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1.
Front Cardiovasc Med ; 11: 1358066, 2024.
Article En | MEDLINE | ID: mdl-38720918

Background: The prevalence of Type 2 Diabetes Mellitus (T2D) and its significant role in increasing Coronary Heart Disease (CHD) risk highlights the urgent need for effective CHD screening within this population. Despite current advancements in T2D management, the complexity of cardiovascular complications persists. Our study aims to develop a comprehensive CHD screening model for T2D patients, employing multimodal data to improve early detection and management, addressing a critical gap in clinical practice. Methods: We analyzed data from 699 patients, including 471 with CHD (221 of these also had T2D) and a control group of 228 without CHD. Employing strict diagnostic criteria, we conducted significance testing and multivariate analysis to identify key indicators for T2D-CHD diagnosis. This led to the creation of a neural network model using 21 indicators and a logistic regression model based on an 8-indicator subset. External validation was performed with an independent dataset from an additional 212 patients to confirm the models' generalizability. Results: The neural network model achieved an accuracy of 90.7%, recall of 90.78%, precision of 90.83%, and an F-1 score of 0.908. The logistic regression model demonstrated an accuracy of 90.13%, recall of 90.1%, precision of 90.22%, and an F-1 score of 0.9016. External validation reinforced the models' reliability and effectiveness in broader clinical settings. Conclusion: Our AI-driven diagnostic models significantly enhance early CHD detection and management in T2D patients, offering a novel, efficient approach to addressing the complex interplay between these conditions. By leveraging advanced analytics and comprehensive patient data, we present a scalable solution for improving clinical outcomes in this high-risk population, potentially setting a new standard in personalized care and preventative medicine.

2.
Environ Pollut ; 351: 124099, 2024 May 02.
Article En | MEDLINE | ID: mdl-38703980

Rivers play a significant role in the global nitrous oxide (N2O) budget. However, the microbial sources and sinks of N2O in river systems are not well understood or quantified, resulting in the prolonged neglect of nitrification. This study investigated the isotopic signatures of N2O, thereby quantifying the microbial source of N2O production and the degree of N2O reduction in the Yellow River. Although denitrification has long been considered to be the dominant pathway of N2O production in rivers, our findings indicated that denitrification only accounted for 18.3% (8.2%-43.0%) of the total contribution to N2O production in the Yellow River, with 50.2%-80.2% being concurrently reduced. The denitrification contribution to N2O production (R2 = 0.44, p < 0.01) and N2O reduction degree (R2 = 0.70, p < 0.01) were positively related to the dissolved organic carbon (DOC) content. Similar to urban rivers and eutrophic lakes, denitrification was the primary process responsible for N2O production (43.0%) in certain reaches with high organic content (DOC = 5.29 mg/L). Nevertheless, the denitrification activity was generally constrained by the availability of electron donors (average DOC = 2.51 mg/L) throughout the Yellow River basin. Consequently, nitrification emerged as the primary contributor in the well-oxygenated Yellow River. Additionally, our findings further distinguished the respective contribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to N2O emissions. Although AOB dominated the N2O production in the Yellow River, the AOA specie abundance (AOA/(AOA + AOB)) contributed up to 32.6%, which resulted in 25.6% of the total nitrifier-produced N2O, suggesting a significant occurrence of AOA in the oligotrophic Yellow River. Overall, this study provided a non-invasive approach for quantifying the microbial sources and sinks to N2O emissions, and demonstrated the substantial role of nitrification in the large oligotrophic rivers.

