SYBR Green Assay Research Articles

Isolation and molecular detection of pigeon pox virus in Assiut and New Valley governorates

Pigeon Poxvirus (PPV) was detected in eight pigeons suffering from wart like nodular lesions in two Egyptian governorates (Assiut and New Valley) during summer 2018. Different serological and molecular techniques were carried out for isolation and detection of the virus on chorio-allantoic membranes (CAM) of specific-pathogen-free (SPF) embryonated chicken eggs. The characteristic pock lesions were detected on CAMs, whereas PPV was isolated. Electron microscopy revealed enveloped brick shaped Avipoxvirions. The neutralizing antibodies against PPV were detected in six out of eight samples. Serum neutralization test revealed a neutralization index of ≥ 1.6, while ELISA revealed an S/P ratio of ≥ 1.4 in the affected pigeons. Nucleotide sequence of P4b of Pigeon poxvirus isolated from nodule 1 sample (PPVNV1), revealed 100 % nucleotide identity to PPV and only 90 % nucleotide identity with Fowl poxvirus (FPV). P4b locus based SYBR green QPCR produced PPV amplicons of 77.33–77.83 °C melting temperature (Tm). QPCR SYBR green assay successfully differentiated PPV from FPV amplicon which revealed a dissociation curve of Tm =75.85 °C. This is the first report discriminating PPV from FPV based on SYBR green qPCR approach of P4b locus. This isolated local Egyptian strain can be used in vaccine production for optimal vaccination strategy.

Development of a Recombinase Polymerase Amplification (RPA) assay for acute hepatopancreatic necrosis disease (AHPND) detection in Pacific white shrimp (Penaeus vannamei)

Acute hepatopancreatic necrosis disease (AHPND) is currently the most important bacterial disease of shrimp that has caused enormous losses to the shrimp industry worldwide. The causative agent of AHPND are Vibrio spp. Carrying plasmids containing the pirA and pirB genes which encode binary toxins, PirAB. Currently, AHPND is mostly diagnosed by PCR-based platforms which require the use of sophisticated laboratory instrumentation and are not suitable for a point-of-care diagnostics. Therefore, the availability of an alternative method based on isothermal amplification would be suitable for AHPND detection outside a laboratory setting and extremely useful at a pond side location. Isothermal amplification is based on the nucleic acid amplification at a single temperature and does not require the use of a thermal cycler. In this study, we developed an isothermal Recombinase Polymerase Amplification (RPA) assay for AHPND detection targeting both pirA and pirB genes, simultaneously and evaluated the specificity and sensitivity of the assay. The assay could detect AHPND without any cross-reaction with other microbial pathogens and Specific Pathogen Free (SPF) shrimp. The limit of detection of the assay was 5 copies of pirAB genes. To evaluate the reliability of the assay in detecting AHPND, DNA from Penaeus vannamei shrimp displaying acute and chronic infection were analyzed by the RPA assay and the results were compared with SYBR Green real-time PCR assay. While there was a 100% conformity between the two assay while detecting acute phase infection, RPA appeared to be more sensitive in detecting chronic phase infection. The data suggest that RPA assay described here would be a reliable method in detecting AHPND outside a standard laboratory setting.

Development of cost-effective quantitative PCR method for parallel detection of porcine circovirus2 and porcine parvovirus in perspective of North-eastern India.

Pig farming performs as an intricate part in the socio-economic situation in the north-eastern region of India. This region contributes 38% (3.95 million) of total pigs in India. In spite of this, the region unables to flourish as an enterprise as per the expectation due to a low productivity rate. Porcine infectious pathogens like porcine cirovirus2 (PCV2) and porcine parvovirus (PPV) have a direct economic impact on pig farming through slow growth rate, abortion, and mortality and ultimately maximize the production cost by increasing the usage of antibiotic or antiviral drugs. The veterinary diagnostic infrastructure is a fundamental aspect of the development of livestock status by rapid and effective detection of pathogens. Quantitative PCR (qPCR) is a precise and fast-track technique used for the routine diagnostic method. Hence, we developed a highly precise and comparatively cost-effective SYBR Green reporter dye-based qPCR assay for parallel identification of PCV2 and PPV. In the present assay, the correlation coefficient (R2) value was 0.99, and 10 copies of the gene/μl were the least limit of detection (LOD) concerning both viruses. Melt curve analysis of this study represented PCV2-specific melt curve (Tm) at 81.2 °C and PPV-specific melt curve (Tm) at 73.5 °C. Therefore, the assay easily differentiates the true positive amplicons of PCV2 and PPV through specific Tm values. Among the 50 field samples, 26 (52%) samples were PCV2 positive, 18 (36%) samples PPV positive, and 11 (22%) samples were co-infected of both the viruses. This method is cost-effective, precise, and sensitive to diagnose the concurrent or individual infection of the PCV2 and PPV in the pig. Hence, considering the impact of pig farming in the north-eastern part of the country, the present assay gives an unprecedented achievement in disease diagnosis.

