Marker Genes Research Articles

Potential ameliorative effect of Dapagliflozin on systemic inflammation-induced cardiovascular injury via endoplasmic reticulum stress and autophagy pathway.

Dapagliflozin (DPG) is a sodium-glucose cotransporter-2 inhibitor and is used in the treatment of diabetes. In this study, we aimed to investigate the effect of DPG on cardiotoxicity caused by systemic inflammation via endoplasmic reticulum (ER) stress and autophagy. Four groups of thirty-two Wistar Albino rats were created: Control (1ml oral physiological saline for five days and intraperitoneal saline on the 5th day), LPS (1ml oral physiological saline for five days and intraperitoneal 5mg/kg of LPS on the 5th day), LPS + DPG (10mg/kg of DPG orally for five days and 5mg/kg of LPS intraperitoneally on the 5th day), and DPG (10mg/kg of DPG orally for five days and 5mg/kg of SF intraperitoneally on the 5th day). Histopathological and immunohistochemical analyses were performed on heart and aorta tissues. ER stress and autophagy gene markers in heart tissues were evaluated by RT-qPCR. Oxidative stress in heart tissues and serum cardiac enzymes were analyzed by spectrophotometric method. The heart and aortic tissues of the LPS group showed increased expressions of Tumor Necrosis Factor-α (TNF-α) and Caspase-3 (Cas-3), along with mild hyperemia, slight inflammatory cell infiltrations, and myocardial cell damage. The heart tissues also showed genetically increased expressions of include binding immunoglobulin protein (BiP/ GRP78), protein kinase RNA-like ER Kinase (PERK), inositol-requiring enzyme 1 (IRE-1), activating transcription factors 4 (ATF-4), activating transcription factors 4 (ATF6), C/EBP homologous protein (CHOP), and BECLIN 1. Furthermore, Creatine kinase-MB (CK-MB) and Lactate dehydrogenase (LDH) levels in blood tissue significantly increased, according to biochemical analysis. With DPG therapy, all of these findings were reversed. In conclusion, DPG protects against the cardiotoxic effect of systemic inflammation with its antioxidant and anti-inflammatory properties by regulating ER stress and autophagy pathways.

Inhibitory Effect of Luteolin on Spike S1 Glycoprotein-Induced Inflammation in THP-1 Cells via the ER Stress-Inducing Calcium/CHOP/MAPK Pathway.

The global SARS-CoV-2 outbreak has escalated into a critical public health emergency, with the spike glycoprotein S1 subunit of SARS-CoV-2 (spike-S1) linked to inflammation in lung tissue and immune cells. Luteolin, a flavone with anti-inflammatory properties, shows promise, but research on its effectiveness against long-COVID-related inflammation and spike protein-induced responses remains limited. This study aims to elucidate the underlying mechanisms of inflammation in THP-1 cells induced by the spike-S1. Additionally, it seeks to assess the potential of luteolin in mitigating inflammatory responses induced by the spike-S1 in a THP-1 macrophage model. The gene expression profiles of spike-S1 in THP-1 cells were analyzed by transcriptome sequencing. The inhibitory effect of luteolin on ER stress and inflammation in spike-S1-induced THP-1 cells was investigated using Western blotting, RT-PCR, and ELISA. The candidate genes (CAMK2A, SIGLEC7, PPARGC1B, SEC22B, USP28, IER2, and TIRAP) were upregulated in the spike-S1-induced THP-1 group compared to the control group. Among these, calcium/calmodulin-dependent protein kinase II alpha (CAMK2A) was identified as the most promising molecule in spike-S1-induced THP-1 cells. Our results indicate that the spike S1 significantly increased the expression of ER-stress markers at both gene and protein levels. Luteolin significantly reduced ER stress by decreasing the expression of ER-stress marker genes and ER-stress marker proteins (p < 0.01). Additionally, luteolin exhibited anti-inflammatory properties upon spike S1-induction in THP-1 cells by significantly suppressing IL-6, IL-8, and IL-1β cytokine secretion in a dose-dependent manner (p < 0.05). Furthermore, our results revealed that luteolin exhibited the downregulation of the MAPK pathway, as evidenced by modulating the phosphorylation of p-ERK1/2, p-JNK and p-p38 proteins (p < 0.05). The results from this study elucidate the mechanisms by which the spike S1 induces inflammation in THP-1 cells and supports the use of naturally occurring bioactive compounds, like luteolin, against inflammation-related SARS-CoV-2 infection.

