Kinetic and Thermodynamic Control of Supramolecular Aggregation of Near Infrared Pyrrolopyrrole Cyanine Fluorophores Confined in Colloidal Nanoparticles.

Control of the intermolecular aggregation of organic π-conjugated molecules as chromophores is crucial for tuning their physical properties such as light absorption/emission, and energy and charge transfer. Lots of advances have been achieved in control of intermolecular aggregation of organic chromophores in solid states where an indefinitely large number of molecules are involved. However, much less understanding has been gained at a mesoscale of aggregates formed by well-defined organization of a deterministic number of chromophores, which has been realized in natural photosynthetic systems but still remains rare in manmade materials. Here, we report both the kinetic and the thermodynamic control of the supramolecular aggregation of a near-infrared cyanine dye, PPcy, and its derivatives confined in colloidal nanoparticles stabilized by surfactants in aqueous media. Our results demonstrate that both the aggregation number, the aggregation state and the optical properties of the PPcy chromophores are controllable through optimization of the alkyl and polymer chains tethered from PPcy, the effective concentration of the chromophore inside each particle, and the surfactants utilized to stabilize the colloids in water.

Maternal exposure to E 551 during pregnancy leads to genome-wide DNA methylation changes and metabolic disorders in the livers of pregnant mice and their fetuses.

The widespread use of nanoparticles in the food industry has raised concerns regarding their potential adverse effects on human health, particularly in vulnerable populations, including pregnant mothers and fetuses. However, studies evaluating the reproductive and developmental toxicity of food-grade nanomaterials are limited. This study investigated the potential risks of prenatal dietary exposure to food-grade silica nanoparticles (E 551) on maternal health and fetal growth using conventional toxicological and epigenetic methods. The results showed that prenatal exposure to a high-dose of E 551 induces fetal resorption. Moreover, E 551 significantly accumulates in maternal and fetal livers, triggering a hepatic inflammatory response. At the epigenetic level, global DNA methylation is markedly altered in the maternal and fetal livers. Genome-wide DNA methylation sequencing revealed affected mCG, mCHG, and mCHH methylation landscapes. Subsequent bioinformatic analysis of the differentially methylated genes suggests that E 551 poses a risk of inducing metabolic disorders in maternal and fetal livers. This is further evidenced by impaired glucose tolerance in pregnant mice and altered expression of key metabolism-related genes and proteins in maternal and fetal livers. Collectively, the results of this study highlighted the importance of epigenetics in characterizing the potential toxicity of maternal exposure to food-grade nanomaterials during pregnancy.

Comparison of ARIMA model, DNN model and LSTM model in predicting disease burden of occupational pneumoconiosis in Tianjin, China.

BACKGROUND: This study aims to explore appropriate model for predicting the disease burden of pneumoconiosis in Tianjin by comparing the prediction effects of Autoregressive Integrated Moving Average (ARIMA) model, Deep Neural Networks (DNN) model and multivariate Long Short-Term Memory Neural Network (LSTM) models. METHODS: Disability adjusted life year (DALY) was used to evaluate the disease burden of occupational pneumoconiosis. ARIMA model, DNN model and multivariate LSTM model were used to establish prediction model. Three performance evaluation metrics including Root Mean Squared Error (RMSE), Mean Absolute Error (MAE) and Mean Absolute Percentage Error (MAPE) were used to compare the prediction effects of the three models. RESULTS: From 1990 to 2021, there were 10,694 cases of pneumoconiosis patients in Tianjin, resulting in a total of 112,725.52 person-years of DALY. During this period, the annual DALY showed a fluctuating trend, but it had a strong correlation with the number of pneumoconiosis patients, the average age of onset, the average age of receiving dust and the gross industrial product, and had a significant nonlinear relationship with them. The comparison of prediction results showed that the performance of multivariate LSTM model and DNN model is much better than that of traditional ARIMA model. Compared with the DNN model, the multivariate LSTM model performed better in the training set, showing lower RMES (42.30 vs. 380.96), MAE (29.53 vs. 231.20) and MAPE (1.63% vs. 2.93%), but performed less stable than the DNN on the test set, showing slightly higher RMSE (1309.14 vs. 656.44), MAE (886.98 vs. 594.47) and MAPE (36.86% vs. 22.43%). CONCLUSION: The machine learning techniques of DNN and LSTM are an innovative method to accurately and efficiently predict the burden of pneumoconiosis with the simplest data. It has great application prospects in the monitoring and early warning system of occupational disease burden.