Establishment of Duplex SYBR Green I-based Real-time PCR Assay for Simultaneous Detection of Duck Hepatitis A Virus-1 and Duck Astrovirus-3.

Duck viral hepatitis (DVH) mainly affects ducklings under 1 month of age, causes liver necrosis, enlargement, and hemorrhage, and is highly lethal, seriously jeopardizing the duck industry. The prevalence of duck hepatitis A virus (DHAV-1) and duck astrovirus type 3 (DAstV-3) is increasing, and coinfection is common. Moreover, the similar clinical characteristics of the DHAV-1 and DAstV-3 infections and the high frequency of coinfection make diagnosis difficult. In this study, to establish a method for the rapid, simultaneous detection of DHAV-1 and DAstV-3, two pairs of specific primers were designed according to their conserved gene regions. An SYBR® Green I-based qPCR assay was successfully established that can quickly and differentially detect the two viruses. Moreover, the assay is highly specific and does not show cross-reaction with other common viruses. The detection limit of the method is 7.34 × 101 copies/µl and 3.78 × 101 copies/µl for DHAV-1 and DAstV-3, respectively, indicating high sensitivity. A total of 34 clinical samples were tested using the established method; the positive rates for DHAV-1 and DAstV-3 were 14.71% and 8.82%, respectively, and that for coinfection was 2.94% (1/34), which was better than that obtained with conventional PCR. In summary, the SYBR Green I-based qPCR assay established in this study has high specificity, good sensitivity and accuracy, high feasibility, and is rapid. Thus, it can be a powerful tool for the coinfection detection of DHAV-1 and DAstV-3 and for future epidemiologic studies.

Duplex SYBR Green I-based real-time PCR assay for the rapid detection of canine kobuvirus and canine astrovirus

A duplex SYBR Green I-based real-time PCR assay was established for the simultaneous detection of canine kobuvirus (CaKoV) and canine astrovirus (CaAstV). This assay can easily distinguish the two viruses according to their different melting temperatures (Tm) of 80 °C for CaKoV and 86.5 °C for CaAstV; other canine enteroviruses used as controls showed no specific melting peaks. The detection limit of this assay was determined to be 101 copies/μL for both viruses. This method exhibited high repeatability and reproducibility, with a coefficient of variation less than 1.5 %. A total of 48 fecal samples were collected for clinical testing by real-time PCR and confirmed by sequencing. Real-time PCR assay showed a 10.4 % CaKoV-positive rate and a 4.2 % CaAstV-positive rate, and the positive rate of co-infection of the two viruses was 2.1 %, which was consistent with the sequencing results. This assay has many advantages over conventional PCR: it is rapid, sensitive, specific, and reliable for detecting these two viruses in one sample, and it can be used as a tool to detect CaKoV and CaAstV infection or co-infection in clinical settings.

Detection and genetic characteristics of porcine bocavirus in central China.

To investigate the epidemic profile and genetic diversity of porcine bocavirus (PBoV), 281 clinical samples, including 236intestinal tissue samples and 45 fecal samples were collected from diarrheic piglets on 37 different pig farms in central China, and two SYBR Green I-based quantitative PCR assays were developed to detect PBoV1/2 and PBoV3/4/5, respectively. One hundred forty-eight (52.67%) of the 281 clinical samples were positive for PBoV1/2, 117 (41.63%) were positive for PBoV3/4/5, 55 (19.57%) were positive for both PBoV1/2 and PBoV3/4/5, and 86.49% (32/37) of the pig farms were positive for PBoV. Overall, the prevalence of PBoV was 74.73% (210/281) in central China. Subsequently, nearly full-length genomic sequences of two PBoV strains (designated CH/HNZM and PBoV-TY) from two different farms were determined. Phylogenetic analysis demonstrated that the two PBoV strains obtained in this study belonged to the PBoV G2 group and had a close relationship to 10 other PBoV G2 strains but differed genetically from PBoV G1, PBoV G3, and seven other bocaviruses. CH/HNZM and PBoV-TY were closely related to the PBoV strain GD18 (KJ755666), which may be derived from the PBoV strains 0912/2012 (MH558677) and 57AT-HU (KF206160) through recombination. Compared with reference strain ZJD (HM053694)-China, more amino acid variation was found in the NS1 proteins of CH/HNZM and PBoV-TY. These data extend our understanding of the molecular epidemiology and evolution of PBoV.

