Evolution and post-transcriptional regulation insights of m6A writers, erasers, and readers in plant epitranscriptome.

As a dynamic and reversible post-transcriptional marker, N6-methyladenosine (m6A) plays an important role in the regulation of biological functions, which are mediated by m6A pathway components including writers (MT-A70, FIP37, VIR and HAKAI family), erasers (ALKBH family) and readers (YTH family). There is an urgent need for a comprehensive analysis of m6A pathway components across species at evolutionary levels. In this study, we identified 4062 m6A pathway components from 154 plant species including green algae, utilizing large-scale phylogenetic to explore their origin and evolution. We discovered that the copy number of writers was conserved among different plant lineages, with notable expansions in the ALKBH and YTH families. Synteny network analysis revealed conserved genomic contexts and lineage-specific transpositions. Furthermore, we used Direct RNA Sequencing (DRS) to reveal the Poly(A) length (PAL) and m6A ratio profiles in six angiosperms species, with a particular focus on the m6A pathway components. The ECT1/2-Poeaece4 sub-branches (YTH family) with unique genomic contexts exhibited significantly higher expression level than genes of other ECT1/2 poeaece sub-branches (ECT1/2-Poeaece1-3), accompanied by lower m6A modification and PAL. Besides, conserved m6A sites distributed in CDS and 3'UTR were detected in the ECT1/2-Poaceae4, and the dual-luciferase assay further demonstrated that these conserved m6A sites in the 3'UTR negatively regulated the expression of Firefly luciferase (LUC) gene. Finally, we developed transcription factor regulatory networks for m6A pathway components, using yeast one-hybrid assay demonstrated that PheBPC1 could interact with the PheECT1/2-5 promoter. Overall, this study presents a comprehensive evolutionary and functional analysis of m6A pathway components and their modifications in plants, providing a valuable resource for future functional analysis in this field.

Construction of Boron Difluoride Complexes with Asymmetric N,N'-Bidentate Ligands.

Boron difluoride (BF2) complexes with asymmetrical N,N'-bidentate ligands have received increasing attention due to their fascinating properties and broad applications. They are generally constructed in two steps: ligand formation, followed by boron complexation. This review focuses on categorizing these BF2 complexes based on the key synthetic strategies that have been applied in the ligand formation steps. The post-functionalization, properties and applications of different types of BF2 complexes are presented. Their challenges and opportunities are also discussed. This should help the future rational design and synthesis of BF2 complexes with intriguing properties and practical applications.

Synthesis, Structures and Photophysical Properties of Asymmetric Fulvene-[b]-fused BODIPYs.

Herein, we developed a one-pot procedure to synthesize novel fulvene-[b]-fused BODIPYs from α-(2-alkynylphenyl)-pyrrole and acylpyrrole, using 5-exo cyclization as the key transformation. Compared to benzene-[b]-fused BODIPYs, although they have similar chemical compositions, their structures and properties significantly differ from each other, which can be attributed to the less aromaticity of the fulvene linker than benzene. Notably, fulvene-[b]-fused BODIPY 1 b exhibits helical-twisted core skeleton, intensified red-shifted absorption, and peak fluorescence. In addition, the pathway of this one-pot reaction and the mechanism of POCl3 mediated 5-exo cyclization have been proposed by a combining experimental and computational study.

2-Deoxy-D-glucose simultaneously targets glycolysis and Wnt/ß-catenin signaling to inhibit cervical cancer progression.

