Quantitative Reverse transcription-PCR Assay Research Articles

AgrA directly binds to the promoter of vraSR and downregulates its expression in Staphylococcus aureus.

Staphylococcus aureus is an important human pathogen and vancomycin is widely used for the treatment of S. aureus infections. The global regulator agr is known as a well-described virulence regulator. Previous studies have found that agr-dysfunction strains are more likely to develop into vancomycin-resistant strains, but the mechanism for this phenomenon remains unknown. VraSR is a two-component regulatory system related to vancomycin resistance. In this study, we found that the expression levels of vraR were higher in agr-dysfunction clinical strains than in the agr-functional strains. We knocked out agr in a clinical strain, and quantitative reverse transcription PCR and β-galactosidase activity assays revealed that agr repressed transcription of vraR. After vancomycin exposures, population analysis revealed larger subpopulations displaying reduced susceptibility in agr knockout strain compared with wild-type strain, and this pattern was also observed in agr-dysfunction clinical strains compared with the agr-functional strains. Electrophoretic mobility experiment demonstrated binding of purified AgrA to the promoter region of vraR. In conclusion, our results indicated that the loss of agr function in S. aureus may contribute to the evolution of reduced vancomycin susceptibility through the downregulation of vraSR.

APR-246 enhances the anticancer effect of doxorubicin against p53-mutant AsPC-1 pancreatic cancer cells

Pancreatic cancer (PC) is a disease with a high mortality rate, and the early diagnosis of PC is still challenging. The 5-year relative survival rate remains below 8%, and therapeutic strategies are ineffective at increasing patient survival rates. In PC cells, resistance to treatment has been associated with genetic changes that initiate aberrant developmental signaling pathways; therefore, new strategies for treating PC are warranted. Here, we sought to explore the small molecule p53 reactivator, APR-246, either as a mono-drug or combined with doxorubicin (Doxo) in the p53 mutant (p53-mut) AsPC-1 PC cell line. Cytotoxicity of APR-246 and Doxo was studied alone or in combination with the AsPC-1 cell line with MTT assay. CalcuSyn software was used to calculate the combination index (CI), which was based on the Chou and Talalay technique. Apoptosis was assessed after staining with Acridine orange/ethidium bromide (AO/EB). Morphological alterations were examined under a 200x magnification by an inverted microscope. Gene expression was quantified using quantitative reverse transcription PCR assay (RT-qPCR). APR-246 alone exhibited modest anti-proliferative effects, while Doxo combined with APR-246 showed synergistic effects associated with morphological change; no more enhanced apoptosis was observed, as supported by NOXA gene levels. In conclusion, APR-246, whether monotherapy or combined with Doxo, was hindering the proliferation of p53-mut AsPC-1 PC cells, and further in vitro and in vivo research is warranted.

Tackling strong biofilm and multi-virulent vancomycin-resistant Staphylococcus aureus via natural alkaloid-based porous nanoparticles: perspective towards near future eradication.

As a growing direction, nano-based therapy has become a successful paradigm used to address the phytogenic delivery-related problems in overcoming multivirulent vancomycin-resistant Staphylococcus aureus (VRSA) infection. Hence, our aim was to develop and assess a novel nanocarrier system (mesoporous silica nanoparticles, MPS-NPs) for free berberine (Free-BR) as an antimicrobial alkaloid against strong biofilm-producing and multi-virulent VRSA strains using in vitro and in vivo mouse model. Our outcomes demonstrated vancomycin resistance in 13.7% of Staphylococcus aureus (S. aureus) strains categorized as VRSA. Notably, strong biofilm formation was observed in 69.2% of VRSA strains that were all positive for icaA gene. All strong biofilm-producing VRSA strains harbored a minimum of two virulence genes comprising clfA and icaA with 44.4% of them possessing all five virulence genes (icaA, tst, clfA, hla, and pvl), and 88.9% being multi-virulent. The study findings affirmed excellent in vitro antimicrobial and antibiofilm properties of BR-loaded MPS-NPs. Real-time quantitative reverse transcription PCR (qRT-PCR) assay displayed the downregulating role of BR-loaded MPS-NPs on strong biofilm-producing and multi-virulent VRSA strains virulence and agr genes in both in vitro and in vivo mice models. Additionally, BR-loaded MPS-NPs supplementation has a promising role in attenuating the upregulated expression of pro-inflammatory cytokines' genes in VRSA-infected mice with attenuation in pro-apoptotic genes expression resulting in reduced VRSA-induced apoptosis. In essence, the current study recommends the future scope of using BR-loaded MPS-NPs as auspicious alternatives for antimicrobials with tremendous antimicrobial, antibiofilm, anti-quorum sensing (QS), and anti-virulence effectiveness against problematic strong biofilm-producing and multi-virulent VRSA-associated infections.

