An integrated software solution for real-time PCR analysis based on microfluidic biochip

Characterization of Aberrant Melting Peaks in Unlabeled Probe Assays

Replication-deficient Adenovirus Induces Host Topoisomerase I Activity: Implications for Adenovirus-mediated Gene Expression

To evaluate the quantitative real-time polymerase chain reaction (qRT-PCR) analysis in herpes simplex virus (HSV) keratitis with and without epithelial involvement. This cross-sectional study was performed on 70 patients with different HSV types and an active ocular lesion in Farabi Eye Hospital, Tehran, Iran. From these 70 patients, 171 samples were collected, including seventy tear samples and 33 scraping samples from involved eyes; and 68 samples from uninvolved fellow eyes. Samples were frozen at - 70 °C until DNA extraction was performed. Quantity of HSV was measured using qRT-PCR in all three samples. The mean age of HSV patients was 52.19 ± 20.42years (range, 4-85years). Forty-one (58.6%) HSV patients had epithelial involvement, and 29 (41.4%) patients did not have epithelial involvement. In PCR-positive cases, the mean number of viruses in affected eyes' tears (8,831,234 ± 4,051,979) was significantly higher than uninvolved eyes' tears (182,603 ± 69,141) (P = 0.02). The mean of PCR in HSV patients with and without epithelial involvement was 10,320,269 ± 5,329,800 and 1,469,419 ± 1,070,396, respectively (P = 0.04). The qRT-PCR of involved tears in both groups (with and without epithelial involvement) was significantly higher than unaffected eyes' tears (P < 0.0001 and P = 0.01, respectively). In cases with and without epithelial involvement, the cutoff points of viral load in involved eyes' tears were 281,000 and 126,000 copies, respectively. The results indicated that qRT-PCR is an excellent method for the detection of herpes simplex keratitis.

Cynanchum wilfordii (Asclepiadaceae) is widely distributed throughout Korea, Japan, and China. Dried roots of this plant have been used as a tonic to promote renal function. Due to the morphological similarities of the dried roots of this plant to those of Cynanchum auriculatum, which is used as a substitute herbal medicine for C. wilfordii, distinguishing these two species is extremely difficult. The present study was conducted to develop molecular markers to distinguish C. wilfordii and C. auriculatum by using conventional polymerase chain reaction (PCR) and realtime PCR analyses. Comparative analysis based on the sequence of the trnL-trnF intergenic spacer revealed 4 base-pair variations, and the inter-individual sequences of the 2 species separately showed 100% homology. According to these results, the variations were divided into 2 groups. The 2 species were further distinguished using a sequence-characterized amplified region marker developed based on a randomly amplified polymorphic DNA-PCR product, and then a single nucleotide polymorphism marker was designed based on the trnL-trnF intergenic spacer for more efficient detection in real-time PCR. The results showed that speciesspecific molecular markers might allow accurate discrimination of C. wilfordii and C. auriculatum.

BACKGROUNDResistance training (RT) is the main modality of exercise used to induce hypertrophic and neuromuscular adaptations. RT done at high intensities (HI‐RT) is also capable of inducing epigenetic modifications leading to altered protein expression. HI‐RT increases protein expression of many enzymes that play key roles in disease prevention and treatment. Inflammation is one pathology that is associated with many disease states that can be altered by the effects of HI‐RT. Both pro‐ and anti‐inflammatory cytokines are upregulated after a bout of exercise. Long term training leads to increases in anti‐inflammatory cytokines such as muscle‐derived interleukin‐6 (IL‐6). Current recommendations state that each muscle group should be exercised 2‐3 nonconsecutive days per week to allow time for recovery. HI‐RT protocols including training much higher training volumes and frequencies have been used by advanced athletes for decades, the effects of these protocols on health outcomes are not reflected in the literature.STUDY OBJECTIVEThe objective of this case report is to determine the effects of high‐frequency and high‐volume HI‐RT on RNA expression linked to inflammatory cytokines.HYPOTHESISIt is hypothesized that both the pro‐inflammatory and anti‐inflammatory cytokines will be upregulated following a high‐frequency high‐volume HI‐RT program due to increased muscle damage and macrophage infiltration.METHODSThe participant (N = 1; 24 years; 192 cm; 107.7 kg; 25.6% body fat) had leg circumference measured at 50% of the length of the femur. Then, a muscle biopsy was performed on the right leg vastus lateralis (VL). Muscle samples were stored at ‐80°C for later analysis. The participant completed a high‐frequency, high‐volume HI‐RT program for one month, which included barbell squats 5 days per week. After the training program was completed, leg circumference was measured again and a second biopsy of the right leg VL was taken. RNA was isolated from the samples for real‐time polymerase chain reaction (RT‐PCR) analysis of IL‐6 and tumor necrosis factor alpha (TNF‐α).RESULTSThe participant experienced a 4 cm increase in thigh circumference (6.4%). Due to time constraints, RT‐PCR analysis was delayed. Analysis will be concluded prior to the conference meeting.CONCLUSIONSTo be updated after analysis is complete.

