The noncoding RNA HIDDEN TREASURE 1 promotes phytochrome B-dependent seed germination by repressing abscisic acid biosynthesis.

Light is a major environmental factor for seed germination. Red light-activated phytochrome B (phyB) promotes seed germination by modulating the dynamic balance of two phytohormones, gibberellic acid (GA) and abscisic acid (ABA). How phyB modulates ABA biosynthesis after perceiving a light signal is not yet well understood. Here, we identified the noncoding RNA HIDDEN TREASURE 1 (HID1) as a repressor of ABA biosynthesis acting downstream of phyB during Arabidopsis thaliana seed germination. Loss of HID1 function led to delayed phyB-dependent seed germination. Photoactivated phyB promoted the accumulation of HID1 in the radicle within 48 h of imbibition. Our transcriptomics analysis showed that HID1 and phyB co-regulate the transcription of a common set of genes involved in ABA and GA metabolism. Through a forward genetic screen, we identified three ABA biosynthesis genes, ABA DEFICIENT 1 (ABA1), ABA2, and ABA3, as suppressors of HID1. We further demonstrated that HID1 directly inhibits the transcription of 9-CIS-EPOXYCAROTENOID DIOXYGENASE (NCED9), a gene encoding a key rate-limiting enzyme of ABA biosynthesis. HID1 interacts with ARABIDOPSIS TRITHORAX-RELATED7 (ATXR7), an H3K4me3 methyltransferase, inhibiting its occupancy and H3K4me3 modification at the NCED9 locus. Our study reveals a nuclear mechanism of phyB signaling transmitted through HID1 to control the internal homeostasis of ABA and GA, which gradually optimizes the transcriptional network during seed germination.

SlRBP1 promotes translational efficiency via SleIF4A2 to maintain chloroplast function in tomato.

Many glycine-rich RNA-binding proteins (GR-RBPs) have critical functions in RNA processing and metabolism. Here, we describe a role for the tomato (Solanum lycopersicum) GR-RBP SlRBP1 in regulating mRNA translation. We found that SlRBP1 knockdown mutants (slrbp1) displayed reduced accumulation of total chlorophyll and impaired chloroplast ultrastructure. These phenotypes were accompanied by deregulation of the levels of numerous key transcripts associated with chloroplast functions in slrbp1. Furthermore, native RNA immunoprecipitation-sequencing (nRIP-seq) recovered 61 SlRBP1-associated RNAs, most of which are involved in photosynthesis. SlRBP1 binding to selected target RNAs was validated by nRIP-qPCR. Intriguingly, the accumulation of proteins encoded by SlRBP1-bound transcripts, but not the mRNAs themselves, was reduced in slrbp1 mutants. Polysome profiling followed by RT-qPCR assays indicated that the polysome occupancy of target RNAs was lower in slrbp1 plants than in wild-type. Furthermore, SlRBP1 interacted with the eukaryotic translation initiation factor SleIF4A2. Silencing of SlRBP1 significantly reduced SleIF4A2 binding to SlRBP1-target RNAs. Taking these observations together, we propose that SlRBP1 binds to and channels RNAs onto the SleIF4A2 translation initiation complex and promotes the translation of its target RNAs to regulate chloroplast functions.

The Arabidopsis DREAM complex antagonizes WDR5A to modulate histone H3K4me2/3 deposition for a subset of genome repression.