Network analysis uncovers the master role of WRKY transcription factors in Arabidopsis thaliana response to N-acyl homoserine lactones

BackgroundPlants can perceive bacterial molecules such as the quorum sensing signals N-acyl homoserine lactones (AHL), thus modifying their fitness in response to environmental factors. Even though the benefits conferred by AHL depend on various hormone signaling pathways, the understanding of AHL signaling, especially the response to AHL presence, remains largely unknown.MethodsWeighted gene co-expression network analysis (WGCNA), multi-omics network analysis, and reverse transcription quantitative PCR (RT-qPCR) assays were used to identify key genes in AHL signaling.ResultsTo obtain comprehensive insights on AHL signaling, we integrated available transcriptome data from Arabidopsis thaliana exposed to different single or multiple AHL molecules and performed a weighted gene co-expression network analysis. We identified several key genes regulated in plants exposed to multiple AHL molecules. Multi-omics network analysis and RT-qPCR assay revealed a potential role of WRKY transcription factors.ConclusionsResults presented here offer good indications for exploring the mechanism of plants' response to bacterial signaling molecules, which could further support the application of AHL-producing bacteria in sustainable agriculture.

Association of DNA methylation/demethylation with the functional outcome of stroke in a hyperinflammatory state.

JOURNAL/nrgr/04.03/01300535-202410000-00024/figure1/v/2024-02-06T055622Z/r/image-tiff Inflammation is closely related to stroke prognosis, and high inflammation status leads to poor functional outcome in stroke. DNA methylation is involved in the pathogenesis and prognosis of stroke. However, the effect of DNA methylation on stroke at high levels of inflammation is unclear. In this study, we constructed a hyperinflammatory cerebral ischemia mouse model and investigated the effect of hypomethylation and hypermethylation on the functional outcome. We constructed a mouse model of transient middle cerebral artery occlusion and treated the mice with lipopolysaccharide to induce a hyperinflammatory state. To investigate the effect of DNA methylation on stroke, we used small molecule inhibitors to restrain the function of key DNA methylation and demethylation enzymes. 2,3,5-Triphenyltetrazolium chloride staining, neurological function scores, neurobehavioral tests, enzyme-linked immunosorbent assay, quantitative reverse transcription PCR and western blot assay were used to evaluate the effects after stroke in mice. We assessed changes in the global methylation status by measuring DNA 5-mc and DNA 5-hmc levels in peripheral blood after the use of the inhibitor. In the group treated with the DNA methylation inhibitor, brain tissue 2,3,5-triphenyltetrazolium chloride staining showed an increase in infarct volume, which was accompanied by a decrease in neurological scores and worsening of neurobehavioral performance. The levels of inflammatory factors interleukin 6 and interleukin-1 beta in ischemic brain tissue and plasma were elevated, indicating increased inflammation. Related inflammatory pathway exploration showed significant overactivation of nuclear factor kappa B. These results suggested that inhibiting DNA methylation led to poor functional outcome in mice with high inflammation following stroke. Further, the effects were reversed by inhibition of DNA demethylation. Our findings suggest that DNA methylation regulates the inflammatory response in stroke and has an important role in the functional outcome of hyperinflammatory stroke.

Injectable thermosensitive hydrogel loading erythropoietin and FK506 alleviates gingival inflammation and promotes periodontal tissue regeneration.

Background: Periodontitis is a chronic multifactorial inflammatory disease associated with dysbiotic plaque biofilms and characterized by progressive destruction of the tooth-supporting apparatus. Therefore, there is significant potential in the discovery of drugs that inhibit periodontal inflammatory responses and promote periodontal regeneration. Methods: In this study, we generated a periodontitis rat model to detect the effects of chitosan/β-sodium glycerophosphate (β-GP)/glycolic acid (GA) hydrogel carried Erythropoietin and FK506 (EPO-FK506-CS/β-GP/GA). A total of forty-eight male Wistar rats were used to establish the periodontitis model. Drug injection was administered every 3days for a total of five times over a 2-week period. After a period of 2weeks following implantation, the rats underwent anesthesia, and a section of their maxillae encompassing the maxillary first and secondmolars, along with the alveolar bone, was obtained. micro-CT scanning, histopathology, immunohistochemistry and reverse transcription-quantitative PCR (RT-qPCR) assays were performed. Meanwhile, ELISA assay was performed to detect the levels of inflammatory mediators (TNF-α, IL-6 and IL-1β). Results: The synthesis and characterization of EPO-FK506-CS/β-GP/GA revealed that the hydrogel has stability and sustained release of drugs. The application of FK506+EPO was found to significantly enhance new bone formation in the defect area, as evidenced by the results of HE staining. Additionally, the use of FK506+EPO in the treated groups led to a notable increase in the density of alveolar bone, as observed through micro-CT analysis, when compared to the Model group. EPO-FK506-CS/β-GP/GA hydrogel exhibited notable efficacy in modulating inflammatory mediators (TNF-α, IL-6 and IL-1β). Furthermore, the osteoinductive properties of the EPO-FK506-CS/β-GP/GA hydrogel were extensive, as evidenced by a significant upregulation in the expression of key markers (Collagen I, Runx2, OPN, and OCN) associated with osteoblastic differentiation. Conclusion: Taken together, EPO-FK506-CS/β-GP/GA hydrogel alleviates gingival inflammation and promotes periodontal tissue regeneration in the periodontitis.

