Real-time Polymerase Chain Reaction System Research Articles

An Interdisciplinary Design Project for Undergraduate Engineering Training – Portable Real-Time Polymerase Chain Reaction System

Our world has been permanently changed by the pandemic outbreak of COVID-19 starts around the end of 2019. In the first few months of 2020, the whole world was in urgent need of an effective, easy, and quick method for the identification of the infection of the new virus. Polymerase Chain Reaction (PCR) machine, which can test DNA samples by rapidly making millions of copies of a specific DNA sample through the PCR process, including the COVID-19 virus, can perfectly fit this demand. In this study, a design project on PCR is introduced for undergraduate education in electrical and mechanical engineering. The objective of this project is to develop a low-cost, ease-of-use, wallet-size, portable real-time PCR (RT-PCR) machine for accurate testing of various bacteria or viruses. The key function of the PT-PCR system is to precisely control and maintain the temperature of the biosample solution within a range between 55°C and 95°C. This project provides students opportunities in studying and practicing a wide range of engineering technics and skills, including mechanical design, electronics design, microcomputer programming, data acquisition and processing, etc. Students can gain comprehensive understanding of the design of multiphysics system after they overcome various challenges emerging in the project. From the view of engineering education, the process of this project development has demonstrated the importance and benefits of adopting complex interdisciplinary engineering problems for student teams to solve, especially those involve contemporary issues.

Role of Glutaminase 2 in Promoting CD4+ T Cell Production of Interleukin-2 by Supporting Antioxidant Defense in Systemic Lupus Erythematosus.

Glutaminase (GLS) isoenzymes GLS1 and GLS2 catalyze the first step of glutaminolysis. GLS1 is requisite for Th17 cell differentiation, and its inhibition suppresses autoimmune disease in animals, but the function of GLS2 is not known. The aim of this study was to investigate the role of GLS2 in CD4+ T cell function and systemic lupus erythematosus (SLE) pathogenesis. We measured reactive oxygen species (ROS) levels, lipid peroxidation, and mitochondrial mass and polarization by flow cytometry, interleukin-2 (IL-2) production by a dual luciferase assay, and CpG DNA methylation of Il2 by a real-time polymerase chain reaction system. The impact of the overexpression of wild-type GLS1, wild-type GLS2, or mutated GLS2 at the PDZ domain-binding motif in CD4+ T cells was examined. Furthermore, GLS2 expression in CD4+ T cells from lupus-prone mice and patients with SLE was analyzed by Western blotting. GLS2, but not GLS1, reduced ROS levels and lipid peroxidation and restored mitochondrial function in T cells. GLS2 promoted IL-2 production through the demethylation of the Il2 promoter. Mutation of the PDZ domain-binding motif abated the ability of GLS2 to regulate IL-2 and ROS levels. In lupus-prone mice and patients with SLE, the expression of GLS2 was decreased in CD4+ T cells. Finally, GLS2 overexpression corrected ROS levels and restored IL-2 production by CD4+ T cells from lupus-prone mice and SLE patients. Our findings suggest that GLS2 has a crucial role in IL-2 production by CD4+ T cells by supporting antioxidant defense, and they offer a new approach to correcting IL-2 production by T cells in SLE.

Low-Cost, Real-Time Polymerase Chain Reaction System for Point-of-Care Medical Diagnosis.

Global health crises due to the prevailing Coronavirus Disease 2019 (COVID-19) pandemic have placed significant strain on health care facilities such as hospitals and clinics around the world. Further, foodborne and waterborne diseases are not only spreading faster, but also appear to be emerging more rapidly than ever before and are able to circumvent conventional control measures. The Polymerase Chain Reaction (PCR) system is a well-known diagnostic tool for many applications in medical diagnostics, environmental monitoring, and food and water quality assessment. Here, we describe the design, development, and testing of a portable, low-cost, and real-time PCR system that can be used in emergency health crises and resource-poor situations. The described PCR system incorporates real-time reaction monitoring using fluorescence as an alternative to gel electrophoresis for reaction analysis, further decreasing the need of multiple reagents, reducing sample testing cost, and reducing sample analysis time. The bill of materials cost of the described system is approximately $340. The described PCR system utilizes a novel progressive selective proportional–integral–derivative controller that helps in reducing sample analysis time. In addition, the system employs a novel primer-based approach to quantify the initial target amplicon concentration, making it well-suited for food and water quality assessment. The developed PCR system performed DNA amplification at a level and speed comparable to larger and more expensive commercial table-top systems. The fluorescence detection sensitivity was also tested to be at the same level as commercially available multi-mode optical readers, thus making the PCR system an attractive solution for medical point-of-care and food and water quality assessment.

