Hyperoxia exposure promotes endothelial-mesenchymal transition and inhibits regulatory T cell function in human pulmonary microvascular endothelial cells.

Objective: This study aims to investigate the effects of hyperoxia exposure on TGF-ß1-induced endothelial-mesenchymal transition (EndoMT) and regulatory T cell (Treg)-mediated immunomodulation in human pulmonary microvascular endothelial cells (HPMECs), which could provide a theoretical basis for further studies of the pathogenesis of bronchopulmonary dysplasia (BPD). Methods: A BPD cell model was established by exposing HPMECs to hyperoxia. Flow cytometry was used to isolate CD4 + CD3 + CD25 + CD127- Tregs from the peripheral blood samples of preterm infants. HPMECs were divided into four groups based on whether they were exposed to hyperoxia and/or co-cultured with Tregs. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA) were used to test the expression levels of TGF-ß1, α-SMA, Foxp3, IL-10, and reactive oxygen species (ROS). Results: The results showed that the expression levels of TGF-ß1 and α-SMA in HPMECs increased at 24 h, 48 h, and 72 h of hyperoxia exposure. In the co-culture group of HPMECs and Tregs, Foxp3 and IL-10 expressions decreased at 48 h and 72 h of hyperoxia exposure. ROS expression increased in the hyperoxia group of HPMECs at 24 h, 48 h, and 72 h of hyperoxia exposure, which were higher than those in the hyperoxia group of HPMECs and Tregs. Conclusion: These findings suggest that hyperoxia exposure promotes EndoMT in HMPECs and inhibits the immunosuppressive effect of Tregs. Despite this, Tregs still seem could protect HPMECs from oxidative stress injury.

[Role and mechanism of epithelial-mesenchymal transition in a rat model of bronchopulmonary dysplasia induced by hyperoxia exposure]. / 上皮-间å è´¨è½¬åŒ–åœ¨é«˜æ°§è¯±å¯¼å¤§é¼ æ”¯æ°”ç®¡è‚ºå‘è‚²ä¸è‰¯æ¨¡åž‹ä¸­çš„ä½œç”¨åŠæœºåˆ¶ç ”ç©¶.

OBJECTIVES: To investigate the role and mechanism of epithelial-mesenchymal transition (EMT) in a rat model of bronchopulmonary dysplasia (BPD). METHODS: The experiment consisted of two parts. (1) Forty-eight preterm rats were randomly divided into a normoxia group and a hyperoxia group, with 24 rats in each group. The hyperoxia group was exposed to 85% oxygen to establish a BPD model, while the normoxia group was kept in room air at normal pressure. Lung tissue samples were collected on days 1, 4, 7, and 14 of the experiment. (2) Rat type II alveolar epithelial cells (RLE-6TN) were randomly divided into a normoxia group (cultured in air) and a hyperoxia group (cultured in 95% oxygen), and cell samples were collected 12, 24, and 48 hours after hyperoxia exposure. Hematoxylin-eosin staining was used to observe alveolarization in preterm rat lungs, and immunofluorescence was used to detect the co-localization of surfactant protein C (SPC) and α-smooth muscle actin (α-SMA) in preterm rat lung tissue and RLE-6TN cells. Quantitative real-time polymerase chain reaction and protein immunoblotting were used to detect the expression levels of EMT-related mRNA and proteins in preterm rat lung tissue and RLE-6TN cells. RESULTS: (1) Compared with the normoxia group, the hyperoxia group showed blocked alveolarization and simplified alveolar structure after 7 days of hyperoxia exposure. Co-localization of SPC and α-SMA was observed in lung tissue, with decreased SPC expression and increased α-SMA expression in the hyperoxia group at 7 and 14 days of hyperoxia exposure compared to the normoxia group. In the hyperoxia group, the mRNA and protein levels of TGF-ß1, α-SMA, and N-cadherin were increased, while the mRNA and protein levels of SPC and E-cadherin were decreased at 7 and 14 days of hyperoxia exposure compared to the normoxia group (P<0.05). (2) SPC and α-SMA was observed in RLE-6TN cells, with decreased SPC expression and increased α-SMA expression in the hyperoxia group at 24 and 48 hours of hyperoxia exposure compared to the normoxia group. Compared to the normoxia group, the mRNA and protein levels of SPC and E-cadherin in the hyperoxia group were decreased, while the mRNA and protein levels of TGF-ß1, α-SMA, and E-cadherin in the hyperoxia group increased at 48 hours of hyperoxia exposure (P<0.05). CONCLUSIONS: EMT disrupts the tight connections between alveolar epithelial cells in a preterm rat model of BPD, leading to simplified alveolar structure and abnormal development, and is involved in the development of BPD. Citation:Chinese Journal of Contemporary Pediatrics, 2024, 26(7): 765-773.