3.
J Exp Clin Cancer Res ; 43(1): 143, 2024 May 14.
Article En | MEDLINE | ID: mdl-38745179

BACKGROUND: Sorafenib is a standard first-line treatment for advanced hepatocellular carcinoma (HCC), yet its effectiveness is often constrained. Emerging studies reveal that sorafenib triggers ferroptosis, an iron-dependent regulated cell death (RCD) mechanism characterized by lipid peroxidation. Our findings isolate the principal target responsible for ferroptosis in HCC cells and outline an approach to potentially augment sorafenib's therapeutic impact on HCC. METHODS: We investigated the gene expression alterations following sgRNA-mediated knockdown induced by erastin and sorafenib in HCC cells using CRISPR screening-based bioinformatics analysis. Gene set enrichment analysis (GSEA) and the "GDCRNATools" package facilitated the correlation studies. We employed tissue microarrays and cDNA microarrays for validation. Ubiquitination assay, Chromatin immunoprecipitation (ChIP) assay, RNA immunoprecipitation (RIP) assay, and dual-luciferase reporter assay were utilized to delineate the specific mechanisms underlying ferroptosis in HCC cells. RESULTS: Our study has revealed that pleiomorphic adenoma gene 1 (PLAG1), a gene implicated in pleomorphic adenoma, confers resistance to ferroptosis in HCC cells treated with sorafenib. Sorafenib leads to the opposite trend of protein and mRNA levels of PLAG1, which is not caused by affecting the stability or ubiquitination of PLAG1 protein, but by the regulation of PLAG1 at the transcriptional level by its upstream competitive endogenous long non-coding RNA (lncRNA) plasmacytoma variant translocation 1 (PVT1). Data from 139 HCC patients showed a significant positive correlation between PLAG1 and GPX4 levels in tumor samples, and PLAG1 is instrumental in redox homeostasis by driving the expression of glutathione peroxidase 4 (GPX4), the enzyme that reduces lipid peroxides (LPOs), which further leads to ferroptosis inhibition. CONCLUSIONS: Ferroptosis is a promising target for cancer therapy, especially for patients resistant to standard chemotherapy or immunotherapy. Our findings indicate that PLAG1 holds therapeutic promise and may enhance the efficacy of sorafenib in treating HCC.


Carcinoma, Hepatocellular , DNA-Binding Proteins , Ferroptosis , Liver Neoplasms , Phospholipid Hydroperoxide Glutathione Peroxidase , Sorafenib , Humans , Sorafenib/pharmacology , Sorafenib/therapeutic use , Ferroptosis/drug effects , Carcinoma, Hepatocellular/drug therapy , Carcinoma, Hepatocellular/metabolism , Carcinoma, Hepatocellular/pathology , Carcinoma, Hepatocellular/genetics , Liver Neoplasms/drug therapy , Liver Neoplasms/metabolism , Liver Neoplasms/pathology , Liver Neoplasms/genetics , Phospholipid Hydroperoxide Glutathione Peroxidase/metabolism , Phospholipid Hydroperoxide Glutathione Peroxidase/genetics , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , MicroRNAs/genetics , MicroRNAs/metabolism , Mice , Animals , Cell Line, Tumor , Gene Expression Regulation, Neoplastic/drug effects , Male
4.
Mol Neurobiol ; 2024 May 14.
Article En | MEDLINE | ID: mdl-38743209

Intracerebral hemorrhage (ICH) is a subtype of stroke with the highest fatality and disability rate. Up to now, commonly used first-line therapies have limited value in improving prognosis. Angiogenesis is essential to neurological recovery after ICH. Recent studies have shown that microRNA-451(miR-451) plays an important role in angiogenesis by regulating the function of vascular endothelial cells. We found miR-451 was significantly decreased in the peripheral blood of ICH patients in the acute stage. Based on the clinical findings, we conducted this study to investigate the potential regulatory effect of miR-451 on angiogenesis after ICH. The expression of miR-451 in ICH mouse model and in a hemin toxicity model of human brain microvascular endothelial cells (hBMECs) was decreased the same as in ICH patients. MiR-451 negatively regulated the proliferation, migration, and tube formation of hBMECs in vitro. MiR-451 negatively regulated the microvessel density in the perihematoma tissue and affected neural functional recovery of ICH mouse model. Knockdown of miR-451 could recovered tight junction and protect the integrity of blood-brain barrier after ICH. Based on bioinformatic programs, macrophage migration inhibitory factor (MIF) was predicted to be the target gene and identified to be regulated by miR-451 inhibiting the protein translation. And p-AKT and p-ERK were verified to be downstream of MIF in angiogenesis. These results all suggest that miR-451 will be a potential target for regulating angiogenesis in ICH.

5.
Org Lett ; 2024 May 15.
Article En | MEDLINE | ID: mdl-38747898

Enamides and their derivatives are prominent bioactive pharmacophores found in various bioactive molecules. Herein we report a palladium-catalyzed oxidative N-α,ß-dehydrogenation of amides to produce a range of enamides with high yields and excellent tolerance toward different functional groups. Mechanistic studies indicate that the reaction involves allylic C(sp3)-H activation followed by ß-H elimination. The effectiveness of this approach is demonstrated through late-stage functionalization of bioactive molecules and the synthesis of valuable compounds through product elaboration.

