PCR Results Research Articles

Concordance of non-invasive plasma cell-free DNA with invasive diagnostics for diagnosis of invasive fungal disease.

Mold plasma cell-free DNA (cfDNA) PCR is a promising non-invasive diagnostic modality for early diagnosis of invasive mold disease (IMD) in immunocompromised patients. Although mold cfDNA PCR has been shown to be highly accurate, the value of invasive procedures to collect specimens for conventional fungal diagnostics following plasma cfDNA testing remains unclear. This retrospective single-center cohort study included patients with mold plasma cfDNA PCR performed 7 days before or 2 days after invasive specimen collection. Mold PCR detected Aspergillus species, Mucorales agents, Fusarium species, and Scedosporium species. Invasive procedures included tissue biopsy and bronchoscopy. The primary endpoint was the concordance of mold plasma cfDNA PCR results with results of conventional fungal tests performed on tissue and bronchoalveolar lavage fluid (BAL). Five hundred and six patients with mold plasma cfDNA PCR resulting ahead of invasive specimen (123 tissue and 426 BAL) results were included, and 437 (86.4%) were immunocompromised. After adjudicating discordant results based on the EORTC/MSGERC definitions for IMD, mold plasma cfDNA PCR and invasive test results were 88.5% (448/506) concordant. In proven cases, 64.7% (11/17) of negative mold plasma cfDNA PCR results occurred in patients with fungal sinusitis (8) and limb infection (3). Non-hematologic malignancy and non-neutropenic states were statistically associated with negative mold plasma cfDNA PCR in patients with proven or probable IMD. Non-invasive mold plasma cfDNA PCR results were highly concordant with invasive specimen fungal test results, thus indicating risk-prone invasive specimen collection can be safely curtailed in immunocompromised patients with suspected IMD.

Genome-wide analyses of the NAC transcription factor gene family in Acer palmatum provide valuable insights into the natural process of leaf senescence.

Acer palmatum is a deciduous shrub or small tree. It is a popular ornamental plant because of its beautiful leaves, which change colour in autumn. This study revealed 116 ApNAC genes within the genome of A. palmatum. These genes are unevenly distributed on the 13 chromosomes of A. palmatum. An analysis of the phylogenetic tree of Arabidopsis thaliana NAC family members revealed that ApNAC proteins could be divided into 16 subgroups. A comparison of ApNAC proteins with NAC genes from other species suggested their potential involvement in evolutionary processes. Studies suggest that tandem and segmental duplications may be key drivers of the expansion of the ApNAC gene family. Analysis of the transcriptomic data and qRT‒PCR results revealed significant upregulation of most ApNAC genes during autumn leaf senescence compared with their expression levels in summer leaves. Coexpression network analysis revealed that the expression profiles of 10 ApNAC genes were significantly correlated with those of 200 other genes, most of which are involved in plant senescence processes. In conclusion, this study contributes to elucidating the theoretical foundation of the ApNAC gene family and provides a valuable basis for future investigations into the role of NAC genes in regulating leaf senescence in woody ornamental plants.

SOX11 Silence Inhibits Atherosclerosis Progression in ApoE-Deficient Mice by Alleviating Endothelial Dysfunction.

SRY-Box Transcription Factor-11 (SOX11) is a transcriptional regulatory factor that plays a crucial role in inflammatory responses. However, its involvement in atherosclerosis (AS), a cardiovascular disease driven by endothelial cell inflammation, remains unknown. This study aims to elucidate the role of SOX11 in AS. The expression of SOX11 was found to be elevated in the aortic tissue of AS mice induced by feeding ApoE-deficient mice a high-fat diet. Knockdown of SOX11 using lentiviral-mediated SOX11-specific shRNA via tail vein injection resulted in a reduction in plaque area and lipid deposition within plaques at the aortic root. Furthermore, silencing SOX11 led to decreased expression of cell adhesion factors Intercellular Cell Adhesion Molecule-1 and Vascular Cell Adhesion Molecule-1, as well as reduced levels of inflammatory factors Interleukin (IL)-6, IL-1β, and chemokine Monocyte Chemotactic Protein-1. In the human umbilical vein endothelial cells (HUVECs) induced by Tumor Necrosis Factor (TNF)-α, increased inflammation was observed at the cellular level, along with enhanced monocyte adhesion. Infection of HUVECs with lentivirus carrying specific shRNA targeting SOX11 inhibited inflammatory response. Mechanistically, chromatin immunoprecipitation (ChIP)-PCR results revealed that SOX11 bound to the promoters of downstream target genes Tumor Necrosis Factor Receptor-Associated Factor-1 (TRAF1), Cluster of Differentiation (CD)40, and CD36, positively regulating their transcription. In conclusion, SOX11 plays a pivotal role in promoting endothelial cell inflammation. Suppression of SOX11 reduces endothelial cell inflammation by inhibiting the transcription of TRAF1, CD40, and CD36, thereby impeding the progression of atherosclerosis.

