High-level Gene Expression Research Articles

Linalool and 1,8-Cineole as Constitutive Disease-Resistant Factors of Norway Spruce Against Necrotrophic Pathogen Heterobasidion Parviporum.

Norway spruce is an important coniferous species in boreal forests. Root and stem rot diseases caused by the necrotrophic pathogen Heterobasidion parviporum threaten the wood production of Norway spruce which necessitates the search for durable control and management strategies. Breeding for resistant traits is considered a viable long-term strategy. However, identification of potential resistant traits and markers remains a major challenge. In this study, short-term disease resistance screening was conducted using 218 Norway spruce clones from 17 families. Disease resistance was evaluated based on the size of necrosis lesion length following infection with the pathogen. A subset of needles/branches from clones with small (partial resistant) or large (susceptible) lesions were used for terpene analysis and transcriptomic profiling. The results revealed that the content of monoterpene linalool and 1,8-cineole and their respective encoded genes were significantly more abundant and highly expressed in the partial resistant group. Furthermore, linalool and 1,8-cineole were demonstrated to have inhibitory effect on the growth of the pathogen H. parviporum, with morphological distortion of the hyphae. RNAseq analysis revealed that transcript of pathogen genes involved in the regulation of carbohydrate metabolism and stress responses were significantly decreased in presence of the terpenes. The results suggest the relevance of monoterpenes together with jasmonic acid precursor and some genes involved in phenylpropanoid biosynthesis, as constitutive tolerance factors for Norway spruce tolerance against necrotrophic pathogen. The high level of necrosis related cell death gene expression might be factors critical for host susceptibility and disease development.

Functional role of the c-terminal domains of the msl2 protein of drosophila melanogaster

Dosage compensation complex, consisting of five proteins and two non-coding RNAs roX, specifically binds to the X chromosome in males, providing a higher level of gene expression, which is necessary to compensate for the monosomy of the sex chromosome in male Drosophila compared to two X chromosomes in females. The MSL2 protein contains an N-terminal RING domain, which acts as an E3 ligase in the ubiquitination of proteins and is the only subunit of the complex that is expressed only in males. The functional role of two C-terminal domains of the MSL2 protein, enriched with proline (P-domain) and basic amino acids (B-domain), was investigated. As a result, it was shown that the B-domain destabilizes the MSL2 protein, which is associated with the presence of two lysines whose ubiquitination is under the control of the RING domain of MSL2. The unstructured proline-rich domain stimulates transcription of the roX2 gene, which is necessary for the effective formation of the dosage compensation complex.

Distribution of progesterone receptors and the membrane component of progesterone receptor in various organs and tissues of male and female rats

Progesterone regulates reproductive processes and affects many functions of various non-reproductive organs. Its effects in mammals and humans are mediated by nuclear (nPRs) and membrane progesterone receptors (mPRs). The action of progesterone through different types of receptors may differ significantly and has tissue specific features. The expression of known types and subtypes of progesterone receptors in the tissues of male and female rats has been studied fragmentarily. The purpose of our work was to study the expression of five mPRs genes, as well as the nPRs gene and the membrane component of the progesterone receptor PGRMC I in the reproductive organs and in 17 non-reproductive tissues of male and female rats using reverse transcription followed by real-time PCR. In this study, it was shown that a high level of nPRs gene expression in rats is found not only in reproductive organs of females (uterus, ovary, mammary glands), but also in seminal vesicles of males, in the brain and trachea of both sexes, in blood vessels, and in the pancreas of females. The highest level of expression of mPRs genes of all subtypes was found in the testes, while expression of the gene encoding nPRs was practically undetectable in them. Expression of genes encoding mPRs was also detected in the liver and spleen of male and female rats, while expression of the gene encoding nPRs was at background levels. Virtually no expression of nPRs, mPRs, and membrane component of progesterone receptor (PGRMC I) genes was detected in muscle, and its level was very low in the heart in animals of both sexes. We found sex-specific differentiation of nuclear and membrane receptor mRNA levels in rats in non-reproductive tissues, characterized by a predominance of nPRs transcripts and three subtypes of mPRs (α, β, δ) in females and two subtypes of mPRs (γ, ε) in males. Data on the presence of progesterone receptors in tissues not involved in reproduction confirm the effect of progesterone on these organs. High levels of mRNA for various progesterone receptors in the tissues of male rats, such as the pancreas, lungs, kidney, and trachea, indicate an important physiological role of progestins not only in females, but also in males, which is still poorly understood. The work also discusses the known functions of progesterone receptors in the tissues studied.

