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The model moss species Physcomitrium patens has long been used for studying divergence of land plants spanning from bryophytes to angiosperms. In addition to its phylogenetic relationships, the limited number of differential tissues, and comparable morphology to the earliest embryophytes provide a system to represent basic plant architecture. Based on plant-fungal interactions today, it is hypothesized these kingdoms have a long-standing relationship, predating plant terrestrialization. Mortierellaceae have origins diverging from other land fungi paralleling bryophyte divergence, are related to arbuscular mycorrhizal fungi but are free-living, observed to interact with plants, and can be found in moss microbiomes globally. Due to their parallel origins, we assess here how two Mortierellaceae species, Linnemannia elongata and Benniella erionia, interact with P. patens in coculture. We also assess how Mollicute-related or Burkholderia-related endobacterial symbionts (MRE or BRE) of these fungi impact plant response. Coculture interactions are investigated through high-throughput phenomics, microscopy, RNA-sequencing, differential expression profiling, gene ontology enrichment, and comparisons among 99 other P. patens transcriptomic studies. Here we present new high-throughput approaches for measuring P. patens growth, identify novel expression of over 800 genes that are not expressed on traditional agar media, identify subtle interactions between P. patens and Mortierellaceae, and observe changes to plant-fungal interactions dependent on whether MRE or BRE are present. Our study provides insights into how plants and fungal partners may have interacted based on their communications observed today as well as identifying L. elongata and B. erionia as modern fungal endophytes with P. patens.

The sacred datura plant (Solanales: Solanaceae: Datura wrightii) has been used to study plant-herbivore interactions for decades. The wealth of information that has resulted leads it to have potential as a model system for studying the ecological and evolutionary genomics of these interactions. We present a de novo Datura wrightii genome assembled using PacBio HiFi long-reads. Our assembly is highly complete and contiguous (N50 = 179Mb, BUSCO Complete = 97.6%). We successfully detected a previously documented ancient whole genome duplication using our assembly and have classified the gene duplication history that generated its coding sequence content. We use it as the basis for a genome-guided differential expression analysis to identify the induced responses of this plant to one of its specialized herbivores (Coleoptera: Chrysomelidae: Lema daturaphila). We find over 3000 differentially expressed genes associated with herbivory and that elevated expression levels of over 200 genes last for several days. We also combined our analyses to determine the role that different gene duplication categories have played in the evolution of Datura-herbivore interactions. We find that tandem duplications have expanded multiple functional groups of herbivore responsive genes with defensive functions, including UGT-glycosyltranserases, oxidoreductase enzymes, and peptidase inhibitors. Overall, our results expand our knowledge of herbivore-induced plant transcriptional responses and the evolutionary history of the underlying herbivore-response genes.

Rice production is severely hampered by drought stress, which causes enormous economic losses. The issue of global climate change is gaining importance, and hence development of rice genotypes tolerant to drought stress is becoming more critical. To address this issue, backcross inbred lines (BILs) developed were subjected to drought stress, and their molecular mechanism was studied. The drought‐tolerant parent Apo and drought‐susceptible, high‐yielding IR64 along with two BILs, namely, CB 229 (qDTY2.2 + qDTY3.1 + qDTY8.1) and CB 193‐3 (qDTY3.1 + qDTY8.1) were tested in a greenhouse for their response to drought. In this study, CB 229 showed better performance under water stress irrigated conditions; it was on par with IR64. Drought‐responsive transcriptome profiling was carried out in both the parents and the superior BIL CB 229 through the RNA‐Seq approach. About 3050 differentially expressed genes (DEGs) (2021 upregulated and 1029 downregulated) were detected in tolerant BIL CB 229 in drought stress. Most of the DEGs were involved in carbohydrate metabolism and the formation of cell walls, as well as genes associated with metabolite adaptability, ROS homeostasis and post‐transcriptional regulation. Genes such as chaperone protein, senescence‐induced receptor‐like serine, mannose‐6‐phosphate isomerase, aquaporin and heat shock proteins (LOC_Os02g26840, LOC_Os02g25720, LOC_Os07g35570, LOC_Os01g64970, etc.) were upregulated in the tolerant Apo and CB 229. It was observed that the BIL CB 229 yielded higher grains than both parents under moisture stress. Ninety‐four genes in the quantitative trait loci (QTLs) region were found to be differentially regulated in CB 229, Apo and IR64. Out of 94, nine genes co‐localized within the QTL qDTY2.2, 12 genes within qDTY3.1 and four genes within qDTY8.1 were differentially upregulated in CB 229 and downregulated in the susceptible genotype. The study revealed that the QTLs qDTY2.2, qDTY3.1 and qDTY8.1 are found to have complementary effects and offer enhanced levels of tolerance against drought due to complementation. Additionally, this analysis discovered new DEGs that may be involved in functions related to drought tolerance but lack function annotations. Future research can focus on a few of the significant DEGs found in this study. Taken together, our findings provide insight into drought tolerance mechanisms and could assist the development of novel strategies for improving drought tolerance in rice. [ABSTRACT FROM AUTHOR]

Multiple Sclerosis (MS) is an autoimmune neurodegenerative disease affecting approximately 3 million people globally. Despite rigorous research on MS, aspects of its development and progression remain unclear. We utilized a publicly available RNA-seq dataset (GSE138614) consisting of the post-mortem white matter tissues of five donors without any neurological disorders and ten MS patient donors. We investigated gene expression levels correlated with tissue inflammation and alternative splicing to identify possible pathological isoforms in MS tissues. We identified RNA-binding motifs, differentially expressed RNA-binding proteins, and single-nucleotide polymorphisms (SNPs) to unravel possible mechanisms of alternative splicing. Genes with expression changes that were positively correlated with tissue inflammation were enriched in the immune system and receptor interaction pathways. Genes showing a negative correlation were enriched in nervous system development and in metabolic pathways. A comparison of normal-appearing white matter (NAWM) and active or chronic active lesions within the same donors identified genes playing roles in immunity, white matter injury repair, and remyelination. We identified exon skipping events and spontaneous SNPs in membrane-associated ring-CH-type finger-1 (MARCHF1), UDP glycosyltransferase-8 (UGT8), and other genes important in autoimmunity and neurodegeneration. Overall, we identified unique genes, pathways, and novel splicing events that can be further investigated as potential novel drug targets for MS treatment. [ABSTRACT FROM AUTHOR]

• We screened the expression profiles of miRNAs in the late stage of RBC preservation. • We identified miRNAs that changed during different storage times as well as potential target genes. • We predicted the potential regulatory effects of these differential miRNAs through bioinformatics. To detect the differentially expressed regulatory miRNAs in the late stage of red blood cell (RBC) preservation and predict their roles. Suspended RBCs with different storage periods of 35 day, 42 day, and 50 day were collected for routine blood tests, RNA extraction, and preparation of small RNA sequencing libraries. The constructed libraries were sequenced and the biological functions of differential miRNAs in RBCs in the late storage were analyzed by bioinformatics. Routine indicators of RBCs in the late stage were not significantly affected by preservation time. The Pearson correlation analysis performing on RBC miRNAs with different storage days revealed that RBC miRNAs changed with the increase of storage days. RBC miRNAs from day 35 (D35), day 42 (D42) and day 50 (D50) showed significant differences (P < 0.05). Compared RBC miRNAs from D42 with these from D35, there were 690 up-regulated miRNAs and 82 down-regulated miRNAs; compared RBC miRNAs from D50 with these from D35, there were 638 up-regulated miRNAs and 123 down-regulated miRNAs; compared RBC miRNAs from D42 with these from D50, there were 271 up-regulated miRNAs and 515 down-regulated miRNAs. GO enrichment analysis of target genes of differential miRNAs were mainly involved in cell metabolism, biosynthesis, protein modification, gene expression and transcriptional regulation of biological processes. KEGG pathway enrichment analysis of miRNA target genes showed that differential miRNA target genes were closely related to pathways in cancer. MiRNAs were differentially expressed in the late stage of RBC preservation, and may be involved in various biological processes, especially cancer. [ABSTRACT FROM AUTHOR]