FerroLigandDB: A Ferroptosis Ligand Database of Structure-Activity Relations.

Ferroptosis is an iron-dependent programmed cell death characterized by lipid peroxidation that is linked to the pathophysiological processes in many diseases, such as neurodegenerative diseases, cancers, ischemia-reperfusion injuries, and organ damages. Many proteins are associated with ferroptosis signal transduction pathways. Novel chemical compounds are demanded to explore and regulate these pathways. Therefore, a ferroptosis ligand database, which holds relations among chemical structures, targets, bioactivities, and diseases, is needed for discovering and designing new ferroptosis regulators. This work reports FerroLigandDB, a manually curated database for small-molecular ferroptosis regulators. The database comprises 466 ferroptosis inducer entries (with 380 unique molecular structures) and 539 ferroptosis inhibitor entries (with 468 unique molecular structures) (note: one compound can be recorded as multiple entries due to the different assays). Each ferroptosis ligand entry is detailed with compound IDs, structure attributes, bioactivity values, test objects, target information, associated diseases, and references. The fields in the FerroLigandDB database implicitly contain relationships among chemical structures, bioactivities, targets, and diseases. Thus, FerroLigandDB is a comprehensive resource for scientists to design and discover novel ferroptosis regulators. The user interface of FerroLigandDB is implemented with query features and data visualization facilities. With compound identifiers, the compounds are linked to the records of other chemoinformatics databases (such as PubChem and SciFinder). The FerroLigandDB database is freely accessible at http://ferr.gulab.org.cn/.

The relationship between the psychological resilience and post-traumatic growth of college students during the COVID-19 pandemic: a model of conditioned processes mediated by negative emotions and moderated by deliberate rumination.

BACKGROUND: The mental health of university students during the COVID-19 pandemic has attracted the attention of researchers. For the present study researchers constructed a mediation model to explore the relationship between psychological resilience and post-traumatic growth, the mediating role of negative emotions and the moderating role of deliberate rumination in students. METHODS: The Psychological Resilience Scale, Posttraumatic Growth Inventory, Depression-Anxiety-Stress Scale (DASS-21) and Event Related Rumination Inventory were used in a survey of 881 college students. The data were analyzed using SPSS 26.0 and the PROCESS plugin (version 3.3). RESULTS: (1) Psychological resilience is positively related with post-traumatic growth. Deliberate rumination is positively related to psychological resilience, posttraumatic growth, and negative emotions. Psychological resilience, post-traumatic growth and negative emotions are negatively related. (2) Negative emotions mediated the relationship between psychological resilience and post-traumatic growth. (3) Deliberate rumination plays a moderating role in psychological resilience affecting negative emotions. Deliberate rumination plays a moderating role in the extent to which psychological resilience influences PTG through negative emotions. CONCLUSIONS: Psychological resilience affects post-traumatic growth directly and also indirectly through negative emotions. With the increase of mental resilience, the level of negative emotion tended to decrease. When individuals are experiencing negative emotions, high levels of active rumination are more likely to promote post-traumatic growth. This study helps to explore the factors affecting the mental health of college students during the epidemic, thus providing guidance for appropriate mental health interventions.

