Gene Profiling Research Articles

Effects of moringa (Moringa oleifera) leaf powder supplementation on growth performance, haematobiochemical parameters and gene expression profile of stinging catfish, Heteropneustes fossilis

Moringa oleifera is a popular edible protein source due to its high concentration of micronutrients, macronutrients, and antioxidants. The present study investigated the effects of M. oleifera leaf at various levels on the growth performance, haematobiochemical response, and SOD2 and HSP70 gene expression of Heteropneustes fossilis for 90 days. The fish were randomly distributed into 12 glass aquaria (66×36×36 cm) at 50 fish/aquarium in triplicate treatments Four dietary groups were used to feed the H. fossilis, each group containing graded levels of M. oleifera leaf meal (0, 10 %, 20 %, and 40 %) with a basal diet. It was observed that H. fossilis fed a diet supplemented with 10 % MOLM produced the highest final weight, specific growth rate, condition factor, and survivability. Hemoglobin and red blood cell levels were significantly higher in the fish treatment fed with a 10 % M. oleifera diet compared to the other treatments. Significantly lower levels of ALT and AST were detected in the fish that were fed a diet containing 10 % MOLM. Frequencies of ECA and ENA were significantly higher at 40 % M. oleifera inclusion. The relative mRNA expression profile of SOD2 and HSP70 gene were significantly higher at 10 % MOLM supplementation diet in comparison to the control group. The results of the PCA showed that adding 10 % MOLM supplementation had a beneficial effect on the nutritional and haematobiochemical parameters. Overall, it can be stated that 10 % MOLM treated with basal diet as a supplement on stinging catfish have positive impact on growth performance, haematobiochemical response, and immune gene expression.

Computational dissection of the regulatory mechanisms of aberrant metabolism in remodeling the microenvironment of breast cancer.

The composition of T cell subsets and tumor-specific T cell interactions within the tumor microenvironment (TME) contribute to the heterogeneity observed in breast cancer. Moreover, aberrant tumor metabolism is often intimately linked to dysregulated anti-tumor immune function of T cells. Identifying key metabolic genes that affect immune cell interactions thus holds promise for uncovering potential therapeutic targets in the treatment of breast cancer. This study leverages single-cell transcriptomic data from breast cancer to investigate tumor-specific T-cell subsets and their interacting subnetworks in the TME during cancer progression. We further assess the metabolic pathway activities of tumor-specifically activated T-cell subsets. The results reveal that metabolic pathways involved in insulin synthesis, secretion, degradation, as well as fructose catabolism, significantly influence multiple T cell interactions. By integrating the metabolic pathways that significantly up-regulate T cells in tumors and influence their interactions, we identify key abnormal metabolic genes associated with T-cell collaboration and further develop a breast cancer risk assessment model. Additionally, using gene expression profiles of prognosis-related genes significantly associated with aberrant metabolism and drug IC50 values, we predict targeted drugs, yielding potential candidates like GSK-J4 and PX-12. This study integrate the analysis of abnormal T-cell interactions and metabolic pathway abnormalities in the breast cancer TME, elucidating their roles in cancer progression and providing leads for novel breast cancer therapeutic strategies.

A Four-Gene Autophagy-Related Prognostic Model Signature and Its Association With Immune Phenotype in Lung Squamous Cell Carcinoma.

In the era of immunotherapy, there is a critical need for effective biomarkers to improve outcome prediction and guide treatment decisions for patients with lung squamous cell carcinoma (LUSC). We hypothesized that the immune contexture of LUSC may be influenced by tumor intrinsic events, such as autophagy. We aimed to develop an autophagy-related risk signature and assess its predictive value for immune phenotype. Expression profiles of autophagy-related genes (ARGs) in LUSC samples were obtained from the TCGA and GEO databases. Survival analyses were conducted to identify survival-related ARGs and construct a risk signature using the Random Forest algorithm. Four ARGs (CFLAR, RGS19, PINK1, and CTSD) with the most significant prognostic value were selected to construct the risk signature. Patients in the high-risk group exhibited worse prognosis than those in the low-risk group (p < 0.0001 in TCGA; p < 0.01 in GEO) and the risk score was identified as an independent prognostic factor. We observed that the high-risk group displayed an immune-suppressive status and showed higher levels of infiltrating regulatory T cells and macrophages, which are associated with poorer outcomes. Additionally, the risk score exhibited a significantly positive correlation with the expression of PD-1 and CTLA4, as well as the estimate score and immune score. This study provided an effective autophagy-related prognostic signature, which could also predict the immune phenotype.