WD40 proteins PaTTG1 interact with both bHLH and MYB to regulate trichome formation and anthocyanin biosynthesis in Platanus acerifolia.

Trichome development and anthocyanin accumulation are regulated by a complex regulatory network, the MBW complexes consist of MYB, bHLH, and WD40 transcription factors. In this study, two sequences, named PaTTG1.1, and PaTTG1.2, were cloned and functionally characterized from Platanus acerifolia. Quantitative real-time PCR results showed that PaTTG1 genes were expressed in the trichomes and red leaves. Overexpression of PaTTG1.1 and PaTTG1.2 genes in Arabidopsis ttg1 mutants restored the phenotypes of ttg1 mutants that were glabrous and lacked purple anthocyanins in hypocotyls and seeds. In transgenic plants, the expression levels of the trichome regulation-related genes AtCPC, AtTRY, AtETC1, AtMYB23, and AtGL2, as well as early and late biosynthetic genes related to anthocyanin biosynthesis, were significantly upregulated. The results of the yeast two-hybrid showed that PaTTG1.1 and PaTTG1.2 proteins could physically interact with both bHLH and R2R3-MYB transcription factors from Arabidopsis and P. acerifolia. Taken together, the results presented in this study suggest that the two PaTTG1 genes share similar functions in the regulation of trichomes and anthocyanins in different species. However, there may be some differences in their regulatory mechanisms.

MGB probe-based multiplex droplet digital PCR for the interspecific identification of Notopterygii Rhizoma et Radix in herbal materials and preparations.

Owing to high sensitivity and ability for absolute quantification, the droplet digital polymerase chain reaction (ddPCR) is widely used for viral and bacterial detection. However, few studies have been conducted on the application of ddPCR to identify the original plant species used in traditional Chinese medicine and Chinese patent medicine. In this study, we investigated the feasibility of using ddPCR to differentiate between Notopterygium incisum and N. franchetii to establish a sensitive and quantitative method for quality control of herbal materials and preparations. Specific minor groove binding (MGB) probes and primers were designed based on stable single nucleotide polymorphisms. The ddPCR experimental conditions were designed and optimised according to the results of multiplex PCR and qPCR, which ultimately confirmed the limits of detection and quantification (LOD and LOQ, respectively) of the method for Notopterygii Rhizoma et Radix. Additionally, the original plant species of Notopterygii Rhizoma et Radix in Jiuwei Qianghuo pills circulating in the market were identified. The results of the multiplex PCR and qPCR indicated that the probes and primers were specific. Furthermore, a Qsep analyser and Sanger sequencing were used to confirm that the specific amplification products of N. incisum and N. franchetii were 283 and 206 bp, respectively. The optimised ddPCR system was employed to determine the LOD to be 0.000816 ng/µl, and LOQ of N. incisum and N. franchetii to be 0.00408 and 0.003312 ng/µl, respectively. In addition, Notopterygii Rhizoma et Radix in four Jiuwei Qianghuo pills was amplified and successfully identified using ddPCR assays. This study established a multiplex ddPCR method using MGB probes to identify Notopterygii Rhizoma et Radix, providing a foundation for the identification and quantification of multi-source Chinese herbal medicines.

ALOX15-Driven Ferroptosis: The key target in Dihydrotanshinone I's epigenetic Battle in hepatic stellate cells against liver fibrosis.