Comparable Results of Helicobacter pylori Antibiotic Resistance Testing of Stools vs Gastric Biopsies Using Next-Generation Sequencing

Comparable Results of Helicobacter pylori Antibiotic Resistance Testing of Stools vs Gastric Biopsies Using Next-Generation Sequencing

A hand-held, real-time, AI-assisted capillary convection PCR system for point-of-care diagnosis of African swine fever virus

A hand-held, low-cost and real-time convection polymerase chain reaction (CPCR) system is developed for point-of-care diagnosis of African swine fever (ASF) virus. In CPCR amplification, the reagent is transferred to denaturation, annealing and extension stages of the reaction repeatedly due to thermal convection. Two different modes of fiber-based optical detection are compared, and it shows that the detection sensitivity, repeatability, and consistency can be significantly improved with bottom collection comparing to sidewall collection. Each capillary tube is illuminated by its own LED from the top through a common optical filter, and meanwhile, a camera equipped with another optical filter is adopted to detect the fluorescence signal from optical fibers. To handle the untypical real-time fluorescence curves of negative tests due to non-specific amplification, AI-based classification methods, for example, artificial neural network (ANN) is adopted to improve the detection specificity up to 97.50% comparing to 47.5% or 75.0% which is achieved with Ct-based method. A smartphone is adopted to run the AI algorithm and custom software, as well as to report an ASF event with the geographical information. Experimental results show that with the hand-held CPCR system, within 30 min, ASF viruses can be successfully detected with acceptable sensitivity and specificity.

Clinicopathologic features and KRAS mutation incidence of gastric carcinomas

Objectives: This study aims to determine the frequency of KRAS mutations in patients with gastric adenocarcinoma (GAC) in Hatay province, and to determine the relationship of this mutation with some pathological and clinical parameters and to guide the diagnosis and treatment planning of patients. Methods: Formalin-fixed, paraffin-embedded, and histologically confirmed samples were used in the assessment of KRAS mutation. Sections were taken from the archive tissue samples of each case. Real-Time Polymerase Chain Reaction (RT-PCR) system was used to identify mutations of codons 12 and 13 (exon 2) of the RAS gene. Mutations of GLY12ALA (G12A), GLY12ASP (G12D), GLY12ARG (G12R), GLY12CYS (G12C), GLY12SER (G12S), GLY12VAL (G12V), GLY13ASP (G13D) were performed. Results: The mutation rate of KRAS was 2% and only one substitution, G12D, was detected. In this case, the tumor was located in the small curvature. Since the number of cases with mutations was low, statistical comparison could not be made between KRAS mutation and clinicopathological factors. A significant difference was found between tumor differentiation and WHO-2010 typing and primary tumor stage. Conclusions: We found the incidence of KRAS mutation to be 2%. We also estimate that the G12D mutation may be associated with GAC site and surgical margin. Although KRAS mutation in GAC alone is not a prognostic or predictive marker, subtype-specific analysis may provide data that may affect the diagnosis, management and treatment of the disease

Association between genetic variants and depression in a Romanian cohort.