Abscisic acid-dependent PMT1 expression regulates salt tolerance by alleviating abscisic acid-mediated reactive oxygen species production in Arabidopsis.

Phosphocholine (PCho) is an intermediate metabolite of nonplastid plant membranes that is essential for salt tolerance. However, how PCho metabolism modulates response to salt stress remains unknown. Here, we characterize the role of phosphoethanolamine N-methyltransferase 1 (PMT1) in salt stress tolerance in Arabidopsis thaliana using a T-DNA insertional mutant, gene-editing alleles, and complemented lines. The pmt1 mutants showed a severe inhibition of root elongation when exposed to salt stress, but exogenous ChoCl or lecithin rescued this defect. pmt1 also displayed altered glycerolipid metabolism under salt stress, suggesting that glycerolipids contribute to salt tolerance. Moreover, pmt1 mutants exhibited altered reactive oxygen species (ROS) accumulation and distribution, reduced cell division activity, and disturbed auxin distribution in the primary root compared with wild-type seedlings. We show that PMT1 expression is induced by salt stress and relies on the abscisic acid (ABA) signaling pathway, as this induction was abolished in the aba2-1 and pyl112458 mutants. However, ABA aggravated the salt sensitivity of the pmt1 mutants by perturbing ROS distribution in the root tip. Taken together, we propose that PMT1 is an important phosphoethanolamine N-methyltransferase participating in root development of primary root elongation under salt stress conditions by balancing ROS production and distribution through ABA signaling.

Mussel-Inspired Surface Coating to Stabilize and Functionalize Supramolecular J-Aggregate Nanotubes Composed of Amphiphilic Cyanine Dyes.

We report a mussel-inspired strategy of polydopamine (PDA) coating to stabilize and functionalize J-aggregate nanotubes (NTs) formed by supramolecular self-assembly of an amphiphilic cyanine dye called C8S3 in aqueous media. Optimization of the coating condition by changing the incubation time in a slightly basic media of dopamine with different concentrations leads to conformal wrapping of the PDA layer with controllable thickness on the surface of the NTs. Compared to noncoated pristine C8S3 NTs, these PDA-coated NTs show enhanced stability against dilution, heating, and photobleaching. Moreover, the PDA layer wrapping around the NTs serves as an adhesive for the adsorption of a variety of metal ions and electroless deposition of the metal nanoparticles. Such stabilized and functionalized NT composites may offer a robust synthetic J-aggregate system to mimic the structure and function of light-harvesting complexes and reaction centers in photosynthetic systems.

Estimating the Impacts of Plant Internal Nitrogen Deficit at Key Top Dressing Stages on Corn Productivity and Intercepted Photosynthetic Active Radiation.