6.
Aging Dis ; 2024 Apr 07.
Article En | MEDLINE | ID: mdl-38607739

End-stage liver disease (ESLD), stemming from a spectrum of chronic liver pathologies including chronic liver failure, acute cirrhosis decompensation and hepatocellular carcinoma, imposes a significant global healthcare burden. Liver transplantation (LT) remains the only treatment for ESLD. However, the escalating mortality on transplant waitlists has prompted the utilization of marginal liver grafts in LT procedures. These grafts primarily encompass elderly livers, steatotic livers, livers from donation after circulatory death, split livers and those infected with the hepatitis virus. While the expansion of the donor pool offers promise, it also introduces concomitant risks. These encompass graft failure, biliary and cardiovascular complications, the recurrence of liver disease and reduced patient and graft survival. Consequently, various established strategies, ranging from improved donor-recipient matching to surgical interventions, have emerged to mitigate these risks. This article undertakes a comprehensive assessment of the current landscape, evaluating the viability of diverse marginal liver grafts. Additionally, it synthesizes approaches aimed at enhancing the quality of such marginal liver grafts. The overarching objective is to augment the donor pool and ameliorate the risk factors associated with the shortage of liver grafts.

7.
Am J Transl Res ; 16(3): 864-872, 2024.
Article En | MEDLINE | ID: mdl-38586099

OBJECTIVE: To analyze the efficacy of arthroscopic treatment for patients with rotator cuff injuries and frozen shoulder combined with rotator cuff injuries and assess the factors influencing patient prognosis. METHODS: A retrospective analysis was performed on 85 patients who underwent arthroscopic surgery at Hanzhong Central Hospital between October 2016 and October 2021, including 42 patients treated for rotator cuff injuries alone (Group A), and 43 patients for frozen shoulder combined with rotator cuff injuries (Group B). Both groups underwent general anesthesia with controlled hypotension during surgery. Treatment outcomes, including shoulder joint functional scores, pain scores, shoulder joint range of motion, and muscle strength were assessed and compared between the two groups before treatment, as well as at 2 weeks and 2 months post-treatment. Quality of life was also evaluated and compared at 2 months post-treatment. Patients were categorized into good and poor prognosis groups based on their outcome, and factors influencing patient prognosis were analyzed. RESULTS: Before treatment, both groups exhibited relatively low shoulder joint function scores and external rotation angles, coupled with higher pain scores; however, these differences were not significant between groups (all P>0.05). The surgery duration for Group B was notably longer than that of Group A (P<0.05). Nevertheless, there was no significant variance in intraoperative blood loss between the two groups (P>0.05). After a 2-week treatment duration, both groups demonstrated a significant improvement in shoulder joint function score, pain score, and shoulder joint range of motion compared to baseline, but with no statistically significant intergroup differences. However, two months after the treatment, patients in Group A exhibited marked improvements in shoulder joint function score, pain score, shoulder joint range of motion, and overall quality of life compared to Group B (all P<0.05). Furthermore, the therapeutic efficacy in Group A was superior to that in Group B at the 2-month follow-up (P<0.05). Age, comorbid diabetes, metabolic disorders such as thyroid dysfunction, and the extent of shoulder cuff injury were identified as independent risk factors influencing prognosis. CONCLUSION: Arthroscopic treatment is effective for both frozen shoulder combined with rotator cuff injury and rotator cuff injury alone, with better outcomes observed in patients with rotator cuff injury only. This technique warrants further promotion.

8.
iScience ; 27(5): 109682, 2024 May 17.
Article En | MEDLINE | ID: mdl-38660403

The aryl hydrocarbon receptor (AhR) pathway may play an important role in the regulation of osteoclasts, but there are still conflicting studies on this aspect, and the specific mechanism of action has not been fully elucidated. Therefore, we conducted this study to find a drug to treat osteoporosis that targets AhR. We found that StemRegenin 1 inhibited RANKL-induced osteoclastogenesis in a concentration-dependent and time-dependent manner. Through further experiments, we found that SR1 can inhibit nuclear transcription of AhR and inhibit c-src phosphorylation, and ultimately regulates the activation of the NF-κB and p-ERK/mitogen-activated protein kinase pathways. Therefore, for the first time, we discovered the way in which the AhR-c-src-NF-κB/p-ERK MAPK-NFATc1 signaling pathway regulates the expression of osteoclast differentiation-associated proteins. Finally, SR1 was shown to successfully reverse bone loss in OVX mice. These studies provide us with ideas for finding new way to treat osteoporosis.