The master transcriptional repressor DREAM (dimerization partner, RB-like, E2F and multivulval class B) complex regulates the cell cycle in eukaryotes, but much remains unknown about how it transmits repressive signals on chromatin to the primary transcriptional machinery (e.g., RNA polymerase II [Pol II]). Through a forward genetic screen, we identified BTE1 (barrier of transcription elongation 1), a plant-specific component of the DREAM complex. The subsequent characterization demonstrated that DREAM complex containing BTE1 antagonizes the activity of Complex Proteins Associated with Set1 (COMPASS)-like complex to repress H3K4me3 occupancy and inhibits Pol II elongation at DREAM target genes. We showed that BTE1 is recruited to chromatin at the promoter-proximal regions of target genes by E2F transcription factors. DREAM target genes exhibit characteristic enrichment of H2A.Z and H3K4me2 modification on chromatin. We further showed that BTE1 directly interacts with WDR5A, a core component of COMPASS-like complex, repressing WDR5A chromatin binding and the elongation of transcription on DREAM target genes. H3K4me3 is known to correlate with the Pol II transcription activation and promotes efficient elongation. Thus, our study illustrates a transcriptional repression mechanism by which the DREAM complex dampens H3K4me3 deposition at a set of genes through its interaction with WDR5A.

A dataset resource for clinically associated phosphosites in hepatocellular carcinoma.

Phosphorylation is one of the most common post-translational modifications (PTMs) and is closely related to protein activity and function, playing a critical role during cancer development. Quantitative phosphoproteomic strategies have been widely used to study the underlying mechanisms of cancer progression or drug resistance. In this report, we analyzed the association of phosphosite levels originated from our previously reported proteogenomic study in hepatocellular carcinoma (HCC) with clinical parameters, including prognosis, recurrence, and Tumor-Node-Metastasis (TNM) stages. By using both the log-rank test and univariate Cox proportional hazards regression analysis, we found that the abundance levels of 1712 phosphosites were associated with prognosis and those of 393 phosphosites associated with recurrence. Besides, 692 phosphosites had different abundance levels among TNM stages (I, II, III+IV) by Analysis of Variance (ANOVA) test. Gene ontology (GO) biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using proteins with these statistically significant phosphosites. In conclusion, we provided a dataset resource for clinically associated phosphosites in HCC, which may be beneficial to liver cancer related basic research.

Online Alkaline-pH Reverse Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Conventional Low-pH Method for Global Proteomic Analysis.

The global proteome analysis was limited by the identification of peptides with low abundance or specific physiochemical properties. Here, a one-dimensional online alkaline-pH reverse phase nanoelectrospray-tandem mass spectrometry (alkaline-pH-MS/MS) method was developed and optimized for global proteomic analysis. In this method, peptides were separated on a nanoflow C18 column with an alkaline-pH mobile phase (pH = 8.0) and directly injected into the mass spectrometer. The unique peptides overlapped between alkaline-pH-MS/MS and conventional online low-pH reverse phase nanoelectrospray-tandem mass spectrometry (low-pH-MS/MS) were as low as 45%, strongly indicating that these two methods were complementary to each other. In addition, alkaline-pH-MS/MS showed identification capacity for a higher proportion of peptides with negative grand average of hydropathy (GRAVY) or high isoelectric point (pI). Compared to low-pH-MS/MS, alkaline-pH-MS/MS enabled enrichment preference toward histidine-, lysine-, methionine-, and proline-containing peptides. The complementarity of alkaline-pH-MS/MS and low-pH-MS/MS was further demonstrated for the analysis of tryptic digests from 15 intrahepatic cholangiocarcinoma (iCCA) cell lines. The alternating 60 min alkaline-pH-MS/MS plus 60 min low-pH-MS/MS method outperformed the conventional 120 min low-pH-MS/MS method in both the identification of amino acid variants and protein groups. Therefore, we established the alkaline-pH-MS/MS method as a simple, competitive, alternative method to low-pH-MS/MS for global proteomic analysis.

"Two Birds One Stone" Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.

Core fucosylation and O-GlcNAcylation are the two most famous protein glycosylation modifications that regulate diverse physiological and pathological processes in living organisms. Here, a "two birds one stone" strategy has been described for the site-specific analysis of core fucosylation and O-GlcNAcylation. Taking advantage of two mutant endoglycosidases (EndoF3-D165A and EndoCC-N180H), which efficiently and specifically recognize core fucose and O-GlcNAc, glycopeptides can be labeled using a biantennary N-glycan probe bearing azido and oxazoline groups. Then, a temperature-sensitive poly(N-isopropylacrylamide) polymer functionalized with dibenzocyclooctyne was introduced to facilitate the enrichment of the labeled glycopeptides from the complex mixture. The captured glycopeptides can be further released enzymatically by wild-type endoglycosidases (EndoF3 and EndoCC) in a traceless manner for mass spectrometry (MS) analysis. The described strategy allows simultaneous profiling of core-fucosylated glycoproteome and O-GlcNAcylated glycoproteome from one complex sample by MS technology and searching the database using different variable modifications.

