Transcriptome- and genome-wide systematic identification of expansin gene family and their expression in tuberous root development and stress responses in sweetpotato (Ipomoea batatas).

Introduction: Expansins (EXPs) are essential components of the plant cell wall that function as relaxation factors to directly promote turgor-driven expansion of the cell wall, thereby controlling plant growth and development and diverse environmental stress responses. EXPs genes have been identified and characterized in numerous plant species, but not in sweetpotato. Results and methods: In the present study, a total of 59 EXP genes unevenly distributed across 14 of 15 chromosomes were identified in the sweetpotato genome, and segmental and tandem duplications were found to make a dominant contribution to the diversity of functions of the IbEXP family. Phylogenetic analysis showed that IbEXP members could be clustered into four subfamilies based on the EXPs from Arabidopsis and rice, and the regularity of protein motif, domain, and gene structures was consistent with this subfamily classification. Collinearity analysis between IbEXP genes and related homologous sequences in nine plants provided further phylogenetic insights into the EXP gene family. Cis-element analysis further revealed the potential roles of IbEXP genes in sweetpotato development and stress responses. RNA-seq and qRT-PCR analysis of eight selected IbEXPs genes provided evidence of their specificity in different tissues and showed that their transcripts were variously induced or suppressed under different hormone treatments (abscisic acid, salicylic acid, jasmonic acid, and 1-aminocyclopropane-1-carboxylic acid) and abiotic stresses (low and high temperature). Discussion: These results provide a foundation for further comprehensive investigation of the functions of IbEXP genes and indicate that several members of this family have potential applications as regulators to control plant development and enhance stress resistance in plants.

ATP Hydrolases Superfamily Protein 1 (ASP1) Maintains Root Stem Cell Niche Identity through Regulating Reactive Oxygen Species Signaling in Arabidopsis.

The maintenance of the root stem cell niche identity in Arabidopsis relies on the delicate balance of reactive oxygen species (ROS) levels in root tips; however, the intricate molecular mechanisms governing ROS homeostasis within the root stem cell niche remain unclear. In this study, we unveil the role of ATP hydrolase superfamily protein 1 (ASP1) in orchestrating root stem cell niche maintenance through its interaction with the redox regulator cystathionine ß-synthase domain-containing protein 3 (CBSX3). ASP1 is exclusively expressed in the quiescent center (QC) cells and governs the integrity of the root stem cell niche. Loss of ASP1 function leads to enhanced QC cell division and distal stem cell differentiation, attributable to reduced ROS levels and diminished expression of SCARECROW and SHORT ROOT in root tips. Our findings illuminate the pivotal role of ASP1 in regulating ROS signaling to maintain root stem cell niche homeostasis, achieved through direct interaction with CBSX3.

[Matrix solid-phase dispersion extraction of organophosphorus flame retardants in soil based on response surface methodology].

