Differential Patterns Research Articles

Differential Expression Analyses on Human Aortic Tissue Reveal Novel Genes and Pathways Associated With Abdominal Aortic Aneurysm Onset and Progression.

Abdominal aortic aneurysms (AAAs) are focal dilatations of the abdominal aorta that expand progressively, increasing their risk of rupture. Rupture of an AAA is associated with high mortality rates, but the mechanisms underlying the initiation, expansion, and rupture of AAAs are not yet fully understood. We aimed to characterize the pathophysiology of AAAs and identify new genes associated with AAA initiation and progression. This study used RNA sequencing data on 140 samples, becoming the largest RNA sequencing data set for differential expression studies of AAAs. We performed differential expression analyses and analyses of differential splicing between dilated and nondilated aortic tissue samples, and between AAAs of different diameters. We identified 3002 differentially expressed genes between AAAs and controls that were independent of ischemic time, 1425 of which were new. Additionally, 8 genes (EXTL3, ZFR, DUSP8, DISP1, USP33, VPS37C, ZNF784, RFX1) were differentially expressed between AAAs of varying diameters and between AAAs and control samples. Finally, 7 genes (SPP1, FHL1, GNAS, MORF4L2, HMGN1, ARL1, RNASE4) with differential splicing patterns were also differentially expressed genes between AAAs and controls, suggesting that splicing differences in these genes may contribute to the observed expression changes and disease development. This study identifies new genes and splicing patterns associated with AAAs and validates previous relevant pathways on AAAs. These findings contribute to the understanding of the complex mechanisms underlying AAAs and may provide potential targets to limit AAA progression and mortality risk.

Clinicopathological significance of SOX2 and FOXG1 expression patterns in ovarian immature teratomas

Objective: To investigate the relationship between the expression patterns of SOX2 and FOXG1 and the differentiation/development level of neural components in immature teratoma and to determine the clinical significance and potential application of this correlation in a clinical setting. Methods: We conducted a comprehensive whole transcriptome sequencing analysis to identify differentially expressed genes (DEGs) across various subtypes of ovarian germ cell tumors. Additionally, immunohistochemical staining of paraffin-embedded tissue sections was employed to assess the nuclear staining pattern of SOX2 and FOXG1 proteins within the tumor tissues. Results: The transcriptome sequencing data showed that transcription factors SOX2 and FOXG1 exhibited high levels of expression typically in immature teratoma and occupied a pivotal position within the protein-protein interaction network. Immunohistochemical staining revealed the absence of both SOX2 and FOXG1 protein expression in dysgerminoma and yolk sac tumor samples. In immature teratoma, immunohistochemical staining demonstrated diffuse expression of SOX2 and FOXG1 proteins within the inner layer of densely-arranged primitive neuroepithelial tubules. This pattern of expression suggested the presence of stem cell-like properties within these tumor cells. In the sparsely peripheral neurogliocytes, FOXG1 maintained a diffuse nuclear staining pattern resembling that of neuroepithelial cells, while SOX2 exhibited a scattered pattern of positive staining, hinting at a neural lineage differentiation potential. This spatial differential expression pattern of SOX2 and FOXG1 proteins in immature teratoma suggested that primitive neural components within these tumors often recapitulated the trajectory of neural formation and cortical development that was typically observed during embryogenesis. The primitive neural tube acted as the center that constantly moved from inside to outside, with a dynamic shift from the interior to the exterior, paralleled by the sequential differentiation of cell lineages from primitive neuroepithelial stem cells to radial glia, intermediate progenitor cells, and ultimately to precursor glia. Conclusions: This spatial expression pattern of SOX2 and FOXG1 proteins observed in immature teratoma mirrors the lineage differentiation and migration trajectories of primitive neuroepithelial components typically seen in embryonic neurogenesis and cortical development. In daily practice, the combined application of SOX2 and FOXG1 SOX2 and FOXG1 helps identify the primitive neuroepithelial components in immature teratoma, avoid misjudgment of similar morphologies, and thereby assist in the histological grading and clinical decision-making.

Exploring the Biological Effects of Polystyrene Nanoplastics on Spermatogenesis: Insights From Transcriptomic Analysis in Mouse Spermatocytes.