9.
Environ Sci Pollut Res Int ; 31(20): 28939-28949, 2024 Apr.
Article En | MEDLINE | ID: mdl-38564128

Encouraging the recycling of plastic packaging materials in express delivery is a necessary step toward environmentally friendly industrial development. In this study, we present a framework for analyzing the flow of materials in express plastic packaging, from production and manufacturing to consumption and recycling. In examining the use of recycled materials in post-consumer express plastic packaging and the destination of consumer packaging waste in 2020 and 2021, we found that 44.4% (1613.6 Gg) of the studied express plastic packaging was incinerated. Additionally, approximately 1296.6 Gg of express plastic packaging flowed into rural areas. Our calculations showed that the ΔRSE in 2020 was 15.1%, and on the condition that 25% separated collection with 80% recycling, ΔRSE would be - 0.5%. Results verified that separated collection is an important step in the recycling strategy for packaging materials. Survey data from universities in Beijing indicate that currently, 26% of college students are participating in the separate collection of packaging.


Entropy , Plastics , Product Packaging , Recycling , China
10.
Inorg Chem ; 63(18): 8171-8179, 2024 May 06.
Article En | MEDLINE | ID: mdl-38655575

Although 1,10-phenanthroline has been proven to hold a strong complexing capacity for f-block elements and their derivatives have been applied in many fields, research on more highly or completely rigid phenanthroline ligands is still rare due to the challenging syntheses. Here, we reported three tetradentate ligands 2,9-di(pyridin-2-yl)-1,10-phenanthroline (L1), 12-(pyridin-2-yl)-5,6-dihydroquinolino[8,7b][1,10]phenanthroline (L2), and 5,6,11,12-tetrahydrobenzo[2,1-b:3,4-b']bis([1,10]phenanthroline) (L3) with increasing preorganization on the side chain; among which, L3 is fully preorganized. Their complexation reactions with Eu(III) were systematically investigated by electrospray ionization mass spectrometry (ESI-MS), UV-vis titrations, and single-crystal structures. It is found that all three ligands form only 1:1 M/L complexes with Eu(III). The single-crystal structures revealed that the three ligands hold similar coordination modes, while their stability constants determined by UV-vis titrations were L3 (4.80 ± 0.01) > L2 (4.38 ± 0.01) > L1 (3.88 ± 0.01). This trend is supported not only by the thermodynamic stability of rigid ligands compared to free ligands but also by the conclusion that rigid ligands exhibit faster reaction rates (lower energy barrier) than free ligands kinetically. This work is helpful in providing theoretical guidance for the subsequent development of highly preorganized chelating ligands with strong coordination ability and high selectivity for f-block elements.

11.
Heart Lung ; 66: 86-93, 2024.
Article En | MEDLINE | ID: mdl-38593678

BACKGROUND: Previous observational studies have suggested associations between Coronary Heart Disease (CHD) and Mental Health Disorders (MHD). However, the causal nature of these relationships has remained elusive. OBJECTIVE: The purpose of this study is to elucidate the causal relationships between eight distinct types of CHD and six types of MHD using Mendelian randomization (MR) analysis. METHODS: The MR analysis employed a suite of methods including inverse variance-weighted (IVW), MR-Egger, weighted mode, weighted median, and simple mode techniques. To assess heterogeneity, IVW and MR-Egger tests were utilized. MR-Egger regression also served to investigate potential pleiotropy. The stability of IVW results was verified by leave-one-out sensitivity analysis. RESULTS: We analyzed data from over 2,473,005 CHD and 803,801 MHD patients, informed by instrumental variables from large-scale genomic studies on European populations. The analysis revealed a causal increase in the risk of Major Depressive Disorder and Mania associated with Coronary Artery Disease and Myocardial Infarction. Heart Failure was found to causally increase the risk for Bipolar Disorder and Schizophrenia. Atrial Fibrillation and Ischemic Heart Diseases were positively linked to Generalized Anxiety Disorder and Mania, respectively. There was no significant evidence of an association between Hypertensive Heart Disease, Hypertrophic Cardiomyopathy, Pulmonary Heart Disease, and MHD. Reverse MR analysis indicated that MHD do not serve as risk factors for CHD. CONCLUSIONS: The findings suggest that specific types of CHD may act as risk factors for certain MHDs. Consequently, incorporating psychological assessments into the management of patients with CHD could be advantageous.