Organophosphorus flame retardants (OPFRs) are widely used in commercial products owing to their exceptional flame-retarding and plasticizing properties. However, OPFRs are also well recognized as emerging persistent organic pollutants (POPs) because of their environmental persistence, biological concentration, and potential toxicity. Thus, the accurate detection of OPFRs in environmental media is critical for analyzing their fate, transport, and ecological risk. However, very few OPFR detection methods are currently available, and the types of OPFRs detected may vary from site to site. In this study, matrix solid-phase dispersion extraction (MSPD), a simple, rapid, and versatile technique for preparing solid, semisolid, liquid, and viscous samples, was combined for the first time with gas chromatography-tandem mass spectrometry (GC-MS/MS) to analyze 10 OPFRs in soil, namely, tripropyl phosphate (TPrP), tri-n-butyl phosphate (TnBP), tri-iso-butyl phosphate (TiBP), tris(2-chloroisopropyl) phosphate (TCIPP), tris(2-chloroethyl) phosphate (TCEP), tris(1,3-dichloro-2-propyl) phosphate (TDCPP), triphenyl phosphate (TPHP), 2-ethylhexyl diphenyl phosphate (EHDPP), triphenylphosphine oxide (TPPO), and trimethylphenyl phosphate (TCP). The GC-MS/MS system was equipped with a Bruker-5MS capillary column coupled with a triple quadrupole mass spectrometer operated in multiple reaction monitoring (MRM) mode. Prior to detection, a mixed standard solution was fortified with 10 ng of13C-PCB208 as an internal standard. The optimal conditions under which MSPD could achieve high selectivity for OPFRs were determined. In addition, single-factor analysis was used to examine the influence of the sorbent (i. e., C18, PSA, Florisil, GCB, and multiwalled carbon nanotubes (MWCNTs)) as well as the dosage, type, and volume of the eluent on the extraction efficiency of the method for the 10 OPFRs. When GCB and ethyl acetate were used as the adsorbent and solvent, respectively, during elution, high extraction recoveries for the OPFRs were achieved. Optimization via response surface methodology (RSM) was adopted to further analyze the impact of three key factors, namely, the adsorbent dosage, eluent volume, and grinding time, as well as their interactions, on OPFR recoveries. Under the optimal conditions of 0.3 g of GCB as the adsorbent, 10 mL of ethyl acetate as the eluent, and 5 min of grinding time, the relative average recovery of the OPFRs was 87.5%. Furthermore, the 10 OPFRs showed good linear relationships under five concentration gradients, with correlation coefficients greater than 0.998. The limits of detection (LODs) and quantification (LOQs) were calculated as signal-to-noise ratios (S/N) of 3 and 10, respectively, and found to be in the ranges of 0.006-0.161 and 0.020-0.531 ng/g, respectively. The performance of the proposed method was verified by determining the recoveries and relative standard deviations (RSDs) of the OPFRs in soils spiked at low, medium, and high levels (10, 20, and 100 ng/g, respectively). The recoveries of the OPFRs ranged from 70.4% to 115.4%, with RSDs ranging from 0.7% to 6.7%. Compared with the conventional accelerated solvent extraction (ASE) method, MSPD presents higher efficiency, simpler operation, and less solvent requirements. The developed method was applied to determine OPFRs in soil samples collected from different sites in Suzhou, including an electronics factory, an auto-repair factory, a paddy field, and a school field. The results revealed that the contents of OPFRs in the soils from the electronics and auto-repair factories were significantly higher than those in the soils from the paddy and school fields. The main pollutants in the soil samples collected from the electronics and auto-repair factories were TCIPP, TPPO, TCEP, and TDCPP. Moreover, the contents of these compounds were 5.30, 4.44, 4.54, and 4.20 ng/g, in soils from the electronics factory and 2.70, 3.93, 7.60, and 5.04 ng/g, in soils from the auto-repair factory. To the best of our knowledge, this study is the first to determine high concentrations of TPPO in industrial soils. Thus, the combination of MSPD and GC-MS/MS adopted in this study can provide useful insights into the detection of the 10 OPFRs in soil.

Thermally activated persulfate (TAP)-enhanced tris(2-chloroethyl) phosphate removal in real-world waters based on a response-surface approach as well as toxicological evaluation on its degradation products.