Toward Efficient Wound Management: Bioinspired Microfluidic and Microneedle Patch.

Microneedle (MN) patches hold demonstrated prospects in intelligent wound management. Herein, inspired by the highly folded structure of insect wings, a three-dimensional (3D) origami MN patch with superfine miniature needle structures, microfluidic channels, and multiple functions was reported to detect biomarkers, release drugs controllably and monitor motions to facilitate wound healing. By simply replicating the pre-stretched silicone rubber (Ecoflex) molds patterned by a laser engraving machine, the superfine structure MN patch with microfluidic channels was obtained from the restored molds. The bioinspired origami structure endows the MN patch with a high degree of functional integration, including microfluidic channels and electrocircuits. The microfluidic channels combined with the pH value and glucose concentration indicators enable the patch with the capability of biomarker sensing detection. Porous structures, a temperature-responsive hydrogel, and a photothermal-sensitive agent are utilized to form a controllable drug release system on the MN patch. Meanwhile, MXene electrocircuits were printed on the MN patch for motion sensing. In addition, the ability of the MN patch to accelerate wound healing was demonstrated by a mouse model experiment with full-thickness skin wounds. These results indicate that the multifunctional 3D origami MN patch is a valuable intelligent strategy for wound management.

Ultrasensitive detection of thiram based on surface-enhanced Raman scattering via Au@Ag@Ag core/shell/shell bimetallic nanorods.

We developed a highly sensitive and stable SERS-active substrate of Au@Ag@Ag core/shell/shell nanorods, formed by encapsulating Au nanorods (Au NRs) into a bilayer silver shell with Raman reporter molecules (4-mercaptobenzoic acid (4-MBA) and thiram) in the shell-shell gap. The core/shell/shell nanostructures demonstrated a high SERS enhancement and easy assembly. The important role of the bilayer silver shell in boosting the SERS intensity and detection sensitivity was revealed by comparing the performances of the Au@Ag@4-MBA@Ag NRs, Au@Ag@4-MBA NRs, and Au@4-MBA NRs. The obtained Au@Ag@4-MBA@Ag NRs exhibited a significantly promoted SERS intensity, which could reach around 2.6 times and 240 times that of the Au@Ag@4-MBA NRs and Au@4-MBA NRs, where the enhancement factor was found to be strongly correlated with the shell thickness. The controllable plasma properties and SERS effect of the Au@Ag@4-MBA@Ag NRs could be optimized by adjusting the dose of silver nitrate. The SERS substrate comprising core/shell/shell nanorods was highly reproducible and stable (retaining 83% SERS intensity after one month). Moreover, the highly sensitive detection of the pesticide thiram with a detection limit as low as 1.74 × 10-9 M was achieved by taking advantage of the great SERS response of the core/shell/shell nanostructures, which was 1-2 orders of magnitude lower than for other SERS substrates. The developed SERS substrate could be readily extended to embed other target analytes into the core/shell/shell nanostructure for novel and sensitive detection. This study could enable fresh approaches toward next-generation ultrasensitive analyte detection.

Recent advances on low-Co and Co-free high entropy layered oxide cathodes for lithium-ion batteries.

