Uncovering the pharmacological mechanisms of Patchouli essential oil for treating ulcerative colitis.

ETHNOPHARMACOLOGICAL RELEVANCE: Pogostemonis Herba has long been used in traditional Chinese medicine to treat inflammatory disorders. Patchouli essential oil (PEO) is the primary component of Pogostemonis Herba, and it has been suggested to offer curative potential when applied to treat ulcerative colitis (UC). However, the pharmacological mechanisms of PEO for treating UC remain to be clarified. AIM OF THE STUDY: To elucidate the pharmacological mechanisms of PEO for treating UC. METHODS AND RESULTS: In the present study, transcriptomic and network pharmacology approaches were combined to clarify the mechanisms of PEO for treating UC. Our results reveal that rectal PEO administration in UC model mice significantly alleviated symptoms of UC. In addition, PEO effectively suppressed colonic inflammation and oxidative stress. Mechanistically, PEO can ameliorate UC mice by modulating gut microbiota, inhibiting inflammatory targets (OPTC, PTN, IFIT3, EGFR, and TLR4), and inhibiting the PI3K-AKT pathway. Next, the 11 potential bioactive components that play a role in PEO's anti-UC mechanism were identified, and the therapeutic efficacy of the pogostone (a bioactive component) in UC mice was partially validated. CONCLUSION: This study highlights the mechanisms through which PEO can treat UC, providing a rigorous scientific foundation for future efforts to develop and apply PEO for treating UC.

Integrated transcriptomic and metabolic analyses reveal the early response mechanism of Pinus tabulaeformis to pine wood nematodes.

Pine wilt disease (PWD) is a devastating disease of pine trees caused by the pine wood nematode (Bursapherenchus xylophilus, PWN). To study how Pinus tabulaeformis responds to PWD infection, we collected 3-year-old P. tabulaeformis seedlings at 2 days, 5 days, and 8 days after being infected with B. xylophilus. We identified genes and metabolites early responding to infection using transcriptome and metabolomic data obtained by high-throughput mRNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based assays, respectively. The following results were obtained: (1) After inoculation with PWN, the average number of days taken for 3-year-old P. tabulaeformis seedlings to develop symptoms was 8 days. (2) Combined transcriptome and metabolome analysis revealed that phenylpropanoid biosynthesis and flavonoid biosynthesis are critically important pathways for P. tabulaeformis to respond to PWD. (3) The response of P. tabulaeformis to stress was mainly through positive regulation of gene expression, including some key genes related to plant hormones or transcription factors that have been widely studied. Genes related to pathways such as photosynthesis, plant-pathogen interactions, and DNA replication were downregulated. (4) Terpenoid biosynthesis genes involved during the development of pine wilt disease. This study demonstrated the defence and pathogenic mechanisms of P. tabulaeformis against PWD, providing a reference for the early diagnosis of PWD.

Enhancing protective immunity against bacterial infection via coating nano-Rehmannia glutinosa polysaccharide with outer membrane vesicles.

With the coming of the post-antibiotic era, there is an increasingly urgent need for safe and efficient antibacterial vaccines. Bacterial outer membrane vesicles (OMVs) have received increased attention recently as a potential subunit vaccine. OMVs are non-replicative and contain the principle immunogenic bacterial antigen, which circumvents the safety concerns of live-attenuated vaccines. Here, we developed a novel nano-vaccine by coating OMVs onto PEGylated nano-Rehmannia glutinosa polysaccharide (pRL) in a structure consisting of concentric circles, resulting in a more stable vaccine with improved immunogenicity. The immunological function of the pRL-OMV formulation was evaluated in vivo and in vitro, and the underlying mechanism was studied though transcriptomic analysis. The pRL-OMV formulation significantly increased dendritic cell (DC) proliferation and cytokine secretion. Efficient phagocytosis of the formulation by DCs was accompanied by DC maturation. Further, the formulation demonstrated superior lymph node targeting, contributing to a potent mixed cellular response and bacterial-specific antibody response against Bordetella bronchiseptica infection. Specifically, transcriptomic analysis revealed that the immune protection function correlated with T-cell receptor signalling and Th1/Th2/Th17 differentiation, among other markers of enhanced immunological activity. These findings have implications for the future application of OMV-coated nano-carriers in antimicrobial immunotherapy.

Study on the effect of ascorbic acid on the biosynthesis of pigment and citrinin in red yeast rice based on comparative transcriptomics.

