes, defined as PgERF001 through PgERF189, were identified and these PgERF genes were spliced into 397 transcripts. The 93 PgERF genes that have complete AP2 domains in open reading frame were classified into five subfamilies, DREB, ERF, AP2, RAV and Soloist. The DREB subfamily and ERF subfamily were further clustered into four and six groups, respectively, compared to the 12 groups of these subfamilies found in Arabidopsis thaliana. Gene ontology categorized these 397 transcripts of the 189 PgERF genes into eight functional subcategories, suggesting their functional differentiation, and they have been especially enriched for the subcategory of nucleic acid binding transcription factor activity. The expression activity and networks of the 397 PgERF transcripts have substantially diversified across tissues, developmental stages and genotypes. The expressions of the PgERF genes also significantly varied, when ginseng was subjected to cold stress, as tested using six PgERF genes, PgERF073, PgERF079, PgERF110, PgERF115, PgERF120 and PgERF128, randomly selected from the DREB subfamily. This result suggests that the DREB subfamily genes play an important role in plant response to cold stress. Finally, we studied the responses of the PgERF genes to methyl jasmonate (MeJA). We found that 288 (72.5%) of the 397 PgERF gene transcripts responded to the MeJA treatment, with 136 up-regulated and 152 down-regulated, indicating that most members of the PgERF gene family are responsive to MeJA. These results, therefore, provide new resources and knowledge necessary for family-wide functional analysis of the PgERF genes in ginseng and related species.

Selection and validation of reference genes desirable for gene expression analysis by qRT-PCR in MeJA-treated ginseng hairy roots.

Ginseng is a valuable herb of traditional Chinese medicine and ginsenosides, the main bioactive components of ginseng, have been proven to have multiple functions in human therapies and health. Methyl jasmonate (MeJA) is an elicitor that has been demonstrated to have a vital influence on ginsenoside biosynthesis. Quantitative real-time polymerase chain reaction (qRT-PCR) has been widely used in quantification of gene expressions. Here, we report the selection and validation of reference genes desirable for normalization of gene expressions quantified by qRT-PCR in ginseng hairy roots treated with MeJA. Twelve reference genes were selected as candidate genes, and their expressions were quantified by qRT-PCR, and analyzed by geNorm, NormFinder and BestKeeper. CYP and EF-1α were shown to be the most stable reference genes in geNorm, CYP was the most stable reference gene in NormFinder, and 18S was the most stable reference gene in BestKeeper. On this basis, we further quantified the relative expression levels of four genes encoding key enzymes that are involved in ginsenoside biosynthesis using CYP and 18S as the reference genes, respectively. Moreover, correlation analysis was performed between the quantified expressions of four genes and the ginsenoside content in MeJA-treated ginseng hairy roots. The results of relative expressions of the four genes quantified using CYP as the reference gene and their significant correlations with the ginsenoside content were better than those using 18S as the reference gene. The CYP gene, hence, was concluded as the most desirable reference gene for quantification of the expressions of genes in MeJA-treated ginseng hairy roots. This finding, therefore, provides information useful for gene research in ginseng, particularly in MeJA-treated ginseng hairy roots, which includes identification and characterization of genes involved in ginsenoside biosynthesis.

Transcriptome analysis identifies strong candidate genes for ginsenoside biosynthesis and reveals its underlying molecular mechanism in Panax ginseng C.A. Meyer.

Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal herbs for human health and medicine in which ginsenosides are known to play critical roles. The genes from the cytochrome P450 (CYP) gene superfamily have been shown to play important roles in ginsenoside biosynthesis. Here we report genome-wide identification of the candidate PgCYP genes for ginsenoside biosynthesis, development of functional SNP markers for its manipulation and systems analysis of its underlying molecular mechanism. Correlation analysis identified 100 PgCYP genes, including all three published ginsenoside biosynthesis PgCYP genes, whose expressions were significantly correlated with the ginsenoside contents. Mutation association analysis identified that six of these 100 PgCYP genes contained SNPs/InDels that were significantly associated with ginsenosides biosynthesis (P ≤ 1.0e-04). These six PgCYP genes, along with all ten published ginsenoside biosynthesis genes from the PgCYP and other gene families, formed a strong co-expression network, even though they varied greatly in spatio-temporal expressions. Therefore, this study has identified six new ginsenoside biosynthesis candidate genes, provided a genome-wide insight into how they are involved in ginsenoside biosynthesis and developed a set of functional SNP markers useful for enhanced ginsenoside biosynthesis research and breeding in ginseng and related species.

[Advances in plant stem cell culture].

Plant stem cells are the cells that are located in meristems and are kept in a state of undifferentiation. Plant stem cell possesses lower vacuolization, higher mitochondrial activity, more genetic stability and stronger self-renewal capacity compared with calli. Plant stem cell culture has a wide application in pharmaceutical, functional food as well as cosmetic industries. Here we describe the procedure of induction, isolation and identification of plant stem cells, to provide a reference for further research in this field.

Structural Variation, Functional Differentiation, and Activity Correlation of the Cytochrome P450 Gene Superfamily Revealed in Ginseng.

Ginseng ( C.A. Mey.) is one of the most important medicinal herbs for human health and medicine, for which ginsenosides are the major bioactive components. The cytochrome P450 genes, , form a large gene superfamily; however, only three genes have been identified from ginseng and shown to be involved in ginsenoside biosynthesis, indicating the importance of the gene superfamily in the process. Here we report genome-wide identification and systems analysis of the genes in ginseng, defined as genes. We identified 414 genes, including the three published genes. These genes formed a superfamily consisting of 41 gene families, with a substantial diversity in phylogeny and dramatic variation in spatiotemporal expression. Gene ontology (GO) analysis categorized the gene superfamily into 12 functional subcategories distributing among all three primary functional categories, suggesting its functional differentiation. Nevertheless, the majority of its gene members expressed correlatively and tended to form a coexpression network and some of them were commonly regulated in expression across tissues and developmental stages. These results have led to genome-wide identification of genes useful for genome-wide identification of the genes involved in ginsenoside biosynthesis in ginseng and provided the first insight into how a gene superfamily functionally differentiates and acts correlatively in plants.