It is known that ferroptosis promotes hepatic stellate cells (HSCs) inactivation. Arachidonate 15-Lipoxygenase (ALOX15), a ferroptosis driver gene, participates in disease progression. Dihydrotanshinone I (DHI), an active compound from Salvia miltiorrhiza, effectively regulates HSC inactivation. Nonetheless, there still needs to be clear understanding of how DHI affects HSC ferroptosis. This study primarily investigates DHI's protective effects on liver fibrosis in vivo and in vitro. Additionally, we explored the molecular mechanisms by which DHI promotes ferroptosis in HSCs. The relationship between ALOX15 level and methylation was examined. Molecular docking was performed to confirm the targeting between early growth response protein 1 (EGR1) and DHI. DHI exhibited a mitigating effect on liver fibrosis in vivo. DHI-induced inactivation of HSC by promoting ferroptosis, accompanied by an elevation in intracellular iron and reactive oxygen species (ROS) levels. Results of transcriptome sequencing and quantitative real-time PCR (qRT-PCR) confirmed the elevation of ALOX15 (a ferroptosis driver gene) in HSCs with DHI. Loss of ALOX15 inhibited DHI-induced ferroptosis. Interestingly, DNA methyltransferase 1 (DNMT1), an essential DNA methyltransferase, was downregulated by DHI. Overexpression of DNMT1 resulted in decreased ALOX15 expression in cells with DHI. Notably, transcription factor EGR1 was demonstrated to regulate DNMT1 expression. EGR1 deficiency led to an increase in DNMT1 expression, which inhibited DHI-induced ferroptosis. Molecular docking confirmed that EGR1 could serve as a direct pharmacological target of DHI. DHI upregulates EGR1 level, leading to decreased DNMT1 expression and increased ALOX15 demethylation, thereby promoting HSC ferroptosis and inactivation.

Optimizations of Placenta Extracellular Matrix-Loaded Silk Fibroin/Alginate 3D-Printed Scaffolds Structurally and Functionally for Bone Tissue Engineering.

Recent interest has been focused on extracellular matrix (ECM)-based scaffolds totreat critical-sized bone injuries. In this study, urea was used to decellularize and solubilize human placenta tissue. Then, different concentrations of ECM were composited with 8% alginate (Alg) and 12% silk fibroin (SF) for printing in order to produce a natural 3D construct that resembled bone tissue. The physical and biological features of the printed structures were evaluated entirely in vitro. Finally, a rat model was employed to examine the optimal 3D printed scaffold (5% ECM) as a bone transplant for the healing of cranial bone lesions. The present investigation demonstrated that decellularizing placental tissue fragments led to efficient removal of cell debris. In addition, a remarkable improvement in the printed scaffolds' mechanical and biological properties was observed by increasing the ECM concentration. The histology studies and real-time PCR results demonstrated the acceleration of bone regeneration in the bone lesions treated with 5%ECM-SF/Alg at 4 and 8 weeks after implantation. Overall, these results proved that the placental ECM-printed scaffolds could potentially construct biomimetic grafts to reconstruct significant bone defects and now promise to proceed with clinical studies.

Exosomes derived from umbilical cord mesenchymal stem cells promote healing of complex perianal fistulas in rats

BackgroundComplex perianal fistulas, challenging to treat and prone to recurrence, often require surgical intervention that may cause fecal incontinence and lower quality of life due to large surgical wounds and potential sphincter damage. Human umbilical cord-derived MSCs (hUC-MSCs) and their exosomes (hUCMSCs-Exo) may promote wound healing.MethodsThis study assessed the efficacy, mechanisms, and safety of these exosomes in treating complex perianal fistulas in SD rats. We established a rat model, divided rats with fistulas into the control and the exosome groups. We assessed treatment efficacy through ultrasound, clinical observations, and histopathological analysis. We also evaluated the activation of the HIF-1α/TGF-β/Smad signaling pathway via PCR and Western blot and assessed serological markers for HIF-1α and inflammatory indices through ELISA. We analyzed gut microbiota and the systemic metabolic environment via untargeted metabolomics.ResultsThe hUCMSCs-Exo effectively promoted healing of wound, regulated the immune balance enhanced collagen synthesis and angiogenesis in the perianal fistulas model of rats, and regulated the gut microbiota and metabolomic profiles. Results of PCR and Western blot analyses indicated that the exosomes activated HIF-1α/TGF-β/Smad signaling pathways. To the dosages tested, the 10ug/100ul concentration (medium dose) was found to be the most effective to the treatment of complex perianal fistulas.ConclusionsThe hUCMSCs-Exo significantly promoted the healing of wound in perianal fistulas of rats and demonstrated higher safety. The underlying mechanism facilitating the healing process was likely associated with the activation of the HIF-1α/TGF-β/Smad signaling pathway.Graphical abstract