GW3, encoding a member of the P450 subfamily, controls grain width by regulating the GA4 content in spikelets of rice (Oryza sativa L.).

A stable QTL, GW3, controlling grain width was identified in two populations. Its causal gene LOC_Os03g04680 was verified by gene-based haplotype analysis, expression analysis, gene knockout and complementation transgenic tests. Grain width (GW) is one of the key traits affecting grain size and determines grain yield and appearance quality in rice. Mining gene loci and elite alleles controlling GW is necessary. The GW phenotypes of the two populations were investigated in three environments, which showed abundant phenotypic variation. GW3, encoding a P450 subfamily protein, was identified and validated as a causal gene by gene-based haplotype analysis, expression analysis, gene knockout and complementation transgenic tests. The accessions with large GW values had high gene expression levels. In addition, the GW of the accessions with the GG allele was significantly greater than that of the accessions with the AA allele. The Hap 1 and Hap 3 were identified as elite haplotypes, which can increase GW. The expression levels of OsKO1, OsGA3ox1, OsGA20ox1 and OsGA20ox2 in the young panicle of A7444 were significantly greater than those in the young panicle of the mutants, indicating that GW3 may be involved in the gibberellins (GA) biosynthesis pathway to regulate GW. GA4 content detection and electron scanning analysis revealed that GA4 regulates GW by affecting glume cell size. These results provide new insights for studying the genetic mechanism of rice GW and provide a material basis for breeding high-yield rice varieties.

Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis

The discovery of Lactylation may pave the way for novel approaches to investigating sepsis. This study focused on the prognostic and diagnostic significance of lactylated genes in sepsis. RNA sequencing was performed on blood samples from 20 sepsis patients and 10 healthy individuals at Southwest Medical University in Luzhou, Sichuan, China. Genes associated with sepsis were identified through analysis of RNA sequencing data. Afterward, the genes that were expressed differently were compared with the lactylation genes, resulting in the identification of 55 lactylation genes linked to sepsis. The overlapping genes underwent analysis using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Protein-Protein Network Interactions were used to screen for the core genes. The datasets GSE65682, GSE69528, GSE54514, GSE63042, and GSE95233 were obtained from the GEO database to validate core genes. Survival analysis evaluated the predictive significance of central genes in sepsis, while Receiver Operating Characteristic (ROC) Curve analysis was employed to establish the diagnostic value of genes. Additionally, a meta-analysis was conducted to confirm the precision of RNA-seq data. We obtained five peripheral blood samples, including two from healthy individuals, one from a patient with systemic inflammatory response syndrome (SIRS), and two from patients with sepsis. These samples were used to identify the specific location of core genes using 10×single-cell sequencing. High-throughput sequencing and bioinformatics techniques identified two lactylation-related genes (S100A11 and CCNA2) associated with sepsis. Survival analysis indicated that septic patients with reduced levels of S100A11 had a decreased 28-day survival rate compared to those with elevated levels. Conversely, individuals exhibiting decreased CCNA2 levels demonstrated a greater likelihood of surviving for 28 days than those in the high expression category, indicating a favorable association with survival rates among sepsis patients (P < 0.05). Both genes showed high sensitivity and specificity based on the ROC curve, with AUC values of 0.961 for S100A11 and 0.890 for CCNA2. The meta-analysis revealed that S100A11 exhibited high levels of expression in the sepsis survivors, whereas it displayed low levels of expression in the non-survivors; on the other hand, CCNA2 demonstrated low expression in the sepsis survivors and high expression in the non-survivors (P < 0.05). Single-cell RNA sequencing ultimately showed that monocyte macrophages, T cells, and B cells exhibited high expression levels of the crucial genes associated with sepsis-induced lactylation. In conclusion, the lactylation genes S100A11 and CCNA2 are strongly linked to sepsis and could be valuable markers for diagnosing, predicting outcomes, and providing guidance for sepsis.

