Real-time TaqMan Research Articles

Genetic Associations of Plasminogen Activator Inhibitor-1-Related miRNA Variants with Coronary Artery Disease.

Coronary artery disease (CAD) is one of the most common types of cardiovascular disease and can lead to a heart attack as plaque gradually builds up inside the coronary arteries, blocking blood flow. Previous studies have shown that polymorphisms in the PAI-1 gene are associated with CAD; however, studies of the PAI-1 3'-untranslated region, containing a miRNA binding site, and the miRNAs that interact with it, are insufficient. To investigate the association between miRNA polymorphisms and CAD in the Korean population based on post-transcriptional regulation, we genotyped five polymorphisms in four miRNAs targeting the 3'-untranslated region of PAI-1 using real-time PCR and TaqMan assays. We found that the mutant genotype of miR-30c rs928508 A > G was strongly associated with increased CAD susceptibility. In a genotype combination analysis, the combination of the homozygous mutant genotype (GG) of miR-30c rs928508 with the wild-type genotype (GG) of miR-143 rs41291957 resulted in increased risk for CAD. Also, in an allele combination analysis, the combination of the mutant allele (G) of miR-30c rs928508 and the wild-type allele (G) of miR-143 rs41291957 resulted in increased risk for CAD. Furthermore, metabolic syndrome and diabetes mellitus showed synergistic effects on CAD risk when combined with miR-30c rs928508. These results can be applied to identify CAD prognostic biomarkers among miRNA polymorphisms and various clinical factors.

Enhanced Transcription of Human Endogenous Retroviruses and TRIM28 Downregulation in Patients with Inflammatory Bowel Disease.

Inflammatory bowel disease (IBD) includes patients affected by Crohn's disease or ulcerative colitis. IBD is thought to be a chronic immune-mediated disease, but its origin remains elusive, and this limits new therapeutic approaches. Human endogenous retroviruses (HERVs) originate from ancestral infections and represent 8% of the human genome. HERVs are no longer infectious, but some retroviral sequences can be activated, and their aberrant expressions have been implicated in inflammatory and autoimmune disorders. HERV transcription is regulated by TRIM28 and SETDB1, which are also directly involved in epigenetic processes and modulation of the immune response. Using a PCR real-time Taqman amplification assay, we assessed, for the first time, the transcription levels of pol genes of HERV-H, -K, and -W families of env genes of syncytin 1 (SYN1), SYN2, and HERV-W, as well as of TRIM28 and SETDB1 in the whole blood of 48 patients with Crohn's disease (CD), 20 with ulcerative colitis (UC), and in healthy controls (HC) of comparable age. The transcriptional levels of HERV-H-pol (p = 0.0003) and HERV-K-pol (p = 0.001) were significantly higher in IBD patients compared with HC, with no differences between patients with CD and UC. No significant differences were found for the remaining HERVs between IBD patients and HC. The transcript levels of TRIM28 were significantly downregulated in IBD patients (p < 0.001), without differences between CD and UC, while the SETDB1 levels were preserved. The enhanced transcription of HERV-H-pol and HERV-K-pol, as well as the impaired activation of TRIM28, were not influenced by clinical disease activity and type of treatment. The overexpression of HERVs and impaired transcription of TRIM28 in patients affected by CD or UC suggest that they might be the main actors in the pathophysiology of IBD, opening the way to innovative targeted interventions.

&lt;i&gt;CDKN2B-AS1&lt;/i&gt; polymorphism rs1333049 is associated with advanced carotid artery atherosclerosis in a Slovenian population

Several studies have reported an association between the 9p21 region in the human genome and atherosclerosis. The rs1333049 polymorphism is a single nucleotide polymorphism (SNP) in CDKN2B-AS1, located in the 9p21 region. The aim of our study was to investigate the association between the rs1333049 polymorphism and advanced carotid atherosclerosis, as well as its effect on CDKN2B expression in endarterectomy sequesters. In our case-control study, we included 881 participants, divided into two groups. The case group comprised 308 participants with advanced atherosclerosis of the internal or common carotid artery (stenosis &gt; 75 %) who underwent a revascularization procedure. The control group included 573 participants without hemodynamically significant carotid atherosclerosis. We analyzed the rs1333049 polymorphism using the StepOne real-time polymerase chain reaction (PCR) and TaqMan SNP genotyping assay. We found a statistically significant association according to the co-dominant (P=0.014, OR=3.29, 95% CI: 1.32-8.91, and P=0.015, OR=2.50, 95% CI: 1.22-5.37) and dominant (P=0.006, OR=2.74, 95% CI: 1.36-5.71) models. We performed immunohistochemical analysis of CDKN2B expression on 26 endarterectomy sequesters. The C allele of rs1333049 was associated with a lower numerical area density of CDKN2B-positive cells in atherosclerotic plaques. In conclusion, the C allele of the rs1333049 SNP is associated with an increased risk of developing advanced carotid atherosclerosis and lower CDKN2B expression in the plaques.