The presence of polystyrene plastics in the human testis has raised concerns, yet their biological activity remains poorly characterized. This study aimed to investigate the biological effects and potential regulatory genes of polystyrene nanoplastics on spermatocyte line, GC-2spd(ts). After a 24-h exposure to polystyrene nanoplastics, the results indicated cell membrane disruption, impairment of mitochondrial membrane potential, increased levels of reactive oxygen species (ROS), and induced DNA damage. Furthermore, a comprehensive transcriptomic analysis was conducted, revealing differential gene expression patterns in GC-2spd(ts) cells in response to polystyrene nanoplastics. A total of 134 differentially expressed genes (DEGs) were identified, with 48 genes upregulated and 86 genes downregulated. The Gene Ontology analysis highlighted the involvement of these genes in various spermatogenesis-related biological processes, including acrosome reaction, sperm mitochondrial organization, sperm annulus, and outer acrosomal membrane. Subsequently, the quantification of gene expression through qRT-PCR identified five key genes (NSUN7, SEPTIN4, TRIM36, EQTN, and SYT8) screened from the DEGs. In conclusion, this study provides valuable insights into the biological effects of polystyrene nanoplastics on mouse spermatocytes using comprehensive transcriptomic analysis, contributing to the establishment of a foundation for future investigations into these relevant pathways.

Study on Spatial Differentiation Characteristics and Driving Mechanism of Sustainable Utilization of Cultivated Land in Tarim River Basin

The sustainable utilization of cultivated land is a crucial prerequisite for ensuring food security and achieving sustainable socioeconomic development. This study employed a dataset to evaluate sustainable land use and utilized a combination of multi-factor comprehensive evaluation models, structural equation modeling, geographically weighted regression, and Pearson correlation analysis to systematically investigate the overall level, spatial differentiation characteristics, and driving mechanisms of sustainable cultivated land utilization in the Tarim River Basin. Additionally, we compared and tested three spatial interpolation methods using high-resolution data to address the modifiable areal unit problem (MAUP) and enhance the quality of spatial predictions for cultivated land utilization, ultimately identifying inverse distance weighting (IDW) as the optimal method. The results indicate the following: (1) The level of sustainable cultivated land utilization is moderately high, with an average index of 0.581, exhibiting a “U-shaped” trend from the upper to lower reaches of the Tarim River Basin. The highest levels are found in the Kashgar River–Yarkant River Basin, followed by the Hotan River Basin and the Kaidu–Peacock River Basin, while the mainstream area has the lowest levels. (2) The relationships among various cultivated land environmental systems and sustainability demonstrate distinct response characteristics and spatial differentiation patterns. Cultivated land use and management exert the most significant influence on sustainability, followed by soil quality and water resource systems, with climatic factors having the least impact. The effects of each system reveal inverted “U”, inverted “N”, “U”, and “W” patterns from the lower reaches to the upper reaches, respectively. (3) As the complexity of interactions and integrative mechanisms within the regional cultivated land system increases, the sensitivity and vulnerability of the system also rise, resulting in lower levels of sustainable utilization. (4) Based on the current challenges facing the cultivated land environmental system and the primary mechanisms influencing its sustainability, we propose regulatory measures focused on “suitable consolidation”, “suitable resting”, and “suitable planting”. These findings provide valuable insights for formulating differentiated land protection strategies, policies, and spatial planning initiatives.

Influence of differential source patterns in the detection of signals of disproportionate reporting for PARP inhibitors

