RefMetaPlant: a reference metabolome database for plants across five major phyla.

Plants are unique with tremendous chemical diversity and metabolic complexity, which is highlighted by estimates that green plants collectively produce metabolites numbering in the millions. Plant metabolites play crucial roles in all aspects of plant biology, like growth, development, stress responses, etc. However, the lack of a reference metabolome for plants, and paucity of high-quality standard compound spectral libraries and related analytical tools, have hindered the discovery and functional study of phytochemicals in plants. Here, by leveraging an advanced LC-MS platform, we generated untargeted mass spectral data from >150 plant species collected across the five major phyla. Using a self-developed computation protocol, we constructed reference metabolome for 153 plant species. A 'Reference Metabolome Database for Plants' (RefMetaPlant) was built to encompass the reference metabolome, integrated standard compound mass spectral libraries for annotation, and related query and analytical tools like 'LC-MS/MS Query', 'RefMetaBlast' and 'CompoundLibBlast' for searches and profiling of plant metabolome and metabolite identification. Analogous to a reference genome in genomic research, RefMetaPlant provides a powerful platform to support plant genome-scale metabolite analysis to promote knowledge/data sharing and collaboration in the field of metabolomics. RefMetaPlant is freely available at https://www.biosino.org/RefMetaDB/.

CropMetabolome: a comprehensive metabolome database for major crops cross eight categories.

Chemical compositions of crops are of great agronomical importance, as crops serve as resources for nutrition, energy, and medicines for human and livestock. For crop metabolomics research, the lack of crop reference metabolome and high-quality reference compound mass spectra, as well as utilities for metabolic profiling, has hindered the discovery and functional study of phytochemicals in crops. To meet these challenging needs, we have developed the Crop Metabolome database (abbreviated as CropMetabolome) that is dedicated to the construction of crop reference metabolome, repository, and dissemination of crop metabolomic data, and profiling and analytic tools for metabolomics research. CropMetabolome contains a metabolomics database for more than 50 crops (belonging to eight categories) that integrated self-generated raw mass spectral data and public-source datasets. The reference metabolome for 59 crop species was constructed, which have functions that parallel those of reference genome in genomic studies. CropMetabolome also contains 'Standard compound mass spectral library', 'Flavonoids library', 'Pesticide library', and a set of related analytical tools that enable metabolic profiling based on a reference metabolome (CropRefMetaBlast), annotation and identification of new metabolites (CompoundLibBlast), deducing the structure of novel flavonoid derivatives (FlavoDiscover), and detecting possible residual pesticides in crop samples (PesticiDiscover). In addition, CropMetabolome is a repository to share and disseminate metabolomics data and a platform to promote collaborations to develop reference metabolome for more crop species. CropMetabolome is a comprehensive platform that offers important functions in crop metabolomics research and contributes to improve crop breeding, nutrition, and safety. CropMetabolome is freely available at https://www.cropmetabolome.com/.

KINASE-INDUCIBLE DOMAIN INTERACTING 8 regulates helical pod morphology in Medicago truncatula.

Leguminosae exhibits a wide diversity of legume forms with varying degrees of spiral morphologies, serving as an ideal clade for studying the growth and development of spiral organs. While soybean (Glycine max) develops straight pods, the pod of the model legume Medicago truncatula is a helix structure. Despite the fascinating structures and intensive description of the pods in legumes, little is known regarding the genetic mechanism underlying the highly varied spirality of the legume pods. In this study, we found that KINASE-INDUCIBLE DOMAIN INTERACTING 8 (MtKIX8) plays a key role in regulating the pod structure and spirality in M. truncatula. Unlike the coiled and barrel-shaped helix pods of the wild type, the pods of the mtkix8 mutant are loose and deformed and lose the topologic structure as observed in the wild-type pods. In the pods of the mtkix8 mutant, the cells proliferate more actively and overly expand, particularly in the ventral suture, resulting in uncoordinated growth along the dorsal and ventral sutures of pods. The core cell cycle genes CYCLIN D3s are upregulated in the mtkix8 pods, leading to the prolonged growth of the ventral suture region of the pods. Our study revealed the key role of MtKIX8 in regulating seed pod development in M. truncatula and demonstrates a genetic regulatory model underlying the establishment of the helical pod in legumes.