Droplet Digital PCR for Acinetobacter baumannii Diagnosis in Bronchoalveolar Lavage Samples from Patients with Ventilator-Associated Pneumonia.

Advanced diagnostic technologies have made accurate and precise diagnosis of pathogens easy. Herein, we present a new diagnostic method, droplet digital PCR (ddPCR), to detect and quantify Acinetobacter baumannii in mini bronchoalveolar lavage (mini-BAL) samples. A. baumannii causes ventilator-associated pneumonia (VAP), a severe healthcare infection affecting patients' lungs. VAP carries a high risk of morbidity and mortality, making its timely diagnosis crucial for prompt and effective management. Methodology. The assay performance was evaluated by comparing colonization data, quantitative culture results, and different generations of PCR (traditional PCR and Real-Time PCR-qPCR Taqman® and SYBR® Green). The ddPCR and qPCR Taqman® prove to be more sensitive than other molecular techniques. Reasonable analytical specificity was obtained with ddPCR, qPCR TaqMan®, and conventional PCR. However, qPCR SYBR® Green technology presented a low specificity, making the results questionable in clinical samples. DdPCR detected/quantified A. baumanni in more clinical samples than other methods (38.64% of the total samples). This emerging ddPCR technology offers promising advantages such as detection by more patients and direct quantification of pathogens without calibration curves.

Association of FOXO3 (rs17069665) gene polymorphism and childhood acute lymphoblastic leukemia in Egypt

BackgroundAcute lymphoblastic leukemia (ALL) is the most common malignancy in children. Genetic variations, particularly gene polymorphisms, have been closely linked to increased susceptibility to ALL. One of those genes is Forkhead box O3 (FOXO3), which is considered a potential tumor suppressor gene. AimThis study intended to examine the potential significance of the FOXO3 (rs17069665) single nucleotide polymorphism (SNP) as a risk factor for childhood ALL, in addition to its effect on the laboratory results, clinical manifestations and the clinical outcome after induction of chemotherapy. Subjects and methodsSixty-six newly diagnosed ALL children and 70 healthy children of matched age and sex as controls were recruited. FOXO3 (rs17069665) polymorphism was detected using TaqMan real time PCR. ResultsHigher frequencies of the (AG) genotype and G-allele of FOXO3 (rs17069665) variant were present in ALL patients in comparing with the controls (16.7 % vs. 4.3 %, p = 0.017 and 11.4 % vs. 2.1 %, p = 0.003, respectively). The frequencies of the FOXO3 (rs17069665) SNP reflected a noticeably higher risk of ALL under diverse genetic models, including the co-dominant model (AG vs. AA, OR = 2.55), dominant (AG + GG vs. AA, OR = 2.81), and allelic (G-allele vs. A-allele, OR = 2.9) models. The single case of c-MYC mutation was observed with the (GG) genotype. No significant association between FOXO3 (rs17069665) SNP polymorphism and response to chemotherapy was found. ConclusionOur findings showed that the FOXO3 (rs17069665) polymorphism was associated with a greater incidence of ALL in Egyptian children, which might be a potential biomarker for ALL susceptibility.

Association of glutamine synthetase polymorphisms rs2296521, rs10911021 and rs12136955 with plasma ammonia concentration in valproic acid-treated Egyptian epilepsy patients.