Pigment is one of the most important metabolites in red yeast rice. However, citrinin may accumulate and cause quality security issues. In the present study, the effect of ascorbic acid (EAA) on the pigment and citrinin was studied, and the metabolic mechanism was discussed using comparative transcriptomics. The introduction of EAA increased the pigment by 58.2% and decreased citrinin by 65.4%. The acid protease activity, DPPH scavenging rate, and total reducing ability also increased by 18.7, 9.0, and 26.7%, respectively. Additionally, a total of 791 differentially expressed genes were identified, and 79 metabolic pathways were annotated, among which carbon metabolism, amino acid metabolism, and fatty acid metabolism were closely related to the biosynthesis of pigment and citrinin. Ethanol dehydrogenase (M pigC), oxidoreductase (M pigE), reductase (M pigH), and monooxygenase (M pigN) may be related to the increase of pigment. ctnC and pksCT contributed to the decline of citrinin.

Pilot study: Understanding canine transmissible venereal tumor through its transcriptional profile.

Canine transmissible venereal tumor (CTVT) is transmitted through the implantation of tumor cells. CTVT was the first tumor described with contagious characteristics and remains one of the few tumors with this capability. This study aimed to map the transcriptomic profile of CTVT to elucidate the potential mechanisms through which this tumor implants and evades host immune surveillance. For this study, 11 dogs aged ≥ 2 years diagnosed with CTVT were selected. Tumor biopsies were performed, RNA was extracted and converted into complementary DNA, followed by RT-qPCR analysis. The transcriptomic profile of CTVT revealed a wide array of differentially expressed genes. However, only the most relevant genes from an oncological perspective were discussed. IL-8, CXCL13, NCAM1, RNASEL, COROA1, and CBLB demonstrated potential associations with immune system evasion and transmission via implantation. Therefore, studying these genes may contribute to the development of targeted therapies that prevent contagion and immune evasion.

Exogenous gibberellin suppressed taproot secondary thickening by inhibiting the formation and maintenance of vascular cambium in radish (Raphanus sativus L.).

Introduction: The thickening of radish taproots is primarily determined by secondary growth driven by the vascular cambium and is a highly intricate process regulated by plant hormones, transcription factors, and many metabolic pathways. Gibberellin (GA), a plant hormone associated with cell elongation, is essential in secondary growth. However, the mechanism through which exogenous GA3 regulates secondary taproot growth in radishes remains unclear. Methods: Integrated morphological, anatomical, hormonal, and transcriptomic analyses of taproots in radishes treated with GA3 and its biosynthesis inhibitor paclobutrazol (PBZ) were performed to explore their effects on taproot secondary growth and key regulatory pathways. Results: GA3 significantly hindered taproot thickening by inhibiting the formation and maintenance of the vascular cambium, and PBZ promoted root development by increasing root length rather than root diameter. Transcriptome analysis revealed 2,014, 948, and 1,831 differentially expressed genes identified from the control vs. GA3, control vs. PBZ, and GA3 vs. PBZ comparisons, respectively. Kyoto Encyclopedia of Genes and Genome pathway enrichment analysis revealed that differentially expressed genes were primarily involved in the biosyntheses of secondary metabolites and metabolic pathways. GA3 significantly increased the levels of endogenous indole-acetic acid and the expression of auxin synthesis and signal transduction genes. Discussion: Exogenous GA3 significantly inhibited the expression of genes involved in the maintenance and differentiation of vascular cambium, including WOX14, ER/ERL1, and XCP2. Exogenous GA3 affects root thickening in radishes primarily by regulating hormone signal transduction pathways, vascular cambium activity, and substance and energy metabolisms. Our findings provide insights into the mechanisms underlying taproot thickening in radishes and provide a valuable gene database for future studies.

Exploring the transcriptomic landscape of moyamoya disease and systemic lupus erythematosus: insights into crosstalk genes and immune relationships.