IntroductionCurrent individual case safety report (ICSR) databases contain almost 56 million unique spontaneous declarations of drug-event associations by health professionals but also by patients themselves. These databases have become a useful source for detecting signals of disproportionate reporting (SDR). However, since health professionals use a medical jargon that is often distant from the more colloquial terms used by patients, they usually report more frequently certain adverse events than patients and vice versa. The main objective of this work is to illustrate the existence of different reporting patterns among drugs within a class and to analyze their potential impact on SDR detection.MethodsFour ICSR databases were considered, namely, FAERS, VAERS, JADER, and VigiBase, with reports up until March 2024. They were all integrated in a single database following a careful deduplication and COVID-19 correction protocol. Measures of reporting odds ratio, proportional reporting ratio and empirical Bayesian geometric mean were used to evaluate disproportionate reporting.ResultsThe reporting patterns of four marketed oncology drugs, namely, olaparib, rucaparib, niraparib, and talazoparib, and an investigational drug, veliparib, were compared to those of a diverse set of eight clinically observed SDR, namely, fatigue, asthenia, anaemia, thrombocytopenia, neutropenia, insomnia, intestinal obstruction, and pneumonitis. The source pattern analysis revealed that olaparib and talazoparib are most frequently reported by physicians, and physicians are the main reporters of events such as neutropenia and pneumonitis, predisposing these events to be detected as SDR for those PARP inhibitors. In contrast, rucaparib and niraparib are most frequently reported by American consumers, and American consumers are the main reporters of events such as insomnia and intestinal obstruction, facilitating their detection as SDR for those two drugs. SDR detection was found to be robust to ICSR data completeness.DiscussionMatched reporting patterns between drugs and events may predispose certain drugs to be disproportionally associated with adverse events. Therefore, SDR detected from matched drug-event source patterns in ICSR databases should be challenged during signal validation. Class SDR for drugs with differential source patterns (such as fatigue, asthenia, anaemia, thrombocytopenia, and neutropenia for all PARP inhibitors) usually involve correcting opposite drug-event source patterns.

Human liver organoids are susceptible to Plasmodium vivax infection

BackgroundThe eradication of Plasmodium vivax malaria is complicated due to the presence of hypnozoites, the hidden dormant form of the parasite that is present in the liver. Currently available drug regimens are effective at killing hypnozoites but cause side effects and are difficult to administer. Studies testing drugs for liver-stage malaria remain rare and mainly rely on the use of cancerous or immortalized hepatic cells and primary hepatocytes.MethodsOrganoids were used as platform to model liver-stage vivax malaria. Hepatic endoderm cells, endothelial progenitor cells and mesenchymal cells were generated from human induced pluripotent stem cells and self-assembled into liver organoids on top of Matrigel layer. Liver characteristic and maturity were examined through genes and proteins expression of liver markers, and liver functional tests before infected with Plasmodium vivax sporozoites. The infection was then verified by the detection of parasitophorous vacuole membrane proteins, Upregulated in Infectious Sporozoite 4 (UIS4), and blood-stage infection following co-culture with human reticulocytes.ResultsGenerated liver organoids showed upregulation of liver specific transcripts including hepatic nuclear factor 4A (HNF4A), alpha-fetoprotein (AFP), and albumin (ALB) which also confirmed by the protein expression. Furthermore, those organoids resembled mature hepatocytes in terms of albumin secretion, fat and glycogen storage and cytochrome activity. Following invasion of P. vivax sporozoites, PvUIS4 was detected and the hepatic merozoites could develop into ring-stage and early trophozoites in human reticulocytes. Moreover, differential expression patterns of genes involved in lipid and cholesterol synthesis were also detected.ConclusionsStem cell-derived liver organoids resemble mature liver cells in terms of liver functions and are susceptible to infection with P. vivax sporozoites, paving the way for studies on the mechanism of hypnozoite formation and testing of possible hypnozoitocidal drugs.

Prospective Evaluation of Autonomic Function and Intestinal Blood Flow in Health and Irritable Bowel Syndrome Shows Differences Limited to Patients With Constipation Predominance.

Autonomic dysfunction may contribute to symptom generation in irritable bowel syndrome (IBS), possibly driven by psychological morbidity and activation of the hypothalamic-pituitary-adrenal axis. Previous data are conflicting, perhaps due to lack of accounting for differential bowel patterns in IBS (constipation vs. diarrhea) or by diverse methodologies used to measure autonomic function. Our aim was to determine if autonomic response differed between IBS subtypes and healthy controls. Forty female volunteers (20 IBS and 20 healthy) underwent comprehensive autonomic testing, fasting and postprandially, and in response to cold pressor and deep breathing challenges. Pulse transit time (PTT) and ultrasound measurements of intestinal blood flow were used as measures of systemic and local autonomic function, respectively. Outcomes were adjusted for baseline psychological comorbidities and gastric emptying (measured concurrently with scintigraphy). Findings, confined to IBS patients with predominant constipation (IBS-C), included (1) lower fasting and a trend to larger postprandial increase in superior mesenteric artery end-diastolic velocity; (2) lower fasting PTT, suggesting higher sympathetic tone, but no difference in postprandial PTT change; and (3) attenuated increase in postprandial aortic peak systolic velocity. Response to systemic autonomic challenges did not differ between IBS and health. Some psychological factors mediated differences between groups in the fasting, but not postprandial, state. IBS-C patients display systemic and local autonomic imbalance providing some support for recent therapies aimed at modulating autonomic state specifically in this patient group (e.g., acustimulation).