Utility of Cand PCR in the Diagnosis of Vulvovaginal Candidiasis in Pregnant Women

Vulvovaginal candidiasis (VVC) can lead to multiple complications when it occurs during pregnancy, so it is necessary to diagnose it promptly for effective treatment. Traditional methods for identifying Candida spp. are often too time-consuming and have limited specificity and sensitivity. In this work, we evaluated the diagnostic utility of an endpoint PCR assay (Cand PCR) in vaginal swab specimens. Using a cotton swab, 108 vaginal swab samples were taken from pregnant women who consented to participate in the study. The samples were inoculated in Sabouraud agar plates (the gold standard) and subsequently used to extract DNA directly from the exudate. The yeasts isolated from the Sabouraud agar were identified in CHROMagar™ Candida. DNA extracted from vaginal swabs was amplified by Cand PCR. Based on the results of the Cand PCR and the gold standard, sensitivity (S), specificity (E), positive predictive values (PPVs), and negative predictive values (NPVs) were determined. Cand PCR presented an S = 65%, E = 100%, PPV = 100% and NPV = 91%. Cand PCR showed low sensitivity for detecting Candida spp. directly from vaginal swabs, but it was useful for identifying the etiologic agent and reducing the time to obtain the result, which is usually at least 48 h.

Diagnosing gastrointestinal infections based on cycle threshold cut-offs of PCR.

This study compared the performance of molecular vs stool culture assays for gastrointestinal infection (GII) detection, with focus on defining cycle threshold (Ct) cut-off values for positive culture results. A total of 6,000 records of patients with suspected GII between October 2022 and February 2023 and registered at Clalit HealthCare Services in Haifa, Israel, were reviewed. Stool samples were collected from all patients with suspected GII. PCR was performed with the Seegene Allplex GI-Bacteria (I) assay kit. PCR-positive samples were cultured on bacteria-specific agar media. Out of 356 PCR-positive samples, 196 (55.1%) were culture-positive. Significant differences were noted between the mean Ct of culture-positive vs culture-negative samples for Shigella spp. (P < 0.0001), E. coli O157 (P = 0.0001), and Campylobacter spp. (P = 0.004). Shigella had the lowest Ct cutoff (27.14). Negative culture results for PCR-positive samples may result from low bacterial load. At the same time, false-positive PCR results may exist. Thus, PCR result should be considered along with clinical presentation and with Ct value consideration.IMPORTANCEGII diagnostic procedures have shifted from traditional- to molecular-based assays, which may increase missdiagnosis due to the high PCR sensitivity and false positives. This study suggests to consider a Ct threshold for each pathogen in order to reduce inaccurate diagnosis. Alternatively, culture should be performed for PCR-positive samples.

Identification and Analysis of the Plasma Membrane H+-ATPase Gene Family in Cotton and Its Roles in Response to Salt Stress.

Plant plasma membrane (PM) H+-ATPase functions as a proton-motive force by exporting cellular protons to establish a transmembrane chemical gradient of H+ ions and an accompanying electrical gradient. These gradients are crucial for plant growth and development and for plant responses to abiotic and biotic stresses. In this study, a comprehensive identification of the PM H+-ATPase gene family was conducted across four cotton species. Specifically, 14 genes were identified in the diploid species Gossypium arboreum and Gossypium raimondii, whereas 39 and 43 genes were identified in the tetraploid species Gossypium hirsutum and Gossypium barbadense, respectively. The characteristics of this gene family were subsequently compared and analyzed using bioinformatics. Chromosomal localization and collinearity analyses elucidated the distribution characteristics of this gene family within the cotton genomes. Gene structure and phylogenetic analyses demonstrated the conservation of this family across cotton species, whereas the examination of cis-acting elements in gene promoters highlighted their involvement in environmental stress and hormone response categories. An expression profile analysis revealed eight genes whose expression was upregulated under salt stress conditions, and quantitative real-time PCR results suggested that the cotton PM H+-ATPase genes may play crucial roles in conferring resistance to salt stress. These findings establish a robust foundation for subsequent investigations into the functions of cotton PM H+-ATPase genes and may offer valuable insights for selecting genes for resistance breeding programs.