As the price of the precious metal cobalt continues to rise, there is an urgent need for a cobalt-free or low-cobalt electrode material to reduce the cost of lithium-ion batteries, which are widely used commercially, while maintaining their performance as much as possible. With the introduction of the new concept of high entropy (HE) materials into the battery field, low cobalt and cobalt free HE novel lithium-ion batteries have attracted great attention. It possesses important research value to use HE materials to reduce the use of cobalt metal in electrode materials. In this perspective, the comparison between the new cathode materials of low cobalt and cobalt-free HE lithium-ion battery and traditional cathode materials and the latest progress in maintaining structural stability and conductivity are introduced. It is believed that low cobalt and cobalt-free and HE layered oxides can be used to replace the function of cobalt in the cathode materials of lithium-ion batteries. Finally, the future research directions and the synthesis method of HE cathode materials for lithium-ion batteries are also discussed.

Profiling of RNA ribose methylation in Arabidopsis thaliana.

Eukaryotic rRNAs and snRNAs are decorated with abundant 2'-O-methylated nucleotides (Nm) that are predominantly synthesized by box C/D snoRNA-guided enzymes. In the model plant Arabidopsis thaliana, C/D snoRNAs have been well categorized, but there is a lack of systematic mapping of Nm. Here, we applied RiboMeth-seq to profile Nm in cytoplasmic, chloroplast and mitochondrial rRNAs and snRNAs. We identified 111 Nm in cytoplasmic rRNAs and 19 Nm in snRNAs and assigned guide for majority of the detected sites using an updated snoRNA list. At least four sites are directed by guides with multiple specificities as shown in yeast. We found that C/D snoRNAs frequently form extra pairs with nearby sequences of methylation sites, potentially facilitating the substrate binding. Chloroplast and mitochondrial rRNAs contain five almost identical methylation sites, including two novel sites mediating ribosomal subunit joining. Deletion of FIB1 or FIB2 gene reduced the accumulation of C/D snoRNA and rRNA methylation with FIB1 playing a bigger role in methylation. Our data reveal the comprehensive 2'-O-methylation maps for Arabidopsis rRNAs and snRNAs and would facilitate study of their function and biosynthesis.

From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants.

The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.

A Sensitive and Reversible Labeling Strategy Enables Global Mapping of the Core-Fucosylated Glycoproteome on Cell Surfaces.

Core fucosylation, the attachment of α1,6-fucose to the innermost N-acetylglucosamine (GlcNAc) residue of N-glycans, has a strong relationship with tumor growth, invasion, metastasis, prognosis, and immune evasion by regulating many membrane proteins. However, details about the functional mechanism are still largely unknown due to the lack of an effective analytical method to identify cell-surface core-fucosylated glycoproteins, and especially glycosylation sites. Here, we developed a sensitive and reversible labeling strategy for probing core fucosylation, by which core-fucosylated glycoproteins that located on cell-surface were selectively tagged by a biotinylated probe with high sensitivity. The labeled probe can be further broken enzymatically after the capture by affinity resin. The on-bead traceless cleavage allowed the global mapping of core-fucosylated glycoproteins and glycosylation sites by mass spectrometry (MS). The profile of core-fucosylated glycoproteome provides an in-depth understanding of the biological functions of core fucosylation.

Intelligent Patches for Wound Management: In Situ Sensing and Treatment.

Intelligent wound patches have the potential properties of ultra-adhesion, self-healing ability, biosensing, antibacterial, anti-inflammatory, etc. In situ sensing (biosensing and monitoring) and intelligent drug delivery deserve more exploration, and new strategies of these two factors are of great importance. In this Feature, a comprehensive set of the progress in the area of intelligent wound patches, especially those based on multiple biosensing and electronics, and their potentials in drug release is deliberated. In addition, the major challenges in this field and opinions on its future developments are portrayed.

Horseradish peroxidase-repeat assay based on tyramine signal amplification for highly sensitive H2O2 detection by surface-enhanced Raman scattering.