As a typical organophosphorus flame retardant, tris(2-chloroethyl) phosphate (TCEP) is refractory in aqueous environment. The application of TAP is a promising method for removing pollutants. Herein, the removal of TCEP using TAP was rigorously investigated, and the effects of some key variables were optimized by the one-factor-at-a-time approach. To further evaluate the interactions among variables, the response surface methodology (RSM) based on central composite design was employed. Under optimized conditions (pH 5, [PS]0: [TCEP]0 = 500:1), the maximum removal efficiency (RE) of TCEP reached up to 90.6%. In real-world waters, the RE of TCEP spanned the range of 56%- 65% in river water, pond water, lake water and sanitary sewage. The low-concentration Cl- (0.1 mM) promoted TCEP degradation, but the contrary case occurred when the high-concentration Cl-, NO3-, CO32-, HCO3-, HPO42-, H2PO4-, NH4+ and humic acid were present owing to their prominently quenching effects on SO4•-. Both EPR and scavenger experiments revealed that the main radicals in the TAP system were SO4•- and •OH, in which SO4•- played the most crucial role in TCEP degradation. GC-MS/MS analysis disclosed that two degradation products appeared, sourcing from the replacement, oxidation, hydroxylation and water-molecule elimination reactions. The other two products were inferred from the comprehensive literature. As for acute toxicity to fish, daphnid and green algae, product A displayed the slightly higher toxicity, whereas other three products exhibited the declining toxicity as compared to their parent molecule. These findings offer a theoretical/practical reference for high-efficiency removal of TCEP and its ecotoxicological risk evaluation.

A dual-emitting fluoroprobe fabricated by aloe leaf-based N-doped carbon quantum dots and copper nanoclusters for nitenpyram detection in waters by virtue of inner filter effect and static quenching principles.

Fluorescence sensing technique has been used in environmental analysis due to its simplicity, low cost, and visualization. Although the fruit pulp-based biomass carbon quantum dots (CQDs) have excellent luminescent properties, aloe leaves possess the superiority of being easily accessible in all seasons compared to fruit pulp. Thus, we fabricated Aloe carazo leaf-based nitrogen doping-CQDs (N-CQDs) using a facile hydrothermal approach, which emitted bright blue fluorescence with a quantum yield of 21.4 %. By comparison, the glutathione-encapsulated copper nanoclusters (GSH-CuNCs) displayed strong red fluorescence. A blue/red dual emission based on the N-CQDs/CuNCs mixture was established for nitenpyram detection. At the 350-nm excitation, the N-CQD/CuNCs system produced dual-wavelength emitting peaks at 440 and 660 nm, respectively. Moreover, when nitenpyram was introduced into the system, the fluorescence intensities (FIs) of N-CQDs significantly decreased, whereas the FIs of GSH-CuNCs varied slightly; simultaneously, the solution color changed from bright blue to dark red. Both the spectral overlapping between nitenpyram's UV-Vis absorption and N-CQDs' excitation and almost unchanged fluorescence lifetimes indicated the occurrence of inner-filtering effect (IFE) in the dual-emitting fluoroprobe. In addition, the Stern-Volmer constant (Ksv = 6.92 × 103 M-1), temperature effect, as well as UV-Vis absorption of N-CQD/CuNCs before and after the addition of nitenpyram corroborated the static-quenching behavior. Consequently, the fluorescence-quenching of N-CQDs by nitenpyram was attributable to the joint IFE and static-quenching principles. A good linearity existed between the F660/F440 values and nitenpyram concentrations (0.5-200 µM) with a method detection limit of 0.15 µM. The dual-emitting fluoroprobe provided the satisfactory recoveries (95.0%-107.0 %) for nitenpyram detection in real-world waters, which were comparable with the results of traditional liquid chromatography coupled to tandem mass spectrometry method. Owing to its simple operations, low-cost, and adaptability for on-site outdoor monitoring, the newly developed dual-emitting fluoroprobe possesses great potential applications in routine monitoring of nitenpyram under field conditions.

Hericium coralloides Ameliorates Alzheimer's Disease Pathologies and Cognitive Disorders by Activating Nrf2 Signaling and Regulating Gut Microbiota.