Systematics and Phylogeny of Myxomycetes: Yesterday, Today, Tomorrow

Myxomycetes are amoeboid fungus-like organisms (Amoebozoa) with a unique life cycle characterized by a great morphological diversity of fruiting bodies. Due to the similarity of these structures to the fruiting bodies of some representatives of Ascomycota and Basidiomycota, myxomycetes have been classified as fungi since the first known scientific description in 1654. Only in the XIX century, when their life cycle was studied, the difference of this group from fungi became clear. During the same period, microscopic structures of fruiting bodies, as well as ornamentation of the spore surface, began to be considered as diagnostic features. Due to this, in the period from the end of XIX to the middle of XX century, a rather stable system was formed. However, as further studies have shown, both macro- and micromorphological characters are often quite variable, depend on environmental conditions, and often result from a convergent evolution, which causes difficulties in defining species and taxonomic units of higher ranks. Since the first decade of the 21st century, thanks to the development of molecular genetic methods and accumulation of data on nucleotide sequences of marker genes together with the improvement of microscopic studies, it has been possible to obtain data on the evolutionary relationships of different groups of myxomycetes. A milestone in this process was the publication of the first phylogenetic system of myxomycetes in 2019. This work was the starting point for a number of studies on the relationships of different groups of myxomycetes at a lower taxonomic level. Thus, there has been a surge in the number of studies that bring us closer to constructing a natural system. The latest iteration of the myxomycete system, incorporating all modifications and enhancements as of June 2024, is presented.

Performance of different wheat varieties and their associated microbiome under contrasting tillage and fertilization intensities: Insights from a Swiss long-term field experiment

Winter wheat is an important global cereal crop. However, conventional farming practices, characterised by intensive tillage and high fertilizer inputs, pose significant threats to the environment. In response, more conservative management practices are being applied aiming to maintain wheat production while promoting a beneficial microbiome. Here, we evaluated the suitability of three different wheat varieties for less intensive agricultural systems, focusing on reduced tillage and fertilizer intensity. The study was conducted over two consecutive years in a Swiss long-term field experiment comparing conventional versus reduced tillage and full fertilization versus half fertilization. In addition, we investigated the composition of plant-associated microbial communities using amplicon sequencing of phylogenetic marker genes, specifically targeting bacteria and fungi in rhizosphere samples and fungi in root samples. Our results revealed that in our study wheat variety most strongly predicted grain yield and quality, independent of tillage and fertilization intensity. Specifically, wheat varieties demonstrated higher yields and N uptake in plots subjected to conventional ploughing and full fertilization compared to those under reduced tillage and half fertilization. We found no significant effect of wheat variety on the composition of microbial communities. However, tillage emerged as the primary factor influencing microbial community composition in the rhizosphere, while fertilization intensity significantly impacted fungal communities in the root system. These findings underscore the complex interplay between agronomic practices, plant genetics, and microbial dynamics in agroecosystems, emphasizing the need for holistic and adaptive approaches and their further development to ensure sustainable crop production.