An adaptive learning method for long-term gesture recognition based on surface electromyography.

The surface electromyography (EMG) signal reflects the user's intended actions and has become the important signal source for human-computer interaction. However, classification models trained on EMG signals from the same day cannot be applied for different days due to the time-varying characteristics of the EMG signal and the influence of electrodes shift caused by device wearing for different days, which hinders the application of commercial prosthetics. This type of gesture recogni-tion for different days is usually referred to as long-term gesture recognition.
Approach. To address this issue, we propose a long-term gesture recognition method by optimizing feature extraction, dimensionality reduction, and classification model calibration in EMG signal recognition. Our method extracts differential common spa-tial patterns (CSP) features and then conduct dimensionality reduction with non-negative matrix factorization (NMF), effectively reducing the influence of the non-stationarity of the EMG signals. Based on clustering and classification self-training(CCST) scheme, we select samples with high confidence from unlabeled sam-ples to adaptively updates the model before daily formal use. 
Main results. We verify the feasibility of our method on a dataset consisting of 30 days of gesture data. The proposed gesture recognition scheme achieves accuracy over 90%, similar to the performance of daily calibration with labeled data. However, our method needs only one repetition of unlabeled gestures samples to update the classifi-cation model before daily formal use. 
Significance. From the results we can conclude that the proposed method can not only ensure superior performance, but also greatly facilitate the daily use, which is especially suitable for long-term application.&#xD.

Genome-wide DNA methylation analysis reveals a unique methylation pattern for pleural mesothelioma compared to healthy pleura and other lung diseases

BackgroundPleural mesothelioma (PM) is a rare and aggressive cancer type, typically diagnosed at advanced stages. Distinguishing PM from other lung diseases is often challenging. There is an urgent need for biomarkers that can enable early detection. Interest in the field of epigenetics has increased, particularly in the context of tumour development and biomarker discovery. This study aims to identify specific changes in DNA methylation from healthy pleural tissue to PM and to compare these methylation patterns with those found in other lung diseases.ResultsEPIC methylation array data (850 K) were generated for 11 PM and 29 healthy pleura in-house collected samples. This is the first time such a large dataset of healthy pleura samples has been generated. Additional EPIC methylation array data (850 K) for pleural mesothelioma and other lung-related diseases were downloaded from public databases. We conducted pairwise differential methylation analyses across all tissue types, which facilitated the identification of significantly differentially methylated CpG sites. Extensive differential methylation between PM and healthy pleura was observed, identifying 81,968 differentially methylated CpG sites across all genomic regions. Among these, five CpG sites located within four genes (MIR21, RNF39, SPEN and C1orf101) exhibited the most significant and pronounced methylation differences between PM and healthy pleura. Moreover, our analysis delineated distinct methylation patterns specific to PM subtypes. Finally, the methylation profiles of PM were distinctly different from those of other lung cancers, enabling accurate differentiation.ConclusionsDNA methylation analyses provide a robust method for distinguishing PM from healthy pleural tissues, and specific methylation patterns exist within PM subtypes. These methylation differences underscore their importance in understanding disease progression and may serve as viable biomarkers or therapeutic targets. Moreover, differential methylation patterns between PM and other lung cancers highlights its diagnostic potential. These findings necessitate further translational studies to explore their clinical applications.

