Explore the vast range of titles available.

The dung microbiome is a complex system that is highly influenced by species and diet. This study characterized the dung bacterial and fungal communities of five herbivore species inhabiting the National Park Zuid‐Kennemerland, the Netherlands. The five selected herbivore species were rabbit (Oryctolagus cuniculus L.), cow (Bos taurus L.), horse (Equus ferus caballus L.), fallow deer (Dama dama L.), and European bison (Bison bonasus L.). We explored the effects of distinct digestive physiology (ruminants vs. non‐ruminants) and diverse dietary preferences on the microbial community composition of herbivore dung. Firmicutes and Bacteroidetes were dominant bacterial phyla in the dung of all five herbivore species, and Ascomycota was the predominant fungal phylum. Verrucomicrobiota and Mucoromycota were more present in horse dung and Proteobacteria were more abundant in rabbit dung than the three ruminant dung types. There were few significant differences in the microbial community structure among the three ruminant dung types. The alpha and beta diversity of dung microbial communities significantly differed between ruminants and non‐ruminants, especially in bacterial communities. Based on MetaCyc pathways, we found that the primary functions of bacteria in herbivore dung were focused on biosynthesis, various super pathways, and degradation, with a few differences between ruminant and non‐ruminant dung. FUNGuild analysis showed that horse dung had more saprotrophic fungi, while the fungi in fallow deer dung had more symbiotrophic properties, with the fungal functions of bison, cow, and rabbit dung somewhere in between. There was also a correlation between microbial community and nutrient composition of the substrate in herbivore dung. Understanding the dung microbial community composition of these herbivore species can enrich the database of mammalian gut microbiomes for studying the mechanisms of microbial community variation while preparing for exploring a new perspective to study the impact of herbivores on ecosystems through dung deposition.

Aims Microbial-driven biogeochemical cycles of phosphorus (P) in wetlands subjected to global climate warming result in a downstream eutrophication risk. However, how warming influences P associated with microbial shifts in wetland soils is largely unknown. Methods A custom-built, novel microcosm that simulated climate warming was established under ambient temperature and elevated wanning conditions (+ 3 °C). 31P nuclear magnetic resonance (31P–NMR) technology was used to characterize different P forms and highthroughput sequencing of 16S rRNA gene was used to identify microbial community and functional potentials in wetland soils varied with nutrition status. Results Soil P forms were dominated by orthophosphate. The dynamic changes of different P forms in response to warming were mainly observed in high nutrition wetlands. The relative abundance of orthophosphate and polyphosphate (inorganic) significantly (p < 0.05) decreased, which was accompanied with increased phosphonate (organic) under warming. Consistently, soil microbial community shifts were also found in high nutrition wetlands, especially in fall with significantly (p < 0.05) increased relative abundance of Alphaproteobacteria and Betaproteobacteria and decreased Clostridia under warming. The microbial functions related to catabolism, the transport, degradation and release of P were enriched under warming. Changed microbial community may have altered the overall functional potentials which were responsible for P dynamics. Conclusions Soil microbial community shifts in response to experimental warming were season-based. Microbial changes and P shifts from high nutrition wetlands were more sensitive to warming. The changed microbial community under warming conditions may trigger the loss of orthophosphate through the altered functional potentials. These findings aid to better understand microbial-driven biogeochemical cycles of P in wetland soils under future climate changes.

Background Lung cancer is the second most common cancer with the highest mortality in the world. Calumenin as a molecular chaperone that not only binds various proteins within the endoplasmic reticulum but also plays crucial roles in diverse processes associated with tumor development. However, the regulatory mechanism of calumenin in lung adenocarcinoma remains elusive. Here, we studied the impact of calumenin on lung adenocarcinoma and explored possible mechanisms. Methods 5-ethynyl-2’-deoxyuridine assay, colony formation, transwell and wound healing assays were performed to explore the effects of calumenin on the proliferation and migration of lung adenocarcinoma cells. To gain insights into the underlying mechanisms through which calumenin knockdown inhibits the migration and proliferation of lung adenocarcinoma, we performed Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Gene Set Enrichment Analysis and Ingenuity Pathway Analysis based on transcriptomics by comparing calumenin knockdown with normal A549 cells. Results The mRNA and protein levels of calumenin in lung adenocarcinoma are highly expressed and they are related to an unfavorable prognosis in this disease. Calumenin enhances the proliferation and migration of A549 and H1299 cells. Gene Set Enrichment Analysis revealed that knockdown of calumenin in A549 cells significantly inhibited MYC and V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog signaling pathways while activating interferon signals, inflammatory signals, and p53 pathways. Ingenuity pathway analysis provided additional insights, indicating that the interferon and inflammatory pathways were prominently activated upon calumenin knockdown in A549 cells. Conclusions The anti-cancer mechanism of calumenin knockdown might be related to the inhibition of MYC and KRAS signals but the activation of interferon signals, inflammatory signals and p53 pathways.

