Since the Fourth edition of the WHO classification, PPGLs have been recognized for their metastatic potential, though no clear features can accurately predict this behavior. The prognostic value of Ki-67 in assessing the risk of progression, relapse, or metastasis in PPGLs remains debated.

This cohort study included 501 patients diagnosed with PPGLs at the First Hospital of Jilin University between 2000 and 2022, with clinical data, treatment details, pathological indicators, and germline gene test results collected. Bulk sequencing was performed on formalin-fixed paraffin-embedded (FFPE) primary tumor samples from 87 patients. Progression-free survival (PFS) was analyzed using multivariable Cox regression.

Among the 119 enrolled patients with PPGLs, the average age was 45.7 ± 14.0 years, and the median follow-up time was 46 months. A significant finding was the high expression of CDK1, a gene known to be significantly associated with the metastatic risk of PPGLs, in samples with Ki-67 ≥ 3% (p < 0.0001). More importantly, patients with PPGLs and a Ki-67 level ≥ 3% had a 3.59-fold higher risk of progression, relapse or metastasis compared to those with Ki-67 < 3% (HR = 4.59, 95% CI: 1.06-11.95), after adjusting for all confounding factors. In the composite model, the addition of Ki-67 enhanced the predictive ability of the combined model of SDHB, primary site, tumor size, and invade neighboring tissue (AUC = 0.888, 95% CI: 0.808-0.967 vs. AUC = 0.874, 95% CI: 0.783-0.965).

A Ki-67 level ≥ 3% is associated with an increased risk of progression, relapse or metastasis in patients with PPGLs.

JOURNAL/nrgr/04.03/01300535-202507000-00024/figure1/v/2024-09-09T124005Z/r/image-tiff Differentiation of oligodendrocyte progenitor cells into mature myelin-forming oligodendrocytes contributes to remyelination. Failure of remyelination due to oligodendrocyte progenitor cell death can result in severe nerve damage. Ferroptosis is an iron-dependent form of regulated cell death caused by membrane rupture induced by lipid peroxidation, and plays an important role in the pathological process of ischemic stroke. However, there are few studies on oligodendrocyte progenitor cell ferroptosis. We analyzed transcriptome sequencing data from GEO databases and identified a role of ferroptosis in oligodendrocyte progenitor cell death and myelin injury after cerebral ischemia. Bioinformatics analysis suggested that perilipin-2 (PLIN2) was involved in oligodendrocyte progenitor cell ferroptosis. PLIN2 is a lipid storage protein and a marker of hypoxia-sensitive lipid droplet accumulation. For further investigation, we established a mouse model of cerebral ischemia/reperfusion. We found significant myelin damage after cerebral ischemia, as well as oligodendrocyte progenitor cell death and increased lipid peroxidation levels around the infarct area. The ferroptosis inhibitor, ferrostatin-1, rescued oligodendrocyte progenitor cell death and subsequent myelin injury. We also found increased PLIN2 levels in the peri-infarct area that co-localized with oligodendrocyte progenitor cells. Plin2 knockdown rescued demyelination and improved neurological deficits. Our findings suggest that targeting PLIN2 to regulate oligodendrocyte progenitor cell ferroptosis may be a potential therapeutic strategy for rescuing myelin damage after cerebral ischemia.

Walnut (Juglans sigillata), an economically significant ecotype of the Juglans genus in the Juglandaceae family, is cultivated mainly in southwest China, a region prone to seasonal drought. Drought significantly reduced both the yield and quality of walnuts in this area. Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi that colonize plant roots and play crucial roles in enhancing plant drought resistance. This study investigated the effects of AMF on the alleviation of drought stress. Compared to non-inoculated drought-stressed plants, AMF inoculation improved plant growth, increased photosynthetic capacity, enhanced reactive oxygen species (ROS) scavenging ability, and significantly activities of superoxide Dismutase, peroxidase, and catalase were significantly increased by 19.90 %, 18.43 %, and 8.39 %, respectively. malondialdehyde, Superoxide anion, and Hydrogen peroxide levels decreased by 18.39 %, 20.75 %, and 21.44 %, respectively, and soluble sugar and proline concentrations also significantly increased (P < 0.05), helping to maintain the osmotic balance. In addition, transcriptome results showed that ATP-binding cassette transporter related to drought resistance were significantly enriched in plants inoculated with AMF, and genes related to growth, such as IAA and CKT synthesis, transcription factors (BZIP, WRKY, and GTE), and related antioxidant enzymes. The mitogen-activated protein kinases pathway-related genes were upregulated in the inoculated drought treatment group, whereas pinobanksin and homoeriodictyol were upregulated in the inoculated drought treatment group, both of which provide support for drought resistance. In summary, AMF alleviated drought stress and promoted Juglans sigillata growth by modulating key physiological, biochemical, and molecular mechanisms involved in drought resistance. This study offers important theoretical insights that support the application of AMF in sustainable agricultural practices.

The Gulf of Maine, home to American lobster, Homarus americanus, is experiencing rapid ocean warming (OW) and acidification (OA) due to climate change. While some studies have investigated the effects of either ocean acidification (OA) or warming (OW) on lobsters, few explore the interaction of these stressors, particularly on gene expression. We evaluated the effects of OA and OW on early benthic juvenile lobster transcriptomics using RNA sequencing and RT-qPCR through two distinct aquarium experiments. Lobsters were reared under OW/OA conditions aligned with values predicted for 2100: decrease in pH by 0.3-0.4 units; mean sea surface warming of 2.89 °C. RNA was isolated from carapace hypodermal tissue in both experiments. The multi-stressor treatment in the RNAseq experiment had the greatest differential expression. Genes of interest pertaining to calcification and cuticle development were primarily downregulated under high temperature but upregulated under acidified and multi-stressor conditions. In the RT-qPCR experiment, crustin alone was significantly downregulated and only under the most extreme multi-stressor treatment. This gene along with the prophenoloxidase activating enzyme had expression that trended toward downregulation across all treatments, suggesting a possible correlation to immune suppression. Expression profiles for crustin and the calcification gene, carbonic anhydrase differed across treatments based on molt cycle timing, indicating that stressor impacts may vary depending on the molt cycle phase. Elevated temperature had a greater effect on the expression of calcification and cuticle development genes, though the direction of expression reversed with multiple stressors. These results indicate the impacts of OW and OA on early benthic juvenile lobsters are complex, possibly synergistic, vary with molt cycle, and potentially interfere with normal cuticle development, which may increase susceptibility to injury or disease.

