Imaging of pH distribution inside individual microdroplet by stimulated Raman microscopy.

Aerosol microdroplets as microreactors for many important atmospheric reactions are ubiquitous in the atmosphere. pH largely regulates the chemical processes within them; however, how pH and chemical species spatially distribute within an atmospheric microdroplet is still under intense debate. The challenge is to measure pH distribution within a tiny volume without affecting the chemical species distribution. We demonstrate a method based on stimulated Raman scattering microscopy to visualize the three-dimensional pH distribution inside single microdroplets of varying sizes. We find that the surface of all microdroplets is more acidic, and a monotonic trend of pH decreasing is observed in the 2.9-µm aerosol microdroplet from center to edge, which is well supported by molecular dynamics simulation. However, bigger cloud microdroplet differs from small aerosol for pH distribution. This size-dependent pH distribution in microdroplets can be related to the surface-to-volume ratio. This work presents noncontact measurement and chemical imaging of pH distribution in microdroplets, filling the gap in our understanding of spatial pH in atmospheric aerosol.

Cloning and functional mechanism of the dwarf gene gba affecting stem elongation and cellulose biosynthesis in jute (Corchorus olitorius).

Plant height (PH) is an important factor affecting bast fiber yield in jute. Here, we report the mechanism of dwarfism in the 'Guangbaai' (gba) of jute. The mutant gba had shorter internode length and cell length compared to the standard cultivar 'TaiZi 4' (TZ4). Exogenous GA3 treatment indicated that gba is a GA-insensitive dwarf mutant. Quantitative trait locus (QTL) analysis of three PH-related traits via a high-density genetic linkage map according to re-seq showed that a total of 25 QTLs were identified, including 13 QTLs for PH, with phenotypic variation explained ranging from 2.42 to 74.16%. Notably, the functional mechanism of the candidate gene CoGID1a, the gibberellic acid receptor, of the major locus qPHIL5 was evaluated by transgenic analysis and virus-induced gene silencing. A dwarf phenotype-related single nucleotide mutation in CoGID1a was identified in gba, which was also unique to the dwarf phenotype of gba among 57 cultivars. Cogid1a was unable to interact with the growth-repressor DELLA even in the presence of highly accumulated gibberellins in gba. Differentially expressed genes between transcriptomes of gba and TZ4 after GA3 treatment indicated up-regulation of genes involved in gibberellin and cellulose synthesis in gba. Interestingly, it was found that up-regulation of CoMYB46, a key transcription factor in the secondary cell wall, by the highly accumulated gibberellins in gba promoted the expression of cellulose synthase genes CoCesA4 and CoCesA7. These findings provide valuable insights into fiber development affected by endogenous gibberellin accumulation in plants.

Significantly Accelerated Photosensitized Formation of Atmospheric Sulfate at the Air-Water Interface of Microdroplets.

The multiphase oxidation of sulfur dioxide (SO2) to form sulfate is a complex and important process in the atmosphere. While the conventional photosensitized reaction mainly explored in the bulk medium is reported to be one of the drivers to trigger atmospheric sulfate production, how this scheme functionalizes at the air-water interface (AWI) of aerosol remains an open question. Herein, employing an advanced size-controllable microdroplet-printing device, surface-enhanced Raman scattering (SERS) analysis, nanosecond transient adsorption spectrometer, and molecular level theoretical calculations, we revealed the previously overlooked interfacial role in photosensitized oxidation of SO2 in humic-like substance (HULIS) aerosol, where a 3-4 orders of magnitude increase in sulfate formation rate was speculated in cloud and aerosol relevant-sized particles relative to the conventional bulk-phase medium. The rapid formation of a battery of reactive oxygen species (ROS) comes from the accelerated electron transfer process at the AWI, where the excited triplet state of HULIS (3HULIS*) of the incomplete solvent cage can readily capture electrons from HSO3- in a way that is more efficient than that in the bulk medium fully blocked by water molecules. This phenomenon could be explained by the significantly reduced desolvation energy barrier required for reagents residing in the AWI region with an open solvent shell.

