Identification of cuproptosis-related biomarkers and analysis of immune infiltration in allograft lung ischemia-reperfusion injury

Background: Allograft lung ischemia-reperfusion injury (ALIRI) is a major cause of early primary graft dysfunction and poor long-term survival after lung transplantation (LTx); however, its pathogenesis has not been fully elucidated. Cell death is a mechanism underlying ALIRI. Cuproptosis is a recently discovered form of programmed cell death. To date, no studies have been conducted on the mechanisms by which cuproptosis-related genes (CRGs) regulate ALIRI. Therefore, we explored the potential biomarkers related to cuproptosis to provide new insights into the treatment of ALIRI.Materials and methods: Datasets containing pre- and post-LTx lung biopsy samples and CRGs were obtained from the GEO database and previous studies. We identified differentially expressed CRGs (DE-CRGs) and performed functional analyses. Biomarker genes were selected using three machine learning algorithms. The ROC curve and logistic regression model (LRM) of these biomarkers were constructed. CIBERSORT was used to calculate the number of infiltrating immune cells pre- and post-LTx, and the correlation between these biomarkers and immune cells was analyzed. A competing endogenous RNA network was constructed using these biomarkers. Finally, the biomarkers were verified in a validation set and a rat LTx model using qRT-PCR and Western blotting.Results: Fifteen DE-CRGs were identified. GO analysis revealed that DE-CRGs were significantly enriched in the mitochondrial acetyl-CoA biosynthetic process from pyruvate, protein lipoylation, the tricarboxylic acid (TCA) cycle, and copper-transporting ATPase activity. KEGG enrichment analysis showed that the DE-CRGs were mainly enriched in metabolic pathways, carbon metabolism, and the TCA cycle. NFE2L2, NLRP3, LIPT1, and MTF1 were identified as potential biomarker genes. The AUC of the ROC curve for each biomarker was greater than 0.8, and the LRM provided an excellent classifier with an AUC of 0.96. These biomarkers were validated in another dataset and a rat LTx model, which exhibited good performance. In the CIBERSORT analysis, differentially expressed immune cells were identified, and the biomarkers were associated with the immune cells.Conclusion:NFE2L2, NLRP3, LIPT1, and MTF1 may serve as predictors of cuproptosis and play an important role in the pathogenesis of cuproptosis in ALIRI

The water lily genome and the early evolution of flowering plants

Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms1–3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.Supplementary Tables: This file contains Supplementary Tables 1-21.National Natural Science Foundation of China, the open funds of the State Key Laboratory of Crop Genetics and Germplasm Enhancement (ZW201909) and State Key Laboratory of Tree Genetics and Breeding, the Fujian provincial government in China, the European Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant Agreement and the Special Research Fund of Ghent University.http://www.nature.com/naturecommunicationsam2021BiochemistryGeneticsMicrobiology and Plant Patholog

Data from: Trophic dynamics of filter feeding bivalves in the Yangtze Estuarine Intertidal Marsh: stable isotope and fatty acid analyses

Benthic bivalves are important links between primary production and consumers, and are essential intermediates in the flow of energy through estuarine systems. However, information on the diet of filter feeding bivalves in estuarine ecosystems is uncertain, as estuarine waters contain particulate matter from a range of sources and as bivalves are opportunistic feeders. We surveyed bivalves at different distances from the creek mouth at the Yangtze estuarine marsh in winter and summer, and analyzed trophic dynamics using stable isotope (SI) and fatty acid (FA) techniques. Different bivalve species had different spatial distributions in the estuary. Glauconome chinensis mainly occurred in marshes near the creek mouth, while Sinonovacula constricta preferred the creek. Differences were found in the diets of different species. S. constricta consumed more diatoms and bacteria than G. chinensis, while G. chinensis assimilated more macrophyte material. FA markers showed that plants contributed the most (38.86 ± 4.25%) to particular organic matter (POM) in summer, while diatoms contributed the most (12.68 ± 1.17%) during winter. Diatoms made the largest contribution to the diet of S. constricta in both summer (24.73 ± 0.44%) and winter (25.51 ± 0.59%), and plants contributed no more than 4%. This inconsistency indicates seasonal changes in food availability and the active feeding habits of the bivalve. Similar FA profiles for S. constricta indicated that the bivalve had a similar diet composition at different sites, while different δ13C results suggested the diet was derived from different carbon sources (C4 plant Spartina alterniflora and C3 plant Phragmites australis and Scirpus mariqueter) at different sites. Species-specific and temporal and/or spatial variability in bivalve feeding may affect their ecological functions in intertidal marshes, which should be considered in the study of food webs and material flows in estuarine ecosystems

