Promising Genes Research Articles

Investigating The Circadian Rhythm Signaling Pathway in HTLV-1 Pathogenesis Using Boolean Analysis.

The Human T-cell lymphotropic virus type 1 (HTLV-1), an oncogenic virus belonging to the Deltaretrovirus genus, expresses various proteins, including Tax and HBZ, which can affect many cellular pathways. In this study, we have investigated the role of the circadian rhythm signaling pathway, a key regulator of human health, in the pathogenesis of HTLV-1 using Boolean Network analysis and laboratory methods. After an extensive search of the circadian rhythm pathway, we analyzed the relationships between the genes of this pathway using the R programming language and the BoolNet package. Subsequently, we examined the impact of viral proteins on the cellular clock rhythm genes. Finally, we identified three genes, PER2, CRY1, and DEC1, as the main checkpoints from the attractors obtained. These three genes and two viral genes, Tax and HBZ, were quantitatively assessed on two groups of individuals, including ten asymptomatic carriers infected with HTLV-1 and ten healthy individuals using the qRT-PCR method. Our results showed that the expression level of PER2 and DEC1 genes was significantly higher in the asymptomatic carriers compared to the healthy control group. Also, we recorded positive correlations between PER2 and DEC1, CRY1 and DEC1, and negative correlations between HBZ and CRY1 and DEC1. In this study, we suggested that in asymptomatic carriers, the virus might try to induce a chronic infection by escaping from the immune system due to an alteration in circadian rhythm pathways. We also detected three promising genes in this pathway that could have therapeutic or diagnostic value in these individuals. However, this possibility requires further research in different periods, different groups (e.g., ATLL and HAM/TSP), and examining a more significant number of circadian rhythm genes.

Mechanism of Radix Bupleuri and Hedysarum Multijugum Maxim drug pairs on liver fibrosis based on network pharmacology, bioinformatics and molecular dynamics simulation.

A number of studies demonstrate the therapeutic effectiveness of Radix Bupleuri (RB) and Hedysarum Multijugum Maxim (HMM) in treating liver fibrosis, but the exact molecular mechanisms remain unclear. This study aims to explore the mechanism of RB-HMM drug pairs in treating liver fibrosis by using network pharmacology, bioinformatics, molecular docking, molecular dynamics simulation technology and in vitro experiments. Totally, 155 intersection targets between RB-HMM and liver fibrosis were identified. In the protein-protein interaction (PPI) network, the top 10 hub targets with the highest node connection values were TNF, IL-6, AKT1, EGFR, HIF1A, PPARG, CASP3, SRC, MMP9 and HSP90AA1. GO functional and KEGG pathway enrichment analysis involved 335 biological processes, 39 cellular components, 78 molecular functions, and 139 signaling pathways. The bioinformatics analysis indicated that TNF, IL-6, PPARG and MMP9 were promising candidate genes that can serve as diagnostic and prognostic biomarkers for liver fibrosis. Moreover, the molecular docking and molecular dynamic simulation of 50 ns well complemented the binding affinity and strong stability between the three common compounds MOL000098 (quercetin), MOL000354 (isorhamnetin) and MOL000422 (kaempferol) and four final hub targets (TNF, IL-6, PPARG and MMP9). Calculation of binding free energy and decomposition free energy using MM_PBSA and MM_GBSA also validated the strong binding affinity and stability of 12 systems. MOL000098 (quercetin) was selected via MTT assay and western blot assay verified MOL000098 (quercetin) treatments remarkably decreased the protein levels of TNF and IL-6 in TGFβ stimulated LX2 cells. In conclusion, RB-HMM drug pairs can affect the progression of liver fibrosis through multiple components, multiple targets and multiple pathways, and treat liver fibrosis possibly through anti-inflammatory and affecting cell apoptosis.