A new and simple surface-enhanced Raman scattering (SERS) biosensor based on the tyramine signal amplification (TSA)-triggered formation of horseradish peroxidase (HRP) repeats on a gold sensing chip was designed for the highly sensitive detection of hydrogen peroxide (H2O2). Initially, gold wafers were functionalized with HRP as sensing chips. Then, the HRP immobilized on the chips triggers the TSA reaction to transform the tyramine-HRP conjugate into a tyramine-HRP repeat array. With the aid of the target H2O2, the HRP repeats catalyze the oxidation of o-phenylenediamine (OPD) and produce an enzyme catalytic product with a different chemical structure, thus altering the fingerprint of the SERS spectra from that of OPD. H2O2 can be quantitatively analyzed according to the change in SERS signal intensity. On the basis of the TSA strategy, the proposed method allows the detection of H2O2 with a limit of detection (LOD) of 0.8 × 10-8 M. The as-prepared SERS sensor can achieve high-sensitivity H2O2 detection with a small amount of sample for each analysis. Therefore, this sensor exhibits significant potential for application in bioanalysis.

Characterizing the dissemination of misinformation on social media in health emergencies: An empirical study based on COVID-19.

The dissemination of misinformation in health emergencies poses serious threats to public health and increases health anxiety. To understand the underlying mechanism of the dissemination of misinformation regarding health emergencies, this study creatively draws on social support theory and text mining. It also explores the roles of different types of misinformation, including health advice and caution misinformation and health help-seeking misinformation, and emotional support in affecting individuals' misinformation dissemination behavior on social media and whether such relationships are contingent on misinformation ambiguity and richness. The theoretical model is tested using 12,101 textual data about COVID-19 collected from Sina Weibo, a leading social media platform in China. The empirical results show that health caution and advice, help seeking misinformation, and emotional support significantly increase the dissemination of misinformation. Furthermore, when the level of ambiguity and richness regarding misinformation is high, the effect of health caution and advice misinformation is strengthened, whereas the effect of health help-seeking misinformation and emotional support is weakened, indicating both dark and bright misinformation ambiguity and richness. This study contributes to the literature on misinformation dissemination behavior on social media during health emergencies and social support theory and provides implications for practice.

The false smut pathogen Ustilaginoidea virens requires rice stamens for false smut ball formation.

Rice false smut has emerged as a serious grain disease in rice production worldwide. The disease is characterized by the transformation of individual rice florets into false smut balls, which is caused by the fungal pathogen Ustilaginoidea virens. To date, little is known about the host factors required for false smut ball formation by U. virens. In this study, we identified histological determinants for the formation of false smut balls by inoculating U. virens into rice floral mutants defective with respect to individual floral parts. The results showed that U. virens could form mature false smut balls in rice floral mutants with defective pistils, but failed to develop false smut balls in the superwoman mutant lacking stamens, identifying that U. virens requires rice stamens to complete its infection cycle. Comparative transcriptome analysis indicated a list of candidate host genes that may facilitate nutrient acquisition by U. virens from the rice stamens, such as SWEET11, SWEET14 and SUT5, and genes involved in the biosynthesis of trehalose and raffinose family sugars. These data pinpoint rice stamens as the key target organ of U. virens infection and provide a valuable starting point for dissecting the molecular mechanism of false smut ball formation.

A simple enzyme-free SERS sensor for the rapid and sensitive detection of hydrogen peroxide in food.

A simple enzyme-free method based on surface-enhanced Raman scattering (SERS) was developed for the first time to detect H2O2 in food by etching a self-assembled film of silver nanoparticles (Ag NPs) on a glass substrate. H2O2 is able to oxidize Ag NPs to yield Ag+ ions; this process reduces the size of the Ag NPs and ultimately leads to a decrease in the SERS signal of the Raman probe. The intensities of the SERS spectra were strongly correlated with H2O2 concentration, which indicated that the Ag NP self-assembled SERS sensor can be successfully used for the quantitative analysis of H2O2. The main advantage of this SERS sensor is that it can directly detect H2O2 without introducing complex enzymatic reactions. This easy-to-operate and fast-response detection technology has great potential for the sensitive detection of H2O2 in food.

Arabidopsis small nucleolar RNA monitors the efficient pre-rRNA processing during ribosome biogenesis.