Genomic and metabolomic insights into the selection and differentiation of bioactive compounds in citrus

Bioactive compounds are playing an increasingly prominent role in breeding functional and nutritive fruit crops such as citrus. However, the genomic and metabolic basis for the selection and differentiation underlying bioactive compounds variations in citrus remain poorly understood. Here, we constructed a species-level variation atlas of genomes and metabolomes using 299 citrus accessions. A total of 19,829 significant SNPs were targeted to 653 annotated metabolites, among which multiple significant signals were identified for secondary metabolites, especially flavonoids. Significantly differential accumulation of bioactive compounds in phenylpropane pathway, mainly flavonoids and coumarins, were unveiled across ancestral citrus species during differentiation, which is likely associated with the divergent haplotype distribution and/or expression profiles of relevant genes, including p-coumaroyl coenzyme A 2'-hydroxylases, flavone synthases, cytochrome P450 enzymes, prenyltransferases and UDP-glycosyltransferases. Moreover, we elucidated the citrus varieties with excellent antioxidant and anticancer capacities, clarifying the robust associations between distinct bioactivities and specific metabolites. Thus, these findings provide citrus breeding options for enrichment of beneficial flavonoids and avoidance of the potential risk of coumarins. This study will illuminate the application of genomic and metabolic engineering strategies in developing modern healthy citrus cultivars.

Fat mass and obesity associated gene and homeobox transcription factor iriquois-3 mRNA profiles in the metabolic tissues of zebrafish are modulated by feeding and food deprivation

Fat mass and obesity associated gene (FTO) has been strongly associated with obesity, and it is functionally linked to the homeobox transcription factor iriquois-3 (IRX3). In mammals, FTO and IRX3 are involved in the regulation of food intake and metabolism. This study aimed to determine whether FTO and IRX3are affected by feeding and food unavailability. FTO and IRX3 mRNA and protein were found widely distributed in all tissues examined, including the brain, muscle, gut, and liver. Postprandial increase in the abundance of FTO and IRX3 mRNAs was observed in metabolic tissues of both male and female zebrafish at 1 h post-feeding. Meanwhile, their expression in the brain and gut decreased at 3 h post-feeding, reaching preprandial levels. Additionally, FTO and IRX3 mRNA abundance in examined tissues increased after 7 days of food deprivation, but substantially decreased after refeeding for 24 h. In summary, we report that both FTO and IRX3 are meal-sensitive genes in zebrafish. The fasting-induced increase suggests a possible appetite regulatory role for FTO and IRX3 in zebrafish. These findings highlight the importance of FTO and IRX3 in appetite and metabolic regulation in zebrafish.

Impact of gonadotropin on certain testis-related genes identified through testicular transcriptome analysis in the Asian and the African catfish

Induction of spawning in catfish is well demonstrated in females while stimulation of spermiation in males seems difficult. This has led to least understanding of gene profile changes during testicular maturation. Expression of the factors after hormonal induction that control reproductive processes has become an intense research area in fish endocrinology. In view of this, de novo assemblies of testicular transcriptomes of the Asian catfish, Clarias batrachus and the African catfish, C. gariepinus, were performed to identify genes/factors involved in testicular maturation. For testicular induction, human chorionic gonadotropin (hCG) was administered in vivo to both the catfish species during active phase of reproduction. 1,68,071 and 1,26,232 assembled transcripts were obtained from C. batrachus and C. gariepinus testicular transcriptomes and were annotated using different databases. Further, in silico analysis suggested the presence of several transcripts that were involved in steroidogenesis and male reproduction. Comparison of transcriptomes of both species revealed the presence of certain unique genes related to reproduction differentially. Expression profiles after hCG induction in testis showed higher expression of certain steroidogenesis related genes such as star, cyp11b1, cyp17a and cyp21a in both the species. Further, expression levels of crucial factors related to testis, such as sox9, dmrt1/2/3, were also found to be significantly higher after gonadotropin induction. However, amh, tgfα and dmrt4/5 expression levels were significantly low. Factors related to male reproduction i.e., tekt1, tekt2, spag1, spata2 and spata7 were found to be upregulated in hCG treated testicular tissue. Histology analysis indicated that the gonadotropin induction either short or long term is a better strategy to highlight expression profile changes during testicular maturation in teleost.