QTL mapping and candidate gene analysis of element accumulation in rice grains via genome-wide association study and population genetic analysis

BackgroundToxic heavy metal elements in soils are major global environmental issues and easily migrate to crop grains to cause severe problems in human health, whereas moderately essential elements such as selenium are beneficial for human health. The accumulation of heavy metals and essential elements in rice grains and their genetic mechanisms are still poorly understood.ResultsWe conducted genetic dissection of four toxic heavy metal elements (lead, cadmium, mercury, and chromium), one quasi metallic element (arsenic), and one essential element (selenium) in grains of 290 Xian and 308 Geng rice accessions through a genome-wide association study (GWAS) based on three statistical models and assays of element concentrations from three environments. A total of 99 quantitative trait loci (QTLs) were identified. Among these QTLs, 18.2% overlapped between/among two or more elements, indicating that some QTLs related to the accumulation of certain elements may depend on other heavy metal elements or be involved in the collaborative transport of other elements. Moreover, at least 14 QTLs/regions were identified in the same regions, containing 12 cloned genes reported to be associated with element accumulation or tolerance-related traits, while the remaining 85 were new QTLs. A total of 62 promising candidate genes were identified from 50 major QTLs, of which 25 genes were newly discovered in this study. More importantly, population genetic analysis revealed 26 and 15 intraspecies divergent regions affecting element concentrations in the Xian and Geng subspecies, respectively, including 25 QTLs identified in this study and 13 previously reported and cloned genes.ConclusionsOur findings will facilitate further gene cloning and dissection of the genetic mechanisms of element accumulation in rice grains to improve grain quality.

Identification of candidate genes for leaf size by QTL mapping and transcriptome sequencing in Brassica napus L

Leaf is the main photosynthetic organ at the seedling stage of rapeseed and leaf size is a crucial agronomic trait affecting rapeseed yield. Understanding the genetic mechanisms underlying leaf size is therefore important for rapeseed breeding. In this study, QTL mapping for three traits related to leaf size, i.e., leaf width (LW), leaf length (LL) and leaf area (LA), was performed using a recombinant inbred line (RIL) population and four QTLs for LW, two QTLs for LL and four QTLs for LA were detected. Transcriptome analysis revealed that differentially expressed genes (DEGs) were enriched in the GO terms related to microtubules, and the expression level of several genes involved in cell division also showed significant differences. Microscopic analysis suggested that the cell number was the main factor regulating leaf size. Combining QTL mapping and RNA sequencing, four promising candidate genes, including BnaA10G0085600ZS, BnaA10G0156900ZS, BnaC03G0441700ZS, and BnaC08G0410600ZS, were proposed to control leaf size by regulating cell division. The results of QTL, transcriptome analysis, and anatomical observation were highly consistent, collectively revealing that genes related to cell division played a crucial role in regulating the leaf size traits in rapeseed. These findings provided further insights into the genetic mechanism of leaf size and built fundamental theory basis for high-density tolerance breeding in rapeseed.

Naturally occurring variation in a cytochrome P450 modifies thiabendazole responses independently of beta-tubulin.

Widespread anthelmintic resistance has complicated the management of parasitic nematodes. Resistance to the benzimidazole (BZ) drug class is nearly ubiquitous in many species and is associated with mutations in beta-tubulin genes. However, mutations in beta-tubulin alone do not fully explain all BZ resistance. We performed a genome-wide association study using a genetically diverse panel of Caenorhabditis elegans strains to identify loci that contribute to resistance to the BZ drug thiabendazole (TBZ). We identified a quantitative trait locus (QTL) on chromosome V independent of all beta-tubulin genes and overlapping with two promising candidate genes, the cytochrome P450 gene cyp-35D1 and the nuclear hormone receptor nhr-176. Both genes were previously demonstrated to play a role in TBZ metabolism. NHR-176 binds TBZ and induces the expression of CYP-35D1, which metabolizes TBZ. We generated single gene deletions of cyp-35D1 and nhr-176 and found that both genes play a role in TBZ response. A predicted high-impact lysine-to-glutamate substitution at position 267 (K267E) in CYP-35D1 was identified in a sensitive strain, and reciprocal allele replacement strains in different genetic backgrounds were used to show that the lysine allele conferred increased TBZ resistance. Using competitive fitness assays, we found that neither allele was deleterious, but the lysine allele was selected in the presence of TBZ. Additionally, we found that the lysine allele significantly increased the rate of TBZ metabolism compared to the glutamate allele. Moreover, yeast expression assays showed that the lysine version of CYP-35D1 had twice the enzymatic activity of the glutamate allele. To connect our results to parasitic nematodes, we analyzed four Haemonchus contortus cytochrome P450 orthologs but did not find variation at the 267 position in fenbendazole-resistant populations. Overall, we confirmed that variation in this cytochrome P450 gene is the first locus independent of beta-tubulin to play a role in BZ resistance.