Alzheimer's disease (AD) is prone to onset and progression under oxidative stress conditions. Hericium coralloides (HC) is an edible medicinal fungus that contains various nutrients and possesses antioxidant properties. In the present study, the nutritional composition and neuroprotective effects of HC on APP/PS1 mice were examined. Behavioral experiments showed that HC improved cognitive dysfunction in APP/PS1 mice. Immunohistochemical and Western blotting results showed that HC reduced the levels of p-tau and amyloid-ß deposition in the brain. By altering the composition of the gut microbiota, HC promoted the growth of short-chain fatty acid-producing bacteria and suppressed the growth of Helicobacter. Metabolomic results showed that HC decreased D-glutamic acid and oxidized glutathione levels. In addition, HC reduced the levels of reactive oxygen species, enhanced the secretion of superoxide dismutase, catalase, and glutathione peroxidase, inhibited the production of malondialdehyde and 4-hydroxynonenal, and activated the nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway. Collectively, HC demonstrated antioxidant activity by activating Nrf2 signaling and regulating gut microbiota, further exerting neuroprotective effects. This study confirms that HC has the potential to be a clinically effective AD therapeutic agent and offers a theoretical justification for both the development and use of this fungus.

A pretreatment method combined matrix solid-phase dispersion with dispersive liquid-liquid micro-extraction for polybrominated diphenyl ethers in vegetables through quantitation of gas chromatography-tandem mass spectrometry (GC-MS).

Herein, a novel pretreatment method for extraction of polybrominated diphenyl ethers (PBDEs) using matrix solid phase dispersion (MSPD) and depth purification using dispersive liquid-liquid micro-extraction (DLLME) from vegetables was designed. The vegetables included three leafy vegetables (Brassica chinensis, Brassica rapa var. glabra Regel and Brassica rapa L.), two root vegetables (Daucus carota and Ipomoea batatas (L.) Lam.), and Solanum melongena L. First, the freeze-dried powders of vegetables and sorbents were evenly ground to a mixture, which was then loaded into a solid phase column containing two molecular sieve spacers, one positioned at the top and the other at the bottom. The PBDEs were eluted with a small amount of solvent, concentrated, redissolved in acetonitrile, and then mixed with extractant. Next, 5 mL water was added to form an emulsion and centrifuged. Finally, the sedimentary phase was collected and injected into a gas chromatography-tandem mass spectrometry (GC-MS) system. The main factors such as the type of adsorbent, ratio of sample mass and adsorbents, volume of elution solvent used in the MSPD process, as well as the types and volume of dispersant and the, extractant used in DLLME were all evaluated using the single factor method. Under optimal conditions, the proposed method showed good linearity (R2 > 0.999) within the range of 1 to 1000 g kg-1 for all PBDEs and satisfactory recoveries of spiked samples (82.9-113.8%, except for BDE-183 (58.5-82.5%)) and matrix effects (-3.3-18.2%). The limits of detection and the limits of quantification were in the range of 1.9-75.1 g kg-1 and 5.7-25.3 g kg-1, respectively. Moreover, the total pretreatment and detection time was within 30 min. This method proved to be a promising alternative to other high-cost and time-consuming and multi-stage procedures for determination of PBDEs in vegetables.

The physiological effect of organophosphate flame retardants (OPFRs) on wheat (Triticum aestivum L.) seed germination and seedling growth under the presence of copper.