Coronary Disease , Mendelian Randomization Analysis , Mental Disorders , Humans , Mendelian Randomization Analysis/methods , Coronary Disease/psychology , Coronary Disease/epidemiology , Coronary Disease/genetics , Coronary Disease/complications , Risk Factors , Mental Disorders/epidemiology , Mental Disorders/genetics , Male , Female
12.
Nat Genet ; 56(5): 846-860, 2024 May.
Article En | MEDLINE | ID: mdl-38641644

Methylation quantitative trait loci (mQTLs) are essential for understanding the role of DNA methylation changes in genetic predisposition, yet they have not been fully characterized in East Asians (EAs). Here we identified mQTLs in whole blood from 3,523 Chinese individuals and replicated them in additional 1,858 Chinese individuals from two cohorts. Over 9% of mQTLs displayed specificity to EAs, facilitating the fine-mapping of EA-specific genetic associations, as shown for variants associated with height. Trans-mQTL hotspots revealed biological pathways contributing to EA-specific genetic associations, including an ERG-mediated 233 trans-mCpG network, implicated in hematopoietic cell differentiation, which likely reflects binding efficiency modulation of the ERG protein complex. More than 90% of mQTLs were shared between different blood cell lineages, with a smaller fraction of lineage-specific mQTLs displaying preferential hypomethylation in the respective lineages. Our study provides new insights into the mQTL landscape across genetic ancestries and their downstream effects on cellular processes and diseases/traits.


DNA Methylation , East Asian People , Quantitative Trait Loci , Female , Humans , Male , East Asian People/genetics , Genetic Predisposition to Disease , Genome-Wide Association Study/methods , Multifactorial Inheritance , Polymorphism, Single Nucleotide
13.
Ren Fail ; 46(1): 2344655, 2024 Dec.
Article En | MEDLINE | ID: mdl-38685582

The association between blood flow rate (BFR) and clinical outcomes in patients undergoing maintenance hemodialysis (MHD) is inconclusive. This retrospective study included 175 patients undergoing MHD treatment between July 2015 and March 2022, divided into two groups based on time-averaged effective blood flow rate (eBFR) median value. We investigated arteriovenous fistula (AVF) outcomes and the association of eBFR with all-cause mortality and new major adverse cardiovascular events (MACE). Mean ± SD and median time-averaged eBFR values were 276 ± 24 and 275 mL/min, respectively. After adjusting for relevant factors including age, sex, vintage, diabetes, CVD, receiving hemodiafiltration (HDF) treatment and spKt/V, Cox models indicated a low time-averaged eBFR (≤ 275 ml/min) was associated with increased risks of all-cause mortality (hazard ratio [HR] 14.18; 95% confidence interval [CI], 3.14-64.1) and new MACE (HR 3.76; 95% CI, 1.91-7.40) in MHD patients. Continuous Cox models demonstrated each 20 ml/min increase in eBFR linked to a 63% decrease in the risk of all-cause mortality (HR: 0.37, 95% CI: 0.23-0.59) and a 38% decrease in the occurrence of new MACE (HR: 0.62, 95% CI: 0.46-0.84). There was no significant difference in AVF outcomes between the two groups. Our study noted higher eBFR (>275 mL/min) is associated with lower risks of both all-cause mortality and new MACE compared with low eBFR (≤275 mL/min). Increased eBFR is not associated with a higher risk of AVF failure.


Kidney Failure, Chronic , Renal Dialysis , Humans , Female , Male , Middle Aged , Retrospective Studies , Aged , Kidney Failure, Chronic/therapy , Kidney Failure, Chronic/mortality , Blood Flow Velocity , Arteriovenous Shunt, Surgical/adverse effects , Proportional Hazards Models , Cardiovascular Diseases/etiology , Cardiovascular Diseases/mortality , Treatment Outcome , Hemodiafiltration/methods , Hemodiafiltration/adverse effects
14.
Life Sci ; 342: 122540, 2024 Apr 01.
Article En | MEDLINE | ID: mdl-38428568

Transcatheter arterial chemoembolisation (TACE) is the standard of care for intermediate-stage hepatocellular carcinoma and selected patients with advanced hepatocellular carcinoma. However, TACE does not achieve a satisfactory objective response rate, and the concept of TACE refractoriness has been proposed to identify patients who do not fully benefit from TACE. Moreover, repeated TACE is necessary to obtain an optimal and sustained anti-tumour response, which may damage the patient's liver function. Therefore, studies have recently been performed to improve the effectiveness of TACE. In this review, we summarise the detailed molecular mechanisms associated with TACE responsiveness and relapse after this treatment to provide more effective targets for adjuvant therapy while helping to improve TACE regimens.