Co-culture of benzalkonium chloride promotes the biofilm formation and decreases the antibiotic susceptibility of a Pseudomonas aeruginosa strain.

Benzalkonium chloride (BAC) is a disinfectant with broad-spectrum antibacterial properties, yet despite its widespread use and detection in the environment, the effects of BAC exposure on microorganisms remain poorly documented. Herein, the impacts of BAC on a Pseudomonas aeruginosa strain Jade-X were systematically investigated. The results demonstrated that the minimum inhibitory concentration (MIC) of BAC against strain Jade-X was 64 mg L-1. Exposure to BAC concentrations of 8, 16, 32, and 64 mg L-1 significantly augmented biofilm formation by 2.03-, 2.43-, 2.96-, and 2.56-fold respectively. The swimming and twitching abilities, along with the virulence factor production, were inhibited. Consistently, quantitative reverse transcription PCR assays revealed significant downregulation of genes related to flagellate- and pili-mediated motilities (flgD, flgE, pilB, pilQ, and motB), as well as phzA and phzB genes involved in pyocyanin production. The results of disk diffusion and MIC assays demonstrated that BAC decreased the antibiotic susceptibility of ciprofloxacin, levofloxacin, norfloxacin, and tetracycline. Conversely, an opposite trend was observed for polymyxin B and ceftriaxone. Genomic analysis revealed that strain Jade-X harbored eleven resistance-nodulation-cell division efflux pumps, with mexCD-oprJ exhibiting significant upregulation while mexEF-oprN and mexGHI-opmD were downregulated. In addition, the quorum sensing-related regulators LasR and RhlR were also suppressed, implying that BAC might modulate the physiological and biochemical behaviors of strain Jade-X by attenuating the quorum sensing system. This study enhances our understanding of interactions between BAC and P. aeruginosa, providing valuable insights to guide the regulation and rational use of BAC.

Circular RNA circEZH2 Promotes Lung Adenocarcinoma Progression by Regulating microRNA-495-3p/Tumor Protein D52 Axis and Activating Nuclear Factor-Kappa B Pathway.

It has been increasingly recognized that circular RNAs (circRNAs) act as a pivotal factor in the onset and progression of human malignancies. Yet, the specific activities and mechanistic roles of these RNAs in the context of lung adenocarcinoma (LUAD) are not fully understood. Microarray analysis identified a novel LUAD-associated circular RNA, termed hsa_circ_0006357 (also referred to as circEZH2). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was utilized for the analysis of circEZH2 expression in tissues and cell lines. The characteristics of circEZH2 were verified by RNase R treatment and fluorescence in situ hybridization (FISH) assays. The functions of circEZH2 were detected by Cell Counting Kit-8 (CCK-8), colony formation, wound healing, and Transwell assays. The molecular mechanism of circEZH2 was clarified through bioinformatics analysis as well as RNA pulldown, dual-luciferase reporter, RT-qPCR, and immunoblotting assays. The role of circEZH2 in vivo was investigated using a xenograft model. This investigation revealed that circEZH2 expression was elevated in LUAD cell lines and tumor samples. This elevation was associated with enhanced cell proliferation, migratory capacity, epithelial-mesenchymal transition (EMT), and invasion in vitro. Conversely, silencing of circEZH2 in vivo resulted in a notable decrease in LUAD tumorigenesis, whereas its overexpression led to the opposite effects. Mechanistically, circEZH2 appeared to act as a sponge for miR-495-3p, facilitating the upregulation of tumor protein D52 (TPD52) and triggering the nuclear factor kappa B (NF-κB) signaling pathway, thus contributing to the progression of LUAD. These findings indicate that circEZH2 may function as a competitive endogenous RNA (ceRNA), driving the progression of LUAD by manipulating the miR-495-3p/TPD52 axis and activating the NF-κB pathway.