High-resolution whole-genome DNA methylation revealed unique signatures of painful diabetic neuropathy.

The aim of this work was to describe the DNA methylation signature and to identify genes associated with neuropathic pain in type 2 diabetes mellitus. We analyzed two independent diabetic neuropathy cohorts: PROPGER consisting of 72 painful and 67 painless patients recruited at the German Diabetes Center in Düsseldorf (DE), and PROPENG comprising 27 painful and 65 painless diabetic neuropathy patients recruited at the University of Manchester (UK). Genome-wide methylation data was generated using Illumina Infinium Methylation EPIC v1.0 BeadChip. We used four different selection criteria to identify promising pain-related genes. Our findings revealed significant differences in methylation patterns between painful and painless diabetic neuropathy and identified a set of individual CpG sites of unique candidate genes associated with the painful phenotype. Several of these genes, including GCH1, MYT1L and MED16, have been previously linked to pain-related phenotypes or diabetes. Through pathway enrichment analysis, we demonstrated that specific epigenetic signatures could contribute to the complex phenotype of diabetic neuropathy and cluster analyses highlighted significant epigenetic dissimilarities between painful and painless phenotypes. Our results uncovered epigenetic differences between painful and painless diabetic neuropathy patients and identified targeted genes linked to neuropathic pain through DNA methylation mechanisms. This approach holds promise for investigating other chronic pain conditions, such as secondary chronic pain from cancer treatment, thoracic surgery, and various transplant settings.

Bioinformatics-Based Analysis and Verification of Chromatin Regulators and the Mechanism of Immune Infiltration Associated with Myocardial Infarction.

Recent studies have shown that dysfunction in chromatin regulators (CRs) may be an important mechanism of myocardial infarction (MI). They are thus expected to become a new target in the diagnosis and treatment of MI. However, the diagnostic value of CRs in MI and the mechanisms are not clear. CRs-related differentially expressed genes (DEGs) were screened between healthy controls and patients with MI via GSE48060, GSE60993, and GSE66360 datasets. DEGs were further analyzed for enrichment analysis. Hub genes were screened by least absolute shrinkage and selection operator (LASSO) regression and weighted gene co-expression network analysis (WGCNA). GSE61144 datasets were further used to validate hub genes. RT-qPCR examined peripheral blood mononuclear cells (PBMCs) to verify expressions of hub genes. In addition, a correlation between hub genes and immune cell infiltration was identified by CIBERSORT and single-sample gene set enrichment analysis (ssGSEA). Finally, we constructed a diagnostic nomogram and ceRNA network and found possible therapeutic medicines which were based on hub genes. Firstly, 16 CR-related DEGs were identified. Next, Dual-specificity phosphatase 1 (DUSP1), growth arrest and DNA damage-inducible 45 (GADD45A), and transcriptional regulator Jun dimerization protein 2 (JDP2) were selected as hub genes by LASSO and WGCNA. Receiver operating characteristic curves in the training and test data sets verified the reliability of hub genes. Results of RT-qPCR confirmed the upregulation of hub genes in MI. Subsequently, the immune infiltration analysis indicated that DUSP1, GADD45A, and JDP2 were correlated with plasmacytoid dendritic cells, natural killer cells, eosinophils, effector memory CD4 T cells, central memory CD4 T cells, activated dendritic cells, and activated CD8 T cells. Furthermore, a nomogram that included DUSP1, GADD45A, and JDP2 was created. The calibration curve, decision curve analysis, and the clinical impact curve indicated that the nomogram could predict the occurrence of MI with high efficacy. The results of the ceRNA network suggest that hub genes may be cross-regulated by various lncRNAs and miRNAs. In addition, 10 drugs, including 2H-1-benzopyran, Nifuroxazide, and Bepridil, were predicted to be potential therapeutic agents for MI. Our study identifies three promising genes associated with the progression of chromatin regulators (CRs)-related myocardial infarction (MI) and immune cell infiltration, including Dual-specificity phosphatase 1 (DUSP1), growth arrest and DNA damage-inducible 45 (GADD45A), and Jun dimerization protein 2 (JDP2), which might be worthy of further study.