Development of a Multilayer Film Including the Soluble Eggshell Membrane Fraction for the Treatment of Oral Mucosa Lesions

Background/Objectives: Oral diseases causing mucosal lesions are normally treated with local or systemic anti-inflammatory, analgesic and antimicrobial agents. The development of topical formulations, including wound-healing promoters, might speed up the recovery process, improving patients’ quality of life, and reduce the risk of deterioration in health conditions. In this study, a mucoadhesive multilayer film, including a novel biocompatible substance (solubilized eggshell membrane, SESM), was rationally designed. Methods: The SESM preparation procedure was optimized and its biological effects on cell proliferation and inflammation marker gene expression were evaluated in vitro; preformulation studies were conducted to identify the most promising polymers with film-forming properties; then, trilayer films, consisting of an outer layer including chlorhexidine digluconate as a model drug, a supporting layer and a mucoadhesive layer, incorporating SESM, were prepared using the casting method and their mechanical, adhesion and drug release control properties were evaluated. Results: SESM proved to possess a notable wound-healing capacity, inducing a wound closure of 84% in 24 h without inhibiting blood clotting. The films revealed a maximum detachment force from porcine mucosa of approx. 1.7 kPa and maximum in vivo residence time of approx. 200–240 min; finally, they released up to 98% of the loaded drug within 4 h. Conclusions: The formulated trilayer films were found to possess adequate properties, making them potentially suitable for protecting oral lesions and favoring their rapid healing, while releasing antimicrobial substances that might be beneficial in reducing the risk of bacterial infections.

TGFB2 mRNA Levels Prognostically Interact with Interferon-Alpha Receptor Activation of IRF9 and IFI27, and an Immune Checkpoint LGALS9 to Impact Overall Survival in Pancreatic Ductal Adenocarcinoma

The treatment of pancreatic ductal adenocarcinoma (PDAC) is an unmet challenge, with the median overall survival rate remaining less than a year, even with the use of FOLFIRINOX-based therapies. This study analyzed archived macrophage-associated mRNA expression using datasets deposited in the UCSC Xena web platform to compare normal pancreatic tissue and PDAC tumor samples. The TGFB2 gene exhibited low mRNA expression levels in normal tissue, with less than one TPM. In contrast, in tumor tissue, TGFB2 expression levels exhibited a 7.9-fold increase in mRNA expression relative to normal tissue (p &lt; 0.0001). Additionally, components of the type-I interferon signaling pathway exhibited significant upregulation of mRNA levels in tumor tissue, including Interferon alpha/beta receptor 1 (IFNAR1; 3.4-fold increase, p &lt; 0.0001), Interferon regulatory factor 9 (IRF9; 4.2-fold increase, p &lt; 0.0001), Signal transducer and activator of transcription 1 (STAT1; 7.1-fold increase, p &lt; 0.0001), and Interferon Alpha Inducible Protein 27 (IFI27; 66.3-fold increase, p &lt; 0.0001). We also utilized TCGA datasets deposited in cBioportal and KMplotter to relate mRNA expression levels to overall survival outcomes. These increased levels of mRNA expression were found to be prognostically significant, whereby patients with high expression levels of either TGFB2, IRF9, or IFI27 showed median OS times ranging from 16 to 20 months (p &lt; 0.01 compared to 72 months for patients with low levels of expression for both TGFB2 and either IRF9 or IFI27). Examination of the KMplotter database determined the prognostic impact of TGFB2 mRNA expression levels by comparing patients expressing high versus low levels of TGFB2 (50th percentile cut-off) in low macrophage TME. In TME with low macrophage levels, patients with high levels of TGFB2 mRNA exhibited significantly shorter OS outcomes than patients with low TGFB2 mRNA levels (Median OS of 15.3 versus 72.7 months, p &lt; 0.0001). Furthermore, multivariate Cox regression models were applied to control for age at diagnosis. Nine genes exhibited significant increases in hazard ratios for TGFB2 mRNA expression, marker gene mRNA expression, and a significant interaction term between TGFB2 and marker gene expression (mRNA for markers: C1QA, CD74, HLA-DQB1, HLA-DRB1, HLA-F, IFI27, IRF9, LGALS9, MARCO). The results of our study suggest that a combination of pharmacological tools can be used in treating PDAC patients, targeting both TGFB2 and the components of the type-I interferon signaling pathway. The significant statistical interaction between TGFB2 and the nine marker genes suggests that TGFB2 is a negative prognostic indicator at low levels of the IFN-I activated genes and TAM marker expression, including the immune checkpoint LGALS9 (upregulated 16.5-fold in tumor tissue; p &lt; 0.0001).

