Fungal names: a comprehensive nomenclatural repository and knowledge base for fungal taxonomy.

Fungal taxonomy is a complex and rapidly changing subject, which makes proper naming of fungi challenging for taxonomists. A registration platform with a standardized and information-integrated database is a powerful tool for efficient research on fungal taxonomy. Fungal Names (FN, https://nmdc.cn/fungalnames/; launched in 2011) is one of the three official fungal nomenclatural repositories authorized by the International Nomenclature Committee for Fungi (NCF). Currently, FN includes >567 000 taxon names from >10 000 related journals and books published since 1596 and covers >147 000 collection records of type specimens/illustrations from >5000 preserving agencies. FN is also a knowledge base that integrates nomenclature information with specimens, culture collections and herbaria/fungaria, publications and taxonomists, and represents a summary of the history and recent advances in fungal taxonomy. Published fungal names are categorized based on well-accepted nomenclature rules and can be readily searched with different keywords and strategies. In combination with a standardized name checking tool and a sequence alignment-based identification package, FN makes the registration and typification of nomenclatural novelties of fungi convenient and accurate.

NOVA1 prevents overactivation of the unfolded protein response and facilitates chromatin access during human white adipogenesis.

The molecular mechanism underlying white adipogenesis in humans has not been fully elucidated beyond the transcriptional level. Here, we found that the RNA-binding protein NOVA1 is required for the adipogenic differentiation of human mesenchymal stem cells. By thoroughly exploring the interactions between NOVA1 and its binding RNA, we proved that NOVA1 deficiency resulted in the aberrant splicing of DNAJC10 with an in-frame premature stop codon, reduced DNAJC10 expression at the protein level and hyperactivation of the unfolded protein response (UPR). Moreover, NOVA1 knockdown abrogated the down-regulation of NCOR2 during adipogenesis and up-regulated the 47b+ splicing isoform, which led to decreased chromatin accessibility at the loci of lipid metabolism genes. Interestingly, these effects on human adipogenesis could not be recapitulated in mice. Further analysis of multispecies genomes and transcriptomes indicated that NOVA1-targeted RNA splicing is evolutionarily regulated. Our findings provide evidence for human-specific roles of NOVA1 in coordinating splicing and cell organelle functions during white adipogenesis.

Transcriptome data analysis provides insights into the conservation of Michelia lacei, a plant species with extremely small populations distributed in Yunnan province, China.

BACKGROUND: Michelia lacei W.W.Smith (Magnoliaceae), was classified as a Plant Species with Extremely Small Populations (PSESP) by the Yunnan Provincial Government in both action plans of 2012 and 2021. This evergreen tree is known for its high ornamental and scientific value, but it faces significant threats due to its extremely small population size and narrow geographical distribution. The study aims to understand the genetic structure, diversity, and demographic history of this species to inform its conservation strategies. RESULTS: The analysis of transcriptome data from 64 individuals across seven populations of M. lacei identified three distinct genetic clusters and generated 104,616 single-nucleotide polymorphisms (SNPs). The KM ex-situ population, originating from Longling County, exhibited unique genetic features, suggesting limited gene flow. The genetic diversity was substantial, with significant differences between populations, particularly between the KM lineage and the OTHER lineage. Demographic history inferred from the data indicated population experienced three significant population declines during glaciations, followed by periods of recovery. We estimated the effective population size (Ne) of the KM and OTHER lineages 1,000 years ago were 85,851 and 416,622, respectively. Gene flow analysis suggested past gene flow between populations, but the KM ex-situ population showed no recent gene flow. A total of 805 outlier SNPs, associated with four environmental factors, suggest potential local adaptation and showcase the species' adaptive potential. Particularly, the BZ displayed 515 adaptive loci, highlighting its strong potential for adaptation within this group. CONCLUSIONS: The comprehensive genomic analysis of M. lacei provides valuable insights into its genetic background and highlights the urgent need for conservation efforts. The study underscores the importance of ex-situ conservation methods, such as seed collection and vegetative propagation, to safeguard genetic diversity and promote population restoration. The preservation of populations like MC and BZ is crucial for maintaining the species' genetic diversity. In-situ conservation measures, including the establishment of in-situ conservation sites and community engagement, are essential to enhance protection awareness and ensure the long-term survival of this threatened plant species.