Carcinoma, Hepatocellular , Chemoembolization, Therapeutic , Liver Neoplasms , Humans , Carcinoma, Hepatocellular/therapy , Carcinoma, Hepatocellular/pathology , Liver Neoplasms/therapy , Liver Neoplasms/pathology , Chemoembolization, Therapeutic/methods , Arteries/pathology , Combined Modality Therapy
15.
Bioresour Technol ; 399: 130574, 2024 May.
Article En | MEDLINE | ID: mdl-38471631

Widespread use of nanomaterials raises concerns. The underlying mechanism by which graphene oxide (GO) nanoparticles causes poor settleability of activated sludge remains unclear. To explore this mechanism, three reactors with different GO concentrations were established. Extended Derjaguin-Landau-Verwey-Overbeek theory indicated that GO destroyed the property of extracellular polymeric substances (EPS), increasing the energy barrier between bacteria. Low levels of uronic acid and hydrogen bonding in exopolysaccharide weakened the EPS gelation increasing aggregation repulsion. Lager amounts of hydrophilic amino acid and looser structure of extracellular proteins for exposing inner hydrophilic groups significantly contributed to the hydrophilicity of EPS. Both changes implied deterioration in EPS structure under GO stress. Metagenome demonstrated a decrease in genes responsible for capsular polysaccharide colonization and genes regulated the translocation of loose proteins were increased, which increased repulsion between bacteria. This study elucidated that changes in EPS secretion under GO exposure are the underlying causes of poor settleability.


Extracellular Polymeric Substance Matrix , Graphite , Sewage/chemistry , Proteins
16.
Microbiol Spectr ; 12(3): e0360223, 2024 Mar 05.
Article En | MEDLINE | ID: mdl-38315121

Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.


Gene Transfer, Horizontal , Metagenomics , Animals , Humans , Mice , Metagenomics/methods , Computational Biology/methods , Metagenome , Bacteria/genetics , DNA
17.
Cell Rep ; 43(2): 113786, 2024 Feb 27.
Article En | MEDLINE | ID: mdl-38363684

Type 1 innate lymphoid cells (ILC1s) possess adaptive immune features, which confer antigen-specific memory responses against haptens and viruses. However, the transcriptional regulation of memory ILC1 responses is currently not known. We show that retinoic acid receptor-related orphan receptor alpha (RORα) has high expression in memory ILC1s in murine contact hypersensitivity (CHS) models. RORα deficiency diminishes ILC1-mediated CHS responses significantly but has no effect on memory T cell-mediated CHS responses. During sensitization, RORα promotes sensitized-ILC1 expansion by suppressing expression of cell-cycle repressors in draining lymph nodes. RORα programs gene-expression patterns related to cell survival and is required for the long-term maintenance of memory ILC1s in the liver. Our findings reveal RORα to be a key transcriptional factor for sensitized-ILC1 expansion and long-term maintenance of memory ILC1s.


Immunity, Innate , Lymphocytes , Animals , Mice , Cell Survival , Liver , Lymph Nodes , Transcription Factors
18.
J Biol Chem ; 300(3): 105779, 2024 Mar.
Article En | MEDLINE | ID: mdl-38395305