The aim of this study was to analyse the expression of 1,25-dihydroxyvitamin D3 receptor (VDR) in oral cancers are squamous cell carcinomas (OSCC) to evaluate whether oral tissue may be a new potential target for biologically active 1,25-(OH)2D3 or its analogues. Expression of VDR was analysed in OSCC specimen (n=191) and cancer cell lines (BICR3, BICR56) by immunohistochemistry, real-time polymerase chain reaction (RT-PCR) analysis, and Western blotting. Scanned images were digitally analysed using ImageJ and the immunomembrane plug-in. VDR expression on protein level was correlated with proliferation marker Ki-67, clinical characteristics and impact on survival. VDR was co-labelled with CD44 and Ki-67 in double labeling experiments. Expression subgroups were identified by receiver operating characteristics (ROC) analysis. Low VDR expression was significantly associated with recurrence of the tumour. Multivariate analysis demonstrated low VDR expression as an independent prognostic factor (p=0.0005). Immunohistochemical double staining revealed VDR expression by CD44+ cancer cells. An inverse correlation of VDR+ expressing cancer cells with Ki-67 has been found, which was indicated by immunofluorescence double labeling. VDR specificity was confirmed by Western blot and RT-PCR analysis. For the first time, our study provides evidence that decreased VDR expression in OSCC might be associated with tumour relapse. Tumour cells of a putative CD44+ cancer stem cell compartment express VDR indicating a potential Achilles' heel for the treatment of OSCC although, our results do not allow any conclusion on the function of VDR. Adjuvant chemoprevention by using 1,25-(OH)2D3 or its analogues can be a successful tool targeting adjuvant residual tumour cells and will likely help therapeutic optimization for cancer patients in the clinic. However, this hypothesis requires further in vitro and in vivo studies.

Background . Sexually transmitted infections (STIs) caused by the Gram-negative bacteria Chlamydia trachomatis and Neisseria gonorrhoeae are associated with an increased risk of HIV acquisition in South African women. HIV infection involves binding of the virus to CD4 + receptors on host cells and subsequent binding to a chemokine co-receptor that mediates fusion with the host target cell membrane. Objective . To investigate the potential impact of STIs on HIV receptor expression in cervical epithelial cells, and the molecular pathways mediating this effect. Methods . Expression of Toll-like receptor 4 (TLR4), CD4 + and CCR5 was investigated in HPV type 18-positive (HeLa) and HPV-negative (C33A) cervical epithelial cells, uterine adenocarcinoma cells (Ishikawa), cervical squamous cell carcinoma tissue and normal cervical tissue by real-time polymerase chain reaction (RT-PCR) analysis. HIV receptor expression in HeLa cells was investigated in the presence/absence of 10 μg/mL bacterial lipopolysaccharide (LPS) and chemical inhibitors of epidermal growth factor receptor (EGFR), extracellular signal regulated kinase (ERK1/2) or cyclo-oxygenase-2 (COX-2) by RT-PCR analysis. Results . TLR4, CD4 + and CCR5 expression was elevated in HeLa, C33A and Ishikawa cell lines and carcinoma tissue, compared with normal cervical tissue. Treatment of HeLa cells with LPS increased expression of the primary HIV chemokine co-receptor CCR5 ( p <0.01) and several alternative HIV receptors including CCR2b (p<0.01), CXCR6 ( p <0.05) and GPR1 ( p <0.05), but not CD4 + . We found that LPSmediated CCR5 expression occurred via induction of the EGFR, ERK1/2 and COX-2 signalling pathways. Conclusion . Our findings suggest that STIs have the potential to enhance susceptibility to HIV infection in women by regulating expression of HIV receptors in cervical epithelial cells.

A simple and powerful microfluidic array chip-based electrophoresis system, which is composed of a 3-D microfluidic array chip, a microvacuum pump-based negative pressure sampling device, a high-voltage supply and an LIF detector, was developed. The 3-D microfluidic array chip was fabricated with three glass plates, in which a common sample waste bus (SW(bus)) was etched in the bottom layer plate to avoid intersecting with the separation channel array. The negative pressure sampling device consists of a microvacuum air pump, a buffer vessel, a 3-way electromagnet valve, and a vacuum gauge. In the sample loading step, all the six samples and buffer solutions were drawn from their reservoirs across the injection intersections through the SW(bus) toward the common sample waste reservoir (SW(T)) by negative pressure. Only 0.5 s was required to obtain six pinched sample plugs at the channel crossings. By switching the three-way electromagnetic valve to release the vacuum in the reservoir SW(T), six sample plugs were simultaneously injected into the separation channels by EOF and electrophoretic separation was activated. Parallel separations of different analytes are presented on the 3-D array chip by using the newly developed sampling device.