Distinct regional vulnerability to Aβ and iron accumulation in post mortem AD brains.

The paramagnetic iron, diamagnetic amyloid beta (Aβ) plaques and their interaction are crucial in Alzheimer's disease (AD) pathogenesis, complicating non-invasive magnetic resonance imaging for prodromal AD detection. We used a state-of-the-art sub-voxel quantitative susceptibility mapping method to simultaneously measure Aβ and iron levels in post mortem human brains, validated by histology. Further transcriptomic analysis using Allen Human Brain Atlas elucidated the underlying biological processes. Regional increased paramagnetic and diamagnetic susceptibility were observed in medial prefrontal, medial parietal, and para-hippocampal cortices associated with iron deposition (R=0.836, p=0.003) and Aβ accumulation (R=0.853, p=0.002) in AD brains. Higher levels of gene expression relating to cell cycle, post-translational protein modifications, and cellular response to stress were observed. These findings provide quantitative insights into the variable vulnerability of cortical regions to higher levels of Aβ aggregation, iron overload, and subsequent neurodegeneration, indicating changes preceding clinical symptoms. The vulnerability of distinct brain regions to amyloid beta (Aβ) and iron accumulation varies. Histological validation was performed on stained sections of ex-vivo human brains. Regional variations in susceptibility were linked to gene expression profiles. Iron and Aβ levels in ex-vivo brains were simultaneously quantified.

Inducible overexpression of MYB118-like gene improves anthocyanin production in Populus × canescens

Anthocyanins are secondary metabolites which contribute different colors to the leaves. Anthocyanin biosynthesis is regulated by MYB transcription factors, which have been extensively studied and characterized in a diversity of plants. In this study, we identified a novel MYB transcription factor MYB118L, from Populus 'Zhonghua Hongye', which showed an elevated accumulation of anthocyanin than Populus clone ZL-2025. Subcellular localization analyses revealed that MYB118L-GFP fusion protein was specifically located in the nucleus. Transgenic plants overexpressing MYB118L driven by the stress-inducible Rd29A promoter showed a significant increase in anthocyanin production, resulting in a red coloration of the leaves under drought stress conditions. These plants also exhibited higher expression levels of genes involved in anthocyanin biosynthesis compared to the wild type, suggesting that MYB118L positively regulates the expression of these genes. Y1H and dual-luciferase assays confirmed that MYB118L can directly activate the promoters of LAR1 gene. Our findings suggest that MYB118L is an essential transcription factor involved in the regulation of anthocyanin biosynthesis in poplar and could be utilized for genetic engineering of colorful tree species.

Development and validation of a droplet digital PCR method for quantifying lentiviral vector infectious titer

Lentiviruses, with their high transduction efficiency and gene expression levels, are widely used as gene delivery vectors in the development of chimeric antigen receptor T cells (CAR-T) and other genetically modified cell therapies. Accurate determination of the lentiviral vector infectious titer is essential to ensure effective transduction and product consistency. In this study, we developed an efficient method for lentiviral vector titration based on digital droplet polymerase chain reaction (ddPCR) technology, enabling absolute quantification of the target gene. Benzonase treatment of non-transduced plasmids substantially shortened the experimental period, reducing cell culture duration from 10-14 days–3 days. The method was rigorously validated by assessing specificity, working range, limit of quantification, precision, accuracy, and robustness. This study demonstrates the feasibility of combining enzymatic digestion with ddPCR to quantify lentiviral vector infectious titer and provides a detailed and readily adaptable methodology for the scientific community.

Systemic comparison of molecular characteristics in different skin fibroblast senescent models.

