PCR Method Research Articles

New insights into the role of the CHI3L2 protein in invasive ductal breast carcinoma

AbstractChitinase-like proteins have multiple biological functions that promote tumor growth, angiogenesis and metastasis. Expression of CHI3L2, which is similar in structure to CHI3L1, is detected in glioma cells and tumor-associated macrophages (TAMs) in glioma and breast cancer. However, its exact role remains unclear. We analyzed the expression of CHI3L2 in 74 invasive ductal breast carcinoma (IDC) tumors, breast cancer and macrophages cell cultures using immunohistochemistry, immunofluorescence, Western blot and PCR methods. Clinicopathologic data were included in the analysis. The results obtained show that CHI3L2 expression decreases with increasing degree of tumor grade and negative status of estrogen (ER) and progesterone receptors (PR). Furthermore, CHI3L2 is significantly and positively correlated with phosphorylation of STAT-3 and ERK1/2 signaling pathways, but negatively correlated with macrophage infiltration. CHI3L2 is expressed both in the cytoplasm of cancer cells and in macrophages and may regulate STAT-3 and ERK1/2 phosphorylation in breast cancer cell lines. Analysis of the clinicopathologic data revealed that CHI3L2 levels had no effect on patient survival. CHI3L2 expression may be specific for cancer cells in IDC and involved in cross-talk with the tumor microenvironment. Our study has shown that IDC cancer cells express the CHI3L2 protein, possibly indicating a novel function of this protein.

Improving onchocerciasis elimination surveillance: trials of odour baited Esperanza Window Traps to collect black fly vectors and real-time qPCR detection of Onchocerca volvulus in black fly pools

Abstract Background Entomological data for onchocerciasis surveillance relies on sampling black flies through human landing collectors in the field and laboratory testing of the flies for infection using pooled screening O-150 PCR-ELISA assay. Both techniques require improvements. This study aimed to optimize the Esperanza Window Trap (EWT) for black fly collection. We tested alternative carbon dioxide (CO2) mimics to attract black flies to the traps. Additionally, we evaluated new quantitative PCR (qPCR) methods that target mitochondrial DNA markers and have been proposed to enhance the sensitivity and specificity for detecting Onchocerca volvulus infections in blackflies. Methods Traps baited with low, medium and high release rates of either 2-butanone or cyclopentanone as CO2 mimics were field tested against traps baited with organically generated CO2 in four ecological zones in Nigeria: Guinea savannah, derived savannah, rainforest and montane forest. The performance of EWTs baited with CO2 or in combination with 2-butanone (low release) were subsequently evaluated against the human landing collection (HLC). Trap scaling was also pilot tested by comparing two EWTs to a single HLC team. Collected black flies were used to test detection of O. volvulus in black flies using Ov ND5 real-time PCR (qPCR) compared to the conventional pool screening O-150 PCR. Results EWTs baited with 2-butanone caught similar numbers of black flies (Simulium damnosum s.l.) to those baited with CO2, while cyclopentanone collected significantly fewer flies in all locations. The low release of 2-butanone was the most effective overall, although HLCs collected higher numbers of black flies than EWT baited with CO2 either singly or in combination with low-release 2-butanone. The combination of two EWTs baited with CO2 and deployed 100 m apart from each other collected similar numbers of flies as one HLC. More black fly pools were positive for O. volvulus by Ov ND5 qPCR compared with O-150 PCR in derived savannah (31.15 vs. 15.57%), montane forest (11.54 vs. 0%) and rainforest (23.08 vs. 2.56%), with only one positive pool in Guinea savannah detected by both methods. Conclusions The 2-butanone has potential to be used in xenomonitoring as a standardized replacement for organically generated CO2. Ov ND5 qPCR detected more positive pools than O-150 PCR. The positive pools found in foci hitherto considered to have interrupted/eliminated onchocerciasis highlight the need for more sensitive and specific methods that support programmatic assessments to identify and combat recrudescence. Graphical Abstract