BIOINFORMATICALLY ANALYZED RELATIONSHIPS BETWEEN SPECIFIC HUMAN GENES ASSOCIATED WITH HIV ATTACHMENT

Introduction. Assessing interaction between the human immunodeficiency virus (HIV) and human factors is crucial for understanding the disease pathogenesis. HIV triggers an immune response that involves numerous cellular and molecular processes related to inflammation, cell migration, and disrupted tissue barrier functions. Such reactions build up a cascade in which chemokines and cognate co-receptors, as well as other molecules regulating the immune response, play a key role. However, the interaction between HIV and the human organism cannot be reduced to a simple mechanism because it represents a multilayered system where crucial molecules and events may be unknown or require further study. Objective: to assess a significance of candidate genes potentially involved in the pathogenesis of HIV infection during the phase of viral attachment to cell, based on assessing gene expression, localization, and involvement in biological pathways and processes. Materials and methods. The study compared the characteristics of the 100 most promising candidate genes (CG) according to the HumanNet web resource with background genes (CCR5, CXCR4, CCR2, CD4), known to be reliably linked to HIV attachment. Expression data, localization, and involvement in various cellular pathways and processes for the candidate and background genes were analyzed. A scoring system was developed to assess the significance of each gene in the context of its role in immune and inflammatory responses. Results. A total of 100 candidate genes were analyzed. Using the developed scoring system, a number of genes were identified as significant based on the analyzed parameter: 17 candidates – significant by expression profile; 7 – by localization; 17 – by involvement in biological pathways; and 25 – by involvement in biological processes. The final ranking revealed 55 candidate genes. The identified candidate genes were classified into the following functional groups: chemokine co-receptors and their ligands; genes and proteins associated with G-proteins; and a group for which a common functional role or family could not be established. Conclusions. The identified correlations between the candidate genes and background genes highlight the need to further investigate CG interactions in HIV pathogenesis allowing for a more detailed assessment of the contribution of both individual genes and entire systems, which, in the future, will expand our understanding of the molecular mechanisms behind HIV infection and, hypothetically, accelerate the discovery of new (or the expansion of existing) therapeutic models.

Promising candidate drug target genes for repurposing in cervical cancer: A bioinformatics-based approach.

Cervical cancer is the fourth most common cancer among women globally, and studies have shown that genetic variants play a significant role in its development. A variety of germline and somatic mutations are associated with cervical cancer. However, genomic data derived from these mutations have not been extensively utilized for the development of repurposed drugs for cervical cancer. The objective of this study was to identify novel potential drugs that could be repurposed for cervical cancer treatment through a bioinformatics approach. A comprehensive genomic and bioinformatics database integration strategy was employed to identify potential drug target genes for cervical cancer. Using the GWAS and PheWAS databases, a total of 232 genes associated with cervical cancer were identified. These pharmacological target genes were further refined by applying a biological threshold of six functional annotations. The drug target genes were then cross-referenced with cancer treatment candidates using the DrugBank database. Among the identified genes, LTA, TNFRSF1A, PRKCZ, PDE4B, and PARP were highlighted as promising targets for repurposed drugs. Notably, these five target genes overlapped with 12 drugs that could potentially be repurposed for cervical cancer treatment. Among these, talazoparib, a potent PARP inhibitor, emerged as a particularly promising candidate. Interestingly, talazoparib is currently being investigated for safety and tolerability in other cancers but has not yet been studied in the context of cervical cancer. Further clinical trials are necessary to validate this finding and explore its potential as a repurposed drug for cervical cancer.

Potential New Expression Biomarkers for Anorexia Nervosa.