Introduction: The advent of RNA sequencing (RNA-Seq) has significantly advanced our understanding of the transcriptomic landscape, revealing intricate gene expression patterns across biological states and conditions. However, the complexity and volume of RNA-Seq data pose challenges in identifying differentially expressed genes (DEGs), critical for understanding the molecular basis of diseases like cancer. Methods: We introduce a novel Machine Learning-Enhanced Genomic Data Analysis Pipeline (ML-GAP) that incorporates autoencoders and innovative data augmentation strategies, notably the MixUp method, to overcome these challenges. By creating synthetic training examples through a linear combination of input pairs and their labels, MixUp significantly enhances the model's ability to generalize from the training data to unseen examples. Results: Our results demonstrate the ML-GAP's superiority in accuracy, efficiency, and insights, particularly crediting the MixUp method for its substantial contribution to the pipeline's effectiveness, advancing greatly genomic data analysis and setting a new standard in the field. Discussion: This, in turn, suggests that ML-GAP has the potential to perform more accurate detection of DEGs but also offers new avenues for therapeutic intervention and research. By integrating explainable artificial intelligence (XAI) techniques, ML-GAP ensures a transparent and interpretable analysis, highlighting the significance of identified genetic markers. [ABSTRACT FROM AUTHOR]

Differential expression analysis of single-cell RNA sequencing (scRNA-seq) data is central for characterizing how experimental factors affect the distribution of gene expression. However, distinguishing between biological and technical sources of cell-cell variability and assessing the statistical significance of quantitative comparisons between cell groups remain challenging. We introduce Memento, a tool for robust and efficient differential analysis of mean expression, variability, and gene correlation from scRNA-seq data, scalable to millions of cells and thousands of samples. We applied Memento to 70,000 tracheal epithelial cells to identify interferon-responsive genes, 160,000 CRISPR-Cas9 perturbed T cells to reconstruct gene-regulatory networks, 1.2 million peripheral blood mononuclear cells (PBMCs) to map cell-type-specific quantitative trait loci (QTLs), and the 50-million-cell CELLxGENE Discover corpus to compare arbitrary cell groups. In all cases, Memento identified more significant and reproducible differences in mean expression compared with existing methods. It also identified differences in variability and gene correlation that suggest distinct transcriptional regulation mechanisms imparted by perturbations. [Display omitted] • A statistical model for scRNA-seq decouples measurement and expression noise • Highly efficient resampling allows for well-calibrated hypothesis testing • Memento enables studying coordinated expression of genes in response to perturbations • Memento maps loci associated with gene expression mean, variability, and correlation Memento implements a statistical model and a fast resampling procedure to estimate and compare the mean, variability, and correlation of gene expression, allowing for the study of transcription in a deeper yet accurate fashion compared with traditional differential expression. [ABSTRACT FROM AUTHOR]

SUMMARY Somatic embryogenesis (SE) is a powerful model system for studying embryo development and an important method for scaling up availability of elite and climate‐adapted genetic material of Norway spruce (Picea abies L. Karst). However, there are several steps during the development of the somatic embryo (Sem) that are suboptimal compared to zygotic embryo (Zem) development. These differences are poorly understood and result in substantial yield losses during plant production, which limits cost‐effective large‐scale production of SE plants. This study presents a comprehensive data resource profiling gene expression during zygotic and somatic embryo development to support studies aiming to advance understanding of gene regulatory programmes controlling embryo development. Transcriptome expression patterns were analysed during zygotic embryogenesis (ZE) in Norway spruce, including separated samples of the female gametophytes and Zem, and at multiple stages during SE. Expression data from eight developmental stages of SE, starting with pro‐embryogenic masses (PEMs) up until germination, revealed extensive modulation of the transcriptome between the early and mid‐stage maturing embryos and at the transition of desiccated embryos to germination. Comparative analysis of gene expression changes during ZE and SE identified differences in the pattern of gene expression changes and functional enrichment of these provided insight into the associated biological processes. Orthologs of transcription factors known to regulate embryo development in angiosperms were differentially regulated during Zem and Sem development and in the different zygotic embryo tissues, providing clues to the differences in development observed between Zem and Sem. This resource represents the most comprehensive dataset available for exploring embryo development in conifers. [ABSTRACT FROM AUTHOR]

Vitamin C, also referred to as ascorbic acid (AsA), is recognized for its capacity to cure and avert scurvy, and it is crucial for regular human growth and development. In various crops, AsA participates in stress response mechanisms mediated by abscisic acid and has been discovered to have a crucial function in the morphogenesis, growth, development, and production of male gametes in plants. GDP-D-mannose 3′,5′-epimerase (GME) is essential in the synthesis of vitamin C. Our research identified 91, 83, 51, and 46 genes, respectively, found in G. barbadense (GbGMEs), G. hirsutum (GhGMEs), G. arboretum (GaGMEs), and G. raimondii (GrGMEs). Plants resulting from VIGS infection with GhGME31D clearly showed yellowing, water loss and wilting of leaves and black spots on stems. Measurement of MDA and AsA levels indicated that the plants were more damaged. This indicates that AsA has a substantial impact on plant growth and development. [ABSTRACT FROM AUTHOR]

Taxanes are one of the most widely used classes of breast cancer (BC) therapeutics. Despite the long history of clinical usage, the molecular mechanisms of their action and cancer resistance are still not fully understood. Here we aimed to identify gene expression and molecular pathway activation biomarkers of BC sensitivity to taxane drugs paclitaxel and docetaxel. We used to our knowledge the biggest collection of clinically annotated publicly available literature BC gene expression data (12 datasets, n = 1250) and the experimental clinical BC cohort (n = 12). Seven literature datasets were used for biomarker discovery (n = 914), and the remaining five literature plus one experimental datasets (n = 336) – for the validation. We totally found 34 genes and 29 molecular pathways which could strongly discriminate good and poor responders to taxane treatments. The biomarker genes and pathways were associated with molecular processes related to formation of mitotic spindle and centromeres, and with the spindle assembly mitotic checkpoint. Furthermore, we created gene expression and pathway activation signatures predicting BC response to taxanes. These signatures were tested on the validation BC cohort and demonstrated strong biomarker potential reflected by mean AUC values of 0.76 and 0.77, respectively, which outperforms previously reported analogs. Taken together, these findings can deepen our understanding of mechanism of action of taxanes and potentially improve personalization of treatment in BC. [ABSTRACT FROM AUTHOR]

Background/Objectives: We present hidecan, an R package for generating visualisations that summarise the results of one or more genome-wide association studies (GWAS) and differential expression analyses, as well as manually curated candidate genes, e.g., extracted from the literature. This tool is applicable to all ploidy levels; we notably provide functionalities to facilitate the visualisation of GWAS results obtained for autotetraploid organisms with the GWASpoly package. Results: We illustrate the capabilities of hidecan with examples from two autotetraploid potato datasets. Conclusions: The hidecan package is implemented in R and is publicly available on the CRAN repository and on GitHub. A description of the package, as well as a detailed tutorial, is made available alongside the package. It is also part of the VIEWpoly tool for the visualisation and exploration of results from polyploids computational tools. [ABSTRACT FROM AUTHOR]

Differences between orbital and subcutaneous abdominal fat in the same patient have been noted but not formally investigated, previously. The objective of this research was to compare the differential expression of protein profiles in subcutaneous abdominal and orbital adipose tissues. In this cross-sectional, observational study, orbital fat tissue was sampled from 10 patients who underwent blepharoplasty and agreed to provide a small sample of subcutaneous abdominal fat. Shotgun mass spectrometry was performed on the extracted proteome. Data were analyzed using protein appearance patterns, differential expression and statistical enrichment. Protein analysis revealed significant differences in proteomics and differential expression between the orbital and subcutaneous abdominal adipose tissues, which presented five proteins that were uniquely expressed in the orbital fat and 18 in the subcutaneous abdominal fat. Gene Ontology analysis identified significantly different cellular processes and components related to the extracellular matrix or basement membrane components. This analysis shows the differences between orbital and subcutaneous abdominal fat found in proteomics differential expression, uniquely expressed proteins, and cellular processes. Further research is needed to correlate specific proteins and cellular processes to the mechanism of fat accumulation and obesity. [ABSTRACT FROM AUTHOR]

Abstract Background Circular RNAs (circRNAs) function as essential regulatory elements with pivotal roles in various biological processes. However, their expression profiles and functional regulation during the differentiation of goat myoblasts have not been thoroughly explored. This study conducts an analysis of circRNA expression profiles during the proliferation phase (cultured in growth medium, GM) and differentiation phase (cultured in differentiation medium, DM1/DM5) of skeletal muscle satellite cells (MuSCs) in goats. Results A total of 2,094 circRNAs were identified, among which 84 were differentially expressed as determined by pairwise comparisons across three distinct groups. Validation of the expression levels of six randomly selected circRNAs was performed using reverse transcription PCR (RT-PCR) and quantitative RT-PCR (qRT-PCR), with confirmation of their back-splicing junction sites. Enrichment analysis of the host genes associated with differentially expressed circRNAs (DEcircRNAs) indicated significant involvement in biological processes such as muscle contraction, muscle hypertrophy, and muscle tissue development. Additionally, these host genes were implicated in key signaling pathways, including Hippo, TGF-beta, and MAPK pathways. Subsequently, employing Cytoscape, we developed a circRNA-miRNA interaction network to elucidate the complex regulatory mechanisms underlying goat muscle development, encompassing 21 circRNAs and 47 miRNAs. Functional assays demonstrated that circTGFβ2 enhances myogenic differentiation in goats, potentially through a miRNA sponge mechanism. Conclusion In conclusion, we identified the genome-wide expression profiles of circRNAs in goat MuSCs during both proliferation and differentiation phases, and established that circTGFβ2 plays a role in the regulation of myogenesis. This study offers a significant resource for the advanced exploration of the biological functions and mechanisms of circRNAs in the myogenesis of goats.