ObjectivesThe heterogeneity of meniscus cells and the mechanism of meniscus degeneration is not well understood. Here, single-cell RNA sequencing (scRNA-seq) was used to identify various meniscus cell subsets and investigate the mechanism of meniscus degeneration.MethodsscRNA-seq was used to identify cell subsets and their gene signatures in healthy human and degenerated meniscus cells to determine their differentiation relationships and characterise the diversity within specific cell types. Colony-forming, multi-differentiation assays and a mice meniscus injury model were used to identify meniscus progenitor cells. We investigated the role of degenerated meniscus progenitor (DegP) cell clusters during meniscus degeneration using computational analysis and experimental verification.ResultsWe identified seven clusters in healthy human meniscus, including five empirically defined populations and two novel populations. Pseudotime analysis showed endothelial cells and fibrochondrocyte progenitors (FCP) existed at the pseudospace trajectory start. Melanoma cell adhesion molecule ((MCAM)/CD146) was highly expressed in two clusters. CD146+ meniscus cells differentiated into osteoblasts and adipocytes and formed colonies. We identified changes in the proportions of degenerated meniscus cell clusters and found a cluster specific to degenerative meniscus with progenitor cell characteristics. The reconstruction of four progenitor cell clusters indicated that FCP differentiation into DegP was an aberrant process. Interleukin 1β stimulation in healthy human meniscus cells increased CD318+ cells, while TGFβ1 attenuated the increase in CD318+ cells in degenerated meniscus cells.ConclusionsThe identification of meniscus progenitor cells provided new insights into cell-based meniscus tissue engineering, demonstrating a novel mechanism of meniscus degeneration, which contributes to the development of a novel therapeutic strategy.

The “one-to-many” problem is a typical challenge that faced by many machine learning aided inverse nanophotonics designs where one target optical response can be achieved by many solutions (designs). Although novel training approaches, such as tandem network, and network architecture, such as the mixture density model, have been proposed, the critical problem of solution degeneracy still exists where some possible solutions or solution spaces are discarded or unreachable during the network training process. Here, we report a solution to the “one-to-many” problem by employing a conditional generative adversarial network (cGAN) that enables generating sets of multiple solution groups to a design problem. Using the inverse design of a transmissive Fabry–Pérot-cavity-based color filter as an example, our model demonstrates the capability of generating an average number of 3.58 solution groups for each color. These multiple solutions allow the selection of the best design for each color which results in a record high accuracy with an average index color difference Δ of 0.44. The capability of identifying multiple solution groups can benefit the design manufacturing to allow more viable designs for fabrication. The capability of our cGAN is verified experimentally by inversely designing the RGB color filters. We envisage this cGAN-based design methodology can be applied to other nanophotonic structures or physical science domains where the identification of multi-solution across a vast parameter space is required.