Ribosome production in eukaryotes requires the complex and precise coordination of several hundred assembly factors, including many small nucleolar RNAs (snoRNAs). However, at present, the distinct role of key snoRNAs in ribosome biogenesis remains poorly understood in higher plants. Here we report that a previously uncharacterized C (RUGAUGA)/D (CUGA) type snoRNA, HIDDEN TREASURE 2 (HID2), acts as an important regulator of ribosome biogenesis through a snoRNA-rRNA interaction. Nucleolus-localized HID2 is actively expressed in Arabidopsis proliferative tissues, whereas defects in HID2 cause a series of developmental defects reminiscent of ribosomal protein mutants. HID2 associates with the precursor 45S rRNA and promotes the efficiency and accuracy of pre-rRNA processing. Intriguingly, disrupting HID2 in Arabidopsis appears to impair the integrity of 27SB, a key pre-rRNA intermediate that generates 25S and 5.8S rRNA and is known to be vital for the synthesis of the 60S large ribosomal subunit and also produces an imbalanced ribosome profile. Finally, we demonstrate that the antisense-box of HID2 is both functionally essential and highly conserved in eukaryotes. Overall, our study reveals the vital and possibly conserved role of a snoRNA in monitoring the efficiency of pre-rRNA processing during ribosome biogenesis.

Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light.

Seedling photomorphogenesis is a sophisticated developmental process that is controlled by both the transcriptional and posttranscriptional regulation of gene expression. Here, we identify an Arabidopsis noncoding RNA, designated hidden treasure 1 (HID1), as a factor promoting photomorphogenesis in continuous red light (cR). We show that HID1 acts through phytochrome-interacting factor 3 (PIF3), which encodes a basic helix-loop-helix transcription factor known to be a key repressor of photomorphogenesis. Knockdown of HID1 in hid1 mutants leads to a significant increase in the expression of PIF3, which in turn drives the development of elongated hypocotyls in cR. We identified two major stem-loops in HID1 that are essential for its modulation of hypocotyl growth in cR-grown seedlings. Furthermore, our data reveal that HID1 is assembled into large nuclear protein-RNA complex(es) and that it associates with the chromatin of the first intron of PIF3 to repress its transcription. Strikingly, phylogenetic analysis reveals that many land plants have conserved homologs of HID1 and that its rice homolog can rescue the mutant phenotype when expressed in Arabidopsis hid1 mutants. We thus concluded that HID1 is a previously uncharacterized noncoding RNA whose function represents another layer of regulation in the precise control of seedling photomorphogenesis.

Assessment of the Effects of Total Emission Control Policies on Surface Water Quality in China: 2004 to 2014.

Water quality deterioration is a problem throughout the globe, especially in China. The Chinese government established national total emission control (TEC) policies related to the nation's surface water quality over the past 10 yr to restore, protect, and promote healthy water quality. The objective of this study is to evaluate the effects of China's TEC policies by analyzing three water quality constituents (ammonium nitrogen [NH-N], dissolved oxygen [DO], and the permanganate index [COD]) at 73 monitoring stations, which account for most of the surface waters of eastern China. The seasonal Mann-Kendall test revealed that approximately 60, 50, and 65% of stations had nonsignificant trends for COD, NH-N, and DO, respectively. Concentrations of COD and NH-N significantly (α = 0.05) decreased by 27.4 and 38.4% at the monitoring stations over the 11-yr study period, whereas DO significantly (α = 0.05) increased by 24.7%. Correlation analysis indicated that the water quality improved at approximately 30% (COD) and 20% (NH-N) of monitoring sites with the reduction of water pollutant emissions from industrial sources. A seasonal pattern was observed for the three water quality parameters at most of the stations but not at a regional scale. Results also indicated that COD concentrations decreased significantly (α = 0.05) at most river stations but increased significantly (α = 0.05) at nearly all lake stations, suggesting that TEC in China might be more effective for rivers than for lakes and reservoirs. Although there are many nonsignificant relationships with the water quality constituents selected as top pollutants in China, a few noticeable significant relationships were established.