The use of valproic acid (VPA) in the treatment of some psychiatric and neurological disorders such as bipolar disorder, migraines, and epilepsy is associated with hyperammonemia. However, the mechanism of this negative effect of VPA is unclear. In this study, we investigate gene glutamate-ammonia ligase (GLUL) polymorphisms for the glutamine synthetase (GS) enzyme, a key enzyme that catalyzes the removal of ammonia by incorporating it with glutamate to form glutamine, and we investigate whether it has a relationship with the emergence of hyperammonemia during VPA-based therapy. We enrolled 180 Egyptian epilepsy patients in this study. Patient history, general and neurological examination and blood samples from arm veins were taken. Real time TaqMan PCR polymorphism for three polymorphism SNPs (rs2296521, rs10911021 and rs12136955) of GLUL was done. We assessed the relationship between the patient features, including three GLUL polymorphisms, and the development of hyperammonemia during VPA-based therapy. We found that the ammonia levels showed a positive correlation with VPA treatment duration (p = 0.015) and a negative correlation with carbamazepine total dose per day (p = 0.027) and with WBCs count (p = 0.026). Also, female patients having rs2296521 SNPs with the A allele and patients having rs10911021 SNPs with the C allele were at high risk for elevated plasma ammonia levels. Moreover, patients having rs12136955 SNPs with the A allele or associated hypertension as a co-morbidity were at high risk for elevated plasma ammonia levels. Female patients who have rs2296521 with the A allele, rs10911021 with the C allele, or rs12136955 with the A allele, are independent risk factors for elevated plasma ammonia levels during VPA-based therapy. Moreover, carbamazepine combined therapy may protect against the development of hyperammonemia in VPA-treated patients.

Testing Reported Associations of Gene Variants with Non-Syndromic Orofacial Clefts in the Polish Population.

Orofacial clefts (OFCs) are the second most common birth defect worldwide. The etiology of OFCs involves complex interactions between genetics and environment. Advances in genomic technologies have identified gene variants associated with OFCs. This study aimed to investigate whether selected SNPs in the MYH9, MTHFR, MAFB, and SUMO1 genes influence the occurrence of non-syndromic OFCs in the Polish population. The study included 209 individuals with non-syndromic OFCs and 418 healthy controls. Saliva and umbilical cord blood samples were collected for DNA extraction. Four SNPs in the MYH9, MTHFR, MAFB, and SUMO1 genes were genotyped using real-time PCR-based TaqMan assays. Statistical analysis was performed using logistic regression to assess the association between SNPs and OFCs. A significant association was found between the rs7078 CC polymorphism and OFCs (OR = 3.22, CI 1.68-6.17, p < 0.001). No significant associations were identified for the rs1081131, rs13041247, and rs3769817 polymorphisms. The research indicates that the rs7078 polymorphism significantly influences the occurrence of orofacial cleft palate in the Polish population, whereas the rs3769817, rs1801131, and rs13041247 SNPs do not show such a correlation.

P-266 Profiling redox effects induced by micro-nanoplastics in the female reproductive system: insights from human granulosa cells

Abstract Study question Are nano-microplastics (NMPs) taken up into human granulosa cells causing redox alterations? Summary answer NMPs enter into human granulosa cells and influence viability, energy production and antioxidant response. What is known already In recent decades, anthropogenic activities have increased the production of global plastic with millions of tons produced every year. Under the action of different physical, chemical or biological agents, plastic waste breaks down into (NMP) particles that propagate in the environment posing threats for human health. NMPs translocate from digestive tract to circulatory systems reaching organs and cells, including female gonads. Nevertheless, there is insufficient knowledge of their effects on reproductive functions in mammals to allow for an accurate risk assessment to be conducted and any risks managed in animal and human being contexts. Study design, size, duration Human ovarian granulosa cells (KGN cell line) were exposed to NMPs of different sizes (40 nm, 70 nm, 100 nm, and 200 nm) at concentrations ranging from 5 to 1000 μg/ml for 24 h and then processed for cellular and biochemical analyses Participants/materials, setting, methods NMPs uptake by granulosa cells was tested by the employment of fluorescent NMPs and observation under confocal laser scanning microscopy. Cell viability was assed by Cell Counting Kit8. The effects of NMPs on mitochondrial bioenergetics was evaluated by MitoStress kit (Seahorse Xfe96, Agilent). ATP production was evaluated by Cell Titer-Glo ATP assay kit (Promega). Key enzymes of antioxidant response were analysed at transcript and protein level by using real-time Taqman PCR and Western blotting, respectively. Main results and the role of chance We demonstrated that NMPs are taken up by granulosa cells at all tested concentrions along with significant decrease of cell vitality with all sizes and concentrations. Seahorse analysis revealed an altered bioenergetic profiles. ATP levels increase at 70, 100 and 200 nm (one way ANOVA p = 0.001) at all tested concentrations (one way ANOVA p &amp;lt; 0.001). The gene and protein expression of catalase (CAT) superoxide dismutase 1 (SOD1) and superoxide dismutase 2 (SOD2) increased at 5 and 100 µg/ml with all sizes except 100 nm, whereas the level of sirtuins (SIRT1 and SIRT3) transcripts and protein decreased. Reduced levels of phosphorylated NRF2, the transcription factor that activates antioxidant responsive elements (ARE)-mediated gene expression were observed. Limitations, reasons for caution The use of human cell lines requires careful consideration when transferring to human testing. Wider implications of the findings Our results contribute to understanding the effects of NMPs on mammalian fertility in order to find possible protective approaches. Considering that the level of susceptibility of mammalian female germ cells to NMPs is still unknown, present results contribute to evidence-based strategies allowing living and working in a health promoting environment. Trial registration number Effects of combined exposure to nano/microplastics and plastic additives on mammalian female fertility (CUP E53D2301100006)