Sexually transmitted infections in sexually abused children: an audit project to implement PCR tests in a child advocacy center in Türkiye

Background. Sexual abuse in children can sometimes result in sexually transmitted infections (STIs), which can serve as crucial forensic evidence. Although PCR methods are now accepted as the gold standard for STI screening, they have not yet widely replaced traditional culture methods in Türkiye. This study aims to assess the necessity of implementing PCR-based STI testing at Child Advocacy Centers in Türkiye, where such testing is not routinely available. Methods. Conducted between February and November 2023, this study included children who presented to the Child Advocacy Center of Marmara University Pendik Training and Research Hospital. High-risk victims were identified based on criteria including a history of penetrative sexual abuse and factors such as multiple perpetrators or significant age disparity. Serological tests and genital swabs were collected and analyzed using both bacterial culture methods and a comprehensive STI PCR panel. Results. The study included 20 victims, with a median age of 16 years. STI PCR testing detected pathogens in 19 out of 21 samples, including Chlamydia trachomatis (20%) and Neisseria gonorrhoeae (5%). In contrast, culture methods identified no sexually transmitted pathogens. Conclusion. PCR testing demonstrated significantly higher sensitivity for detecting STIs compared to traditional bacterial culture methods, as expected. Implementing PCR-based STI testing in Child Advocacy Centers is an urgent and essential need for providing an accurate diagnosis and robust forensic evidence, enhancing the care and legal protection of sexually abused children.

Does DNA extraction affect the specificity of a PCR method claiming the specific detectability of a genome-edited plant?

ABSTRACT Under current EU legislation, genetically modified organisms (GMOs) and derived food and feed products must be authorized as GM food, feed, or seed and appropriate detection methods must be made available for use in official controls. A Real-Time PCR method has recently been published by Chhalliyil et al. claiming to be specific for the detection and identification of genome-edited oilseed rape (OSR) lines commercialized in North America. In a previous study, we have independently assessed this method in three reference laboratories for sensitivity, specificity, and robustness. We found that the method does not meet all the minimum performance requirements (MPR) for GMO testing in the EU, which contradicts the claims of the method developer. Here we show, in addition to the previously published method assessment study that a modified DNA extraction is not the reason for the contradictory findings and does not affect the specificity of the method. We also discuss the procedures recently proposed by the method developers for interpreting PCR results with high Cq values.

Prevalence, genotyping and phylogenetic analysis of HPV infecting Palestinian women.

Human Papillomavirus (HPV) is a significant global public health concern due to its association with cervical, other anogenital, and oropharyngeal cancers. This study aimed to evaluate the prevalence and the phylogenetic relationships of HPV among Palestinian in order to inform public health strategies. A cross-sectional study was conducted between September 2023 and April 2024 involving 379 Palestinian women over the age of 18 from 11 governorates in the West Bank. Cervical swabs were collected and analyzed using nested PCR and Sanger sequencing methods to detect and genotype HPV. The study also included phylogenetic analysis to understand the genetic relationships between HPV strains. The overall HPV prevalence was 14.5%. The highest prevalence was observed in the 20-29 age group (19.6%), the Middle region of the West Bank (19.0%), and lower educational attainment. Genotyping revealed a diverse distribution of HPV types, with HPV 11 and HPV 6 being the most common low-risk types, while HPV 16 was the most common high-risk type. About 21.8% of the detected strains were high-risk strains. Phylogenetic analysis indicated significant regional clustering of HPV strains. The study highlights the need for targeted public health interventions, including vaccination and regular screening, particularly for younger women and those with lower educational attainment. Continued surveillance and research are essential to reduce the burden of HPV-related diseases in the West Bank, Palestine.

Live-Cell Imaging of miRNAs with the Combination of CHA and HCR Techniques.