Effects of Liquiritin on Mitochondrial Dynamics in Cerebral Ischemia–Reperfusion Injury by Regulating Nurr1 via the YAP-INF2-Mitochondrial Fission Pathway

This study investigated whether liquiritin can alleviate cerebral ischemia–reperfusion injury by regulating Nurr1 to mediate mitochondrial homeostasis. SH-SY5Y cells were subjected to glucose deprivation and reperfusion to establish a cerebral ischemia–reperfusion injury model in vitro. Cell viability and apoptosis were then determined using a cell counting kit and flow cytometry analysis. The degree of mitochondrial swelling was evaluated using a cell mitochondria isolation kit. Reactive superoxide generation, mitochondrial membrane potential, adenosine triphosphate (ATP) content, and mitochondrial ultrastructure were analyzed using dihydroethidium, JC-1 (5,5′,6,6′-tetrachloro1,1′,3,3′-tetramethylbenzimidazolylcarbocyanine iodide), luciferase-based ATP bioluminescent assays, and transmission electron microscopy, respectively. Quantitative reverse transcription PCR and western blot assays were conducted to detect levels of mitochondrial fission-related factors. Glucose deprivation and reperfusion exposure significantly reduced the viability and induced apoptosis of SH-SY5Y cells, indicating that glucose deprivation and reperfusion exposure successfully induced cerebral ischemia–reperfusion injury. Glucose deprivation and reperfusion exposure also increased the degree of mitochondrial swelling, promoted an increase in superoxide, and decreased mitochondrial membrane potential and ATP enzyme levels. Cerebral ischemia–reperfusion injury also significantly increases Drp1 and Fis1 protein expression, reduces mitofusin-2 and optic atrophy 1 levels, increases nuclear receptor-related 1 and inverted formin-2 expression, and decreases yes-associated protein expression. Electron microscopy further revealed sparse mitochondria and broken cristae. However, these findings were reversed by liquiritin in a dose-dependent manner and were further abolished after carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone treatment. Our study suggests that the protective effects of liquiritin on cerebral ischemia–reperfusion injury are linked to nuclear receptor-related 1 upregulation, followed by the regulation of yes-associated protein-inverted formin-2-mitochondrial fission pathways. Liquiritin may represent a novel therapeutic agent for treating cerebral ischemia–reperfusion injury.Graphical

Acidovorax citrulli Type IV Pili PilR Interacts with PilS and Regulates the Expression of the pilA Gene

Acidovorax citrulli can cause bacterial fruit blotch of watermelon, melon, and other cucurbits, and has the potential to cause severe economic losses to growers throughout the world. This article investigated the functions and interactions of the pilR and pilS genes, two important genes in bacterial type IV pili systems, in A. citrulli. For each gene, deletion mutants and complementary strains were constructed via homologous recombination, and their phenotypes were determined. The results showed that the absence of pilR and pilS could significantly reduce the pathogenicity and twitching motility of A. citrulli while increasing the swimming motility, biofilm formation, and in vitro growth. Conversely, complementary strains were no different than the wild-type strain. Using quantitative reverse transcription PCR and promoter activity assays, we confirmed that the deletion of pilR and pilS genes leads to a significant decrease in the transcription level of pilA. Meanwhile, three methods including yeast two-hybrid, glutathione S-transferase pull-down, and luciferase complementation imaging assays were used to verify the direct interaction between the PilR and PilS proteins. These findings revealed the biological function of the pilR and pilS and confirms their regulatory role on pilA.

KCNH2A561V Heterozygous Mutation Inhibits KCNH2 Protein Expression via The Activation of UPR Mediated by ATF6.