Anorexia nervosa (AN) is a psychiatric disorder with an estimated heritability of around 70%. Although the largest meta-analysis of genome-wide association studies on AN identified independent risk-conferring loci for the disorder, the molecular mechanisms underlying the genetic basis of AN remain to be elucidated. To investigate AN, we performed transcriptome profiling in peripheral blood mononuclear cells from 15 AN patients and 15 healthy controls. We validated our mean results in a mouse model of chronic food restriction, which mimics several aspects of AN. In this exploratory study, we identified 673 significantly differentially expressed genes in AN. Among these genes, we identified seven genes previously found to be dysregulated in IPSC-derived neurons from AN individuals and the Vanin-1 (Vnn1) gene, which appears to play an important role in the regulation of several metabolic pathways. We confirmed underexpression of Vnn1, particularly in the liver, in a mouse model of chronic food restriction. These results indicate that quantitative food restriction affects Vnn1 expression, suggesting that this gene may contribute to the anorexic phenotype in the chronic food restriction mouse model as well as in patients with AN. We believe that this report highlights promising candidate genes and gene pathways for AN, and although we did not obtain a significant result in the replication cohort, it identifies Vnn1 as a potential biomarker that may be used as a molecular target to predict and/or to understand AN.

Distinct effects of PTST2b and MRC on starch granule morphogenesis in potato tubers.

The molecular mechanisms underpinning the formation of the large, ellipsoidal starch granules of potato tuber are poorly understood. Here, we demonstrate the distinct effects of PROTEIN TARGETING TO STARCH2b (PTST2b) and MYOSIN RESEMBLING CHLOROPLAST PROTEIN (MRC) on tuber starch granule morphology. A gene duplication event in the Solanaceae resulted in two PTST2 paralogs (PTST2a and PTST2b). PTST2b is expressed in potato tubers, and unlike PTST2a, it had no detectable interaction with STARCH SYNTHASE 4. MRC expression was detectable in leaves, but not in tubers. Using transgenic potato lines in the variety Clearwater Russet, we demonstrate that MRC overexpression leads to the formation of granules with aberrant shapes, many of which arise from multiple initiation points. Silencing PTST2b led to the production of striking near-spherical granules, each arising from a single, central initiation point. Contrary to all reported PTST2 mutants in other species, we observed no change in the number of granules per cell in these lines, suggesting PTST2b is specifically involved in the control of starch granule shape. Starch content and tuber yield per plant were not affected by PTST2b silencing, but MRC overexpression led to strong decreases in both parameters. Notably, the spherical granules in PTST2b silencing lines had a distinctively altered pasting profile, with higher peak and final viscosity than the wild type. Thus, PTST2b and MRC are promising target genes for altering starch granule size and shape in potato tubers, and can be used to create novel starches with altered physicochemical and/or functional properties.

Genetic control of root/shoot biomass partitioning in barley seedlings.

The process of allocating resources to different plant organs in the early stage of development can affect their adaptation to drought conditions, by influencing water uptake, transpiration, photosynthesis, and carbon storage. Early barley development can affect the response to drought conditions and mitigate yield losses. A distinct behavior of biomass partitioning between two Spanish barley landraces (SBCC073 and SBCC146) was observed in a previous rhizotron experiment. An RIL population of approximately 200 lines, derived from the cross of those lines, was advanced using speed breeding. We devised an experiment to test if seedling biomass partitioning was under genetic control, growing the seedlings in pots filled with silica sand, in a growth chamber under controlled conditions. After 1 week, the shoot and root were separated, oven dried, and weighted. There were genotypic differences for shoot dry weight, root dry weight, and root-to-shoot ratio. The population was genotyped with a commercial 15k SNP chip, and a genetic map was constructed with 1,353 SNP markers. A QTL analysis revealed no QTL for shoot or root dry weight. However, a clear single QTL for biomass partitioning (RatioRS) was found, in the long arm of chromosome 5H. By exploring the high-confidence genes in the region surrounding the QTL peak, five genes with missense mutations between SBCC146 and SBCC073, and differential expression in roots compared to other organs, were identified. We provide evidence of five promising candidate genes with a role in biomass partitioning that deserve further research.