Orthogonal Radical and Cationic Single-Unit Monomer Insertions for Engineering Polymer Architectures.

The single-unit monomer insertion (SUMI), derived from living/controlled polymerization, can be directly functionalized at the end or within the chain of polymers prepared by living/controlled polymerization, offering potential applications in the preparation of polymers with complex architectures. Many scenarios demand the simultaneous incorporation of monomers suitable for different polymerization methods into complex polymers. Therefore, it becomes imperative to utilize SUMI technologies with diverse mechanisms, especially those that are compatible with each other. Here, we reported the orthogonal SUMI technique, seamlessly combining radical and cationic SUMI approaches. Through the careful optimization of monomer and chain transfer agent pairs and adjustments to reaction conditions, we can efficiently execute both radical and cationic SUMI processes in one pot without mutual interference. The utilization of orthogonal SUMI pairs facilitates the integration of radical and cationic reversible addition-fragmentation chain transfer (RAFT) polymerization in various configurations. This flexibility enables the synthesis of diblock, triblock, and star polymers that incorporate both cationically and radically polymerizable monomers. Moreover, we have successfully implemented a mixing mechanism of free radicals and cations in RAFT step-growth polymerization, resulting in the creation of a side-chain sequence-controlled polymer brushes.

Universal crRNA Acylation Strategy for Robust Photo-Initiated One-Pot CRISPR-Cas12a Nucleic Acid Diagnostics.

Spatiotemporal regulation of clustered regularly interspaced short palindromic repeats (CRISPR) system is attractive for precise gene editing and accurate molecular diagnosis. Although many efforts have been made, versatile and efficient strategies to control CRISPR system are still desirable. Here, we proposed a universal and accessible acylation strategy to regulate the CRISPR-Cas12a system by efficient acylation of 2'-hydroxyls (2'-OH) on crRNA strand with photolabile agents (PLGs). The introduction of PLGs confers efficient suppression of crRNA function and rapid restoration of CRISPR-Cas12a reaction upon short light exposure regardless of crRNA sequences. Based on this strategy, we constructed a universal PhotO-Initiated CRISPR-Cas12a system for Robust One-pot Testing (POIROT) platform integrated with recombinase polymerase amplification (RPA), which showed two orders of magnitude more sensitive than the conventional one-step assay and comparable to the two-step assay. For clinical sample testing, POIROT achieved high-efficiency detection performance comparable to the gold-standard quantitative PCR (qPCR) in sensitivity and specificity, but faster than the qPCR method. Overall, we believe the proposed strategy will promote the development of many other universal photo-controlled CRISPR technologies for one-pot assay, and even expand applications in the fields of controllable CRISPR-based genomic editing, disease therapy, and cell imaging.

Identifying eleven new ferroptosis inhibitors as neuroprotective agents from FDA-approved drugs.

With increasing evidence that ferroptosis is associated with diverse neurological disorders, targeting ferroptosis offers a promising avenue for developing effective pharmaceutical agents for neuroprotection. In this study, we identified ferroptosis inhibitors as neuroprotective agents from US Food and Drug Administration (FDA)-approved drugs. 1176 drugs have been screened against erastin-induced ferroptosis in HT22 cells, resulting in 89 ferroptosis inhibitors. Among them, 26 drugs showed significant activity with EC50 below10 µM. The most active ferroptosis inhibitor is lumateperone tosylate at nanomolar level. 11 drugs as ferroptosis inhibitors were not reported previously. Further mechanistic studies revealed that their mechanisms of actions involve free radical scavenging, Fe2+ chelation, and 15-lipoxygenase inhibition. Notably, the active properties of some drugs were firstly revealed here. These ferroptosis inhibitors increase the chemical diversity of ferroptosis inhibitors, and offer new therapeutic possibilities for the treatments of related neurological diseases.

3D Printing Drug-Free Scaffold with Triple-Effect Combination Induced by Copper-Doped Layered Double Hydroxides for the Treatment of Bone Defects.