Spodoptera frugiperda is a major invasive pest that poses a serious threat to crops worldwide. Low temperature is a key factor limiting the survival and reproduction for this pest. To study the responses of S. frugiperda to low-temperature stress, high-throughput sequencing was used to perform transcriptomic analysis on the 6th instar larvae under low-temperature stress at 5 °C and 10 °C, along with 25 °C as a control. As a result, 215 differentially expressed genes (DEGs) were identified under different low-temperature stresses. Upon functional annotation of the DEGs in KEGG and GO databases, the number of DEGs annotated in control vs. LT10 comparison was the largest (n = 150), whereas fewer DEGs (n = 89) were annotated in control vs. LT5 comparison. This discrepancy suggested that S. frugiperda might adopt different strategies to cope with low-temperature stress. The DEGs in the GO database were particularly associated with cell catalytic activity, cell anatomical entity process, cell apoptosis, and cell binding channel. KEGG annotation analysis of the different low-temperature stresses showed that most of the enriched pathways were related to carbon metabolism, oxidative phosphorylation, and lipid metabolism. The results will be the basis for mastering the cold tolerant mechanism of S. frugiperda, and is of great significance for its prevention.

A significant area of computer science called artificial intelligence (AI) is successfully applied to the analysis of intricate biological data and the extraction of substantial associations from datasets for a variety of biomedical uses. AI has attracted significant interest in biomedical research due to its features: (i) better patient care through early diagnosis and detection; (ii) enhanced workflow; (iii) lowering medical errors; (v) lowering medical costs; (vi) reducing morbidity and mortality; (vii) enhancing performance; (viii) enhancing precision; and (ix) time efficiency. Quantitative metrics are crucial for evaluating AI implementations, providing insights, enabling informed decisions, and measuring the impact of AI-driven initiatives, thereby enhancing transparency, accountability, and overall impact. The implementation of AI in biomedical fields faces challenges such as ethical and privacy concerns, lack of awareness, technology unreliability, and professional liability. A brief discussion is given of the AI techniques, which include Virtual screening (VS), DL, ML, Hidden Markov models (HMMs), Neural networks (NNs), Generative models (GMs), Molecular dynamics (MD), and Structure-activity relationship (SAR) models. The study explores the application of AI in biomedical fields, highlighting its enhanced predictive accuracy, treatment efficacy, diagnostic efficiency, faster decision-making, personalised treatment strategies, and precise medical interventions.

This study seeks to explore the molecular regulatory mechanism within Dosinia corrugata in response to extreme high-temperature conditions, aiming to enhance the sustainable development of the D. corrugata aquaculture industry. To identify heat-responsive genes and elucidate adaptive mechanisms, we conducted transcriptional profiling of D. corrugata gills after 12 h and 24 h of acute heat stress. At 12 h and 24 h under acute heat stress, we detected 6842 and 1112 differentially expressed genes (DEGs), respectively. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed that co-enriched pathways at both time points included Apoptosis-multiple species, Ubiquitin-mediated proteolysis, Tumor Necrosis Factor (TNF) signaling pathway, and Retinoic acid-inducible Gene I (RIG-I)-like receptor signaling pathway in response to acute heat stress. It is noteworthy that at 12 h of acute heat stress, metabolic pathways were significantly enriched, while at 24 h, immune-related pathways showed significant enrichment. Based on the co-enrichment pathways identified at both time points during acute heat stress (12 h and 24 h), we constructed a potential regulatory network for differentially expressed genes under heat stress. This study offers valuable insights into comprehending the potential molecular regulatory mechanisms that underlie D. corrugata's response to elevated temperatures.

The field of RNA research has experienced significant changes and is now at the forefront of contemporary drug development. This narrative overview explores the scientific developments and historical turning points in RNA research, emphasising the field's critical significance in the development of novel therapeutics. Important discoveries like antisense oligonucleotides (ASOs), mRNA therapies, and RNA interference (RNAi) have created novel treatment options that can be targeted, such as the ground-breaking mRNA vaccinations against COVID-19. Advances in high-throughput sequencing, single-cell RNA sequencing, and epitranscriptomics have further unravelled the complexity of RNA biology, shedding light on the intricacies of gene regulation and cellular diversity. The integration of computational tools and bioinformatics has propelled the identification of RNA-based biomarkers and the development of RNA therapeutics. Despite significant progress, challenges such as RNA stability, delivery, and off-target effects persist, necessitating continuous innovation and ethical considerations. This review provides a critical insight into the current state and prospects of RNA research, emphasising its transformative potential in drug discovery. By examining the interplay between technological advancements and therapeutic applications, we underscore the promising horizon for RNA-based interventions in treating a myriad of diseases, marking a new era in precision medicine.

Lymantria xylina is the most important defoliator, damaging the effective coastal windbreak tree species Casuarina equisetifolia. However, the underlying genetic mechanisms through which C. equisetifolia responds to L. xylina attacks remain unknown. Here, we compared the transcriptional, phytohormone and metabolic differences between susceptible (S) and resistant (R) C. equisetifolia cultivars in response to L. xylina feeding. The main L. xylina-induced resistance in C. equisetifolia was a jasmonate (JA) response and JA synthesis was highly induced by L. xylina feeding at both the transcriptional and metabolic levels, thus promoting flavonoid accumulation. The JA response was highly activated by L. xylina feeding on the R but not in the S cultivar, although the JA signalling pathway was intact in both cultivars. We found a single amino acid mutation in the homologues of glutamate receptor-like protein 3.6 (CeGLR3.6T807I) in the S cultivar. Compared with the GLR3.6 homologues in the R cultivar, phosphorylation of CeGLR3.6T807I was not induced by insect feeding, leading to a decreased JA response in the S cultivar. Collectively, this study provides new insights into the function of CeGLR3.6 in regulating the JA response of C. equisetifolia to L. xylina feeding.

Excessive stress is a known contributor to cardiovascular diseases (CVD), and ferulic acid (FA), a natural phenolic compound, has demonstrated significant antioxidant and anti-inflammatory properties. This study investigates the protective effects of FA against stress-induced myocardial injury (SIMI) and elucidates the underlying mechanisms. An acute SIMI model was established in mice using low-temperature water immersion restraint. Cardiac function was assessed via cardiac index and histopathological analysis. Serum levels of corticosterone (CORT), lactate dehydrogenase (LDH), and brain natriuretic peptide (BNP) were quantified using enzyme-linked immunosorbent assay (ELISA), along with inflammatory markers TNF-α and IL-1β. The oxidative stress parameters, including malondialdehyde (MDA), glutathione (GSH), superoxide dismutase (SOD), and reactive oxygen species (ROS), were analyzed using colorimetric methods and fluorescent probes. Immunohistochemistry (IHC) and Western Blot were used to analyze the expression of proteins related to TNF, MAPK, PPAR-α/PGC-1α, and Nrf2 signaling pathways. Results indicated that FA pretreatment improved cardiac index, myocardial structural integrity, and reduced inflammatory cell infiltration. Serum levels of LDH, BNP, CORT, TNF-α, and IL-1β were significantly decreased in FA-treated SIMI mice. Elevated MDA and ROS levels, along with decreased GSH and SOD levels in the SIMI group, were reversed by FA pretreatment, likely through activation of the PPARα/PGC-1α and Nrf2 signaling pathways. Additionally, FA inhibited the TNF-α/TNFR1 and ERK/JNK MAPK pathways, contributing to its protective effects. In conclusion, FA mitigates SIMI by alleviating oxidative stress and inflammatory responses.