Senescent human skin primary fibroblast (FB) models have been established for studying aging-related, proliferative, and inflammatory skin diseases. The aim of this study was to compare the transcriptome characteristics of human primary dermal FBs from children and the elderly with four senescence models. Human skin primary FBs were obtained from healthy children (FB-C) and elderly donors (FB-E). Senescence models were generated by ultraviolet B irradiation (FB-UVB), D-galactose stimulation (FB-D-gal), atazanavir treatment (FB-ATV), and replication exhaustion induction (FB-P30). Flow cytometry, immunofluorescence staining, real-time quantitative polymerase chain reaction, co-culturing with immune cells, and bulk RNA sequencing were used for systematic comparisons of the models. In comparison with FB-C, FB-E showed elevated expression of senescence-related genes related to the skin barrier and extracellular matrix, proinflammatory factors, chemokines, oxidative stress, and complement factors. In comparison with FB-E, FB-UVB and FB-ATV showed higher levels of senescence and expression of the genes related to the senescence-associated secretory phenotype (SASP), and their shaped immune microenvironment highly facilitated the activation of downstream immune cells, including T cells, macrophages, and natural killer cells. FB-P30 was most similar to FB-E in terms of general transcriptome features, such as FB migration and proliferation, and aging-related characteristics. FB-D-gal showed the lowest expression levels of senescence-related genes. In comparisons with the single-cell RNA sequencing results, FB-E showed almost complete simulation of the transcriptional spectrum of FBs in elderly patients with atopic dermatitis, followed by FB-P30 and FB-UVB. FB-E and FB-P30showed higher similarity with the FBs in keloids. Each senescent FB model exhibited different characteristics. In addition to showing upregulated expression of natural senescence features, FB-UVB and FB-ATV showed high expression levels of senescence-related genes, including those involved in the SASP, and FB-P30showed the greatest similarity with FB-E. However, D-galactose-stimulated FBs did not clearly present aging characteristics.

Identification of Cold Tolerance Transcriptional Regulatory Genes in Seedlings of Medicago sativa L. and Medicago falcata L.

Alfalfa species Medicago sativa L. (MS) and Medicago falcata L. (MF), globally prominent perennial leguminous forages, hold substantial economic value. However, our comprehension of the molecular mechanisms governing their resistance to cold stress remains limited. To address this knowledge gap, we scrutinized and compared MS and MF cold-stress responses at the molecular level following 24 h and 120 h low-temperature exposure (4 °C). Our study revealed that MF had superior physiological resilience to cold stress compared with MS, and its morphology was healthier under cold stress, and its malondialdehyde content and superoxide dismutase activity increased, first, and then decreased, while the soluble sugar content continued to accumulate. Transcriptome analysis showed that after 120 h of exposure, there were different gene-expression patterns between MS and MF, including 1274 and 2983 genes that were continuously up-regulated, respectively, and a total of 923 genes were included, including star cold-resistant genes such as ICE1 and SIP1. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed numerous inter-species differences in sustained cold-stress responses. Notably, MS-exclusive genes included a single transcription factor (TF) gene and several genes associated with a single DNA repair-related pathway, whereas MF-exclusive genes comprised nine TF genes and genes associated with 14 pathways. Both species exhibited high-level expression of genes encoding TFs belonging to AP2-EREBP, ARR-B, and bHLH TF families, indicating their potential roles in sustaining cold resistance in alfalfa-related species. These findings provide insights into the molecular mechanisms governing cold-stress responses in MS and MF, which could inform breeding programs aimed at enhancing cold-stress resistance in alfalfa cultivars.

Insights into the Detoxification of Spruce Monoterpenes by the Eurasian Spruce Bark Beetle.