The abnormal expression of miRNA-21 is closely related to many cancers, and its sensitive detection plays an important role in the diagnosis and treatment of cancers. In the report, we designed a non-enzymatic amplification sensing system based on the catalytic hairpin assembly (CHA) and palindrome-based hybridization chain reaction (PHCR) technique for the detection and imaging of miRNA in living cells. Based on PHCR technology, two ingeniously designed palindrome-contained fluorescently labeled hairpin probes are sequentially opened upon the stimulation of short oligonucleotide triggers, promoting the autonomous assembly of cross-linked network-like structures (CNSs) and generating fluorescence resonance energy transfer (FRET) signal. Moreover, the PHCR technique can be combined with CHA technology to sufficiently improve amplification efficiency and signal output. By utilizing the CHA-PHCR sensing system, one miRNA-21 activates many triggers through CHA process and in turn initiates the assembly of CNSs by PHCR reaction, efficiently amplifying the FRET signal output. As such, the sensing system can detect target miRNAs down to 10pm with high detection specificity. Moreover, the CNS exhibits the enhanced intracellular stability, enabling the living cell imaging of miRNA-21. The CHA-PHCR sensing system can also screen the expression level of miRNA-21 in different living cells and differentiate cancer cells from healthy cells, which is consistent with the gold-standard PCR method.

Abstract A035: A real-time PCR method for the detection of cancer-specific methylation patterns in cfDNA

Abstract Non-invasive liquid biopsy tests are proving to be the next frontier in cancer diagnostics with methylation emerging as a reliable biomarker for low levels of circulating tumor DNA (ctDNA). There is a rising interest in sensitive, low-cost liquid biopsy assays to detect low copies of hypermethylated ctDNA in an excess background of non-cancer-associated hypomethylated cell- free DNA (cfDNA). Real-time quantitative methylation-specific PCR (qMSP) allows for the detection of low abundance methylated fragments. qMSP approaches have previously been developed but are predominantly designed to target a specific CpG site. To date we are not aware of any qMSP approaches that target pan-cancer-associated methylation patterns across multiple CpG sites. Harbinger Health has developed a qMSP method with locked nucleic acid (LNA) blockers that target methylation haplotypes, allowing for multiplex enrichment and quantification of cancer-specific methylation patterns. Using targeted bisulfite sequencing, we identified ten pan-cancer-informative CpG-dense regions which showed consistent contiguous elevated methylation states in cancer cfDNA and low levels of methylation in non-cancer cfDNA. We designed qMSP assays for these regions and LNA blockers which bind to unmethylated target CpG sites, outcompeting the hydrolysis probe through a high Tm differential. This prevented non-specific probe hybridization. The qMSP-LNA assays were evaluated in simplex and multiplex using cell line DNA in a titration of hypermethylated “ctDNA” spiked into hypomethylated “cfDNA” to simulate varying ctDNA levels, and then validated with cancer and non-cancer cfDNA samples at 5 ng input, equivalent to 1450 haploid copies. The percentage of methylated DNA was estimated by the ratio of methylated copies (qMSP-LNA) to total copies (internal reference), which were quantified by standard curves. The qMSP-LNA assays detected low abundance methylated DNA fragments down to 23 target copies. LNA blockers completely depleted background signal originating from unmethylated DNA with high specificity, showing no inhibition of methylated DNA detection. When tested in cfDNA samples which varied in conversion efficiency, discordant methylation states, and methylation abundance, the assays reproducibly amplified and detected highly methylated fragments which correspond to cancer signal. Harbinger Health has developed qMSP-LNA assays for contiguous CpG biomarkers which differentiate cancer and non-cancer samples from only ten pan-cancer-informative regions. The qMSP-LNA method detected low abundance fragments with specific methylation patterns with high specificity and sensitivity. The assay reproducibly detected methylated DNA in cfDNA samples that represent a clinically relevant range of methylation signal and will be further validated in a larger cohort of cancer and non-cancer cfDNA samples. Due to the high specificity and sensitivity, this cost-effective PCR method may provide utility and improve access for early cancer detection and monitoring. Citation Format: Emily Neaga, Caitlin Gilley, Sarah Falotico, Mayur Gurnani, Zhenyu Zhang, Jocelyn Charlton, Miguel Williams, Anthony Shuber. A real-time PCR method for the detection of cancer-specific methylation patterns in cfDNA [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A035.