Tissue-engineered poly(l-lactide) (PLLA) scaffolds have been widely used to treat bone defects; however, poor biological activities have always been key challenges for its further application. To address this issue, introducing bioactive drugs or factors is the most commonly used method, but there are often many problems such as high cost, uncontrollable and monotonous drug activity, and poor bioavailability. Here, a drug-free 3D printing PLLA scaffold with a triple-effect combination induced by surface-modified copper-doped layered double hydroxides (Cu-LDHs) is proposed. In the early stage of scaffold implantation, Cu-LDHs exert a photothermal therapy (PTT) effect to generate high temperature to effectively prevent bacterial infection. In the later stage, Cu-LDHs can further have a mild hyperthermia (MHT) effect to stimulate angiogenesis and osteogenic differentiation, demonstrating excellent vascularization and osteogenic activity. More importantly, with the degradation of Cu-LDHs, the released Cu2+ and Mg2+ provide an ion microenvironment effect and further synergize with the MHT effect to stimulate angiogenesis and osteogenic differentiation, thus more effectively promoting the healing of bone tissue. This triple-effect combined scaffold exhibits outstanding antibacterial, osteogenic, and angiogenic activities, as well as the advantages of low cost, convenient procedure, and long-term efficacy, and is expected to provide a promising strategy for clinical repair of bone defects.

The utility of long non-coding RNAs in chronic obstructive pulmonary disease: a comprehensive analysis.

OBJECTIVES: Chronic obstructive pulmonary disease (COPD) is one of the main causes of morbidity and mortality in the world. However, there are some patients who are not diagnosed early and correctly through routine methods because of inconspicuous or serious symptoms. This study aims to assess the diagnostic role of long non-coding RNA (lncRNA) in COPD. METHODS: We searched literature from electronic databases, after excluding non-COPD literature, the bibliometric analysis was performed, and VOSviewer software was used to represent the data analyzed. Literature evaluating the diagnostic test accuracy of lncRNA for COPD was eligible, and the QUADAS-2 checklist was used to evaluate the quality. The pooled sensitivity (SEN), specificity (SPE), diagnostic odds ratio (DOR), and summary receiver operating characteristic curve (sROC) were used to analyze the overall diagnostic performance. Subgroup and meta-regression analyses were performed to explore the heterogeneity, and a funnel plot was assessed for publication bias. Also, lncRNAs related to COPD were identified and explored for their potential biological function. RESULTS: An increased annual growth rate of literature on this subject from 2016 focused on COPD, humans, RNA, and lncRNA. The meta-analysis enrolled 17 literature indicated that the SEN, SPE, and DOR differentiating COPD patients from normal controls (NCs) were 0.86 (95% CI [0.80, 0.90]), 0.78 (95% CI [0.67, 0.86]), and 21.59 (95% CI [11.39, 40.91]), respectively. Meanwhile, lncRNAs had the ability to distinguish acute exacerbations of COPD (AECOPD) patients from COPD; the SEN, SPE, and DOR were 0.75 (95% CI [0.62, 0.85]), 0.81 (95% CI [0.71, 0.89]), and 13.02 (95% CI [7.76, 21.85]), respectively. The area under the sROC were calculated to be greater than 0.8 at least. Subgroup and meta-regression analysis showed that the types of specimens and dysregulated lncRNAs might affect the diagnostic accuracy. The funnel plot showed there was a certain publication bias. 41 lncRNAs related to COPD were identified and mainly located in the nucleus and cytoplasm, associated with proliferation, invasion, and prognosis. These lncRNA-binding proteins were involved in the spliceosome, Rap1 signaling pathway, MAPK signaling pathway, and so on. CONCLUSION: LncRNA suggests potential diagnostic biomarkers and therapeutic targets for COPD patients.

Virome Profiling, New Virus Identification and the Prevalence and Distribution of Viruses Infecting Chieh-Qua (Benincasa hispida Cogn. var. chieh-qua How) in China.