Polyethylene Upgrading to Liquid Fuels Boosted by Atomic Ce Promoters.

Hydrocracking catalysis is a key route to plastic waste upgrading, but the acid site-driven C-C cleavage step is relatively sluggish in conventional bifunctional catalysts, dramatically effecting the overall efficiency. We demonstrate here a facile and efficient way to boost the reactivity of acid sites by introducing Ce promoters into Pt/HY catalysts, thus achieving a better metal-acid balance. Remarkably, 100 % of low-density polyethylene (LDPE) can be converted with 80.9 % selectivity of liquid fuels over the obtained Pt/5Ce-HY catalysts at 300 °C in 2 h. For comparison, Pt/HY only gives 38.8 % of LDPE conversion with 21.3 % selectivity of liquid fuels. Through multiple experimental studies on the structure-performance relationship, the Ce species occupied in the supercage are identified as the actual active sites, which possess remarkably-improved adsorption capability towards short-chain intermediates.

Dual-Site Metal Catalysts for Electrocatalytic CO2 Reduction Reaction.

Electrocatalytic CO2 reduction reaction (CO2 RR) is a promising and green approach for reducing atmospheric CO2 concentration and achieving high-valued conversion of CO2 under the carbon-neutral policy. In CO2 RR, the dual-site metal catalysts (DSMCs) have received wide attention for their ingenious design strategies, abundant active sites, and excellent catalytic performance attributed to the synergistic effect between dual-site in terms of activity, selectivity and stability, which plays a key role in catalytic reactions. This review provides a systematic summary and detailed classification of DSMCs for CO2 RR, describes the mechanism of synergistic effects in catalytic reactions, and also introduces in situ characterization techniques commonly used in CO2 RR. Finally, the main challenges and prospects of dual-site metal catalysts and even multi-site catalysts for CO2 recycling are analyzed. It is believed that based on the understanding of bimetallic site catalysts and synergistic effects in CO2 RR, well-designed high-performance, low-cost electrocatalysts are promising for achieving CO2 conversion, electrochemical energy conversion and storage in the future.

Vorinostat Corrects Cognitive and Non-Cognitive Symptoms in a Mouse Model of Fragile X Syndrome.

BACKGROUND: Fragile X syndrome (FXS) is caused by mutations in the FMR1 gene. It is a form of heritable intellectual disability and autism. Despite recent advance in elucidating disease mechanisms, there is no efficacious medication. Because de novo drug development is a lengthy process, repurposing the existing FDA-approved drugs offers an opportunity to advance clinical intervention for FXS. Our previous study with transcriptome analysis predicts potential therapeutic effects of vorinostat on FXS. METHODS: We analyzed the vorinostat-induced transcriptome changes and confirmed its similarity to that induced by trifluoperazine, which was previously shown to correct pathological outcomes associated with FXS. To validate the therapeutic efficacy, we examined vorinostat's effect on correcting the key behavioral and cellular symptoms in a mouse model of FXS. RESULTS: We found that vorinostat restores object location memory and passive avoidance memory in the Fmr1 knockout mice. For the non-cognitive behavioral symptoms, vorinostat corrected the autism-associated alterations, including repetitive behavior and social interaction deficits. In the open field test, vorinostat dampened hyperactivity in the center area of the arena. Surprisingly, vorinostat did not correct the abnormally elevated protein synthesis in cultured Fmr1 knockout hippocampal neurons, suggesting that different aspects of pathological outcomes may respond differently to a specific therapeutic intervention. CONCLUSIONS: We used the drug-induced transcriptome signature to predict new application of existing drugs. Our data reveal the therapeutic effects of the FDA-approved drug vorinostat in a mouse model of FXS.

Spatiotemporal Resolved Live Cell Membrane Tracking through Photo-click Reactions Enriched in Lipid Phase.