Abstract Vitamin C, also referred to as ascorbic acid (AsA), is recognized for its capacity to cure and avert scurvy, and it is crucial for regular human growth and development. In various crops, AsA participates in stress response mechanisms mediated by abscisic acid and has been discovered to have a crucial function in the morphogenesis, growth, development, and production of male gametes in plants. GDP-D-mannose 3′,5′-epimerase (GME) is essential in the synthesis of vitamin C. Our research identified 91, 83, 51, and 46 genes, respectively, found in G. barbadense (GbGMEs), G. hirsutum (GhGMEs), G. arboretum (GaGMEs), and G. raimondii (GrGMEs). Plants resulting from VIGS infection with GhGME31D clearly showed yellowing, water loss and wilting of leaves and black spots on stems. Measurement of MDA and AsA levels indicated that the plants were more damaged. This indicates that AsA has a substantial impact on plant growth and development.

Abstract Single-cell RNA-sequencing (scRNA-seq) provides gene expression profiles of individual cells from complex samples, facilitating the detection of cell type-specific marker genes. In scRNA-seq experiments with multiple donors, the population level variation brings an extra layer of complexity in cell type-specific gene detection, for example, they may not appear in all donors. Motivated by this observation, we develop a statistical model named scCTS to identify cell type-specific genes from population-level scRNA-seq data. Extensive data analyses demonstrate that the proposed method identifies more biologically meaningful cell type-specific genes compared to traditional methods.

Abstract Background The study aims to comprehensively combine colorectal cancer data cohorts in order to analyze the effects of various DNA methylation-coding genes on colorectal cancer patients. The annual incidence and mortality of colorectal cancer are very high, and there are no effective treatments for advanced colorectal cancer. DNA methylation is a method widely used to regulate epigenetics in the molecular mechanism study of tumors. Method Three single-cell cohorts GSE166555, GSE146771, and EMTAB8107, and five transcriptome cohorts GSE17536, GSE39582, GSE72970, and TCGA-CRC (TCGA-COAD and TCGA-READ) were applied in this study. 2 erasers (ALKBH5 and FTO), There are 7 writers (METTL3, METTL14, WTAP, VIRMA, RBM15, RBM15B, and ZC3H13) and 11 readers (YTHDC1, IGF2BP1, IGF2BP2, IGF2BP3, YTHDF1, YTHDF3, YTHDC2, and HNRNPA2B1, YTHDF2, HNRNPC and RBMX), a total of 20 M6A regulators, were used as the basis of the dataset in this study and were applied to the construction of molecular typing and prognostic models. Drugs that are differentially sensitive in methylation-regulated gene-related prognostic models were identified using the ConsensusClusterPlus package, which was also used to identify distinct methylation regulatory expression patterns in colorectal cancer and to model the relationship between tissue gene expression profiles and drug IC50 values. Finally, TISCH2 assessed which immune cells were significantly expressed with M6A scores. The immunosuppression of M6A methylation is spatially explained. Results This study used data from 583 CRC patients in the TCGA-CRC cohort. Firstly, the mutation frequency and CNV variation frequency of 20 m6A modification-related factors were analyzed, and the corresponding histogram and heat map were drawn. The study next analyzed the expression variations between mutant and wild forms of the VIRMA gene and explored differences in the expression of these variables in tumor and normal tissues. In addition, the samples were divided into different subgroups by molecular clustering method based on m6A modification, and each subgroup’s expression and clinicopathological characteristics were analyzed. Finally, we compared prognostic differences, tumor microenvironment (TME) characteristics, immune cell infiltration, and gene function enrichment among different subpopulations. We also developed a colorectal cancer m6A-associated gene signature and validated its prognostic effects across multiple cohorts. Finally, using single-cell RNA sequencing data, we confirmed that tumor cells show elevated expression of m6A-related gene signatures. Discussion This study explored the mutation frequency, expression differences, interactions, molecular clustering, prognostic effect, and association with tumor characteristics of m6A modification-related factors in CRC and validated them at the single-cell level. These results clarify the association between m6A alteration and colorectal cancer (CRC) and offer important insights into the molecular recognition and management of cancer.

Abstract [Objective] WRKY is one of the plant specific transcription factor families, involved in various plant life activities. However, currently there are few reports related to the WRKY70 gene in strawberry. Analyzing the role of WRKY70 homologous genes in strawberry in response to stress will help accelerate the application of molecular breeding technology and cultivate new strawberry germplasm resources. [Methods] The FaWRKY70 gene was cloned from ‘Benihoppe’ strawberry fruits using homologous cloning method. Its conserved domain, physicochemical properties, protein structure, and evolutionary relationship were analyzed using bioinformatics. Expression pattern analysis was performed using qRT-PCR. [Results] The FaWRKY70 gene had a length of 1 020 bp and encodes 339 amino acids. Homologous gene alignment revealed that FaWRKY70 had a high degree of amino acid sequence similarity with species in the same family such as apple and peony. The homologous genes were mostly related to plant responses to biotic and abiotic stress, suggesting that FaWRKY70 may be involved in resistance to stress. FaWRKY70 was expressed in different organs of strawberry, with significant differences. The expression level was highest in flowers and lowest in fruits. Under salicylic acid treatment, the FaWRKY70 gene was quickly responded, reaching its highest expression level after 3 hours, and gradually decreased thereafter. Under the treatment with methyl jasmonate, the FaWRKY70 gene showed a slight degree of induction and an overall downward trend. [Conclusion] FaWRKY70 is involved in growth and hormone signal transduction through different response modes in strawberry.

Background: The study aims to comprehensively combine colorectal cancer data cohorts in order to analyze the effects of various DNA methylation-coding genes on colorectal cancer patients. The annual incidence and mortality of colorectal cancer are very high, and there are no effective treatments for advanced colorectal cancer. DNA methylation is a method widely used to regulate epigenetics in the molecular mechanism study of tumors. Method: Three single-cell cohorts GSE166555, GSE146771, and EMTAB8107, and five transcriptome cohorts GSE17536, GSE39582, GSE72970, and TCGA-CRC (TCGA-COAD and TCGA-READ) were applied in this study. 2 erasers (ALKBH5 and FTO), There are 7 writers (METTL3, METTL14, WTAP, VIRMA, RBM15, RBM15B, and ZC3H13) and 11 readers (YTHDC1, IGF2BP1, IGF2BP2, IGF2BP3, YTHDF1, YTHDF3, YTHDC2, and HNRNPA2B1, YTHDF2, HNRNPC and RBMX), a total of 20 M6A regulators, were used as the basis of the dataset in this study and were applied to the construction of molecular typing and prognostic models. Drugs that are differentially sensitive in methylation-regulated gene-related prognostic models were identified using the ConsensusClusterPlus package, which was also used to identify distinct methylation regulatory expression patterns in colorectal cancer and to model the relationship between tissue gene expression profiles and drug IC50 values. Finally, TISCH2 assessed which immune cells were significantly expressed with M6A scores. The immunosuppression of M6A methylation is spatially explained. Results: This study used data from 583 CRC patients in the TCGA-CRC cohort. Firstly, the mutation frequency and CNV variation frequency of 20 m6A modification-related factors were analyzed, and the corresponding histogram and heat map were drawn. The study next analyzed the expression variations between mutant and wild forms of the VIRMA gene and explored differences in the expression of these variables in tumor and normal tissues. In addition, the samples were divided into different subgroups by molecular clustering method based on m6A modification, and each subgroup's expression and clinicopathological characteristics were analyzed. Finally, we compared prognostic differences, tumor microenvironment (TME) characteristics, immune cell infiltration, and gene function enrichment among different subpopulations. We also developed a colorectal cancer m6A-associated gene signature and validated its prognostic effects across multiple cohorts. Finally, using single-cell RNA sequencing data, we confirmed that tumor cells show elevated expression of m6A-related gene signatures. Discussion: This study explored the mutation frequency, expression differences, interactions, molecular clustering, prognostic effect, and association with tumor characteristics of m6A modification-related factors in CRC and validated them at the single-cell level. These results clarify the association between m6A alteration and colorectal cancer (CRC) and offer important insights into the molecular recognition and management of cancer. [ABSTRACT FROM AUTHOR]