Bioinformatics investigation of the prognostic value and mechanistic role of CD9 in glioma

In recent years, CD9 has been extensively studied as a potential biomarker for cancer. However, the biological role of CD9 in gliomas remains unclear. This study investigates the function of CD9 in gliomas and its molecular mechanisms. Utilizing pan-cancer analysis with TCGA, CGGA, and GEO databases, differential expression of CD9 was observed in 11 tumor types within the TCGA cohort, and it was associated with patient survival rates. Analysis of the CGGA glioma database revealed that patients with high CD9 expression had lower survival rates. The area under the ROC curve (AUC) for GSE16011 was greater than 0.7, indicating a high discriminative ability. Through gene set enrichment analysis (GSEA), immune-related analysis, and CD9 mutation detection, CD9 was found to have the strongest correlation with neutrophil involvement (cor = 0.30, P < 0.05), and the high CD9 expression group exhibited higher rejection responses and TIDE scores, suggesting a lower likelihood of successful immunotherapy. The high CD9 expression group was more sensitive to 81 drugs, indicating potential therapeutic effects for gliomas. Furthermore, overexpression of CD9 in gliomas may be associated with gene mutations. Down-regulation or up-regulation of CD9 expression in the glioblastoma cell line LN229 showed that CD9 could positively regulate the migratory ability of LN229 cells. Further, several marker genes, such as VEGFR-2, TGF-β1, CASP1 and PI3K, were down regulated in CD9 knockdown cell lines and up regulated in CD9 overexpression cell lines, compared with control cell line. This study preliminarily explores the role of CD9 in gliomas and its prognostic value, providing new insights for personalized treatment strategies in glioma therapy.

TMEM175 plays a crucial role in osteoblast differentiation by regulating lysosomal function and autophagy

Bone provides structural support, enables movement, protects internal organs, regulates calcium and phosphorus levels, and contains bone marrow essential for hematopoiesis. Osteoblasts are specialized cells responsible for bone formation through the secretion of extracellular matrix components. Transmembrane protein 175 (TMEM175), which functions as an endosomal/lysosomal K+ channel and a lysosomal H+ channel, regulates lysosomal function and autophagy. Despite the recognized importance of lysosomes and autophagy in osteoblast differentiation, the specific role of TMEM175 in osteoblast differentiation has not been revealed. In this study, we investigated whether TMEM175 is associated with human bone mineral densityand fracture and examined the role of TMEM175 in osteoblast differentiation. In analyses of single nucleotide polymorphismsof pore ion channel genes using the mouse2human database, a significant correlation between TMEM175 single nucleotide polymorphisms and human bone mineral density and fracture was identified. TMEM175 expression levels were found to increase during osteoblast differentiation from bone chip-derived mesenchymal stem cells (BMSCs). Knockdown of TMEM175 in BMSCs suppressed osteoblast differentiation, as evidenced by decreased matrix mineralization and lower expression levels of osteoblast marker genes. Further analysis indicated that TMEM175 deficiency leads to lysosomal dysfunction and partially impairs autophagic clearance during osteoblast differentiation. Moreover, the TMEM175 inhibitor 4-aminopyridinedecreased osteoblast differentiation of BMSCs. Taken together, this study reveals that TMEM175 plays an important role in osteoblast differentiation by regulating lysosomal function and autophagic clearance.

Single-cell sequencing technology to characterize stem T-cell subpopulations in acute T-lymphoblastic leukemia and the role of stem T-cells in the disease process.