Major depressive disorder (MDD) is beyond doubt a common, disabling, and costly condition. MDD associates hypothalamic–pituitary–adrenal (HPA) axis alterations. We sought to investigate two candidate variants which could have a role in the genetic susceptibility for stress or corticoid-induced MDD: glucocorticoid receptor (GR) – nuclear receptor subfamily 3 group C member 1 (NR3C1) rs41423247 and brain-derived neurotrophic factor rs6265 BDNF:c.442G>A Val66Met. We enrolled 82 Romanian subjects, 1:2 male to female ratio, 53.54±8.98 years old, diagnosed with an episode of major depression at the Clinical Neuropsychiatry Hospital in Craiova, Romania, and 286 healthy controls, 34.28±16.34 years old. All subjects were genotyped using specific ThermoFisher Scientific assays on a ViiA™ 7 real-time polymerase chain reaction (PCR) system. The impact of certain genetic variants may be ethnic-specific. In our Romanian cohort, rs41423247 NR3C1:c.1184+646C>G has a minor allele frequency of 29.2%, and rs6265 BDNF:c.442G>A of 22.2%. Neither reached significance in our study, under any of the association models – dominant, recessive, or allelic. Interpretation of our negative findings requires caution: literature provides arguably more evidence for the association between the analyzed polymorphisms; our study has sample size challenges, from which refined phenotyping limitations derive.

Interleukin-1 gene (IL-1) polymorphism in patients with Behçet’s Disease, and its relationship with disease manifestations

Objective The objective of this study was to investigate whether interleukin-1 (IL-1) gene polymorphisms are associated with susceptibility to Behçet’s disease (BD) and clinical manifestations of the disease. Methods In this cross-sectional study, we enrolled 110 patients with BD and age-and gender-matched 120 healthy controls. Five polymorphic regions of the IL-1 gene including rs 1800587 (IL1A-889 C/T), rs 2234650 (IL1R1), rs 16944 (IL1B-511 C/T), rs 315952 (IL1RN), and rs1143634 (IL1B-3954 C/T) were analyzed by using the real-time polymerase chain reaction system. Allele frequencies and genotypes were compared between groups. p ≤ 0.05 was accepted as statistically significant. Results The mean age of the patients with BD was 41 ± 12.4 years. The two groups were similar in terms of the age and gender distribution. The vast majority of BD patients had mucocutaneous involvement. The mean disease duration was 83.7 ± 67.8 months among the patients. The frequencies of each polymorphism in the IL-1 gene were similar between patients with BD and healthy controls. Conclusion The frequencies of variable IL-1 gene polymorphisms were similar between patients with BD and healthy controls.

LoopTag FRET Probe System for Multiplex qPCR Detection of Borrelia Species.

Background: Laboratory diagnosis of Lyme borreliosis refers to some methods with known limitations. Molecular diagnostics using specific nucleic acid probes may overcome some of these limitations. Methods: We describe the novel reporter fluorescence real-time polymerase chain reaction (PCR) probe system LoopTag for detection of Borrelia species. Advantages of the LoopTag system include having cheap conventional fluorescence dyes, easy primer design, no restrictions for PCR product lengths, robustness, high sequence specificity, applicability for multiplex real-time PCRs, melting curve analysis (single nucleotide polymorphism analysis) over a large temperature range, high sensitivity, and easy adaptation of conventional PCRs. Results: Using the LoopTag probe system we were able to detect all nine tested European species belonging to the Borrelia burgdorferi (sensu lato) complex and differentiated them from relapsing fever Borrelia species. As few as 10 copies of Borrelia in one PCR reaction were detectable. Conclusion: We established a novel multiplex probe real-time PCR system, designated LoopTag, that is simple, robust, and incorporates melting curve analysis for the detection and in the differentiation of European species belonging to the Borrelia burgdorferi s.l. complex.

Plasma interleukin-22 level, variants in interleukin-22 gene polymorphism, and the severity of systemic lupus erythematosus among Egyptian pediatric and adolescents.