Genomic and cytogenetic analyses reveal satellite repeat signature in allotetraploid okra (Abelmoschus esculentus).

BACKGROUND: Satellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome evolution, and speciation. As a consequence, the composition, abundance and chromosome distribution of satellite repeats often exhibit variability across various species, genome, and even individual chromosomes. However, we know little about the satellite repeat evolution in allopolyploid genomes. RESULTS: In this study, we investigated the satellite repeat signature in five okra (Abelmoschus esculentus) accessions using genomic and cytogenetic methods. In each of the five accessions, we identified eight satellite repeats, which exhibited a significant level of intraspecific conservation. Through fluorescence in situ hybridization (FISH) experiments, we observed that the satellite repeats generated multiple signals and exhibited variations in copy number across chromosomes. Intriguingly, we found that five satellite repeats were interspersed with centromeric retrotransposons, signifying their involvement in centromeric satellite repeat identity. We confirmed subgenome-biased amplification patterns of these satellite repeats through existing genome assemblies or dual-color FISH, indicating their distinct dynamic evolution in the allotetraploid okra subgenome. Moreover, we observed the presence of multiple chromosomes harboring the 35 S rDNA loci, alongside another chromosomal pair carrying the 5 S rDNA loci in okra using FISH assay. Remarkably, the intensity of 35 S rDNA hybridization signals varied among chromosomes, with the signals predominantly localized within regions of relatively weak DAPI staining, associated with GC-rich heterochromatin regions. Finally, we observed a similar localization pattern between 35 S rDNA and three satellite repeats with high GC content and confirmed their origin in the intergenic spacer region of the 35 S rDNA. CONCLUSIONS: Our findings uncover a unique satellite repeat signature in the allotetraploid okra, contributing to our understanding of the composition, abundance, and chromosomal distribution of satellite repeats in allopolyploid genomes, further enriching our understanding of their evolutionary dynamics in complex allopolyploid genomes.

Phase State Regulates Photochemical HONO Production from NaNO3/Dicarboxylic Acid Mixtures.

Field observations of daytime HONO source strengths have not been well explained by laboratory measurements and model predictions up until now. More efforts are urgently needed to fill the knowledge gaps concerning how environmental factors, especially relative humidity (RH), affect particulate nitrate photolysis. In this work, two critical attributes for atmospheric particles, i.e., phase state and bulk-phase acidity, both influenced by ambient RH, were focused to illuminate the key regulators for reactive nitrogen production from typical internally mixed systems, i.e., NaNO3 and dicarboxylic acid (DCA) mixtures. The dissolution of only few oxalic acid (OA) crystals resulted in a remarkable 50-fold increase in HONO production compared to pure nitrate photolysis at 85% RH. Furthermore, the HONO production rates (PHONO) increased by about 1 order of magnitude as RH rose from <5% to 95%, initially exhibiting an almost linear dependence on the amount of surface absorbed water and subsequently showing a substantial increase in PHONO once nitrate deliquescence occurred at approximately 75% RH. NaNO3/malonic acid (MA) and NaNO3/succinic acid (SA) mixtures exhibited similar phase state effects on the photochemical HONO production. These results offer a new perspective on how aerosol physicochemical properties influence particulate nitrate photolysis in the atmosphere.

Nanoplastics Detected in Commercial Sea Salt.

People of all ages consume salt every day, but is it really just salt? Plastic nanoparticles [nanoplastics (NPs)] pose an increasing environmental threat and have begun to contaminate everyday salt in consumer goods. Herein, we developed a combined surface enhanced Raman scattering (SERS) and stimulated Raman scattering (SRS) approach that can realize the filtration, enrichment, and detection of NPs in commercial salt. The Au-loaded (50 nm) anodic alumina oxide substrate was used as the SERS substrate to explore the potential types of NP contaminants in salts. SRS was used to conduct imaging and quantify the presence of the NPs. SRS detection was successfully established through standard plastics, and NPs were identified through the match of the hydrocarbon group of the nanoparticles. Simultaneously, the NPs were quantified based on the high spatial resolution and rapid imaging of the SRS imaging platform. NPs in sea salts produced in Asia, Australasia, Europe, and the Atlantic were studied. We estimate that, depending on the location, an average person could be ingesting as many as 6 million NPs per year through the consumption of sea salt alone. The potential health hazards associated with NP ingestion should not be underestimated.