The cucurbit vegetable chieh-qua (Benincasa hispida var. chieh-qua How) is an important crop in South China and southeast Asian countries. Viral diseases cause substantial loss of chieh-qua yield. To identify the viruses that affect chieh-qua in China, ribosomal RNA-depleted total RNA sequencing was performed using chieh-qua leaf samples with typical viral symptoms. The virome of chieh-qua comprises four known viruses (melon yellow spot virus (MYSV), cucurbit chlorotic yellows virus (CCYV), papaya ringspot virus (PRSV) and watermelon silver mottle virus (WSMoV) and two novel viruses: cucurbit chlorotic virus (CuCV) in the genus Crinivirus and chieh-qua endornavirus (CqEV) in the genus Alphaendornavirus. The complete genomes of the two novel viruses in chieh-qua and three other isolates of CuCV in pumpkin, watermelon and cucumber were determined and the recombination signals of pumpkin and watermelon isolates of CuCV were detected. A reverse transcriptase PCR indicated that the dominant viruses of chieh-qua in Hainan are MYSV (66.67%) and CCYV (55.56%), followed by CuCV (27.41%), WSMoV (7.41%), cucumber mosaic virus (8.15%), zucchini yellow mosaic virus (6.67%), PRSV (6.67%) and CqEV (35.56%). Our findings support diagnostic and prevalence studies of viruses infecting chieh-qua in China, enabling sustainable control strategies for cucurbit viruses worldwide.

Using an In-Sample Addition of Medronic Acid for the Analysis of Purine- and Pyrimidine-Related Derivatives and Its Application in the Study of Lung Adenocarcinoma A549 Cell Lines by LC-MS/MS.

Intracellular purine- and pyrimidine-related derivatives are vital molecules for preserving genetic information and are essential for cellular bioenergetics and signal transduction. This study developed a practical liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for quantifying intracellular purine- and pyrimidine-related derivatives. To solve the distorted peak shape related to di- and triphosphate nucleotides, in-sample addition of medronic acid and ammonium phosphate was performed. Using the BEH-amide column, the results showed that adding 0.5 mM medronic acid to the sample significantly improved the peak shape without causing an obvious ion suppressive effect. Method validation confirmed that the coefficients of determination (R2) values for linearity evaluation were above 0.94 for all analytes. The intraday and interday accuracies ranged from 85.1 to 128.4%, with the precision below 16.6%. The validated method was successfully applied in characterizing the alterations of purine- and pyrimidine-related derivatives in the A549 cell line with perturbed mitochondrial fission or blockade of the electron transport chain. Collectively, this study demonstrates that the strategy of in-sample medronic acid addition is effective in improving the quantification of intracellular purine- and pyrimidine-related derivatives. We believe that our proposed platform can facilitate the development of novel drugs targeting purine and pyrimidine metabolism in the future.

The effect of research on life satisfaction in middle-aged and older adults: physical disability and physical activity as a parallel and serial mediation analysis.

BACKGROUND AND OBJECTIVE: Maintaining the life satisfaction of frail middle-aged and older adults when they experience physical disability, lower activity status, or complex conditions that are related to each other is now an urgent issue. Therefore, the purpose of this study was to provide evidence for the impact of frailty in middle-aged and older adults on life satisfaction under the simultaneous occurrence and correlation of physical disability and physical activity status. METHODS: Data from the 2015 Taiwan Longitudinal Study in Ageing (TLSA) were analyzed by PROCESS in SPSS to explore three different mediation models (N = 4,421). The first was a parallel mediation model for exploring life satisfaction in middle-aged and older adults with frailty through physical disability or physical activity. The second was a serial mediation model for examining physical disability and physical activity in causal chains linked with a specific direction of flow and to test all combinations. The third was a moderated mediation model for testing whether the indirect effect of frailty status on life satisfaction through physical disability or physical activity was moderated by age stratification. RESULTS: Physical disability and physical activity partially mediated the relationship between frailty status and life satisfaction (IEOVERALL = -0.196, 95% CI: -0.255 to -0.139). The causal path with the highest indirect effect was found to be that between frailty and physical disability; increased frailty led to higher physical disability, which in turn affected physical activity, leading to lower life satisfaction (IE = 0.013, 95% CI: 0.008 to 0.019). The different stratifications by age significantly increased the mediating effect of physical activity (Index of Moderated Mediation = -0.107, SE = 0.052, 95% CI: -0.208 to -0.005) but did not reduce the mediating effect of physical disability. CONCLUSION: This study provides evidence that physical activity and physical disability influence the development of frailty. It also has a significant impact on the life satisfaction of middle-aged and older adults.