The newly discovered zoonotic coronavirus swine acute diarrhea syndrome coronavirus (SADS-CoV) causes acute diarrhea, vomiting, dehydration, and high mortality rates in newborn piglets. Although SADS-CoV uses different strategies to evade the host's innate immune system, the specific mechanism(s) by which it blocks the interferon (IFN) response remains unidentified. In this study, the potential of SADS-CoV nonstructural proteins (nsp) to inhibit the IFN response was detected. The results determined that nsp1 was a potent antagonist of IFN response. SADS-CoV nsp1 efficiently inhibited signal transducer and activator of transcription 1 (STAT1) phosphorylation by inducing Janus kinase 1 (JAK1) degradation. Subsequent research revealed that nsp1 induced JAK1 polyubiquitination through K11 and K48 linkages, leading to JAK1 degradation via the ubiquitin-proteasome pathway. Furthermore, SADS-CoV nsp1 induced CREB-binding protein degradation to inhibit IFN-stimulated gene production and STAT1 acetylation, thereby inhibiting STAT1 dephosphorylation and blocking STAT1 transport out of the nucleus to receive antiviral signaling. In summary, the results revealed the novel mechanisms by which SADS-CoV nsp1 blocks the JAK-STAT signaling pathway via the ubiquitin-proteasome pathway. This study yielded valuable findings on the specific mechanism of coronavirus nsp1 in inhibiting the JAK-STAT signaling pathway and the strategies of SADS-CoV in evading the host's innate immune system.


Alphacoronavirus , Coronavirus Infections , Proteasome Endopeptidase Complex , Swine Diseases , Viral Nonstructural Proteins , Animals , Acetylation , Alphacoronavirus/physiology , Coronavirus Infections/veterinary , Coronavirus Infections/virology , Janus Kinase 1/genetics , Janus Kinase 1/metabolism , Phosphorylation , Proteasome Endopeptidase Complex/metabolism , STAT1 Transcription Factor/genetics , STAT1 Transcription Factor/metabolism , Swine , Ubiquitins/metabolism , Swine Diseases/metabolism , Swine Diseases/virology , HEK293 Cells , Vero Cells , Humans , Chlorocebus aethiops , Viral Nonstructural Proteins/metabolism
19.
Water Res ; 253: 121318, 2024 Apr 01.
Article En | MEDLINE | ID: mdl-38387270

Although rivers are increasingly recognized as essential sources of greenhouse gases (GHG) to the atmosphere, few systematic efforts have been made to reveal the drivers of spatiotemporal variations of dissolved GHG (dGHG) in large rivers under increasing anthropogenic stress and intensified hydrological cycling. Here, through a source-to-estuary survey of the Yangtze River in March (spring) and October (autumn) of 2018, we revealed that labile dissolved organic matter (DOM) and nitrogen inputs remarkably modified the spatiotemporal distribution of dGHG. The average partial pressure of CO2 (pCO2), CH4 and N2O concentrations of all sampling sites in the Yangtze River were 1015 ± 225 µatm, and 87.5± 36.5 nmol L-1, and 20.3 ± 6.6 nmol L-1, respectively, significantly lower than the global average. In terms of longitudinal and seasonal variations, higher GHG concentrations were observed in the middle-lower reach in spring. The dominant drivers of spatiotemporal variations in dGHG were labile, protein-like DOM components and nitrogen level. Compared with the historical data of dGHG from published literature, we found a significant increase in N2O concentrations in the Yangtze River during 2004-2018, and the increasing trend was consistent with the rising riverine nitrogen concentrations. Our study emphasized the critical roles of labile DOM and nitrogen inputs in driving the spatial hotspots, seasonal variations and annual trends of dGHG. These findings can contribute to constraining the global GHG budget estimations and controls of GHG emission in large rivers in response to global change.


Greenhouse Gases , Greenhouse Gases/analysis , Estuaries , Dissolved Organic Matter , Rivers , Nitrogen , China
20.
Nanotechnology ; 35(31)2024 May 17.
Article En | MEDLINE | ID: mdl-38387100

As device feature sizes continue to decrease and fin field effect transistors reach their physical limits, gate all around field effect transistors (GAAFETs) have emerged with larger gate control areas and stackable characteristics for better suppression of second-order effects such as short-channel effects due to their gate encircling characteristics. Traditional methods for studying the electrical characteristics of devices are mostly based on the technology computer-aided design. Still, it is not conducive to developing new devices due to its time-consuming and inefficient drawbacks. Deep learning (DL) and machine learning (ML) have been well-used in recent years in many fields. In this paper, we propose an integrated learning model that integrates the advantages of DL and ML to solve many problems in traditional methods. This integrated learning model predicts the direct current characteristics, capacitance characteristics, and electrical parameters of GAAFET better than those predicted by DL or ML methods alone, with a linear regression factor (R2) greater than 0.99 and very small root mean square error. The proposed integrated learning model achieves fast and accurate prediction of GAAFET electrical characteristics, which provides a new idea for device and circuit simulation and characteristics prediction in microelectronics.

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