Integrated data driven analysis identifies potential candidate genes associated with PCOS

Polycystic ovary syndrome (PCOS) is one of the most common anovulatory disorder observed in women presenting with infertility. Several high and low throughput studies on PCOS have led to accumulation of vast amount of information on PCOS. Despite the availability of several resources which index the advances in PCOS, information on its etiology still remains inadequate. Analysis of the existing information using an integrated evidence based approach may aid identification of novel potential candidate genes with a role in PCOS pathophysiology. This work focuses on integrating existing information on PCOS from literature and gene expression studies and evaluating the application of gene prioritization and network analysis to predict missing novel candidates. Further, it assesses the utility of evidence-based scoring to rank genes for their association with PCOS. The results of this study led to identification of ~2000 plausible candidate genes associated with PCOS. Insilico validation of these identified candidates confirmed the role of 938 genes in PCOS. Further, experimental validation was carried out for four of the potential candidate genes, a high-scoring (PROS1), two mid-scoring (C1QA and KNG1), and a low-scoring gene (VTN) involved in the complement and coagulation pathway by comparing protein levels in follicular fluid in women with PCOS and healthy controls. While the expression of PROS1, C1QA, and KNG1 was found to be significantly downregulated in women with PCOS, the expression of VTN was found to be unchanged in PCOS. The findings of this study reiterate the utility of employing insilico approaches to identify and prioritize the most promising candidate genes in diseases with a complex pathophysiology like PCOS. Further, the study also helps in gaining clearer insights into the molecular mechanisms associated with the manifestation of the PCOS phenotype by contributing to the existing repertoire of genes associated with PCOS.

Genome-wide association study identified QTLs and genes underlying early seedling vigour in aus rice (Oryza sativa L.).

Early seedling vigour (ESV) is a key trait that enhances early establishment, stress tolerance, and grain yield in rice, especially in direct-seeded rice (DSR) systems. The aus varietal groups is known for its high seedling vigour. The screening of aus diversity panel for ESV traits and subsequent genome-wide association study (GWAS) can lead to the identification of genetic components of ESV. Here, we report the genetic variation in seven ESV traits along with days to 50% flowering and grain yield in a panel of 181 aus accessions evaluated under field conditions. We observed significant variations in the studied traits. The vegetative vigour, scored visually, was significantly correlated with most of the traits, suggesting its impact on overall plant performance. Comparative analysis of aus genetic groups revealed significant variations, and the subpopulation that includes early maturing drought tolerant genotypes was the most vigorous, and thus ideal for donor selection. GWAS using 918, 863 single nucleotide polymorphism (SNP) markers identified 14 significant QTLs, including seven novel ones, linked to vegetative vigour, average growth rate and seedling biomass. Candidate genes like OsPDR1, NCKAP1, and OsSAUR10, involved in jasmonic acid biosynthesis, ABA signaling, and brassinosteroid pathways, were identified to be associated with ESV regulation. This study provides insights into the genetic basis of ESV in aus rice, identifying promising germplasm and genes that could improve seedling vigour and yield in DSR systems. Future research should validate these findings and integrate them into breeding programs for enhanced rice performance in various environments.

Uncovering immune cell-associated genes in breast cancer: based on summary data-based Mendelian randomized analysis and colocalization study

BackgroundBreast cancer, which is the most prevalent form of cancer among women globally, encompasses various subtypes that demand distinct treatment approaches. The tumor microenvironment and immune response are of crucial significance in the development and progression of breast cancer. Nevertheless, there has been scant evidence concerning the genes within breast cancer - specific immune cells.MethodsWe utilized summary data-based Mendelian randomization (SMR) to identify genes associated with breast cancer by utilizing expression quantitative trait loci (eQTL) datasets for 14 different immune cell types and genome-wide association studies (GWAS) for overall breast cancer and its subtypes. Furthermore, colocalization analysis was carried out to evaluate whether the observed association in SMR analyses is influenced by the same causal variant. Replication analysis and bulk RNA sequencing (bulkRNA-seq) analysis were employed to validate promising immune genes as potential drug targets.ResultsAfter correcting for the rate of false discovery, we discovered a total of 17 genes in 9 immune cell types that were significantly associated with overall breast cancer and its subtypes. The genes KCNN4, L3MBTL3, ZBTB38, MDM4, and TNFSF10 were identified in overall breast cancer and its subtypes. Colocalization analyses provided robust evidence in support of these associations. Notably, the KCNN4 gene in non-classical MONOcytes (MONOnc) was further validated through replication analysis and bulkRNA-seq analysis.ConclusionIn summary, our research has revealed a repertoire of genes within diverse immune cells associated with breast cancer. KCNN4 gene in non-classical MONOcytes (MONOnc) exhibited a negative association with overall breast cancer and its subtypes, which was identified as a potential drug target for breast cancer, opening up new avenues for therapeutic interventions.