Cervical cancer is one of the most common female malignant tumors, with typical cancer metabolism characteristics of increased glycolysis flux and lactate accumulation. 2-Deoxy-D-glucose (2-DG) is a glycolysis inhibitor that acts on hexokinase, the first rate-limiting enzyme in the glycolysis pathway. In this research, we demonstrated that 2-DG effectively reduced glycolysis and impaired mitochondrial function in cervical cancer cell lines HeLa and SiHa. Cell function experiments revealed that 2-DG significantly inhibited cell growth, migration, and invasion, and induced G0/G1 phase arrest at non-cytotoxic concentrations. In addition, we found that 2-DG down-regulated Wingless-type (Wnt)/ß-catenin signaling. Mechanistically, 2-DG accelerated the degradation of ß-catenin protein, which resulted in the decrease of ß-catenin expression in both nucleus and cytoplasm. The Wnt agonist lithium chloride and ß-catenin overexpression vector could partially reverse the inhibition of malignant phenotype by 2-DG. These data suggested that 2-DG exerted its anti-cancer effects on cervical cancer by co-targeting glycolysis and Wnt/ß-catenin signaling. As expected, the combination of 2-DG and Wnt inhibitor synergistically inhibited cell growth. It is noteworthy that, down-regulation of Wnt/ß-catenin signaling also inhibited glycolysis, indicating a similar positive feedback regulation between glycolysis and Wnt/ß-catenin signaling. In conclusion, we investigated the molecular mechanism by which 2-DG inhibits the progression of cervical cancer in vitro, elucidated the interregulation between glycolysis and Wnt/ß-catenin signaling, and preliminarily explored the effect of combined targeting of glycolysis and Wnt/ß-catenin signaling on cell proliferation, which provides more possibilities for the formulation of subsequent clinical treatment strategies.

Molecular identification and functional verification of SPL9 and SPL15 of Lilium.

The transformation of plants from juveniles to adults is a key process in plant growth and development, and the main regulatory factors are miR156 and SQUAMOSA promoter binding protein-like (SPL) transcription factors. Lilium is an ornamental bulb, but it has a long maturation time. In this experiment, Lilium bulbs were subjected to a temperature treatment of 15 °C for 4 weeks to initiate vegetative phase change. Transmission electron microscopy indicated the cell wall of bud core tissue undergoing vegetative phase change became thinner, the starch grains were reduced, and the growth of the juvenile stage was accelerated. The key transcription factors LbrSPL9 and LbrSPL15 were cloned, and the phylogenetic analysis showed they possessed high homology with other plant SPLs. Subcellular localization and transcription activation experiments confirmed LbrSPL9 and LbrSPL15 were mainly located in the nucleus and exhibited transcriptional activity. The results of in situ hybridization showed the expression levels of LbrSPL9 and LbrSPL15 were increased after temperature change treatment. The functional verification experiment of the transgenic plants confirmed that the overexpression of LbrSPL9 and LbrSPL15 could shorten maturation time. These findings help elucidate the regulatory mechanisms of phase transition in Lilium and provide a reference for breeding research in other bulbous flowers.

L. johnsonii, L. plantarum, and L. rhamnosus alleviated Enterohaemorrhagic Escherichia coli-induced diarrhoea in mice by regulating gut microbiota.

Enterohaemorrhagic Escherichia coli (EHEC) is a prominent foodborne pathogen that causes infectious intestinal diarrhoea. Lactobacillus is a recognized probiotic that inhibits intestinal pathogens and maintains the balance of the intestinal flora. The purpose of this study was to investigate the regulatory effects of three Lactobacillus strains, L. johnsonii, L. plantarum, and L. rhamnosus, on the intestinal flora of EHEC-infected mice. The initial weight and diarrhoea index of the mice were recorded. After 21 days, the faeces of the mice were subjected to 16S rDNA high-throughput sequencing. The diarrhoea index of mice treated with Lactobacillus improved, their body weight continued to rise, and their liver index gradually decreased. The α diversity analysis showed that the intestinal flora diversity and abundance were lower in mice infected with EHEC than in healthy mice. L. plantarum, L. johnsonii, and L. rhamnosus significantly improved the diversity of the flora species. In terms of flora composition, the three main phyla present were Bacteroidetes, Firmicutes, and Proteobacteria. The abundance of these three phyla was reduced to 93.81% after infection and restored to over 96.30% after treatment. At the genus level, Lactobacillus reduced the abundance of Bacteroides, Helicobacter pylori, and Shigella, while increasing the abundance of butyric acid-producing bacteria and Lactobacillus. Finally, a heat map and non-metric multidimensional scaling analysis showed that the intestinal flora structures in the L. johnsonii, L. plantarum, and L. rhamnosus treatment groups were closest to those of healthy mice. In conclusion, L. johnsonii, L. plantarum, and L. rhamnosus regulated and improved the structure of intestinal flora and relieved diarrhoea caused by EHEC infection.