Caenorhabditis elegans males undergo sex-specific tail tip morphogenesis (TTM) under the control of the DM-domain transcription factor DMD-3. To find genes regulated by DMD-3, we performed RNA-seq of laser-dissected tail tips. We identified 564 genes differentially expressed (DE) in wild-type males versus dmd-3(-) males and hermaphrodites. The transcription profile of dmd-3(-) tail tips is similar to that in hermaphrodites. For validation, we analyzed transcriptional reporters for 49 genes and found male-specific or malebiased expression for 26 genes. Only 11 DE genes overlapped with genes found in a previous RNAi screen for defective TTM. GO enrichment analysis of DE genes finds upregulation of genes within the unfolded protein response pathway and downregulation of genes involved in cuticle maintenance. Of the DE genes, 40 are transcription factors, indicating that the gene network downstream of DMD-3 is complex and potentially modular. We propose modules of genes that act together in TTM and are co-regulated by DMD-3, among them the chondroitin synthesis pathway and the hypertonic stress response. [ABSTRACT FROM AUTHOR]

Drought is a major abiotic stress factor that reduces agricultural productivity. Understanding the molecular regulatory network of drought response in winter rape is of great significance for molecular Brassica rapa. In order to comprehensively analyze the network expression of DEGs and DEMIs in winter rape under drought stress, in this study we used Longyou 7 as the experimental material to identify DEGs and DEMIs related to drought stress by transcriptome and miRNA sequencing. A total of 14–15 key differential mRNA genes related to drought stress and biological stress were screened out under different treatments in the three groups. and 32 differential miRNAs were identified through targeted regulatory relationships, and the mRNA expression of 20 target genes was negatively regulated by the targeting regulatory relationship. It is mainly enriched in starch and sucrose metabolism, carbon metabolism and other pathways. Among them, gra-MIR8731-p3_2ss13GA18GA regulated the expression of multiple mRNAs in the three treatments. miRNA is mainly involved in the drought resistance of Chinese cabbage winter rape by regulating the expression of target genes, such as starch and sucrose metabolism, amino acid biosynthesis, and carbon metabolism. These miRNAs and their target genes play an indispensable role in winter rapeseed drought stress tolerance regulation. [ABSTRACT FROM AUTHOR]

To analyze the N6-methyladenosine (m6A) modification profile in systemic lupus erythematosus (SLE) using bioinformatics methods and public databases. We establish an SLE m6A modification expression profile and analyze the potential roles of m6A-related differentially expressed genes (DEGs) in SLE using public data. DEGs are obtained from the ADEx database, and the m6A modification profile in SLE is analyzed using the m6A GEO dataset (GSE173312). Additionally, we perform GO/Pathway annotation analysis of m6A DEGs using DAVID. In SLE patients, the expression of the m6A writer components RBM15B and the eraser enzyme FTO are downregulated, while the expression of the reader IGFBP3 is upregulated. The SLE m6A modification profile include 181 genes, with 123 genes upregulated and 58 genes downregulated in expression. These genes are primarily involved in biological processes such as cell apoptosis and cell cycle pathways, type I interferon signaling pathway, DNA replication, and B cell MHC II molecule regulation. Abnormalities in PBMCs cell m6A modification are observed in SLE patients and may potentially contribute to the development and occurrence of the disease [ABSTRACT FROM AUTHOR]

Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and serve crucial regulatory functions in both animals and plants. Nevertheless, there is limited understanding of lncRNAs and their patterns of expression and roles in sharks. In the current study, we systematically identified and characterized lncRNAs in the blue shark (Prionace glauca) from four tissues (liver, spleen, muscle, and kidney) using high-throughput sequencing and bioinformatics tools. A total of 21,932 high-confidence lncRNAs were identified, with 8984 and 3067 stably and tissue-specific expressed lncRNAs, respectively. In addition, a total of 45,007 differentially expressed (DE) lncRNAs were obtained among tissues, with kidney versus muscle having the largest numbers across tissues. DE lncRNAs trans target protein-coding genes were predicted, and functional gene ontology enrichment of these genes showed GO terms such as muscle system processes, cellular/metabolic processes, and stress and immune responses, all of which correspond with the specific biological functions of each tissue analyzed. These results advance our knowledge of lncRNAs in sharks and present novel data on tissue-specific lncRNAs, providing key information to support future functional shark investigations. [ABSTRACT FROM AUTHOR]

Introduction: Chronic alcoholism is one of the most common neurological diseases in modern society. However, the key mechanisms underlying learning and memory impairments caused by chronic alcohol exposure remain unclear. In this study, a microRNA-messenger RNA (miRNA-mRNA) network was constructed to explore the potential function of key genes in chronic alcohol exposure, their effects on the hippocampus, and their mechanisms which facilitate brain injury in mice. Methods: The Morris water maze test was used to assess the learning ability of mice in each group. Mitochondrial ATPase activity and H2S levels in the hippocampi of mice were determined. Differentially expressed miRNAs and mRNAs in the mouse hippocampus were identified using second-generation sequencing. Using the TargetScan, miRTarBase, and miRDB databases, we predicted miRNA target genes and constructed a miRNA-mRNA regulatory network. Furthermore, using the Gene Ontology and KEGG databases we performed functional enrichment and protein-protein interaction analyses. Real-time quantitative polymerase chain reaction (qPCR) and other methods were employed to verify the mRNA expression of related genes. Results: The Morris water maze test revealed that mice exposed to chronic alcohol exhibited a significantly reduced learning ability compared to the control group (p < 0.05). Compared with the control group, the activity of mitochondrial ATPase in the hippocampal tissue of alcohol-treated mice was significantly decreased (p < 0.01), suggesting brain injury. In the model group, H2S significantly increased in the mice hippocampi (p < 0.01), indicating that chronic alcohol exposure could activate cystathionine β-synthase (CBS) and catalyze the mass formation of H2S, suggesting brain injury. A total of 208 differentially expressed miRNAs and 377 differentially expressed mRNAs were screened through bioinformatic analysis. Enrichment analysis indicated that the main pathways were involved in neurodegeneration and regulation of the Wnt signaling pathway. The PCR detected a significant down regulation in the expressions of FOS and EGR1 genes. Discussion: Consequently, chronic alcohol exposure may regulate the expression of FOS and EGR1 in the hippocampus through miR-222-3p, miR- 132-3p, miR-212-3p, and miR-191-5p, reduce the activity of hippocampal mitochondrial ATPase, activate CBS, catalyze the large amount of H2S formation, and destroy the mitochondrial structure, resulting in decreased learning ability. Our findings revealed valuable genes and miRNAs for the study of chronic alcohol exposure. [ABSTRACT FROM AUTHOR]

By analyzing two large atlases of almost 4 million cells, we show that immune‐senescence involves a gradual loss of cellular identity, reflecting increased cellular heterogeneity, for effector, and cytotoxic immune cells. The effects are largely similar in both males and females and were robustly reproduced in two atlases, one assembled from 35 diverse studies including 678 adults, the other the OneK1K study of 982 adults. Since the mean transcriptional differences among cell‐types remain constant across age deciles, there is little evidence for the alternative mechanism of convergence of cell‐type identity. Key pathways promoting activation and stemness are down‐regulated in aged T cells, while CD8 TEM and CD4 CTLs exhibited elevated inflammatory, and cytotoxicity in older individuals. Elevated inflammatory signaling pathways, such as MAPK and TNF‐alpha signaling via NF‐kB, also occur across all aged immune cells, particularly amongst effector immune cells. This finding of lost transcriptional identity with age carries several implications, spanning from a fundamental biological understanding of aging mechanisms to clinical perspectives on the efficacy of immunomodulation in elderly people. [ABSTRACT FROM AUTHOR]