Transcriptome Analysis of Porcine Immune Cells Stimulated by Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Caesalpinia sappan Extract.

The current level of knowledge on transcriptome responses triggered by Caesalpinia sappan (CS) extract in porcine peripheral blood mononuclear cells (PBMCs) after porcine reproductive and respiratory syndrome virus (PRRSV) infection is limited. Therefore, in the present study, we aimed to detect significant genes and pathways involved in CS extract supplementation responsiveness of PBMCs after PRRSV infection. RNA sequencing was conducted on PBMCs, which were isolated from six weaned piglets. The resultant transcriptional responses were examined by mRNA sequencing. Differential expression analysis identified 263 and 274 differentially expressed genes (DEGs) between the PRRSV and CTRL groups, and the PRRSV+CS and CTRL groups, respectively. Among these, ZNF646 and KAT5 emerged as the most promising candidate genes, potentially influencing the interaction between PRRSV-infected PBMCs and CS extract supplementation through the regulation of gene networks and cellular homeostasis during stress. Two pathways were detected to be associated with CS extract supplementation responsiveness: the cellular response to stress pathway and the NF-kB signaling pathway. Consequently, our study reveals a novel mechanism underlying cellular stress response and the NF-κB signaling pathway in PRRSV-infected PBMCs, and identifies a potential application of CS extract for activating the NF-κB signaling pathway. In conclusion, by supplementing CS extract in PBMC cells infected with PRRSV, we found that CS extract modulates PRRSV infection by inducing cellular stress, which is regulated by the NF-κB signaling pathway. This induced stress creates an adverse environment for PRRSV survival. This study contributes to a deeper understanding of the therapeutic targets and pathogenesis of PRRSV infection. Importantly, our results demonstrate that CS extract has the potential to be a candidate for modulating PRRSV infection.

Chromosome-scale genome assembly of Apocynum pictum, a drought-tolerant medicinal plant from the Tarim Basin.

Apocynum pictum Schrenk is a semishrub of the Apocynaceae family with a wide distribution throughout the Tarim Basin that holds significant ecological, medicinal, and economic values. Here, we report the assembly of its chromosome-level reference genome using Nanopore long-read, Illumina HiSeq paired-end, and high-throughput chromosome conformation capture sequencing. The final assembly is 225.32 Mb in length with a scaffold N50 of 19.64 Mb. It contains 23,147 protein-coding genes across 11 chromosomes, 21,148 of which (91.36%) have protein functional annotations. Comparative genomics analysis revealed that A. pictum diverged from the closely related species Apocynum venetum approximately 2.2 million years ago and has not undergone additional polyploidizations after the core eudicot WGT-γ event. Karyotype evolution analysis was used to characterize interchromosomal rearrangements in representative Apocynaceae species and revealed that several A. pictum chromosomes were derived entirely from single chromosomes of the ancestral eudicot karyotype. Finally, we identified 50 members of the well-known stress-responsive WRKY transcription factor family and used transcriptomic data to document changes in their expression at 2 stages of drought stress, identifying a number of promising candidate genes. Overall, this study provides high-quality genomic resources for evolutionary and comparative genomics of the Apocynaceae, as well as initial molecular insights into the drought adaptation of this valuable desert plant.

Transcriptome analysis of mammary epithelial cell between Sewa sheep and East FriEsian sheep from different localities.