FST and genetic diversity in an island model with background selection

Background selection, by which selection on deleterious alleles reduces diversity at linked neutral sites, influences patterns of total neutral diversity, πT, and genetic differentiation, FST, in structured populations. The theory of background selection may be split into two regimes: the background selection regime, where selection pressures are strong and mutation rates are sufficiently low such that deleterious alleles are at a deterministic mutation-selection balance, and the interference selection regime, where selection pressures are weak and mutation rates are sufficiently high that deleterious alleles accumulate and interfere with another, leading to selective interference. Previous work has quantified the effects of background selection on πT and FST only for deleterious alleles in the background selection regime. Furthermore, there is evidence to suggest that migration reduces the effects of background selection on FST, but this has not been fully explained. Here, we derive novel theory to predict the effects of migration on background selection experienced by a subpopulation and extend previous theory from the interference selection regime to make predictions in an island model. Using simulations, we show that this theory best predicts FST and πT. Moreover, we demonstrate that background selection may generate minimal increases in FST under sufficiently high migration rates, because migration reduces correlated effects on fitness over generations within subpopulations. However, we show that background selection may still cause substantial reductions in πT, particularly for metapopulations with a larger effective population size. Our work further extends the theory of background selection into structured populations, and suggests that background selection will minimally confound locus-to-locus FST scans.

Approximating the semantic space: word embedding techniques in psychiatric speech analysis

Large language models provide high-dimensional representations (embeddings) of word meaning, which allow quantifying changes in the geometry of the semantic space in mental disorders. A pattern of a more condensed (‘shrinking’) semantic space marked by an increase in mean semantic similarity between words has been recently documented in psychosis across several languages. We aimed to explore this pattern further in picture descriptions provided by a transdiagnostic German sample of patients with schizophrenia spectrum disorders (SSD) (n = 42), major depression (MDD, n = 43), and healthy controls (n = 44). Compared to controls, both clinical groups showed more restricted dynamic navigational patterns as captured by the time series of semantic distances crossed, while also showing differential patterns in the total distances and trajectories navigated. These findings demonstrate alterations centred on the dynamics of the flow of meaning across the semantic space in SSD and MDD, preserving previous indications towards a shrinking semantic space in both cases.

Electroencephalographic power ratio and peak frequency difference associate with central sensitization in chronic pain.

Central sensitization, or increased responsiveness of the central nervous system to sensory input, is present in many chronic pain patients. Clinically, it is detected through subjective, patient-reported measures. There is a need for reliable, direct measurements of neural response to controlled stimuli to quantify neuronal dysfunction in pain. The goal of this work is to investigate cortical activity, recorded via electroencephalogram (EEG), during objective and calibrated painful stimulation in chronic pain patients.&#xD;Approach. Chronic pain patients (N=8) and healthy controls (N=8) participated in this study. We recorded electroencephalography (EEG) at rest (baseline) and during evoked pain tasks, including thermal and mechanical stimuli. The evoked pain was applied following the quantitative sensory testing (QST) protocol, which is a research technique that applies objective, calibrated painful stimuli. &#xD;Main results. Peak alpha frequency at rest was significantly lower in chronic pain patients compared to healthy controls (p<0.0002), while EEG alpha/theta and alpha/beta power ratios at rest were higher in patients (p<0.0002). During thermal QST, these power ratios decreased in patients and increased in controls (p<0.0002 for both). During mechanical QST, power ratios decreased or did not change. Furthermore, the peak theta-beta frequency difference at baseline was significantly lower in patients compared to controls (p<0.0002). During thermal QST, this difference increased in patients and decreased in controls; during mechanical QST, this difference increased in both patients and controls (p<0.0002). Functional connectivity analysis showed that controls had greater baseline theta connectivity strength that increased during mechanical QST (p<0.0002).&#xD;Significance. This work demonstrates differential patterns of EEG activity at rest and during acute painful stimulation in chronic pain patients compared to healthy controls. These measures may quantify an individual's tendency to experience chronic pain and central sensitization and serve as diagnostic biomarkers.

Uncovering Genetic Signatures of the Walser Migration in the Alps: Patterns of Diversity and Differentiation

Uncovering Genetic Signatures of the Walser Migration in the Alps: Patterns of Diversity and Differentiation

Crosstalk Between Cancer-associated Fibroblasts and Myeloid Cells Shapes the Heterogeneous Microenvironment of Gastric Cancer.