Design, Synthesis and Hydrogen Bonding of B3 N6 -[4]Triangulene.

Replacement of the allylic C=C-C unit with a N-B-N unit at each of the three zigzag edges of [4]triangulene gives rise to B3 N6 -[4]triangulene, which is envisioned to represent a key structural unit of a new hypothetical boron carbon nitride (BC4 N). A tert-butylated B3 N6 -[4]triangulene has been successfully synthesized by three-fold nitrogen-directed borylation, and the X-ray crystallographic analysis indicates that its slightly bent triangular polycyclic framework can be viewed as a 1,3,5-triphenylbenzene connected by three 4π-electron N-B-N units. The HN-B-NH moiety provides a dual hydrogen-bond donor, which forms H-bonds with halide or carboxylate anions in solution, and form DD-AA hydrogen-bond arrays with 2,7-di(tert-butyl)-pyrene-4,5,9,10-tetraone in the co-crystal. Moreover, the blue fluorescence of B3 N6 -[4]triangulene in solution is responsive to binding p-nitrobenzoate anion through hydrogen bonds.

Carbazole-Fused Polycyclic Aromatics Enabled by Regioselective Scholl Reactions.

The synthesis of new carbazole-fused polycyclic aromatics with interesting geometry and useful properties was explored using Scholl reactions. As found from the Scholl reactions of substrates having two carbazole units linked at different positions through o-phenylene, oxidative coupling of carbazole units occurred in a regioselective manner with new carbon-carbon bonds preferably formed at C3 and C4 in N-alkyl carbazoles. A new N-containing aromatic bowl was characterized by single-crystal X-ray crystallography, and new p-type organic semiconductors exhibited field effect mobility of up to 0.070 cm2 V-1 s-1 in solution-processed thin-film transistors.

Trifluoromethylation of Anthraquinones for n-Type Organic Semiconductors in Field Effect Transistors.

This study puts forth a new design of n-type organic semiconductors, which has trifluoromethylethynyl groups attached to 9,10-anthraquinone at different positions. These electron-deficient anthraquinones are synthesized by trifluoromethylation of the corresponding trimethylsilyl-protected alkynes with fluoroform-derived CuCF3, and their π-π stacking in the crystals is tunable by varying the positions of trifluoromethylethynyl groups. It is found that most of these trifluoromethylated anthraquinones function as n-type semiconductors in solution-processed field effect transistors with electron mobility of up to 0.28 cm2 V-1 s-1.

Revisiting Indolo[3,2-b]carbazole: Synthesis, Structures, Properties, and Applications.

Indolo[3,2-b]carbazole presents a π-skeleton with a remarkable electronic structure and interesting potential applications. It is, however, also associated with ambiguity and controversy. Herein, new derivatives of indolo[3,2-b]carbazole are reported and they have enabled a comprehensive study on the electronic structure of indolo[3,2-b]carbazole and the development of a new n-type organic semiconductor. Experimental and computational studies show that indolo[3,2-b]carbazole has a largely localized p-benzoquinonediimine moiety and significant antiaromaticity. When substituted with (4-silylethynyl)phenyl groups, the indolo[3,2-b]carbazole exhibits one-dimensional π-π stacking and functions as an n-type organic semiconductor in solution-processed field effect transistors.

Gut microbiome interventions in human health and diseases.

Ongoing studies have determined that the gut microbiota is a major factor influencing both health and disease. Host genetic factors and environmental factors contribute to differences in gut microbiota composition and function. Intestinal dysbiosis is a cause or a contributory cause for diseases in multiple body systems, ranging from the digestive system to the immune, cardiovascular, respiratory, and even nervous system. Investigation of pathogenesis has identified specific species or strains, bacterial genes, and metabolites that play roles in certain diseases and represent potential drug targets. As research progresses, gut microbiome-based diagnosis and therapy are proposed and applied, which might lead to considerable progress in precision medicine. We further discuss the limitations of current studies and potential solutions.