Glycation is a non-enzymatic posttranslational modification coming from the reaction between reducing sugars and free amino groups in proteins, where early glycation products (fructosyl-lysine, FL) and advanced glycation end products (AGEs) are formed. The occurrence of glycation and accumulation of AGEs have been closely associated with hepatocellular carcinoma (HCC). Here, we reported the characterization of differential glycation in HCC using tissue proteomics with stable isotopic labeling; early glycation-modified peptides were enriched with boronate affinity chromatography (BAC), and AGEs-modified peptides were fractionated with basic reversed-phase separation. By this integrated approach, 3717 and 1137 early and advanced glycated peptides corresponding to 4007 sites on 1484 proteins were identified with a false discovery rate (FDR) of no more than 1%. One hundred fifty-five sites were modified with both early and advanced end glycation products. Five early and 7 advanced glycated peptides were quantified to be differentially expressed in HCC tissues relative to paired adjacent tissues. Most (8 out of 10) of the proteins corresponding to the differential glycated peptides have previously been reported with dysregulation in HCC. The results together may deepen our knowledge of glycation as well as provide insights for therapeutics. [ABSTRACT FROM AUTHOR]

Introduction: The purpose of this study was to explore the regulatory mechanisms of FGF2 in carotid atherosclerotic plaque development using bioinformatics analysis. Material and methods: Expression profiles of 32 atheroma plaque (AP) and 32 paired distant macroscopically intact (DMI) tissues samples in the GSE43292 dataset were downloaded from the Gene Expression Omnibus database. Following identification of differential expression genes (DEGs), correlation analysis of fibroblast growth factor 2 (FGF2) and DEGs was conducted. Subsequently, functional enrichment analysis and the proteinprotein interaction network for FGF2 significantly correlated DEGs were constructed. Then, microRNAs (miRNAs) that regulated FGF2 and regulatory pairs of long noncoding RNA (lncRNA)-miRNA were predicted to construct the lncRNA-miRNA-FGF2 network. Results: A total of 101 DEGs between AP and DMI samples were identified, and 31 DEGs were analyzed to have coexpression relationships with FGF2, including 23 positively correlated and 8 negatively correlated DEGs. VAV3 had the lowest r value among all FGF2 negatively correlated DEGs. FGF2 positively correlated DEGs were closely related to "regulation of smooth muscle contraction" (e.g., calponin 1 (CNN1)), while FGF2 negatively correlated DEGs were significantly associated with "platelet activation" (e.g., Vav guanine nucleotide exchange factor 3 (VAV3)). In addition, a total of 12 miRNAs that regulated FGF2 were predicted, and hsa-miR-15a-5p and hsamiR-16-5p were highlighted in the lncRNA-miRNA-FGF2 regulatory network. Conclusions: CNN1 might cooperate with FGF2 to regulate smooth muscle contractility during CAP formation. VAV3 might cooperate with FGF2 to be responsible for the development of CAP through participating in platelet activation. Hsa-miR-15a-5p and hsa-miR-16-5p might participate in the development of CAP via regulating FGF2. [ABSTRACT FROM AUTHOR]

Transcription factors (TFs) play a crucial role in gene expression, and studying them can lay the foundation for future research on the functional characterization of TFs involved in various biological processes. In this study, we conducted a genome-wide identification and analysis of TFs in the thermotolerant basidiomycete fungus, Coriolopsis trogii. The TF repertoire of C. trogii consisted of 350 TFs, with C2H2 and Zn2C6 being the largest TF families. When the mycelia of C. trogii were cultured on PDA and transferred from 25 to 35 °C, 14 TFs were up-regulated and 14 TFs were down-regulated. By analyzing RNA-seq data from mycelia cultured at different temperatures and under different carbon sources, we identified 22 TFs that were differentially expressed in more than three comparisons. Co-expression analysis revealed that seven differentially expressed TFs, including four Zn2C6s, one Hap4_Hap_bind, one HMG_box, and one Zinc_knuckle, showed significant correlation with 729 targeted genes. Overall, this study provides a comprehensive characterization of the TF family and systematically screens TFs involved in the high-temperature adaptation of C. trogii, laying the groundwork for further research into the specific roles of TFs in the heat tolerance mechanisms of filamentous fungi. [ABSTRACT FROM AUTHOR]

Ras-related Rap1A GTPase is implicated in pancreas β-cell insulin secretion and is stimulated by the cAMP sensor Epac2, a guanine exchange factor and activator of Rap1 GTPase. In this study, we examined the differential proteomic profiles of pancreata from C57BL/6 Rap1A-deficient (Null) and control wild-type (WT) mice with nanoLC-ESI-MS/MS to assess targets of Rap1A potentially involved in insulin regulation. We identified 77 overlapping identifier proteins in both groups, with 8 distinct identifier proteins in Null versus 56 distinct identifier proteins in WT mice pancreata. Functional enrichment analysis showed four of the eight Null unique proteins, ERO1-like protein β (Ero1lβ), triosephosphate isomerase (TP1), 14-3-3 protein γ, and kallikrein-1, were exclusively involved in insulin biogenesis, with roles in insulin metabolism. Specifically, the mRNA expression of Ero1lβ and TP1 was significantly (p < 0.05) increased in Null versus WT pancreata. Rap1A deficiency significantly affected glucose tolerance during the first 15–30 min of glucose challenge but showed no impact on insulin sensitivity. Ex vivo glucose-stimulated insulin secretion (GSIS) studies on isolated Null islets showed significantly impaired GSIS. Furthermore, in GSIS-impaired islets, the cAMP-Epac2-Rap1A pathway was significantly compromised compared to the WT. Altogether, these studies underscore an essential role of Rap1A GTPase in pancreas physiological function. [ABSTRACT FROM AUTHOR]

Background: Fold change is a common metric in biomedical research for quantifying group differences in omics variables. However, inconsistent calculation methods and inadequate reporting lead to discrepancies in results. This study evaluated various fold-change calculation methods aiming at a recommendation of a preferred approach. Methods: The primary distinction in fold-change calculations lies in defining group expected values for log ratio computation. To challenge method interchangeability in a "stress test" scenario, we generated diverse artificial data sets with varying distributions (identity, uniform, normal, log-normal, and a mixture of these) and compared calculated fold-changes to known values. Additionally, we analyzed a multi-omics biomedical data set to estimate to what extent the findings apply to real-world data. Results: Using arithmetic means as expected values for treatment and reference groups yielded inaccurate fold-change values more frequently than other methods, particularly when subgroup distributions and/or standard deviations differed significantly. Conclusions: The arithmetic mean method, often perceived as standard or picked without considering alternatives, is inferior to other definitions of the group expected value. Methods using median, geometric mean, or paired fold-change combinations are more robust against violations of equal variances or dissimilar group distributions. Adhering to methods less sensitive to data distribution without trade-offs and accurately reporting calculation methods in scientific reports is a reasonable practice to ensure correct interpretation and reproducibility. [ABSTRACT FROM AUTHOR]

BACKGROUND: There are differentially expressed genes in acute intracerebral hemorrhage, which are related to the occurrence and development of intracerebral hemorrhage OBJECTIVE: To screen differentially expressed genes and key genes in brain tissue of a rat model with acute intracerebral hemorrhage, to validate them through qPCR, and to analyze the relationships between key genes and the neurological function and brain tissue water content after intracerebral hemorrhage. METHODS: Seventy-eight Sprague-Dawley rats were randomly divided into two groups: in intracerebral hemorrhage group, a rat model of acute intracerebral hemorrhage was made using collagenase injection at the right caudate nucleus; and in sham-operated group, rats were injected with equal amount of saline at the same site. RNA was extracted from rat brain tissues of both groups using the TRIzol method and transcriptome sequencing technology was used to identify differentially expressed genes in brain tissues of acute intracerebral hemorrhage, which were then verified by qPCR and analyzed for the relationships between the genes and neurological function and brain tissue water content after intracerebral hemorrhage. And the key genes were analyzed by GO and KEGG functional enrichment analysis in combination with bioinformatics. RESULTS AND CONCLUSION: Ten key genes were identified, including CXCL8, SERPINE1, TFPI2, CXCR4, GDA, KCNQ5, ERICH3, SCN3B, CACNA1E, and CCL20. The contents of GDA, KCNQ5, ERICH3, SCN3B, and CACNA1E in the intracerebral hemorrhage group were lower than those in the sham-operated group (P < 0.05). The contents of CXCL8, SERPINE1, TFPI2, CXCR4 and CCL20 in the intracerebral hemorrhage group were higher than those in the sham-operated group (P < 0.05). The contents of GDA, KCNQ5, ERICH3, SCN3B, and CACNA1E were positively correlated with brain tissue water content and neurologic deficit score (P < 0.05), while the contents of CXCL8, SERPINE1, TFPI2, CXCR4 and CCL20 were negatively correlated with brain tissue water content and neurologic deficit score (P < 0.05). GO analysis indicated that differentially expressed genes were mainly enriched in two biological processes (leukocyte chemotaxis and chemokine-mediated signaling pathways), two cell components (cation channel complexes and ion channel complexes), and two molecular functions (gated channel activity and ion channel activity). KEGG analysis indicated that differentially expressed genes were concentrated in tumor necrosis factor signaling pathway, glutamatergic synapses and GABAergic synapses. To conclude, the differentially expressed genes in intracerebral hemorrhage include CXCL8, SERPINE1, TFPI2, CXCR4, GDA, KCNQ5, ERICH3, SCN3B, CACNA1E, and CCL20, and these genes are related to brain tissue water content and neurological function after intracerebral hemorrhage. These genes are mainly enriched in cell components, binding functions, cellular protrusions, and other related biological functions. [ABSTRACT FROM AUTHOR]