Targeted therapies have improved the clinical outcomes of most patients with cancer. However, the heterogeneity of gastric cancer remains a major hurdle for precision treatment. Further investigations into tumor microenvironment heterogeneity are required to resolve these problems. In this study, bioinformatic analyses, including metabolism analysis, pathway enrichment, differentiation trajectory inference, regulatory network construction, and survival analysis, were applied to gain a comprehensive understanding of tumor microenvironment biology within gastric cancer using single-cell RNA-seq and public datasets and experiments were carried out to confirm the conclusions of these analyses. We profiled heterogeneous single-cell atlases and identified eight cell populations with differential expression patterns. We identified two cancer-associated fibroblasts (CAFs) subtypes, with particular emphasis on the role of inflammatory cancer-associated fibroblasts (iCAFs) in EMT and lipid metabolic crosstalk within the tumor microenvironment. Notably, we detected two differentiation states of iCAFs that existed in different tissues with discrepant expression of genes involved in immuno-inflammation or ECM remodeling. Moreover, investigation of tumor-infiltrating myeloid cells has revealed the functional diversity of myeloid cell lineages in gastric cancer. Of which a proliferative cell lineage named C1QC+MKI67+TAMs was recognized with high immunosuppressive capacities, suggesting it has immune suppression and cell proliferation functions in the tumor niche. Finally, we explored regulatory networks based on ligand-receptor pairs and found crucial pro-tumor crosstalk between CAFs and myeloid cells in the tumor microenvironment (TME). These findings provide insights for future cancer treatments and drug discovery.

Full-length transcriptome reveals alternative splicing regulation pattern of skin color variant in red tilapia (Oreochromis spp.)

The hybrid species red tilapia (Oreochromis spp.) is favored in aquaculture for its bright color, rapid growth, and high market value. However, color variation hinders market development, which is influenced by both genetic and environmental factors. We aim to identify candidate genes and pathways related to pigmentation, uncovering the molecular basis of these color variations in red tilapia by employing third-generation full-length transcriptome sequencing combined with second-generation transcriptome analysis. Our analysis focused on three distinct phenotypic classes: whole pink, pink with black blotch, and whole black. Pigment cell and pigment composition analysis highlighted that the pigment pattern in red tilapia is primarily determined by the distribution and interaction of various pigment cells, including melanophores, xanthophores, erythrophores, and iridophores. The whole pink individuals were characterized by an absence of melanophores and a high concentration of carotenoids, while the whole black individuals exhibited active melanogenesis. Transcriptomic data indicated that genes associated with melanin synthesis (wnt, fzd7, lef, tcf7, tyrp1, oca2, pmel, bmp2, cbs) were up-regulated in whole black individuals, while genes related to carotenoid uptake and deposition (scarb1, ldlr, ttc39b, stard5, stard10, plin2, fitm2, bscl2), as well as pteridine synthesis (gch1, ptps), were more actively expressed in whole pink individuals. Retinol metabolism was identified as a mediator of the interaction between melanin synthesis and carotenoid deposition. Further, alternative splicing (AS) act as a crucial post-transcriptional mechanism regulating body coloration, beyond transcriptional differences. Analysis of AS events identifies multiple splice variants of pigment-related genes (scarb1, pax7, ctnnb1, rxrb, bscl2, gjb10, bmp4, frzb) that exhibit differential expression and splicing patterns across different color phenotypes. Notably, AS events of the scarb1 gene, related to carotenoid deposition, and the polr2d gene, associated with the transcription machinery, may significantly influence pigment deposition patterns in red tilapia. Our work not only deepens the genetic understanding of pigmentation in red tilapia but also establishes a solid foundation for improving color stability through selective breeding and genetic improvement programs across various hybrid species in aquaculture, which is crucial for marketability and consumer attraction.

Interparental and Parent-Teen Relationships during Adolescence as Predictors of Intra- and Interpersonal Emotion Regulation in Young Adulthood.