Linkage Effect Induced by Hierarchical Architecture in Magnetic MXene-based Microwave Absorber.

Hierarchical architecture engineering is desirable in integrating the physical-chemical behaviors and macroscopic properties of materials, which present great potential for developing multifunctional microwave absorption materials. However, the intrinsic mechanisms and correlation conditions among cellular units have not been revealed, which are insufficient to maximize the fusion of superior microwave absorption (MA) and derived multifunctionality. Herein, based on three models (disordered structure, porous structure, lamellar structure) of structural units, a range of MXene-aerogels with variable constructions are fabricated by a top-down ice template method. The aerogel with lamellar structure with a density of only 0.015 g cm-3 exhibits the best MA performance (minimum reflection loss: -53.87 dB, effective absorption bandwidth:6.84 GHz) at a 6 wt.% filling ratio, which is preferred over alternative aerogels with variable configurations. This work elucidates the relationship between the hierarchical architecture and the superior MA performance. Further, the MXene/CoNi Composite aerogel with lamellar structure exhibits >90% compression stretch after 1000 cycles, excellent compressive properties, and elasticity, as well as high hydrophobicity and thermal insulation properties, broadening the versatility of MXene-based aerogel applications. In short, through precise microstructure design, this work provides a conceptually novel strategy to realize the integration of electromagnetic stealth, thermal insulation, and load-bearing capability simultaneously.

Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome.

Soil and plant-associated protistan communities play a key role in shaping bacterial and fungal communities, primarily through their function as top-down predators. However, our understanding of how pathogen invasion influences these protistan communities and their relationships with bacterial and fungal communities remains limited. Here, we studied the protistan communities along the soil-plant continuum of healthy chilli peppers and those affected by Fusarium wilt disease (FWD), and integrated bacterial and fungal community data from our previous research. Our research showed that FWD was associated with a significant enrichment of phagotrophic protists in roots, and also increased the proportion and connectivity of these protists (especially Cercozoa and Ciliophora) in both intra- and inter-kingdom networks. Furthermore, the microbiome of diseased plants not only showed a higher relative abundance of functional genes related to bacterial anti-predator responses than healthy plants, but also contained a greater abundance of metagenome-assembled genomes with functional traits involved in this response. The increased microbial inter-kingdom associations between bacteria and protists, coupled with the notable bacterial anti-predator feedback in the microbiome of diseased plants, suggest that FWD may catalyse the associations between protists and their microbial prey. These findings highlight the potential role of predatory protists in influencing microbial assembly and functionality through top-down forces under pathogenic stress.

Association of NOTCH3 With Elastic Fiber Dispersion in the Infrarenal Abdominal Aorta of Cynomolgus Monkeys.

BACKGROUND: The regional heterogeneity of vascular components and transcriptomes is an important determinant of aortic biology. This notion has been explored in multiple mouse studies. In the present study, we examined the regional heterogeneity of aortas in nonhuman primates. METHODS: Aortic samples were harvested from the ascending, descending thoracic, suprarenal, and infrarenal regions of young control monkeys and adult monkeys with high fructose consumption for 3 years. The regional heterogeneity of aortic structure and transcriptomes was examined by histological and bulk RNA sequencing analyses, respectively. RESULTS: Immunostaining of CD31 and αSMA (alpha-smooth muscle actin) revealed that endothelial and smooth muscle cells were distributed homogeneously across the aortic regions. In contrast, elastic fibers were less abundant and dispersed in the infrarenal aorta compared with other regions and associated with collagen deposition. Bulk RNA sequencing identified a distinct transcriptome related to the Notch signaling pathway in the infrarenal aorta with significantly increased NOTCH3 mRNA compared with other regions. Immunostaining revealed that NOTCH3 protein was increased in the media of the infrarenal aorta. The abundance of medial NOTCH3 was positively correlated with the dispersion of elastic fibers. Adult cynomolgus monkeys with high fructose consumption displayed vascular wall remodeling, such as smooth muscle cell loss and elastic fiber disruption, predominantly in the infrarenal region. The correlation between NOTCH3 and elastic fiber dispersion was enhanced in these monkeys. CONCLUSIONS: Aortas of young cynomolgus monkeys display regional heterogeneity of their transcriptome and the structure of elastin and collagens. Elastic fibers in the infrarenal aorta are dispersed along with upregulation of medial NOTCH3.