Our purpose was to investigate, for the first time, genotypes and alleles distribution of two single nucleotide polymorphisms (SNPs) of interleukin 22 (IL-22) (rs1012356 and rs2227485) in Egyptian pediatric and adolescents with systemic lupus erythematosus (SLE) and to evaluate the plasma IL-22 levels and their association with gene polymorphism and SLE risk and severity. The TaqMan™ SNP genotyping assay on a real-time polymerase chain reaction (PCR) system was employed to evaluate the polymorphism's genotypes. Plasma IL-22 levels were determined by using an enzyme-linked immunoabsorbent assay (ELISA). The frequencies and genotypes of rs2227485 and rs1012356 in IL-22 between SLE patients and controls also haplotypes formed by the same SNPs revealed no statistically significant difference (p > 0.05). Otherwise, logistic regression analysis revealed that patients carrying rs1012356 "TA + AA" genotype had increased risk for prediction of SLE activity (OR = 1.610, 95% CI = 1.339-2.760, p = 0.034) by lowering plasma IL-22 level. Among Egyptian pediatric and adolescents, we confirm a combined model "TA + AA" in rs1012356 (A/T) of IL-22 in regression analysis, as an independent predictor for SLE activity by lowering IL-22 plasma levels. Despite neither SNP rs2227485 A/G in IL-22 gene nor haplotypes formed by the same two SNPs (rs2227485 A/G and rs1012356 A/T) were significantly associated with the clinical and/or laboratory manifestations of SLE.

Botanical authentication of globe artichoke-containing foods: Differentiation of Cynara scolymus by a novel HRM approach

Cynara scolymus L., known as globe artichoke, is a medicinal plant widely used in plant food supplements (PFS) and herbal infusions due to its beneficial health properties. The high demand for artichoke-containing products can lead to adulteration practices. In this work, a real-time polymerase chain reaction (PCR) system coupled to high-resolution melting (HRM) analysis was proposed to differentiate C. scolymus from other Cynara species. Hence, a Cynara-specific real-time PCR assay was successfully developed with high analytical performance, achieving a sensitivity of 0.4 pg of globe artichoke DNA. HRM analysis enabled the discrimination of C. scolymus, with a high level of confidence (>98%), corroborating sequencing data. Application results to artichoke-containing PFS and mixed herbal infusions allowed confirming the presence of C. scolymus in 38% of the samples, suggesting the substitution/mislabelling of globe artichoke in 2 samples and the need for further efforts to increase DNA amplifiability of PFS.

COVID-19 Testing Pipeline: Lesson Learned

The transmission of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) in Indonesia is seen to be uncontrollably increasing that urges the government to leverage the capacity for the disease detections. Real-time polymerase chain reaction (RT-PCR), rapid test and computed tomography (CT) scan are the most common methods to determine if one has been infected regardless of whether or not the common symptoms of such Corona Virus Disease 2019 (COVID-19) surface. Among these three, RT-PCR is considered the gold standard for qualitative and quantitative assessment of SARS CoV-2 detection. The present paper aims at elaborating the framework of Roche’s RT-PCR machine employed specifically for SARS CoV-2 detection performed by Genetics Indonesia which is deemed to be efficient and relatively quicker than other detection kits. RT-PCR machine detected SARS Cov-2 with RNA amplification curve equals to 10 copies RNA below the cut off value of Crossing point (Cp) positive control. Also elucidated in the paper is the implementations of EAV RNA and LightCycler® 96 RT-PCR System through which analysis time, amounts of individual required sample, as well as the reagents, can be accordingly reduced.

The African Network for Improved Diagnostics, Epidemiology and Management of common infectious Agents