Genomic and transcriptomic sequencing technologies have revolutionized our ability to characterize prostate cancer at the molecular level. The underlying premise of next-generation sequencing technologies and their current and evolving applications in prostate cancer management are provided in the review.

Improved methodologies are allowing timely sequencing of the coding regions or both the coding and noncoding regions of the genome to help identify potential mutations and structural variations in the prostate cancer genome, some of which are currently also targetable therapeutically. DNA microarray- based differential gene expression has been supplanted by RNA sequencing (RNA-seq), which not only allows for more accurate quantitation but also nucleotide-level resolution to investigate the entire transcriptome, including alternative gene spliced transcripts and noncoding RNA transcripts, whose full clinical implications have yet to be fully understood and realized. Gene classifier platforms that predict risk of recurrence or metastasis are being incorporated into prostate cancer management algorithms. In the appropriate clinical context, not only somatic but also germline mutation testing is being recommended.

Continued clinical integration of sequencing technologies and ongoing research will lead to improved understanding of prostate cancer biology and prostate cancer treatment.

The neocortical development process includes cell proliferation, differentiation, migration, and maturation, supported by precise genetic regulation. To understand these processes at the cellular and molecular levels, it is necessary to characterize the fundamental anatomical structures by gene expression. However, markers established in the adult brain sometimes behave differently in the fetal brain, actively changing during development. The spatial transcriptome is a powerful analytical method that enables sequence analysis while retaining spatial information. However, a deeper understanding of these data requires computational estimation, including integration with single-cell transcriptome data and aggregation of spots at the single-cell cluster level. The application of such analysis to biomarker discovery has only begun recently, and its application to the developing fetal brain is largely unexplored. In this study, we performed a spatial transcriptome analysis of the developing mouse brain to investigate spatio-temporal regulation of gene expression during development. Using these data, we conducted an integrated study with publicly available mouse data sets. Our data-driven analysis identified novel molecular markers of the choroid plexus, piriform cortex, and thalamus. Furthermore, we identified a novel molecular marker that can determine the dorsal endopiriform nucleus (DEn) of the developmental stage in the claustrum/DEn complex.

In 2023, the Global Initiative for Chronic Obstructive Lung Disease (GOLD) introduced a provision regarding preserved ratio-impaired spirometry (PRISm), a presumed pre-stage of Chronic Obstructive Pulmonary Disease (COPD), into the COPD guidelines. However, further research in this area is needed. Our study aimed to investigate the epigenetic differences between PRISm and COPD. EWAS (n = 572) and RNA-sequencing (n = 60) were performed on blood samples from the COPD registry, and EWAS was replicated in the KoGES cohort data (n = 98). Our findings revealed significant epigenetic differences between patients with PRISm and COPD. 39,980 CpG-sites displayed differential methylation between PRISm and COPD. Seven gene regions-EEF1A2, EMP2, EPCAM, MTSS1L, ARHGEF10, HYDIN, and FADS2 were not only differentially methylated but also exhibited differential expression. The consistency of differential methylation of CpG sites in five genes, excluding ARHGEF10 and MTSS1L, was replicated in the KoGES study, affirming the distinction between COPD and PRISm. Our research identified seven gene regions as critical contributors related to the modulation of gene expression, including CpG sites that differentiate COPD from PRISm. These results highlight the significance of DNA methylation changes in distinguishing PRISm from COPD and shed light on potential mechanisms by which methylation alterations impact lung function.

Diatoms are a crucial component of marine ecosystems, recognized for their broad environmental adaptability and wide temperature tolerance. However, the molecular mechanisms underlying their adaptability to diverse temperatures are unknown. In this study, we discover that heat shock transcription factors (HSFs) are potentially important for thermal tolerance in diatoms. Our study focuses on PtHSF2, annotated as HSF2 in Phaeodactylum tricornutum's genome, which is ubiquitous in diatoms. Overexpression of PtHSF2 markedly enhances thermal tolerance and increases cell size; causes significant differential expression of several genes, including cell division cycle protein 45-like (PtCdc45-like), ATM (ataxia telangiectasia mutated), ATR (ataxia telangiectasia and Rad3-related), light-harvesting complex protein 2 (Lhcx2), and fatty acid desaturase. Cleavage Under Targets and Tagmentation (CUT&Tag) and CUT&Tag-qPCR analyses demonstrate that PtHSF2 directly targets and upregulates PtCdc45-like and Lhcx2 while downregulating ATP-binding cassette transporter. Functional validation of PtCdc45-like shows that its overexpression results in larger cell size, enhances antioxidant capacity, and improves cell survival at elevated temperatures. Collectively, our findings elucidate the molecular mechanism by which PtHSF2 mediates high-temperature tolerance in diatoms and validate the functions of its target gene PtCdc45-like. These results highlight the importance of HSFs in diatom temperature adaptation and provide insights into temperature acclimation in microalgae.

Breast cancer is the most prevalent malignancy and the leading cause of cancer-related deaths among women worldwide. Several case reports have shown that some breast cancer patients subsequently develop acute myeloid leukemia (AML) within a short period. However, the causal relationship and pathogenic mechanisms between breast cancer and AML remain incompletely understood.

Mendelian randomization (MR) analyses were conducted to explore the bidirectional causal relationships between breast cancer and AML. Additionally, we applied the Bayesian Weighted Mendelian Randomization (BWMR) approach to validate the results of the MR analysis. Subsequently, we utilized RNA-seq data from various sources to explore the potential molecular signaling pathways between breast cancer and AML.

Both IVW method and BWMR approach demonstrated that data from three distinct sources consistently indicated breast cancer as a risk factor for AML, with all sources showing statistically significant results (all P < 0.05, Odds Ratios [ORs] > 1). Bioinformatic analyses suggested that extracellular vesicle functions and p53 signaling pathway may mediate molecular links between breast cancer and AML. Using machine learning, we identified 8 genes with high diagnostic efficacy for predicting the occurrence of AML in breast cancer patients.

MR analyses indicated a causal relationship between breast cancer and AML. Additionally, transcriptome analysis offered a theoretical basis for understanding the potential mechanisms and therapeutic targets of AML in breast cancer patients.