Protective effect of N-(E)-p-coumaroyltyrosine on LPS-induced acute inflammatory injury and signaling pathway analysis.

N-trans-p-coumaroyltyrosine (N-(E)-p-coumaroyltyrosine, NPCT), extracted and purified from Abri Mollis Herba, is an amino acid amide. The defense mechanism of NPCT against inflammatory response is still unknown. In this study, lipopolysaccharide (LPS)-induced zebrafish acute inflammatory injury model was established to observe the inhibitory effect of NPCT on the aggregation of inflammatory cells in the yolk sac of zebrafish, as well as the inhibitory effect of NPCT on inflammatory and gas signaling factors. Results show that NPCT could inhibit inflammatory cell infiltration in zebrafish yolk sac, the migration and aggregation of macrophages and neutrophils to the site of inflammation, and the release of Nitric Oxide (NO) and Reactive Oxygen Species (ROS) in zebrafish, indicating that NPCT could substantially significantly prevent the development of LPS-induced acute systemic inflammation. In addition, the analysis results of RNA-seq showed that in the model group versus the administered group, the differentially expressed genes were mainly enriched to inflammatory signaling pathways, such as the NOD-like receptor signaling pathway and Toll-like receptor signaling pathway, which were down-regulated in the administered group. The TLR4, MyD88, IRAK4, NF-κB, IκB, NLRP3, Caspase-1, ASC, IL-1ß, and IL-6 genes were significantly different in the transcripts, and the overall trend of the qPCR results was consistent with the transcriptome sequencing results. Therefore, NPCT had a significant inhibitory effect on LPS-induced acute inflammatory injury in zebrafish, and its anti-inflammatory mechanism may be through the regulation of key genes on the NOD-like receptor signaling pathway and Toll-like receptor signaling pathway, thereby affecting the release of relevant inflammatory cytokines.

Role of Bridging Groups in Regulating the Luminescence and Charge Transfer Properties of Thermally Activated Delayed Fluorescence Molecules: A Theoretical Perspective.

Organic emitters with a simultaneous combination of aggregation-induced emission (AIE) and thermally activated delayed fluorescence (TADF) characteristics are in great demand due to their excellent comprehensive performances toward efficient organic light-emitting diodes (OLEDs), biomedical imaging, and the telecommunications field. However, the development of efficient AIE-TADF materials remains a substantial challenge. In this work, light-emitting properties of two AIE-TADF molecules with different bridging groups ICz-BP and ICz-DPS are theoretically investigated in the solid state with the combined quantum mechanics/molecular mechanics (QM/MM) method and the thermal vibration correlation function (TVCF) theory. The research indicates that the C═O bridging bond in ICz-BP is more favorable than the S═O bridging bond in ICz-DPS for enhancing the planarity of the acceptor, increasing conjugation, and thereby elevating the transition dipole moment density. Simultaneously, the stacking pattern of ICz-BP in the solid facilitates a reduction in energy gap between S1 and T1 (ΔEST), achieving rapid reverse intersystem crossing rate (kRISC). Furthermore, compared to toluene, the stacking patterns of ICz-BP and ICz-DPS in the solid effectively suppress the out-of-plane wagging vibration of the acceptor, thereby inhibiting the loss of nonradiative energy in the excited state and realizing aggregation-induced emission. Moreover, the charge transport properties of both electrons and holes in ICz-BP are found to be higher than the corresponding rates in ICz-DPS, attributed to the smaller internal reorganization energy of ICz-BP in the solid state. Additionally, the calculations reveal a more balanced charge transport characteristic in ICz-BP, contributing to efficient exciton recombination and emission and ultimately mitigating efficiency roll-off. Based on these computational results, we aim to unveil the relationship between molecular structure and light-emitting properties, aiding in the design and development of efficient AIE-TADF devices.