BackgroundIn sub-Saharan Africa, acute respiratory infections (ARI), acute gastrointestinal infections (GI) and acute febrile disease of unknown cause (AFDUC) have a large disease burden, especially among children, while respective aetiologies often remain unresolved. The need for robust infectious disease surveillance to detect emerging pathogens along with common human pathogens has been highlighted by the ongoing novel coronavirus disease 2019 (COVID-19) pandemic. The African Network for Improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA) is a sentinel surveillance study on the aetiology and clinical characteristics of ARI, GI and AFDUC in sub-Saharan Africa.MethodsANDEMIA includes 12 urban and rural health care facilities in four African countries (Côte d’Ivoire, Burkina Faso, Democratic Republic of the Congo and Republic of South Africa). It was piloted in 2018 in Côte d’Ivoire and the initial phase will run from 2019 to 2021. Case definitions for ARI, GI and AFDUC were established, as well as syndrome-specific sampling algorithms including the collection of blood, naso- and oropharyngeal swabs and stool. Samples are tested using comprehensive diagnostic protocols, ranging from classic bacteriology and antimicrobial resistance screening to multiplex real-time polymerase chain reaction (PCR) systems and High Throughput Sequencing. In March 2020, PCR testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and analysis of full genomic information was included in the study. Standardised questionnaires collect relevant clinical, demographic, socio-economic and behavioural data for epidemiologic analyses. Controls are enrolled over a 12-month period for a nested case-control study. Data will be assessed descriptively and aetiologies will be evaluated using a latent class analysis among cases. Among cases and controls, an integrated analytic approach using logistic regression and Bayesian estimation will be employed to improve the assessment of aetiology and associated risk factors.DiscussionANDEMIA aims to expand our understanding of ARI, GI and AFDUC aetiologies in sub-Saharan Africa using a comprehensive laboratory diagnostics strategy. It will foster early detection of emerging threats and continued monitoring of important common pathogens. The network collaboration will be strengthened and site diagnostic capacities will be reinforced to improve quality management and patient care.

Quantitative Analysis of Fluorescence Detection Using a Smartphone Camera for a PCR Chip

Most existing commercial real-time polymerase chain reaction (RT-PCR) instruments are bulky because they contain expensive fluorescent detection sensors or complex optical structures. In this paper, we propose an RT-PCR system using a camera module for smartphones that is an ultra small, high-performance and low-cost sensor for fluorescence detection. The proposed system provides stable DNA amplification. A quantitative analysis of fluorescence intensity changes shows the camera’s performance compared with that of commercial instruments. Changes in the performance between the experiments and the sets were also observed based on the threshold cycle values in a commercial RT-PCR system. The overall difference in the measured threshold cycles between the commercial system and the proposed camera was only 0.76 cycles, verifying the performance of the proposed system. The set calibration even reduced the difference to 0.41 cycles, which was less than the experimental variation in the commercial system, and there was no difference in performance.

Influence of SLCO1B1 521T>C, UGT2B7 802C>T and IMPDH1 −106G>A Genetic Polymorphisms on Mycophenolic Acid Levels and Adverse Reactions in Chinese Autoimmune Disease Patients

IntroductionMycophenolate mofetil (MMF), a new type of immunosuppressant, has emerged as a frontline agent for treating autoimmune diseases. Mycophenolic acid (MPA) is an active metabolite of MMF. MPA exposure varies greatly among individuals, which may lead to adverse drug reactions such as gastrointestinal side effects, infection, and leukopenia. Genetic factors play an important role in the variation of MPA levels and its side effects. Although many published studies have focused on MMF use in patients after organ transplant, studies that examine the use of MMF in patients with autoimmune diseases are still lacking.MethodsThis study will not only explore the genetic factors affecting MPA levels and adverse reactions but also investigate the relationships between UGT1A9 −118(dT)9/10, UGT1A9 - 1818T>C, UGT2B7 802C>T, SLCO1B1 521T>C, SLCO1B3 334T>G, IMPDH1 −106G>A and MPA trough concentration (MPA C0), along with adverse reactions among Chinese patients with autoimmune diseases. A total of 120 patients with autoimmune diseases were recruited. The MPA trough concentration was detected using the enzyme multiplied immunoassay technique (EMIT). Genotyping was performed using a real-time polymerase chain reaction (PCR) system and validated allelic discrimination assays. Clinical data were collected for the determination of side effects.ResultsSLCO1B1 521T>C demonstrated a significant association with MPA C0/d (p=0.003), in which patients with the CC type showed a higher MPA C0/d than patients with the TT type (p=0.001) or the CT type (p=0.000). No significant differences were found in MPA C0/d among the other SNPs. IMPDH1 −106G>A was found to be significantly related to infections (p=0.006). Subgroup analysis revealed that UGT2B7 802C>T was significantly related to Pneumocystis carinii pneumonia infection (p=0.036), while SLCO1B1 521T>C was associated with anemia (p=0.029).ConclusionFor Chinese autoimmune disease patients, SLCO1B1 521T>C was correlated with MPA C0/d and anemia. IMPDH1 −106G>A was significantly related to infections. UGT2B7 802C>T was significantly related to Pneumocystis carinii pneumonia infection.