A polymer-based probe for specific discrimination of cysteine.

A novel optically active methacrylic polymer with an amide-linked acrylate appendage as a chemosensor was synthesized by atom transfer radical polymerization (ATRP) followed by post-modification through a bottom-up design. The sensing behavior of the polymeric probe to various α-amino acids has been investigated through fluorescence, absorption, circular dichroism (CD), and visual color changes at physiological pH. It was found that the sensor exhibits specificity for the fluorescent recognition of cysteine against other amino acids and thiols in a turn-on mode, being significantly more effective than the corresponding small molecule counterpart. The detection limit was estimated to be in the micromolar range. In addition, the use of this chiral polymer allows the selective discrimination of cysteine enantiomers based on either fluorescence or CD spectral responses. Interestingly, the cysteine assay could also be visualized by the naked eye in the presence of small amounts of ferric ions.

Generation, division and training: A promising method for source-free unsupervised domain adaptation.

Conventional unsupervised domain adaptation (UDA) methods often presuppose the existence of labeled source domain samples while adapting the source model to the target domain. Nevertheless, this premise is not always tenable in the context of source-free UDA (SFUDA) attributed to data privacy considerations. Some existing methods address this challenging SFUDA problem by self-supervised learning. But inaccurate pseudo-labels are always unavoidable to degrade the performance of the target model among these methods. Therefore, we propose a promising SFUDA method, namely Generation, Division and Training (GDT) which aims to promote the reliability of pseudo-labels for self-supervised learning and encourage similar features to have closer predictions than dissimilar ones by contrastive learning. Specifically in our GDT method, we first refine pseudo-labels with deep clustering for target samples and then split them into reliable samples and unreliable samples. After that, we adopt self-supervised learning and information maximization for reliable samples training. And for unreliable samples, we conduct contrastive learning via the perspective of similarity and disparity to attract similar samples and repulse dissimilar samples, which helps pull the similar features closed and push the dissimilar features away, leading to efficient feature clustering. Thorough experimentation on three benchmark datasets substantiates the excellence of our proposed approach.

Improving Structural, Physical, and Sensitive Properties of Sodium Alginate-Purple Sweet Potato Peel Extracts Indicator Films by Varying Drying Temperature.

Sodium alginate (SA)-purple sweet potato peel extracts (PPE) from industrial waste indicator films were developed at different drying temperatures (25, 30, 35, 40, 45, 50, and 55 °C). The effects of drying temperatures on the film's structural, physical, and sensitive properties were investigated. On the structural properties, scanning electron microscopy, Fourier transform infrared spectroscopy, and X-ray diffraction indicated that compactness, intermolecular interactions, and crystallinity of indicator films were improved at a lower drying temperature. On the physical properties, with the drying temperature increasing, elongation at the break increased significantly (p < 0.05); ΔE and water-vapor permeability decreased significantly (p < 0.05); and thickness and tensile strength initially increased significantly (90.46 → 98.46, 62.99 → 95.73) and subsequently decreased significantly (98.46 → 71.93, 95.73 → 55.44) (p < 0.05), with the maximum values obtained at 30 °C. On sensitivity, the corresponding colors of the films became lighter as the drying temperature increased, and the films exhibited relatively excellent pH and NH3 sensitivity, with easily discernible color changes at lower temperatures. The results of this paper revealed that the overall film characteristics are improved at lower drying temperatures, which will provide valuable references for selecting the drying temperature for preparing indicator films as a guide for industrialized production.

Multi-omics Analysis Identifies Hypoxia Subtypes and S100A2 as an Immunosuppressive Factor in Cervical Cancer.