Rotational stability of monofocal and diffractive multifocal toric intraocular lens with identical design and material: a propensity score based prospective comparative study.

PURPOSE: To compare the rotational stability of a monofocal and a diffractive multifocal toric intraocular lens(IOLs) with identical design and material. METHODS: This prospective study enrolled patients who underwent plate-haptic toric IOL (AT TORBI 709 M and AT LISA 909 M) implantation. Propensity score matching (PSM) was performed to balance baseline factors. Follow-up examinations were conducted at 1 h, 1 day, 3 days, 1 week, 2 weeks, 1 month, and 3 months postoperatively. A linear mixed model of repeated measures was used to investigate the changes in IOL rotation over time. A 2-week timeframe was utilized to assess differences in IOL rotation between the two groups. RESULT: After PSM, a total of 126 eyes were selected from each group for further analysis. Postoperatively, the time course of IOL rotation change in the two groups remained consistent, with the greatest rotation occurring between 1 h and 1 day postoperatively. At the 2-week postoperative mark, the monofocal toric IOL exhibited a higher degree of rotation compared to the multifocal toric IOL (5.40 ± 7.77° vs. 3.53 ± 3.54°, P = 0.015). In lens thickness(LT) ≥ 4.5 mm and white-to-white distance(WTW) ≥ 11.6 mm subgroups, the monofocal toric IOL rotated greater than the multifocal toric IOL (P = 0.026 and P = 0.011, respectively). CONCLUSION: The diffractive multifocal toric IOL exhibits superior rotational stability compared to the monofocal toric IOL, especially in subgroups LT ≥ 4.5 mm and WTW ≥ 11.6 mm. Moreover, the time course of IOL rotation change is consistent for both, with the maximum rotation occurring between 1 h and 1 day postoperatively.

Adaptive Clustering for Point Cloud.

The point cloud segmentation method plays an important role in practical applications, such as remote sensing, mobile robots, and 3D modeling. However, there are still some limitations to the current point cloud data segmentation method when applied to large-scale scenes. Therefore, this paper proposes an adaptive clustering segmentation method. In this method, the threshold for clustering points within the point cloud is calculated using the characteristic parameters of adjacent points. After completing the preliminary segmentation of the point cloud, the segmentation results are further refined according to the standard deviation of the cluster points. Then, the cluster points whose number does not meet the conditions are further segmented, and, finally, scene point cloud data segmentation is realized. To test the superiority of this method, this study was based on point cloud data from a park in Guilin, Guangxi, China. The experimental results showed that this method is more practical and efficient than other methods, and it can effectively segment all ground objects and ground point cloud data in a scene. Compared with other segmentation methods that are easily affected by parameters, this method has strong robustness. In order to verify the universality of the method proposed in this paper, we test a public data set provided by ISPRS. The method achieves good segmentation results for multiple sample data, and it can distinguish noise points in a scene.

Sucralose regulates postprandial blood glucose in mice through intestinal sweet taste receptors Tas1r2/Tas1r3.