The β-tubulin (benA) gene is a promising target for the identification of Aspergillus species. Assessment of the clinical implementation and performance of benA gene-based Aspergillus polymerase chain reaction (PCR) remains warranted. In this study, we assessed the analytical performance of the BenA probe PCR in comparison with the Aspergenius kit. We prospectively collected bronchoalveolar lavage (BAL) fluid via diagnostic bronchoscopy from adult patients with hematologic diseases. BenA gene-based multiplex real-time PCR and sequential melting temperature analysis were performed to detect the azole resistance of Aspergillus fumigatus. In total, 76 BAL fluids in 75 patients suspicious of invasive pulmonary aspergillosis (IPA) were collected. Before the application of PCR, the prevalence of proven and probable IPA was 32.9%. However, after implementing the benA gene-based PCR, 15.8% (12 out of 76) of potential IPA cases were reclassified as probable IPA. The analytical performance of the BenA probe PCR in BAL samples was comparable to that of the Aspergenius kit. The diagnostic performance was as follows: sensitivity, 52.0%; specificity, 64.7%; positive predictive value, 41.9%; negative predictive value, 73.3%; positive likelihood ratio, 1.473; and negative likelihood ratio, 0.741. Moreover, benA gene-based Aspergillus PCR discriminated all major sections of Aspergillus, including cryptic species such as Aspergillus tubingensis. Sequential melting temperature analysis successfully detected 2 isolates (15.4%) of A. fumigatus carrying resistant mutations. BenA gene-based Aspergillus PCR with melting temperature analysis enhances diagnostic accuracy and detects not only cryptic species but also resistant mutations of A. fumigatus. It shows promise for clinical applications in the diagnosis of IPA.

Background: It is of great importance to quickly and accurately detect Brucella abortus and Brucella melitensis from clinical and non-clinical samples because of their high prevalence and high risk in causing brucellosis, a life-threating infectious disease affecting both humans and animals. Methods: The current study describes a new method for the detection of brucellosis in clinical samples using real-time polymerase chain reaction (PCR) and high-resolution melt (HRM) curve analysis. This study was conducted on 70 human and 55 animal isolates with more than 1/80 serum antibody titers. Additionally, the accuracy and specificity of the methods were compared. Results: The mean range [cycles threshold±standard deviation (CT±SD)] for the amplified samples was 15.39–25.15 by real-time PCR. The melting peak range (°C) ±SD for B. abortus and B. melitensis was 90.10±0.4 and 89.70±0.4, respectively, and 10 was reported on peak height. Conclusions: The results of HRM analysis can be used for species differentiation and bacterial genotyping according to nucleotide polymorphism. This molecular method could help in diagnosing Brucella quickly and precisely. Quick recognition of Brucella species could decrease its prevalence among humans and animals and mitigate economic loss.

To examine the detection performance of a peptide nucleic acid (PNA) probe-based real-time time polymerase chain reaction (PCR) assay to detect common aneuploidies. Using amniotic fluid samples, PNA probe based real-time PCR (Patio DEP Detection Kit; SeaSun Biomaterials, Korea) assay was performed. PNA probe was designed to hybridize to similar sequences located on different segments of target chromosomes (21, 18, and 13) and a reference chromosome. Amplification of target sequences and melting curve analysis was performed. When analyzing the melting curve, the ratio of the peak height of the target and reference chromosome was calculated and determined as aneuploidy if the ratio of peak height was abnormal. All the results from the PNA probe-based real-time PCR and melting curve analyses were compared to those from conventional karyotyping. Forty-two cases with common aneuploidies (24 of trisomy 21, 12 of trisomy 18, and 6 of trisomy 13) and 131 cases with normal karyotype were analyzed. When comparing the karyotyping results, the sensitivity and specificity of the PNA probe-based real-time PCR assay were both 100%. The level of agreement was almost perfect (k = 1.00). PNA real-time PCR assay is a rapid and easy method for detecting common aneuploidies.