Accurate and timely appraisal of plant nitrogen (N) demand is imperative to regulate the canopy structure and corn production. The strength and time of plant N deficit can be quantified by critical N concentration. The study was aimed to analyze nitrogen nutrition index (NNI), nitrogen deficit content (NDC), plant nitrogen productivity (PNP), and a fraction of intercepted photosynthetic active radiation (FIPAR) across different N treatments and to develop NNI-NDC, NNI-PNP, NNI-FIPAR, NDC-PNP, and NDC-FIPAR relationships from V6 to V12 stages of corn to quantify the suitable PNP and FIPAR values under the optimal plant N condition. Four multi-N rates (0, 75, 90, 150, 180, 225, 270, and 300 kg N ha-1) field experiments were conducted with two cultivars of corn in Henan province of China. Results indicated that N fertilization affected yield, plant biomass, plant N content, and leaf area index. The values of NNI and NDC were from 0.54 to 1.28 kg ha-1 and from -28.13 to 21.99 kg ha-1 under the different treatments of N rate, respectively. The NDC and NNI showed significantly negative relationships from V6 to V12 stages. The values of PNP and FIPAR increased gradually with the crop growth process. The PNP values gradually declined while the FIPAR values of every leaf layer increased with the increase of N supply. The NDC-PNP and NNI-FIPAR relationships were significantly positive; however, the relationships between NNI-PNP and NDC-FIPAR were significantly negative during the vegetative period of corn. The coefficient of determination (R 2) based on NNI was better than that on NDC. The FIPAR values were ~0.35, 0.67, and 0.76% at the upper, middle, and bottom of leaf layers, respectively, and PNP values were ~39, 44, and 51 kg kg-1 at V6, V9, and V12 stages, respectively, when NNI and NDC values were equal to 1 and 0 kg ha-1, respectively. This study described the quantitative information about the effect of a plant's internal N deficit on plant N productivity and canopy light intercept. The projected results would assist in predicting the appropriate plant growth status during key N top-dressing stages of corn, which can optimize N application and improve N use efficiency.

Genome-Wide Identification and Gene Expression Analysis of Acyl-Activating Enzymes Superfamily in Tomato (Solanum lycopersicum) Under Aluminum Stress.

In response to changing environments, plants regulate gene expression and subsequent metabolism to acclimate and survive. A superfamily of acyl-activating enzymes (AAEs) has been observed in every class of creatures on planet. Some of plant AAE genes have been identified and functionally characterized to be involved in growth, development, biotic, and abiotic stresses via mediating diverse metabolic pathways. However, less information is available about AAEs superfamily in tomato (Solanum lycopersicum), the highest value fruit and vegetable crop globally. In this study, we aimed to identify tomato AAEs superfamily and investigate potential functions with respect to aluminum (Al) stress that represents one of the major factors limiting crop productivity on acid soils worldwide. Fifty-three AAE genes of tomato were identified and named on the basis of phylogenetic relationships between Arabidopsis and tomato. The phylogenetic analysis showed that AAEs could be classified into six clades; however, clade III contains no AAE genes of tomato. Synteny analyses revealed tomato vegetable paralogs and Arabidopsis orthologs. The RNA-seq and quantitative reverse-transcriptase PCR (qRT-PCR) analysis indicated that 9 out of 53 AAEs genes were significantly up- or downregulated by Al stress. Numerous cis-acting elements implicated in biotic and abiotic stresses were detected in the promoter regions of SlAAEs. As the most abundantly expressed gene in root apex and highly induced by Al, there are many potential STOP1 cis-acting elements present in the promoter of SlAAE3-1, and its expression in root apex was specific to Al. Finally, transgenic tobacco lines overexpressing SlAAE3-1 displayed increased tolerance to Al. Altogether, our results pave the way for further studies on the functional characterization of SlAAE genes in tomato with a wish of improvement in tomato crop in the future.

Genome-Wide DNA Methylation Alterations and Potential Risk Induced by Subacute and Subchronic Exposure to Food-Grade Nanosilica in Mice.

The intensive application of nanomaterials in the food industry has raised concerns about their potential risks to human health. However, limited data are available on the biological safety of nanomaterials in food, especially at the epigenetic level. This study examined the implications of two types of synthetic amorphous silica (SAS), food-grade precipitated silica (S200) and fumed silica Aerosil 200F (A200F), which are nanorange food additives. After 28-day continuous and intermittent subacute exposure to these SAS via diet, whole-genome methylation levels in mouse peripheral leukocytes and liver were significantly altered in a dose- and SAS type-dependent manner, with minimal toxicity detected by conventional toxicological assessments, especially at a human-relevant dose (HRD). The 84-day continuous subchronic exposure to all doses of S200 and A200F induced liver steatosis where S200 accumulated in the liver even at HRD. Genome-wide DNA methylation sequencing revealed that the differentially methylated regions induced by both SAS were mainly located in the intron, intergenic, and promoter regions after 84-day high-dose continuous exposure. Bioinformatics analysis of differentially methylated genes indicated that exposure to S200 or A200F may lead to lipid metabolism disorders and cancer development. Pathway validation experiments indicated both SAS types as potentially carcinogenic. While S200 inhibited the p53-mediated apoptotic pathway in mouse liver, A200F activated the HRAS-mediated MAPK signaling pathway, which is a key driver of hepatocarcinogenesis. Thus, caution must be paid to the risk of long-term exposure to food-grade SAS, and epigenetic parameters should be included as end points during the risk assessment of food-grade nanomaterials.