Genetic variants in LGALS3 are related to lower galectin-3 serum levels and clinical outcomes in systemic sclerosis patients: A case-control study

Introduction Systemic sclerosis (SSc) is a rare complex disease characterized by vascular damage, autoimmunity, and extensive skin and internal organs fibrosis. Galectin-3 (Gal-3) is encoded by gene LGALS3 (Lectin, Galactoside-Binding, Soluble, 3; 14q22.3) and it has been reported to play a central role in self-tolerance, inflammation, and fibrosis. Objective To investigate associations among LGALS3 single nucleotide polymorphisms (SNPs) and serum levels Gal-3 and SSc susceptibility and their clinical features. Methods A case-control study with 88 patients and 151 matched controls was performed. LGALS3 variants were analyzed by the TaqMan real-time polymerase chain reaction (PCR) system whereas Gal-3 serum levels were measured by sandwich enzyme linked immunosorbent assay (ELISA). Associations among genotypes, clinical features, and Gal-3 levels were performed by univariable and multivariable analysis through statistical packages. Results The LGALS3 rs4652 A/C genotype was more frequent in SSc patients than controls according to overdominant model [OR 1.89 (CI 95% 1.01 − 3.52); p = .046]. Also, LGALS3 rs4652 C/C polymorphic genotype was associated with lower patient Gal-3 levels (p = .03) and control group (p = 0.005), as noted by generalized linear model (GLM). The LGALS3 rs1009977 G/T controls showed higher Gal-3 levels than wild-type and polymorphic genotypes (p = .03); however, in SSc patients, no difference was found. None of the LGALS3 SNPs or Gal-3 levels was associated with clinical manifestations in SSc patients. Considering only the SSc group, GLM analysis pointed LGALS3 rs4652 and rs2075601, pulmonary arterial hypertension (PAH), myopathy, and health assessment questionnaire (HAQ) and scleroderma health assessment questionnaire (SHAQ) as important predictors for Gal-3 levels. Conclusion The LGALS3 rs4652 A/C was more frequent in SSc patients and related to lower Gal-3 levels. These findings were corroborated through a GLM to estimate Gal-3 values. Also, by model equations, Gal-3 levels may be predicted by HAQ, SHAQ, PAH, myopathy, and LGALS3 rs4652 and rs2075601 factors. In these ways, we suggest that galectins may be promising biomarkers to identify susceptibility to SSc as well as to identify HAQ, SHAQ, PAH, and myopathy outcomes.

Association of hsa-mir-328-3p Expression in Whole Blood With Optical Density of Retinal Pigment Epithelial Cells.

To investigate the association of the pair box 6 gene (PAX6) and hsa-miR-328-3p with optical density of macular pigment. We evaluated 112 individuals (34 with moderate myopia, eight with high-degree myopia, and 70 healthy individuals). The optical density of macular pigment was measured using single-wavelength reflectometry. DNA and RNA were extracted from whole blood samples. Expression of hsa-miR-328-3p and genotyping of single-nucleotide polymorphism of PAX6 (rs662702) were performed using Applied Biosystems 7900HT real-time polymerase chain reaction system. Optical density of retinal pigment epithelial cells was evaluated using Fundus plus camera. In the group with myopia, with increasing ∆Ct hsa-miR-328-3p, the median optical density of the retinal pigment epithelium decreased statistically significantly (p<0.032). No statistically significant association was found between SNP rs662702 genotype variant of the PAX6 gene and the optical density of the retinal pigment epithelium. The increased expression of hsa-miR-328-3p in the blood indicates a decrease in the optical density of the retinal pigment epithelium in those with myopia.