Parents' contributions to their children's emotion regulation during adolescence has been a relatively understudied interpersonal context of development, even though parents' roles as sources of social and emotional learning persist from childhood into adolescence and the complexity of teens' lives grows during this time. This study aims to investigate the differential predictive utility of qualities and behaviors in interparental and parent-teen relationships during adolescence for predicting youths' development of intra- and interpersonal emotion regulation over a 13-year period. To assess these hypotheses, data were obtained from a longitudinal, multi-method, multi-informant study of 184 adolescents (107 Caucasian, 53 African American, and 24 mixed/other ethnicity; median family income of USD 40,000-60,000/year in 1999, equivalent to about USD 75,000-112,000/year when accounting for inflation) and their parents. The results provide support for a differential pattern of prediction; qualities of interparental relationships in early adolescence were significant predictors of young adult interpersonal emotion regulation, whereas behaviors in interparental and parent-teen relationships in late adolescence were significant predictors of both young adult positive intra- and interpersonal emotion regulation. Notably, some father-reported relationship predictors during late adolescence had unexpected relations with later intrapersonal emotion regulation. The results are discussed in terms of the helpfulness of these specific relationship factors during each part of adolescence for supporting positive intra- and interpersonal emotional regulation development.

Study on the protective mechanism of Xuemaitong Capsule against acute myocardial ischemia rat based on network pharmacology and metabolomics

BackgroundXuemaitong Capsule (XMT) is a widely recognized traditional Miao medicine extensively utilized in Chinese clinical settings. Previous studies have demonstrated XMT protective effects against acute myocardial ischemia (AMI). However, the mechanism by which XMT provides protection to AMI rats is yet to be fully understood. Aim of the studyThe purpose of this study was to investigate the protective mechanism of XMT on AMI rats through network pharmacology, traditional pharmacodynamics and metabolomics. Material and methodsThe components and potential targets of XMT were identified through the application of traditional Chinese medicine system pharmacology and traditional Chinese medicine molecular mechanism bioinformatics analysis tools. We constructed herb-composition-target networks and analyzed protein–protein interaction (PPI) networks. The potential mechanism was explored by pathway enrichment analysis. Subsequently, the AMI model was constructed by ligation of the anterior descending branch of the left coronary artery, and XMT protective effects on AMI rats were evaluated by analyzing the myocardial enzyme profiles, electrocardiograms(ECG), Triphenyltetrazolium chloride(TTC) staining, and Hematoxylin-Eosin (HE) staining in AMI rats. Metabolomics based on UHPLC-Q-Exactive Orbitrap MS was used to observe the protective effect of XMT on the serum metabolic profile of AMI, and multivariate statistical analysis further revealed the differential patterns of metabolites after XMT treatment. Finally, integrated pathway analysis was carried out to reveal the biological metabolic mechanism. ResultsA total of 392 active components of XMT acted with 624 targets for treating AMI. Pathway enrichment analysis revealed that XMT could treat AMI through TNF, MAPK and PI3K-Akt signaling pathways. Further, XMT could effectively prevent ST-segment elevation in the ECG, reduce the size of myocardial infarction, decrease cardiac weight index and cardiac enzyme levels, and mitigate histological damage in the hearts of AMI rats. In addition, XMT callback 117 metabolites and four metabolic pathways, including taurine and hypotaurine metabolism, phenylalanine metabolism, pyrimidine metabolism and retinol metabolism. Through integrating network pharmacology and metabolomics, we explored the biological mechanism by which XMT treats AMI. It was speculated that the mechanism of XMT is to regulate TNF signaling, PI3K-Akt pathway and MAPK signaling pathway, and participate in cell apoptosis, oxidative stress, immune and inflammatory reaction and other biological processes. ConclusionXMT plays a protective role in AMI rats by regulating multiple metabolic biomarkers, multiple targets and pathways. Therefore, XMT may provide a potential strategy for the treatment of AMI.

Genome-Wide Identification, Classification, Expression Analysis, and Screening of Drought and Heat Resistance-Related Candidates of the Rboh Gene Family in Wheat