The inhibition effect of psoralen on prostate cancer PC3 cells via down-regulation of long non-coding RNA ENST00000510619.

New medications are needed to improve outcomes of castration-resistant prostate cancer (CRPC). Psoralen has been reported to have anti-cancer properties for various tumors, but there are limited reports about psoralen treatment in prostate cancer (PCa). This study aimed to investigate the effect of psoralen on PC3 cells and to investigate potential underlying mechanisms of action. The effect of psoralen on the proliferation and cell cycle progression of PC3 cells was determined using Cell Counting Kit-8 (CCK-8) test and flow cytometry, respectively. The differential gene profiles in PC3 cells treated with psoralen were determined with microarray analyses. The effect of psoralen on long non-coding RNA (lncRNA) ENST00000510619 expression in PC3 cells was detected by real-time quantitative polymerase chain reaction (RT-qPCR). The effect of psoralen and transfection of small interfering lnc-RNA (si-lncRNA) ENST00000510619 on cell viability, invasion ability, and migratory activity of PC3 cells were evaluated using the CCK-8 test, transwell assay, and wound healing, respectively. Psoralen significantly inhibited PC3 cells in a concentration- and time-dependent manner and caused G1 phase and G2/M phase cycle arrests. When screened with a fold change (FC) of ≥2 and a P value of <0.05, 1,716 lncRNAs and 1,160 messenger RNAs (mRNAs) were significantly up-regulated, whereas 3,269 lncRNAs and 3,263 mRNAs were significantly down-regulated in PC3 cells after psoralen treatment. Among the differentially down-regulated lncRNAs in which the signal of the probe showed significant differences compared to the background, lncRNA ENST00000510619 had the highest FC. The expression of lncRNA ENST00000510619 was shown to be down-regulated by psoralen in a concentration-dependent manner. CCK-8 assay, wound healing, and transwell assay showed that both psoralen and si-lncRNA ENST00000510619 transfection significantly inhibited the activity, invasion, and migration of PC3 cells (P<0.01 for all). Psoralen was confirmed to inhibit proliferation and block the cell cycle in PC3 cells in this in vitro study. The molecular mechanism involves multiple differentially expressed lncRNAs and mRNAs and is related to the down-regulation of lncRNA ENST000000510619 expression. This study provides the experimental basis for the development of psoralen as a novel anti-CRPC drug and for the consideration of lncRNA ENST00000510619 as a potential clinical target for CRPC.

Determination of Pathogenic E. coli and Antimicrobial Resistance Genes in dogs and human Semen: Evidence of Multidrug-Resistance and Antimicrobial Resistance Gene Profiles

Determination of Pathogenic E. coli and Antimicrobial Resistance Genes in dogs and human Semen: Evidence of Multidrug-Resistance and Antimicrobial Resistance Gene Profiles

The antimicrobial resistance profile in poultry of Central and Southern India is evolving with distinct features

Antimicrobial resistance (AMR) is fast emerging and is depleting antibiotics repertoire. Poultry is a major source for AMR because focus to enhance its production by modern practices widely uses antibiotics. India and China are major producers of meat and have hotspots of AMR. The Central and Southern India were predicted as emerging hotspots for AMR in poultry but no data available to substantiate it. To this end, we collected chicken feces from poultry farms in these regions and isolated genomic DNA. Further, shotgun whole genome sequencing was performed for metagenomics analysis. For the first time, we report the AMR gene profiles in poultry from Kerala and Telangana. The samples exhibited a higher prevalence of gram-negative and anaerobic species. The high priority pathogens in India were detected, like E.coli, Clostridium perfringens, Klebsiella pneumonia Staphylococcus aureus, Enterococcous faecalis, Pseudomonas aeruginosa, Bacteriodes fragiles. Conspicuously, the Southern India had the highest abundance of AMR genes than the Central India. E.coli was significantly more prevalent in the southernmost zone of India than in other sites. Our data had many common AMR profile features of the European Union (EU) poultry farms but lacked mcr-1, which was a lately emerged AMR gene in E.coli. Our data revealed the extent of AMR gene evolved in the Central and Southern India. It is comparable to the EU data but severity is lesser than in the EU.

Analysis of Meis2 knockout mice reveals Sonic hedgehog-mediated patterning of the cochlear duct.