Defect dynamics for self-propelled rods in a doublet of circular confinement

Rod-shaped active micro/nano-particles, such as bacterial and bipolar metallic micro/ nano-motors, exhibit emergent collective phenomena far from equilibrium state compared to passive particles. We apply a simulation approach —dissipative particle dynamics (DPD)— to explore the collectively ordered states of self-propelled rods (SPRs) which rely on the defect dynamics in the rod cluster. The SPRs are confined in a doublet of circular confinement and repel each other when two rods touch each other. When the rod flow in the connecting passage of the circles is suppressed, namely the small passage width, the steady vortex pattern is obtained in the two circles for weak activity. In binary-passage system, long single-passage system, and short single-passage system, ferromagnetic vortices (FMV), uncorrelated vortices (UV), and anti-ferromagnetic vortices (AFMV) can be obtained, respectively. For intermediate activity, a regular periodic oscillation of the rod number nr in one circle can be seen clearly. For strong activity, mixing of high- and low-frequency oscillation is observed. The amplitude of the rod current in the passage Ip follows the relation $I_{p}{\sim}F_{a}$ , where Fa denotes the self-propelled force

Punicalagin Protects Diabetic Nephropathy by Inhibiting Pyroptosis Based on TXNIP/NLRP3 Pathway

Diabetic nephropathy is a diabetic complication caused by chronic inflammation. As the primary polyphenol in pomegranate, punicalagin is believed to have significant anti-inflammatory properties. In this study, we established a mice model for diabetes induced by high-fat diet (HFD)/ streptozotocin (STZ) to verify the protective effect of punicalagin in vivo. The results show that the blood urea nitrogen (BUN), serum creatinine (CREA), and the urine albumin to creatinine ratio (UACR) were significantly decreased in diabetic mice after punicalagin intervention, and the symptoms of glomerular interstitial hyperplasia and glomerular hypertrophy were alleviated. Pyroptosis is an essential manner of programmed cell death in the inflammatory response; the expression of pyroptosis-related proteins such as interleukin-1 (IL-1β), cysteinyl aspartate-specific protease-1 (caspase-1), gasdermin D (GSDMD), and nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain containing protein 3 (NLRP3) was decreased in our study, which proved that the administration of punicalagin for eight weeks can significantly inhibit pyroptosis in mice. In addition, punicalagin reduced high glucose-mediated protein expressions of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase 4 (NOX4) and alleviated mitochondria damage. Low expression of NOX4 inhibits the dissociation of thioredoxin (Trx) and thioredoxin-interacting protein (TXNIP) and the suppression of NLRP3 inflammasome activation. To summarize, our study provided evidence that punicalagin can alleviate diabetic nephropathy, and the effect is associated with downregulating the expression of NOX4, inhibiting TXNIP/NLRP3 pathway-mediated pyroptosis, suggesting its therapeutic implications for complications of diabetes

Sesamol promotes browning of white adipocytes to ameliorate obesity by inducing mitochondrial biogenesis and inhibition mitophagy via β3-AR/PKA signaling pathway

Background: Obesity is defined as an imbalance between energy intake and expenditure, and it is a serious risk factor of non-communicable diseases. Recently many studies have shown that promoting browning of white adipose tissue (WAT) to increase energy consumption has a great therapeutic potential for obesity. Sesamol, a lignan from sesame oil, had shown potential beneficial functions on obesity treatment. Objective: In this study, we used C57BL/6J mice and 3T3-L1 adipocytes to investigate the effects and the fundamental mechanisms of sesamol in enhancing the browning of white adipocytes to ameliorate obesity. Methods: Sixteen-week-old C57BL/6J male mice were fed high-fat diet (HFD) for 8 weeks to establish the obesity models. Half of the obese mice were administered with sesamol (100 mg/kg body weight [b.w.]/day [d] by gavage for another 8 weeks. Triacylglycerol (TG) and total cholesterol assay kits were used to quantify serum TG and total cholesterol (TC). Oil red O staining was used to detect lipid droplet in vitro. Mito-Tracker Green was used to detect the mitochondrial content. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) was used to detect the levels of beige-specific genes. Immunoblotting was used to detect the proteins involved in beige adipocytes formation. Results: Sesamol decreased the content of body fat and suppressed lipid accumulation in HFD-induced obese mice. In addition, sesamol significantly upregulated uncoupling protein-1 (UCP1) protein in adipose tissue. Further research found that sesamol also significantly activated the browning program in mature 3T3-L1 adipocytes, manifested by the increase in beige-specific genes and proteins. Moreover, sesamol greatly increased mitochondrial biogenesis, as proved by the upregulated protein levels of mitochondrial biogenesis, and the inhibition of the proteins associated with mitophagy. Furthermore, β3-adrenergic receptor (β3-AR), protein kinase A-C (PKA-C) and Phospho-protein kinase A (p-PKA) substrate were elevated by sesamol, and these effects were abolished by the pretreatment of antagonists β3-AR. Conclusion: Sesamol promoted browning of white adipocytes by inducing mitochondrial biogenesis and inhibiting mitophagy through the β3-AR/PKA pathway. This preclinical data promised the potential to consider sesamol as a metabolic modulator of HFD-induced obesity