Quantification and Characterization of Fine Plastic Particles as Considerable Components in Atmospheric Fine Particles.

The negative effects of air pollution, especially fine particulate matter (PM2.5, particles with an aerodynamic diameter of ≤2.5 µm), on human health, climate, and ecosystems are causing significant concern. Nevertheless, little is known about the contributions of emerging pollutants such as plastic particles to PM2.5 due to the lack of continuous measurements and characterization methods for atmospheric plastic particles. Here, we investigated the levels of fine plastic particles (FPPs) in PM2.5 collected in urban Shanghai at a 2 h resolution by using a novel versatile aerosol concentration enrichment system that concentrates ambient aerosols up to 10-fold. The FPPs were analyzed offline using the combination of spectroscopic and microscopic techniques that distinguished FPPs from other carbon-containing particles. The average FPP concentrations of 5.6 µg/m3 were observed, and the ratio of FPPs to PM2.5 was 13.2% in this study. The FPP sources were closely related to anthropogenic activities, which pose a potential threat to ecosystems and human health. Given the dramatic increase in plastic production over the past 70 years, this study calls for better quantification and control of FPP pollution in the atmosphere.

Evolution and expression analysis of the caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) gene family in jute (Corchorus L.).

BACKGROUND: Jute is considered one of the most important crops for fiber production and multipurpose usages. Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is a crucial enzyme involved in lignin biosynthesis in plants. The potential functions of CCoAOMT in lignin biosynthesis of jute have been reported in several studies. However, little is known about the evolution of the CCoAOMT gene family, and either their expression level at different developing stages in different jute cultivars, as well as under abiotic stresses including salt and drought stress. RESULTS: In the present study, 66 CCoAOMT genes from 12 species including 12 and eight CCoAOMTs in Corchorus olitorius and C. capsularis were identified. Phylogenetic analysis revealed that CCoAOMTs could be divided into six groups, and gene expansion was observed in C. olitorius. Furthermore, gene expression analysis of developing jute fibers was conducted at different developmental stages (15, 30, 45, 60, and 90 days after sowing [DAS]) in six varieties (Jute-179 [J179], Lubinyuanguo [LB], and Qiongyueqing [QY] for C. capsularis; Funong No.5 [F5], Kuanyechangguo [KY], and Cvlv [CL] for C. olitorius). The results showed that CCoAOMT1 and CCoAOMT2 were the dominant genes in the CCoAOMT family. Of these two dominant CCoAOMTs, CCoAOMT2 showed a constitutive expression level during the entire growth stages, while CCoAOMT1 exhibited differential expression patterns. These two genes showed higher expression levels in C. olitorius than in C. capsularis. The correlation between lignin content and CCoAOMT gene expression levels indicated that this gene family influences the lignin content of jute. Using real-time quantitative reverse transcription PCR (qRT-PCR), a substantial up-regulation of CCoAOMTs was detected in stem tissues of jute 24 h after drought treatment, with an up to 17-fold increase in expression compared to that of untreated plants. CONCLUSIONS: This study provides a basis for comprehensive genomic studies of the entire CCoAOMT gene family in C. capsularis and C. olitorius. Comparative genomics analysis among the CCoAOMT gene families of 12 species revealed the close evolutionary relationship among Corchorus, Theobroma cacao and Gossypium raimondii. This study also shows that CCoAOMTs are not only involved in lignin biosynthesis, but also are associated with the abiotic stress response in jute, and suggests the potential use of these lignin-related genes to genetically improve the fiber quality of jute.

Strategies and Challenges of Identifying Nanoplastics in Environment by Surface-Enhanced Raman Spectroscopy.