The mechanisms underlying the formation of complex structures such as during the outgrowth of the cochlear duct are still poorly understood. We have analyzed the morphological and molecular changes associated with cochlear development in mouse mutants for the transcription factor Meis2, which show defective coiling of the cochlea. These morphological abnormalities were accompanied by the formation of ectopic and extra rows of sensory hair cells. Gene profiling of otic vesicles from Meis2 mutants revealed a dysregulation of genes that are potentially involved in Sonic hedgehog (Shh)-mediated patterning of the cochlear duct. Like in Shh mutants, Meis2 defective mice showed a loss of genes that are expressed in the apical part of the cochlear duct. Taken together, these data reveal that the loss of Meis2 leads to a phenotype that resembles Shh mutants, suggesting that Meis2 is instrumental for cochlear Shh signaling. The modulation of the same subset of genes provides an interesting insight into which Shh responsive genes are essential for outgrowth and patterning of the cochlear duct.

Sex specific gene expression is present prior to metamorphosis in the sea urchin

A profound collaboration between the germline and somatic cells of an organism is the creation of a functional gonad. Here we establish a foundation for studying molecular gonadogenesis in the sea urchin by use of RNA-seq, quantitative mRNA measurements, and in-situ hybridizations throughout the life cycle of the variegated sea urchin, Lytechinus variegatus (Lv). We found through three distinct analyses that the ovary and testis of this echinoderm expresses unique transcripts involved in gametogenesis, and also discovered uncharacterized gene products unique to each gonad. We further developed a pipeline integrating timepoint RNA-seq data throughout development to identify hallmark gene expression in gonads. We found that meiotic and candidate genes involved in sex determination are first expressed surprisingly early during larval growth, and well before metamorphosis. We further discovered that individual larvae express varying amounts of male- or female- hallmarks before metamorphosis, including germline, oocyte, sperm, and meiotic related genes. These distinct male- or female- gonad gene profiles may indicate the onset of, and commitment to, development of a bipotential gonad primordium, and may include metabolic differences, supported by the observation that transcripts involved in glycolysis are highly enriched in the ovary compared to the testis. Together these data support a hypothesis that sex determination is initiated prior to metamorphosis in the sea urchin and that the many uncharacterized genes unique to each gonad type characterized herein may reveal unique pathways and mechanisms in echinoderm reproduction.

Selection of Reference Genes and HSP17.9A Expression Profiling in Heat-Stressed Grapevine Varieties

Background: “Touriga Franca” (TF) and “Touriga Nacional” (TN) are grapevine varieties cultivated in the ‘Douro Superior’ subregion (Northern Portugal) that experience stressful environmental conditions during the summer. Objectives: Aiming to profile the expression of stress-responsive genes by quantitative real-time PCR (qPCR) in TF and TN plants growing naturally, three candidate reference genes were first tested under controlled conditions. Methods: To simulate a summer’s day, TF and TN in vitro plants were exposed to 32 °C–3 h (heat acclimation) and 42 °C–1 h (severe heat stress, HS) followed by two recovery periods (32 °C–3 h and 24 °C–24 h). Leaf samples were collected at the end of each phase. Control plants were kept at 24 °C. Results: Among the candidate reference genes, the UBC and VAG pair showed the highest stability. The suitability of these genes for qPCR was validated by heat shock protein 17.9A (HSP17.9A) gene profiling. The HSP17.9A expression was up-regulated in both varieties and all experimental phases except in TF control plants. TN showed the highest HSP17.9A relative expression ratio after severe HS. Conclusions: TN responded faster than TF to the induced heat shocks. The UBC, VAG, and HSP17.9A genes revealed to be suitable for further qPCR assays in TF and TN grapevine varieties.

Adaptive capability of slow-growing backyard poultry as indicated by physiological and molecular responses in a hot and humid coastal climate