BACKGROUND: Non-nutritive sweeteners (such as sucralose) bind to sweet receptors Tas1r2/Tas1r3 on intestinal endocrine L cells after diets to upregulate blood glucose. However, the mechanism by which sucralose regulates postprandial blood glucose (PBG) has not been clarified to date. We hypothesized that the gut sweet taste receptor was one of the targets for sucralose to regulate PBG. The aim of this study was to examine the effect of sucralose on PBG based on the gut sweet taste receptor signaling pathway and to explore the mechanism. Therefore, we examined PBG, genes, and proteins associated with the gut sweet receptor pathway in sucralose-exposed mice. RESULTS: The results showed that after 12 weeks of sucralose exposure the PBG of mice increased significantly, and the expression of intestinal sweet taste receptors increased correspondingly. Within the concentration range of this experiment, a significant increase of PBG was observed in mice fed on sucralose with a concentration equal to or higher than 0.33 g L-1 . CONCLUSION: Long-term consumption of sucralose may increase body weight and the risk of elevated PBG, resulting in overexpression of sweetness receptors and glucose transporters. The mechanism of these effects might be the result of non-nutritive sweeteners binding to sweetness receptors Tas1r2/Tas1r3 in gut endocrine cells and upregulating Slc5a1 and Slc2a2. But we cannot rule out that the rise in PBG is the result of a combination of sweet receptors and gut microbes. Therefore, the effect of gut microbes on PBG needs to be studied further. © 2023 Society of Chemical Industry.

Enhancement of functional properties, digestive properties, and in vitro digestion product physiological activity of extruded corn gluten meal by enzymatic modification.

BACKGROUND: Enzymatic modification is an effective means of improving the functional properties, digestive properties, and in vitro digestion product physiological activity of proteins, thus significantly expanding protein uses in various food applications. RESULTS: In this study, the addition of chymotrypsin (CT) at pH 9.0 and 11.0 was found to significantly improve the functional properties (solubility, foaming properties, water holding capacity, oil holding capacity, etc.) and digestive properties of extruded corn gluten meal (ECGM). Similar changes were observed when treating ECGM with glutaminase, protein glutaminase, and papain. These changes were likely due to the increase in number of carboxyl groups and the multiple effects of change in protein net charge and conformation caused by enzymatic deamidation. Of note, ECGM deamidated by CT showed the highest degree of deamidation, solubility, and gastrointestinal digestibility at pH 11.0, up to 44.92%, 43.75%, and 82.22%, respectively. In addition, CT-ECGM digestion product exhibited strong antioxidant activity and potential to promote alcohol metabolism in both a static digestion model and dynamic digestion model, even comparable to commercial corn peptides (CCP), while being inexpensive and of low bitterness compared to CCP. Meanwhile, the physiological activity enhanced as the molecular weight of digestion product decreased with the digested component having strongest activity. CONCLUSION: This study may promote the application of ECGM as a food component in the food industry or even as a substitute for CCP. © 2023 Society of Chemical Industry.

Buccal Fat Pad Augmentation for Midfacial Rejuvenation: Modified Fat Grafting Technique and Ogee Line Remodeling.

BACKGROUND: The volume and position of the buccal fat pad (BFP) change with age, which manifests as a hollow midface. Previous studies showed that autologous fat grafting for BFP augmentation could effectively ameliorate midfacial hollowing. OBJECTIVES: The aim of this study was to introduce a modified fat grafting technique for female patients with midfacial hollowing to restore the volume of BFP, and to evaluate the safety and effectiveness of this approach. METHODS: Two cadavers were used for the dissection of the BFP and to demonstrate the surgical procedures. Forty-eight patients were treated for midfacial hollowing with the modified grafting strategy. The BFP was filled through a percutaneous zygomatic incision and an immediate amelioration in the hollow area was observed. Improvements were evaluated from measurements of the ogee line and ogee angle, FACE-Q questionnaires, and 3-party satisfaction ratings. Clinical profiles were reviewed and statistically analysed. RESULTS: The mean [standard deviation] ogee angle was 6.6° [1.9°] preoperatively and 3.9° [1.4°] postoperatively (average reduction, 2.7°). Patients' ogee lines were smoother postoperatively, with marked improvements in overall appearance, psychological well-being, and social confidence. Patients reported high satisfaction with decision-making and postoperative outcomes and felt 6.61 [2.21] years younger. Overall, 88%, 76%, and 83% of the cases were graded as good or excellent in improvement by surgeon, patient, and the third party, respectively. CONCLUSIONS: For age-dependent midfacial hollowing in female patients, the modified percutaneous grafting technique described here was safe and efficacious in restoring BFP volume. This technique produced a smoother ogee line and a natural, younger midfacial contour.