Plant defence mechanisms, including physical barriers like toughened bark and chemical defences like allelochemicals, are essential for protecting them against pests. Trees allocate non-structural carbohydrates (NSCs) to produce secondary metabolites like monoterpenes, which increase during biotic stress to fend off pests like the Eurasian spruce bark beetle, ESBB (Ips typographus). Despite these defences, the ESBB infests Norway spruce, causing significant ecological damage by exploiting weakened trees and using pheromones for aggregation. However, the mechanism of sensing and resistance towards host allelochemicals in ESBB is poorly understood. We hypothesised that the exposure of ESBB to spruce allelochemicals, especially monoterpenes, leads to an upsurge in the important detoxification genes like P450s, GSTs, UGTs, and transporters, and at the same time, genes responsible for development must be compromised. The current study demonstrates that exposure to monoterpenes like R-limonene and sabiene effectively elevated detoxification enzyme activities. The differential gene expression (DGE) analysis revealed 294 differentially expressed (DE) detoxification genes in response to R-limonene and 426 DE detoxification genes in response to sabiene treatments, with 209 common genes between the treatments. Amongst these, genes from the cytochrome P450 family 4 and 6 genes (CP4 and CP6), esterases, glutathione S-transferases family 1 (GSTT1), UDP-glucuronosyltransferase 2B genes (UDB), and glucose synthesis-related dehydrogenases were highly upregulated. We further validated 19 genes using RT-qPCR. Additionally, we observed similar high expression levels of detoxification genes across different monoterpene treatments, including myrcene and α-pinene, suggesting a conserved detoxification mechanism in ESBB, which demands further investigation. These findings highlight the potential for molecular target-based beetle management strategies targeting these key detoxification genes.

Gene expression associated with chlorophyll degradation and color transformation in a spontaneous bud mutation of navel orange

Color mutations on citrus skin are a common occurrence and can serve as indicators of fruit maturation in citrus. In this study, a new early maturing navel orange cultivar, Lei Zao 1 Hao (MT), was identified as a spontaneous bud mutation from the Leibo Navel Orange (WT). To assess the differences between these two cultivars, the coloration of the fruit, the sugar content, and the levels of acid were examined throughout the ripening process. The study findings revealed that over the course of the fruit's development, the external peel color progressively turned orange. MT exacerbated the decline in H° while increasing L*, a*, and b*, and the chlorophyll level of the MT peel was continuously lower than that of WT, which coincided with a decrease in chlorophylls a and b. Compared to WT, MT had higher expression levels of genes linked to chlorophyll degradation, including CitCLH, CitNYC1, CitPPH, CitPAO, CitCAB1, and CitCAB2. The elevated expression of these genes in MT may potentially be associated with the initial color transformation process. In addition, the MT accelerated the accumulation of TSS and total sugar, especially before the 189 DAF of ripening. In short, ‘Lei Zao 1 Hao’ is a new option of navel orange available with extremely early maturity and a higher sugar content.

Transcriptomic Analysis Reveals Diverse Expression of Scorpion Toxin Genes in Mesobuthus martensii.

Scorpions, an ancient group of venomous invertebrates, have existed for over 430 million years. Their toxins, important for predation and defense, exhibit a variety of biological and pharmacological activities. Research on scorpion toxins has spanned decades. Notably, the toxin genes of Mesobuthus martensii (Scorpiones: Buthidae), a well-known Chinese herbal medicine, have been described at genomic and proteomic levels. However, previous studies primarily focused on the toxin genes expressed in the venom glands, overlooking their expression in multiple tissues. This study analyzed transcriptomes from 14 tissues of M. martensii. Gene annotation revealed 83 toxin and toxin-like genes, including those affecting sodium, potassium, calcium, and chloride ion channels. Approximately 70% of toxin genes were highly expressed in the vesicle; additionally, some exhibited low or no expression in the vesicle while showing high expression in other tissues. Beyond the vesicle, high expression levels of toxin genes were observed in metasoma segments II-V, blood, lateral eyes, chelicerae, legs, pedipalp chelae, femurs, and patellae. This expression pattern suggests that toxin genes are recruited from multiple tissues and may help prevent intraspecific harm during courtship and competition for prey. These findings inspire further research into the evolutionary recruitment process of scorpion toxins.