Precursor T-cell acute lymphoblastic leukemia (Pre-T ALL) is a malignant neoplastic disease in which T-cells proliferate in the bone marrow. Single-cell sequencing technology could identify characteristic cell types, facilitating the study of the therapeutic mechanisms in Pre-T ALL. The single-cell sequencing data (scRNA-seq) of Pre-T ALL were obtained from public databases. Key immune cell subpopulations involved in the progression of Pre-T ALL were identified by clustering and annotating the cellular data using AUCell. Next, pseudo-temporal analysis was performed to identify the differentiation trajectories of immune cell subpopulations using Monocle. Copy number mutation landscape of cell subpopulations was characterized by inferCNV. Finally, cellphoneDB was used to analyze intercellular communication relationships. A total of 10 cellular subpopulations were classified, with Pre-T ALL showing a higher proportion of NK/T cells. NK/T cells were further clustered into two subpopulations. Stem T cells showed a high expression of marker genes related to hematopoietic stem cells, Naive T cells had a high expression of CCR7, CCR7, RCAN3, and NK cells high-expressed KLRD1, TRDC. The cell proliferation was reduced and the activation of T cell was increased during the differentiation of stem T cells to Naive T cells. We observed interaction between stem T cells with dendritic cells such as CD74-COPA, CD74-MIF as well as co-inhibition-related interactions such as LGALS9-HAVCR2, TGFB1-TGFBR3. Stem T cells were involved in the development of Pre-T-ALL through the regulatory effects of transcription factors (TFs) KLF2 and FOS and multiple ligand-receptor pairs.

Agrobacterium virulence factors induce the expression of host DNA repair-related genes without promoting major genomic damage

This study aimed to investigate whether the plant DNA damage levels and DNA damage response (DDR) are regulated during Agrobacterium infection and potentially manipulated by Agrobacterium to facilitate T-DNA integration. We investigated the plant genomic response to Agrobacterium infection by measuring gamma H2AX levels, which reflect the levels of double-strand DNA breaks (DSBs), and by characterizing transcription of three major DNA repair marker genes NAC82, KU70, and AGO2. These experiments revealed that, globally, Agrobacterium infection did not result in a major increase in DSB content in the host genome. The transcription of the DNA damage repair genes, on the other hand, was elevated upon the wild-type Agrobacterium infection. This transcriptional outcome was largely negated by a mutation in the bacterial virB5 gene which encodes the virulence (Vir) protein B5, a minor component of Agrobacterium pilus necessary for the translocation of Vir effector proteins into the host cell, suggesting that the transcriptional activation of the cellular DNA damage repair machinery requires the transport into the host cell of the Agrobacterium effectors, i.e., the VirD2, VirD5, VirE2, VirE3, and VirF proteins. Most likely, a combination of several of these Vir effectors is required to activate the host DNA repair as their individual loss- or gain-of-function mutants did not significantly affect this process.

Doubled Haploid Technology: Generation of Doubled Haploid Maize Lines Using Haploid Inducers.

Doubled haploid (DH) technology allows for the development of completely homozygous lines from heterozygous plants in only two generations. This approach has been widely adopted in maize breeding programs, as it expedites the generation of inbred lines compared to traditional methods. The DH approach is based on the use of maize genotypes that have the ability to induce haploid seeds when used as the pollen parent. The most common method for producing maize haploid plants for the generation of DH lines is in vivo maternal haploid induction. The process involves pollination with a haploid inducer maize line to generate haploid seeds. Then, haploids are screened for and identified (typically via the expression of a particular marker gene), germinated, treated with an exogenous doubling agent to induce genome duplication, and transplanted to the field. Following successful self-pollination, seeds harvested from the ear represent fully homozygous lines. The seed set at this stage, however, is often low, necessitating one or two additional rounds of self-pollination to increase the number of fully homozygous inbred lines. Here, we describe a protocol for the generation of maize DH lines using maternal haploid-inducing maize lines. We outline the steps for setting up the donor material, performing induction crosses, selecting haploids based on two different marker alleles, treating seedlings with colchicine to double the genome, transplanting the treated seedlings to the field, and self-pollinating the treated plants.