Optimized and validated protocol to the detection of the invasive bivalve Limnoperna fortunei from eDNA plankton samples

Abstract: We optimized a methodology for plankton environmental DNA detection of the invasive golden mussel and validated it in samples from a Southern Brazil reservoir. Limnoperna fortunei is a successful invasive alien species that causes significant impacts on freshwater ecosystems. We adjusted and validated the methodology to detect L. fortunei in plankton samples, with a SYBR Green assay. Based on the standard curve analysis, the observed theoretical minimal qPCR detection level was 0.0005625 ng.µL-1 (R2 = 0.99) at a PCR quantification cycle of 14.09–29.56. We also presented a practical guide to be used in monitoring and detection of L. fortunei. The optimized protocol was efficient in detecting L. fortunei and can be used to monitor already infested environments or invasions in new environments.

Specialized antiplasmodial secondary metabolites from Aspergillus niger 58, an endophytic fungus from Terminalia catappa

Ethnopharmacological relevanceTerminalia catappa L. (West Indian-Almond) is a medicinal plant used in traditional medicine for the treatment of infectious diseases. Moreover, various organic extracts prepared from this plant have been reported to exhibit antiplasmodial activity. Aim of the studyThe need for new antimalarials is still an urgency driven by the alarmingly high burden of malaria in endemic regions, with multitude of people dying annually. We have previously identified an endophytic fungus Aspergillus niger 58 harboured by T. catappa as having promising specialized secondary metabolites against the malaria parasites. In the present study, we report the antiplasmodial activity-guided chromatographic isolation of some metabolites secreted by this endophytic fungus. Materials and methodsThe SYBR Green I-based fluorescence microtiter plate assay was used to monitor the growth of Plasmodium falciparum parasites in culture in the presence and absence of inhibitors and results were validated by microscopic analysis of Giemsa-stained culture smears. Giemsa-stain microscopy was also used to study the cell cycle stage-specific action of selected fractions. ResultsThe results revealed that the multidimensional purification of the crude extract (IC50: 4.03 μg/mL) provided RPHPLC F17 (IC50: 0.09 μg/mL) and RPHPLC F18 (IC50: 0.1 μg/mL) with activity against P. falciparum 3D7 (Pf3D7) strain. Moreover, both fractions at IC99 (0.5 μg/mL) exhibited multi-stages action by targeting all the three stages of the life cycle of blood-stage Pf3D7. Two compounds, flavasperone (1) and aurasperone A (2) were isolated, of which aurasperone A exhibited good potency against Pf3D7 (IC50: 4.17 μM) and P. falciparum INDO (PfINDO) (IC50: 3.08 μM). ConclusionOur study adds credence to the notion that endophytic extracts are potential storehouses for potent specialized secondary metabolites that can be harnessed to fight the malaria parasite and reduce the burden of this disease worldwide. An endophyte that can be cultured in laboratory with ability to secrete promising metabolites of medicinal value holds the promise of conserving Nature from the threat of annihilation of flora for medicinal purposes.

In vitro and in vivo antiplasmodial activity of hydroethanolic bark extract of Bridelia atroviridis müll. Arg. (Euphorbiaceae) and lc-ms-based phytochemical analysis