The Stress Response of Aphids to the Accumulation of Heavy Metals Along Vicia faba L. Under Cadmium Treatment.

Due to the intensification of human activities, the ecosystems are being polluted by heavy metals. The pollution of heavy metals in agricultural systems has become a serious issue of global concern. This study detected the bioaccumulation of cadmium (Cd) in broad beans and aphids through continuous exposure to varying concentrations of Cd pollution (0, 3.125, 6.25, 12.5, 25, 50 mg/L) and subsequently examined its effects on aphid energy metabolism and reproductive ability. The results showed that Cd can be transmitted and accumulated between Vicia faba L. and aphids along the food chain, and the amount of accumulation was related to the Cd treatment concentration. Quantitative real-time PCR results showed that the expression levels of trehalase (TRE) and trehalose-6-phosphate synthase (TPS) in F1 were significantly upregulated, and those of vitellogenin (Vg) were varied across the five generations of aphids after Cd treatment, which were up-regulated, and others down-regulated. Compared with the control group, the glycogen content and two types of trehalase activities of the first-generation Cd-treatment aphids were decreased, while trehalose content increased; there was no significant change in the carbohydrate content and trehalase activity of the fourth and fifth generations of aphids. In addition, the reproduction of female aphids was inhibited. This research is helpful for studying the toxic effects of heavy metals on insects and the adaptation mechanisms of insects to extreme environments. It also provides a theoretical basis for further exploring the molecular mechanisms of Cd homeostasis in plants and insects under Cd stress.

Tropisetron-Induced Apoptosis: A Study on SKOV3 Cell Viability and Gene Expression

Background: Ovarian tumors account for 1% of all childhood neoplasms and are the most common genital neoplasm in children. Considering the role of serotonin in the promotion of tumor growth and metastasis in some cancers, tropisetron as a 5-hydroxytryptamine (5-HT3) receptor antagonist can exert anti-neoplastic effects. The current study seeks to determine the association between the use of tropisetron and ovarian cancer­cell lines (SKOV3) by evaluating apoptotic regulators. Materials and Methods: In this experimental study, after the addition of tropisetron to SKOV3 cancer cells at the concentrations of 1, 10, and 100 μM, the MTT assay was employed to assess the cell viability percentage within 24, 48, and 72 hours. The level of expression of Bcl2 and Bax genes after 24 hours were determined by Real Time-PCR, and Caspase 3 enzyme activity was measured by the ELISA method. Differences between groups were statistically analyzed by one-way analysis of variance (ANOVA). A p-value less than 0.05 is considered to be statistically significant. Results: Based on the MTT test, tropisetron significantly decreased the viability of SKOV3 cancer cells. It decreased the levels of Bcl2 expression according to real-time PCR results (P =0.0015) but increased the expression levels of Bax (P = 0.011) in SKOV3 cells. Both caspase-3 enzyme activity and the ratio of Bax to Bcl2 expression (Bax/Bcl2) were increased (P = 0.008 and P = 0.011, respectively). Conclusion: Tropisetron could inhibit tumor cell growth via apoptosis induction and exert proapoptotic effects in an ovarian cancer ¬cell line. Therefore, it seems that it can be considered as a possible chemotherapy drug for ovarian cancer. However, more studies should be conducted in this regard.

Diagnostic Models for Differentiating COVID-19-Related Acute Ischemic Stroke Using Machine Learning Methods.