USE OF TAQMAN ARRAY TO INVESTIGATE INFECTION IN DIABETIC FOOT WOUNDS

IntroductionDiabetic foot disease is a major public health problem with an annual NHS expenditure in excess of £1 billion. Infection increases risk of major amputation fivefold. Due to the polymicrobial nature of diabetic foot infections, it is often difficult to isolate the correct organism with conventional culture techniques, to deliver appropriate narrow spectrum antibiotics. Rapid DNA-based technology using multi-channel arrays presents a quicker alternative and has previously been used effectively in intensive care and respiratory medicine.MethodsWe gained institutional and Local Ethics Committee approval for a prospective cohort study of patients with clinically infected diabetic foot wounds. They all had deep tissue samples taken in clinic processed with conventional culture and real-time PCR TaqMan array.Results50 samples were taken from 39 patients between October 2020 and March 2022. 84% of patient were male, 88% had type 2 diabetes. The ulcers were of variable chronicity prior to sampling (range 1–113 weeks) and mean HbA1c was 67.2mmol/mol. Ulcers were on the heel (3), midfoot (6) and forefoot (41). Minimum follow up was 3 months. 6 ulcers healed, 24 patients were admitted due to foot disease, there were 2 major amputations and 4 deaths. TaqMan array results were available a mean of 4.3 days earlier than culture results. 9 patients had negative conventional cultures and 8 were negative onarray testing. 17 patients had the same organisms detected on culture and array. 16 of these 17 had additional organisms detected by array. The most frequent organisms detected on array that were not detected by culture were Staphylococcus spp., Enterobacter, Pseudomonas and fungi.ConclusionTaqMan array shows promise in detecting infecting organisms from diabetic foot wounds and providing earlier results than standard culture, which may enable appropriate and timely antibiotic therapy.

Evaluation of a pleiotropic cytokinin polymorphism with cerebral infarction in a Chinese male population.

Cardiovascular diseases, particularly stroke, are a leading cause of morbidity and mortality worldwide. Genetic variations in genes associated with inflammation have been implicated in the pathogenesis of stroke. Interleukin-6 (IL-6), a pleiotropic cytokine with diverse biological functions, has been linked to cardiovascular diseases and stroke. The relationship between cerebral ischemia and inflammation is well-established, suggesting a potential role for IL-6 polymorphisms in stroke susceptibility. In the context of this study, the focus is on evaluating a pleiotropic cytokinin polymorphism, specifically IL-6-572GC, and its association with cerebral infarction in a Chinese male population. The investigation aims to elucidate the genetic correlation between IL-6 polymorphisms and stroke risk, particularly in the context of hemorrhagic subtype of stroke. The study utilizes a case-control design, comparing stroke patients with healthy controls while adjusting for classic risk factors associated with stroke. The methodology employed includes the detection of IL-6 polymorphisms using Real Time Taq Man Probe and PCR-RFLP methods. The results suggest an association between the IL-6-572GC genotype and an increased risk of stroke, particularly in the hemorrhagic subtype. However, the relationship between another IL-6 polymorphism, IL-6-174GC, and stroke remains inconclusive, except for a potential correlation with one allele. The findings underscore the potential role of IL-6-572GC genotype as a genetic risk factor for stroke in the Chinese male population under study. Further research involving larger cohorts is warranted to validate these results and clarify the role of IL-6-174GC polymorphism in stroke susceptibility. Understanding the genetic underpinnings of stroke can provide valuable insights for risk assessment and personalized treatment strategies in affected populations.