Ethnopharmacological relevanceMalaria is a life-threatening health problem worldwide and treatment remains a major challenge. Natural products from medicinal plants are credible sources for better anti-malarial drugs.Aim of the study: This study aimed at assessing the in vitro and in vivo antiplasmodial activities of the hydroethanolic extract of Bridelia atroviridis bark. Materials and methodsThe phytochemical characterization of Bridelia atroviridis extract was carried out by High-Performance Liquid Chromatography-Mass spectrometry (HPLC-MS). The cytotoxicity test on Vero cells was carried out using the resazurin-based assay while the in vitro antiplasmodial activity was determined on Plasmodium falciparum (Dd2 strain, chloroquine resistant) using the SYBR green I-based fluorescence assay. The in vivo assay was performed on Plasmodium berghei-infected rats daily treated for 5 days with distilled water (10 mL/kg) for malaria control, 25 mg/kg of chloroquine sulfate for positive control and 50, 100 and 200 mg/kg of B. atroviridis extract for the three test groups. Parasitaemia was daily monitored using 10% giemsa-staining thin blood smears. At the end of the treatment, animals were sacrificed, blood was collected for hematological and biochemical analysis while organs were removed for biochemical and histopathological analyses. ResultsThe HPLC-MS analysis data of B. atroviridis revealed the presence of bridelionoside D, isomyricitrin, corilagin, myricetin and 5 others compounds not yet identified. Bridelia atroviridis exhibited good in vitro antiplasmodial activity with the IC50 evaluated at 8.08 μg/mL and low cytotoxicity with the median cytotoxic concentration (CC50) higher than 100 μg/mL. B. atroviridis extract significantly reduced the parasitemia (p < 0.05) with an effective dose-50 (ED-50) of 89 mg/kg. B. atroviridis also prevented anemia, leukocytosis and liver and kidneys impairment by decrease of transaminases, ALP, creatinine, uric acid, and triglycerides concentrations. As well, B. atroviridis extract decreased some pro-inflammatory cytokines (TNF-α, IL-1β, IL-6) levels and significantly improved the anti-inflammatory status (P < 0.01) of infected animals marked by a decrease of IL-10 concentration. These results were further confirmed by the improved of antioxidant status and the quasi-normal microarchitecture of the liver, kidneys and spleen in test groups. Overall, the hydroethanolic bark extract of Bridelia atroviridis demonstrated antimalarial property and justified its use in traditional medicine to manage malaria disease.

Assessment of in vitro and in vivo antimalarial efficacy and GC-fingerprints of selected medicinal plant extracts

A hallmark of mortality and morbidity, malaria is affecting nearly half of the world's population. Emergence of drug-resistant strains of malarial parasite prompts identification and evaluation of medicinal plants and their constituents that may hold the key to a new and effective anti-malarial drug. In this context, nineteen methanolic extracts from seventeen medicinal plants were evaluated for anti-plasmodial potential against Plasmodium falciparum strain 3D7 (Chloroquine (CQ) sensitive) and INDO (CQ resistant) using fluorescence based SYBR-Green assay and for cytotoxic effects against mammalian cell lines. Leaf extract of two plants showed promising in vitro anti-malarial activity (Pf3D7 IC50 ≤ 10 μg/ml); one plant extract showed good activity (Pf3D7 IC50 = 10.1–20 μg/ml); seven were moderately active (IC50 = 20.1–50 μg/ml), four plant extracts showed poor activity (PfD7 IC50 = 50.1–100 μg/ml) and five extracts showed no activity up to IC50 = 100 μg/ml. Further, six extracts were found equipotent to PfINDO (resistance index ranging 0.4–2) and relatively nontoxic to mammalian cell lines HEK293 (cytotoxicity index ranging 1.4–12.5). Based on good resistance and selectivity indices, three extracts were evaluated for in vivo activity in Plasmodium berghei ANKA infected mice at a dose of 500 mg/kg and they showed significant suppression of P. berghei parasitemia. Further, these active plant extracts were fractionated using silica-gel chromatography and their fractions were evaluated for anti-plasmodial action. Obtained fractions showed enrichment in antimalarial activity. Active fractions were analyzed by gas chromatography and mass-spectrometery. Results suggests that the three active plant extracts could serve as potent source of anti-malarial agent and therefore require further analysis.

Estimation of the number of Anisakis larvae in commercial fish using a descriptive model based on real‐time PCR

Seafood parasitation by Anisakis (Anisakidae) larvae has been reported in most of the oceans and seas worldwide. The presence of these nematodes in commonly consumed fish represents a potential hazard for consumers as they can provoke gastrointestinal symptoms and allergic reactions. In the present work, the capacity of a SYBR Green qPCR protocol to quantify Anisakis larvae in commercial fish was evaluated using experimentally spiked samples with different numbers (0-50) of A. simplex third-stage larvae (L3). To verify the agreement of the obtained results, 25 naturally infected fish specimens of Atlantic blue whiting underwent a parallel visual inspection. The logarithmic behavior of the Cq data obtained from the experimentally spiked samples allowed the development of a descriptive mathematical model that correlates the Cq value with the number of Anisakis larvae (R2 = 0.9908, CV = 2.37%). In the commercial blue whiting specimens there was a high correlation between the results of the molecular technique and the visual inspection (R2 = 0.9912); the Bland-Altman analysis showed that 94% of the differences were within the limits of agreement (-4.98 and 6.68), indicating the reliability of the descriptive mathematical model based on the SYBR Green qPCR technique. The descriptive function presented based on the SYBR Green qPCR assay is promising as a sensitive and accurate tool for measuring the Anisakis larval load in commercial fish, with a potential application not only in the food industry but also in prevention programs for public health. © 2020 Society of Chemical Industry.