Transcriptomics analysis of the role of SdiA in desiccation tolerance of Cronobacter sakazakii in powdered infant formula

The quorum-sensing receptor SdiA is vital for regulating the desiccation tolerance of C. sakazakii, yet the specific mechanism remains elusive. Herein, transcriptomics and phenotypic analysis were employed to explore the response of C. sakazakii wild type (WT) and sdiA knockout strain (ΔsdiA) under drying conditions. Following 20 days of drying in powdered infant formula (PIF), WT exhibited 4 log CFU/g higher survival rates compared to ΔsdiA. Transcriptome revealed similar expression patterns between csrA and sdiA, their interaction was confirmed both by protein-protein interaction analysis and yeast two-hybrid assays. Notably, genes associated with flagellar assembly and chemotaxis (flg, fli, che, mot regulon) showed significantly higher expression levels in WT than in ΔsdiA, indicating a reduced capacity for flagellar synthesis in ΔsdiA, which was consistent with cellular morphology observations. Similarly, genes involved in trehalose biosynthesis (ostAB, treYZS) and uptake (thuEFGK) exhibited similar expression patterns to sdiA, with higher levels of trehalose accumulation observed in WT under desiccation conditions compared to ΔsdiA. Furthermore, WT demonstrated enhanced protein and DNA synthesis capabilities under desiccation stress. Higher expression levels of genes related to oxidative phosphorylation were also noted in WT, ensuring efficient cellular ATP synthesis. This study offers valuable insights into how SdiA influences the desiccation tolerance of C. sakazakii, paving the way for targeted strategies to inhibit and control this bacterium.

Single-Cell RNA Sequencing Revealing that MMP12+ Macrophages are Associated with Cancer Liver Metastasis.

We aimed to explore the MMP12+ macrophages function in liver metastasis of Colorectal cancer [CRC]. CRC has a high incidence, and a great many patients develop liver metastases. Some studies have found that macrophages may participate in the liver metastasis of CRC. This study aimed to determine the factors and major signaling pathways of MMP12+ macrophages affecting liver metastasis of CRC. The single-cell RNA sequencing [scRNA-seq] data of CRC and bulk transcriptome data were downloaded. After filtering scRNA-seq data, dimensionality reduction and clustering were performed to identify different cell subgroups. The FindAll- Markers function was used to calculate the differentially expressed genes in each cell subgroup, and the genes in the promising set were uploaded to the DAVID database to analyze the biological processes to which these genes were enriched. Differentially expressed genes among macrophage subgroups were selected by the AverageExpression function. Then, the CIBERSORT algorithm was used to compute the proportion of each macrophage subgroup in each bulk tissue and determine the most significant macrophage subgroup. The dynamic changes of gene expression in macrophage subgroup were computed by Pseudotime. Finally, CellChat was applied to investigate the effect of the macrophage subgroup on epithelial cells and the ligand-receptor effect of B cells and T cells. Clustering scRNA-seq data showed a larger proportion of macrophages in liver metastases. The proportion of MMP12+ macrophage subtypes increased gradually among normal, tumor, and liver metastasis groups, and MMP12+ macrophages were associated with angiogenesis, cell migration, and inhibited T cell proliferation. The Pseudotime showed higher expression levels of genes related to angiogenesis and enhanced TGF-β signaling pathway and the negative regulation of T cell proliferation with the occurrence of liver metastasis in MMP12+ macrophages. MMP12+ macrophages can promote the proliferation of epithelial cells and inhibit the activation of T cells and B cells. MMP12+ macrophages promoted liver metastasis of CRC by influencing angiogenesis, TGF-β signaling pathway expression, and regulation of T cells and B cells.

Precision and efficacy of RNA-guided DNA integration in high-expressing muscle loci

Gene replacement therapies primarily rely on adeno-associated virus (AAV) vectors for transgene expression. However, episomal expression can decline over time due to vector loss or epigenetic silencing. CRISPR-based integration methods offer promise for long-term transgene insertion. While the development of transgene integration methods has made substantial progress, identifying optimal insertion loci remains challenging. Skeletal muscle is a promising tissue for gene replacement owing to low invasiveness of intramuscular injections, relative proportion of body mass, the multinucleated nature of muscle, and the potential for reduced adverse effects. Leveraging endogenous promoters in skeletal muscle, we evaluated two highly expressing loci using homology-independent targeted integration (HITI) to integrate reporter or therapeutic genes in mouse myoblasts and skeletal muscle tissue. We hijacked the muscle creatine kinase (Ckm) and myoglobin (Mb) promoters by co-delivering CRISPR-Cas9 and a donor plasmid with promoterless constructs encoding green fluorescent protein (GFP) or human Factor IX (hFIX). Additionally, we deeply profiled our genome and transcriptome outcomes from targeted integration and evaluated the safety of the proposed sites.This study introduces a proof-of-concept technology for achieving high-level therapeutic gene expression in skeletal muscle, with potential applications in targeted integration-based medicine and synthetic biology.