Plant respiratory burst oxidase homologs (Rbohs) are key enzymes that produce reactive oxygen species (ROS), which serve as signaling molecules regulating plant growth and stress responses. In this study, 39 TaRboh genes (TaRboh01–TaRboh39) were identified. These genes were distributed unevenly among the wheat genome’s fourteen chromosomes, with the exception of homoeologous group 2 and 7 and chromosomes 4A, as well as one unidentified linkage group (Un). TaRbohs were classified into ten distinct clades, each sharing similar motif compositions and gene structures. The promoter regions of TaRbohs contained cis-elements related to hormones, growth and development, and stresses. Furthermore, five TaRboh genes (TaRboh26, TaRboh27, TaRboh31, TaRboh32, and TaRboh34) exhibited strong evolutionary conservation. Additionally, a Ka/Ks analysis confirmed that purifying selection was the predominant force driving the evolution of these genes. Expression profiling and qPCR results further indicated differential expression patterns of TaRboh genes between heat and drought stresses. TaRboh11, TaRboh20, TaRboh22, TaRboh24, TaRboh29, and TaRboh34 were significantly upregulated under multiple stress conditions, whereas TaRboh30 was only elevated in response to drought stress. Collectively, our findings provide a systematic analysis of the wheat Rboh gene family and establish a theoretical framework for our future research on the role of Rboh genes in response to heat and drought stress.

Genome-Wide Identification of FCS-Like Zinc Finger (FLZ) Family Genes in Three Brassica Plant Species and Functional Characterization of BolFLZs in Chinese Kale Under Abiotic Stresses

FCS-like zinc finger (FLZ) proteins are plant-specific regulatory proteins, which contain a highly conserved FLZ domain, and they play critical roles in plant growth and stress responses. Although the FLZ family has been systematically characterized in certain plants, it remains underexplored in Brassica species, which are vital sources of vegetables, edible oils, and condiments for human consumption and are highly sensitive to various abiotic stresses. Following the whole-genome triplication events (WGT) in Brassica, elucidating how the FLZ genes have expanded, differentiated, and responded to abiotic stresses is valuable for uncovering the genetic basis and functionality of these genes. In this study, we identified a total of 113 FLZ genes from three diploid Brassica species and classified them into four groups on the basis of their amino acid sequences. Additionally, we identified 109 collinear gene pairs across these Brassica species, which are dispersed among different chromosomes, suggesting that whole-genome duplication (WGD) has significantly contributed to the expansion of the FLZ family. Subcellular localization revealed that six representative BolFLZ proteins are located in the nucleus and cytoplasm. Yeast two-hybrid assays revealed that 13 selected BolFLZs interact with BolSnRK1α1 and BolSnRK1α2, confirming the conservation of the SnRK1α-FLZ module in Brassica species. Expression profile analysis revealed differential expression patterns of BolFLZ across various tissues. Notably, the expression levels of seven BolFLZ genes out of the fifteen genes analyzed changed significantly following treatment with various abiotic stressors, indicating that the BolFLZ genes play distinct physiological roles and respond uniquely to abiotic stresses in Brassica species. Together, our results provide a comprehensive overview of the FLZ gene family in Brassica species and insights into their potential applications for enhancing stress tolerance and growth in Chinese kale.

Transcriptome Analysis Reveals the lncRNA-mRNA Co-expression Network Regulating the Aestivation of Sea Cucumber.

LncRNAs are long non-coding RNAs that are widely recognized as crucial regulators of gene expression and metabolic control, involved in numerous dormancy-related processes. Aestivation is a common hypometabolism strategy of sea cucumber (Apostichopus japonicus) in response to high-temperature conditions and is typically characterized by the degradation of the intestine and respiratory tree. Although the aestivation process has been extensively studied in sea cucumbers, the role of lncRNAs in the context of aestivation states remains a conspicuous knowledge gap. Here, we identified and characterized 14,711 lncRNAs in A. japonicus and analyzed their differential expression patterns during the aestivation process in the intestine and respiratory tree. The results revealed the physiological differences, especially the metabolic processes, between the intestine and respiratory tree during the aestivation. The co-expression network of lncRNA-mRNA suggested the dominant role of lncRNA in regulating the differential response of the intestine and respiratory trees. Differentially co-expressed factors were significantly enriched in the deep-aestivation stage-specific modules. Conserved co-expressed factors included several transcription factors known to be involved in rhythm regulation, such as Klf2 and Egr1. Furthermore, a specific trans-acting lncRNA (lncrna.1393.1) was identified as a potential regulator of Klf2 and Egr1. Overall, the systematic identification, characterization, and expression analysis of lncRNAs in A. japonicus enhanced our knowledge of long non-coding regulation of aestivation in sea cucumber and provided new clues for understanding the common "toolkit" of dormancy regulatory mechanisms.