Nanoplastics (<1000 nm) have been evidenced to be universal in a variety of environmental media. They pose a potential cytotoxicity and health risk due to their tiny size, which allows them to easily penetrate biological barriers and enter cells. Here, we briefly review the various prevalent analytical techniques or tools for identifying nanoplastics, and further move to focus on their advantages and disadvantages. Surface-enhanced Raman spectroscopy (SERS) has been implemented for the identification of individual nanoparticles because of its high sensitivity to molecules and ease of rapid characterization. Therefore, we introduce the SERS technique in the following aspects, (1) principles of SERS; (2) strategies and advances in SERS detection of nanoplastics; and (3) applying SERS to real environmental samples. We put our effort into the summarization of efficient SERS substrates that essentially enable the better detection of nanoplastics, and extend to discuss how the reported nanoplastics pretreatment methodologies can bring SERS analysis to practical applications. A further step moving forward is to investigate the problems and challenges of currently applied SERS detection methods and to look at future research needs in nanoplastics detection employing SERS analysis.

Sunlight Induces the Production of Atmospheric Volatile Organic Compounds (VOCs) from Thermokarst Ponds.

Ground subsidence caused by permafrost thawing causes the formation of thermokarst ponds, where organic compounds from eroding permafrost accumulate. We photolyzed water samples from two such ponds in Northern Quebec and discovered the emission of volatile organic compounds (VOCs) using mass spectrometry. One pond near peat-covered permafrost mounds was organic-rich, while the other near sandy mounds was organic-poor. Compounds up to C10 were detected, comprising the atoms of O, N, and S. The main compounds were methanol, acetaldehyde, and acetone. Hourly VOC fluxes under actinic fluxes similar to local solar fluxes might reach up to 1.7 nmol C m-2 s-1. Unexpectedly, the fluxes of VOCs from the organic-poor pond were greater than those from the organic-rich pond. We suggest that different segregations of organics at the air/water interface may partly explain this observation. This study indicates that sunlit thermokarst ponds are a significant source of atmospheric VOCs, which may affect the environment and climate via ozone and aerosol formation. Further work is required for understanding the relationship between the pond's organic composition and VOC emission fluxes.

Significantly Accelerated Photochemical Perfluorooctanoic Acid Decomposition at the Air-Water Interface of Microdroplets.

The efficient elimination of per- and polyfluoroalkyl substances (PFASs) from the environment remains a huge challenge and requires advanced technologies. Herein, we demonstrate that perfluorooctanoic acid (PFOA) photochemical decomposition could be significantly accelerated by simply carrying out this process in microdroplets. The almost complete removal of 100 and 500 µg/L PFOA was observed after 20 min of irradiation in microdroplets, while this was achieved after about 2 h in the corresponding bulk phase counterpart. To better compare the defluorination ratio, 10 mg/L PFOA was used typically, and the defluorination rates in microdroplets were tens of times faster than that in the bulk phase reaction system. The high performances in actual water matrices, universality, and scale-up applicability were demonstrated as well. We revealed in-depth that the great acceleration is due to the abundance of the air-water interface in microdroplets, where the reactants concentration enrichment, ultrahigh interfacial electric field, and partial solvation effects synergistically promoted photoreactions responsible for PFOA decomposition, as evidenced by simulated Raman scattering microscopy imaging, vibrational Stark effect measurement, and DFT calculation. This study provides an effective approach and highlights the important roles of air-water interface of microdroplets in PFASs treatment.

Automatic Identification of Individual Nanoplastics by Raman Spectroscopy Based on Machine Learning.

The increasing prevalence of nanoplastics in the environment underscores the need for effective detection and monitoring techniques. Current methods mainly focus on microplastics, while accurate identification of nanoplastics is challenging due to their small size and complex composition. In this work, we combined highly reflective substrates and machine learning to accurately identify nanoplastics using Raman spectroscopy. Our approach established Raman spectroscopy data sets of nanoplastics, incorporated peak extraction and retention data processing, and constructed a random forest model that achieved an average accuracy of 98.8% in identifying nanoplastics. We validated our method with tap water spiked samples, achieving over 97% identification accuracy, and demonstrated the applicability of our algorithm to real-world environmental samples through experiments on rainwater, detecting nanoscale polystyrene (PS) and polyvinyl chloride (PVC). Despite the challenges of processing low-quality nanoplastic Raman spectra and complex environmental samples, our study demonstrated the potential of using random forests to identify and distinguish nanoplastics from other environmental particles. Our results suggest that the combination of Raman spectroscopy and machine learning holds promise for developing effective nanoplastic particle detection and monitoring strategies.