Establishment of a duplex SYBR green I-based real-time polymerase chain reaction assay for the rapid detection of canine circovirus and canine astrovirus

The similar clinical characteristics of canine circovirus (CaCV) and canine astrovirus (CaAstV) infections and high frequency of co-infection make diagnosis difficult. In this study, a duplex SYBR Green I-based real-time polymerase chain reaction (PCR) assay was established for the rapid, simultaneous detection of CaCV and CaAstV. Two pairs of specific primers were designed based on the Rep gene of CaCV and the Cap gene of CaAstV. By using the real-time PCR assay method, the two viruses can be distinguished by the difference in melting temperatures, 79 °C and 86 °C for CaCV and CaAstV, respectively. This assay had high specificity, showing no cross-reaction with other common canine viruses, as well as high sensitivity, with minimum detection limits of 9.25 × 101 copies/μL and 6.15 × 101 copies/μL for CaCV and CaAstV, respectively. Based on the mean coefficient of variation, the method had good reproducibility and reliability. In a clinical test of 57 fecal samples, the rates of positive detection by real-time PCR were 14.04% (8/57) and 12.28% (7/57) for CaCV and CaAstV, respectively, and the rate of co-infection was 8.77% (5/57). In conclusion, the newly established duplex SYBR Green I-based real-time PCR assay is sensitive, specific, reliable, and rapid and is an effective tool for the detection of co-infections with CaCV and CaAstV.

Detection of spore forming Paenibacillus macerans in raw milk

Paenibacillus macerans can cause spoilage of milk during extended storage. However, the natural milk microbiota interferes with the enumeration of Paenibacillus species in raw milk. In this study, a qualitative SYBR Green real-time PCR assay based on the groEL gene was developed for detecting P. macerans (PMassay) in raw milk and compared with one designed for total Paenibacillus detection (TPassay). The specificity of the PMassay was confirmed against a panel of dairy-related spore forming isolates. In the presence of background DNA substituted up to 95%, P. macerans DNA could still be detected by the PMassay although interference occurred as non-target DNA substitution increased. The PMassay was sensitive (detection limit of 2 log CFU/ml in milk) and specific as non-P. macerans isolates gave a Ct > 30. After enrichment of raw milk for 7 days at 37 °C in Reinforced Clostridial Medium with D-cycloserine (RCM-D) under anaerobiosis, Paenibacillus was detected in 10 of the 16 raw milk samples tested. Enrichment in RCM-D yielded about 0.5 to 5.8 log CFU/ml total Paenibacillus and 0.3 to 4.6 log CFU/ml P. macerans in the samples. The assay could be useful in commercial settings, allowing a sensitive detection of P. macerans.

A modified two-color flow cytometry assay to quantify in-vitro reinvasion and determine invasion phenotypes at low Plasmodium falciparum parasitemia

Invasion of human red blood cells (RBCs) by Plasmodium parasites is a crucial yet poorly characterised phenotype. Two-color flow cytometry (2cFCM) promises to be a very sensitive and high throughput method for phenotyping parasite invasion. However, current protocols require high (~1.0%) parasitemia for assay set-up and need to be adapted for low parasitemia samples, which are becoming increasingly common in low transmission settings. Background fluorescence from nuclei-containing uninfected RBCs and high autologous reinvasion rates (merozoite invasion of donor uninfected RBCs present at 50% assay volume) are some of the limitations to the method's sensitivity to enumerate low parasitemia (<0.5%) with nucleic acid-based stains. Here, we describe modifications for plating unlabeled donor to labeled target RBCs per assay well and for gating parasitemia, that produces accurate quantifications of low reinvasion parasitemia. Plasmodium falciparum 3D7, Dd2 and field isolates at various low and high parasitemia (0.05%–2.0%) were used to set-up SyBr Green 1-based 2cFCM invasion assays. Target RBCs were labeled with CTFR proliferation dye. We show that this dye combination allowed for efficient parasite invasion into target RBCs and that a 1:3 ratio of unlabeled to labeled RBCs per assay greatly skewed autologous reinvasion (p < 0.001). Accuracy of quantifying reinvasion was limited to an assay parasitemia of 0.02% with minimal background interference. Invasion inhibition by enzymatic treatments increased averagely by 10% (p<0.05) across the entire parasitemia range. The effect was greater for samples with <0.5% parasitemia. Overall, a more sensitive method for phenotyping invasion of low P. falciparum parasitemia is described.