Assessing the adaptability of slow-growing rural chickens for improving thermotolerance to suit the global climate change is a major research need. This work was aimed to evaluate the adaptability of CARI-Debendra chickens and to identify the polymorphism as well as expression profiling of thermotolerant genes (HSP70 and GRP78) under prevailing temperature-humidity indices and thermal stress in a coastal environment. One hundred sixty straight run chicks were reared at THI≥75 (control) and THI>80 under coastal climate till 12 weeks. Polymorphism of HSP70 and GRP78 candidate genes were explored using restriction enzymes TaqI and HaeIII to identify possible thermotolerance markers. Expression profiling of both the genes in liver, intestine and pectoralis muscle was determined through quantitative real-time PCR. Rectal and body surface temperature recorded in the neck and back showed significant differences (P < 0.01) with higher temperature in THI>80 group. Comparatively lower live weights (P < 0.05) and poor FCR were recorded in THI>80 group. The villi height in all intestinal segments was significantly lower (P < 0.01), but deeper crypt depth was observed in THI>80 than control group. A lowest thymus weight (P < 0.05) was noted with no significant differences in immune response in treatment group. Serum levels of cholesterol, activities of lactate dehydrogenase, creatinine kinase and concentration of potassium, sodium and thyroxine hormone were not different between the 2 groups. The concentration of triiodothyronine and chloride ion was lower in THI>80 group indicating adaptive changes for thermoregulation. HSP70 gene expressions in the three tissues were differentially increased (P < 0.01) by temperature-humidity indices, but the expression of GRP78 was not different between the 2 groups. The results concluded that the environmental factors interact with genetics on adaptability towards thermotolerance in slow-growing chickens.

Autophagy-associated biomarkers ULK2, UVRAG, and miRNAs miR-21, miR-126, and miR-374: Prognostic significance in glioma patients.

As the pioneering study from Pakistan, our research distinctly focuses on validating the roles of autophagy-associated genes and MicroRNAs (miRs) in the unique context of our population for glioma prognosis. The study delves into the nuanced interplay of autophagy within a miR-modulated environment, prompting an exploration of its potential impact on glioma development and survival. Employing real-time PCR (qPCR), we meticulously assessed the expression profiles of autophagy genes and miRs in glioma tissues, complemented by immunohistochemistry on Formalin-fixed paraffin-embedded tissues from the same patients. Our comprehensive statistical analyses, including the data normality hypothesis Shapiro-Wilk test, the Mann-Whitney U-test, Spearman correlation test, and Kaplan-Meier survival analysis, were tailored to unravel the intricate associations specific to low- and high-grade glioma within our population. Clinicopathological analysis revealed a predominance of male patients (66%) with a median age of 35 years. Glioblastoma (32%) and Astrocytoma (36%) were the most prevalent histopathological subtypes. Molecular analysis showed significant correlations between prognostic markers (Ki-67, IDH-1, p53) and clinicopathological factors, including age, histological type, radiotherapy, and chemotherapy. In high-grade glioma, increased expression of AKT and miR-21, coupled with reduced ULK2 and LC3 expression was distinctly observed. While correlation analysis identified a strong positive correlation between ULK2 and UVRAG, PTEN, miR-7, and miR-100 in low-grade glioma, unveiling distinctive molecular signatures unique to our study. Furthermore, a moderate positive correlation emerged between ULK2 and mTOR, miR-7, miR-30, miR-100, miR-204, and miR-374, also between miR-21 and miR-126. Similarly, a positive correlation appeared between ULK2 and AKT, LC3, PI3K, PTEN, ULK1, VPS34, mTOR, Beclin1, UVRAG, miR-7 and miR-374. AKT positively correlated with LC3, PI3K, PTEN, ULK1, VPS34, mTOR, Beclin1, UVRAG, miR-7, miR-30, miR-204, miR-374, miR-126 and miR-21 weakly correlated with AKT and miR-30 in high-grade glioma, providing further insights into the autophagy pathway within our population. The enrichment analysis for miR-21, miR-126, and miR-374 showed MAPK pathway as a common pathway along with Ras, PI3K, and mTOR pathway. The low ULK2, UVRAG, and miR-374 expression group exhibited significantly poor overall survival in glioma, while miR-21 over-expression indicated a poor prognosis in glioma patients, validating it in our population. This study provides comprehensive insights into the molecular landscape of gliomas, highlighting the dysregulation of autophagy genes ULK2, and UVRAG and the associated miR-21, miR-126 and miR-374 as potential prognostic biomarkers and emphasizing their unique significance in shaping survival outcomes in gliomas within the specific context of the Pakistani population.

Assessment of housekeeping genes stability for gene transcription regulation analysis of Spodoptera littoralis (Lepidoptera: Noctuidae) under Spodoptera littoralis nucleopolyhedrovirus viral infection.