Background: Systemic Lupus Erythematosus (SLE) is acknowledged for its significant influence on systemic health. This study sought to explore potential crosstalk genes, pathways, and immune cells in the relationship between SLE and moyamoya disease (MMD). Methods: We obtained data on SLE and MMD from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were conducted to identify common genes. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on these shared genes. Hub genes were further selected through the least absolute shrinkage and selection operator (LASSO) regression, and a receiver operating characteristic (ROC) curve was generated based on the results of this selection. Finally, single-sample Gene Set Enrichment Analysis (ssGSEA) was utilized to assess the infiltration levels of 28 immune cells in the expression profile and their association with the identified hub genes. Results: By intersecting the important module genes from WGCNA with the DEGs, the study highlighted CAMP, CFD, MYO1F, CTSS, DEFA3, NLRP12, MAN2B1, NMI, QPCT, KCNJ2, JAML, MPZL3, NDC80, FRAT2, THEMIS2, CCL4, FCER1A, EVI2B, CD74, HLA-DRB5, TOR4A, GAPT, CXCR1, LAG3, CD68, NCKAP1L, TMEM33, and S100P as key crosstalk genes linking SLE and MMD. GO analysis indicated that these shared genes were predominantly enriched in immune system process and immune response. LASSO analysis identified MPZL3 as the optimal shared diagnostic biomarkers for both SLE and MMD. Additionally, the analysis of immune cell infiltration revealed the significant involvement of activation of T and monocytes cells in the pathogenesis of SLE and MMD. Conclusion: This study is pioneering in its use of bioinformatics tools to explore the close genetic relationship between MMD and SLE. The genes CAMP, CFD, MYO1F, CTSS, DEFA3, NLRP12, MAN2B1, NMI, QPCT, KCNJ2, JAML, MPZL3, NDC80, FRAT2, THEMIS2, CCL4, FCER1A, EVI2B, CD74, HLA-DRB5, TOR4A, GAPT, CXCR1, LAG3, CD68, NCKAP1L, TMEM33, and S100P have been identified as key crosstalk genes that connect MMD and SLE. Activation of T and monocytes cells-mediated immune responses are proposed to play a significant role in the association between MMD and SLE.

Meta-transcriptomic analysis reveals the geographical expansion of known sugarbeet-infecting viruses and the occurrence of a novel virus in sugarbeet in the United States.

In this study, meta-transcriptome sequencing was conducted on a total of 18 sugarbeet (Beta vulgaris L. subsp. vulgaris) sample libraries to profile the virome of field-grown sugarbeet to identify the occurrence and distribution of known and potentially new viruses from five different states in the United States. Sugarbeet roots with symptoms resembling rhizomania caused by beet necrotic yellow vein virus (BNYVV), or leaves exhibiting leaf-curling, yellowing to browning, or green mosaic were collected from the sugarbeet growing areas of California, Colorado, Idaho, Minnesota, and North Dakota. In silico analysis of de novo assembled contigs revealed the presence of nearly full-length genomes of BNYVV, beet soil-borne virus (BSBV), and beet soil-borne mosaic virus (BSBMV), which represent known sugarbeet-infecting viruses. Among those, BNYVV was widespread across the locations, whereas BSBV was prevalent in Minnesota and Idaho, and BSBMV was only detected in Minnesota. In addition, two recently reported Beta vulgaris satellite virus isoforms (BvSatV-1A and BvSatV-1B) were detected in new locations, indicating the geographical expansion of this known virus. Besides these known sugarbeet-infecting viruses, the bioinformatic analysis identified the widespread occurrence of a new uncharacterized Erysiphe necator-associated abispo virus (En_abispoV), a fungus-related virus that was identified in all 14 libraries. En_abispoV contains two RNA components, and nearly complete sequences of both RNA1 and RNA2 were obtained from RNASeq and were further confirmed by primer-walking RT-PCR and Sanger sequencing. Phylogenetic comparison of En_abispoV isolates obtained in this study showed varying levels of genetic diversity within RNA1 and RNA2 compared to previously reported isolates. The undertaken meta-transcriptomic approach revealed the widespread nature of coexisting viruses associated with field-grown sugarbeet exhibiting virus disease-like symptoms in the United States.

Degradation of lignocellulose by different bacterial and fungal co-cultures.

Long seen as non-valorisable waste, agricultural co-products are increasingly used in biorefinery processes. Co-culture appears as new trend for to improve the degradation of lignocellulose and improve the production of bioproducts. The goal of the study was to setup inter-domain co-cultures with high capabilities of lignocellulose degradation using a pluridisciplinary approach combining bioinformatics, enzymology, transcriptomics. Different individual lignocellulolytic strains: Trichoderma reesei QM6a and three bacteria (Streptomyces coelicolor A3(2), Rhizobium sp.XylPr11 and Sphingobacterium prati AraPr2 affiliated from different phyla) were used in that study . Synergic activities have been observed and quantified in co-culture conditions, particularly for xylanases and peroxidases activities. The enzymatic activities for the co-cultures in the most interesting co-culture (T. reesei QM6a/S. coelicolor A3(2)) reached more up to 2 IU/mL and 430 IU/mL respectively for the xylanase and peroxidase. Furthermore, ATR-FTIR analysis showed a real impact of co-culture condition on the substrate compared to the monoculture specially for hemicellulose degradation. Transcriptomics of S. coelicolor A3(2) either in mono or co-culture showed a relative similar pattern profile whatever the condition analysed with a specific overexpression of certain CAZyme genes involved in glycolysis due to the hydrolytic role played by the fungal partner. This work provided the proof of concept for technological feasibility, pertinence and usefulness of interdomain co-culture.