[Research Progress of Regulatory T Cells in the Pathogenesis of Multiple Myeloma --Review].

The multiple myeloma (MM), the second most common hematologic malignancy, is malignant proliferative disease of plasma cells. Although the application of many targeted drugs has significantly prolonged the survival time of MM patients, it is still an incurable disease. In recent years, the immunosuppression caused by interaction between tumor microenvironment(TME) and tumor cells has attracted people's attention gradually. As a kind of immunosuppressive cells in TME, regulatory T cells (Treg) play an important role in the progress of MM. Treg is related to the proliferation and metastasis of tumors, and can lead to the progress of MM by promoting the angiogenesis and generating immunosuppressive TME. In this review, we briefly summarized the latest research progress on the impact of Treg on the pathogenesis of MM.

Rare Pattern of Myelodysplastic Syndrome (MDS) with Serum Monoclonal Immunoglobulin: Case Report.

Background: Myelodysplastic syndromes (MDS) are clonal hematopoietic stem cell disorders characterized by bone marrow dysplasia, ineffective hematopoiesis, and cytopenias. Monoclonal gammopathy of undetermined significance (MGUS) and multiple myeloma (MM) patients have a high risk of secondary MDS or acute myeloid leukemia (AML) compared to healthy persons, and chemotherapy or transplantation may result in secondary treatment-related MDS. Methods: A patient was diagnosed with both MDS and MGUS, which was treated using thalidomide, dexamethasone, and danazol. A follow-up blood test was conducted to determine leukocyte and hemoglobin levels. Results: Immunoprotein electrophoresis showed M protein peak with IgA+ κ components. Nuclear cells proliferated actively in bone marrow aspirates. Bone marrow analysis suggested a myelodysplastic syndrome with myeloblastoma (MDS-RS) and a new plasmacytoma. The immunophenotype was shown as follows: R5 cells (red) are about 15.5%. Among the CD38+CD45 cells, about 95.9% of cKappa cells and 1.7% of cLambda cells are considered as plasmacytoma. Gene detection showed that the patient carried 14 gene mutations, and karyotype analysis showed that they had normal male chromosome structure. The patient was diagnosed as MDS and MGUS, and finally discharged after treatment with thalidomide (75 mg daily), dexamethasone (3 mg daily), and danazol (200 mg twice daily). Within 1 year, the disease has stabilized. Conclusion: The combination of plasma cell disease and myeloid malignancy may increase mortality. This is uncommon and may be easily misdiagnosed if not detected early. When a myeloid neoplasm tests positive for MDS and serum M protein, clinicians should evaluate for other plasma cell disease.

Efficacy of ultrasound-guided acupotomy for knee osteoarthritis: A systematic review and meta-analysis of randomized controlled trials.