Cervical cancer is a common gynecological oncology. Growing evidence indicates hypoxia plays an important role in tumor progression and immunity. However, no study has examined the hypoxia landscape in cervical cancer. In this study, using hierarchical clustering, we identified three hypoxia subtypes in cervical cancer samples from The Cancer Genome Atlas dataset according to formerly described hypoxia-related genes. The overall survival time, hypoxic features, genomics, and immunological characteristics of these subtypes existed distinct differences. We also created a hypoxia score by principle component analysis for dimension reduction. The hypoxiaScore was an effective prognostic biomarker validated by GSE44001 and was associated with immunotherapy response. Furthermore, combined with single-cell RNA-sequence (scRNA-seq) and experiments, S100A2 was identified as an immunosuppressive factor induced by hypoxia and regulated expression of PD-L1. S100A2 also served as an oncogene promoting the proliferation and migration of cervical cancer cells. These findings depicted a new hypoxia-based classification and identified S100A2 as a potential therapeutic target for cervical cancer, thereby advancing the understanding of immunotherapy resistance mechanisms and cervical cancer genetic markers.

Double-layer microcapsules based on shellac for enhancing probiotic survival during freeze drying, storage, and simulated gastrointestinal digestion.

Probiotics are susceptible to diverse conditions during processing, storage, and digestion. Here, shellac (SC), sodium alginate (SA), coconut oil (CO), soybean oil (SO), and trehalose (AL) were used to prepare microcapsules aiming to improve the survival of Lactiplantibacillus plantarum KLDS1.0318 during freeze-drying, storage process, and gastrointestinal digestion. The results showed that for SA/AL/SC/CO and SA/AL/SC/SO, the survival loss decreased by 51.2 % and 51.0 % after a freeze-drying process compared with microcapsules embedded by SA; the viable bacteria count loss decreased by 4.36 and 4.24 log CFU/mL compared with free cell (CON) during storage for 28 d under 33%RH at 25 °C, respectively; while for simulating digestion in vitro, the survival loss decreased by 3.05 and 2.70 log CFU/mL, 0.63 and 0.55 log CFU/mL after digestion at simulated gastric fluid for 120 min and small intestine fluid for 180 min, respectively (P < 0.05). After microcapsules were added to fermented dairy stored at 4 °C for 21 d, the viable bacteria count of SA/AL/SC/CO and SA/AL/SC/SO significantly increased by 2.10 and 1.70 log CFU/mL compared with CON, respectively (P < 0.05). In conclusion, the current study indicated that shellac-based probiotic microcapsules have superior potential to protect and deliver probiotics in food systems.

Predictive value of the Adult Comorbidity Evaluation 27 on adverse surgical outcomes and survival in elderly with advanced epithelial ovarian cancer undergoing cytoreductive surgery.

OBJECTIVE: We aimed to evaluate the ability of Adult Comorbidity Evaluation 27 (ACE-27) to predict perioperative outcomes and survival in elderly women with advanced epithelial ovarian cancer (AEOC) undergoing cytoreductive surgery. METHODS: We collected patients with AEOC in our hospital between January 1, 2012 and January 1, 2021. Patients younger than 65 years old or those with non-epithelial ovarian cancer were excluded. ACE-27 was applied retrospectively to assess comorbidities in the selected patients, who were then classified into two groups based on their ACE-27 scores: low ACE-27 score group (none to mild) and high ACE-27 score group (moderate to severe). RESULTS: A total of 222 elderly women with AEOC were included, of whom 164 patients accepted debulking surgery. Among those who have undergone surgery, Clavien-Dindo grade III + perioperative complications or unintended intensive care unit (ICU) admission occurred more often in patients of high ACE-27 score group, with statistically significant difference (odds ratio [OR]: 4.21, 95% confidence interval [CI], 1.28-14.35, p = 0.018). Further stratified analyses by age, BMI, FIGO stage and pathology also prove that OS of patients graded severe was shorter than patients graded none to moderate in cohort of age < 70, BMI < 25 kg/m2, FIGO III stage and pathology of serous, respectively. Kaplan-Meier survival curves analyzed by log-rank test showed that the overall survival (OS) of patients with severe comorbidities were shorter than with none to moderate (HR 3.25, 95%CI 1.55-6.79, p = 0.002). CONCLUSIONS: Our findings demonstrate the ability of ACE-27 to predict grade III + perioperative complications or unintended ICU admission and survival in elderly patients with AEOC. This highlights the possibility for ACE-27 to play an instrumental role in identifying AEOC patients who are more susceptible to adverse surgical outcomes and have a poor survival rate and assisting in decisions regarding treatment.