Cellular deconvolution of bulk RNA-sequencing data using single cell/nuclei RNA-seq reference data is an important strategy for estimating cell type composition in heterogeneous tissues, such as the human brain. Here, we generate a multi-assay dataset in postmortem human dorsolateral prefrontal cortex from 22 tissue blocks, including bulk RNA-seq, reference snRNA-seq, and orthogonal measurement of cell type proportions with RNAScope/ImmunoFluorescence. We use this dataset to evaluate six deconvolution algorithms. Bisque and hspe were the most accurate methods. The dataset, as well as the Mean Ratio gene marker finding method, is made available in the DeconvoBuddies R/Bioconductor package.

Advancements in RNA sequencing have expanded our ability to study gene expression profiles of biological samples in bulk tissue and single cells. Deconvolution of bulk data with single-cell references provides the ability to study relative cell-type proportions, but most methods assume a reference is present for every cell type in bulk data. This is not true in all circumstances-cell types can be missing in single-cell profiles for many reasons. In this study, we examine the impact of missing cell types on deconvolution methods.

Using paired single-cell and single-nucleus data, we simulate realistic scenarios where cell types are missing since single-nucleus RNA sequencing is able to capture cell types that would otherwise be missing in a single-cell counterpart. Single-nucleus sequencing captures cell types absent in single-cell counterparts, allowing us to study their effects on deconvolution. We evaluate three different methods and find that performance is influenced by both the number and similarity of missing cell types. Additionally, missing cell-type profiles can be recovered from residuals using a simple non-negative matrix factorization strategy. We also analyzed real bulk data of cancerous and non-cancerous samples. We observe results consistent with simulation, namely that expression patterns from cell types likely to be missing appear present in residuals.

We expect our results to provide a starting point for those developing new deconvolution methods and help improve their to better account for the presence of missing cell types. Our results suggest that deconvolution methods should consider the possibility of missing cell types.

Understanding disease progression is crucial for detecting critical transitions and finding trigger molecules, facilitating early diagnosis interventions. However, the high dimensionality of data and the lack of aligned samples across disease stages have posed challenges in addressing these tasks. We present a computational framework, Gaussian Graphical Optimal Transport (GGOT), for analyzing disease progressions. The proposed GGOT uses Gaussian graphical models, incorporating protein interaction networks, to characterize the data distributions at different disease stages. Then we use population-level optimal transport to calculate the Wasserstein distances and transport between stages, enabling us to detect critical transitions. By analyzing the per-molecule transport distance, we quantify the importance of each molecule and identify trigger molecules. Moreover, GGOT predicts the occurrence of critical transitions in unseen samples and visualizes the disease progression process. We apply GGOT to the simulation dataset and six disease datasets with varying disease progression rates to substantiate its effectiveness. Compared to existing methods, our proposed GGOT exhibits superior performance in detecting critical transitions.

Long noncoding RNAs (lncRNAs) have been recognized as significant modulators of gene expression and are essential for various biological functions, even though they don't appear to have the ability to encode proteins. Originally considered dark matter, lncRNAs have been recognized as being dysregulated and contributing to the onset, progression, and resistance to treatment of acute myeloid leukemia (AML). AML is a prevalent type of leukemia characterized by the disruption of myeloid cell differentiation, leading to an increased number of immature myeloid progenitor cells. Currently, the need for novel biomarkers and treatment targets to enhance therapeutic alternatives has led to a focus on lncRNAs as possible indicators for prognostic, therapeutic, and diagnostic systems in various human cancers, including AML. Recent research has recognized a limited set of lncRNAs as possible prognostic biomarkers or diagnoses in AML. This review evaluates the key research that highlights the significance of lncRNAs in AML and discusses their roles and impacts on the disease. Furthermore, we intend to underscore the importance of lncRNAs as new and trustworthy markers for the diagnosis, prediction, drug resistance, and targets for treatment in AML.

Fertilization triggers a cascade of events, including a rise in egg cytosolic calcium that marks the onset of embryonic development. In mammals and birds, this critical process is mediated by the sperm-derived phospholipase C zeta (PLCζ), which is pivotal in releasing calcium from the endoplasmic reticulum in the egg and initiating embryonic activation. Intriguingly, Xenopus laevis, a key model organism in reproductive biology, lacks an annotated PLCZ1 gene, prompting questions about its calcium release mechanism during fertilization. Using bioinformatics and RNA sequencing of adult X. laevis testes, we investigated the presence of a PLCZ1 ortholog in amphibians. While we identified PLCZ1 homologs in 25 amphibian species, including 14 previously uncharacterized orthologs, we found none in X. laevis or its close relative, Xenopus tropicalis. Additionally, we found no compensatory expression of other PLC isoforms in these species. Synteny analysis revealed a PLCZ1 deletion in species within the Pipidae family and another intriguing deletion of potential sperm factor PLCD4 in the mountain slow frog, Nanorana parkeri. Our findings indicate that the calcium release mechanism in frog eggs involves a signaling pathway distinct from the PLCζ-mediated process observed in mammals.

Spongy moth, Lymantria dispar Linnaeus (Lepidoptera: Erebidae), stands as a pervasive international threat, marked by its designation as one of the "world's 100 worst invasive species" by IUCN, owing to its voracious leaf-eating habits encompassing over 500 plant species. Its strong flight ability facilitates its spread and invasion. The present study aims to uncover differential gene expression, utilizing the Illumina Novaseq6000 sequencing platform for comprehensive transcriptome sequencing and bioinformatic analysis of total RNA extracted from larvae and pupae. Results revealed pivotal processes of protein functional structure conformation, transport, and signal transduction in functional gene annotation during the 2 developmental stages of spongy moth. 18 functional genes, namely, Distal-less (Dll), Wingless (Wg), Decapentaplegic (Dpp), Hedgehog (Hh), Cubitus interruptus (Ci), Patched (Ptc), Apterous (Ap), Serrate (Ser), Fringe (Fng), Achaete (Ac), Engrailed (En), Vestigial (Vg), Scute (Sc), Invected (Inv), Scalloped (Sd), Ultrabithorax (Ubx), Serum Response Factor (SRF), and Spalt-major, associated with wing development were identified, and their expression levels were meticulously assessed through real-time quantitative PCR (RT-qPCR) in 1st-6th instar larvae and male and female pupae wing discs. The results showed that 18 genes exhibited expression. Furthermore, the relative expression values of wing development-related genes were significantly higher in the pupae stage than in the larval stage. The relative expression values of male and female pupae were also significantly different. The RT-qPCR results were in general agreement with the results of transcriptome analysis. This study establishes a foundational understanding of the developmental mechanisms governing the formation of spongy moth wings.

