Integrated metabolomic and transcriptomic analysis of triterpenoid accumulation in the roots of Codonopsis pilosula var. modesta (Nannf.) L.T.Shen at different altitudes.

INTRODUCTION: Codonopsis Radix is a beneficial traditional Chinese medicine, and triterpenoid are the major bioactive constituents. Codonopsis pilosula var. modesta (Nannf.) L.T.Shen (CPM) is a precious variety of Codonopsis Radix, which is distributed at high mountain areas. The environment plays an important role in the synthesis and metabolism of active ingredients in medicinal plants, but there is no report elaborating on the effect of altitude on terpenoid metabolites accumulation in CPM. OBJECTIVES: This study aims to analyse the effects of altitude on triterpenoid biosynthetic pathways and secondary metabolite accumulation in CPM. MATERIAL AND METHODS: The untargeted metabolomics based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) and 10 triterpenoids based on ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) method were analysed at the low-altitude (1480 m) and high-altitude (2300 m) CPM fresh roots. The transcriptome based on high-throughput sequencing technology were combined to analyse the different altitude CPM triterpenoid biosynthetic pathways. RESULTS: A total of 17,351 differentially expressed genes (DEGs) and 55 differentially accumulated metabolites (DAMs) were detected from the different altitude CPM, and there are significant differences in the content of the 10 triterpenoids. The results of transcriptome study showed that CPM could significantly up-regulate the gene expression levels of seven key enzymes in the triterpenoid biosynthetic pathway. CONCLUSIONS: The CPM at high altitude is more likely to accumulate triterpenes than those at low altitude, which was related to the up-regulation of the gene expression levels of seven key enzymes. These results expand our understanding of how altitude affects plant metabolite biosynthesis.

Antitumor Effect of Anti-c-Myc Aptamer-Based PROTAC for Degradation of the c-Myc Protein.

Targeting "undruggable" targets with intrinsically disordered structures is of great significance for the treatment of disease. The transcription factor c-Myc controls global gene expression and is an attractive therapeutic target for multiple types of cancers. However, due to the lack of defined ligand binding pockets, targeted c-Myc have thus far been unsuccessful. Herein, to address the dilemma of lacking ligands, an efficient and high throughput aptamer screening strategy is established, named polystyrene microwell plate-based systematic evolution of ligands by exponential enrichment (microwell-SELEX), and identify the specific aptamer (MA9C1) against c-Myc. The multifunctional aptamer-based Proteolysis Targeting Chimeras (PROTAC) for proteolysis of the c-Myc (ProMyc) is developed using the aptamer MA9C1 as the ligand. ProMyc not only significantly degrades c-Myc by the ubiquitin-proteasome system, but also reduces the Max protein, synergistically inhibiting c-Myc transcriptional activity. Combination of the artificial cyclization and anti-PD-L1 aptamer (PA1)-based delivery system, circular PA1-ProMyc chimeras achieve tumor regression in the xenograft tumor model, laying a solid foundation for the development of efficacious c-Myc degrader for the clinic. Therefore, this aptamer-based degrader provides an invaluable potential degrader in drug discovery and anti-tumor therapy, offering a promising degrader to overcome the challenge of targeting intractable targets.

Leveraging CRISPR/Cas12 signal amplifier to sensitive detection of apurinic/apyrimidinic endonuclease 1 and high-throughput inhibitor screening.

As an essential protein in DNA repair, apurinic/apyrimidinic endonuclease 1 (APE1) plays multiple critical functions in maintaining homeostasis, making it a significant biomarker and therapeutic target for many disorders. Here, we describe a simple method to detect APE1 based on the Releasing-Extension-Signal amplification Test (REST) strategy that leverages the dsDNA as the activator to fully unlock the trans-cleavage activity of CRISPR/Cas12a. This assay provides a rapid and specific APE1 detection with a detection limit down to 1.05 × 10-5 U/mL. We also combined this method with an automated pipetting platform and a microplate reader for high-throughput screening of potential inhibitors of APE1. Besides, by changing the modification on the probe, the REST strategy was easily repurposed to detect various DNA glycosylases. Taken together, the simplicity and robustness of the method offer a new choice for APE1 detection and inhibitor screening, showing great potential in practical use. Furthermore, the REST strategy devised in this study provides a new example of applying CRISPR/Cas12a signal amplifier to non-nucleic acid biosensing and inhibitor screening, which broadens the CRISPR-Dx toolbox.