Delocalized Orbitals Over Metal Clusters and Organic Linkers Enable Boosted Charge Transfer in Metal-Organic Framework for Overall CO2 Photoreduction.

The conversion of CO2 to C2 through photocatalysis poses significant challenges, and one of the biggest hurdles stems from the sluggishness of the multi-electron transfer process. Herein, taking metal-organic framework (PFC-98) as a model photocatalyst, we report a new strategy to facilitate charge separation. This strategy involves matching the energy levels of the lowest unoccupied node and linker orbitals of the MOF, thereby creating the lowest unoccupied crystal orbital (LUCO) delocalized over both the node and linker. This feature enables the direct excitation of electrons from photosensitive linker to the catalytic centers, achieving a direct charge transfer (DCT) pathway. For comparison, an isoreticular MOF (PFC-6) based on analogue components but with far apart frontier energy level was synthesized. The delocalized LUCO caused the presence of an internal charge-separated state (ICS), prolonging the excited state lifetime and further inhibiting the electron-hole recombination. The presence of an internal charge-separated state (ICS) prolongs the excited state lifetime and further inhibits the electron-hole recombination. Moreover, it also induced abundant electrons accumulating at the catalytic sites, enabling the multi-electron transfer process. As a result, the material featuring delocalized LUCO exhibits superior overall CO2 photocatalytic performance with high C2 production yield and selectivity.

Fine-Tuning Crystal Structures of Lead Bromide Perovskite Nanocrystals through Trace Cadmium(II) Doping for Efficient Color-Saturated Green LEDs.

Decreasing perovskite nanocrystal size increases radiative recombination due to the quantum confinement effect, but also increases the Auger recombination rate which leads to carrier imbalance in the emitting layers of electroluminescent devices. Here, we overcome this trade-off by increasing the exciton effective mass without affecting the size, which is realized through the trace Cd2+ doping of formamidinium lead bromide perovskite nanocrystals. We observe an ~2.7 times increase in the exciton binding energy benefiting from a slight distortion of the [BX6]4- octahedra caused by doping in the case of that the Auger recombination rate is almost unchanged. As a result, bright color-saturated green emitting perovskite nanocrystals with a photoluminescence quantum yield of 96 % are obtained. Cd2+ doping also shifts up the energy levels of the nanocrystals, relative to the Fermi level so that heavily n-doped emitters convert into only slightly n-doped ones; this boosts the charge injection efficiency of the corresponding light-emitting diodes. The light-emitting devices based on those nanocrystals reached a high external quantum efficiency of 29.4 % corresponding to a current efficiency of 123 cd A-1, and showed dramatically improved device lifetime, with a narrow bandwidth of 22 nm and Commission Internationale de I'Eclairage coordinates of (0.20, 0.76) for color-saturated green emission for the electroluminescence peak centered at 534 nm, thus being fully compliant with the latest standard for wide color gamut displays.

Association of Tumor Cell Metabolic Subtype and Immune Response With the Clinical Course of Hepatocellular Carcinoma.