BACKGROUND: This systematic review aimed to evaluate the effectiveness and safety of ultrasound-guided acupotomy (UGAT) therapy in the treatment of patients with knee osteoarthritis (KOA). METHODS: We conducted online researches in the databases including PubMed, the Cochrane Library, EMBASE, China national knowledge infrastructure, China biomedical literature database, and Wan Fang data. All data were collected until January 1, 2022. Relevant randomized controlled trials on the effectiveness of UGAT for the treatment of KOA were included. Meta-analyses were carried out by RevMan 5.3 software. Evidence quality was evaluated by the grading of recommendations, assessment development, and evaluation. RESULTS: Eight studies including 543 participants were analyzed in this study. The pooled analysis indicated that UGAT was significantly more efficient than the control group in decreasing the visual analogue scale score (mean difference = -0.81, 95% confidence interval (CI) = [-1.15, -0.47], P < .00001, 8 studies), improving knee function on the Lysholm knee score (mean difference = 8.26, 95% CI = [1.56, 14.97], P = .02, 2 studies), and increasing clinical effective rate (relative risk = 1.14, 95% CI = [1.06, 1.23], P = .0005, 6 studies). For adverse events, UGAT was also associated with lower incidence of adverse event (odds ratio = 0.27, 95% CI = [0.12, 0.63], P = .002, 4 studies) compared to traditional acupotomy. CONCLUSION: Current evidence suggested that UGAT therapy was effective and safe in the clinical treatments of KOA, thus could be suggested in the clinical managements of KOA. However, considering the unsatisfactory quality of the available trials, more large-scale, and better quality randomized controlled trials were recommend in future.

Genetic Analysis of Colletotrichum siamense Populations from Different Hosts and Counties in Hainan, China, Using Microsatellite Markers.

Colletotrichum siamense was demonstrated as the dominant species among Colletotrichum spp. that infected rubber tree, areca palm, and coffee in Hainan, China. However, the extent of genetic differentiation within the species C. siamense in relation to geographical regions and host species is not known. In this study, 112 C. siamense isolates were genotyped with 12 microsatellite markers. In total, there were 99 multilocus genotypes. Results from permutational multivariate analysis of variance and analysis of molecular variance indicated that there was no significant genetic differentiation between fungal populations with respect to host, location (county), and year. Discriminant analysis of principal components and STRUCTURE analysis showed that C. siamense isolates grouped into three clusters; further analysis confirmed that there were significant (P < 0.001) genetic differences among the three clusters. However, each cluster had isolates from different hosts, counties, or years, supporting the lack of genetic differentiation with respect to host, county, and year. Statistical analyses of allelic associations indicated some evidence for recombination within the populations defined on the basis of host or county. The present findings provide insights into the genetic structure of C. siamense on the three perennial host species in Hainan and suggest that the disease on these three crops can be effectively considered as one disease and, hence, needs to be controlled simultaneously in mixed plantations.

Codon usage bias in chloroplast genes implicate adaptive evolution of four ginger species.

Codon usage bias (CUB) refers to different codons exhibiting varying frequencies of usage in the genome. Studying CUB is crucial for understanding genome structure, function, and evolutionary processes. Herein, we investigated the codon usage patterns and influencing factors of protein-coding genes in the chloroplast genomes of four sister genera (monophyletic Roscoea and Cautleya, and monophyletic Pommereschea and Rhynchanthus) from the Zingiberaceae family with contrasting habitats in southwestern China. These genera exhibit distinct habitats, providing a unique opportunity to explore the adaptive evolution of codon usage. We conducted a comprehensive analysis of nucleotide composition and codon usage on protein-coding genes in the chloroplast genomes. The study focused on understanding the relationship between codon usage and environmental adaptation, with a particular emphasis on genes associated with photosynthesis. Nucleotide composition analysis revealed that the overall G/C content of the coding genes was ˂ 48%, indicating an enrichment of A/T bases. Additionally, synonymous and optimal codons were biased toward ending with A/U bases. Natural selection is the primary factor influencing CUB characteristics, particularly photosynthesis-associated genes. We observed differential gene expressions related to light adaptation among sister genera inhabiting different environments. Certain codons were favored under specific conditions, possibly contributing to gene expression regulation in particular environments. This study provides insights into the adaptive evolution of these sister genera by analyzing CUB and offers theoretical assistance for understanding gene expression and regulation. In addition, the data support the relationship between RNA editing and CUB, and the findings shed light on potential research directions for investigating adaptive evolution.