The sperm‐associated antigen 11a (Spag11a) gene is exclusively expressed in the caput epididymis. Our previous studies demonstrated that small interfering RNA (siRNA)‐mediated ablation of this gene resulted in increased proliferation of epididymal epithelial cells. Further, active immunization‐mediated ablation of SPAG11A protein increased the susceptibility of male reproductive tract tissues to diethylnitrosamine (DEN)‐induced tumorigenesis. In this study, we report that the caput epididymis of Spag11a knockout mice displayed hyperplasia and inflammation, while the caput epididymis of wild‐type mice exhibited normal anatomical structure. Global transcriptome analyses in the caput epididymis of knockout mice indicated differential expression of genes involved in a variety of cellular processes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses suggested that the absence of Spag11a may activate microRNAs associated with cancer, chemical carcinogenesis‐receptor activation, and chemical carcinogenesis‐DNA adducts pathways; which may contribute to the promotion of tumorigenesis in the epididymis. The susceptibility of caput epididymis to chemically induced carcinogenesis in Spag11a knockout mice was analyzed. Histological analyses indicated that while the epididymis of wild‐type mice did not show any signs of tumorigenesis, knockout mice displayed hyperplasia, anaplasia, dysplasia, neoplasia, and inflammation in the caput epididymis. Our results provide concrete evidence that deletion of Spag11a induces histopathological and molecular changes that contribute to tumorigenesis. It is possible that the expression of Spag11a gene could be one of the reasons for the rarity of epididymal cancers. The involvement of an epididymal gene in tumorigenesis is being demonstrated for the first time. Significance statement: Epididymal cancers are rare, and it was proposed that a large number of factors that are specifically expressed in the epididymis contribute to this unique property. The Spag11a gene is specifically expressed in the epididymis. We demonstrated that ablation of Spag11a gene in epididymal primary cells induced proliferation, while overexpression in an immortalized caput‐derived cell line inhibited proliferation. We also demonstrated that ablation of SPAG11A protein by active immunization rendered the microenvironment of the epididymis favorable for tumorigenesis. We propose that Spag11a gene could be one of the factors that renders the epididymis resistant to tumorigenesis. In‐depth analysis on the role of this gene could provide strategies to address tumorigenesis in other organ systems as well. [ABSTRACT FROM AUTHOR]

Ramie is one of the most important fiber crops in China, with fibers extracted from stem barks having been used as textile materials for thousands of years. DNA methylation is an important epigenetic modification involved in plant growth and development. However, the role of methylation in ramie fiber growth remains poorly understood. In the present study, we investigated the DNA methylation landscape of the nuclear genome in bark sections taken from the top (TPS) and the middle (MPS) of the stems of ramie plants, which represent different stages of fiber growth, using whole-genome bisulfite sequencing. We detected 7,709,555 and 8,508,326 5-methylcytosines in the TPS and MPS genomes, respectively. The distribution of methylation across three sequence contexts, CG, CHG, and CHH, varied greatly among gene elements, with methylation at CHH being the most prevalent. Comparison of methylation levels between the TPS and MPS genomes revealed 23.162 Mb of differentially methylated genomic regions, encompassing 9485 genes. Among these differentially methylated genes, 841 exhibited altered expression in the MPS genome. Notably, an SND2 ortholog Bni05G006779 showed a negative correlation between its expression and methylation levels. Overexpression of Bni05G006779 in Arabidopsis dramatically increased the number of xylem fibers and the secondary wall thickness of the fibers in the stems of transgenic plants. These findings provide important insights into the involvement of DNA methylation in regulating ramie fiber growth. [ABSTRACT FROM AUTHOR]

Extracellular vesicles (EVs) are of growing interest in the context of screening for highly informative cancer markers. We have previously shown that uterine aspirate EVs (UA EVs) are a promising source of ovarian cancer (OC) diagnostic markers. In this study, we first conducted an integrative analysis of EV-miRNA profiles from UA, malignant ascitic fluid (AF), and a conditioned medium of cultured ascites cells (ACs). Using three software packages, we identified 79 differentially expressed miRNAs (DE-miRNAs) in UA EVs from OC patients and healthy individuals. To narrow down this panel and select miRNAs most involved in OC pathogenesis, we aligned these molecules with the DE-miRNA sets obtained by comparing the EV-miRNA profiles from OC-related biofluids with the same control. We found that 76% of the DE-miRNAs from the identified panel are similarly altered (differentially co-expressed) in AF EVs, as are 58% in AC EVs. Interestingly, the set of miRNAs differentially co-expressed in AF and AC EVs strongly overlaps (40 out of 44 miRNAs). Finally, the application of more rigorous criteria for DE assessment, combined with the selection of miRNAs that are differentially co-expressed in all biofluids, resulted in the identification of a panel of 29 miRNAs for ovarian cancer screening. [ABSTRACT FROM AUTHOR]

Papaya ringspot virus (PRSV) is one of the most devastating viruses of papaya that has significantly hampered papaya production across the globe. Although PRSV resistance is known in some of its wild relatives, such as Vasconcellea cauliflora and in some of the improved papaya genotypes, the molecular basis of this resistance mechanism has not been studied and understood. Plant microRNAs are an important class of small RNAs that regulate the gene expression in several plant species against the invading plant pathogens. These miRNAs are known to manifest the expression of genes involved in resistance against plant pathogens, through modulation of the plant's biochemistry and physiology. In this study we made an attempt to study the overall expression pattern of small RNAs and more specifically the miRNAs in different papaya genotypes from India, that exhibit varying levels of tolerance or resistance to PRSV. Our study found that the expression of some of the miRNAs was differentially regulated in these papaya genotypes and they had entirely different miRNA expression profile in healthy and PRSV infected symptomatic plants. This data may help in improvement of papaya cultivars for resistance against PRSV through new breeding initiatives or biotechnological approaches such as genome editing. [ABSTRACT FROM AUTHOR]

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IntroductionAphids are phloem sap-sucking insects and are a serious destructive pest of several crop plants. Aphids are categorized as “generalists” or “specialists” depending on their host range. Myzus persicae (Sulz.) is a generalist aphid with a broad host range while Lipaphis erysimi (Kalt.), a specialist aphid, has a narrow host range. Aphid infestation involves several sequential stages including host recognition and selection, overcoming primary plant defence barriers, feeding on phloem sap and detoxification of host defence responses. Information on the molecular basis of variations between generalist and specialist aphids with reference to the above processes is limited.MethodsIn the current study, we generated transcriptome data of M. persicae and L. erysimi from adult and nymph stages and analysed the differential expression of genes between adults of the generalist and specialist aphid and similarly, between nymphs of the two aphid species. We categorized these differentially expressed genes into nine different categories namely, chemosensation-related, plant cell wall degrading enzymes, detoxification-related, digestive enzymes, peptidases, carbohydrate-, lipid-, amino acid-metabolism and reproduction. We also identified putative effector molecules in both M. persicae and L. erysimi from the transcriptome data,Results and discussionGene expression analysis identified 7688 and 8194 differentially expressed unigenes at adult and nymph stages, respectively of M. persicae and L. erysimi. M. persicae showed significantly higher levels of expression in a greater number of unigenes (5112 in adults and 5880 in nymphs) in contrast to the specialist, L. erysimi (2576 in adults and 2314 in nymphs) in both developmental stages. In addition, M. persicae displayed a greater number (350 in adults and 331 in nymphs) of upregulated unigenes involved in important processes such as host recognition, plant cell wall degradation, detoxification, digestion and metabolism, which correlate with its dynamic and polyphagous nature in contrast to the specialist (337 in adults and 251 in nymphs). We also observed a greater number of putative effectors in M. persicae (948 in adults and 283 in nymphs) than L. erysimi (797 in adults and 245 in nymphs). Based on our analysis, we conclude that the generalist aphid, M. persicae has a more diversified and stronger arsenal of genes that influence its polyphagous feeding behaviour and effective response to plant defence mechanisms against insect-herbivory. Our study provides a compendium of such candidate genes that would be most useful in studies on aphid biology, evolution and control.