New Transcriptomic Biomarkers for Detection of the Recombinant Human Erythropoietin (rHuEPO) MirCERA in Horses.

Detection and monitoring of biomarkers related to doping is particularly suitable for the development of analytical strategies dedicated to indirect detection of banned substances. Previous studies in horses have already allowed the investigation of transcriptomic biomarkers in equine blood associated with reGH and rHuEPO administrations. Our most recent developments continue to focus on the discovery and monitoring of transcriptomic biomarkers for the control of ESAs, and a collaborative study with WADA-accredited doping control laboratories has recently been initiated to conduct a pilot study. In humans, three mRNAs (ALAS2, CA1, and SLC4A1) were previously observed to be differentially expressed after blood doping and were associated with immature red blood cells, the so-called circulating reticulocytes. In horses, circulating reticulocytes are rarely observed even after rHuEPO administration. With the improved primers that detect the equine orthologues of the human mRNAs from the ALAS2, CA1, and SLC4A1 genes, we can now report the first evidence of the detection of the three biomarkers in equine blood. In addition, an upregulation of the mRNA levels of the three genes was observed after analysis of blood samples collected from MirCERA-treated animals, with kinetics similar to those previously documented in humans. Our data suggest that ALAS2 and CA1 are promising indirect biomarkers for the detection of recombinant EPO abuse in horses, as observed in humans.

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.

Transcriptomic analysis reveals key molecular signatures across recovery phases of hemorrhagic fever with renal syndrome.

BACKGROUND: Hemorrhagic fever with renal syndrome (HFRS), a life-threatening zoonosis caused by hantavirus, poses significant mortality risks and lacks specific treatments. This study aimed to delineate the transcriptomic alterations during the recovery phases of HFRS. METHODS: RNA sequencing was employed to analyze the transcriptomic alterations in peripheral blood mononuclear cells from HFRS patients across the oliguric phase (OP), diuretic phase (DP), and convalescent phase (CP). Twelve differentially expressed genes (DEGs) were validated using quantitative real-time PCR in larger sample sets. RESULTS: Our analysis revealed pronounced transcriptomic differences between DP and OP, with 38 DEGs showing consistent expression changes across all three phases. Notably, immune checkpoint genes like CD83 and NR4A1 demonstrated a monotonic increase, in contrast to a monotonic decrease observed in antiviral and immunomodulatory genes, including IFI27 and RNASE2. Furthermore, this research elucidates a sustained attenuation of immune responses across three phases, alongside an upregulation of pathways related to tissue repair and regeneration. CONCLUSION: Our research reveals the transcriptomic shifts during the recovery phases of HFRS, illuminating key genes and pathways that may serve as biomarkers for disease progression and recovery.

Transcriptomic analysis of profibrinolytic and fibrinolytic inhibitor genes in COVID-19 patients.

The immunopathogenesis of COVID-19 infection is initiated by the entry of the SARS-CoV-2 virus into the human body through droplets, entering the lungs and binding to the ACE-2 receptor. Activated macrophages stimulate an immune and inflammatory response, leading to the activation of the coagulation cascade, including profibrinolytic and fibrinolytic inhibitor processes. One of the proteins involved in profibrinolytic is encoded by the PLAUR gene, while fibrinolytic inhibitor proteins are encoded by the A2M and SERPINE1 genes. This research aims to assess the transcriptomic analysis of genetic expression data of profibrinolytic genes, fibrinolytic inhibitor genes and their correlation with serum D-dimer levels, which describe the clinical condition of coagulation in COVID-19 patients. This cross-sectional study included 25 patients each for mild and moderate-to-severe COVID-19 at Dr. M. Djamil Padang General Hospital, Padang, Indonesia. Inter-group gene expression comparisons will be analyzed using log2 folds change, and bivariate tests will be analyzed using correlation. The results show that the PLAUR gene has higher expression in moderate-to-severe compared to mild cases. Similarly, the SERPINE1 and A2M genes expressions are higher in moderate-to-severe compared to mild cases. Furthermore, there is a significant correlation between serum D-dimer levels and profibrinolytic factor (PLAUR gene) expression in COVID-19 patients. The correlation between serum D-dimer levels with fibrinolytic inhibitor factor (SERPINE1 and A2M genes) expression was found. These conclude that there is a significant difference in the expression of the profibrinolytic and fibrinolytic inhibitor genes between mild and moderate-to-severe cases in COVID-19, demonstrating COVID-19 infection affects coagulation activities.