Expression levels of some genes in the MAPK pathway (DUSP1, DUSP2, DUSP4, DUSP6 and DUSP10) in eyelid tumor tissue

Abstract Objectives To control mitogen-activated protein kinases (MAPK) signaling pathways involved in the onset and progression of cancer, dual specificity phosphatases (DUSPs/MKP) are essential. This study seeks to detect the correlation between eyelid tumors and the genes DUSPs, known for their influence on MAPK signaling pathways. Additionally, we aim to juxtapose our findings with analyses from various bioinformatics databases. Methods Expression levels of relevant genes in cDNA samples were determined by quantitative PCR method. Open-access databases were used for mutation analysis of relevant genes, mRNA expression changes, and survival analyses, and the STRING database was used for protein-protein interactions. Results It was found that the expression of DUSP1 and DUSP2 showed a significant decrease in the tumor tissue, while a significant increase was detected in the DUSP4 and DUSP6 genes. Additionally, when we compared the study genes with the Cancer Genome Atlas program cancer cohorts, it was found that the DUSP1 and DUSP10 gene expression profiles were downregulated in uveal melanoma compared to other cancer cohorts. Conclusions Significant and obvious changes were observed in the DUSP genes we studied in eyelid tumors. However, the relationship between these genes and cancer must be studied more. Considering that these enzymes are effective in cell proliferation, differentiation, and apoptosis, it would be appropriate to plan comprehensive studies on their interactions with other proteins they interact with in the MAPK pathway.

Specific detection of duck adeno-associated virus using a TaqMan-based real-time PCR assay

Duck adeno-associated Virus (DAAV) is a novel pathogen that was recently discovered in ducks. To establish a molecular detection assay for DAAV for further epidemiological investigation and pathogenic mechanism. Here, we designed specific primers and probes according to the sequence characteristics of the newly discovered DAAV and then established a TaqMan real-time PCR method (TaqMan-qPCR) for the detection of DAAV. Our data showed that the established TaqMan-qPCR for detecting DAAV had high sensitivity, with the lowest detection limit of 29.1 copies/μL. No cross reaction was found with duck circovirus (DuCV), H9N2 subtype avian influenza virus (AIV), avian Tembusu virus (ATmV). duck hepatitis A virus 1 and 3 (DHAV-1 and DHAV-3), duck adenovirus A (DAdV-A), duck adenovirus 3 (DAdV-3), or duck enteritis virus (DEV). The repeatability was excellent, with the coefficients of variation of repeated intragroup and intergroup tests ranging from 0.12–0.21% and 0.62–1.42%, respectively. Seventy-eight clinical samples collected from diseased or deceased ducklings were tested. The results showed that the DAAV positive rate was 21.79%, and a triple infection (DAAV+MDPV+GPV) was found. These data provide technical support for further molecular epidemiological surveillance and pathogenic mechanism studies of DAAV infection.

Large, but short-term, increase in fecal indicator bacteria following extreme flooding from Hurricane Harvey in Houston, TX

Hurricane Harvey caused widespread flooding along the Texas Gulf Coast in August 2017; some areas of Houston received >150 cm of rainfall within a few days. Due to concerns over fecal contamination of floodwaters, surface water samples were collected at six locations in the southeastern Houston area immediately before and after the hurricane and then every 1 to 2 weeks thereafter over a 2-month period. Total E. coli was enumerated using the IDEXX Quanti-Tray/2000 system. DNA extracted from water samples was analyzed via quantitative real-time PCR (qPCR) for general and source-specific total Bacteroidales and human Bacteroidales markers, and digital PCR (dPCR) for antibiotic resistance genes (ARG) and a plasmid (pBI143) associated with human waste. SourceTracker2 was used to determine human source contributions based on metagenomic analysis of PCR-amplified 16S rRNA gene fragments. Samples collected immediately after the hurricane had elevated levels of E. coli, ranging from 488 to 1,733 CFU 100 ml−1. After 1 week, E. coli levels decreased to <100 MPN 100 ml−1. Total Bacteroidales numbers were elevated immediately following the hurricane and remained high for 12 days. Human-source contributions, as assessed by PCR methods and metagenomic analysis, peaked within 12 days after the hurricane consistently across all sampling sites. Multiple regression analysis of environmental parameters, copies of ARG and pBI143, and metagenomic data confirmed that human waste caused the dramatic, short-term, high levels of fecal contamination of floodwaters generated by Hurricane Harvey. Fecal indicators approached normal background levels approximately 3 weeks after the rainfall ended.