Novel Sm3+-doped La3Ga5MO14 (M = Si or Ge) phosphors for indoor illumination: effects of M cations on photoluminescence.

A series of La3(1-x)Ga5MO14:xSm3+ (M = Si or Ge) orange-red phosphors with high color purity, low correlated color temperature, and good thermal stability were successfully synthesized via a high-temperature solid-phase technique. The phase structure and morphology of La3Ga5SiO14(LGSi):xSm3+ and La3Ga5GeO14(LGGe):xSm3+ were investigated. Sm3+-doped LGSi and LGGe phosphors emitted orange-red light under an excitation of 403 nm, and the optimal doping concentrations were 3 mol% and 2 mol% with excellent color purities of 98.46% and 98.25%, respectively. The concentration quenching mechanism of both the samples was dominated by dipole-dipole interaction, and the effect of Si4+ and Ge4+ on luminescence performance was discussed. The internal quantum efficiencies of LGSi:0.03Sm3+ and LGGe:0.02Sm3+ were calculated to be 27.14% and 56.07%, respectively. The CIE and CCT values indicated that the luminescence of the prepared phosphors was in the orange-red region. Additionally, a white light-emitting diode (w-LED) was fabricated with LGGe:0.02Sm3+ phosphors, which was capable of emitting bright and warm white light and exhibiting a high color rendering index (CRI) of 87.17 and an appropriate correlated color temperature (CCT) of 6108 K. These results indicated that the prepared phosphors with excellent luminescent performances have potential application in indoor illumination.

Chemical constituents of Wikstroemia alternifolia and their neuroprotective activities.

Phytochemical investigation on the plant of Wikstroemia alternifolia led to the isolation of 26 compounds including two new ones, wikstralternifols A and B (1 and 7). Their structures including the absolute configuration were elucidated by spectroscopic data together with analysis of experimental and calculated ECD data. All compounds were isolated from this plant for the first time, and their main structural types were lignans, sesquiterpenoids, and flavonoids. In the sodium nitroprusside-induced rat pheochromocytoma PC-12 cell model, the neuroprotective activities of the selected sesquiterpenoids (1 and 4) and lignans (7 - 14) were screened at the concentration of 10 µM, and 7 - 14 displayed better activities than the positive control edaravone.

Spatiotemporal distribution of community-acquired phenotypic extended-spectrum beta-lactamase Escherichia coli in United States counties, 2010-2019.

Using data from the Veterans' Health Administration from 2010 to 2019, we examined the distribution and prevalence of community-acquired phenotypic extended-spectrum ß-lactamase (ESBL) E. coli in the United States. ESBL prevalence slowly increased during the study period, and cluster analysis showed clustering in both urban and rural locations.

Synthesis of sulfinamides via photocatalytic alkylation or arylation of sulfinylamine.

Sulfinamides are a versatile class of compounds that find applications in both organic synthesis and pharmaceuticals. Here we developed an efficient photocatalytic approach for the convenient preparation of sulfinamides. Commercially available potassium trifluoro(organo)borates and readily available sulfinyl amines are rationally used and converted to a series of alkyl or aryl sulfinamides in moderate to high yields. The reaction allows for the gram-scale preparation of sulfinamides. Moreover, sulfonimidamides, sulfonimidate esters and sulfonyl amides could be obtained in one pot.

A Strategy for Studying Environmental Engineering: Simple Hydrothermal Synthesis of Flower-Shaped Stannous Sulfide Nanomaterials for Efficient Cataluminescence Sensing of Diethyl Ether.