Reduning injection and its effective constituent luteoloside protect against sepsis partly via inhibition of HMGB1/TLR4/NF-κB/MAPKs signaling pathways.

ETHNOPHARMACOLOGICAL RELEVANCE: Reduning injection (RDN), a popular traditional Chinese medicine, formulated by three herbs (i.e., Artemisia carvifolia Buch.-Ham. ex Roxb., Lonicera japonica Thunb., and Gardenia jasminoides J. Ellis), has been widely used to treat upper respiratory infectious diseases in China. AIM OF THE STUDY: To investigate the protective effect of RDN on both lipopolysaccharides (LPS)- and cecal ligation and puncture (CLP)-induced septic mice. To identify the potentially effective constituent, and to determine its protective effect and underlying mechanism in vivo and in vitro. MATERIALS AND METHODS: Male C57BL/6 mice were used to establish septic model by tail intravenous injection of 4 mg/kg LPS or CLP surgery. After modeling, mice were administered by tail intravenous injection of RDN in the dose of 16 or 8 mL/kg/day. The mortality, histopathology, plasma levels of inflammatory cytokines were evaluated respectively. In addition, we screened the potentially effective substances of RDN against sepsis by detecting the nitric oxide (NO) production in LPS-stimulated Raw 264.7 cells and verified the effect of luteoloside in CLP-induced septic mice subsequently. Finally, the underlying mechanisms of RDN and luteoloside were investigated in the inflammatory model in vitro. RESULTS: Administration of RDN significantly reduced the mortality and increased the survival rate in both LPS- and CLP-induced septic mice. Meanwhile, RDN reduced the release of inflammatory cytokines accompanied by alleviating the organs damage of lung, liver, and kidney in CLP-induced septic mice. Moreover, several components from Gardenia jasminoides J. Ellis extract (ZZ) or Lonicera japonica Thunb and Artemisia carvifolia Buch.-Ham. ex Roxb extract (JQ) as well as the constituents of luteoloside, quercetin, and caffeic acid were screened out to have obvious anti-inflammatory activity, which may be the potentially effective substances of RDN against sepsis. We further verified the protective role of luteoloside in CLP-induced septic mice. In addition, RDN and luteoloside significantly inhibited both the secretion and translocation of mobility group box (HMGB)1, and HMGB1-mediated activation of TLR4/NF-κB/MAPKs signaling pathways. CONCLUSION: RDN and its effective constituent luteoloside exhibited a significant protective effect against sepsis, which were potential candidate drugs for treatment of sepsis. The mechanism of antisepsis partly was related to inhibition of HMGB1/TLR4/NF-κB/MAPKs signaling pathways. The results provide an evidence base for the follow-up clinical application of RDN in treatment of sepsis.

A versatile sea anemone-inspired strategy toward 2D hybrid porous carbons from functional molecular brushes.

A generalized and facile strategy toward 2D hybrid porous carbons (2DHPCs) with various highly active functional species (e.g. Co, B, and P) is developed via 2D molecular brushes as biomimetic building blocks. The resulting 2DHPCs present superior electrochemical energy conversion and storage properties.

H2S attenuates injury after ischemic stroke by diminishing the assembly of CaMKII with ASK1-MKK3-p38 signaling module.