Normalization with respect to stable housekeeping genes is important to facilitate gene transcription regulation research and acquire more accurate quantitative polymerase chain reaction (qPCR) data. In the current study, five candidates housekeeping genes of the cotton leafworm, Spodoptera littoralis encoding for Actin (Actin), elongation factor 1-alpha (EF1α), ribosomal protein S3 (RPS3), ribosomal protein 49 (RP49), and Ubiquitin (Ubi), were evaluated as normalization housekeeping genes under Spodoptera littoralis nucleopolyhedrovirus (SpliNPV) viral infection. The qPCR results confirmed the expression of all five housekeeping genes in S. littoralis viral infected larvae. The expression profiles of the housekeeping genes showed that the EF1α, Actin, and RP49 had the minimum average Ct values of 18.41 ± 0.66, 18.84 ± 0.90 and 19.01 ± 0.87 in all infected samples, respectively. While RPS3 and Ubi showed the maximum average Ct of 21.61 ± 0.51 and 21.11 ± 0.82, respectively. According to the results of ΔCt and geNorm analysis, EF1α was ranked as the most stable housekeeping gene during infection time-course. While by using BestKeeper, geNorm and NormFinder, the Ubi, RP49, and RPS3 showed the most genes transcription stability. The obtained results were also validated using the Cytochrome c oxidase (COX) gene transcripts in response to SpliNPV infection. The results revealed that EF1α and Ubi were the most stable housekeeping genes to be used for normalizing S. littoralis gene transcription regulation under SpliNPV infection. These findings, provide a significant addition for gene transcription regulation studies of S. littoralis upon infection using SpliNPV as a bio-agent.

Overexpression of BDNF Suppresses the Epileptiform Activity in Cortical Neurons of Heterozygous Mice with a Transcription Factor Sip1 Deletion.

Since genetic mutations during brain development play a significant role in the genesis of epilepsy, and such genetically determined epilepsies are the most difficult to treat, there is a need to study the mechanisms of epilepsy development with deletions of various transcription factors. We utilized heterozygous mice (Sip1wt/fl) with a neuronal deletion of the transcription factor Sip1 (Smad interacting protein 1) in the cerebral cortex. These mice are characterized by cognitive impairment and are prone to epilepsy. It is known that the brain-derived neurotrophic factor (BDNF) has a neuroprotective effect in various neurodegenerative diseases. Therefore, we created and applied an adeno-associated construct carrying the BDNF sequence selectively in neurons. Using in vitro and in vivo research models, we were able to identify a key gen, the disruption of whose expression accompanies the deletion of Sip1 and contributes to hyperexcitation of neurons in the cerebral cortex. Overexpression of BDNF in cortical neurons eliminated epileptiform activity in neurons obtained from heterozygous Sip1 mice in a magnesium-free model of epileptiform activity (in vitro). Using PCR analysis, it was possible to identify correlations in the expression profile of genes encoding key proteins responsible for neurotransmission and neuronal survival. The effects of BDNF overexpression on the expression profiles of these genes were also revealed. Using BDNF overexpression in cortical neurons of heterozygous Sip1 mice, it was possible to achieve 100% survival in the pilocarpine model of epilepsy. At the level of gene expression in the cerebral cortex, patterns were established that may be involved in the protection of brain cells from epileptic seizures and the restoration of cognitive functions in mice with Sip1 deletion.

Unveiling the Innate and Adaptive Immunity Interplay: Global Transcriptomic Profiling of the Host Immune Response in Candida albicans Endophthalmitis in a Murine Model.

Intraocular fungal infection poses a significant clinical challenge characterized by chronic inflammation along with vision impairment. Understanding the host defense pathways involved in fungal endophthalmitis will play a pivotal role in identifying adjuvant immunotherapy. Clinical isolates of Candida albicans (15,000 CFU/μL) were intravitreally injected in C57BL/6 mice followed by enucleation at 24 and 72 h postinfection. Histopathological analysis was performed to evaluate the retinal changes and the disease severity. RNA-seq analysis was conducted on homogenized eyeballs to assess the relevant gene profiles and their differentially expressed genes (DEGs). Pathway enrichment analysis was performed to further annotate the functions of the DEGs. Histopathological analysis demonstrated a higher disease severity with increased inflammatory cells at 72 hpi and transcriptome analysis revealed 27,717 DEGs, of which 1493 were significant (adj p value ≤0.05, FC ≥ 1.5). Among these, 924 were upregulated, and 569 were downregulated. Majority of the upregulated genes were associated with the inflammatory/host immune response and signal transduction and enriched in the T-cell signaling pathway, natural killer cell-mediated cytotoxicity, C-type receptor signaling pathway, and NOD-like receptor signaling pathway. Furthermore, inflammation-associated genes such as T-cell surface glycoprotein CD3, cathelicidin antimicrobial peptide, and lymphocyte cell-specific protein tyrosine kinase were enriched, while pathways such as MAPK, cAMP, and metabolic pathways were downregulated. Regulating the T-cell influx could be a potential strategy to modulate excessive inflammation in the retina and could potentially aid in better vision recovery in fungal endophthalmitis.

