Search

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.

Background: Chemosensory perception plays a vital role in insect survival and adaptability, driving essential behaviours such as navigation, mate identification, and food location. This sensory process is governed by diverse gene families, including odorant-binding proteins (OBPs), olfactory receptors (ORs), ionotropic receptors (IRs), chemosensory proteins (CSPs), gustatory receptors (GRs), and sensory neuron membrane proteins (SNMPs). The oriental mole cricket (Gryllotalpa orientalis Burmeister), an invasive pest with an underground, phyllophagous lifestyle, causes substantial crop damage. This study characterizes the chemosensory gene repertoire of G. orientalis based on de novo genome assembly and transcriptomic analysis. Results: We present a draft genome of G. orientalis at the scaffold level, spanning 2.94 Gb and comprising 10,497 scaffolds. This assembly encodes 19,155 protein-coding genes, including 158 chemosensory genes: 30 odorant receptors (ORs), 64 ionotropic receptors (IRs), ten gustatory receptors (GRs), 28 odorant-binding proteins (OBPs), 25 chemosensory proteins (CSPs), and a single sensory neuron membrane protein (SNMP). Expression analysis indicated that 71 chemosensory genes were actively expressed in the head, thorax, and legs, with ORs and OBPs showing higher expression in the head and legs. In contrast, GRs and IRs were predominantly expressed in the head. Conclusions: This study provides the first comprehensive identification of chemosensory gene families in the G. orientalis genome, characterized as a scaffold-level draft genome. These findings provide a basis for future functional studies and highlight the role of chemoreception in the subterranean environment. [ABSTRACT FROM AUTHOR]

Introduction: Aphids 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. Methods: In 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 discussion: Gene 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. [ABSTRACT FROM AUTHOR]

Proteins of the TRIM family are involved in both innate immunity and the nervous system processes and may play an important role in the development of neurodegenerative diseases. In this work, we analyzed the expression of 35 genes of the TRIM family in neural progenitors (NPs), terminally differentiated neurons (TDNs) and glial derivatives (NGs) obtained from induced pluripotent stem cells (iPSCs) of healthy donors (HD) and patients with Parkinson's disease (PD), in the absence of inflammatory stimuli and upon the induction of a nonspecific inflammatory response under the influence of TNFα. In NPs and TDNs of PD patients, compared with HD cells, differences in expression were observed for only a small number of TRIM genes. Under the influence of TNFα in TDNs, the expression of individual TRIM genes was activated, which was more significant in the cells of patients with PD compared to cells of HDs. In NGs of PD patients, the expression of many TRIM genes was initially reduced compared to HD cells and remained low or further decreased after exposure to TNFα. The data obtained demonstrate differences in the network of the TRIM family members in PD neurons and glia compared to control, and also show the multidirectional influence of the inflammatory stimulus on the expression of a number of TRIM genes in these types of cells. Considering the important role of many TRIM genes in the functioning of the innate immune system, it can be assumed that, in PD, more significant disturbances in the functioning of genes of this family occur in glia compared to neurons. [ABSTRACT FROM AUTHOR]

Drought stress is an important factor that reduces plant biomass production and quality. The APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) gene family is widely involved in biological processes such as plant growth, development, and stress response. However, the characteristics of the AP2/ERF gene family in hybrid tea rose (Rosa × hybrida) and their potential functions in responding to drought stress are still unclear. In the current study, 127 AP2/ERF genes were identified in hybrid tea rose. Phylogenetic analysis showed that the corresponding 127 AP2/ERF transcription factors belonged to five subfamilies. There was a large number of cis-acting elements in the AP2/ERF gene promoters related to regulation of stress response, growth and development. By examining the RNA sequencing data in the PlantExp database, the RhAP2/ERF genes exhibiting tissue-specific and stress-responsive expression in rose were identified. Furthermore, three candidate RhAP2/ERF genes (RhDREB36, RhERF59, and RhDREB44) that might participate in drought response were determined via qRT-PCR analysis in rose cultivars under drought treatment. Subcellular localization analysis revealed that RhDREB44 was located in the nucleus. These results provide a foundation for exploring the regulatory functions of RhAP2/ERF genes in the growth and development of roses, as well as for selecting key genes for future molecular breeding. [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]

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. Significance Statement: Somatic embryogenesis is used as a model system to study embryo development, however detailed information to verify similarities and explain differences between somatic and zygotic embryogenesis is largely missing for conifers. This data resource provides sequential mRNA transcriptome data from nine stages of conifer zygotic embryo and female gametophyte development, and eight stages of somatic embryo development, to enable exploration of biological questions and comparisons of the two developmental processes. [ABSTRACT FROM AUTHOR]

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]

Many publicly available databases provide disease related data, that makes it possible to link genomic data to medical and meta-data. The cancer genome atlas (TCGA), for example, compiles tens of thousand of datasets covering a wide array of cancer types. Here we introduce an interactive and highly automatized TCGA-based workflow that links and analyses epigenomic and transcriptomic data with treatment and survival data in order to identify possible biomarkers that indicate treatment success. TREMSUCS-TCGA is flexible with respect to type of cancer and treatment and provides standard methods for differential expression analysis or DMR detection. Furthermore, it makes it possible to examine several cancer types together in a pan-cancer type approach. Parallelisation and reproducibility of all steps is ensured with the workflowmanagement system Snakemake. TREMSUCS-TCGA produces a comprehensive single report file which holds all relevant results in descriptive and tabular form that can be explored in an interactive manner. As a showcase application we describe a comprehensive analysis of the available data for the combination of patients with squamous cell carcinomas of head and neck, cervix and lung treated with cisplatin, carboplatin and the combination of carboplatin and paclitaxel. The best ranked biomarker candidates are discussed in the light of the existing literature, indicating plausible causal relationships to the relevant cancer entities. [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]

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.