AIM: Tumor metabolism plays an important role in tumorigenesis and tumor progression. This study evaluated the potential association of tumor cell metabolism and immune cell tumor infiltration with the clinical course of hepatocellular carcinoma (HCC). METHODS: Gene-wise normalization and principal component analysis were performed to evaluate the metabolic system. A tumor microenvironment score system of tumor immune cell infiltration was constructed to evaluate its association with metabolic subtypes. Finally, we analyzed the impact of metabolism and immune cell infiltration on the clinical course of HCC. RESULTS: A total of 673 HCC patients were categorized into cholesterogenic (25.3%), glycolytic (14.6%), mixed (10.4%), and quiescent (49.8%) types based on glycolysis and cholesterol biosynthesis gene expression. The subgroups including the glycolytic genotyping expression (glycolytic and mixed types) showed a higher mortality rate. The glycolytic, cholesterogenic, and mixed types were positively correlated with M0 macrophage, resting mast cell, and naïve B-cell infiltration (P = .013, P = .019, and P = .006, respectively). In TCGA database, high CD8+ T cell and low M0 macrophage infiltration were associated with prolonged overall survival (OS, P = .0017 and P < .0001, respectively). Furthermore, in glycolytic and mixed types, patients with high M0 macrophage infiltration had a shorter OS (P = .03 and P = .013, respectively), and in quiescent type, patients with low naïve B-cell infiltration had a longer OS (P = .007). CONCLUSIONS: Tumor metabolism plays a prognostic role and correlates with immune cell infiltration in HCC. M0 macrophage and CD8+ T cell appear to be promising prognostic biomarker for HCC. Finally, M0 macrophages may represent a useful immunotherapeutic target in patients with HCC.

Advanced graph and sequence neural networks for molecular property prediction and drug discovery.

MOTIVATION: Properties of molecules are indicative of their functions and thus are useful in many applications. With the advances of deep-learning methods, computational approaches for predicting molecular properties are gaining increasing momentum. However, there lacks customized and advanced methods and comprehensive tools for this task currently. RESULTS: Here, we develop a suite of comprehensive machine-learning methods and tools spanning different computational models, molecular representations and loss functions for molecular property prediction and drug discovery. Specifically, we represent molecules as both graphs and sequences. Built on these representations, we develop novel deep models for learning from molecular graphs and sequences. In order to learn effectively from highly imbalanced datasets, we develop advanced loss functions that optimize areas under precision-recall curves (PRCs) and receiver operating characteristic (ROC) curves. Altogether, our work not only serves as a comprehensive tool, but also contributes toward developing novel and advanced graph and sequence-learning methodologies. Results on both online and offline antibiotics discovery and molecular property prediction tasks show that our methods achieve consistent improvements over prior methods. In particular, our methods achieve #1 ranking in terms of both ROC-AUC (area under curve) and PRC-AUC on the AI Cures open challenge for drug discovery related to COVID-19. AVAILABILITY AND IMPLEMENTATION: Our source code is released as part of the MoleculeX library (https://github.com/divelab/MoleculeX) under AdvProp. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Microfat exerts an anti-fibrotic effect on human hypertrophic scar via fetuin-A/ETV4 axis.

BACKGROUND: Hypertrophic scar is a fibrotic disease following wound healing and is characterized by excessive extracellular matrix deposition. Autologous microfat grafting proves an effective strategy for the treatment thereof as it could improve the texture of scars and relieve relevant symptoms. This study aims to explore the potential mechanisms underlying the anti-fibrotic effect of microfat on hypertrophic scars. METHODS: In this study, we injected microfat into transplanted hypertrophic scars in mouse models and investigated the subsequent histological changes and differential expression of mRNAs therein. As for in vitro studies, we co-cultured microfat and hypertrophic scar fibroblasts (HSFs) and analyzed molecular profile changes in HSFs co-cultured with microfat by RNA sequencing. Moreover, to identify the key transcription factors (TFs) which might be responsible for the anti-fibrotic function of microfat, we screened the differentially expressed TFs and transfected HSFs with lentivirus to overexpress or knockdown certain differentially expressed TFs. Furthermore, comparative secretome analyses were conducted to investigate the proteins secreted by co-cultured microfat; changes in gene expression of HSFs were examined after the administration of the potential anti-fibrotic protein. Finally, the relationship between the key TF in HSFs and the microfat-secreted anti-fibrotic adipokine was analyzed. RESULTS: The anti-fibrotic effect of microfat was confirmed by in vivo transplanted hypertrophic scar models, as the number of α-SMA-positive myofibroblasts was decreased and the expression of fibrosis-related genes downregulated. Co-cultured microfat suppressed the extracellular matrix production of HSFs in in vitro experiment, and the transcription factor ETV4 was primarily differentially expressed in HSFs when compared with normal skin fibroblasts. Overexpression of ETV4 significantly decreased the expression of fibrosis-related genes in HSFs at both mRNA and protein levels. Fetuin-A secreted by microfat could also downregulate the expression of fibrosis-related genes in HSFs, partially through upregulating ETV4 expression. CONCLUSIONS: Our results demonstrated that transcription factor ETV4 is essential for the anti-fibrotic effect of microfat on hypertrophic scars, and that fetuin-A secreted by microfat could suppress the fibrotic characteristic of HSFs through upregulating ETV4 expression. Microfat wields an alleviative influence over hypertrophic scars via fetuin-A/ETV4 axis.