Population structure of the B0/W148 Mycobacterium tuberculosis subtype: Phylogenetic analysis and characteristics of genotypic drug resistance

Background. The B0/W148 subtype belongs to the L2phylogenetic lineage of Mycobacterium tuberculosis and is most common in the former Soviet Union. Test systems capable of detecting genetic variants of the pathogen are needed for effective epidemiological surveillance. Studying the genetic diversity of B0/W148 strains and finding molecular markers suitable for their genotyping are key steps in the development of such diagnostic tools.The aim of the work. To study the phylogenetic diversity of the B0/W148 subtype circulating in the territory of the Russian Federation and neighboring countries in order to identify unique clades and search for specific molecular markers suitable for their precise identification.Materials and methods. The study used DNA samples of B0/W148 strains (n = 34) isolated in different regions of the Russian Federation, as well as genomic data obtained from the SRA NCBI (Sequence Read Archive of the National Center for Biotechnology Information) (n = 419). Phylogenetic analysis and principal component analysis (PCA) of whole genome sequencing (WGS) data were used to analyze genetic diversity and to identify molecular markers. An evolutionary reconstruction of the age of the identified clades was carried out.Results. The analysis of the B0/W148 genomes (n = 453) revealed that they are divided into three phylogenetic clades: B – basal, M – minor and P – principal. It was found that specific mutations in the M and P clades allow for their differential diagnosis. The 4137219T&gt;G mutation is unique for the M clade, and the 2241091C&gt;T mutation is unique for the P clade. No characteristic mutations were found among the strains of B clade. In addition, unique mutation profiles in the genes responsible for drug resistance were identified for the clades.Conclusion. The study showed that B0/W148 strains represent a genetically heterogeneous population divided into B, M and P clades. M and P Clades have unique mutations that allow for their identification. It was also found that all clades are characterized by the presence of specific mutation profiles in drug resistance genes.

Unveiling the genetic landscape of Streptococcus agalactiae bacteremia: emergence of hypervirulent CC1 strains and new CC283 strains in Tehran, Iran

BackgroundThe emergence of Streptococcus agalactiae infections in patients with bacteremia is increasing. It is crucial to investigate the epidemiology, molecular characteristics, biofilm status, and virulence analysis of Streptococcus agalactiae in these patients.MethodsIn this cross-sectional study, 61 S. agalactiae isolated from blood infection were subjected to characterization through antimicrobial susceptibility tests, biofilm formation, multilocus sequence typing (MLST), and PCR analysis for detecting resistance (tet and erm family) and virulence genes (alp2/3, alp4, bca, bac, eps, rib, lmb, cylE, and pilus island genes).ResultsOverall, 32.7% of the isolates demonstrated an inducible clindamycin resistance phenotype. The results showed that 49.2, 24.6, and 8.2% of confirmed Streptococcus agalactiae strains were classified as strong, intermediate, and weak biofilm-forming strains, respectively. tet(M) (57.1%) was recovered most, followed by tet(M) + tet(L) (14.3%), tet(S) + tet(K) (10.7%), tet(M) + tet(K) (8.9%), tet(M) + tet(K) + tet(O) (5.4%), and tet(S) + tet(L) + tet(O) (3.6%). Three virulence gene profiles of cylE, lmb, bca, rib (24.6%; 15/61), cylE, lmb, rib, alp3 (19.7%; 12/61), and cylE, lmb, bac, rib (16.4%; 10/61) were detected in approximately two-thirds of the isolates. MLST revealed that the 61 isolates belonged to six clonal complexes, including CC1 (49.2%), followed by CC12 (18%), CC19 (13.1%), CC22 (9.8%), CC17 (6.6%), and CC283 (3.3%), and 11 different sequence types (STs), including ST1 (24.6%), ST7 (14.8%), ST918 (13.1%), ST2118 (9.8%), ST19 (9.8%), ST48 (6.6%), ST1372 (4.9%), ST22 (4.9%), ST40 (4.9%), ST734 (3.3%), and ST283 (3.3%). Remarkably, all CC1 and CC12 isolates, three-fourths of CC19, and half of CC22 were confirmed as biofilm producers. Conversely, CC17 and CC28 isolates were found to be nonproducers. The occurrence of strong biofilm formation was limited to specific CCs, namely CC1 (34.4%), CC12 (8.2%), CC19 (3.3%), and CC22 (3.3%).ConclusionThe high prevalence of CC1 and CC12 clones among S. agalactiae strains reflects the emergence of these lineages as successful clones in Iran, which is a serious concern and poses a potential threat to patients.