In this work, flower-like stannous sulfide (SnS) nanomaterials are synthesized using a hydrothermal method and used as sensitive materials for cataluminescence (CTL)-based detection of diethyl ether. Gas sensors based on SnS nanomaterials are prepared, and the SnS nanomaterials exhibit excellent gas-sensitive behavior towards ether. High sensitivity to ether is achieved at a relatively low operating temperature (153 °C) compared to other common sensors. The response time is 3 s and the recovery time is 8 s. The CTL intensity shows a good linear relationship (R2 = 0.9931) with a detection limit of 0.15 ppm and the concentration of ether in the range of 1.5-60 ppm. The proposed CTL sensor shows good selectivity towards ether. In addition, a highly stable signal is obtained with a relative standard deviation of 1.5%. This study indicates that the SnS-based sensor has excellent gas-sensitive performance and shows potential for applications in the detection of ether.

Rapidly detecting the carcinogen acetaldehyde: preparation and application of a flower-like MoS2 cataluminescence sensor at low working temperature.

In this paper, a cataluminescence (CTL) gas sensor based on flower-like molybdenum disulfide (MoS2) is developed. The experimental results show that it has high sensitivity and selectivity to acetaldehyde. The CTL sensor has the advantage of fast response; the response time is about 3 s and the recovery time is about 40 s. The optimal working temperature of this sensor is 174 °C, which is lower than that of the CTL sensors used for acetaldehyde detection in many other reports. Under the optimized conditions, the CTL signal intensity shows a good linear relationship with acetaldehyde concentration (R2 = 0.9991) within the concentration range of 40-2000 ppm, and the detection limit (LOD) is 3.75 ppm. The selectivity experiment results show that the sensor has an obvious response to acetaldehyde and a very weak response to acetic acid, and has no response to many other VOCs (ether, cyclohexane, butyl ether, carbon tetrachloride, ethanol, toluene, formaldehyde, glycerol, trichloromethane and xylene). After 8 repeated measurements for four weeks, the relative standard deviation (RSD) of the CTL sensor is 1.03%, indicating that it has good reproducibility and stability, which shows that the CTL sensor has a promising prospect for the detection of acetaldehyde.

Pyroelectric catalytic performance of Sm3+-modified Pb(Mg1/3Nb2/3)O3-PbTiO3 for organic dyes: degradation efficiency, kinetics and pyroelectric catalytic mechanism.

The development of photocatalysis is hindered, in part, by the quick recombination of photogenerated carriers and the instability of light sources. In this study, the problem of too-fast electron-hole pair compounding in photocatalysis is effectively regulated by the polarization field of pyroelectric materials using the pyroelectric method. Self-polarized pyroelectric materials that depend on temperature variations can generate usable electrical energy and polarized charge carriers to degrade organic pollutants. Pb(Mg1/3Nb2/3)O3-PbTiO3 (PMN-PT) is a relaxor ferroelectric material with spontaneous polarization characteristics. The PMN-0.30PT:1 mol%Sm3+ catalyst was prepared by applying the high-temperature solid-state reaction method. Under the dark condition and nine cold-hot cycles of 23 °C-68 °C, using H2O2-assisted PMN-0.30PT:1 mol%Sm3+ as a catalyst, the degradation rate of rhodamine 6G (10 mg L-1) was 94.3 ± 2.5%. In addition, the degradation rates of 88.52% and 64.32% were obtained for rhodamine B (10 mg L-1) and methylene blue (10 mg L-1), respectively. This study provides a new approach to the pyroelectric catalytic degradation of organic pollutants.

Live-Cell Imaging of Endogenous RNA with a Genetically Encoded Fluorogenic Allosteric Aptamer.

Imaging and tracking tools for natural cellular RNA with improved biocompatibility, specificity, and sensitivity are critical to understanding RNA function and providing insights into disease therapeutics. We developed a new genetically encoded sensor using fluorogenic allosteric aptamer (FaApt) for the sensitive imaging of the localization and dynamics of RNA targets in live cells. Target RNAs can be specifically recognized with our sensor by forming perfectly complementary duplexes, which in turn can induce allosteric structural changes of the sensor to refold the native conformation of fluorogenic RNA aptamers. We demonstrated the ability of the sensor to monitor the effect of tumor necrosis factor and small-molecule inhibitor on the expression abundance of CXCL1 and survivin mRNA in human cancer cells, respectively. The asymmetrical distribution of endogenous Squint mRNA was confirmed in developing zebrafish embryos through microinjection of FaApt probes. This study provides an effective molecular tool for sensitive imaging and tracking endogenous RNA in living cells. Due to the high specificity and small size of our sensor system, it is expected to be applied to early diagnosis of RNA marker-related diseases and real-time evaluation of the treatment process.