Breast cancer is a leading cause of morbidity and mortality in women, and its progression is closely linked to the tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs), key components of the TME, play a crucial role in promoting tumor growth by driving cancer cell proliferation, invasion, extracellular matrix (ECM) remodeling, inflammation, chemoresistance, and immunosuppression. CAFs exhibit considerable heterogeneity and are classified into subgroups based on different combinations of biomarkers. Single-cell RNA sequencing (scRNA-seq) enables high-throughput and high-resolution analysis of individual cells. Relying on this technology, it is possible to cluster complex CAFs according to different biomarkers to analyze the specific phenotypes and functions of different subpopulations. This review explores CAF clusters in breast cancer and their associated biomarkers, highlighting their roles in disease progression and potential for targeted therapies.

Spatial transcriptomics (ST) has advanced our understanding of tissue regionalization by enabling the visualization of gene expression within whole-tissue sections, but current approaches remain plagued by the challenge of achieving single-cell resolution without sacrificing whole-genome coverage. Here we present Spotiphy (spot imager with pseudo-single-cell-resolution histology), a computational toolkit that transforms sequencing-based ST data into single-cell-resolved whole-transcriptome images. Spotiphy delivers the most precise cellular proportions in extensive benchmarking evaluations. Spotiphy-derived inferred single-cell profiles reveal astrocyte and disease-associated microglia regional specifications in Alzheimer's disease and healthy mouse brains. Spotiphy identifies multiple spatial domains and alterations in tumor-tumor microenvironment interactions in human breast ST data. Spotiphy bridges the information gap and enables visualization of cell localization and transcriptomic profiles throughout entire sections, offering highly informative outputs and an innovative spatial analysis pipeline for exploring complex biological systems.

Casuarina equisetifolia, a crucial species of coastal windbreaks, is highly susceptible to infestation by Anoplophora chinensis. This stem-boring pest poses a significant threat to the health and sustainability of Casuarina equisetifolia forests. Understanding the molecular mechanisms underlying the host preference of A. chinensis to Casuarina equisetifolia is essential for developing effective pest management strategies.

Through field surveys, we identified two cultivars of Casuarina equisetifolia that exhibited differing levels of host preference for A. chinensis. Further analysis of multi-omics data (phenomics, transcriptomics, and metabolomics) from these cultivars revealed that longifolene plays a significant role in attracting A. chinensis to Casuarina equisetifolia. Additionally, the jasmonic acid (JA) signaling pathway was found to suppress longifolene accumulation, primarily through the interaction between the jasmonate ZIM-domain (JAZ) proteins and the terpene synthase (TPS) gene. Moreover, we identified a critical JAZ component, CeJAZ3, whose overexpression led to the down-regulation of TPS expression levels and, consequently, a reduced release of longifolene.

We confirmed that the negative regulator of host preference, CeJAZ3, in the JA signaling pathway can suppress the expression of TPSs, thereby down-regulating the accumulation of longifolene in Casuarina equisetifolia and indirectly suppressing the attraction of host plants to A. chinensis, which provides a basis for the integrated management of A. chinensis. © 2024 Society of Chemical Industry.

Although 70% of patients with estrogen receptor-positive breast cancer benefit from tamoxifen (TAM) therapy, the development of resistance to TAM leads to high rates of metastasis and a poor prognosis. Propofol, a commonly used anesthetic, can inhibit the occurrence and progression of breast cancer. In the present study, the effects of propofol on TAM-resistant (TR) breast cancer cells were evaluated. MCF7-TR cells were treated with or without propofol. Subsequently, cell cycle progression and the induction of apoptosis were detected by flow cytometry, whereas cell proliferation was assessed using Cell Counting Kit-8 and colony formation assays. Furthermore, the potential transcriptional regulatory effects of propofol on MCF7-TR cells were investigated using RNA sequencing. The results indicated that propofol significantly promoted cell cycle arrest, induced apoptosis, and inhibited proliferation and colony formation in MCF7-TR cells. Furthermore, transcriptome sequencing analysis revealed 1,065 differentially expressed genes between propofol-treated MCF7-TR and untreated MCF7-TR cells. Gene Ontology annotation enrichment analysis, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis and Gene Set Enrichment Analysis indicated that propofol affected the expression levels of genes located on the 'plasma membrane' and 'cell periphery', while mainly regulating signals involved in cancer biology, immune response and metabolic pathways. These results identified the potential effects of propofol on TR breast cancer cells and provided a theoretical basis for clinical treatment, particularly for individuals with TAM resistance.

Chronic unpredictable mild stress (CUMS) affects chicken immune system and welfare, causing huge losses of growth performance and welfare. Resveratrol (RSV), an antioxidant and anti-inflammatory natural plant polyphenol, is widely used for the prevention of stress related disease. The aim of this study is to explore the therapeutic effect of RSV on spleen damage in CUMS. We successfully constructed a CUMS model. A total of 288 healthy one-day-old chicks were used in this study and were divided in 3 groups, control, CUMS and CUMS+RSV group. During 42 days of age, spleen tissue samples were collected and analyzed. Transmission electron microscope (TEM), Hematoxylin and eosin (H&E) staining, immunofluorescence, qRT- PCR, Western blots, immunohistochemical staining and RNA- sequencing (RNA-seq) technology was used to determine any changes and analyzed the mRNA and enrichment pathways. Histopathology and ultrastructure showed there was a severe damage of tissues. The results of RNA-seq showed that a total of 206, 267 and 211 DEGs were identified (log2 Fold Change| >1, P < 0.05) in control -vs- CUMS group, CUMS -vs- CUMS+RSV group and control -vs- CUMS+RSV group, respectively. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the SDEGs, two immune/stress- related pathways including PPAR signaling pathway and neuroactive ligand receptor interaction were selected. The genes related to PPAR signaling pathway identified were PLIN1, MMP1, ANGPTL4 and FABP4 and Neuroactive ligand-receptor interaction genes were GRPR, NTSR1, KNG1 and AGT. The PLIN1, MMP1, ANGPTL4, FABP4, GRPR, KNG1 and AGT were up regulated and NTSR1 was down regulated in CUMS group. When compared to CUMS -vs- CUMS+RSV group, PLIN1, FABP4, KNG1 and AGT were down regulated genes and NTSR1 was up regulated gene. Taken together, KEGG pathway analyses of DEGs, verified by qRT-PCR and Western blots, the current study suggested that these data reveal the promising role of RSV in the prevention and therapy of a wide variety of tissue damage and PPAR signaling pathway, neuroactive ligand-receptor interaction in chronic unpredictable mild stress.