Facilitating charge transfer via a giant magnetoresistance effect for high-efficiency photocatalytic hydrogen production

In this work, a CoCu alloy magnetic unit was implanted in a photocatalytic system to improve photoinduced charge separation efficiency by regulating the electron transfer pathway via a giant magnetoresistance (GMR) effect, which achieved significantly enhanced hydrogen production activity driven by visible light. The amount of H-2 produced in 3 h over the Pt@CoCu alloy decorated graphene (G) photocatalyst was about 12.2 times higher than that of Pt/G, and the highest apparent quantum efficiency (AQE) reached 34.4% at 520 nm

Devonian porphyry Cu deposits in NW China: the Xiaotuergen example

<p>The Nuoerte Basin in northern Altay contains numerous mineral discoveries, including the Xiaotuergen porphyry Cu, Kumasu VMS Pb–Zn, and Hongshanzui orogenic Au deposits. This deposit, newly discovered by the 4th Geological Team of XJBGMR – the Xiaotuergen porphyry Cu deposit – is mainly hosted along the contact zone between the granodiorite porphyry and the Nuoerte Formation volcanic-sedimentary rocks. Disseminated, veinlet, veinlet-disseminated, and stockwork Cu mineralization occur in the granodiorite porphyry. Wall-rock alteration styles include mainly potassic (K-feldspar and biotite), silicic, carbonate, sericite, pyrite, chlorite, and epidote alterations. In this study, we used LA-ICP-MS zircon dating for the various rock types in the Xiaotuergen Cu ore district. The tuff at the periphery of the ore district has been newly dated to be ca. 411 Ma. This, together with stratigraphic correlation, suggests that the local stratigraphy is the Lower Devonian Nuoerte Formation, rather than the Lower Carboniferous Hongshanzui Formation as previously assumed. The ore-hosting granodiorite porphyry, quartz porphyry, biotite monzogranite, and granite porphyry are dated to be ca. 405 Ma, 400 Ma, 398 Ma, and 397 Ma, respectively. This constrains the Cu mineralization to be slightly younger than 405 Ma, and indicates that they may have belonged to the same Early Devonian intrusive event. Magmatism at Xiaotuergen had recommenced in the Late Devonian, as represented by minor granite porphyry dikes (ca. 370 Ma) intruding the ore-hosting granodiorite porphyry.</p

To explore the pathogenesis of Bell's palsy using diffusion tensor image

Abstract To explore the pathogenesis of Bell's palsy using the diffusion tensor image on 3.0 T MR. The healthy people and the patients with Bell's palsy underwent intraparotid facial nerve scanning by using the DTI and T1 structural sequence at 3.0 T MR. The raw DTI data were performed affine transformation and nonlinear registration in the common MNI152_T1 space and resampled to the 0.4 mm3 voxel size. A group of 4 spherical seed regions were placed on the intratemporal facial nerves in the common space, bilaterally and symmetrically. The DTI data in the common space were used to track the intratemporal facial nerve fibers by using TrackVis and its Diffusion Toolkit. Each tractography was used to construct the maximum probability map (MPM) according to the majority rule. The fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD) were calculated and extracted on the basis of MPM. For healthy people, there was no significant difference in FA, MD, RD and AD of bilateral facial nerves. For patients with Bell's palsy, there was no significant difference in AD, there was significant difference in FA, MD and RD between the affected nerve and the healthy nerve (P < 0.02). This study showed that the myelin sheath injury of the intratemporal facial nerve is the main cause of Bell's palsy. Most neural axons are not damaged. The results may explain the pathogenesis of the Bell's palsy, which is self-limited for most cases