Spatial transcriptomics of a parasitic flatworm provides a molecular map of drug targets and drug resistance genes

The spatial organization of gene expression dictates tissue functions in multicellular parasites. Here, we present the spatial transcriptome of a parasitic flatworm, the common liver fluke Fasciola hepatica. We identify gene expression profiles and marker genes for eight distinct tissues and validate the latter by in situ hybridization. To demonstrate the power of our spatial atlas, we focus on genes with substantial medical importance, including vaccine candidates (Ly6 proteins) and drug resistance genes (glutathione S-transferases, ABC transporters). Several of these genes exhibit unique expression patterns, indicating tissue-specific biological functions. Notably, the prioritization of tegumental protein kinases identifies a PKCβ, for which small-molecule targeting causes parasite death. Our comprehensive gene expression map provides unprecedented molecular insights into the organ systems of this complex parasitic organism, serving as a valuable tool for both basic and applied research.

Single-cell atlases reveal leaf cell-type-specific regulation of metal transporters in the hyperaccumulator Sedum alfredii under cadmium stress

Hyperaccumulation in plants is a complex and dynamic biological process. Sedum alfredii, the most studied Cd hyperaccumulator, can accumulate up to 9000 mg kg−1 Cd in its leaves without suffering toxicity. Although several studies have reported the molecular mechanisms of Cd hyperaccumulation, our understanding of the cell-type-specific transcriptional regulation induced by Cd remains limited. In this study, the first full-length transcriptome of S. alfredii was generated using the PacBio Iso-Seq technology. A total of 18,718,513 subreads (39.90 Gb) were obtained, with an average length of 2133 bp. The single-cell RNA sequencing was employed on leaves of S. alfredii grown under Cd stress. A total of 12,616 high-quality single cells were derived from the control and Cd-treatment samples of S. alfredii leaves. Based on cell heterogeneity and the expression profiles of previously reported marker genes, seven cell types with 12 transcriptionally distinct cell clusters were identified, thereby constructing the first single-cell atlas for S. alfredii leaves. Metal transporters such as CAX5, COPT5, ZIP5, YSL7, and MTP1 were up-regulated in different cell types of S. alfredii leaves under Cd stress. The distinctive gene expression patterns of metal transporters indicate special gene regulatory networks underlying Cd tolerance and hyperaccumulation in S. alfredii. Collectively, our findings are the first observation of the cellular and molecular responses of S. alfredii leaves under Cd stress and lay the cornerstone for future hyperaccumulator scRNA-seq investigations.

Cold-water coral mortality under ocean warming is associated with pathogenic bacteria

Cold-water corals form vast reefs that are highly valuable habitats for diverse deep-sea communities. However, as the deep ocean is warming, it is essential to assess the resilience of cold-water corals to future conditions. The effects of elevated temperatures on the cold-water coral Lophelia pertusa (now named Desmophyllum pertusum) from the north-east Atlantic Ocean were experimentally investigated at the holobiont level, the coral host, and its microbiome. We show that at temperature increases of + 3 and + 5 °C, L. pertusa exhibits significant mortality concomitant with changes in its microbiome composition. In addition, a metagenomic approach revealed the presence of gene markers for bacterial virulence factors suggesting that coral death was due to infection by pathogenic bacteria. Interestingly, different coral colonies had different survival rates and, colony-specific microbiome signatures, indicating strong colony-specific variability in their response to warming waters. These results suggest that L. pertusa can only survive a long-term temperature increase of < 3 °C. Therefore, regional variations in deep-sea temperature increase should be considered in future estimates of the global distribution of cold-water corals.

Genome‐Wide Association Study Revealed the Genetics of Seed Vigour Traits in Rice (Oryza sativa L.)