Multiplexed imaging mass cytometry reveals distinct tumor-immune microenvironments linked to immunotherapy responses in melanoma.

Background: Single-cell technologies have enabled extensive analysis of complex immune composition, phenotype and interactions within tumor, which is crucial in understanding the mechanisms behind cancer progression and treatment resistance. Unfortunately, knowledge on cell phenotypes and their spatial interactions has only had limited impact on the pathological stratification of patients in the clinic so far. We explore the relationship between different tumor environments (TMEs) and response to immunotherapy by deciphering the composition and spatial relationships of different cell types. Methods: Here we used imaging mass cytometry to simultaneously quantify 35 proteins in a spatially resolved manner on tumor tissues from 26 melanoma patients receiving anti-programmed cell death-1 (anti-PD-1) therapy. Using unsupervised clustering, we profiled 662,266 single cells to identify lymphocytes, myeloid derived monocytes, stromal and tumor cells, and characterized TME of different melanomas. Results: Combined single-cell and spatial analysis reveals highly dynamic TMEs that are characterized with variable tumor and immune cell phenotypes and their spatial organizations in melanomas, and many of these multicellular features are associated with response to anti-PD-1 therapy. We further identify six distinct TME archetypes based on their multicellular compositions, and find that patients with different TME archetypes responded differently to anti-PD-1 therapy. Finally, we find that classifying patients based on the gene expression signature derived from TME archetypes predicts anti-PD-1 therapy response across multiple validation cohorts. Conclusions: Our results demonstrate the utility of multiplex proteomic imaging technologies in studying complex molecular events in a spatially resolved manner for the development of new strategies for patient stratification and treatment outcome prediction.

Influencing factors and mechanism of high-speed railway passenger overall comfort: Insights from source functional brain network and subjective report.

Overall comfort is the priority for the high-speed railway (HSR) passengers, while its influencing factors and mechanism are not yet apparent. According to the source functional brain network and subjective report, this study revealed the potential influencing factors and mechanisms of passengers overall comfort in high-speed railway environments. Here, an ergonomics field test with 20 subjects was conducted where subjective reports and electroencephalography (EEG) were collected. The electric-source imaging and functional connectivity were used to build the source functional brain network from EEG and network indices were extracted. Statistics analysis results showed that static comfort played the most critical role in the overall comfort, followed by emotional valence, emotional arousal, aural pressure comfort, vibration comfort, and noise comfort. Thermal and visual comfort were insignificant due to the well-designed heating, ventilation, and air conditioning (HVAC) and lighting system of HSR. In addition, the source functional brain network of passengers who felt uncomfortable had the higher clustering coefficient, assortativity coefficient and global efficiency, which meant greater activation of brain compared with passengers who were in a state of comfort. According to the local attributes indices analysis, most key brain regions were located in the frontal and hippocampus, which revealed emotion and spatial perception contribute to the whole comfort degradation process. This work proposed novel insights into HSR passengers overall comfort according to subjective and objective methods. Our findings demonstrate emotional regulation and seat improvements are key factors for future improvement of HSR passengers overall comfort.

Insight into Thermodynamic and Kinetic Profiles in Small-Molecule Optimization.

Structure-activity relationships (SARs) and structure-property relationships (SPRs) have been considered the most important factors during the drug optimization process. For medicinal chemists, improvements in the potencies and druglike properties of small molecules are regarded as their major goals. Among them, the binding affinity and selectivity of small molecules on their targets are the most important indicators. In recent years, there has been growing interest in using thermodynamic and kinetic profiles to analyze ligand-receptor interactions, which could provide not only binding affinities but also detailed binding parameters for small-molecule optimization. In this perspective, we are trying to provide an insight into thermodynamic and kinetic profiles in small-molecule optimization. Through a highlight of strategies on the small-molecule optimization with specific cases, we aim to put forward the importance of structure-thermodynamic relationships (STRs) and structure-kinetic relationships (SKRs), which could provide more guidance to find safe and effective small-molecule drugs.