Cerebral ischemia/reperfusion (I/R) injury is a leading cause of learning and memory dysfunction. Hydrogen sulfide (H2S) has been shown to confer neuroprotection in various neurodegenerative diseases, including cerebral I/R-induced hippocampal CA1 injury. However, the underlying mechanisms have not been completely understood. In the present study, rats were pretreated with SAM/NaHS (SAM, an H2S agonist, and NaHS, an H2S donor) only or SAM/NaHS combined with CaM (an activator of CaMKII) prior to cerebral ischemia. The Morris water maze test demonstrated that SAM/NaHS could alleviate learning and memory impairment induced by cerebral I/R injury. Cresyl violet staining was used to show the survival of hippocampal CA1 pyramidal neurons. SAM/NaHS significantly increased the number of surviving cells, whereas CaM weakened the protection induced by SAM/NaHS. The immunohistochemistry results indicated that the number of Iba1-positive microglia significantly increased after cerebral I/R. Compared with the I/R group, the number of Iba1-positive microglia in the SAM/NaHS groups significantly decreased. Co-Immunoprecipitation and immunoblotting were conducted to demonstrate that SAM/NaHS suppressed the assembly of CaMKII with the ASK1-MKK3-p38 signal module after cerebral I/R, which decreased the phosphorylation of p38. In contrast, CaM significantly inhibited the effects of SAM/NaHS. Taken together, the results suggested that SAM/NaHS could suppress cerebral I/R injury by downregulating p38 phosphorylation via decreasing the assembly of CaMKII with the ASK1-MKK3-p38 signal module.

A NAC-type transcription factor confers aluminium resistance by regulating cell wall-associated receptor kinase 1 and cell wall pectin.

Transcriptional regulation is important for plants to respond to toxic effects of aluminium (Al). However, our current knowledge to these events is confined to a few transcription factors. Here, we functionally characterized a rice bean (Vigna umbellata) NAC-type transcription factor, VuNAR1, in terms of Al stress response. We demonstrated that rice bean VuNAR1 is a nuclear-localized transcriptional activator, whose expression was specifically upregulated by Al in roots but not in shoot. VuNAR1 overexpressing Arabidopsis plants exhibit improved Al resistance via Al exclusion. However, VuNAR1-mediated Al exclusion is independent of the function of known Al-resistant genes. Comparative transcriptomic analysis revealed that VuNAR1 specifically regulates the expression of genes associated with protein phosphorylation and cell wall modification in Arabidopsis. Transient expression assay demonstrated the direct transcriptional activation of cell wall-associated receptor kinase 1 (WAK1) by VuNAR1. Moreover, yeast one-hybrid assays and MEME motif searches identified a new VuNAR1-specific binding motif in the promoter of WAK1. Compared with wild-type Arabidopsis plants, VuNAR1 overexpressing plants have higher WAK1 expression and less pectin content. Taken together, our results suggest that VuNAR1 regulates Al resistance by regulating cell wall pectin metabolism via directly binding to the promoter of WAK1 and induce its expression.

Fabrication of Porous Nanonetwork-Structured Carbons from Well-Defined Cylindrical Molecular Bottlebrushes.

Atom transfer radical polymerization was utilized to prepare well-defined cylindrical molecular bottlebrushes which were employed as building blocks and transformed into porous nanonetwork-structured carbons (PNSCs) via hypercross-linking chemistry and shape-regulated carbonization. The as-prepared PNSCs exhibited a unique nanomorphology-tunable characteristic by simply varying carbonization conditions. Because of their three-dimensional network nanomorphologies with well-developed hierarchical porous structures and conductive carbon framework, the PNSCs demonstrated excellent electrochemical performance in lithium-sulfur batteries.

Alleviation by abscisic acid of Al toxicity in rice bean is not associated with citrate efflux but depends on ABI5-mediated signal transduction pathways.