A set of photo-switchable monopeptides derived from cis-ß-dibenzodiazocine-l-alanine (cis-DBDAA) have been designed and synthesized, which are capable of photo-click reacting with diaryltetrazoles or diarylsydnones in a hydrophobic phospholipid bilayer environment. The DBDAA monopeptides include both a hydrophobic tail on C-terminal, providing high affinity toward lipid membrane, and a modularized functional moiety on N-terminal, enabling rapid optimization of the self-assembly strength to form multifunctional supramolecules. With the cis-DBDAA monopeptides photo-switched into trans-configuration, we were able to disrupt the supramolecular assembly through an efficient photo-click reaction across the lipid bilayer of liposomes. We reveal that the performance of the photo-click reactions between the monopeptides and photo-generated nitrile imine intermediates is significantly enhanced by enrichment of both reactants in the hydrophobic membrane lamel of liposomes. Enrichment of the DBDAA monopeptide in lipid phase serves as a convenient method to introduce bioorthogonal chemical handles on live cell membranes, which enables fluorescence labelling of single cell's membrane with high spatiotemporal resolution to facilitate the studies on cell membrane dynamics.

Integrated metabolomics and transcriptomics study of traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients.

BACKGROUND: Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is one of the most common herbs widely used in South and East Asia, to enhance people's health and reinforce vital energy. Despite its prevalence, however, the knowledge about phytochemical compositions and metabolite biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is very limited. RESULTS: An integrated metabolomics and transcriptomics analysis using state-of-the-art UPLC-Q-Orbitrap mass spectrometer and advanced bioinformatics pipeline were conducted to study global metabolic profiles and phytochemical ingredients/biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. A total of 5435 metabolites were detected, from which 2190 were annotated, representing an order of magnitude increase over previously known. Metabolic profiling of Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao tissues found contents and synthetic enzymes for phytochemicals were significantly higher in leaf and stem in general, whereas the contents of the main bioactive ingredients were significantly enriched in root, underlying the value of root in herbal remedies. Using integrated metabolomics and transcriptomics data, we illustrated the complete pathways of phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis, in which some were first reported in the herb. More importantly, we discovered novel flavonoid derivatives using informatics method for neutral loss scan, in addition to inferring their likely synthesis pathways in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. CONCLUSIONS: The current study represents the most comprehensive metabolomics and transcriptomics analysis on traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. We demonstrated our integrated metabolomics and transcriptomics approach offers great potentials in discovering novel metabolite structure and associated synthesis pathways. This study provides novel insights into the phytochemical ingredients, metabolite biosynthesis, and complex metabolic network in herbs, highlighting the rich natural resource and nutritional value of traditional herbal plants.

Photoisomerization-enhanced 1,3-dipolar cycloaddition of carbon-bridged octocyclic azobenzene with photo-released nitrile imine for peptide stapling and imaging in live cells.

A photo-induced 1,3-dipolar cycloaddition between nitrile imine and highly ring-strained N[double bond, length as m-dash]N double bond as a dipolarophile was discovered. The photo-isomerization of carbon-bridged octocyclic azobenzene (CBOA) into its trans-configuration accelerates the ligation reaction at a very rapid rate (28 400 M-1 s-1). The CBOA-based photo-click reaction was proved to be bioorthogonal. In addition, the NoxaB peptide was successfully cross-linked by a CBOA stapler which plays a dual role: photo-control of the conformation of the peptide and photo-conjugation of probes in live cells.

MicroRNA-26b/PTEN Signaling Pathway Mediates Glycine-Induced Neuroprotection in SAH Injury.