Backgrounds: Although COVID-19 is primarily known as a respiratory disease, there is growing evidence of neurological complications, such as ischemic stroke, in infected individuals. This study aims to evaluate the impact of COVID-19 on acute ischemic stroke (AIS) using radiomic features extracted from brain MR images and machine learning methods. Methods: This retrospective study included MRI data from 57 patients diagnosed with AIS who presented to the Department of Radiology at Hacettepe University Hospital between March 2020 and September 2021. Patients were stratified into COVID-19-positive (n = 30) and COVID-19-negative (n = 27) groups based on PCR results. Radiomic features were extracted from brain MR images following image processing steps. Various feature selection algorithms were applied to identify the most relevant features, which were then used to train and evaluate machine learning classification models. Model performance was evaluated using a range of classification metrics, including measures of predictive accuracy and diagnostic reliability, with 95% confidence intervals provided to enhance reliability. Results: This study assessed the performance of dimensionality reduction and classification algorithms in distinguishing COVID-19-negative and COVID-19-positive cases using radiomics data from brain MR scans. Without feature selection, ANN achieved the highest AUC of 0.857 (95% CI: 0.806-0.900), demonstrating strong discriminative power. Using the Boruta method for feature selection, the k-NN classifier attained the best performance, with an AUC of 0.863 (95% CI: 0.816-0.904). LASSO-based feature selection showed comparable results across k-NN, RF, and ANN classifiers, while SVM exhibited excellent specificity and high PPV. The RFE method yielded the highest overall performance, with the k-NN classifier achieving an AUC of 0.882 (95% CI: 0.838-0.924) and an accuracy of 79.1% (95% CI: 73.6-83.8). Among the methods, RFE provided the most consistent results, with k-NN and the ANN identified as the most effective classifiers for COVID-19 detection. Conclusions: The proposed radiomics-based classification model effectively distinguishes AIS associated with COVID-19 from brain MRI. These findings demonstrate the potential of AI-driven diagnostic tools to identify high-risk patients, support optimized treatment strategies, and ultimately improve clinical implications.

Performance and usability evaluation of three LDH-based malaria rapid diagnostic tests in Kédougou, Senegal.

The emergence of pfhrp2/3 -deleted parasites threatens histidine-rich protein 2 (HRP2)-based malaria rapid diagnostic test (RDT) performance. RDTs targeting Plasmodium falciparum ( Pf ) lactate dehydrogenase (LDH) may address current product limitations and improve case management. To evaluate the performance and usability of three LDH-based RDTs in febrile patients. A cross-sectional diagnostic accuracy study was conducted in Kédougou, Senegal. Capillary blood was tested using the SD Bioline Ag Pf (#05FK50) and three LDH-based RDTs: BIOCREDIT Malaria Ag Pf (pLDH), BIOCREDIT Pf (pLDH/HRPII), and BIOCREDIT Pf/Pv (pLDH/pLDH) (Rapigen Inc., Republic of Korea). Venous blood was collected to repeat the BIOCREDIT RDTs and conduct microscopy. Frozen venous specimens were tested using a reference PCR assay. A quantitative multiplex malaria antigen assay measured antigen concentration. RDT performance was determined and analyzed as a function of antigen concentration distribution. Usability of the Pf -only BIOCREDIT tests was evaluated using a questionnaire. 154/220 participants (70%) were Pf -positive by PCR. The Pf (pLDH/HRPII) test demonstrated the highest sensitivity at 78% (70.9%-84.5%); specificity was 89% (79.4%-95.6%). All RDTs performed better than microscopy (53% sensitivity). RDTs performed better when compared to antigen concentration over PCR results. Improved sensitivity of the Pf (pLDH/HRPII) test was driven by the HRP2 line. Line intensity correlated with antigen concentration. Predicted sensitivity using the analytical limit of detection (LOD) was comparable to observed sensitivity. RDTs demonstrated acceptable usability. Both HRP2 and LDH contributed to the sensitivity of the best-performing Pf- RDT. RDT analytical LODs can be used to predict performance in populations with known antigen concentrations.