Roles of microbiota in autoimmunity in Arabidopsis leaves

Over the past three decades, researchers have isolated plant mutants that show constitutively activated defence responses in the absence of pathogen infection. These mutants are called autoimmune mutants and are typically dwarf and/or bearing chlorotic/necrotic lesions. Here, from a genetic screen for Arabidopsis genes involved in maintaining a normal leaf microbiota, we identified TIP GROWTH DEFECTIVE 1 (TIP1), which encodes an S-acyltransferase, as a key player in guarding leaves against abnormal microbiota level and composition under high-humidity conditions. The tip1 mutant has several characteristic phenotypes of classical autoimmune mutants, including a dwarf stature, showing lesions, and having a high basal level of defence gene expression. Gnotobiotic experiments revealed that the autoimmune phenotypes of the tip1 mutant are largely dependent on the presence of microbiota as axenic tip1 plants have markedly reduced autoimmune phenotypes. We found that the microbiota dependency of autoimmune phenotypes is shared by several ‘lesion mimic’-type autoimmune mutants in Arabidopsis. It is worth noting that autoimmune phenotypes caused by mutations in two Nucleotide-Binding, Leucine-Rich Repeat (NLR) genes do not require the presence of microbiota and can even be partially alleviated by microbiota. Our results therefore suggest the existence of at least two classes of autoimmunity (microbiota-dependent versus microbiota-independent) in plants. The observed interplay between autoimmunity and microbiota in the lesion mimic class of autoimmunity is reminiscent of the interactions between autoimmunity and dysbiosis in the animal kingdom. These parallels highlight the intricate relationship between host immunity and microbial communities across various biological systems.

PKR activation-induced mitochondrial dysfunction in HIV-transgenic mice with nephropathy.

HIV disease remains prevalent in the USA and chronic kidney disease remains a major cause of morbidity in HIV-1-positive patients. Host double-stranded RNA (dsRNA)-activated protein kinase (PKR) is a sensor for viral dsRNA, including HIV-1. We show that PKR inhibition by compound C16 ameliorates the HIV-associated nephropathy (HIVAN) kidney phenotype in the Tg26 transgenic mouse model, with reversal of mitochondrial dysfunction. Combined analysis of single-nucleus RNA-seq and bulk RNA-seq data revealed that oxidative phosphorylation was one of the most downregulated pathways and identified signal transducer and activator of transcription (STAT3) as a potential mediating factor. We identified in Tg26 mice a novel proximal tubular cell cluster enriched in mitochondrial transcripts. Podocytes showed high levels of HIV-1 gene expression and dysregulation of cytoskeleton-related genes, and these cells dedifferentiated. In injured proximal tubules, cell-cell interaction analysis indicated activation of the pro-fibrogenic PKR-STAT3-platelet-derived growth factor (PDGF)-D pathway. These findings suggest that PKR inhibition and mitochondrial rescue are potential novel therapeutic approaches for HIVAN.

Stress-induced phosphoprotein 1 (STIP1) gene expression in adenomyosis: An observational case-control study