Subarachnoid hemorrhage (SAH) is a form of stroke associated with high mortality and morbidity. Despite advances in treatment for SAH, the prognosis remains poor. We have previously demonstrated that glycine, a non-essential amino acid is involved in neuroprotection following intracerebral hemorrhage via the Phosphatase and tensin homolog (PTEN)/protein kinase B (AKT) signaling pathway. However, whether it has a role in inducing neuroprotection in SAH is not known. The present study was designed to investigate the role of glycine in SAH. In this study, we show that glycine can reduce brain edema and protect neurons in SAH via a novel pathway. Following a hemorrhagic episode, there is evidence of downregulation of S473 phosphorylation of AKT (p-AKT), and this can be reversed with glycine treatment. We also found that administration of glycine can reduce neuronal cell death in SAH by activating the AKT pathway. Glycine was shown to upregulate miRNA-26b, which led to PTEN downregulation followed by AKT activation, resulting in inhibition of neuronal death. Inhibition of miRNA-26b, PTEN or AKT activation suppressed the neuroprotective effects of glycine. Glycine treatment also suppressed SAH-induced M1 microglial polarization and thereby inflammation. Taken together, we conclude that glycine has neuroprotective effects in SAH and is mediated by the miRNA-26b/PTEN/AKT signaling pathway, which may be a therapeutic target for treatment of SAH injury.

Synthesis and evaluation of photo-activatable ß-diarylsydnone-l-alanines for fluorogenic photo-click cyclization of peptides.

Herein, we design and synthesize a series of photoactivatable ß-diarylsydnone-l-alanines (DASAs), which have excellent photo-reactivity with high fluorescence turn-on toward alkenes in a biocompatible environment. The environmental sensing properties of the resulting fluorescent pyrazoline-alanine facilitate its probing capability. By introducing the DASA residue on the side chain of linear peptides, the macrocyclic peptides resulting from the in situ photo-cyclization toward the alkene residue exhibited fluorogenic translocation through live cell membranes.

Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development.

Seed development is an important process of reproductive development and consists of embryo and endosperm development; both comprise several key processes. To determine and investigate the functions of the dynamic DNA methylome during seed development, we profiled the DNA methylation genome wide in a series of developmental stages of rice (Oryza sativa) embryo and endosperm by methylcytosine immunoprecipitation followed by Illumina sequencing. The results showed that embryo is hypermethylated predominantly around non-transposable element (TE) genes, short DNA-TEs, and short interspersed TEs compared with endosperm, and non-TE genes have the most diverse methylation status across seed development. In addition, lowly expressed genes are significantly enriched in hypermethylated genes, but not vice versa, confirming the crucial role of DNA methylation in suppressing gene transcription. Further analysis revealed the significantly decreased methylation at early developing stages (from 2 to 3 d after pollination), indicating a predominant role of demethylation during early endosperm development and that genes with a consistent negative correlation between DNA methylation change and expression change may be potentially directly regulated by DNA methylation. Interestingly, comparative analysis of the DNA methylation profiles revealed that both rice indica and japonica subspecies showed robust fluctuant profiles of DNA methylation levels in embryo and endosperm across seed development, with the highest methylation level at 6 d after pollination (2 d after pollination of endosperm in japonica as well), indicating that a complex and finely controlled methylation pattern is closely associated with seed development regulation. The systemic characterization of the dynamic DNA methylome in developing rice seeds will help us understand the effects and mechanism of epigenetic regulation in seed development.

Global transcriptome analysis profiles metabolic pathways in traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao.