The article "QUIC-seq: Quick ultra-affordable high-throughput convenient RNA sequencing" introduces a new method for gene expression analysis called QUIC-seq, which is quick, cost-effective, and suitable for high-throughput applications. The method involves extracting RNA, reverse transcription, Tn5 transposase fragmentation, and direct PCR amplification. QUIC-seq simplifies library construction, reduces costs, and offers high reproducibility. The method was used to identify differentially expressed genes in response to nitrogen and phosphorus stress, as well as in exploring gene regulatory networks. QUIC-seq is compared to other RNA-seq methods, showing advantages in cost, throughput, and efficiency. [Extracted from the article]

Abstract Background Recent advances in imaging-based spatially resolved transcriptomics (im-SRT) technologies now enable high-throughput profiling of targeted genes and their locations in fixed tissues. Normalization of gene expression data is often needed to account for technical factors that may confound underlying biological signals. Results Here, we investigate the potential impact of different gene count normalization methods with different targeted gene panels in the analysis and interpretation of im-SRT data. Using different simulated gene panels that overrepresent genes expressed in specific tissue regions or cell types, we demonstrate how normalization methods based on detected gene counts per cell differentially impact normalized gene expression magnitudes in a region- or cell type-specific manner. We show that these normalization-induced effects may reduce the reliability of downstream analyses including differential gene expression, gene fold change, and spatially variable gene analysis, introducing false positive and false negative results when compared to results obtained from gene panels that are more representative of the gene expression of the tissue’s component cell types. These effects are not observed with normalization approaches that do not use detected gene counts for gene expression magnitude adjustment, such as with cell volume or cell area normalization. Conclusions We recommend using non-gene count-based normalization approaches when feasible and evaluating gene panel representativeness before using gene count-based normalization methods if necessary. Overall, we caution that the choice of normalization method and gene panel may impact the biological interpretation of the im-SRT data.

Abstract Background Maedi-visna virus (MVV) is a lentivirus that infects monocyte/macrophage lineage cells in sheep, goats, and wild ruminants and causes pneumonia, mastitis, arthritis, and encephalitis. The immune response to MVV infection is complex, and a complete understanding of its infection and pathogenesis is lacking. This study investigated the in vivo transcriptomic patterns of lung tissues in sheep exposed to MVV using the RNA sequencing technology. Result The results indicated that 2,739 genes were significantly differentially expressed, with 1,643 downregulated genes and 1,096 upregulated genes. Many variables that could be unique to MVV infections were discovered. Gene Ontology analysis revealed that a significant proportion of genes was enriched in terms directly related to the immune system and biological responses to viral infections. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the most enriched pathways were related to virus-host cell interactions and inflammatory responses. Numerous immune-related genes, including those encoding several cytokines and interferon regulatory factors, were identified in the protein-protein interaction network of differentially expressed genes (DEGs). The expression of DEGs was evaluated using real-time polymerase chain reaction and western blot analysis. CXCL13, CXCL6, CXCL11, CCR1, CXCL8, CXCL9, CXCL10, TNFSF8, TNFRSF8, IL7R, IFN-γ, CCL2, and MMP9 were upregulated. Immunohistochemical analysis was performed to identify the types of immune cells that infiltrated MVV-infected tissues. B cells, CD4+ and CD8+ T cells, and macrophages were the most prevalent immune cells correlated with MVV infection in the lungs. Conclusion Overall, the findings of this study provide a comprehensive understanding of the in vivo host response to MVV infection and offer new perspectives on the gene regulatory networks that underlie pathogenesis in natural hosts.

Abstract Background Extrachromosomal circular DNAs (eccDNAs) have been reported to play a key role in the occurrence and development of various diseases. However, the characterization and role of eccDNAs in pulmonary arterial hypertension (PAH) remain unclear. Methods In the discovery cohort, we first explored eccDNA expression profiles by Circle-sequencing analysis. The candidate eccDNAs were validated by routine polymerase chain reaction (PCR), TOPO-TA cloning and Sanger sequencing. In the validation cohort, 30 patients with PAH and 10 healthy controls were recruited for qPCR amplification to detect the candidate eccDNAs. Datas at the baseline were collected, including clinical background, biochemical variables, echocardiography and hemodynamic factors. Receiver operating characteristic curve was used to investigate the diagnostic effect of the eccDNA. Results We identified a total of 21,741 eccDNAs in plasma samples of 3 IPAH patients and 3 individuals in good health, and the expression frequency, GC content, length distribution, and genome distribution of the eccDNAs were thoroughly characterized and analyzed. In the validation cohort, 687 eccDNAs were differentially expressed in patients with IPAH compared with healthy controls (screening threshold: |FC|≥2 and P

Background Expression proteomics involves the global evaluation of protein abundances within a system. In turn, differential expression analysis can be used to investigate changes in protein abundance upon perturbation to such a system. Methods Here, we provide a workflow for the processing, analysis and interpretation of quantitative mass spectrometry-based expression proteomics data. This workflow utilises open-source R software packages from the Bioconductor project and guides users end-to-end and step-by-step through every stage of the analyses. As a use-case we generated expression proteomics data from HEK293 cells with and without a treatment. Of note, the experiment included cellular proteins labelled using tandem mass tag (TMT) technology and secreted proteins quantified using label-free quantitation (LFQ). Results The workflow explains the software infrastructure before focusing on data import, pre-processing and quality control. This is done individually for TMT and LFQ datasets. The application of statistical differential expression analysis is demonstrated, followed by interpretation via gene ontology enrichment analysis. Conclusions A comprehensive workflow for the processing, analysis and interpretation of expression proteomics is presented. The workflow is a valuable resource for the proteomics community and specifically beginners who are at least familiar with R who wish to understand and make data-driven decisions with regards to their analyses.

The widespread availability of high-dimensional biological data has made the simultaneous screening of many biological characteristics a central problem in computational and high-dimensional biology. As the dimensionality of datasets continues to grow, so too does the complexity of identifying biomarkers linked to exposure patterns. The statistical analysis of such data often relies upon parametric modeling assumptions motivated by convenience, inviting opportunities for model misspecification. While estimation frameworks incorporating flexible, data adaptive regression strategies can mitigate this, their standard variance estimators are often unstable in high-dimensional settings, resulting in inflated Type-I error even after standard multiple testing corrections. We adapt a shrinkage approach compatible with parametric modeling strategies to semiparametric variance estimators of a family of efficient, asymptotically linear estimators of causal effects, defined by counterfactual exposure contrasts. Augmenting the inferential stability of these estimators in high-dimensional settings yields a data adaptive approach for robustly uncovering stable causal associations, even when sample sizes are limited. Our generalized variance estimator is evaluated against appropriate alternatives in numerical experiments, and an open source R/Bioconductor package, biotmle, is introduced. The proposal is demonstrated in an analysis of high-dimensional DNA methylation data from an observational study on the epigenetic effects of tobacco smoking.