ABSTRACTA crucial phenotypic attribute for breeding rice for direct seeded condition is rapid uniform germination and build‐up of biomass during the initial period of seedling establishment. Seed vigour constitutes such traits that have gained potential to meet the requirements of breeding for direct seeded rice. In the present study, a set of 295 markers, including 215 candidate gene‐derived markers covering all chromosome, was used to discover the casual alleles for eight rice seed vigour‐related traits. Using a mixed linear model, the study identified 99 significant associations for seed vigour traits. Many associated markers originated from diverse candidate genes in rice. Notably, alleles from genes like RSR1, OsSRS3 and OsSWEET15 exhibited pleiotropic effects, influencing multiple seed vigour traits. This discovery underscores the potential of certain genes to impact various facets of seed vigour simultaneously. The new candidate gene markers associated with seed vigour traits may be utilized to incorporate variable alleles for seed vigour traits through marker‐assisted breeding programmes. Markers identified to be closely associated with more than one trait have significant application in the simultaneous improvement of multiple traits.

Candidatus Desulforudis audaxviator dominates a 975 m deep groundwater community in central Sweden

The continental bedrock contains groundwater-bearing fractures that are home to microbial populations that are vital in mediating the Earth’s biogeochemical cycles. However, their diversity is poorly understood due to the difficulty of obtaining samples from this environment. Here, a groundwater-bearing fracture at 975 m depth was isolated by employing packers in order to characterize the microbial community via metagenomes combined with prokaryotic and eukaryotic marker genes (16S and 18S ribosomal RNA gene). Genome-resolved analyses revealed a community dominated by sulfate-reducing Bacillota, predominantly represented by Candidatus Desulforudis audaxviator and with Wood-Ljungdahl as the most prevalent pathway for inorganic carbon fixation. Moreover, the eukaryotic community had a considerable diversity and was comprised of mainly flatworms, chlorophytes, crustaceans, ochrophytes, and fungi. These findings support the important role of the Bacillota, with the sulfate reducer Candidatus Desulforudis audaxviator as its main representative, as primary producers in the often energy-limited groundwaters of the continental subsurface.

Peripheral mononuclear cells and systemic lupus erythematosus association: Integrated study of single-cell sequencing and mendelian randomization analysis.

Systemic Lupus Erythematosus (SLE) is a complex autoimmune disease predominantly affecting women. Despite advances in treatment, recent developments in single-cell RNA sequencing (scRNA-seq) and Mendelian randomization (MR) continue to facilitate the need for precision medicine. Data obtained from the GSE135779 dataset underwent quality control, normalization, and dimensionality reduction using Seurat and MonacoImmuneData. Marker genes identified subgroups for analysis with CellChat and ClusterProfilerR. MR analysis of these genes' eQTLs was performed to establish causal relationships with SLE using IEU Open GWAS project data. Single-cell analysis revealed distinct cellular subtypes and highlighted increased monocyte levels in patients with SLE. MR analysis revealed 12 genes, particularly interferon induced protein with tetratricopeptide repeats 3 (IFIT3), causally related to SLE. Gene ontology and the Kyoto encyclopedia of genes and genomes analyses identified pathways significant to SLE pathogenesis. Visualization of these genes at the single-cell level revealed their role in disease progression. Cell communication differences between IFIT3-positive and -negative groups were also observed. This study demonstrates the potential of scRNA-seq and MR in identifying critical factors in SLE pathogenesis, thereby supporting the need for targeted therapies. Identifying IFIT3, among other genes, as central to SLE progression opens new avenues for precision medicine approaches in SLE management.

The white gene as a transgenesis marker for the cricket Gryllus bimaculatus.

The cricket Gryllus bimaculatus is an emerging model insect of the order Orthoptera that is used in a wide variety of biological research themes. This hemimetabolous species appears highly complementary to Drosophila and other well-established holometabolous models. To improve transgenesis applications in G. bimaculatus, we have designed a transformation marker gene inspired from the widespread Drosophila mini-white+. Using CRISPR/Cas9, we first generated a loss-of-function mutant allele of the Gb-white gene (Gb-w), which exhibits a white eye coloration at all developmental stages. We then demonstrate that transgenic insertions of a piggyBac vector containing a 3xP3-Gb-w+ cassette rescue eye pigmentation. As an application, we used this vector to generate G. bimaculatus lines expressing a centromeric histone H3 variant (CenH3.1) fused to EGFP and validated EGFP-CenH3.1 detection at cricket centromeres. Finally, we demonstrate that Minos-based germline transformation and site-specific plasmid insertion with the ΦC31 integrase system function in G. bimaculatus.

Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data.

High-throughput sequencing (HTS) technologies have been instrumental in investigating biological questions at the bulk and single-cell levels. Comparative analysis of two HTS data sets often relies on testing the statistical significance for the difference of two negative binomial distributions (DOTNB). Although negative binomial distributions are well studied, the theoretical results for DOTNB remain largely unexplored. Here, we derive basic analytical results for DOTNB and examine its asymptotic properties. As a state-of-the-art application of DOTNB, we introduce DEGage, a computational method for detecting differentially expressed genes (DEGs) in scRNA-seq data. DEGage calculates the mean of the sample-wise differences of gene expression levels as the test statistic and determines significant differential expression by computing the P-value with DOTNB. Extensive validation using simulated and real scRNA-seq data sets demonstrates that DEGage outperforms five popular DEG analysis tools: DEGseq2, DEsingle, edgeR, Monocle3, and scDD. DEGage is robust against high dropout levels and exhibits superior sensitivity when applied to balanced and imbalanced data sets, even with small sample sizes. We utilize DEGage to analyze prostate cancer scRNA-seq data sets and identify marker genes for 17 cell types. Furthermore, we apply DEGage to scRNA-seq data sets of mouse neurons with and without fear memory and reveal eight potential memory-related genes overlooked in previous analyses. The theoretical results and supporting software for DOTNB can be widely applied to comparative analyses of dispersed count data in HTS and broad research questions.

Gene markers generating polygenic resistance in melon-Fusarium wilt-FOM1.2 interaction pathosystem.

Developing melon genotypes with resistance to Fusarium oxysporum f. sp. Melonis-(FOM) race1.2 is a major goal in any breeding program. In this study, we identified the role of 11 gene markers that contribute to polygenic resistance during the FOM1.2-melon interaction. qRT-PCR analysis elucidated upregulation of candidate marker genes AMT, DXPR, Fom-2, GLUC, GalS, GRF3, MLO, PRK, RuBlsCo, TLP and WRKY in resistant 'Shante-F1' and 'Khatouni', and susceptible 'Shante-T' and 'Shahabadi' at 7, 14 and 21 days post-inoculation (dpi). We also studied changes in defence-related enzyme activity: chitinase (CHI), β-1,3-glucanase (GLU) and peroxidase (POX) in melon roots. AMT, GLUC and DXPR transcripts were upregulatied in leaf and root tissues of the resistant 'Shante-F1' and 'Shahabadi'. Transcript levels for GalS and GRF3 increased 6.77- and 6.83-fold in roots of 'Shante-F1' at 7 dpi, whereas in PRK, TLP and WRKY theye increased by 7.84-, 5.15- and 12.26-fold at 14 dpi, respectively. However, transcript levels increased by 5.18-fold for Fom-2 and 8.46-fold for MLO at 21 dpi. Also, RBC transcript level peaked at 14 dpi with 4.9-fold increase in leaves of resistant genotypes, whereas AMT increased 2.94-fold at 21 dpi, and GLUC and DXPR increased 7.11- and 2.91-fold at 14 dpi in 'Shante-F', respectively. Defence-related-enzyme activity was also upregulated three-fold in resistant varieties. The dynamic shifts in the melon transcriptome induced by FOM1.2 emphasize that resistance mechanisms are predominantly regulated through signalling pathways involving CHI, GLU, and POX defence response. Surprisingly, the AMT gene, basically resistant to downy mildew, Pseudoperonospora cubensis; GLUC, MLO and PRK resistant to powdery mildew (Sphaerotheca fusca); TLP and WRKY resistant to Phytophthora blight (Phytophthora capsici); and GRF3 and RBC resistant to root knot nematodes (Meloidogyne spp.) were upregulated in resistant genotypes, indicating a dual role of these genes in resistance to more than one disease at a time.