Lower cost alternatives for molecular diagnosis of COVID-19: conventional RT-PCR and SYBR Green-based RT-qPCR.

In March 2020, WHO declared a pandemic state due to SARS-CoV-2 having spread. TaqMan-based real-time RT-qPCR is currently the gold standard for COVID-19 diagnosis. However, it is a high-cost assay, inaccessible for the majority of laboratories around the world, making it difficult to diagnose on a large scale. The objective of this study was to standardize lower cost molecular methods for SARS-CoV-2 identification. E gene primers previously determined for TaqMan assays by Colman et al. (2020) were adapted in SYBR Green assay and RT-PCR conventional. The cross-reactivity test was performed with 17 positive samples for other respiratory viruses, and the sensibility test was performed with 8 dilutions (10 based) of SARS-CoV-2 isolated and 63 SARS-CoV-2-positive samples. The SYBR Green assays and conventional RT-PCR have not shown amplification of the 17 respiratory samples positives for other viruses. The SYBR Green-based assay was able to detect all 8 dilutions of the isolate. The conventional PCR detected until 107 dilution, both assays detected the majority of the 63 samples, 98.42% of positivity in SYBR Green, and 93% in conventional PCR. The average Ct variation between SYBR Green and TaqMan was 1.92 and the highest Ct detected by conventional PCR was 35.98. Both of the proposed assays are less sensitive than the current gold standard; however, our data shows a low sensibility variation, suggesting that these methods could be used by laboratories as a lower cost molecular method for SARS-CoV-2 diagnosis.Electronic supplementary materialThe online version of this article (10.1007/s42770-020-00347-5) contains supplementary material, which is available to authorized users.

Development of a novel SYBR green I-based quantitative RT-PCR assay for Senecavirus A detection in clinical samples of pigs

Porcine vesicular disease caused by Senecavirus A (SVA) is a newly emerging disease in many countries. Based on clinical signs only, it is very challenging to distinguish SVA infection from other similar diseases, such as foot and mouth disease, swine vesicular disease, and vesicular stomatitis. Therefore, it is crucial to establish a detection assay for the clinical diagnosis of SVA infection. In this study, a pair of specific primers were designed based on the highly conserved L/VP4 gene sequence of SVA. The established SYBR green I-based quantitative reverse transcription polymerase chain reaction (qRT-PCR) method was used to detect SVA nucleic acids in clinical samples. The limit of detection SVA nucleic acids by qRT-PCR was 6.4 × 101 copies/μL, which was significantly more sensitive than that by gel electrophoresis of 6.4 × 103 copes/μL. This assay was specific and had no cross-reaction with other seven swine viruses. Using SYBR green I-based qRT-PCR, the SVA positive rates in experimental animal samples and field samples were 67.60% (96/142) and 80% (24/30) respectively. The results demonstrate that SYBR green I-based qRT-PCR is a rapid and specific method for the clinical diagnosis and epidemiological investigation of related vesicular diseases caused by SVA.

CpG-SNP site methylation regulates allele-specific expression of MTHFD1 gene in type 2 diabetes