The immunoregulatory effects of total glucosides of paeony in autoimmune diseases.

Total glucoside of paeonia (TGP) and its main active ingredient paeoniflorin, extracted from the Chinese herb Paeonia Lactiflora Pallas, exhibit potent immunomodulatory effects. TGP has been shown to inhibit inflammatory responses and disease progression in experimental models of multiple autoimmune diseases (AIDs), including rheumatoid arthritis, systemic lupus erythematosus, Sjogren's syndrome, psoriasis, etc. TGP shows broad immunomodulatory effects on many immune cells such as T cells, macrophages, and dendritic cells, by regulating their activation, proliferation, differentiation, and production of effector molecules. Mechanistically, TGP modulates intracellular signaling transductions including JAK/STAT, NF-κB, MAPK, and PI3K/AKT/mTOR pathways. Moreover, TGP has been applied in the clinical treatment of various AIDs with satisfactory therapeutic outcomes and minor side effects. Thus, available studies have demonstrated that TGP and its bioactive constituents exhibit anti-inflammatory and immunomodulatory functions and may have extensive applications in the treatment of AIDs.

De novo Whole-Genome Assembly of the 10-Gigabase Fokienia Hodginsii Genome to Reveal Differential Epigenetic Events Between Callus and Xylem.

Fokienia hodginsii (F. hodginsii), belonging to the genus Fokienia of the Cupressaceae. F. hodginsii has significant application value due to its wood properties and great research value in evolutionary studies as a gymnosperm. However, the genome of F. hodginsii remains unknown due to the large size of gymnosperms genome. Pacific Bioscience sequencing, Hi-C mapping, whole-genome Bisulfite Sequencing (BS-Seq), long-read isoform sequencing (Iso-Seq), direct RNA sequencing (DRS), quantitative proteomics, and metabonomics analysis are employed to facilitate genome assembly, gene annotation, and investigation into epigenetic mechanisms. In this study, the 10G F. hodginsii genome is assembled into 11 chromosomes. Furthermore, 50 521 protein-coding genes are annotated and determined that 65% of F. hodginsii genome comprises repetitive sequences. It is discovered that transposable element (TE)-including introns is associated with higher expression. The DNA methylome of F. hodginsii reveals that xylem has a higher DNA methylation level compared to callus. Moreover, DRS reveals the significant alterations in RNA full-length ratio, which potentially associated with poly(A) length (PAL) and alternative polyadenylation (APA). Finally, the morphology measurement and metabonomics analysis revealed the difference of 14 cultivars. In summary, the genomes and epigenetics datasets provide a molecular basis for callus formation in the gymnosperm family.

Endo-Lysosomal Network Disorder Reprograms Energy Metabolism in SorL1-Null Rat Hippocampus.

Sortilin-related receptor 1 (SorL1) deficiency is a genetic predisposition to familial Alzheimer's disease (AD), but its pathology is poorly understood. In SorL1-null rats, a disorder of the global endosome-lysosome network (ELN) is found in hippocampal neurons. Deletion of amyloid precursor protein (APP) in SorL1-null rats could not completely rescue the neuronal abnormalities in the ELN of the hippocampus and the impairment of spatial memory in SorL1-null young rats. These in vivo observations indicated that APP is one of the cargoes of SorL1 in the regulation of the ELN, which affects hippocampal-dependent memory. When SorL1 is depleted, the endolysosome takes up more of the lysosome flux and damages lysosomal digestion, leading to pathological lysosomal storage and disturbance of cholesterol and iron homeostasis in the hippocampus. These disturbances disrupt the original homeostasis of the material-energy-subcellular structure and reprogram energy metabolism based on fatty acids in the SorL1-null hippocampus, instead of glucose. Although fatty acid oxidation increases ATP supply, it cannot reduce the levels of the harmful byproduct ROS during oxidative phosphorylation, as it does in glucose catabolism. Therefore, the SorL1-null rats exhibit hippocampal degeneration, and their spatial memory is impaired. Our research sheds light on the pathology of SorL1 deficiency in AD.