Impact of Cd and Pb on the photosynthetic and antioxidant systems of Hemerocallis citrina Baroni as revealed by physiological and transcriptomic analyses.

KEY MESSAGE: Cd induces photosynthetic inhibition and oxidative stress damage in H. citrina, which mobilizes the antioxidant system and regulates the expression of corresponding genes to adapt to Cd and Pb stress. Cd and Pb are heavy metals that cause severe pollution and are highly hazardous to organisms. Physiological measurements and transcriptomic analysis were combined to investigate the effect of 5 mM Cd or Pb on Hemerocallis citrina Baroni. Cd significantly inhibited H. citrina growth, while Pb had a minimal impact. Both Cd and Pb suppressed the expression levels of key chlorophyll synthesis genes, resulting in decreased chlorophyll content. At the same time, Cd accelerated chlorophyll degradation. It reduced the maximum photochemical efficiency of photosystem (PS) II, damaging the oxygen-evolving complex and leading to thylakoid dissociation. In contrast, no such phenomena were observed under Pb stress. Cd also inhibited the Calvin cycle by down-regulating the expression of Rubisco and SBPase genes, ultimately disrupting the photosynthetic process. Cd impacted the light reaction processes by damaging the antenna proteins, PS II and PS I activities, and electron transfer rate, while the impact of Pb was weaker. Cd significantly increased reactive oxygen species and malondialdehyde accumulation, and inhibited the activities of antioxidant enzymes and the expression levels of the corresponding genes. However, H. citrina adapted to Pb stress by the recruitment of antioxidant enzymes and the up-regulation of their corresponding genes. In summary, Cd and Pb inhibited chlorophyll synthesis and hindered the light capture and electron transfer processes, with Cd exerting great toxicity than Pb. These results elucidate the physiological and molecular mechanisms by which H. citrina responds to Cd and Pb stress and provide a solid basis for the potential utilization of H. citrina in the greening of heavy metal-polluted lands.

A Case for the Use of Open Data as a Tool to Incorporate Socioscientific Topics into Neuroscience Education.

Education scholars have called for an increased focus on developing curricula based on culturally relevant pedagogy (Ladson-Billings, 1995). A key tenet of Ladson-Billings' (1995; 2014) theory of culturally relevant pedagogy is the development of students' sociopolitical consciousness, whereby students feel empowered and encouraged to evaluate and solve real-world interdisciplinary problems. Here, we propose that open science datasets could serve as a valuable tool for neuroscience educators to foster their students' sociopolitical consciousness. Using the open data available through the Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) as a case study, this article will explore how open science can be leveraged as a tool to encourage socioscientific thinking amongst neuroscience students. We overview a collection of lessons created by the Allen Institute's Education & Engagement team that provides a scaffolded exploration of an open science resource through a socioscientific lens. We supplement our discussion of the lessons with feedback from students who completed the lessons during a day-long workshop hosted at the Allen Institute in Seattle, WA. We conclude by reflecting on the future role this type of interdisciplinary, open science-based approach to curricula could have across neuroscience education more broadly.

Combined intestinal microbiota and transcriptomic analysis to investigate the effect of different stocking densities on the ability of Pacific white shrimp (Litopenaeus vannamei) to utilize Chlorella sorokiniana.