AbstractThe interaction of genetic and epigenetic mechanisms is one of the underlying causes of phenotypic variability in complex diseases such as type 2 diabetes (T2D). To explore the influence of genetic and epigenetic changes in T2D, we examined the effect of methylation of CpG-SNP sites on allele-specific expression (ASE) in one-carbon metabolism pathway genes in T2D. Case-control study was conducted on 860 individuals (430 T2D and 430 controls). CpG-SNPs shortlisted through in silico analysis were genotyped using tetra ARMS PCR and validated using Sanger DNA sequencing. Global DNA methylation was carried out using RP-HPLC. Promoter DNA methylation and CpG site-specific methylation were carried out using bisulfite sequencing. mRNA expression and ASE were examined by SYBR green and TaqMan assay, respectively. Four exonic CpG-SNPs of MTHFD1, MTRR, and GGH genes were identified in folate pathway genes. Among these, MTHFD1 rs2236225 showed significant association with T2D independent of obesity, displayed ASE, and correlated with CpG-SNP site-specific methylation when compared with controls. Our results demonstrate that SNP rs2236225 in the CpG site of MTHFD1, which regulates allele-specific gene expression in PBMCs is methylation dependent and may perturb one-carbon metabolism pathway in T2D subjects.The interaction of genetic and epigenetic mechanisms is one of the underlying causes of phenotypic variability in diseases like type 2 diabetes. The authors identified the methylation-dependent CpG-SNP in the MTHFD1 gene as a regulator of allele-specific gene expression in peripheral blood mononuclear cells, which may perturb one-carbon metabolism in diabetes.

Development of an SYBR Green I-based real-time PCR assay for the rapid detection of canine kobuvirus

Canine kobuvirus (CaKoV) is a causative agent of gastroenteritis in dogs. Rapid detection of CaKoV is important for preventing and controlling this condition. In this study, an SYBR Green I-based quantitative real-time PCR assay was established for CaKoV detection. Specific primers targeting a highly conserved region of the CaKoV 3D gene were developed. After optimization, the method detected a minimum of 1 × 101 copies/μL with high specificity, stability, and repeatability. Moreover, the entire process only required approximately 1.5 h for completion. Our results were supported by those obtained for clinical samples, in which our developed method was successfully applied. The newly established real-time PCR is a rapid, sensitive, specific, and repeatable method for the quantitative detection of CaKoV and can, therefore, be used in epidemiological studies.

Activities of artesunate-based combinations and tafenoquine against Babesia bovis in vitro and Babesia microti in vivo

BackgroundBabesiosis represents a veterinary and medical threat, with a need for novel drugs. Artemisinin-based combination therapies (ACT) have been successfully implemented for malaria, a human disease caused by related parasites, Plasmodium spp. The aim of this study was to investigate whether ACT is active against Babesia in vitro and in vivo.MethodsMefloquine, tafenoquine, primaquine, methylene blue and lumefantrine, alone or in combination with artesunate, were tested in vitro against Babesia bovis. Parasite growth was verified using a SYBR green I-based fluorescence assay. Mice infected with Babesia microti were treated with mefloquine or tafenoquine, alone or in combination with artesunate, and parasitemia was verified by microscopy and PCR.ResultsAll drugs, except lumefantrine, showed in vitro activity against B. bovis, with methylene blue showing the most potent activity (concentration 0.2 μM). Combination with artesunate led to improved activity, with mefloquine showing a striking 20-fold increase in activity. Tafenoquine (10 mg/kg, base), combined or not with artesunate, but not mefloquine, induced rapid clearance of B. microti in vivo by microscopy, but mice remained PCR-positive. Blood from mice treated with tafenoquine alone, but not with tafenoquine-artesunate, was infective for naive mice upon sub-inoculation.ConclusionsTafenoquine, and most likely other 8-aminoquinoline compounds, are promising compounds for the development of ACT for babesiosis.

Evaluation of a SYBR Green Real-Time PCR Assay for Specific Detection of Pasteurella multocida in Culture and Tissue Samples from Sheep

Pasteurella multocida is one of the bacterial species involved in cases of ovine respiratory complex that has been implicated to cause significant economic losses in sheep production system worldwide. The present study was undertaken with the aim of evaluating a SYBR Green dye based real time PCR assay targeting KMT1 gene for the detection of P. multocida. The analytical specificity and sensitivity of the PCR primers were evaluated. The test showed ten-fold more sensitivity than conventional PCR and detected down to 275.5 fg/ µl of genomic DNA concentration, equivalent to 100 copies of KMT1 gene of P. multocida. The real-time PCR was found to be specific for KMT1 gene of P. multocida, as no cross reactivity was detected with a variety of known bacterial isolates. A total of 52 ovine lung tissue samples were screened for P. multocida, which showed improved level of detection as compared to conventional PCR. It is concluded that, this assay may be used as a valuable diagnostic tool for the rapid and specific detection of P. multocida. By virtue of its high throughput format and its ability to accurately identify as well as quantify the bacterial DNA, the method may be useful in large scale epidemiological studies and clarification of pathogenesis.