Next-generation sequencing (NGS) technologies have revolutionized pain research by providing comprehensive insights into genetic variation across the genome. Recent studies have expanded the known spectrum of mutations in genes such as SCN9A and NTRK1, which are commonly mutated in hereditary sensory neuropathies. NGS has uncovered critical alternative splicing events and facilitated single-cell transcriptomics, revealing cellular heterogeneity within tissues. An NGS-based classifier predicted extremely high opioid requirements with 80 % accuracy, highlighting the importance of tailoring opioid therapy based on genetic profiles. Key genes such as GDF5, COL11A1, and TRPV1 have been linked to osteoarthritis risk and pain sensitivity, while HLA-DRB1, TNF, and P2X7 play critical roles in inflammation and pain modulation in rheumatoid arthritis. Innovative tools, such as an atlas of the somatosensory system in neuropathic pain, have been developed based on NGS data, focusing on the dorsal root and trigeminal ganglia. This approach allows the analysis of cellular changes during the development of chronic pain. In the study of rare variants, NGS outperforms single nucleotide variant candidate studies and classical genome-wide association approaches. The complex data generated by NGS enables integrated multi-omics approaches, allowing deeper exploration of the molecular and cellular basis of pain perception. In addition, the characterization of non-coding RNAs has opened new therapeutic avenues. NGS-based pain research faces challenges related to complex data analysis and interpretation of rare genetic variants with unknown biological functions. Nevertheless, NGS offers significant potential for improving personalized pain management and highlights the need for interdisciplinary collaboration to translate findings into clinical practice.

Carbonic anhydrases (CAs) are critical metalloenzymes, widely exist in organisms, which involve in many physiological processes, including response to adverse environmental conditions. Although CA genes have been comprehensive identified and analyzed in numerous plants, there are a few of reports in cotton. Therefore, we conducted an exhaustive research for CA genes from two tetraploid cotton species and their ancestral species. A total of 138 CA genes were found, and 45 of them belonged to Gossypium hirsutum. Phylogenetic relationships and sequences analysis showed that CA genes were categorized into three distinct subtypes: α-type, β-type and γ-type. The exon numbers of β-type members were highly variable. Various types of cis-elements, including drought inducibility, were identified in CA genes, suggesting that CA genes might be involved in the regulation of drought stress response. qRT-PCR was applied to assess the gene expression level in various tissues under drought stress. The results indicated that the expression levels of GhαCA4-D, GhβCA1-A, GhβCA1-D, GhβCA3-D and GhβCA6-D were significantly higher in leaves than that in stems and roots. The expression of GhαCA4-A, GhαCA8-A, GhαCA4-D, GhβCA3-D, GhβCA6-D and GhγCAL1-D was significantly upregulated in roots at severe drought treatment. The functions of GhαCA4-D, GhβCA6-D and GhγCA2-D were analyzed using virus-induced gene silencing (VIGS) technology. Compared to the controls, GhγCA2-D-silenced upland cotton seedlings were more sensitive to salt stress. However, the drought tolerance of GhαCA4-D and GhβCA6-D silenced plants was significantly decreased. Stomatal density, width and area were significantly higher in TRV:GhβCA6-D compared to TRV:00 inoculated plants. GhαCA4-D silenced plants were susceptible to oxidative stress, and silencing GhαCA4-D induced leave cell death. Our results will assist to make clear the regulatory mechanism of CA genes under abiotic stress.

Shrimp farming, a dominant economic activity in coastal areas, is affected by different abiotic and biotic stress factors. These stressors, under poor management conditions, could affect growth and health of farmed animals. Understanding the common gene expressions in response to stress, regardless of the specific stress factor, holds significant importance in the field of functional genomics. Scope of this study is to identify the core transcriptomic responses in the shrimp species Penaeus vannamei exposed to various abiotic and biotic stress conditions and to decipher their functional importance. To achieve our objective, we gathered and analyzed multiple RNA-seq datasets related to twelve abiotic and nine biotic stress conditions. Through the in silico meta-analysis, we predicted 961 differentially expressed genes (meta-DEGs) for abiotic stress conditions and 517 meta-DEGs for biotic stress conditions, respectively. These meta-DEGs represent genes that are commonly expressed across different stress factors and are indicative of the organism's general response to stress. The annotation of nineteen core up-regulated meta-DEGs revealed their diverse functions in detoxification, cell adhesion, metal ion binding, and oxidative phosphorylation. These genes play a crucial role in stress response and immune defense. For abiotic stress, significant pathways associated with the stress response include tryptophan metabolism, starch and sucrose metabolism, fatty acid degradation, carbohydrate digestion and absorption, phenylalanine metabolism, drug metabolism-other enzymes, arachidonic acid metabolism, and fatty acid elongation. Similarly, for biotic stress, metabolism of xenobiotics by cytochrome P450, pentose and glucuronate interconversions, steroid hormone biosynthesis, and drug metabolism-cytochrome P450 were found to be significant pathway associations. In addition, the study also predicted 17 stress regulatory motifs present in the identified meta-DEGs. These motifs have significance in identifying the stress responses of the organism. The metabolic pathways and regulatory motifs associated with abiotic and biotic stress factors identified through this study could be a valuable resource for developing stress management approaches in shrimp aquaculture.

Walnuts, along with almonds, cashews, and hazelnuts, are renowned as the world's "four famous nuts," with walnuts being the foremost among them. Walnut fruit is rich in nutrients, including proteins, fats, polyphenols, sugars, phospholipids, melatonin, sterols, flavonoids, iron, zinc, manganese, and other trace elements, as well as dietary fiber. However, the codling moth poses a significant threat to walnut fruits as a major pest. Despite its importance, the transcriptomic changes in walnut husk at different times of codling moth infestation have not been fully explored. In this study, we employed the Illumina NovaSeq 6000 platform to sequence the transcriptome of walnut husk at various time points (0, 12, 24, 36, 48, and 72 hours) after codling moth infestation. The RNA-seq libraries yielded between 41,402,492 and 48,358,932 clean reads, resulting in a total of 120.34 Gb of clean data after filtering out low-quality reads. In total, 936 million reads were generated, with approximately 90% aligning uniquely to the reference genome. Differential expression analysis revealed the number of differentially expressed genes (DEGs) at each time point, including 21 genes associated with plant hormone synthesis. The results of this study provide new insights into the transcriptional changes in walnut husk induced by codling moth infestation and lay a foundation for future research on walnut husk defense mechanisms. The raw FASTQ files from this transcriptome experiment are publicly available in the NCBI Sequence Read Archive (SRA) under the BioProject accession number PRJNA1140835.

The nitrate pollution has become an increasingly serious environmental problem worldwide, and the toxic effects of elevated nitrate levels in the environment on aquatic animals remain to be elucidated. The purpose of the present study was to investigate the mechanisms of liver injury to tadpoles after exposure to nitrate from embryonic to metamorphic climax and to assess the recovery process of liver function after cessation of exposure. In the group with continuous nitrate exposure, the livers and thyroid of tadpoles showed remarkably histological lesions, of this with structural disorganization of the hepatocytes, cellular atrophy, and fibrosis, as well as significant reduction in the follicular and colloidal area of the thyroid. Meanwhile, the expression levels of genes related to inflammatory signaling pathways, such as TLR2, TLR6 and NF-κB, were significant elevated. After termination of exposure at Gs23, liver damage (histologic, ultrastructural, and molecular levels) was almost completely recovered, whereas thyroid gland damage was irreversible. Overall, this study shed light on the harmful effects of nitrate pollution on amphibian health and emphasizes the importance of controlling nitrate emissions in the environment.