BACKGROUND: Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao (A. mongolicus, family Leguminosae) is one of the most important traditional Chinese herbs. Among many secondary metabolites it produces, the effective bioactive constituents include isoflavonoids and triterpene saponins. The genomic resources regarding the biosynthesis of these metabolites in A. mongolicus are limited. Although roots are the primary material harvested for medical use, the biosynthesis of the bioactive compounds and its regulation in A. mongolicus are not well understood. Therefore, a global transcriptome analysis on A. mongolicus tissues was performed to identify the genes essential for the metabolism and to profile their expression patterns in greater details. RESULTS: RNA-sequencing was performed for three different A. mongolicus tissues: leaf, stem, and root, using the Illumina Hiseq2000 platform. A total of 159.5 million raw sequence reads were generated, and assembled into 186,324 unigenes with an N50 of 1,524bp. Among them, 129,966 unigenes (~69.7%) were annotated using four public databases (Swiss-Prot, TrEMBL, CDD, Pfam), and 90,202, 63,946, and 78,326 unigenes were found to express in leaves, roots, and stems, respectively. A total of 8,025 transcription factors (TFs) were identified, in which the four largest families, bHLH, MYB, C3H, and WRKY, were implicated in regulation of tissue development, metabolisms, stress response, etc. Unigenes associated with secondary metabolism, especially those with isolavonoids and triterpene saponins biosynthesis were characterized and profiled. Most genes involved in the isoflavonoids biosynthesis had the lowest expression in the leaves, and the highest in the stems. For triterpene saponin biosynthesis, we found the genes in MVA and non-MVA pathways were differentially expressed among three examined tissues, indicating the parallel but compartmentally separated biosynthesis pathways of IPP and DMAPP in A. mongolicus. The first committed enzyme in triterpene saponin biosynthesis from A. mongolicus, cycloartenol synthase (AmCAS), which belongs to the oxidosqualene cyclase family, was cloned by us to study the astragalosides biosynthesis. Further co-expression analysis indicated the candidate CYP450s and glycosyltransferases (GTs) in the cascade of triterpene saponins biosynthesis. The presence of the large CYP450 families in A. mongolicus was further compared with those from Medicago truncatula and Arabidopsis thaliana, and the diversity and phylegenetic relationships of the CYP450 families were established. CONCLUSION: A transcriptome study was performed for A. mongolicus tissues to construct and profile their metabolic pathways, especially for the important bioactive molecules. The results revealed a comprehensive profile for metabolic activities among tissues, pointing to the equal importance of leaf, stem, and root in A. mongolicus for the production of bioactive compounds. This work provides valuable resources for bioengineering and in vitro synthesis of the natural compounds for medical research and for potential drug development.

DiseaseMeth: a human disease methylation database.

DNA methylation is an important epigenetic modification for genomic regulation in higher organisms that plays a crucial role in the initiation and progression of diseases. The integration and mining of DNA methylation data by methylation-specific PCR and genome-wide profiling technology could greatly assist the discovery of novel candidate disease biomarkers. However, this is difficult without a comprehensive DNA methylation repository of human diseases. Therefore, we have developed DiseaseMeth, a human disease methylation database (http://bioinfo.hrbmu.edu.cn/diseasemeth). Its focus is the efficient storage and statistical analysis of DNA methylation data sets from various diseases. Experimental information from over 14,000 entries and 175 high-throughput data sets from a wide number of sources have been collected and incorporated into DiseaseMeth. The latest release incorporates the gene-centric methylation data of 72 human diseases from a variety of technologies and platforms. To facilitate data extraction, DiseaseMeth supports multiple search options such as gene ID and disease name. DiseaseMeth provides integrated gene methylation data based on cross-data set analysis for disease and normal samples. These can be used for in-depth identification of differentially methylated genes and the investigation of gene-disease relationship.

Impact of agricultural irrigation and resettlement practices on carbon storage in arid inland river basins: A case study of the Shule river basin.

Agricultural irrigation and resettlement have significant impacts on carbon storage in arid inland river basins. With the background of "Comprehensive development measures for agricultural irrigation and resettlement in Shule River Basin (SRB)", this paper uses land use data to estimate regional carbon storage through InVEST model and revises the result by using net ecosystem productivity (NEP). The influence of land use change on carbon storage and the driving factors of carbon storage spatial differentiation were analyzed by using the optimal parameters geographical detector (OPGD). It can be inferred from the results that: (1) During 2000-2020, the increase of cropland and grassland area is the main type of land use change in the central oasis area of Yumen City and Guazhou County. Cumulative carbon storage increased by 1.75 × 107 t. (2) NEP in the central oasis area of Yumen City and Guazhou County showed a fluctuating upward trend, and it generally behaves as a carbon sink. The average annual NEP was 1.78 × 105 t, and the carbon sink increased by 0.95 × 105 t. (3) The main factors responsible for driving are vegetation, elevation, potential evapotranspiration, and precipitation. The explanatory power of each factor in carbon storage spatial differentiation was enhanced by the interaction between natural and anthropogenic factors. The interaction between vegetation and the human factor is more significant than that of the human single factor. (4) Agricultural irrigation and resettlement measures did not cause a decline in ecosystem carbon storage in Yumen City and Guazhou County in the central part of SRB. Conversely, the region's ecosystems have seen an increase in carbon storage as a result of the increase in cropland. (5) The introduction of the NEP modification method and the OPGD model improves the accuracy of carbon storage estimation and obtains better driving results in spatial differentiation. The study idea provides a new perspective for the estimation of carbon storage as a whole, and provides a reference basis for the formulation of ecological protection policies.