Characterization and angiogenic potential of CD146+ endometrial stem cells

BackgroundThe human endometrium, lining the inner uterus, regenerates over 400 times uniquely during a woman’s reproductive life. Endometrial stem cells (eSCs) enrich the tissue, resulting in a dense vascular network, significant angiogenic potential, and effective regeneration power. Being of natural angiogenic properties and proven effective in the treatment of vascular disorders, eSCs can be considered safe, reliable, and superior to other post-natal stem cells. Cluster of Differentiation 146 (CD146) has emerged as a pivotal marker associated with pericytes and endothelial cells for promoting angiogenesis. Endometrial cells with high CD146 expression could proliferate and differentiate into multiple lineages. This study will explore the role of CD146 in eSCs, focusing on the potential to boost the angiogenic and regenerative functions of the cells. The novelty of this study lies in the investigation of CD146 on eSC function, which may open new possibilities for eSC-based therapy in regenerative medicine and vascular disorders.MethodsThe study involved obtaining endometrial biopsies from active reproducing women to isolate and cultivate eSCs. eSCs were assessed for growth factor secretion pattern, characterized for their mesenchymal properties. Finally, eSCs were tested for their angiogenic potential by angiogenic gene expression profile and in-ovo chick embryo model. As aimed, to check the role of CD146 in eSC angiogenesis, CD146+ cells were magnetically sorted and cultured. The sorted cells underwent various analyses, including flowcytometry to identify mesenchymal markers and human growth factor panel to analyze growth factor secretion profiles The study evaluated the angiogenic potential of CD146 + cells using functional assays, including ring formation, endothelial differentiation, and wound scratch assays, to evaluate cell migration and healing capabilities. Molecular insights were obtained through chemokine and cytokine investigations In-ovo Chick model assay was conducted to check the angiogenic potential and evaluated through macroscopic as well as through immunohistochemistry.ResultEndometrial stem cells (eSCs) were successfully isolated using a combination of mechanical and enzymatic digestion, followed by culturing in complete DMEM media. The secretion profile of eSCs revealed significant production of various angiogenic growth factors, including Granulocyte macrophage colony-stimulating factor (GM-CSF), granulocyte colony stimulating factor (G-CSF), Vascular endothelial growth factor (VEGF), Fibroblast growth factors (FGF), and Platelet derived growth factor AA (PDGF-AA). The angiogenic gene profile indicated upregulation of several angiogenic genes in eSCs. The mesenchymal nature of eSCs was demonstrated through surface marker analysis (Cluster of differentiation 73, Cluster of differentiation 90, Cluster of differentiation 105) and trilineage differentiation. The in-ovo chick model confirmed the angiogenic potential of eSCs. CD146+ cells, isolated via magnetic sorting, exhibited enhanced angiogenic potential. These cells secreted significant levels of angiogenic growth factors such as VEGF. In Matrigel assays, CD146+ cells formed endothelial ring structures more rapidly and persistently than unsorted eSCs. Semi-quantitative PCR confirmed their endothelial differentiation. CD146+ cells express various angiogenic chemokines such as CXCL5, CXCL8, CCL3, and CCL20 and cytokines such as GM-CSF, Interleukin-1β (IL-1β), Interleukin-6 (IL-6), PDGF AA/BB, Epidermal growth factor (EGF), Endothelin 1, Angiopoietin. In-ovo chick model assay showed that CD146+ cells had superior angiogenesis, with more nodes, junctions, and segments compared to eSCs and controls. Immunohistochemistry confirmed increased expression of endothelial markers (Cluster of differentiation 31, VEGF, Vascular associated protein (VAP), Von Willebrand factor (vWF) in CD146+ cells.ConclusionThe study highlights the angiogenic potential of endometrial stem cells, particularly the CD146+ cell population. These cells promote angiogenesis, secreting growth factors and forming stable blood vessel structures. CD146+ cells have higher expression levels of VEGF and TGF-α, key factors in angiogenesis. This suggests CD146+ eSCs may be promising for therapeutic applications in vascular diseases requiring angiogenesis. Further research is needed.