The potassium channel protein KCNH2 is encoded by KCNH2 gene, and there are more than 300 mutations of KCNH2. Unfolded protein response (UPR) is typically initiated in response to an accumulation of unfolded and/or misfolded proteins in the endoplasmic reticulum (ER). The present study aimed to explore the UPR process and the role of activating transcription factor 6 (ATF6) in the abnormal expression of potassium voltage-gated channel subfamily H member 2 (KCNH2)A561V. The wild-type (wt) KCNH2 and A561V mutant KCNH2 was constructed with his-tag. The 293 cells were used and divided into KCNH2wt+KCNH2A561V, KCNH2wt and KCNH2A561V groups. The expression levels of ATF6 and KCNH2 in different groups were detected by Western blotting, reverse transcription-quantitative PCR, immunofluorescence and immuno-coprecipitation assays. The protein types and abundance of immuno-coprecipitation samples were analyzed by mass spectrometry. The proteomic analysis of the mass spectrometry results was carried out by using the reactome database and GO (Gene Ontology) tool. The mRNA expression levels of KCNH2 and ATF6 in the KCNH2wt+KCNH2A561V group were higher compared with the KCNH2A561V group. However, the full-length protein expression of ATF6 was inhibited, indicating that ATF6 was highly activated and a substantial number of ATF6 was sheared in KCNH2wt+KCNH2A561V group compared with control group. Furthermore, A561V-KCNH2 mutation leading to the accumulation of the immature form of KCNH2 (135 kDa bands) in ER, resulting in the reduction of the ratio of 155 kDa/135 kDa. In addition, the abundance of UPR-related proteins in the KCNH2A561V group was higher compared with the KCNH2wt+KCNH2A561V group. The 'cysteine biosynthetic activity' of GO:0019344 process and the 'positive regulation of cytoplasmic translation activity' of GO:2000767 process in the KCNH2A561V group were higher compared with the KCNH2wt+KCNH2A561V group. Hence, co-expression of wild-type and A561V mutant KCNH2 in 293 cells activated the UPR process, which led to the inhibition of protein translation and synthesis, in turn inhibiting the expression of KCNH2. These results provided a theoretical basis for clinical treatment of Long QT syndrome.

Long non‑coding RNA PEG13 regulates endothelial cell senescence through the microRNA‑195/IRS1 axis.

Atherosclerosis is a chronic inflammatory disease characterized by endothelial dysfunction and plaque formation. The present study aimed to elucidate the pathological role of the long non-coding RNA (lncRNA) paternally expressed 13 (PEG13) in the onset and progression of atherosclerosis. Specifically, its effects on human umbilical vein endothelial cell (HUVEC) proliferation, angiogenesis, senescence and senescence-associated secretory phenotype (SASP)-related factors were investigated using cell proliferation, cellular angiogenesis, β-galactosidase staining, reverse transcription-quantitative PCR and enzyme-linked immunosorbent assays. The results showed that oxidized low-density lipoprotein (ox-LDL) inhibited lncRNA PEG13 expression and HUVEC viability in a dose-dependent manner and PEG13 overexpression partially reversed these effects. Additionally, PEG13 overexpression ameliorated the ox-LDL-induced impairment of angiogenesis, cellular senescence and SASP. Furthermore, lncRNA PEG13 directly targeted microRNA (miR/miRNA)-195-5p, suppressing the ox-LDL-induced upregulation of the miRNA. The gene coding for insulin receptor substrate 1 (IRS1), an activator of the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway, was confirmed as a direct target of miR-195. PEG13 overexpression attenuated the ox-LDL-induced inhibition of IRS1 expression and PI3K/AKT signaling and its protective effects on HUVEC viability, angiogenesis and senescence were partially reversed by small interfering RNAs targeting IRS1. The present study demonstrated that lncRNA PEG13 attenuates ox-LDL-induced senescence in HUVECs by modulating the miR-195/IRS1/PI3K/AKT signaling pathway, suggesting a potential therapeutic target for the treatment of atherosclerosis.

Downregulation of TRPC6 regulates ERK1/2 to prevent sublytic C5b‑9 complement complex‑induced podocyte injury through activating autophagy.

Idiopathic membranous nephropathy (IMN) is a common glomerular disease, in which 50-60% of patients can progress to end-stage renal disease within 10-20 years, seriously endangering human health. Podocyte injury is the direct cause of IMN. Sublytic C5b-9 complement complex induces damage in podocytes' structure and function. In sublytic C5b-9 treated podocytes, the expression of canonical transient receptor potential 6 (TRPC6) is increased. However, the specific mechanism of TRPC6 in sublytic C5b-9 treated podocytes is unclear. The present study aimed to reveal the effect and mechanism of TRPC6 on sublytic C5b-9-induced podocytes. Normal human serum was stimulated using zymosan to form C5b-9. A lactate dehydrogenase release assay was used to examine C5b-9 cytotoxicity in podocytes. The RNA and protein expression levels were analyzed using reverse transcription-quantitative PCR, western blotting and immunofluorescent assay, respectively. Cell Counting Kit-8 assay and flow cytometry were carried out to test the viability and apoptosis of podocytes, respectively. Transmission electron microscopy was used to observe autophagic vacuole. F-actin was tested through phalloidin staining. Sublytic C5b-9 was deposited and TRPC6 expression was boosted in podocytes stimulated through zymosan activation serum. Knockdown of TRPC6 raised the viability and reduced the apoptosis rate of sublytic C5b-9-induced podocytes. Meanwhile, transfection of small-interfering (si)TRPC6 facilitated autophagy progression and enhanced the activation of cathepsin B/L in sublytic C5b-9-induced podocytes. The phosphorylation level of ERK1/2 was receded in siTRPC6 and sublytic C5b-9 co-treated podocytes. Moreover, the addition of the ERK1/2 activator partially reversed the effect of TRPC6 inhibition on sublytic C5b-9-induced podocytes. TRPC6 knockdown reduced the damage of sublytic C5b-9 to podocytes by weakening the ERK1/2 phosphorylation level to activate autophagy. These results indicated that targeting TRPC6 reduced the injury of sublytic C5b-9 on podocytes.