Genome-wide association study reveals loci and candidate genes of flowering time in jute (Corchorus L.).

Suitable flowering time can improve fiber yield and quality, which is of great significance for jute biological breeding. In this study, 242 jute accessions were planted in Fujian for 2 consecutive years, and 244,593 SNPs distributed in jute genome were used for genome-wide association analysis of flowering time. A total of 19 candidate intervals (P < 0.0001) were identified by using GLM and FaST-LMM and were significantly associated with flowering time, with phenotypic variation explained (PVE) ranging from 5.8 to 18.61%. Six stable intervals that were repeatedly detected in different environments were further identified by the linkage disequilibrium heatmap. The most likely 7 candidate genes involved to flowering time were further predicted according to the gene functional annotations. Notably, functional analysis of the candidate gene CcPRR7 of the major loci qFT-3-1, a key factor in circadian rhythm in the photoperiodic pathway, was evaluated by linkage, haplotype, and transgenic analysis. ß-glucuronidase (GUS) and luciferase (LUC) activity assay of the promoters with two specific haplotypes confirmed that the flowering time can be controlled by regulating the expression of CcPRR7. The model of CcPRR7 involved in the photoperiod regulation pathway under different photoperiods was proposed. These findings provide insights into genetic loci and genes for molecular marker-assisted selection in jute and valuable information for genetically engineering PRR7 homologs in plants. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01435-8.

Significantly Accelerated Hydroxyl Radical Generation by Fe(III)-Oxalate Photochemistry in Aerosol Droplets.

Fe(III)-oxalate complexes are ubiquitous in atmospheric environments, which can release reactive oxygen species (ROS) such as H2O2, O•2-, and OH• under light irradiation. Although Fe(III)-oxalate photochemistry has been investigated extensively, the understanding of its involvement in authentic atmospheric environments such as aerosol droplets is far from enough, since the current available knowledge has mainly been obtained in bulk-phase studies. Here, we find that the production of OH• by Fe(III)-oxalate in aerosol microdroplets is about 10-fold greater than that of its bulk-phase counterpart. In addition, in the presence of Fe(III)-oxalate complexes, the rate of photo-oxidation from SO2 to sulfate in microdroplets was about 19-fold faster than that in the bulk phase. The availability of efficient reactants and mass transfer due to droplet effects made dominant contributions to the accelerated OH• and SO42- formation. This work highlights the necessary consideration of droplet effects in atmospheric laboratory studies and model simulations.

Significant Acceleration of Photocatalytic CO2 Reduction at the Gas-Liquid Interface of Microdroplets.

Solar-driven CO2 reduction reaction (CO2 RR) is largely constrained by the sluggish mass transfer and fast combination of photogenerated charge carriers. Herein, we find that the photocatalytic CO2 RR efficiency at the abundant gas-liquid interface provided by microdroplets is two orders of magnitude higher than that of the corresponding bulk phase reaction. Even in the absence of sacrificial agents, the production rates of HCOOH over WO3 ⋅ 0.33H2 O mediated by microdroplets reaches 2536 µmol h-1 g-1 (vs. 13 µmol h-1 g-1 in bulk phase), which is significantly superior to the previously reported photocatalytic CO2 RR in bulk phase reaction condition. Beyond the efficient delivery of CO2 to photocatalyst surfaces within microdroplets, we reveal that the strong electric field at the gas-liquid interface of microdroplets essentially promotes the separation of photogenerated electron-hole pairs. This study provides a deep understanding of ultrafast reaction kinetics promoted by the gas-liquid interface of microdroplets and a novel way of addressing the low efficiency of photocatalytic CO2 reduction to fuel.

Novel Insights into Anthocyanin Synthesis in the Calyx of Roselle Using Integrated Transcriptomic and Metabolomic Analyses.