Background. Endometriosis is distinguished by its high prevalence and significant impact on the quality of life and reproductive health of women; however, its etiology and essential pathogenesis of remain uncertain so far. Modern research is increasingly focusing on immune, hormonal and genetic factors that share a common structure and participate in common metabolism — so-called single nucleotide polymorphisms (SNPs), including stress-induced phosphoprotein 1 (STIP1), which participates in tissue and cellular metabolism through transcription splicing and folding of RNA. The role of this protein, known as heat shock protein (HSP)-organizing protein, is being actively studied in cancer and hyperproliferative diseases. The role of the STIP1 gene and its product in the pathogenesis of adenomyosis appears to be studied insufficiently, thereby determining the relevance of the present study.Objectives. To evaluate the expression of stress-induced phosphoprotein 1 in eutopic endometrium and myometrium in women with isolated adenomyosis, as well as in combination with other benign hyperproliferative diseases of the reproductive system.Methods. Clinical study site: Clinical and Diagnostic Department of Ott Research Institute of Obstetrics, Gynecology and Reproductology. Design: an observational case-control study of patients with verified diagnoses of diffuse adenomyosis, uterine fibroids, and external genital endometriosis (main group — n = 55). The study group (n = 43) was divided into three subgroups: patients with isolated diffuse adenomyosis (AM, n = 16), adenomyosis in combination with uterine fibroids (AM + UF, n = 16), adenomyosis in combination with external genital endometriosis (AM + EGE, n = 11)), a comparison group — patients with uterine fibroids (n = 12) and a control group (n = 17) — women of reproductive age without gynecological diseases. The study was conducted from November 1, 2022 to September 30, 2023. The target indicator of the study was the level of relative mRNA (mRNA) expression of STIP1 gene (in RQ (Relative Quantity) units) in the uterus — adenomyosis glands, surrounding myometrium and endometrium. Histological evaluation of the endometrium served as an additional indicator. Statistical analysis of the results obtained, namely the relative level of mRNA expression, was carried out by the ΔΔСt method using the Expression Suit V1.0.3 program. (https://www.thermofisher.com/ru/ru/home/technical-resources/software-downloads/expressionsuite-software.html). The data analysis was performed using the GraphPad Prizm program (Insight Partners, USA). Differences between groups were evaluated by means of single factor ANOVA analysis (followed by post-hoc pairwise comparisons (Tukey test) of the values in each group. The differences were considered statistically significant at p &lt; 0.05.Results. A high level of STIP1 gene expression was reported in myometrium of patients with isolated adenomyosis (more than 3-fold increase in relation to the comparison group — patients with uterine fibroids). In addition, myometrium of women with adenomyosis combined with uterine fibroids demonstrated a higher expression of STIP1 gene, compared to patients with isolated uterine fibroids (p &lt; 0.01). The evaluation of the expression of mRNA of the STIP1 gene in the eutopic endometrium of patients with adenomyosis and women in the control group revealed no significant differences; however, STIP1 in the endometrium of women with adenomyosis was significantly lower than in the endometrium of both patients with uterine fibroids and women with adenomyosis combined with external genital endometriosis.Conclusion. Increased mRNA expression of STIP1 gene in myometrium in adenomyosis confirms its role in the pathogenesis of this disease. The role of the expression of the STIP1 gene and the corresponding protein is to be further clarified in order to assess its specificity and sensitivity as a diagnostic marker and to identify new approaches to the treatment of adenomyosis.

Abortive and productive infection of CNS cell types following in vivo delivery of VSV

Viral infection is frequently assayed by ongoing expression of viral genes. These assays fail to identify cells that have been exposed to the virus but limit or inhibit viral replication. To address this limitation, we used a dual-labeling vesicular stomatitis virus (DL-VSV), which has a deletion of the viral glycoprotein gene, to allow evaluation of primary infection outcomes. This virus encodes Cre, which can stably mark any cell with even a minimal level of viral gene expression. Additionally, the virus encodes GFP, which distinguishes cells with higher levels of viral gene expression, typically due to genome replication. Stereotactic injections of DL-VSV into the murine brain showed that different cell types had very different responses to the virus. Almost all neurons hosted high levels of viral gene expression, while glial cells varied in their responses. Astrocytes (Sox9+) were predominantly productively infected, while oligodendrocytes (Sox10+) were largely abortively infected. Microglial cells (Iba1+) were primarily uninfected. Furthermore, we monitored the early innate immune response to viral infection and identified unique patterns of interferon (IFN) induction. Shortly after infection, microglia were the main producers of IFNb, whereas later, oligodendrocytes were the main producers. IFNb+ cells were primarily abortively infected regardless of cell type. Last, we investigated whether IFN signaling had any impact on the outcome of primary infection and did not observe significant changes, suggesting that intrinsic factors are likely responsible for determining the outcome of primary infection.