Trans-acting aptazyme for conditional gene knockdown in eukaryotic cells.

Trans-acting hammerhead ribozyme inherits the advantages of being the smallest and best-characterized RNA-cleaving ribozyme, offering high modularity and the ability to cleave any desired sequence without the aid of any protein, as long as the target sequence contains a cleavage site. However, achieving precise control over the trans-acting hammerhead ribozyme would enable safer and more accurate regulation of gene expression. Herein, we described an intracellular selection of hammerhead aptazyme that contains a theophylline aptamer on stem II based on toxin protein IbsC. Based on the intracellular selection, we obtained three new cis-acting hammerhead aptazymes. Moreover, the corresponding trans-acting aptazymes could be efficiently induced by theophylline to knock down different targeted genes in eukaryotic cells. Notably, the best one, T195, exhibited a ligand-dependent and dose-dependent response to theophylline, and the cleavage efficiency could be enhanced by incorporating multiplex aptazymes.

Application of deep reinforcement learning for spike sorting under multi-class imbalance.

Spike sorting is the basis for analyzing spike firing patterns encoded in high-dimensional information spaces. With the fact that high-density microelectrode arrays record multiple neurons simultaneously, the data collected often suffers from two problems: a few overlapping spikes and different neuronal firing rates, which both belong to the multi-class imbalance problem. Since deep reinforcement learning (DRL) assign targeted attention to categories through reward functions, we propose ImbSorter to implement spike sorting under multi-class imbalance. We describe spike sorting as a Markov sequence decision and construct a dynamic reward function (DRF) to improve the sensitivity of the agent to minor classes based on the inter-class imbalance ratios. The agent is eventually guided by the optimal strategy to classify spikes. We consider the Wave_Clus dataset, which contains overlapping spikes and diverse noise levels, and the macaque dataset, which has a multi-scale imbalance. ImbSorter is compared with classical DRL architectures, traditional machine learning algorithms, and advanced overlapping spike sorting techniques on these two above datasets. ImbSorter obtained improved results on the Macro_F1. The results show ImbSorter has a promising ability to resist overlapping and noise interference. It has high stability and promising performance in processing spikes with different degrees of skewed distribution.

How human ecology landscapes shape the circulation of H5N1 avian influenza: A case study in Indonesia.

Background: Highly pathogenic avian influenza H5N1 virus consistently threatens global public health. A better understanding of the virus' circulation mechanism is needed for future epidemic prevention. Previous studies have focused on the correlations between the presence of H5N1 virus and wild bird populations, domestic poultry production, and sociodemographic factors. However, human cultural landscapes and their impact on H5N1 spread have not been adequately explored. Methods: Using 196 HA gene sequences of H5N1 influenza viruses from Indonesia with district-level geographic information, we performed Monmonier barrier and Louvain community detection analyses to explore how human ecological factors impact the circulation of virus and identify barriers to or corridors of dispersal. Results: Spatial discontinuity in the genetic characteristics identified by the Monmonier algorithm were found to mirror the differences in key landscape factors. Our Louvain community detection analysis also found the co-existence of different geographic circulation patterns. The community detection analysis suggests that direct human-related interactions such as poultry transportations between remote areas may result in similar viruses spreading in two distant regions whilst dense localities supported genetically heterogeneous viruses in geographically adjacent areas. Conclusion: Human ecological landscapes shape the circulation mechanism of H5N1 virus in multiple ways contingent upon local context. Physical and cultural barriers may impede its movement between adjacent areas, while natural or human-induced corridors such as wild bird flyways and poultry production networks facilitate its spread between geographically distant areas. Further focus on the importance of cultural landscapes has great potential for increasing our understanding of the circulation of pathogenic H5N1 avian influenza virus in Southeast Asia.

Leveraging Small Molecule-Induced Aptazyme Cleavage for Directed A-to-I RNA Editing.