Application of the Electrical Microbial Growth Analyzer Method for Efficiently Quantifying Viable Bacteria in Ready-to-Eat Sea Cucumber Products

Accurate and efficient quantification of viable bacteria in ready-to-eat food products is crucial for food safety and public health. The rapid and accurate assessment of foodborne bacteria in complex food matrices remains a significant challenge. Herein a culture-based approach was established for easily quantifying viable bacteria in ready-to-eat sea cucumber (RSC) products. Samples of the liquid companion within the package were directly transferred into test tubes to determine bacterial growth curves and growth rate curves, utilizing the electrical microbial growth analyzer. Viable bacteria in the samples were then quantified based on the time required to attain the maximum growth rate indicated on the growth rate curve. At a concentration of 5.0 × 103 CFU/mL of viable bacteria in the liquid companion, the recovery rates were 108.85–112.77% for Escherichia coli (E. coli) and 107.01–130.54% for Staphylococcus aureus (S. aureus), with standard deviations of 1.60 and 3.92, respectively. For the solid content in the package, the quantification was performed using the same methodology following an additional homogenization step. At a concentration of 5.0 × 103 CFU/mL of viable bacteria in the sample, the recovery rates were 91.94–102.24% for E. coli and 81.43–104.46% for S. aureus, with standard deviations of 2.34 and 2.38, respectively. In instances where the viable bacterial concentration was 5.0 × 103 CFU/mL in RSC products, the total time required for the quantification did not exceed 10.5 h. This method demonstrated advantages over traditional plate counting and PCR methods regarding simplicity and efficiency, representing a promising alternative for the quantification of viable bacteria in food like RSC products.

Diagnostic Value of Cross-Priming Amplification Combined with CRISPR-Cas12b in Detecting Cell-Free DNA in Tuberculous Pleural Effusion

Abstract Background Diagnosis of tuberculous pleural effusion (TPE) remains challenging. Studies have shown that detecting cell-free Mycobacterium tuberculosis DNA (cf-TB) in pleural effusion can improve TPE diagnosis. This study aimed to evaluate the diagnostic value of our recently developed Cross-Priming Amplification (CPA) combined with CRISPR-Cas12b (TB One-Pot) assay in detecting cf-TB for TPE. Methods Pleural effusion samples were collected from suspected TPE inpatients at Hangzhou Red Cross Hospital. After centrifugation, the precipitate was used for culture, Xpert, and pleural effusion cytological testing, while the supernatant was used for biochemical and cf-TB assays (including TB One-Pot and the quantitative PCR method (cf-TB-PCR)). Diagnostic performance was assessed based on a comprehensive reference standard (CRS). Results A total of 115 patients were included, comprising 88 CRS-diagnosed TPE cases and 27 non-TPE cases. The sensitivity of TB One-Pot in detecting pleural cf-TB for diagnosing TPE was 64.8%, with an area under the curve (AUC) of 0.805, significantly superior to culture and Xpert (P <0.05). Compared with cf-TB-PCR (sensitivity: 53.4%, AUC: 0.767) and ADA (sensitivity: 52.3%, AUC: 0.761), TB One-Pot demonstrated slightly higher sensitivity and AUC, but the differences were not statistically significant (P >0.05). The specificity of TB One-Pot was 96.3%, while the specificity of other tests was 100%, with no statistically significant differences (P > 0.05). Conclusions cf-TB provides direct evidence of the etiology of TPE. TB One-Pot for detecting cf-TB in diagnosing TPE outperforms existing TB laboratory tests and may represent a more effective approach for TPE diagnosis in resource-limited settings.