Green Printing for Scalable Organic Photovoltaic Modules by Controlling the Gradient Marangoni Flow.

Despite the rapid development in the performances of organic solar cells (OSCs), high-performance OSC modules based on green printing are still limited. The severe Coffee-ring effect (CRE) is considered to be the primary reason for the nonuniform distribution of active layer films. To solve this key printing problem, the cosolvent strategy is presented to deposit the active layer films. The guest solvent Mesitylene with a higher boiling point and a lower surface tension is incorporated into the host solvent o-XY to optimize the rheological properties, such as surface tension and viscosity of the active layer solutions. And the synergistic effect of inward Marangoni flow generation and solution thickening caused by the cosolvent strategy can effectively restrain CRE, resulting in highly homogeneous large-area active layer films. In addition, the optimized crystallization and phase separation of active layer films effectively accelerate the charge transport and exciton dissociation of devices. Consequently, based on PM6:BTP-eC9 system, the device prepared with the co-solvent strategy shows the a power conversion efficiency of 17.80%. Moreover, as the effective area scales to 1 and 16.94 cm2, the recorded performances are altered to 16.71% and 14.58%. This study provides a universal pathway for the development of green-printed high-efficiency organic photovoltaics.

Tailored Fabrication of Full-Color Ultrastable Room-Temperature Phosphorescence Carbon Dots Composites with Unexpected Thermally Activated Delayed Fluorescence.

The development of single-system materials that exhibit both multicolor room-temperature phosphorescence (RTP) and thermally activated delayed fluorescence (TADF) with tunable after glow colors and channels is challenging. In this study, four metal-free carbon dots (CDs) are developed through structural tailoring, and panchromatic high-brightness RTP is achieved via strong chemical encapsulation in urea. The maximum lifetime and quantum yield reaches 2141 ms and 56.55%, respectively. Moreover, CDs-IV@urea, prepared via coreshell interaction engineering, exhibits a dual afterglow of red RTP and green TADF. The degree of conjugation and functional groups of precursors affects the binding interactions of the nitrogen cladding on CDs, which in turn stabilizes triplet energy levels and affects the energy gap between S1 and T1 (ΔEST) to induce multicolor RTP. The enhanced wrapping interaction lowers the ΔEST, promoting reverse intersystem crossing, which leads to phosphorescence and TADF. This strong coreshell interaction fully stabilizes the triplet state, thus stabilizing the material in water, even in extreme environments such as strong acids and oxidants. These afterglow materials are tested in multicolor, time, and temperature multiencryption as well as in multicolor in vivo bioimaging. Hence, these materials have promising practical applications in information security as well as biomedical diagnosis and treatment.

The quality of life in nasopharyngeal carcinoma radiotherapy: A longitudinal study.