Comparison of an Unlabeled Probe High-Resolution Melting Analysis Assay (HRMA) for Factor V Leiden 1691 G/A Mutation to a Fluorogenic 5' Nuclease PCR Hydrolysis Assay.

The clinically significant Factor V Leiden (FVL) point mutation (1691 G/A) causes replacement of Arg with Gln (glutamine), preventing activated protein C from inactivating Factor V leading to a lengthened clotting process. Individuals with the Factor V Leiden mutations have an increased risk for venous thrombosis. The aim of this study is to compare an unlabeled probe high-resolution melting analysis (HRMA) assay for Factor V Leiden mutation to a TaqMan hydrolysis assay (fluorogenic 5' nuclease PCR hydrolysis assay). HRMA is a post-PCR, homogenous, closed-tube system for the detection of sequence variants. Post-PCR, the amplicons are heated gradually until the melting temperature is reached and the fluorescent dye unbinds from the amplicon and exhibits low fluorescence. A melt-curve analysis is generated that is characteristic of a particular sequence variant. Therefore, HRMA allows for comparison of one base changes in genetic sequences based on their differences in melting rate. Blood samples were collected in EDTA tubes and DNA extracted using the Roche MagNaPure. Reactions of both HRMA and TaqMan were carried out on 3 controls (1691 G/G, 1691 G/A, and 1691 G/G and G/A) and 20 samples. The genotypes for 3 reference controls purchased from Coriell (F5 1691 G/G, FVL 1691 G/A, and Heterozygote 1691 G/G and G/A) were confirmed by both the HRMA and TaqMan FVL assays. All 20 samples were confirmed to be F5 1691 G/G by both HRMA and TaqMan assays. Comparing the results of the unlabeled probe HRMA FVL assay with a real-time TaqMan probe end point genotyping assay resulted in 100% sensitivity and 100% specificity for both assays.

SMAD3 rs17228212 Polymorphism Is Associated with Advanced Carotid Atherosclerosis in a Slovenian Population.

Smad proteins influence the TGFβ signaling pathway, which plays an important role in the progression of atherosclerosis. The aim of our study was to investigate the association between the rs17228212 polymorphism of the SMAD3 gene and advanced carotid atherosclerosis in Slovenian subjects and to investigate the effect of the rs17228212 SMAD3 polymorphism on the expression of SMAD3 in endarterectomy sequesters. In this cross-sectional case-control study, 881 unrelated Caucasians were divided into two groups. The first group included 308 patients with advanced carotid atherosclerosis of the common or internal carotid artery with stenosis greater than 75% that underwent a revascularization procedure (cases). The control group consisted of 573 subjects without hemodynamically significant carotid atherosclerosis. We analyzed the rs17228212 polymorphism of the SMAD3 gene using the StepOne real-time polymerase chain reaction system and TaqMan SNP genotyping assay. The results in the two genetic models showed a statistically significant association, codominant (OR 4.05; CI 1.10-17.75; p = 0.037) and dominant (OR 3.60; CI 1.15-15.45; p = 0.045). An immunohistochemical analysis of SMAD3 expression was conducted for 26 endarterectomy specimens. The T allele of the rs17228212 SMAD3 gene was shown to be associated with an increased numerical area density of SMAD3-positive cells in carotid plaques.

Development and field evaluation in African and Asian countries of an hepatitis B virus PCR on open polyvalent platforms to determine treatment eligibility: results from the “Agence Nationale de Recherche sur le Sida et les hépatites” 12327 study