Background The autophagy adapter SQSTM1/p62 is crucial for maintaining homeostasis in various organs and cells due to its protein–protein interaction domains and involvement in diverse physiological and pathological processes. Vascular endothelium cells play a unique role in vascular biology and contribute to vascular health. Methods Using the Cre-loxP system, we generated mice with endothelium cell-specific knockout of p62 mediated by Tek (Tek receptor tyrosine kinase)-cre to investigate the essential role of p62 in the endothelium. In vitro, we employed protein mass spectrometry and IPA to identify differentially expressed proteins upon knockdown of p62. Immunoprecipitation assays were conducted to demonstrate the interaction between p62 and FN1 or LAMC2 in human umbilical vein endothelium cells (HUVECs). Additionally, we identified the degradation pathway of FN1 and LAMC2 using the autophagy inhibitor 3-methyladenine (3-MA) or proteasome inhibitor MG132. Finally, the results of immunoprecipitation demonstrated that the interaction between p62 and LAMC2 was abolished in the PB1 truncation group of p62, while the interaction between p62 and FN1 was abolished in the UBA truncation group of p62. Results Our findings revealed that p62 Endo mice exhibited heart, lung, and kidney fibrosis compared to littermate controls, accompanied by severe cardiac dysfunction. Immunoprecipitation assays provided evidence of p62 acting as an autophagy adapter in the autophagy-lysosome pathway for FN1 and LAMC2 degradation respectively through PB1 and UBA domain with these proteins rather than proteasome system. Conclusions Our study demonstrates that defects in p62 within endothelium cells induce multi-organ fibrosis and cardiac dysfunction in mice. Our findings indicate that FN1 and LAMC2, as markers of (EndoMT), have detrimental effects on HUVECs and elucidate the autophagy-lysosome degradation mechanism of FN1 and LAMC2.

Background Nocardia is a facultative intracellular pathogen that infects the lungs and brains of immunocompromised patients with consequences that can be fatal. The incidence of such infections is rising, immunocompetent individuals are also being infected, and there is a need to learn more about this neglected bacterial pathogen and the interaction with its human host. Results We have applied dual RNA-seq to assess the global transcriptome changes that occur simultaneously in Nocardia farcinica ( N. farcinica ) and infected human epithelial alveolar host cells, and have tested a series of mutants in this in vitro system to identify candidate determinants of virulence. Using a mouse model, we revealed the profiles of inflammation-related factors in the lung after intranasal infection and confirmed that nbtB and nbtS are key virulence genes for Nocardia infection in vivo. Regarding the host response to infection, we found that the expression of many histones was dysregulated during the infection of lung cells, indicating that epigenetic modification might play a crucial role in the host during Nocardia infection. In our mouse model, Nocardia infection led to neurological symptoms and we found that 15 of 22 Nocardia clinical strains tested could cause obvious PD-like symptoms. Further experiments indicated that Nocardia infection could activate microglia and drive M1 microglial polarization, promote iNOS and CXCL-10 production, and cause neuroinflammation in the substantia nigra, all of which may be involved in causing PD-like symptoms. Importantly, the deletion of nbtS in N. farcinica completely attenuated the neurological symptoms. Conclusions Our data contribute to an in-depth understanding of the characteristics of both the host and Nocardia during infection and provide valuable clues for future studies of this neglected human pathogen, especially those addressing the underlying causes of infection-related neurological symptoms.

Background Mitochondrial dysfunction is an important pathogenic event in acute kidney injury (AKI). GCN5L1 is a specific acetyltransferase in mitochondria, which regulates glucose and fatty acid metabolism. However, the role of GCN5L1 in mitochondrial dysfunction and the pathogenesis of ischemic AKI are not fully understood. Methods The protein level of GCN5L1 was detected by western blot assay. Acetylated proteomics was used to explore the level of acetylated TFAM. Duolink proximity ligation assay and co-immunoprecipitation were used to detect the interaction of TFAM and translocase of outer membrane 70 (TOM70). mtDNA copy number, the expression of mitochondrial electron transport chain complexes, the number and morphology of mitochondria were measured. The renal injury of AKI mice was reflected by the levels of creatinine and urea nitrogen and the pathological changes of renal tissue. Results We showed that GCN5L1 was highly expressed in vivo and in vitro and renal tubules specific knockdown of GCN5L1 could effectively attenuate AKI-induced mitochondrial impairment. Besides, acetylated proteomics revealed that acetylated TFAM was significantly upregulated in AKI mice kidney, which reminded us that TFAM might be an acetylating substrate of GCN5L1. Mechanistically, we evidenced that GCN5L1 could acetylate TFAM at its K76 site and subsequently inhibited its binding to TOM70, thereby reducing TFAM import into mitochondria and mitochondrial biogenesis. Clinically, GCN5L1 and acetylated TFAM were positively correlated with disease severity (all p < 0.05). Conclusions In sum, these data demonstrated an unrecognized regulating mechanism of GCN5L1 on TFAM acetylation and its intracellular trafficking, and a potential intervening target for AKI associated mitochondrial disorders as well.