Overview of COVID-19 Test Results (2021–2022) at the Laboratory of the Faculty of Medicine, Universitas Swadaya Gunung Jati, Cirebon, Indonesia

Background: COVID-19 (Coronavirus Disease-19) is a respiratory infection caused by the SARS-CoV-2 virus. In 2020, the World Health Organization (WHO) declared COVID-19 a global pandemic due to the rapid rise in cases and mortality rates worldwide. The pandemic has impacted millions of people and continues to pose a significant global public health threat. Accurate diagnosis of the disease depends on laboratory testing, with RT-PCR widely recognized as the gold standard for confirming COVID-19. Aims: To describe an overview of COVID-19 test results at Laboratory Faculty of Medicine, Universitas Swadaya Gunung Jati, Cirebon, Indonesia, from 2021-2022. Methods: This study used a descriptive observational method. The sample was collected in July 2024 using a total sampling technique. The sample includes all 135,713 patients who had COVID-19 tests at Laboratory Faculty of Medicine Swadaya Gunung Jati Univesity between 2021 and 2022. Data were collected from medical records of COVID-19 test. The variables of this study include gender, age, and COVID-19 test results. A statistical analysis was used to determine frequency distribution. Results: The results of the study showed that among the sample who tested for COVID-19, the majority are male (50.9%) and early adolescent age group (23.9%). RT-PCR test findings were positive in 16.3% of patients and negative in 83.7% of patients. Among PCR positive cases, the majority are female (17.4%), with seniors age groups &gt;65 years accounting for 39.0%. Conclusion: Most of the tested samples are males and early adolescent age groups, with more negative PCR results than positive ones. Among positive cases, the highest number was found in females and seniors age group. It is recommended that females and seniors age groups keep protected during COVID-19 outbreaks. Received: 25 September 2024 | Reviewed: 22 October 2024 | Revised: 30 November 2024 | Accepted: 11 December 2024.

Exploration of the Regulatory Network of Programmed Cell Death Genes in Rheumatoid Arthritis Based on Blood-Derived circRNA Transcriptome Information and Single-Cell Multi-omics Data.

Programmed cell death (PCD) and circular RNA (circRNA) have been found to involve in the pathogenesis of rheumatoid arthritis (RA). The aim of this study was to explore PCD mechanisms and gene regulatory networks in RA. RA related to circRNA, mRNA and single-cell data sets were obtained from the GEO database. The limma package was used to screen differentially expressed circRNA and differentially expressed genes (DEGs) of RA. The PCD gene set from literature was intersected with the DEGs of RA to obtain PCD-related DEGs of RA. The ENCORI database was used to predict and construct a competing endogenous RNAs (ceRNA) regulatory network to obtain key circRNAs and PCD-related DEGs. Hub genes were identified from the key PCD-related DEGs in the ceRNA regulatory network through LASSO regression, and a diagnostic model was constructed based on these hub genes. The expression of hub genes in various cells and stages was analyzed using single-cell datasets. Finally, the expression of key circRNAs and hub genes in peripheral blood of RA patients and healthy individuals was verified by PCR. In this study, a total of 71 differential circRNAs and 221 DEGs in RA were obtained, and 23 PCD-related DEGs were identified. Through ceRNA regulatory network, three key circRNAs (hsa_circ_0001241, hsa_circ_0089761, and hsa_circ_0001654) and four hub PCD-related DEGs. Among them, TXN and RRAGD were highly expressed, and PARP1 and TXNIP were lowly expressed in RA. Single-cell analysis revealed that these genes were significantly differentially expressed in myeloid cell subpopulation. PCR results indicated that among the 7 key factors, the expression of hsa_circ_0001241, hsa_circ_0089761, TXN, and RRAGD in RA was consistent with the results of bioinformatics analysis. Hsa_circ_0001241, hsa_circ_0089761, TXN and RRAGD may be potential biomarkers for RA, and their interactions may have significant implications for the pathology of RA.

Qualitative and Quantitative Detection of Virulence-Associated Genes in Escherichia Coli Isolates from Women with Urinary Tract Infections