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.

Tektins (TEKTs) are constitutive proteins of microtubules associated with flagella, cilia, basal bodies, and centrioles. As one of the testis-specific candidate markers, Tekt1, the first identified member of the TEKT family in mammals, is intimately linked to the formation of sperm flagella and may play a pivotal role in flagellar stability and sperm motility. However, studies on Tekt1 in fish species are still relatively understudied. In this study, the full-length cDNAs of Tekt1 were respectively 1727 bp and 1696 bp in allotriploid crucian carp and diploid red crucian carp, which both comprised a 1209 bp open reading frame (ORF) encoding 402 amino acids. Conversely, the diploid common carp possessed a cDNA length of 1771 bp, characterized by a 1218 bp ORF encoding 405 amino acids. The Western blot analysis revealed that the expression level of Tekt1 protein in the testes of sterile allotriploid crucian carp was markedly decreased in comparison to that of fertile diploid red crucian carp during both pre-spermiation and spermiation periods. The immunohistochemistry analysis revealed abnormalities in the spermiogenesis of allotriploid crucian carp, showcasing a distinctive localization pattern of Tekt1 exclusively present in spermatids, in contrast to diploid red crucian carp, where Tekt1 was detected in both spermatids and spermatozoa. Taken together, these findings suggested differential expression of Tekt1 during spermiogenesis between allotriploid and diploid species, and indicated that the decreased expression of Tekt1 protein in allotriploid crucian carp might be associated with male sterility. Furthermore, these results pave the way for further exploration of reproductive characteristics in male allotriploid crucian carp and offer a theoretical foundation for future research on polyploid breeding.

Phytohormones serve as the ace of regulatory mechanisms in plants during gene expression under different environmental conditions. They are also involved in combating diseases during plant–pathogen interactions. MicroRNAs are a group of small, non-coding and post-transcriptional regulatory RNAs that potentially function in stress tolerance as they target specific mRNAs and promote endonucleolytic cleavage or translational inhibition. Here, we aim to identify potential novel miRNAs that could assist in mitigating leaf rust resistance in wheat to combat rust epidemics. A total of 64 novel miRNAs were identified from Next Generation Sequencing datasets of small RNA libraries prepared from resistant and susceptible wheat near-isogenic lines (NILs) under mock and leaf rust pathogen (Puccinia triticina Eriks.) infected conditions. Eight miRNAs (present post leaf rust infection) complementary RNA cognate targets were predicted through psRNATarget. Ontological annotations and combined pathway analysis were applied to identify their specific functions in different phytohormone biosynthesis or signaling pathways. The miRNA target interaction was successfully validated through degradome mapping. RT-qPCR revealed that most miRNAs (TamiRs) were downregulated in the resistant NIL introgressed with Lr24 gene with an antagonistic upregulation of their phytohormone-associated target genes (AOC, BAGT, BSK3, FAR, GABA, HSF, JUNG, and RPD). However, target gene, RPP showed no such correlation in the presence of microRNA or Lr24 and was upregulated throughout the timepoints of disease progression in both the NILs. This study deciphers the regulatory linkage between the identified novel miRNAs and their phytohormonal target transcripts during leaf rust disease in wheat to assist in rust-resistant breeding programs. [ABSTRACT FROM AUTHOR]

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 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 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.

Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed examination of their statistical methods, case applications, and benefits. A total of 22 tools are categorised by their statistical family (parametric, non-parametric, and probabilistic) and level of analysis (transcript, exon, and event). The central challenges in quantifying alternative splicing include correct splice site identification and accurate isoform deconvolution of transcripts. Benchmarking studies show no consensus on tool performance, revealing considerable variability across different scenarios. Tools with high citation frequency and continued developer maintenance, such as DEXSeq and rMATS, are recommended for prospective researchers. To aid in tool selection, a guide schematic is proposed based on variations in data input and the required level of analysis. Additionally, advancements in long-read RNA sequencing are expected to drive the evolution of differential splicing tools, reducing the need for isoform deconvolution and prompting further innovation.

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]

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]

Objective: This paper explores the role of DNA methylation in α-irradiation damage at the cellular level. Methods: Human normal hepatocytes L-02 were irradiated using a 241 Am α source at doses of 0, 1.0, and 2.0 Gy. The methylation levels of the six differentially methylated genes were examined by pyrophosphate sequencing, and the mRNA expression levels of the six differentially methylated genes were examined by real-time fluorescence quantitative PCR. Results: The rate of γH2AX foci positive cells was significantly higher than that of the control group after irradiation of cells in different dose groups for 1 h and 2 h respectively (P <.05). The proportion of S-phase cells was significantly increased in the 1.0 Gy and 2.0 Gy dose groups compared with the control group (P <.05). The methylation levels of CDK2AP1, PDGFRL, PCDHB16 and FAS genes were significantly increased, while the mRNA expression levels were significantly decreased (P <.05). The expression levels of CDK2Apl, PCDHB16 and FAS were significantly negatively correlated with the methylation levels (P <.05). Conclusion: The α-particle radiation can affect gene expression at the epigenetic level, which led to the speculation that altered methylation levels of CDK2AP1, PCDHB16, and FAS genes may be involved in the α radiation damage process. [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]

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]

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

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.

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.