Under conditions of aluminum (Al) toxicity, which severely inhibits root growth in acidic soils, plants rapidly alter their gene expression to optimize physiological fitness for survival. Abscisic acid (ABA) has been suggested as a mediator between Al stress and gene expression, but the underlying mechanisms remain largely unknown. Here, we investigated ABA-mediated Al-stress responses, using integrated physiological and molecular biology approaches. We demonstrate that Al stress caused ABA accumulation in the root apex of rice bean (Vigna umbellata [Thunb.] Ohwi & Ohashi), which positively regulated Al tolerance. However, this was not associated with known Al-tolerance mechanisms. Transcriptomic analysis revealed that nearly one-third of the responsive genes were shared between the Al-stress and ABA treatments. We further identified a transcription factor, ABI5, as being positively involved in Al tolerance. Arabidopsis abi5 mutants displayed increased sensitivity to Al, which was not related to the regulation of AtALMT1 and AtMATE expression. Functional categorization of ABI5-mediated genes revealed the importance of cell wall modification and osmoregulation in Al tolerance, a finding supported by osmotic stress treatment on Al tolerance. Our results suggest that ABA signal transduction pathways provide an additional layer of regulatory control over Al tolerance in plants.

LeSPL-CNR negatively regulates Cd acquisition through repressing nitrate reductase-mediated nitric oxide production in tomato.

MAIN CONCLUSION: An SPL-type transcription factor, LeSPL-CNR, is negatively involved in NO production by modulating SlNR expression and nitrate reductase activity, which contributes to Cd tolerance. Cadmium (Cd) is a highly toxic pollutant. Identifying factors affecting Cd accumulation in plants is a prerequisite for minimizing dietary uptake of Cd from crops grown with contaminated soil. Here, we report the involvement of a SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) transcription factor LeSPL-CNR in Cd tolerance in tomato (Solanum lycopersicum). In comparison with the wild-type Ailsa Craig (AC) plants, the Colourless non-ripening (Cnr) epimutant displayed increased Cd accumulation and enhanced sensitivity to Cd, which was in well accordance with the repression of LeSPL-CNR expression. Cd stress-induced NO production was inhibited by nitrate reductase (NR) inhibitor, but not NO synthase-like enzyme inhibitor. Expression of LeSPL-CNR was negatively correlated with SlNR expression and the NR activity. We also demonstrated that LeSPL-CNR inhibited the SlNR promoter activity in vivo and bound to SlNR promoter sequence that does not contain a known SBP-binding motif. In addition, expression of an IRON-REGULATED TRANSPORTER1, SlIRT1, was more abundant in Cnr roots than AC roots under Cd stress. LeSPL-CNR may thus provide a molecular mechanism linking Cd stress response to regulation of NR-dependent NO production, which then contributes to Cd uptake via SlIRT1 expression in tomato.

Construction of functional nanonetwork-structured carbon nitride with Au nanoparticle yolks for highly efficient photocatalytic applications.

We report a novel and versatile fabrication strategy for functional nanonetwork-structured carbon nitride with Au nanoparticle yolks (FNNS-C3N4-Au) based on hairy poly(acrylic acid)-grafted SiO2 nanospheres (Au@SiO2-g-PAA). Benefiting from the three-dimensional nanonetwork structure and well-distributed Au nanoparticles, the as-prepared nanocomposites demonstrated excellent photocatalysis performances (degradation rate constant: 1.8 × 10-2 min-1).

Two citrate transporters coordinately regulate citrate secretion from rice bean root tip under aluminum stress.

Aluminum (Al)-induced organic acid secretion from the root apex is an important Al resistance mechanism. However, it remains unclear how plants fine-tune root organic acid secretion which can contribute significantly to the loss of fixed carbon from the plant. Here, we demonstrate that Al-induced citrate secretion from the rice bean root apex is biphasic, consisting of an early phase with low secretion and a later phase of large citrate secretion. We isolated and characterized VuMATE2 as a possible second citrate transporter in rice bean functioning in tandem with VuMATE1, which we previously identified. The time-dependent kinetics of VuMATE2 expression correlates well with the kinetics of early phase root citrate secretion. Ectopic expression of VuMATE2 in Arabidopsis resulted in increased root citrate secretion and Al resistance. Electrophysiological analysis of Xenopus oocytes expressing VuMATE2 indicated VuMATE2 mediates anion efflux. However, the expression regulation of VuMATE2 differs from VuMATE1. While a protein translation inhibitor suppressed Al-induced VuMATE1 expression, it releases VuMATE2 expression. Yeast one-hybrid assays demonstrated that a previously identified transcription factor, VuSTOP1, interacts with the VuMATE2 promoter at a GGGAGG cis-acting motif. Thus, we demonstrate that plants adapt to Al toxicity by fine-tuning root citrate secretion with two separate root citrate transport systems.