Roselle (Hibiscus sabdariffa L.) is an annual herbaceous plant of the genus Hibiscus in family Malvaceae. Roselle calyxes are rich in anthocyanins, which play important roles in human health. However, limited information is available on anthocyanin biosynthesis in the roselle calyx. In this study, transcriptomic and metabolomic analyses were performed to identify the key genes involved in anthocyanin biosynthesis in the roselle calyx. Three roselle cultivars with different calyx colors, including FZ-72 (red calyx, R), Baitao K (green calyx, G), and MG5 (stripped calyx, S), were used for metabolomic analyses with UPLC-Q-TOF/MS and RNA-seq. Forty-one compounds were quantified, including six flavonoids and 35 anthocyanins. The calyx of FZ-72 (red calyx) had the highest contents of anthocyanin derivatives such as delphinidin-3-O-sambubioside (955.11 µg/g) and cyanidin-3-O-sambubioside (531.37 µg/g), which were responsible for calyx color, followed by those in MG5 (stripped calyx) (851.97 and 330.06 µg/g, respectively). Baitao K (green calyx) had the lowest levels of these compounds. Furthermore, RNA-seq analysis revealed 114,415 differentially expressed genes (DEGs) in the calyxes at 30 days after flowering (DAF) for the corresponding cultivars FZ-72 (R), Baitao K (G), and MG5(S). The gene expression levels in the calyxes of the three cultivars were compared at different flowering stages, revealing 11,555, 11,949, and 7177 DEGs in R vs. G, R vs. S, and G vs. S, respectively. Phenylpropanoid and flavonoid biosynthesis pathways were found to be enriched. In the flavonoid pathway, 29, 28, and 27 genes were identified in G vs. R, G vs. S, and S vs. R, respectively. In the anthocyanin synthesis pathway, two, two, and one differential genes were identified in the three combinations; these differential genes belonged to the UFGT gene family. After joint analysis of the anthocyanin content in roselle calyxes, nine key genes belonging to the CHS, CHI, UFGT, FLS, ANR, DFR, CCoAOMT, SAT, and HST gene families were identified as strongly related to anthocyanin synthesis. These nine genes were verified using qRT-PCR, and the results were consistent with the transcriptome data. Overall, this study presents the first report on anthocyanin biosynthesis in roselle, laying a foundation for breeding roselle cultivars with high anthocyanin content.

Electrostatic Secondary-Sphere Interactions That Facilitate Rapid and Selective Electrocatalytic CO2 Reduction in a Fe-Porphyrin-Based Metal-Organic Framework.

Metal-organic frameworks (MOFs) are promising platforms for heterogeneous tethering of molecular CO2 reduction electrocatalysts. Yet, to further understand electrocatalytic MOF systems, one also needs to consider their capability to fine-tune the immediate chemical environment of the active site, and thus affect its overall catalytic operation. Here, we show that electrostatic secondary-sphere functionalities enable substantial improvement of CO2 -to-CO conversion activity and selectivity. In situ Raman analysis reveal that immobilization of pendent positively-charged groups adjacent to MOF-residing Fe-porphyrin catalysts, stabilize weakly-bound CO intermediates, allowing their rapid release as catalytic products. Also, by varying the electrolyte's ionic strength, systematic regulation of electrostatic field magnitude was achieved, resulting in essentially 100 % CO selectivity. Thus, this concept provides a sensitive molecular-handle that adjust heterogeneous electrocatalysis on demand.

Reference genomes of the two cultivated jute species.

Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome-level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each comprised of seven pseudo-chromosomes, with the C. capsularis assembly consisting of 336 Mb with 25,874 genes and the C. olitorius assembly containing 361 Mb with 28 479 genes. Although the two Corchorus genomes exhibit collinearity, the genome of C. olitorius contains 25 Mb of additional sequences than that of C. capsularis with 13 putative inversions, which might give a hint to the difference of phenotypic variants between the two cultivated jute species. Analysis of gene expression in isolated fibre tissues reveals candidate genes involved in fibre development. Our analysis of the population structures of 242 cultivars from C. capsularis and 57 cultivars from C. olitorius by whole-genome resequencing resulted in post-domestication bottlenecks occurred ~2000 years ago in these species. We identified hundreds of putative significant marker-trait associations (MTAs) controlling fibre fineness, cellulose content and lignin content of fibre by integrating data from genome-wide association studies (GWAS) with data from analyses of selective sweeps due to natural and artificial selection in these two jute species. Among them, we further validated that CcCOBRA1 and CcC4H1 regulate fibre quality in transgenic plants via improving the biosynthesis of the secondary cell wall. Our results yielded important new resources for functional genomics research and genetic improvement in jute and allied fibre crops.

Au nanoring arrays as surface enhanced Raman spectroscopy substrate for chemical component study of individual atmospheric aerosol particle.

Monolayer-ordered gold nanoring arrays were prepared by ion-sputtering method and used as surface enhanced Raman spectroscopy (SERS) substrates to test the individual atmospheric aerosols particle. Compared to other methods used for testing atmospheric aerosols particles, the collection and subsequent detection in our work is performed directly on the gold nanoring SERS substrate without any treatment of the analyte. The SERS performance can be tuned by changing the depth of the gold nanoring cavity as originating from coupling of dipolar modes at the inner and outer surfaces of the nanorings. The electric field exhibits uniform enhancement and polarization in the ordered Au nanoring substrate, which can improve the accuracy for detecting atmospheric aerosol particles. Combined with Raman mapping, the information about chemical composition of individual atmospheric aerosols particle and distribution of specific components can be presented visually. The results show the potential of SERS in enabling improved analysis of aerosol particle chemical composition, mixing state, and other related physicochemical properties.

De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis).

BACKGROUND: WRKY is a group of transcription factors (TFs) that play a vital role in plant growth, development, and stress tolerance. To date, none of jute WRKY (CcWRKY) genes have been identified, even if jute (Corchorus capsularis) is one of the most important natural fiber crops in the world. Little information about the WRKY genes in jute is far from sufficient to understand the molecular mechanism of bast fiber biosynthesis. RESULTS: A total of 244,489,479 clean reads were generated using Illumina paired-end sequencing. De novo assembly yielded 90,982 unigenes with an average length of 714 bp. By sequence similarity searching for known proteins, 48,896 (53.74%) unigenes were annotated. To mine the CcWRKY TFs and identify their potential function, the search for CcWRKYs against the transcriptome data of jute was performed, and a total of 43 CcWRKYs were identified in this study. The gene structure, phylogeny, conserved domain and three-dimensional structure of protein were analyzed by bioinformatics tools of GSDS2.0, MEGA7.0, DNAMAN5.0, WebLogo 3 and SWISS-MODEL respectively. Phylogenetic analysis showed that 43 CcWRKYs were divided into three groups: I, II and III, containing 9, 28, and 6 members respectively, according to the WRKY conserved domain features and the evolution analysis with Arabidopsis thaliana. Gene structure analysis indicated that the number of exons of these CcWRKYs varied from 3 to 11. Among the 43 CcWRKYs, 10, 2, 2, and 14 genes showed higher expression in leaves, stem sticks, stem barks, and roots at the vigorous vegetative growth stage, respectively. Moreover, the expression of 21 of 43 CcWRKYs was regulated significantly with secondary cell wall biosynthesis genes using FPKM and RT-qPCR by GA3 stress to a typical GA3 sensitive dwarf germplasm in comparison to an elite cultivar in jute. The Cis-element analysis showed that promoters of these 21 CcWRKYs had 1 to 4 cis-elements involved in gibberellin-responsiveness, suggesting that they might regulate the development of bast fiber in response to GA3 stress. CONCLUSIONS: A total of 43 CcWRKYs were identified in jute for the first time. Analysis of phylogenetic relationship and gene structure revealed that these CcWRKYs might have a functional diversity. Expression analysis showed 21 TFs as GA3 stress responsive genes. The identification of these CcWRKYs and the characterization of their expression pattern will provide a basis for future clarification of their functions in bast fiber development in jute.