As ancient organisms, tree ferns play a crucial role as an evolutionary bridge between lower and higher plant species, providing various utilitarian benefits. However, they face challenges such as overexploitation, climate change, adverse environmental conditions, and insect pests, resulting in conservation concerns. In this study, we provide an overview of metabolic and transcriptomic resources of leaves in two typical tree ferns, A. spinulosa and A. metteniana, and explore the resistance genes for the first time. The landscape of metabolome showed that the compound skimmin may hold medicinal significance. A total of 111 differentially accumulated metabolites (DAMs) were detected, with pathway enrichment analysis highlighting 14 significantly enriched pathways, including 2-oxocarboxylic acid metabolism possibly associated with environmental adaptations. A total of 14,639 differentially expressed genes (DEGs) were found, among which 606 were resistance (R) genes. We identified BAM1 as a significantly differentially expressed R gene, which is one of the core genes within the R gene interaction network. Both the maximum-likelihood phylogenetic tree and the PPI network revealed a close relationship between BAM1, FLS2, and TMK. Moreover, BAM1 showed a significant positive correlation with neochlorogenic acid and kaempferol-7-O-glucoside. These metabolites, known for their antioxidant and anti-inflammatory properties, likely play a crucial role in the defense response of tree ferns. This research provides valuable insights into the metabolic and transcriptomic differences between A. spinulosa and A. metteniana, enhancing our understanding of resistance genes in tree ferns. [ABSTRACT FROM AUTHOR]

With the development of gene testing technology, we have found many different genes, and lncRNA is one of them. LncRNAs refer to a non-protein coding RNA molecule with a length of more than 200bp, which is one of the focuses of research on human malignant diseases such as LUAD. LncRNAs act as an oncogene or inhibitor to regulate the occurrence and progression of tumors. The differential expression of LncRNAs promotes or inhibits the progression of lung adenocarcinoma by affecting cell proliferation, metastasis, invasion, and apoptosis, thus affecting the prognosis and survival rate of patients. Therefore, LncRNAs can be used as a potential target for diagnosis and treatment of cancer. The early diagnosis of the disease was made through the detection of tumor markers. Because lung adenocarcinoma is not easy to diagnose in the early stage and tumor markers are easy to ignore, LncRNAs play an important role in the diagnosis and treatment of lung adenocarcinoma. The main purpose of this article is to summarize the known effects of LncRNAs on lung adenocarcinoma, the effect of differential expression of LncRNAs on the progression of lung adenocarcinoma, and related signal transduction pathways. And to provide a new idea for the future research of lung adenocarcinoma-related LncRNAs. [ABSTRACT FROM AUTHOR]

Banana Fusarium wilt is a devastating disease threatening the production of many agricultural plants, with no effective and radical control measures identified and applied to date. At present, one of the most effective ways to manage the diseases by selecting, breeding, and cultivating banana varieties with very high Fusarium wilt resistance. To this end, this study utilized transcriptome sequencing technology to analyze Fusarium wilt resistance in the root system, leaves, and corms of healthy and diseased Baodaojiao banana (Fusarium wilt resistance variety) plants. The DEGs identified in the roots, leaves, and corms included transcription factors such as bHLH, WRKY, NAC, ERF, the enzymes mannan synthase, alkaline/neutral invertase, galacturonosyltransferase and phosphoenolpyruvate carboxylase kinase, and other related enzyme genes. Additionally, among the differentially expressed enzyme genes involved in plant defense processes (peroxidase, glutathione S-transferase, β-glucosidase, laccase, cellulose synthase, and chitinase), peroxidase was the most abundant. Moreover, most of the differentially expressed genes (DEGs) were expressed at markedly higher levels in healthy plants than in diseased plants, and such peroxidase genes may be significantly associated with plant Fusarium wilt resistance. The results of this study provide the basis for the study of the molecular defense mechanisms of Baodaojiao banana plants against Fusarium wilt; provide reference data for the further exploration of the functions and complex network regulatory mechanisms of Fusarium wilt resistance genes. [ABSTRACT FROM AUTHOR]

Flavonoids are crucial medicinal active ingredients in Ginkgo biloba L. However, the effect of protein post-translational modifications on flavonoid biosynthesis remains poorly explored. Lysine acetylation, a reversible post-translational modification, plays a crucial role in metabolic regulation. This study aims to investigate the potential role of acetylation in G. biloba flavonoid biosynthesis. Through comprehensive analysis of transcriptomes, metabolomes, proteomes and acetylated proteins in different tissues, a total of 11,788 lysine acetylation sites were identified on 4324 acetylated proteins, including 89 acetylation sites on 23 proteins. Additionally, 128 types of differentially accumulated flavonoids were identified among tissues, and a dataset of differentially expressed genes related to the flavonoid biosynthesis pathway was constructed. Twelve (CHI, C3H1, ANR, DFR, CCoAOMT1, F3H1, F3H2, CCoAOMT2, C3H2, HCT, F3′5′H and FG2) acetylated proteins that might be involved in flavonoid biosynthesis were identified. Specifically, we found that the modification levels of CCoAOMT1 and F3′5′H sites correlated with the catalytic production of homoeriodictyol and dihydromyricetin, respectively. Inhibitors of lysine deacetylase (trichostatin A) impacted total flavonoid content in different tissues and increased flavonoid levels in G. biloba roots. Treatment with trichostatin A revealed that expression levels of GbF3′5′H and GbCCoAOMT1 in stems and leaves aligned with total flavonoid content variations, while in roots, expression levels of GbC3H2 and GbFG2 corresponded to total flavonoid content changes. Collectively, these findings reveal for the first time the important role of acetylation in flavonoid biosynthesis. [ABSTRACT FROM AUTHOR]

Research indicates that long noncoding RNAs (lncRNAs) contribute significantly to fibrotic diseases. Although lncRNAs may play a role in hypertrophic scars after burns, its mechanisms remain poorly understood. Using chip technology, we compared the lncRNA expression profiles of burn patients and healthy controls (HCs). Microarray results were examined by quantitative reverse-transcription polymerase chain reaction (RT-PCR) to verify their reliability. The biological functions of differentially expressed mRNAs and the relationships between genes and signaling pathways were investigated by Gene Ontology (GO) and pathway analyses, respectively. In contrast with HCs, it was found that 2738 lncRNAs (1628 upregulated) and 2166 mRNAs (1395 upregulated) were differentially expressed in hypertrophic scars after burn. Results from RT-PCR were consistent with those from microarray. GO and pathway analyses revealed that the differentially expressed mRNAs are mainly associated with processes related to cytokine secretion in the immune system, notch signaling, and MAPK signaling. The lncRNA expression profiles of hypertrophic scars after burn changed significantly compared with HCs. It was believed that the transcripts could be used as potential targets for inhibiting abnormal scar formation in burn patients. ● Chip technology was used to detect the differences in lncRNAs and mRNAs expression. ● The lncRNAs and mRNAs expression profiles of hypertrophic scars after burn differed. ● Processes presented in hypertrophic scars related to immune system、signaling pathway. ● The study may provide ideas for the treatment of hypertrophic scar after burn. [ABSTRACT FROM AUTHOR]

Simple Summary: The oriental fruit fly, Bactrocera dorsalis, has become a major threat to fruit and vegetable production due to the serious damage it causes, its worldwide distribution and invasive capacity, and resistance to commonly used insecticides. Moreover, the fly has a high reproductive capacity, and this prolific reproductive capacity can lead to extreme levels of destruction in affected fruits. Considering the fly's high fertility, targeting the gonads could theoretically be an effective method of pest control. However, the molecular mechanisms underlying gonadal development remain largely unrevealed. To identify gonad-specific expressed genes, an analysis of gonadal transcriptomic sequencing was conducted. A total of 1338, 336, 35, and 479 differentially expressed genes were found in the testis, ovary, female accessory gland, and male accessory gland, respectively. Surprisingly, approximately half of highly expressed gonad-specific genes were uncharacterized. Therefore, the functional motifs or domains of uncharacterized highly expressed gonad-specific genes were predicted, and 23% of novel highly expressed gonad-specific genes encoded proteins that contained signal peptides or transmembrane domains. Furthermore, the spatiotemporal expression and sequence characterization of six novel highly expressed gonad-specific genes were analyzed. Overall, genes associated with gonadal development may aid us in the search for pest control targets to improve pest management approaches. Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) is one of the most devastating agricultural pests worldwide due to its high reproductive and invasive abilities. The elucidation of its gonadal developmental characteristics and the identification of sex-related genes will provide a useful genetic basis for reproductive-based pest control. Here, the gonadal transcriptome of B. dorsalis was sequenced, and novel gonad-specific expressed genes were analyzed. A total of 1338, 336, 35, and 479 differentially expressed genes (DEGs) were found in the testis (TE), ovary (OV), female accessory gland (FAG), and male accessory gland (MAG), respectively. Furthermore, 463 highly expressed gonad-specific genes were identified, with the TE having the highest number of specific highly expressed genes, at 402, followed by 51 in the OV, 9 in the MAG, and only 1 in the FAG. Strikingly, approximately half of highly expressed gonad-specific genes were uncharacterized. Then, it was found that 35, 17, 3, 2, and 1 of 202 uncharacterized highly expressed TE-specific genes encoded proteins that contained transmembrane domains, signal peptides, high-mobility group boxes, the zinc finger domain, and the BTB/POZ domain, respectively. Interestingly, approximately 40% of uncharacterized highly expressed gonad-specific genes encoding proteins were not predicted to possess functional motifs or domains. Finally, the spatiotemporal expression and sequence characterization of six novel highly expressed gonad-specific genes were analyzed. Altogether, our findings provide a valuable dataset for future functional analyses of sex-related genes and potential target sites for pest control. [ABSTRACT FROM AUTHOR]