Usefulness of TrueNat: A Chip-based Real-time PCR Test for COVID-19

Introduction: For the containment of growing Coronavirus Disease (COVID-19) pandemic, rapid diagnostic facilities are need of today. Indigenously developed TrueNat assay is a point-of-care assay developed for early diagnosis of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). It is a portable, fully automated, chip-based, real-time quantitative polymerase chain reaction system with a turnaround time of 1.5-2 hours. Aim: To assess the practical utility and diagnostic accuracy of TrueNat testing for COVID-19 in a pandemic situation. Materials and Methods: A cohort selection cross-sectional study was conducted from July to September 2020 at Department of Biochemistry, Vardhaman Institute of Medical Sciences, Pawapuri, Bihar, India, after obtaining Institutional Ethics Committee (IEC) approval. A total of 296 cases with symptoms of COVID-19 were selected for the study. Assuming real-time Reverse Transcription- Polymerase Chain Reaction (rRT-PCR) to be the gold standard, we collected oropharyngeal swabs from symptomatic COVID-19 suspected cases and tested by both TrueNat and standard RT-PCR. Agreement between both the assays were assessed by overall, Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) and Cohen’s kappa coefficient using Epitools (Ausvet 2020). Results: Out of 296 oropharyngeal swabs taken from suspected COVID-19 patients, 19 were read as “invalid” and discarded; hence only 277 samples were tested by TrueNat and RT-PCR both. Assuming RT-PCR as standard, TrueNat assay demonstrated an overall percent agreement of 99.64%, PPA of 95.65%, NPA 99.81%. The kappa coefficient was 0.9546. Conclusion: TrueNat assay offers a rapid, accurate and affordable technique for COVID-19. It may be deployed for mass screening and confirmation of COVID-19 cases in hospitals and remote areas.

Identification of biomarkers associated with synovitis in rheumatoid arthritis by bioinformatics analyses

Objectives: Rheumatoid arthritis (RA) is the most common inflammatory arthritis in the world, but its underlying mechanism is still unclear. The present study aims to screen and verify the potential biomarkers of RA.Methods: We searched the Gene Expression Omnibus (GEO) database for synovial expression profiling from different RA microarray studies to perform a systematic analysis. Functional annotation of differentially expressed genes (DEGs) was conducted, including GO enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The protein–protein interaction (PPI) networks of the DEGs were constructed based on data from the STRING database. The expression levels of the hub genes in normal membranes and RA synovium were detected by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot system.Results: A total of 444 differential expression genes were identified, including 172 up-regulated and 272 down-regulated genes in RA synovium compared with normal controls. The top ten hub genes; protein tyrosine phosphatase receptor type C (PTPRC), LCK proto-oncogene (LCK), cell division cycle 20 (CDC20), Jun proto-oncogene (JUN), cyclin-dependent kinase 1 (CDK1), kinesin family member 11 (KIF11), epidermal growth factor receptor (epidermal growth factor receptor (EGFR), vascular endothelial growth factor A (VEGFA), mitotic arrest deficient 2 like 1 (MAD2L1), and signal transducer and activator of transcription 1 (STAT1) were identified from the PPI network, and the expression level of VEGFA and EGFR was significantly increased in RA membranes (P<0.05).Conclusion: Our results indicate that the hub genes VEGFA and EGFR may have essential effects during the development of RA and can be used as potential biomarkers of RA.

Comparison of Real-Time PCR Quantification Methods in the Identification of Poultry Species in Meat Products.

Poultry meat is consumed worldwide and is prone to food fraud because of large price differences among meat from different poultry species. Precise and sensitive analytical methods are necessary to control poultry meat products. We chose species–specific sequences of the cytochrome b gene to develop two multiplex real-time polymerase chain reaction (real-time PCR) systems: one for chicken (Gallus gallus), guinea fowl (Numida meleagris), and pheasant (Phasianus colchicus), and one for quail (Coturnix japonica) and turkey (Meleagris gallopavo). For each species, added meat could be detected down to 0.5 % w/w. No cross reactions were seen. For these two real-time PCR systems, we applied three different quantification methods: (A) with relative standard curves, (B) with matrix-specific multiplication factors, and (C) with an internal DNA reference sequence to normalize and to control inhibition. All three quantification methods had reasonable recovery rates from 43% to 173%. Method B had more accepted recovery rates, i.e., in the range 70–130%, namely 83% compared to 75% for method A or C.