As a promising therapeutic approach for the correction of pathogenic mutations, the RNA editing process is reversible and tunable without permanently altering the genome. RNA editing mediated by human ADAR proteins offers distinct advantages, including high specificity and low propensity to cause immunogenicity. Herein, we describe a small molecule-inducible RNA editing strategy by incorporating aptazymes into the guide RNA of ADAR-based RNA editing technology. Once small molecules are added or removed, aptazymes trigger self-cleavage to release the guide RNA, achieving small molecule-controlled RNA editing. To satisfy different RNA editing applications, both turn-on and turn-off A-to-I RNA editing of target mRNA have been realized by using on/off-switch aptazymes. Theoretically speaking, this strategy can be applied to various ADAR-based editing systems, which could improve the safety and potential clinical applications of RNA editing technology.

The aptamer-based RNA-PROTAC.

RNA-binding proteins (RBPs) dysfunction has been implicated in a number of diseases, and RBPs have traditionally been considered to be undruggable targets. Here, targeted degradation of RBPs is achieved based on the aptamer-based RNA-PROTAC, which consists of a genetically encoded RNA scaffold and a synthetic heterobifunctional molecule. The target RBPs can bind to their RNA consensus binding element (RCBE) on the RNA scaffold, while the small molecule can recruit E3 ubiquitin ligase to the RNA scaffold in a non-covalent manner, thereby inducing proximity-dependent ubiquitination and subsequent proteasome-mediated degradation of the target protein. Different RBPs targets, including LIN28A and RBFOX1, have been successfully degraded by simply replacing the RCBE module on the RNA scaffold. In addition, the simultaneous degradation of multiple target proteins has been realized by inserting more functional RNA oligonucleotides into the RNA scaffold.

One-Pot Tandem Oxidative Bromination and Amination of Sulfenamide for the Synthesis of Sulfinamidines.

The sulfinamidines as aza analogues of sulfinamides received limited attention from both organic chemists and pharmaceutical chemists. Herein, we present a tandem oxidative/nucleophilic substitution approach for the synthesis of sulfinamidines in high yield (up to 98%). This cascade reaction method is enabled by N-bromosuccinimide (NBS) as an oxidant and diverse readily available amines as nucleophiles without any additives or catalysts. Notably, this method is highly time-economical, safe to operate, and easy to scale up and has excellent functional group compatibility.

Synthesis of Sulfilimines via Selective S-C Bond Formation in Water.

Sulfilimines are valuable compounds both in organic synthesis and in pharmaceuticals. Here we developed a mild and simplified method for preparation of sulfilimines via selective S-C bond formation rather than traditional S-N bond formation. The method is both attractive and useful for the following reasons: it uses a readily available alkylation reagent such alkyl bromide or alkyl iodide, it uses water as solvent, it is easy to perform, and it is convenient for late-stage diversification of drugs.

Prenylated dihydroflavones from the root barks of Morus alba.

Three new prenylated dihydroflavones, moralbaflavones A-C (1-3), together with four known ones (4a/4b, 5, and 6) were isolated from the root barks of Morus alba L. Their structures including the absolute configurations were determined by the analysis of HRMS, NMR, and ECD data. The neuroprotective properties of these prenylated dihydroflavones were screened at the concentration of 10 µM in the sodium nitroprusside-induced rat pheochromocytoma PC-12 cells, and the results showed moralbaflavone C (3) possessed significant neuroprotective activity, being more potent than the positive control edaravone.

Synthesis of Chiral Sulfonimidoyl Chloride via Desymmetrizing Enantioselective Hydrolysis.

Direct construction of chiral S(VI) from prochiral S(II) is a formidable challenge due to the inevitable formation of stable chiral S(IV). Previous synthetic strategies rely on the conversion of chiral S(IV) or enantioselective desymmetrization of preformed symmetrical S(VI) substrates. Here, we report desymmetrizing enantioselective hydrolysis of in situ-generated symmetric aza-dichlorosulfonium from sulfenamides for the preparation of chiral sulfonimidoyl chlorides, which could be used as a general stable synthon for obtaining a series of chiral S(VI) derivatives.