Effects of TABATA Exercise Volume and Royal Jelly Supplementation on NLRP3 Inflammasome and lncRNA-H19 Expression in Obese Men

Background: Both coding and long non-coding RNAs (lncRNAs) have emerged as vital regulators in almost every cellular process, and their expression can be modulated by external stimuli, such as physical exercise. Objectives: The current research aimed to investigate the effects of different volumes of TABATA-high-intensity interval training (HIIT) exercises combined with royal jelly (RJ) supplementation on the NLRP3 inflammasome and lncRNA-H19 expression in obese males. Methods: Forty-two healthy men [Body Mass Index (BMI) = 30 kg/m², waist-to-hip ratio = 0.95, age range: 40 - 60 years] volunteered to participate in the study. The individuals were randomly divided into five experimental groups (N = 35) and one control + placebo group (N = 7). The high-volume (HV) or low-volume (LV) TABATA exercise programs were performed twice a week for 8 weeks. Participants in the RJ supplementation groups received a 1000 mg capsule once a day for 8 weeks. The expression of NLRP3 and lncRNA-H19 genes was evaluated using the real-time PCR method. Results: The NLRP3 gene expression in the Bruce test, measured before and after the 8-week exercise interventions and RJ supplementation, showed insignificant changes across the different groups. However, the H19 gene expression in the Bruce test showed a significant reduction in the HV-TABATA HIIT intervention groups, which was more pronounced than in the LV groups after 8 weeks: HV group (P = 0.004), RJ group (P = 0.001), HV + RJ group (P = 0.007), and LV + RJ group (P = 0.002). After 8 weeks of non-pharmacological interventions involving exercise training and supplementation, a significant decrease in NLRP3 and a significant increase in H19 gene expression were detected in the HV group compared to the LV group (P = 0.05 and P = 0.010). Significant improvement was also found in the resting H19 levels between the RJ and LV groups (P = 0.011) and the LV + RJ group (P = 0.44). Moreover, a significant reduction in resting NLRP3 gene expression was observed between the RJ + LV and LV groups (P = 0.038). Conclusions: Chronic HV TABATA HIIT exercise, when combined with RJ supplementation, is effective in attenuating inflammatory responses to acute stress.

Parental Reconstruction from a Half-Sib Population of Stoneless Jujube Ziziphus jujuba Mill. Based on Individual Specific SNP Markers Using Multiplex PCR

The selection of unique and individual-specific SNPs is important as compared with universal SNPs for individual identification. Therefore, the main significance of this research is the selection of specific SNPs in male parent and the identification of offspring with these specific SNPs in their genome by multiplex PCR, which is utilized for genotyping of 332 half-sib plants of Ziziphus jujuba.This cost-effective method makes as much as possible to utilize the same amount of each pair of various targeted loci primers. After PCR amplification of targeted genome parts, the mixed products can be directly used in a next-generation sequencing platform. We concomitantly amplified 10 unique SNP loci at 10 different chromosomes of male JingZao 39 plants in 332 half-sib plants and sequenced them on the Illumina Novaseq 6000 platform. Analysis of SNP genotyping accuracy of 332 half-sib plants showed that all 10 unique SNPs in all 332 plants were correctly amplified in this multiplex PCR method. Furthermore, based on Mendelian inheritance, we identified 124 full-sib plants that have 10 unique SNPs in their genomes. These results were further confirmed by whole genome resequencing of 82 randomly selected half-sib plants, and the identity-by-descent values of all full-sib plants were between 0.4399 to 0.5652. This study displayed a cost-effective multiplex PCR method and proper identification of pollen parent through specific SNPs in half-sib progenies and firstly obtained a full-sib population between ‘Wuhezao’ and ‘JingZao 39’, segregating for stone and stoneless fruit.