ObjectivesWidespread testing and treatment are essential to eliminate hepatitis B virus (HBV) infection as a public health concern. However, in resource-limited countries, access to HBV PCR is limited. In this study, we developed a quantitative HBV PCR assay on open molecular platforms and evaluate its performance in diagnosing clinically significant HBV DNA thresholds as defined by the WHO (2000 IU/mL, 20 000 IU/mL, and 200 000 IU/mL). MethodsWe implemented our HBV PCR test in seven African and Asian countries and France, using either an in-house laboratory method or a European conformity for in vitro diagnostic (CE-IVD) marked version of the PCR (Generic HBV Charge Virale, Biocentric). Results were compared with reference tests (Roche Cobas AmpliPrep/Cobas TaqMan and Abbott RealTime on Abbott m2000). ResultsThere was a good agreement between the HBV DNA results of 1015 samples tested by the PCR on open polyvalent platforms and the results from reference tests (mean difference (bias ± standard deviation [SD]): −0.3 ± 0.7 log10 IU/mL and −0.2 ± 0.9 log10 IU/mL when compared with Roche and Abbott tests, respectively). Kappa-Cohen agreements between the HBV PCR on open polyvalent platforms and the Roche/Abbott assays appeared almost perfect for HBV DNA levels ranged from >20 000 to 200 000 IU/mL and >200 000 IU/mL, substantial and moderate for HBV DNA levels ranged from 2000 to 20 000 IU/mL when compared with Abbott and Roche, respectively. The assay's performance was consistent across genotypes A, B, C, D, and E. DiscussionThis field evaluation showed that our HBV PCR test is a valuable alternative to proprietary PCR systems. PCR assays on open platforms contribute to expanding clinical laboratory solutions for diagnosing individuals who meet the viral load criteria for antiviral therapy (>20 000 IU/mL) and mother-to-child prophylaxis (>200 000 IU/mL).

Sex- Specific Effects of Chronic Unpredictable Stress on Renal Mitochondrial Function in C57BL/6 Mice

Background: The kidneys play a central role in long term control of blood pressure. Chronic psychological stress has been linked to hypertension, inflammation, and is associated with both an increased prevalence and progression of renal disease. However, the molecular and cellular mechanisms by which chronic stress alters renal function are not fully understood, and data on sex specific differences in renal and blood pressure responses to stress are limited. The impact of stress to cause local inflammation and mitochondrial dysfunction in the kidneys is not clear and represents a potential mechanism leading to renal dysfunction and hypertension. The chronic unpredictable stress (CUS) model induces psychological stress in rodents thus allowing the study of integrated physiological changes to the kidney in response to stress. Hypothesis: Exposing mice to CUS will lead to increased blood pressure that is associated with decreased renal mitochondrial function and renal inflammation. Methods: To investigate the link between stress, renal mitochondrial function, inflammation, and blood pressure, we exposed adult male and female C57BL/6 mice to CUS for 28 consecutive days. Blood pressure was measured via tail cuff on the 28th day of stress. 24 hours later, mice were euthanized and estrous cycle phase in females was determined by vaginal cytology. Kidney mitochondrial oxygen consumption was assessed using the Oroboros respirometer on the pole ends of the left kidneys. NLR family pyrin domain containing 3 (NLRP3) expression was measured in the right kidney using Real-Time TaqMan PCR. Results: Mean arterial pressure was elevated in both stressed males (in mmHg, 106±4 vs 87±4, n&lt;11, p&lt;0.01) and females (131± 6 vs 94±11 n&lt;4, p&lt;0.01) compared to non-stressed mice. While maximal electron transport capacity (ETS), a measure of mitochondrial function, was unchanged in CUS male kidneys, stressed females in the receptive (estrus and proestrus) phase of the estrous cycle exhibited a significant decrease in renal ETS compared to non-stressed females (in pmol O2/mg protein, 14.4±0.9 vs 11.4±0.7, n=11, p&lt;0.05). Renal mRNA expression of NLRP3 was increased in CUS males (35%± 7.7, n=8, p&lt;0.01) but unchanged in CUS females. Conclusion: These data suggest potential mechanistic differences in stress-induced hypertension in renal mitochondria (decreased ETS in stressed females) and inflammasome level (increased NLRP3 in stressed males) between male and female mice. This work was supported by P20GM109091 (F.H.), R01HL130972-01A1, R01HL5949, BX000168-10A1, BX005320 (F.G.S.), R01DK132948 (C.W. &amp; F.P.) R01 MH129798 (SKW); VA VISN7 RDA (F.H.),, 1U54HL169191-01 &amp; BX002604 (M.J.R.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the abstract. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Validation of a simplified small-scale DNA extraction protocol from wine by quantitative real-time PCR