The microarray and single-cell RNA-sequencing (scRNA-seq) datasets of hepatocellular carcinoma (HCC) were downloaded from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were used to identify HCC-related biomarkers. Based on an analysis of scRNA-seq data, several marker genes expressed on tumor cells have been identified. Three machine-learning algorithms were used to identify shared diagnostic genes. Furthermore, logistic regression analysis was conducted to re-evaluate and identify essential biomarkers, which were then employed to develop a diagnostic prediction model. Additionally, AutoDockTools were used for molecular docking to investigate the association between the most sensitive drug and the core proteins. 44 genes were obtained by intersecting the WGCNA results, marker genes from scRNA-seq data, and up-regulated DEGs. Three machine-learning algorithms refined CDKN3, PPIA, PRC1, GMNN, and CENPW as hub biomarkers. GMNN and PRC1 were further selected by logistic regression analysis to build a nomogram. The molecular docking results showed that the drug NPK76-II-72-1 had a good binding ability with the GMNN and PRC1 proteins. The results highlighted CDKN3, PPIA, PRC1, GMNN, and CENPW as potential detection biomarkers for HCC patients. Our research offers novel insights into the diagnosis and treatment of HCC.

Qingre Sanjie Jiaonang (QRSJ) is a single herbal preparation from Senecio scandens Buch.-Ham.ex D. Don which has been proved to have anti-inflammatory and antioxidant effects. QRSJ has been used in treating upper respiratory tract inflammation and acute bronchitis in China for nearly twenty years.

This study aims to explore the potential effects of QRSJ in alleviating pulmonary fibrosis (PF) and its mechanisms.

A mouse model of PF was induced by intratracheal injection of Bleomycin (BLM, 5 mg/kg), followed by different doses of QRSJ administration (0.5 g/kg, 1.0 g/kg) for 28 days. The lung tissues were collected and prepared for Hematoxylin-Eosin (H&E) staining to observe the pathological changes, while Masson staining was for determining collagen production. RNA sequencing (RNA-seq), flow cytometry and immunofluorescence experiments were employed to investigate the impact of QRSJ on the immune microenvironment. The expression levels of IL-1β, IL-6, CXCL15 (mouse homologue of human IL-8), and TNF-α in the bronchoalveolar lavage fluid (BALF) and serum of mice were observed. Besides, the levels of high mobility group protein B1 (HMGB1), an inflammatory and profibrotic mediator, in the BALF, serum and lung tissues of mice were also detected.

The mouse model of PF was successfully established by checking the pathological examinations. With QRSJ intervention, BLM-induced destruction of alveolar structure and inflammatory cell infiltration were alleviated. H&E results further revealed that the administration of BLM and QRSJ had no impact on kidney histological structure of mice. Meanwhile, QRSJ inhibited the deposition of collagen, decreased the expression of fibronectin and lumican. Next, QRSJ treatment improved immune cell infiltration in the lung, along with the down-regulation of CD45 and Ly6G, and led to a decrease in the immune cell count in BALF. Furthermore, QRSJ alleviated the release of inflammatory factors, including NE, IL-1β, IL-6, CXCL15, and TNF-α. Besides, QRSJ significantly reduced the level of proinflammatory cytokine HMGB1.

This study demonstrated the benefits of QRSJ in improving the pathological abnormalities in a PF model, revealing the new potential of the old drug. It should be attributed to the regulation of abnormal immune microenvironment and HMGB1 release. Future efforts should focus on its specific pharmacological mechanisms and clinical outcomes.

In the domestic cat (Felis catus), the corpus luteum (CL) is the main source of progestogen during pregnancy. Here, we studied gene expression changes in different life cycle stages of the CL of pseudopregnant cats to identify potential regulatory factors. Results revealed no support for different regression substages, which were previously defined on the basis of morphological examination analysis and intraluteal hormone content, as only a very low number of differentially expressed genes and no subclusters in PCA plot were detected. By comparing the regression stage with the developmental/maintenance stage, we detected a total of 6174 differentially expressed genes in the sample set, of which 2882 were upregulated and 3292 were downregulated. The large changes in the expression levels of some genes indicate that the endocrine function of the CL may not be restricted to progesterone (P4) secretion. The findings suggest that domestic cat CLs could also be a source of adipokines such as adiponectin or APELA. The expression of these genes is highly variable and reversed between stages. The life cycle and activity of CLs seem to be regulated by different factors, as genes encoding for the hormone receptors LHCGR and PAQR5 were more highly expressed in the development/maintenance stage, in contrast to this encoding for LEPR, which is higher expressed in regression stage. For regression stage, we identified different potential ways to modulate the cholesterol level and/or P4 concentration. Furthermore, we found differences from previous studies in other species for many genes that were studied in more detail, as well as when analysing functions and pathways. Our findings support the hypothesis that different stages of the CL life cycle in domestic cats can be characterized by changes in gene regulation and that CL life cycles are partly differentially regulated between species.

Helicobacter pylori (H. pylori) infection and the resulting gastric inflammation are major contributors to gastric cancer development. Probiotics, particularly Lactobacillus, are promising for their anti-inflammatory potential, yet their exact mechanisms in inhibiting H. pylori-induced inflammation are unclear. In our previous study, Lactiplantibacillus plantarum ZJ316 (L. plantarum ZJ316) demonstrated strong anti-inflammatory effects against H. pylori infection in vivo, but its precise mechanisms were not fully understood. Here, we aimed to investigate how L. plantarum ZJ316 inhibits the inflammatory response to H. pylori infection. Our results demonstrated that L. plantarum ZJ316 effectively reduced the expression of pro-inflammatory cytokines in H. pylori-infected AGS cells. Mechanistically, L. plantarum ZJ316 inhibited the NF-κB signaling pathway by preventing the degradation of IκBα, suppressing p65 phosphorylation, and blocking the nuclear translocation of phosphorylated p65. Treatment with the NF-κB inhibitor BAY 11-7082 further decreased tumor necrosis factor-α (TNF-α), interleukin-8 (IL-8), and interleukin-1β (IL-1β) levels, confirming the inhibitory effect of L. plantarum ZJ316 on the NF-κB pathway. In H. pylori-infected mice, oral administration of L. plantarum ZJ316 significantly alleviated inflammatory cell infiltration, reduced TNF-α and pepsinogen II (PGII) levels, and increased interleukin-10 (IL-10) levels in serum. A comparative metagenomic analysis of the gastric microbiota revealed a decrease in Prevotella and Desulfovibrio, alongside an increase in Ligilactobacillus and Akkermansia, supporting the protective effects of L. plantarum ZJ316 and correlating with their decreased inflammatory response. In summary, administration of L. plantarum ZJ316 demonstrated robust anti-inflammatory effects against H. pylori infection by suppressing NF-κB signaling and promoting favorable changes in the gastric microbiota composition. Therefore, L. plantarum ZJ316 holds promise as a novel functional food for protecting the body against H. pylori infection.