This study investigated the physiological and biochemical impacts of organophosphate flame retardants (OPFRs) on wheat (Triticum aestivum L.) germination and growth performance in the presence and absence of copper. The study evaluated seed germination, growth, OPFRs concentrations, chlorophyll fluorescence index (Fv/Fm and Fv/F0), and antioxidant enzyme activity. It also calculated the root accumulation of OPFRs and their root-stem translocation. At the germination stage, at a concentration of 20 µg·L-1 OPFR exposure, wheat germination vigor, root, and shoot lengths were significantly decreased compared to the control. However, the addition of a high concentration of copper (60 mg·L-1) decreased by 80%, 82%, and 87% in the seed germination vitality index and root and shoot elongation, respectively, compared to 20 µg·L-1 of OPFR treatment. At the seedling stage, a concentration of 50 µg·L-1 of OPFRs significantly decreased by 42% and 5.4% in wheat growth weight and the photochemical efficiency of photosystem II (Fv/Fm) compared to the control. However, the addition of a low concentration of copper (15 mg·L-1) slightly enhanced the growth weight compared to the other two co-exposure treatments, but the results were not significant (p > 0.05). After 7 days of exposure, the activity of superoxide dismutase (SOD) and malondialdehyde (MDA) (indicates lipid peroxidation) content in wheat roots significantly increased compared to the control and was higher than in leaves. MDA contents in wheat roots and shoots were decreased by 18% and 6.5% when OPFRs were combined with low Cu treatment compared with single OPFRs treatment, but SOD activity was slightly improved. These results suggest that the co-exposure of copper and OPFRs enhances reactive oxygen species (ROS) production and oxidative stress tolerance. Seven OPFRs were detected in wheat roots and stems, with root concentration factors (RCFs) and translocation factors (TFs) ranging from 67 to 337 and 0.05 to 0.33, respectively, for the seven OPFRs in a single OPFR treatment. The addition of copper significantly increased OPFR accumulation in the root and aerial parts. In general, the addition of a low concentration of copper promoted wheat seedling elongation and biomass and did not significantly inhibit the germination process. OPFRs could mitigate the toxicity of low-concentration copper on wheat but had a weak detoxification effect on high-concentration copper. These results indicated that the combined toxicity of OPFRs and Cu had antagonistic effects on the early development and growth of wheat.

Regulatory network of GSK3-like kinases and their role in plant stress response.

Glycogen synthase kinase 3 (GSK3) family members are evolutionally conserved Ser/Thr protein kinases in mammals and plants. In plants, the GSK3s function as signaling hubs to integrate the perception and transduction of diverse signals required for plant development. Despite their role in the regulation of plant growth and development, emerging research has shed light on their multilayer function in plant stress responses. Here we review recent advances in the regulatory network of GSK3s and the involvement of GSK3s in plant adaptation to various abiotic and biotic stresses. We also discuss the molecular mechanisms underlying how plants cope with environmental stresses through GSK3s-hormones crosstalk, a pivotal biochemical pathway in plant stress responses. We believe that our overview of the versatile physiological functions of GSK3s and underlined molecular mechanism of GSK3s in plant stress response will not only opens further research on this important topic but also provide opportunities for developing stress-resilient crops through the use of genetic engineering technology.

Specific detection of RNA mutation at single-base resolution by coupling the isothermal exponential amplification reaction (EXPAR) with chimeric DNA probe-aided precise RNA disconnection at the mutation site.

A chimeric DNA probe-aided RNase H-EXPAR approach is developed for the accurate and specific detection of RNA mutation at single-base resolution through a new site-specific RNase H cleavage mechanism.

A novel restriction endonuclease GlaI for rapid and highly sensitive detection of DNA methylation coupled with isothermal exponential amplification reaction.

Sensitive and accurate detection of site-specific DNA methylation is of critical significance for early diagnosis of human diseases, especially cancers. Herein, for the first time we employ a novel methylation-dependent restriction endonuclease GlaI to detect site-specific DNA methylation in a highly specific and sensitive way by coupling with isothermal exponential amplification reaction (EXPAR). GlaI can only cut the methylated target site with excellent selectivity but leave the unmethylated DNA intact. Then the newly exposed end fragments of methylated DNA can trigger EXPAR for highly efficient signal amplification while the intact unmethylated DNA will not initiate EXPAR at all. As such, only the methylated DNA is quantitatively and faithfully reflected by the real-time fluorescence signal of the GlaI-EXPAR system, and the potential false positive interference from unmethylated DNA can be effectively eliminated. Therefore, by integrating the unique features of GlaI for highly specific methylation discrimination and EXPAR for rapid and powerful signal amplification, the elegant GlaI-EXPAR assay allows the direct quantification of methylated DNA with ultrahigh sensitivity and accuracy. The detection limit of methylated DNA target has been pushed down to the aM level and the whole detection process of GlaI-EXPAR can be accomplished within a short time of 2 h. More importantly, ultrahigh specificity is achieved and as low as 0.01% methylated DNA can be clearly identified in the presence of a large excess of unmethylated DNA. This GlaI-EXPAR is also demonstrated to be capable of determining site-specific DNA methylations in real genomic DNA samples. Sharing the distinct advantages of ultrahigh sensitivity, outstanding specificity and facile operation, this new GlaI-EXPAR strategy may provide a robust and reliable platform for the detection of site-specific DNA methylations with low abundances.