In the present study, we compared a simplified small-scale purification protocol to obtain DNA admixtures out of wine, with our large-scale published method. The extraction methods must provide DNA free of PCR inhibitors, that can interfere with DNA amplification. To evaluate the efficiency of grapevine’s nuclear DNA extraction from wine, the new protocol was also compared in terms of purity and yield to the DNA obtained out of grapevine’s (Vitis vinifera) leaf tissue, using a commercial kit. Two single-copy nuclear genes, nine-cis-epoxy carotenoid dioxygenase 2 (NCED2), and prefoldin subunit 5-like (PS5) were amplified in DNA extracted from wine and grapevine by real-time TaqMan PCR to determine the presence of inhibitors in relation to the diversity of starting biological matrix. This study showed that the small-scale, simpler method for extracting DNA from wine produced effective results in terms of inhibitor presence and purity. Furthermore, even though the initial biological matrix was more complicated, the grapevine nuclear DNA that was removed from wine was qualitatively equivalent to the DNA that was isolated from the leaves.

Linkage between ACE2 Gene Polymorphisms and SARS-CoV-2 infection in Burkina Faso, sub-Saharan Africa

The ACE2 gene polymorphisms (rs143936283, rs146676783, and rs4646116) in infected and noninfected persons by SARS-CoV-2 in Burkina Faso. Our cross-sectional study population comprised 137 SARS-CoV-2 infected persons and 181 non-infected persons. Three ACE2 gene polymorphisms rs143936283, rs146676783, and rs4646116, were genotyped using the real-time PCR standard TaqMan allelic discrimination technique. The association between SARS-CoV-2 infection and the polymorphisms were evaluated by a binary logistic regression. There was no association between the polymorphisms rs143936283, rs4646116 haplotypes, and SARS-CoV-2 infection in our study population. However, in the female population, the heterozygous genotype CT of rs146676783 increased by two and half the risk (OR=2.58 95%CI (1.2-5.48), p= 0.014) of being infected by SARS-CoV-2. Additionally, carrying the homozygous minor allele (genotype TT) of rs146676783 increased by more than five and half the risk (OR=5.57 95%CI (1.64-18.78), p=0.006) of being infected by SARS-CoV-2 among females. This study showed that the ACE2 gene variant rs146676783 was associated with an increased risk of being infected by SARS-CoV-2 in females, suggesting a need for further investigation to contribute to a better understanding of the African COVID-19 enigma.

Investigating the role of VDR gene variants in multiple sclerosis susceptibility: a case–control study in Egypt

BackgroundMultiple sclerosis (MS) is a chronic inflammatory disorder. Vitamin D has a major role in preventing inflammatory disorders as well as its role in the pathophysiology of MS. Vitamin D initiates its biological responses by binding to the nuclear vitamin D receptor (VDR). Several studies have been conducted over the last decade to investigate the relationship between VDR gene variants and the risk of MS, but the results have been inconsistent and inconclusive. The objective of this study is to investigate the association between the VDR gene variants (c.1025-49C>A) and (c.1056A>G) and MS susceptibility in a sample of the Egyptian population, and to shed light on its potential role in preventing inflammatory disorders and its impact on clinical outcomes and treatment using TaqMan Real-Time Polymerase Chain Reaction (PCR). This case-control study was conducted on 100 participants, categorized into two groups. The first group included 50 patients diagnosed with relapsing-remitting multiple sclerosis (RRMS) based on the Revised McDonald MS criteria, and the second group included 50 matched healthy participants. After collecting the blood samples, deoxyribonucleic acid (DNA) was extracted and detection of the VDR: c.1025-49C>A and VDR: c.1056A>G gene variants was done using TaqMan Real-Time PCR on all involved individuals.ResultsThe distribution of the genotypes and alleles of VDR gene variants (c.1025- 49C>A) and (c.1056A>G) did not differ significantly between MS patients and healthy participants (P>0.05 in both). ConclusionHere we show in this study that there was no association between the risk of MS and the VDR gene variants (c.1025-49C>A) and (c.1056A>G) in a group of the Egyptian population which may have impact on MS therapy and outcome.

Evaluation of crAssphages as a potential marker of human viral contamination in environmental water and fresh leafy greens.