Escherichia coli is the most common type of Enterobacteriaceae family that causes urinary tract infections. This bacterium causes diseases due to its many virulence factors. During the study, (150) urine samples were collected for women with symptoms of UTIs aged between (20-50) years from 1/9/2021 to 1/4/2022. Forty-five isolates of E. coli were diagnosed using a biochemical test, a VITEK2 system, and molecular detection using traditional PCR. A molecular study was conducted on 25 of these isolates using conventional PCR and qRT-PCR to investigate the presence of genes included (16S rRNA, uidA, fimA and kpsMTII). The traditional PCR results showed the presence of both 16S rRNA and uidA gene in all 25 isolates of E. coli. In contrast, the results showed that 23 (92%) and 18 (72%) isolates possessed fimA and kpsMTII genes, respectively. Following the extraction of RNA from twenty-five pathogenic isolates of E. coli and ten non-pathogenic isolates, gene expression of fimA and kpsMTII was quantified using quantitative real-time reverse transcription PCR (qRT-PCR). The observed fold change indicates a potential overexpression of the KSPMII and FimA genes in uropathogenic E. coli. The expression of the kpsMTII gene showed the highest level of folding with an average of 22.89 in the case of uropathogenic E.coli isolates compared with non-pathogenic isolates (control) with an average of 4.11. While the expression of the fimA gene with the highest level of fold change with an average of 90.52 in the case of uropathogenic E.coli isolates compared with non-pathogenic isolates (control) with an average of 0.94, Significant differences were observed among the isolates, as indicated by P values less than 0.05. This finding demonstrated that qRT-PCR detects genes that were expressed in comparison with traditional PCR. Also, qRT-PCR is a more sensitive and accurate assay than conventional PCR for determining the quantitative prevalence of E. coli in urine samples.

LncRNA C7orf13 facilitates cell proliferation and metastasis in nasopharyngeal carcinoma via targeting miR‐449c/miR‐28‐5p‐FMNL2 axis

AbstractThis study was to determine the involvement of long non‐coding RNA C7orf13 in nasopharyngeal carcinoma (NPC) and its underlying mechanism. Real‐time quantitative PCR results indicated that C7orf13 was overexpressed in NPC and associated with malignant features. C7orf13 knockdown significantly suppressed the proliferation, migration and invasion of NPC cells. Furthermore, we found that C7orf13 sequestered miR‐449c and miR‐28‐5p in NPC cells by dual‐luciferase reporter assays and RNA immunoprecipitation analysis. Sequent experiments showed that C7orf13 has a positive relationship with formin‐like 2 (FMNL2) in NPC tissues. Moreover, C7orf13 knockdown weakened FMNL2‐mediated cell invasion and migration. Finally, functional experiments revealed that the positive effect of C7orf13 on cell migration and invasion was mediated by the miR‐449c/miR‐28‐5p‐FMNL2 axis. Generally, our study identifies the biological role of long non‐coding RNA C7orf13 in the malignant process of NPC, which may pave a new way for the diagnosis and treatment of NPC.

Research on the influence of radiotherapy-related genes on immune infiltration, immunotherapy response and prognosis in melanoma based on multi-omics.

Skin cutaneous melanoma (SKCM) is a significant oncological challenge due to its aggressive nature and poor treatment outcomes. This study explores the comprehensive effects of radiotherapy (RT) in SKCM, focusing on cell signaling pathways, immune infiltration, immune gene correlations, immunotherapy response, and prognosis. Using the Cancer Genome Atlas (TCGA) database, differentially expressed genes (DEGs) in SKCM patients undergoing RT were identified. A risk score model based on these DEGs was developed to assess the effects of RT-related genes on drug sensitivity, immune cell infiltration, immunotherapy response, and prognosis through multi-omics analysis. Human melanoma cells UACC62 and UACC257 were irradiated with 8 Gy gamma ray to establish an in vitro model, verifying the impact of radiotherapy on gene expression. The risk score demonstrated significant prognostic value and emerged as an independent prognostic factor. miRNA-mRNA and transcription factor regulatory networks underscored its clinical significance. Four key genes were identified: DUSP1, CXCL13, SLAMF7, and EVI2B. Analysis of single-cell and immunotherapy datasets indicated that these genes enhance immune response and immunotherapy efficacy in melanoma patients. PCR results confirmed that gamma rays increased the expression of these genes in human melanoma cells UACC62 and UACC257. Using a multi-omics approach, we analyzed and validated the impact of RT on the immune landscape of melanoma patients. Our findings highlight the critical role of RT-related genes in predicting SKCM prognosis and guiding personalized therapy strategies, particularly in the context of immunotherapy. These contribute to understanding the role of radiotherapy combined with immunotherapy in melanoma.