Evaluation of colorimetric RT-LAMP for screening of SARS-CoV-2 in untreated wastewater

This study compared reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and three reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays targeting the N and E genes of the SARS-CoV-2 genome for detecting RNA in untreated wastewater samples. RT-qPCR assays exhibited consistent amplification down to 2 × 102 GC/reaction, with greater analytical sensitivity at 2 × 101 GC/reaction by US CDC N1 and US CDC N2 assays. In contrast, RT-LAMP exhibited lower sensitivity, detecting SARS-CoV-2 only at or above 2 × 103 GC/reaction. For SARS-CoV-2 seeded wastewater samples, the US CDC N1 assay exhibited greater analytical sensitivity than the US CDC N2, E_Sarbeco, and RT-LAMP assays. Out of 30 wastewater samples, RT-qPCR detected endogenous SARS-CoV-2 RNA in 29 samples, while RT-LAMP identified 27 positive samples, with 20 displaying consistent amplifications in all three RT-LAMP technical replicates. Agreement analysis revealed a strong concordance between RT-LAMP and the US CDC N1 and E_Sarbeco RT-qPCR assays (κ = 0.474) but lower agreement with the US CDC N2 RT-qPCR assay (κ = 0.359). Quantification of SARS-CoV-2 RNA in positive samples revealed a strong correlation between the US CDC N1 and E_Sarbeco assays, while the US CDC N1 and US CDC N2 assays exhibited weak correlation. Logistic regression analysis indicated that RT-LAMP results correlated with RNA quantified by the US CDC N1 and E_Sarbeco assays, with 95 % limits of detection of 3.99 and 3.47 log10 GC/15 mL, respectively. In conclusion, despite lower sensitivity compared to RT-qPCR assays, RT-LAMP may offer advantages for wastewater surveillance, such as rapid results (estimated as twice as fast), and simplicity, making it a valuable tool in the shifting landscape of COVID-19 wastewater surveillance. Furthermore, LAMP positive wastewater samples might be prioritized for SARS-CoV-2 sequencing due to reduced analytical sensitivity. These findings support the use of RT-LAMP as a specific and efficient method for screening wastewater samples for SARS-CoV-2, particularly in resource-limited settings.

Development of highly sensitive one-step reverse transcription-quantitative PCR for SARS-CoV-2 detection in wastewater

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is a major public health concern that has highlighted the need to monitor circulating strains to better understand the coronavirus disease 2019 (COVID-19) pandemic. This study was carried out to monitor SARS-CoV-2 RNA and its variant-specific mutations in wastewater using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). One-step RT-qPCR using the SARS-CoV-2 Detection RT-qPCR Kit for Wastewater (Takara Bio), which amplified two N-gene regions simultaneously using CDC N1 and N2 assays with a single fluorescence dye, demonstrated better performance in detecting SARS-CoV-2 RNA (positive ratio, 66 %) compared to two-step RT-qPCR using CDC N1 or N2 assay (40 % each, and 52 % when combined), with significantly lower Ct values. The one-step RT-qPCR assay detected SARS-CoV-2 RNA in 59 % (38/64) of influent samples collected from a wastewater treatment plant in Japan between January 2021 and March 2022. The correlation between the concentration of SARS-CoV-2 RNA in the wastewater and the number of COVID-19 cases reported each day for 7 days pre- and post-sampling was significant (p < 0.05, r = 0.76 ± 0.03). Thirty-one influent samples which showed two-well positive for SARS-CoV-2 RNA were further tested by six mutations site-specific one-step RT-qPCR (E484K, L452R, N501Y, T478K, G339D, and E484A mutations). The N501Y mutation was detected between March and June 2021 but was replaced by the L452R and T478K mutations between July and October 2021, reflecting the shift from Alpha to Delta variants in the study region. The G339D and E484A mutations were identified in January 2022 and later when the incidence of the Omicron variant peaked. These findings indicate that wastewater-based epidemiology has the epidemiological potential to complement clinical tests to track the spread of COVID-19 and monitor variants circulating in communities.