CrAssphages are human gut bacteriophages with potential use as an indicator of human fecal contamination in water and other environmental systems. We determined the prevalence and abundance of crAssphages in water, food, and fecal samples and compared these estimates with the prevalence of norovirus. Samples were tested using two crAssphage-specific qPCR assays (CPQ056 and TN201-203) and for norovirus using TaqMan realtime RT-PCR. CrAssphage was detected in 40% of human fecal specimens, 61% of irrigation water samples, 58.5% of stream water samples, and 68.5% of fresh leafy greens samples. Interestingly, across all sample categories, crAssphage concentrations were 2-3 log10 higher than norovirus concentrations. The correlation of detection of crAssphage and norovirus was significant for the irrigation water samples (r = 0.74, p = 7.4e-06). Sequences obtained from crAssphage positive samples from human fecal and stream water samples phylogenetically clustered with genotype I crAssphages, whereas sequences derived from irrigation water samples clustered differently from other genotypes. Our data show that crAssphages were prevalent in norovirus-positive water samples and in fresh leafy green samples, there was a strong correlation between the presence of crAssphage and norovirus. CrAssphage genomic copies were consistently higher than norovirus copies in all sample types. Overall, our findings suggest that crAssphages could be used as reliable indicators to monitor fecal-borne virus contamination within the food safety chain.

Shigella Detection and Molecular Serotyping With a Customized TaqMan Array Card in the Enterics for Global Health (EFGH): Shigella Surveillance Study.

Quantitative polymerase chain reaction (qPCR) targeting ipaH has been proven to be highly efficient in detecting Shigella in clinical samples compared to culture-based methods, which underestimate Shigella burden by 2- to 3-fold. qPCR assays have also been developed for Shigella speciation and serotyping, which is critical for both vaccine development and evaluation. The Enterics for Global Health (EFGH) Shigella surveillance study will utilize a customized real-time PCR-based TaqMan Array Card (TAC) interrogating 82 targets, for the detection and differentiation of Shigella spp, Shigella sonnei, Shigella flexneri serotypes, other diarrhea-associated enteropathogens, and antimicrobial resistance (AMR) genes. Total nucleic acid will be extracted from rectal swabs or stool samples, and assayed on TAC. Quantitative analysis will be performed to determine the likely attribution of Shigella and other particular etiologies of diarrhea using the quantification cycle cutoffs derived from previous studies. The qPCR results will be compared to conventional culture, serotyping, and phenotypic susceptibility approaches in EFGH. TAC enables simultaneous detection of diarrheal etiologies, the principal pathogen subtypes, and AMR genes. The high sensitivity of the assay enables more accurate estimation of Shigella-attributed disease burden, which is critical to informing policy and in the design of future clinical trials.

A multiplex direct PCR method for the rapid and accurate discrimination of three species of spider mites (Acari: Tetranychidae) in fruit orchards in Beijing.

Spider mites (Acari: Tetranychidae) are polyphagous pests of economic importance in agriculture, among which the two-spotted spider mite Tetranychus urticae Koch has spread widely worldwide as an invasive species, posing a serious threat to fruit tree production in China, including Beijing. The hawthorn spider mite, Amphitetranychus viennensis Zacher, is also a worldwide pest of fruit trees and woody ornamental plants. The cassava mite, Tetranychus truncatus Ehara, is mainly found in Asian countries, including China, Korea and Japan, and mainly affects fruit trees and agricultural crops. These three species of spider mites are widespread and serious fruit tree pests in Beijing. Rapid and accurate identification of spider mites is essential for effective pest and plant quarantine in Beijing orchard fields. The identification of spider mite species is difficult due to their limited morphological characteristics. Although the identification of insect and mite species based on PCR and real-time polymerase chain reaction TaqMan is becoming increasingly common, DNA extraction is difficult, expensive and time-consuming due to the minute size of spider mites. Therefore, the objective of this study was to establish a direct multiplex PCR method for the simultaneous identification of three common species of spider mites in orchards, A. viennensis, T. truncatus and T. urticae, to provide technical support for the differentiation of spider mite species and phytosanitary measures in orchards in Beijing. Based on the mitochondrial cytochrome c oxidase subunit I (COI) of the two-spotted spider mite and the cassava mite and the 18S gene sequence of the hawthorn spider mite as the amplification target, three pairs of specific primers were designed, and the primer concentrations were optimized to establish a direct multiplex PCR system for the rapid and accurate discrimination of the three spider mites without the need for DNA extraction and purification. The method showed a high sensitivity of 0.047ng for T. truncatus and T. urticae DNA and 0.0002ng for A. viennensis. This method eliminates the DNA extraction and sequencing procedures of spider mite samples, offers a possibility for rapid monitoring of multiple spider mites in an integrated microarray laboratory system, reducing the time and cost of leaf mite identification and quarantine monitoring in the field.