Aiming to investigate the impact of different stocking densities on the ability of Pacific white shrimp (Litopenaeus vannamei) to utilize Chlorella sorokiniana (CHL), a 3 × 2 factorial design stocking experiment was used in this study. Specifically, shrimp was fed with two dietary protein sources (fishmeal [FM] and CHL) at low (LSD; 100 per m3), medium (MSD; 200 per m3) and high (HSD; 300 per m3) stocking densities for 8 weeks. The growth performance and resistance to Vibrio parahaemolyticus (1.0 × 107 CFU/mL) of shrimp decreased with the increase of stocking density, but dietary CHL improved this result. Differences between the CHL and FM groups for V. parahaemolyticus resistance were significant only under high-density conditions (P < 0.05). Significant interactions between stocking density and protein source were found on the activities of catalase (CAT), superoxide dismutase (SOD) and phenol oxidase (PO), and the contents of malondialdehyde (MDA) in the hepatopancreas and the activities of intestinal amylase, most of which were significantly different between CHL and FM groups only at high stocking density (P < 0.05). Analysis of 16S rDNA sequencing showed that dietary CHL increased the alpha diversity of intestinal microbiota, inhibited the colonization of pathogenic bacteria and enhanced the abundance of beneficial bacteria. Transcriptomic results showed that at high stocking densities, differentially expressed genes (DEGs) in the FM vs CHL group were mostly upregulated and primarily enriched in immune and metabolic related pathways including Toll, immune deficiency (Imd) and glycolysis-gluconeogenesis pathways. Pearson correlation analysis revealed significant correlation between the top ten intestinal bacteria at the genus level and markedly enriched DEGs, also more were detected under high density situations. In conclusion, CHL has great potential as a novel protein source in the intensive farming of shrimp.

Machine learning-based analysis of Ebola virus' impact on gene expression in nonhuman primates.

Introduction: This study introduces the Supervised Magnitude-Altitude Scoring (SMAS) methodology, a novel machine learning-based approach for analyzing gene expression data from non-human primates (NHPs) infected with Ebola virus (EBOV). By focusing on host-pathogen interactions, this research aims to enhance the understanding and identification of critical biomarkers for Ebola infection. Methods: We utilized a comprehensive dataset of NanoString gene expression profiles from Ebola-infected NHPs. The SMAS system combines gene selection based on both statistical significance and expression changes. Employing linear classifiers such as logistic regression, the method facilitates precise differentiation between RT-qPCR positive and negative NHP samples. Results: The application of SMAS led to the identification of IFI6 and IFI27 as key biomarkers, which demonstrated perfect predictive performance with 100% accuracy and optimal Area Under the Curve (AUC) metrics in classifying various stages of Ebola infection. Additionally, genes including MX1, OAS1, and ISG15 were significantly upregulated, underscoring their vital roles in the immune response to EBOV. Discussion: Gene Ontology (GO) analysis further elucidated the involvement of these genes in critical biological processes and immune response pathways, reinforcing their significance in Ebola pathogenesis. Our findings highlight the efficacy of the SMAS methodology in revealing complex genetic interactions and response mechanisms, which are essential for advancing the development of diagnostic tools and therapeutic strategies. Conclusion: This study provides valuable insights into EBOV pathogenesis, demonstrating the potential of SMAS to enhance the precision of diagnostics and interventions for Ebola and other viral infections.

Transcriptomic studies unravel the molecular and cellular complexity of systemic lupus erythematosus: A review.

Transcriptomic analysis plays a vital role in investigating Systemic Lupus Erythematosus (SLE), a complex autoimmune disease characterized by diverse clinical manifestations. This approach has yielded valuable insights into gene expression patterns and molecular regulatory mechanisms involved in SLE pathogenesis. Notably, interferon-stimulated gene (ISG) signatures are significantly upregulated in immune cells, skin, and kidney. Although a correlation with serological parameters and clinical symptoms has been proposed, the association with global disease activities remains controversial. Key findings in the field include an upregulated plasmablast signature, which positively correlates with disease activity; a neutrophil signature associated with lupus nephritis; and a decreased lymphocyte signature, reflecting lymphopenia. Tissue-level studies highlight the critical role of infiltrating immune cells in organ damage. Future research should leverage advanced technologies and integrate multi-omics data to deepen our understanding of SLE's molecular underpinnings, facilitating the development of targeted therapies.

Epigenomic, cistromic, and transcriptomic profiling of primary kidney tubular cells.

Spatiotemporal regulation of gene expression is essential for maintaining cellular homeostasis throughout kidney development and disease progression. Transcription factors (TFs) and epigenetic modifications play pivotal roles in controlling gene expression. Profiling chromatin modifications across the genome, along with the distribution and target regulation by TFs in specific kidney cell types, is crucial for understanding the dynamic changes in gene expression. Here, we presented a comprehensive workflow for epigenomic, cistromic, and transcriptomic analyses of primary kidney tubular cells. Specifically, our methodologies included the isolation of primary kidney tubular epithelial cells, RNA extraction, assay for transposase-accessible chromatin using sequencing, ultra-low-input micrococcal nuclease-based native chromatin immunoprecipitation, cleavage under targets and release using nuclease, and subsequent bioinformatic analysis. This protocol provides a methodological framework for investigating the roles of TFs and epigenetic modifications in kidney development and diseases.