Development of a one-step reverse transcription-quantitative polymerase chain reaction assay for the detection of porcine reproductive and respiratory syndrome virus.

Porcine reproductive and respiratory syndrome (PRRS) caused by PRRS virus (PRRSV) is an important disease that severely affects the swine industry and, therefore, warrants rapid and accurate diagnosis for its control. Despite the progress in developing diagnostic tools, including polymerase chain reaction (PCR)-based methods such as reverse transcription quantitative PCR (RT-qPCR) to diagnose PRRSV infection, its diagnosis at the genetic level is challenging because of its high genetic variability. Nevertheless, RT-qPCR is the easiest and fastest method for diagnosing PRRSV. Therefore, this study aimed to develop an RT-qPCR assay for rapid and accurate diagnosis of PRRSV by encompassing all publicly available PRRSV sequences. The developed assay using highly specific primers and probes could detect up to 10 copies of PRRSV-1 and -2 subtypes. Furthermore, a comparison of the performance of the developed assay with those of two commercial kits widely used in South Korea demonstrated the higher efficiency of the developed assay in detecting PRRSV infections in field samples. For PRRSV-1 detection, the developed assay showed a diagnostic agreement of 97.7% with the results of ORF5 sequencing, while for commercial kits, it showed 95.3% and 72.1% agreement. For PRRSV-2, the developed assay showed a diagnostic agreement of 97.7%, whereas the commercial kits showed 93% and 90.7% agreement. In conclusion, we developed an assay with higher accuracy than those of the tested commercial kits, which will contribute markedly to global PRRSV control.

Wolf-Hirschhorn syndrome candidate 1 (Whsc1) methyltransferase signals via a Pitx2-miR-23/24 axis to effect tooth development

Wolf-Hirschhorn syndrome (WHS) is a developmental disorder attributed to a partial deletion on the short arm of chromosome 4. WHS patients suffer from oral manifestations including cleft lip and palate, hypodontia, and taurodontism. WHS candidate 1 (WHSC1) gene is a H3K36-specific methyltransferase that is deleted in every reported case of WHS. Mutation in this gene also results in tooth anomalies in patients. However, the correlation between genetic abnormalities and the tooth anomalies has remained controversial. In our study, we aimed to clarify the role of WHSC1 in tooth development. We profiled the Whsc1 expression pattern during mouse incisor and molar development by immunofluorescence staining and found Whsc1 expression is reduced as tooth development proceeds. Using real-time quantitative reverse transcription PCR, Western blot, chromatin immunoprecipitation, and luciferase assays, we determined that Whsc1 and Pitx2, the initial transcription factor involved in tooth development, positively and reciprocally regulate each other through their gene promoters. miRNAs are known to regulate gene expression posttranscriptionally during development. We previously reported miR-23a/b and miR-24-1/2 were highly expressed in the mature tooth germ. Interestingly, we demonstrate here that these two miRs directly target Whsc1 and repress its expression. Additionally, this miR cluster is also negatively regulated by Pitx2. We show the expression of these two miRs and Whsc1 are inversely correlated during mouse mandibular development. Taken together, our results provide new insights into the potential role of Whsc1 in regulating tooth development and a possible molecular mechanism underlying the dental defects in WHS.

Antimicrobial and antibiofilm effects of essential fatty acids against clinically isolated vancomycin-resistant Enterococcus faecium.

Enterococcus faecium is a leading cause of hospital-acquired infections, which has become a serious public health concern. The increasing incidence of vancomycin-resistant E. faecium (VRE-fm) raises an urgent need to find new antimicrobial agents as a complement to traditional antibiotics. The study aimed to evaluate the antimicrobial and antibiofilm activity of essential fatty acids (EFAs) against VRE-fm, and further explore the molecular mechanism of the antibiofilm activity of EFAs. The microdilution broth method was used for antimicrobial susceptibility testing with traditional antibiotics and EFAs, including α-linolenic acid (ALA), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), linoleic acid (LOA), γ-linolenic acid (GLA), and arachidonic acid (AA). The effect of EFAs on cell morphology of VRE-fm was investigated by scanning electron microscopy. The crystal violet method was used to evaluate the antibiofilm activities of EFAs against VRE-fm. Furthermore, the expression of biofilm-related genes (acm, atlA, esp, and sagA) of VRE-fm isolates under the action of GLA was analyzed using quantitative reverse transcription PCR (qRT-PCR) assay. VRE-fm isolates were highly resistant to most traditional antibiotics, only highly susceptible to quinupristin-dalfopristin (90.0%), tigecycline (100%), and linezolid (100%). EPA, DHA, and GLA exhibited excellent antimicrobial activity. The MIC50/90 of EPA, DHA, and GLA were 0.5/1, 0.25/0.5, and 0.5/1 mM, respectively. SEM imaging showed that strain V27 adsorbed a large number of DHA molecules. Furthermore, all EFAs exhibited excellent inhibition and eradication activities against VRE-fm biofilms. The biofilm inhibition rates of EFAs ranged from 45.3% to 58.0%, and eradication rates ranged from 54.1% to 63.4%, against 6 VRE-fm isolates with moderate biofilm formation ability. GLA exhibited remarkable antibiofilm activity against VRE-fm isolates. The qRT-PCR analysis showed that GLA could significantly down-regulate the expression of the atlA gene (P < 0.01) of VRE-fm. DHA showed the strongest antibacterial activity, while GLA showed the strongest antibiofilm effect among the EFAs with antibacterial activity. Our novel findings indicate that the antibiofilm activity of GLA may be through down-regulating the atlA gene expression in VRE-fm. Therefore, DHA and GLA had the potential to be developed as therapeutic agents to treat infections related to multiple antimicrobial-resistant E. faecium.