Background Metabolic reprogramming plays a pivotal role in tumorigenesis and development of lung adenocarcinoma (LUAD). However, the precise mechanisms and potential targets for metabolic reprogramming in LUAD remain elusive. Our prior investigations revealed that the mitochondrial ribosomal protein MRPL12, identified as a novel mitochondrial transcriptional regulatory gene, exerts a critical influence on mitochondrial metabolism. Despite this, the role and regulatory mechanisms underlying MRPL12’s transcriptional activity in cancers remain unexplored. Methods Human LUAD tissues, Tp53 fl/fl ; Kras G12D -driven LUAD mouse models, LUAD patient-derived organoids (PDO), and LUAD cell lines were used to explored the expression and function of MRPL12. The posttranslational modification of MRPL12 was analyzed by mass spectrometry, and the oncogenic role of key phosphorylation sites of MRPL12 in LUAD development was verified in vivo and in vitro. Results MRPL12 was upregulated in human LUAD tissues, Tp53 fl/fl ; Kras G12D -driven LUAD tissues in mice, LUAD PDO, and LUAD cell lines, correlating with poor patient survival. Overexpression of MRPL12 significantly promoted LUAD tumorigenesis, metastasis, and PDO formation, while MRPL12 knockdown elicited the opposite phenotype. Additionally, MRPL12 deletion in a Tp53 fl/fl ; Kras G12D -driven mouse LUAD model conferred a notable survival advantage, delaying tumor onset and reducing malignant progression. Mechanistically, we discovered that MRPL12 promotes tumor progression by upregulating mitochondrial oxidative phosphorylation. Furthermore, we identified UBASH3B as a specific binder of MRPL12, dephosphorylating tyrosine 60 in MRPL12 (MRPL12 Y60) and inhibiting its oncogenic functions. The decrease in MRPL12 Y60 phosphorylation impeded the binding of MRPL12 to POLRMT, downregulating mitochondrial metabolism in LUAD cells. In-depth in vivo, in vitro, and organoid models validated the inhibitory effect of MRPL12 Y60 mutation on LUAD. Conclusion This study establishes MRPL12 as a novel oncogene in LUAD, contributing to LUAD pathogenesis by orchestrating mitochondrial metabolism reprogramming towards oxidative phosphorylation (OXPHOS). Furthermore, it confirms Y60 as a specific phosphorylation modification site regulating MRPL12’s oncogenic functions, offering insights for the development of LUAD-specific targeted drugs and clinical interventions. Graphical Abstract

Renal cell carcinoma (RCC) is a common urological tumor, with clear cell renal cell carcinoma (ccRCC) being the most prevalent subtype. Metabolic reprogramming plays a critical role in ccRCC progression, making it a promising target for therapeutic intervention, though effective treatments remain unavailable. Our previous studies have shown that mitochondrial ribosomal protein L12 (MRPL12) contributes to various metabolic diseases, including diabetic kidney disease and HCC, by regulating mitochondrial biosynthesis. In this study, we demonstrated that MRPL12 is acetylated at lysine 163 (K163) in ccRCC cells, a key modification that influences its regulatory effect on mitochondrial metabolism. Mechanistically, we clarified that acetylation at the K163 site enhances mitochondrial biosynthesis by promoting MRPL12’s binding to POLRMT, which subsequently increases mitochondrial metabolism and suppresses cellular glycolysis. Additionally, we found that MRPL12 K163 acetylation levels were significantly downregulated in ccRCC and that restoring this acetylation inhibited ccRCC progression in both in vitro and in vivo models. Furthermore, we demonstrated that the acetyltransferase TIP60 and the deacetylase SIRT5 bind to MRPL12 and regulate its acetylation. These findings highlight K163 acetylation as a critical site for MRPL12-mediated regulation of mitochondrial metabolism and reveal that this modification inhibits renal cancer development by promoting mitochondrial biosynthesis, reducing glycolysis, and driving metabolic reprogramming. This study suggests a potential therapeutic strategy for targeting MRPL12 acetylation in ccRCC.