Metatranscriptomics and metabarcoding reveal spatiotemporal shifts in fungal communities and their activities in Chinese coastal waters.

Fungal communities are diverse and abundant in coastal waters, yet, their ecological roles and adaptations remain largely unknown. To address these gaps, ITS2 metabarcoding and metatranscriptomic analyses were used to capture the whole suite of fungal diversity and their metabolic potential in water column and sediments in the Yellow Sea during August and October 2019. ITS2 metabarcoding described successfully the abundance of Dikarya during August and October at the different examined habitats, but strongly underrepresented or failed to identify other fungal taxa, including zoosporic and early-diverging lineages, that were abundant in the mycobiome as uncovered by metatranscriptomes. Metatranscriptomics also revealed enriched expression of genes annotated to zoosporic fungi (e.g., chytrids) mainly in the surface water column in October. This enriched expression was correlated with the two-fold increase in chlorophyll-a intensity attributed to phytoplanktonic species which are known to be parasitized by chytrids. The concurrent high expression of genes related to calcium signalling and GTPase activity suggested that these metabolic traits facilitate the parasitic lifestyle of chytrids. Similarly, elevated expression of phagosome genes annotated to Rozellomycota, an early-diverging fungal phylum not fully detected with ITS2 metabarcoding, suggested that this taxon utilizes a suite of feeding modes, including phagotrophy in this coastal setting. Our data highlight the necessity of using combined approaches to accurately describe the community structure of coastal mycobiome. We also provide in-depth insights into the fungal ecological roles in coastal waters, and report potential metabolic mechanisms utilized by fungi to cope with environmental stresses that occur during distinct seasonal months in coastal ecosystems.

Nanopore sequencing of full rRNA operon improves resolution in mycobiome analysis and reveals high diversity in both human gut and environments.

High-throughput sequencing has substantially improved our understanding of fungal diversity. However, the short read (<500 bp) length of current second-generation sequencing approaches provides limited taxonomic and phylogenetic resolution for species discrimination. Longer sequences containing more information are highly desired to provide greater taxonomic resolution. Here, we amplified full-length rRNA operons (~5.5 kb) and established a corresponding fungal rRNA operon database for ONT sequences (FRODO), which contains ONT sequences representing eight phyla, 41 classes, 109 orders, 256 families, 524 genera and 1116 species. We also benchmarked the optimal method for sequence classification and determined that the RDP classifier based on our FRODO database was capable of improving the classification of ONT reads, with an average of 98%-99% reads correctly classified at the genus or species level. We investigated the applicability of our approach in three representative mycobiomes, namely, the soil, marine and human gut mycobiomes, and found that the gut contains the largest number of unknown species (over 90%), followed by the marine (42%) and soil (33.8%) mycobiomes. We also observed a distinct difference in the composition of the marine and soil mycobiomes, with the highest richness and diversity detected in soils. Overall, our study provides a systematic approach for mycobiome studies and revealed that the previous methods might have underestimated the diversity of mycobiome species. Future application of this method will lead to a better understanding of the taxonomic and functional diversity of fungi in environmental and health-related mycobiomes.