Selection of optimal extraction and RT-PCR protocols for stool RNA detection of colorectal cancer associated immune genes

There is a growing interest in using fecal mRNA transcripts as biomarkers for non-invasive detection of colorectal cancer (CRC). The following study compares different RNA extraction and reverse transcription PCR (RT-PCR) methods for mRNA detection in stool and identifies a robust and sensitive protocol. A combination of the Stool total RNA purification kit (Norgen) and the Superscript III one-step RT-PCR kit (Invitrogen) provided high RNA purity and sensitive and consistent mRNA detection, making them well-suited candidates for large-scale studies. We tested the protocol by detecting the mRNA of several immune genes (CXCL1, IL8, IL1B, IL6, PTGS2, and SPP1) in 22 CRCs, 24 adenomatous polyps, and 22 control stool samples. All these inflammatory markers, except for CXCL1, showed a strong association with CRC. Cancer stool samples showed increased levels of IL1B, IL8, and PTGS2 transcripts compared to polyp and control groups. Thus, this work supports the potential use of fecal mRNA as biomarkers for CRC detection.

Salmonella enterica Enteritidis and Heidelberg serotype-specific molecular detection in poultry samples by a rapid isothermal method

ABSTRACT 1. Loop-mediated isothermal amplification (LAMP) assays were developed to detect Salmonella enterica subspecies enterica serotypes Enteritidis and Heidelberg in poultry farms. These serotype-specific methods were evaluated in comparison with PCR in the analysis of different Salmonella spp. serotypes from a culture collection and poultry farm samples. 2. The results demonstrated the specific amplification of the genetic targets safA in all S. Enteritidis (n = 10) and ACF69659 in all S. Heidelberg (n = 36) isolates from the culture collection. The remaining isolates from other Salmonella spp. serotypes (n = 84) and bacterial species (n = 8) were negative in both LAMP assays. 3. The methods detected DNAs from S. Enteritidis and S. Heidelberg after a single-step pre-enrichment in buffered peptone water of the poultry samples, which agreed with previously developed PCR methods to detect these same two serotypes. 4. In conclusion, LAMP assays were useful for rapid serotype-specific detection, being suitable for surveillance purposes in resource-limited environments such as poultry farms.

Imipenem exposure influence the expression of quorum sensing receptor sdiA in Escherichia coli.

The increasing trend of carbapenem resistance amongst Escherichia coli poses a major public health crisis and requires active surveillance of resistance mechanisms to control the threat. Quorum Sensing system plays a role in bacterial resistance to antibiotics. Quorum Sensing is a cell-cell communication system where bacteria alter their gene expression in response to specific stimuli. Here, in this study we investigated the transcriptional response of quorum sensing receptor, sdiA in E.coli under sub-inhibitory concentration of carbapenem in presence of quorum sensing signal molecules. Two E.coli isolates harbouring blaNDM were subjected to treatment with 10% SDS for 20 consecutive days of which blaNDM encoding plasmid was successfully eliminated from one isolate. Both the wild type and the cured mutant were then allowed to grow under eight different inducing conditions and the transcriptional response of sdiA gene was studied by quantitative real time PCR method. We found different response levels of sdiA in wild type and cured mutant under exogenous AHL and imipenem and when co-cultured with P.aeruginosa under imipenem stress. This study highlighted that sub-inhibitory concentration of imipenem in combination with AHL is acting as signal to SdiA, a quorum sensing receptor in E.coli.

Development of a novel strategy to reduce diagnostic errors in real-time polymerase chain reaction using probe-based techniques