Objective: This article aims to longitudinally compare nasopharyngeal carcinoma (NPC) patients' quality of life (QoL) during radiotherapy (RT) and identify QoL correlates. Methods: This study included 98 patients, with 85 completing full follow-up. Data were collected at baseline (T1), midpoint of RT (T2), and RT completion (T3), between October 2021 and November 2022. QoL was assessed using the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire-Core 30 (EORTC QLQ-C30). RIOM severity was evaluated by the toxicity criteria of Radiation Therapy Oncology Group (RTOG). The nutritional status was evaluated using the Nutritional Risk Screening 2002 (NRS 2002), body mass index (BMI), and the Patient-Generated Subjective Global Assessment (PG-SGA). The generalized estimating equation described the QoL evolution and correlated it with RIOM, nutritional status, and other influential factors. Results: Significant deterioration was observed in various subscales of EORTC QLQ-C30 during RT, including global health status (GHS), physical function, role function, emotional function, fatigue, nausea/vomiting, pain, insomnia, appetite loss, and constipation (all P â€‹< â€‹0.05). Substantial deterioration was also observed in RIOM, nutritional status, and part of hematological indexes (all P â€‹< â€‹0.05). The decline of QoL was associated with gender, age, education level, chemotherapy regimen, Karnofsky performance status (KPS) score, RIOM severity, NRS 2002 score, PG-SGA score, and lymphocyte level (all P â€‹< â€‹0.05). Conclusions: QoL declined during RT and were associated with certain factors. Healthcare professionals should focus on alleviating treatment-related complications and identifying individuals at high risk of malnutrition early to improve outcomes for patients with NPC.

Therapeutic targeting of vimentin by ALD-R491 impacts multiple pathogenic processes to attenuate acute and chronic colitis in mice.

BACKGROUND: Vimentin, an intermediate filament protein, crucially contributes to the pathogenesis of inflammatory bowel disease (IBD) by interacting with genetic risk factors, facilitating pathogen infection, and modulating both innate and adaptive immune responses. This study aimed to demonstrate preclinical proof-of-concept for targeting vimentin therapeutically in IBD across diverse etiologies. METHODS: The small molecule compound ALD-R491 was assessed for vimentin binding using microscale thermophoresis, off-target effects via Eurofins screening, and therapeutic effects in mice with dextran sulfate sodium (DSS)-induced acute colitis and in IL-10 KO with spontaneous colitis. Parameters measured included body weight, survival, disease activity, colon length, and histology. The study analyzed intestinal proinflammatory cytokines, Th17/Treg cells, and epithelial barrier molecules, along with gut microbiota profiling. RESULTS: ALD-R491 specifically bound vimentin with a dissociation constant (KD) of 328 ± 12.66 nM and no off-target effects. In the DSS model, orally administered ALD-R491 exhibited dose-dependent therapeutic effects, superior to 5-ASA and Tofacitinib. In the IL-10 KO model, ALD-R491 significantly delayed colitis onset and progression, with near-zero disease activity index scores over a 15-week treatment. ALD-R491 consistently showed in both models a reduced proinflammatory cytokine expression, including TNF-α, IL-1ß, IL-6, IL-17, IL-22, a rebalanced Th17/Treg axis by reducing RORγt while enhancing FoxP3 expression, and an improved epithelial barrier integrity by increasing intestinal expressions of Mucin-2, ZO-1 and Claudin5. The intestinal dysbiosis was restored with enriched presence of probiotics. CONCLUSIONS: Targeting vimentin exhibits significant therapeutic effects on various facets of IBD pathogenesis, representing a compelling approach for the development of highly effective treatments in IBD.

Revealing epigenetic patterns in gene regulation through integrative analysis of epigenetic interaction network.

Chromatin components and DNA methylation play important roles in regulation of gene expression in mammalian genomes. However, the mechanism underlying how they regulate gene transcription, independently or synergistically, remains largely unknown. We constructed an epigenetic interaction network (EIN) of chromatin components, DNA methylation and gene expression by combining partial correlation coefficient with Pearson correlation coefficient. In EIN, we identified nine direct factors for gene expression. They constitute three interaction modules which synergistically affect gene expression. We introduced a new combination strategy to test how these direct factors in each module regulate gene expression synergistically. We found two inter-attracted patterns and one inter-repulsed patterns among the three modules. Furthermore, we identified 22 indirect factors for gene expression which have effect on gene expression via direct factors. DNA methylation, for example, could regulate gene expression through H3K4me3 and Pol II. Our approach has the potential to help in uncovering inherent relationships between epigenetic factors and gene transcription and guiding experiment.