Genome-Wide Transcriptome Analysis Reveals Conserved and Distinct Molecular Mechanisms of Al Resistance in Buckwheat (Fagopyrum esculentum Moench) Leaves.

Being an Al-accumulating crop, buckwheat detoxifies and tolerates Al not only in roots but also in leaves. While much progress has recently been made toward Al toxicity and resistance mechanisms in roots, little is known about the molecular basis responsible for detoxification and tolerance processes in leaves. Here, we carried out transcriptome analysis of buckwheat leaves in response to Al stress (20 µM, 24 h). We obtained 33,931 unigenes with 26,300 unigenes annotated in the NCBI database, and identified 1063 upregulated and 944 downregulated genes under Al stress. Functional category analysis revealed that genes related to protein translation, processing, degradation and metabolism comprised the biological processes most affected by Al, suggesting that buckwheat leaves maintain flexibility under Al stress by rapidly reprogramming their physiology and metabolism. Analysis of genes related to transcription regulation revealed that a large proportion of chromatin-regulation genes are specifically downregulated by Al stress, whereas transcription factor genes are overwhelmingly upregulated. Furthermore, we identified 78 upregulated and 22 downregulated genes that encode transporters. Intriguingly, only a few genes were overlapped with root Al-regulated transporter genes, which include homologs of AtMATE, ALS1, STAR1, ALS3 and a divalent ion symporter. In addition, we identified a subset of genes involved in development, in which genes associated with flowering regulation were important. Based on these data, it is proposed that buckwheat leaves develop conserved and distinct mechanisms to cope with Al toxicity.

Transcriptome Analysis of Al-Induced Genes in Buckwheat (Fagopyrum esculentum Moench) Root Apex: New Insight into Al Toxicity and Resistance Mechanisms in an Al Accumulating Species.

Relying on Al-activated root oxalate secretion, and internal detoxification and accumulation of Al, buckwheat is highly Al resistant. However, the molecular mechanisms responsible for these processes are still poorly understood. It is well-known that root apex is the critical region of Al toxicity that rapidly impairs a series of events, thus, resulting in inhibition of root elongation. Here, we carried out transcriptome analysis of the buckwheat root apex (0-1 cm) with regards to early response (first 6 h) to Al stress (20 µM), which is crucial for identification of both genes and processes involved in Al toxicity and tolerance mechanisms. We obtained 34,469 unigenes with 26,664 unigenes annotated in the NCBI database, and identified 589 up-regulated and 255 down-regulated differentially expressed genes (DEGs) under Al stress. Functional category analysis revealed that biological processes differ between up- and down-regulated genes, although 'metabolic processes' were the most affected category in both up- and down-regulated DEGs. Based on the data, it is proposed that Al stress affects a variety of biological processes that collectively contributes to the inhibition of root elongation. We identified 30 transporter genes and 27 transcription factor (TF) genes induced by Al. Gene homology analysis highlighted candidate genes encoding transporters associated with Al uptake, transport, detoxification, and accumulation. We also found that TFs play critical role in transcriptional regulation of Al resistance genes in buckwheat. In addition, gene duplication events are very common in the buckwheat genome, suggesting a possible role for gene duplication in the species' high Al resistance. Taken together, the transcriptomic analysis of buckwheat root apex shed light on the processes that contribute to the inhibition of root elongation. Furthermore, the comprehensive analysis of both transporter genes and TF genes not only deep our understanding on the responses of buckwheat roots to Al toxicity but provide a good start for functional characterization of genes critical for Al tolerance.