Real-time PCR assays are valuable tools for the rapid and accurate diagnosis of infectious diseases by identifying the nucleic acid sequences of pathogens. Here, we aimed to develop a recombinant plasmid-based standard for validating the sensitivity of different molecular diagnostic methods adopting the Jonstrup assay (J assay). Chimeric plasmid DNA (cpDNA) harboring various pathogen genes and the target site of the J assay was constructed. Our findings revealed that the J assay could detect a single copy of the target gene similar to digital droplet PCR. The detection sensitivity of each established real-time PCR method for various disease diagnoses was evaluated using the cpDNA. Although most methods showed high sensitivity, similar to that of the J assay, the VHS Garver and SARS-CoV-2 diagnostic methods exhibited detection sensitivities tenfold lower than that of the J assay. To ensure accuracy of results and avoid genetic contamination from positive controls, we introduced an additional probe attachment site emitting distinct fluorescent signals within the cpDNA. Target genes and exogenous sequences within the plasmid DNA were simultaneously detected in a single assay using this unique method. Our approach will help improve the sensitivity of diagnostic methods and develop novel diagnostic methods based on molecular techniques.

Synthesis and Characterization of Thymol Carbon Nanodot Functionalized Silver Nanoparticles (ThCND-AgNPs) and Evaluation of Their Antiproliferative, Anti-Invasive, and Apoptotic Effects on OVCAR-3 Ovarian Cancer Cells.

Ovarian cancer belongs to the category of gynecological malignancies and unfortunately holds the distinction of being the most aggressive among them. It is ranked as the fifth highest cause of cancer-related deaths in women worldwide. The utilization of metal nanoparticles (NPs) linked with natural herbal molecules in biomedical applications has been on the rise. Thymol carbon nanodot functionalized silver nanoparticles (ThCND-AgNPs) were synthesized in an original manner and subjected to thorough characterization, including analysis of their size, morphology, and elemental composition. The aim of this study is to investigate the effects of the ThCND-AgNPs on cell proliferation, invasion, and apoptotic gene expressions in OVCAR-3 ovarian cancer cells. The effect of ThCND-AgNPs on cell viability in OVCAR cells was determined in a dose- and time-dependent manner using the XTT method. The effect on the expression changes of apoptotic-related genes was assessed through the Real-time PCR method, while the anti-invasive activity was measured using the matrigel invasion chamber assay. The ThCND-AgNP molecule exhibited a dose- and time-dependent reduction in cell proliferation in OVCAR-3 cells. The IC50 values were determined to be 388.53 μg/mL at 24 h and 145.683 μg/mL at 48 h. Furthermore, the molecule was found to reduce cell invasion by 51.12% compared with the control group in OVCAR-3 cells. In terms of apoptotic-related genes, Bcl-2 expression was downregulated, while BAX, CASPASE-3, -8, and -9 expressions were unregulated. In conclusion, the obtained data reveal the potential antiproliferative, apoptotic, and anti-invasive effects of our original ThCND-AgNP molecule in ovarian cancer. While these results need further confirmation through more detailed experiments, they will provide insights for future studies.

Biochemical investigation of FOXP3 genetic polymorphism and its association with biochemical parameters in pre-eclampsia patients.

This study addresses the pivotal question of the association between FOXP3 gene polymorphism and pre-eclampsia (PE), employing the Tetra ARMS PCR method for analysis. PE, a multifaceted disorder marked by hypertension and organ dysfunction during pregnancy, led to an exploration of FOXP3 due to its integral role in immune regulation and its implication in various autoimmune and inflammatory disorders. The primary objective was to discern the relationship between FOXP3 gene polymorphism (rs2232365) and the risk of PE. Recruiting 200 PE patients and 100 healthy pregnant women as controls, genomic DNA was extracted from peripheral blood samples, and FOXP3 promoter region polymorphism was meticulously examined using the Tetra ARMS PCR method. The results revealed significant differences in FOXP3 gene polymorphism between PE patients and healthy controls. Specifically, certain alleles and genotypes were more frequent in PE patients, suggesting a potential genetic predisposition to this disorder. Our findings showed that rs2232365 A/G variant was found to be associated with PE under the overdominance model [OR=1.89, CI 95%= 0.99-3.60, P<0.05]. The heterozygous genotype (A/G) of FOXP3 (rs2232365) was associated with increasing the level of clinical and biochemical markers in mild and severe PE patients when compared to controls. Thus, the FOXP3 (rs2232365) A/G variant can be considered a substantial risk factor for PE.