Development and evaluation of PlasmoPod: A cartridge-based nucleic acid amplification test for rapid malaria diagnosis and surveillance.

Malaria surveillance is hampered by the widespread use of diagnostic tests with low sensitivity. Adequate molecular malaria diagnostics are often only available in centralized laboratories. PlasmoPod is a novel cartridge-based nucleic acid amplification test for rapid, sensitive, and quantitative detection of malaria parasites. PlasmoPod is based on reverse-transcription quantitative polymerase chain reaction (RT-qPCR) of the highly abundant Plasmodium spp. 18S ribosomal RNA/DNA biomarker and is run on a portable qPCR instrument which allows diagnosis in less than 30 minutes. Our analytical performance evaluation indicates that a limit-of-detection as low as 0.02 parasites/μL can be achieved and no cross-reactivity with other pathogens common in malaria endemic regions was observed. In a cohort of 102 asymptomatic individuals from Bioko Island with low malaria parasite densities, PlasmoPod accurately detected 83 cases, resulting in an overall detection rate of 81.4%. Notably, there was a strong correlation between the Cq values obtained from the reference RT-qPCR assay and those obtained from PlasmoPod. In an independent cohort, using dried blood spots from malaria symptomatic children living in the Central African Republic, we demonstrated that PlasmoPod outperforms malaria rapid diagnostic tests based on the PfHRP2 and panLDH antigens as well as thick blood smear microscopy. Our data suggest that this 30-minute sample-to-result RT-qPCR procedure is likely to achieve a diagnostic performance comparable to a standard laboratory-based RT-qPCR setup. We believe that the PlasmoPod rapid NAAT could enable widespread accessibility of high-quality and cost-effective molecular malaria surveillance data through decentralization of testing and surveillance activities, especially in elimination settings.

Synovium is a sensitive tissue for mapping the negative effects of systemic iron overload in osteoarthritis: identification and validation of two potential targets

BackgroundThe prevention and treatment of osteoarthritis (OA) pose a major challenge in its research. The synovium is a critical tissue in the systematic treatment of OA. The present study aimed to investigate potential target genes and their correlation with iron overload in OA patients.MethodsThe internal datasets for analysis included the microarray datasets GSE46750, GSE55457, and GSE56409, while the external datasets for validation included GSE12021 and GSE55235. The GSE176308 dataset was used to generate single-cell RNA sequencing profiles. To investigate the expression of the target genes in synovial samples, quantitative reverse transcription-PCR, western blotting, and immunohistochemical assay were conducted. ELISA was used to detect the levels of ferritin and Fe2+ in both serum and synovium.ResultsJUN and ZFP36 were screened from the differentially expressed genes, and their mRNA were significantly reduced in the OA synovium compared to that in normal synovium. Subsequently, complex and dynamically evolving cellular components were observed in the OA synovium. The mRNA level of JUN and ZFP36 differed across various cell clusters of OA synovium and correlated with immune cell infiltration. Moreover, ferritin and Fe2+ were significantly increased in the serum and synovium of OA patients. Further, we found that JUN elevated and ZFP36 decreased at protein level.ConclusionsThe synovium is a sensitive tissue for mapping the adverse effects of systemic iron overload in OA. JUN and ZFP36 represent potential target genes for attenuating iron overload during OA treatment. Some discrepancies between the transcription and protein levels of JUN suggest that post-transcriptional modifications may be implicated. Future studies should also focus on the roles of JUN and ZFP36 in inducing changes in cellular components in the synovium during OA pathogenesis.