Agaricus bisporus is a widely cultivated edible fungus globally. However, the mechanisms underlying the differences in flavor and nutritional traits between wild-type (W) and cultivated-type (C) strains remain unclear, which hinders the artificial breeding of high-quality varieties. This study systematically revealed, for the first time, the molecular and metabolic basis of flavor divergence between wild and cultivated A. bisporus by integrating transcriptomics and metabolomics. A total of 43 strains (23 wild-type and 20 cultivated-type) were analyzed using high-throughput sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to dissect differences in gene expression and metabolite profiles. Results showed that although total protein and amino acid contents exhibited no significant differences, transcriptomic analysis identified significant upregulation of AGABI2DRAFT_188981 and AGABI2DRAFT_191000 (genes associated with high-affinity methionine permease MUP1) in cultivated strains, suggesting their indirect regulation of flavor formation via methionine metabolism. Metabolomic analysis further revealed a marked increase in uridine levels in cultivated strains (3.2-fold higher than wild-type, p < 0.01), indicating potential medicinal value, while wild strains were enriched with flavor precursors such as fumaric acid and isoleucine (fold change ≥ 2.5). In contrast, cultivated strains accumulated metabolites like 2-hydroxybutyric acid and α-ketoglutarate (VIP > 1.5). This study pioneered the construction of a gene-metabolite correlation network, identifying a strong positive correlation between AGABI2DRAFT_191352 (6-phosphofructokinase) and 2-hydroxybutyric acid (r = 0.82), highlighting the regulatory role of glycolytic flux in flavor metabolism. These findings not only elucidate the impact of artificial cultivation on metabolic reprogramming in A. bisporus but also provide critical molecular targets for targeted breeding of strains with enhanced flavor and nutritional value, offering practical significance for advancing the edible fungi industry.

The basal division of posterior pallial amygdala (PoAb) was one important part of the amygdala in birds. PoAb mainly mediated turning behavior. However, the regulating neuromechanisms of PoAb in motor behavior was not clear yet. In this study, we selected septalis lateralis (SL) as the stimulated nucleus because it was closely associated with PoAb and had clear neuroregulatory functions, and we also used unrelated nuclei (entopallium) and unstimulated blank treatment (CK) as controls. We aim to study the neuroregulatory mechanisms of PoAb by investigating the differences of transcriptome level in different groups. A total of 622 differentially expressed genes (DEGs) were obtained from PoAb after comparing the SL stimulating group with the CK control group. GO functional annotation and KEGG pathway enrichment analysis showed that the upregulated 608 DEGs mainly involved energy supply and fluid balance. A total of 345 DEGs were obtained from the PoAb when comparing SL stimulation group and entopallium stimulation group. The upregulated 187 DEGs were mainly involved in cell communication and signal transductions. The study indicated that PoAb may modulate motor behaviour mainly by increasing ATP production and facilitating synaptic transmission, in which genes such as SMAD3, TMED3, GRIA2, HTR1B and SNCG play an important role. We revealed the mechanisms of brain regulation behaviour from gene level, and provided the theoretical foundation for understanding the avian brain.

The NCED (9-cis-epoxy carotenoid dioxygenase) enzyme regulates the biosynthesis of abscisic acid (ABA), which is responsible for plant growth, development, and response to various environmental challenges. However, no genome-wide identification, characterization, functional regulatory element analysis, and expression profiles in response to different abiotic stresses of the NCED gene family have yet to be investigated in an economically important legume plant species, soybean (Glycine max L.). Through comprehensive analysis, 16 NCED genes (named GmNCED1 to GmNCED16) belonging to the RPE65 domain were identified in the soybean genome and found to be unequally distributed over 9 distinct chromosomes. The distinct intron-exon structures of GmNCED genes were categorized into six groups and shared a close relationship with the grapevine. Segmental gene duplication events and the purifying selection process were evident in GmNCED genes, according to evolutionary studies. Cis-acting regulatory element analysis revealed that GmNCED genes were largely associated with light response as well as stress response. ERF, MYB, bZIP, and LBD emerged as the major transcription factors in GmNCED genes. The protein-protein interactions demonstrated the close relationship between GmNCED and Arabidopsis thaliana proteins, while micro-RNA analysis revealed the involvement of GmNCED genes in plant growth and development as well as in the regulation of abiotic stress. The expression profiles of GmNCED2, GmNCED11, and GmNCED12 provided evidence of their engagement in dehydration and sodium salt stress, whereas GmNCED14 and GmNCED15 were up-regulated in drought stress. Moreover, the up-regulation of GmNCED13 and GmNCED14 genes in heat tolerant germinated seed stages at high temperature delta region. More specifically, GmNCED14 might be used as a novel candidate gene under drought stress, and influencing seed germination at high temperature. Overall, this study identified the crucial role of GmNCED in conferring resistance against abiotic stress such as dehydration, salt, and drought, and also uncovering the detailed regulatory mechanism of ABA biosynthesis during seed germination.

Following the recent emergence of RNA as a therapeutic tool, and coupled with an explosion in the development of new RNA technologies, it is rapidly becoming clear that the 21st century is the era of RNA. Neuroscience as a discipline has a long history of embracing new technology to advance the understanding of brain function, particularly in the context of learning and memory. In this short review, we highlight four broad categories of emerging RNA technologies, namely: imaging, isolation, identification and manipulation, and discuss their potential to advance the fundamental understanding of how RNA impacts experience-dependent plasticity, learning, and memory.

Obesity, often driven by high-fat diets (HFDs), is a major global health issue, necessitating effective preventive measures. Tetragonia tetragonoides, a plant with known medicinal properties, has not been extensively studied for its effects on HFD-induced obesity and related genetic changes in mice. This study explores the impact of T. tetragonoides extract (TTE; 300 mg/kg) on obesity-related traits in C57BL/6J male mice, with a focus on transcriptomic changes in the liver and white adipose tissue (WAT). Over 8 weeks, TTE supplementation led to significant reductions in obesity-related phenotypes and modulated gene expression altered by HFD. Key genes like Cd180 and MUPs, linked to immune responses and lipid metabolism, were notably influenced by TTE. The study highlighted TTE's effects on lipid metabolism pathways in the liver and immune processes in WAT, underscoring its potential as an anti-obesity agent, while advocating for further research into its bioactive components.