Mammary epithelial cells, the only milk-producing cell type in the mammary gland, undergo dynamic proliferation and differentiation during pregnancy, culminating in lactation postpartum. The East FriEsian sheep ranks among the world's most prolific dairy breeds, while the Sewa sheep, a unique dual-purpose breed autochthonous to the Qinghai-Tibet Plateau, exhibits significantly lower milk production. Employing tissue culture methods, we successfully established mammary epithelial cell lines from both breeds. Morphological assessment of mammary epithelial cells and immunofluorescence identification of Cytokeratin 7 and Cytokeratin 8 confirmed the epithelial identity of the isolated cells. Subsequent RNA-seq analysis of these in vitro epithelial cell lines revealed 1813 differentially expressed genes (DEGs). Among these, 1108 were significantly up-regulated and 705 were down-regulated in Sewa epithelial sheep cells compared to East FriEsian epithelial cells. KEGG enrichment analysis identified cellular processes, environmental information processing, human diseases, metabolism, and organismal systems as the primary functional categories associated with DEGs. Gene ontology (GO) terms annotation, categorized into molecular function, biological processes, and cellular component, yielded "binding and catalytic activity," "molecular function regulator activity," and "cellular process," "biological regulation," and "regulation of biological process" as the top three terms within each domain, respectively. Clusters of Orthologous Groups of proteins (KOG) classification further revealed that "signal transduction mechanisms" accounted for the largest proportion of DEGs among all KOG categories. Finally, based on these analyses, ATF3 and MPP7 were identified as promising candidate genes for regulating lactation.

Integrated Single-Cell Multiomic Profiling of Caudate Nucleus Suggests Key Mechanisms in Alcohol Use Disorder.

Alcohol use disorder (AUD) induces complex transcriptional and regulatory changes across multiple brain regions including the caudate nucleus, which remains understudied. Using paired single-nucleus RNA-seq and ATAC-seq on caudate samples from 143 human postmortem brains, including 74 with AUD, we identified 17 distinct cell types. We found that a significant portion of the alcohol-induced changes in gene expression occurred through altered chromatin accessibility. Notably, we identified novel transcriptional and chromatin accessibility differences in medium spiny neurons, impacting pathways such as RNA metabolism and immune response. A small cluster of D1/D2 hybrid neurons showed distinct differences, suggesting a unique role in AUD. Microglia exhibited distinct activation states deviating from classical M1/M2 designations, and astrocytes entered a reactive state partially regulated by JUND, affecting glutamatergic synapse pathways. Oligodendrocyte dysregulation, driven in part by OLIG2, was linked to demyelination and increased TGF-β1 signaling from microglia and astrocytes. We also observed increased microglia-astrocyte communication via the IL-1β pathway. Leveraging our multiomic data, we performed cell type-specific expression quantitative trait loci analysis, integrating that with public genome-wide association studies to identify AUD risk genes such as ADAL and PPP2R3C, providing a direct link between genetic variants, chromatin accessibility, and gene expression in AUD. These findings not only provide new insights into the genetic and cellular mechanisms in the caudate related to AUD but also demonstrate the broader utility of large-scale multiomic studies in uncovering complex gene regulation across diverse cell types, which has implications beyond the substance use field.

A novel root hair mutant, srh1, affects root hair elongation and reactive oxygen species levels in wheat.

Root hairs are single-celled projections on root surfaces, critical for water and nutrient uptake. Here, we describe the first short root hair mutant in wheat (Triticum aestivum L.), identified in a mutagenized population and termed here short root hair 1 (srh1). While the srh1 mutant can initiate root hair bulges, lack of subsequent extension results in very short root hairs. Due to its semi-dominant nature, heterozygous lines displayed intermediate root hair lengths compared to wild-type. Bulked segregant analysis in a BC1F3 segregating population genotyped via exome capture sequencing localized the genetic control of this mutant to a region on the long arm of chromosome 3A. Via RNA sequencing and bioinformatic analysis, we identified two promising candidate genes. The first was a respiratory burst oxidase homolog (RBOH) encoding gene TaNOX3-A, orthologous to RBOH genes controlling root hair elongation in rice (OsNOX3) and maize (ZmRTH5), that carries a missense mutation in a conserved region of the predicted protein. RBOHs are membrane bound proteins that produce reactive oxygen species (ROS) which trigger cell wall extensibility, allowing subsequent root hair elongation. Notably, reduced ROS levels were observed in srh1 root hair bulges compared to wild-type. The second candidate was the calreticulin-3 encoding gene TaCRT3-A, located within the wider srh1 interval and whose expression was significantly downregulated in srh1 root tissues. The identification of a major effect gene controlling wheat root hair morphology provides an entry point for future optimization of root hair architecture best suited to future agricultural environments.