One-step detection of microRNA with high sensitivity and specificity via target-triggered loop-mediated isothermal amplification (TT-LAMP).

A novel one-step microRNA assay is developed based on a target-triggered loop-mediated isothermal amplification (TT-LAMP) mechanism, which enables the accurate detection of as low as 100 aM (1 zmol) microRNA with simple one-step operation by using only one-type of DNA polymerase.

Real-time fluorescence ligase chain reaction for sensitive detection of single nucleotide polymorphism based on fluorescence resonance energy transfer.

Most of practical methods for detection of single nucleotide polymorphism (SNP) need at least two steps: amplification (usually by PCR) and detection of SNP by using the amplification products. Ligase chain reaction (LCR) can integrate the amplification and allele discrimination in one step. However, the detection of LCR products still remains a great challenge for highly sensitive and quantitative SNP detection. Herein, a simple but robust strategy for real-time fluorescence LCR has been developed for highly sensitive and quantitative SNP detection. A pair of LCR probes are firstly labeled with a fluorophore and a quencher, respectively. When the pair of LCR probes are ligated in LCR, the fluorophore will be brought close to the quencher, and thus, the fluorescence will be specifically quenched by fluorescence resonance energy transfer (FRET). The decrease of fluorescence intensity resulted from FRET can be real-time monitored in the LCR process. With the proposed real-time fluorescence LCR assay, 10 aM DNA targets or 100 pg genomic DNA can be accurately determined and as low as 0.1% mutant DNA can be detected in the presence of a large excess of wild-type DNA, indicating the high sensitivity and specificity. The real-time measuring does not require the detection step after LCR and gives a wide dynamic range for detection of DNA targets (from 10 aM to 1 pM). As LCR has been widely used for detection of SNP, DNA methylation, mRNA and microRNA, the real-time fluorescence LCR assay shows great potential for various genetic analysis.

Highly sensitive detection of CpG methylation in genomic DNA by AuNP-based colorimetric assay with ligase chain reaction.

We have developed a new ligase chain reaction-based colorimetric assay for detection of DNA methylation with ultrahigh sensitivity and selectivity. Using the proposed assay, as low as 0.01 fM methylated DNA can be detected by visualization of color changes of gold nanoparticles with the naked eye.

Highly sensitive and multiplexed analysis of CpG methylation at single-base resolution with ligation-based exponential amplification.

DNA methylation is a primary epigenetic mechanism for transcriptional regulation during normal development and the occurrence of diseases, including cancers. DNA methylation has been increasingly utilized as a biomarker for cancer detection and differential diagnosis. Generally, one type of cancer is associated with several CpG methylation sites and detection of multiplexed CpG methylation can greatly improve the accuracy of cancer diagnosis. In this paper, we have developed a novel ligase chain reaction (LCR)-based method for multiplexed detection of CpG methylation in genomic DNA at single-base resolution. By rationally designing the two pairs of DNA probes for LCR, the bisulfite-treated methylated DNA target can be exponentially amplified by thermal cycling of the ligation reaction, in which one-base mismatch can be discriminated against, and thus high sensitivity and specificity for the detection of DNA methylation can be achieved. The LCR-based method can accurately determine as low as 10 aM methylated DNA fragment and 10 ng methylated genomic DNA. 0.1% methylated DNA can be detected in the presence of a large excess of unmethylated DNA. Moreover, by simply encoding one of the DNA probes in the LCR with a different length of poly(A) for detection of methylation at different CpG sites, the CpG methylation at different sites can produce LCR products with different lengths, and thus, can be simultaneously detected with one-tube LCR amplification and separation by capillary electrophoresis.