Microsomal prostaglandin E synthase (mPGES)-1, mPGES-2 and cytosolic PGES expression in human gastritis and gastric ulcer tissue

It is becoming increasingly apparent that B cells play an important role in the pathogenesis of rheumatoid arthritis (RA). Due to the scarcity of B cells in RA, it has been technically difficult to functionally characterize B cell apoptosis in this disease. As a necessary first step to identify candidate aberrations, we investigated Fas-mediated signaling events in immortalized peripheral blood B lymphoblastoid cell lines (LCLs) from patients with RA and controls. Cell death was determined by the MTS assay, and apoptosis was detected by the TUNEL assay and DNA laddering. Proteolytic activation of caspase 3 was determined by immunoblotting, and its enzymatic activity was determined by a fluorometric technique. Messenger RNA (mRNA) expression was quantified by real-time polymerase chain reaction (PCR) analysis. The functional role of sphingosine kinase (SPHK) was determined by measuring its enzymatic activity, by quantifying the levels of its product, sphingosine 1-phosphate (S1P), and by investigating the ability of the SPHK inhibitor N,N-dimethylsphingosine and isozyme-specific small interfering RNA (siRNA) oligonucleotides to reverse signaling aberrations. LCLs from patients with RA displayed disease-specific Fas-mediated signal transduction impairment with consequent resistance to cell death. RA LCLs displayed high constitutive SPHK activity and increased levels of S1P. Real-time PCR analysis showed higher SPHK-1 mRNA expression levels in RA patients compared with paired controls. Increased SPHK-1 (but not SPHK-2) mRNA levels were observed in synovial tissue from RA patients. Competitive inhibitors of SPHK reversed the resistance of RA LCLs to Fas-induced apoptosis. Additionally, resistance to Fas-mediated signaling was reversed by siRNA oligonucleotides specific for SPHK-1 but not by oligonucleotides specific for SPHK-2. These findings demonstrate disease-specific resistance to Fas-mediated death signaling in patients with RA and implicate increased SPHK-1 activity as the cause of this aberration.

Tyrosine hydroxylase (TH) is involved in insect melanin and the catecholamine biosynthesis pathway. TH as an enzyme catalyzing the conversion of tyrosine to 3,4-dihydroxyphenylalanine is the first step reaction in the pathway. Although TH has been proven to affect the pigmentation of the epidermis and development in many insects, there is no report about physiological function of the TH gene in Agrotis ipsilon. Here we cloned the TH gene from A. ipsilon. Semi-quantitative real-time polymerase chain reaction (PCR) analysis showed that AiTH was expressed at all development stages. Moreover, its high expression levels in the head and epidermis suggest that it is mainly related to pigment deposition and insect development. Then, we used the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 system to target the AiTH gene: deletion events were detected at the target sites. Compared with the control group, a few mutants with the phenomenon of narrowing in the egg shell and embryos can develop but cannot hatch; the other hatched embryos were seriously dehydrated after hatching and died within the first day. Quantitative real-time PCR analysis revealed that TH was down-regulated in AiTH mutants. Here, our work demonstrated that AiTH plays an important role in growth and development of newly hatched larvae; meanwhile, it would be a promising target to explore a control strategy for A. ipsilon.

AimTo determine the relationship between bilateral allodynia induced by masseter muscle inflammation and P2X3 receptor expression changes in trigeminal ganglia (TRG) and the influence of intramasseteric P2X3 antagonist administration on bilateral masseter allodynia.MethodsTo induce bilateral allodynia, rats received a unilateral injection of complete Freund’s adjuvant (CFA) into the masseter muscle. Bilateral head withdrawal threshold (HWT) was measured 4 days later. Behavioral measurements were followed by bilateral masseter muscle and TRG dissection. Masseter tissue was evaluated histopathologically and TRG tissue was analyzed for P2X3 receptor mRNA expression by using quantitative real-time polymerase chain reaction (PCR) analysis. To assess the P2X3 receptor involvement in nocifensive behavior, two doses (6 and 60 μg/50 μL) of selective P2X3 antagonist A-317491 were administrated into the inflamed masseter muscle 4 days after the CFA injection. Bilateral HWT was measured at 15-, 30-, 60-, and 120-minute time points after A-317491 administration.ResultsHWT was bilaterally reduced after the CFA injection (P < 0.001). Intramasseteric inflammation was confirmed ipsilaterally to the CFA injection. Quantitative real-time PCR analysis demonstrated enhanced P2X3 expression in TRG ipsilaterally to CFA administration (P < 0.01). In comparison with controls, the dose of 6 μg of A-317491 significantly increased bilateral HWT at 15-, 30-, and 60-minute time points after the A-317491 administration (P < 0.001), whereas the dose of 60 μg of A-317491 was efficient at all time points ipsilaterally (P = 0.004) and at 15-, 30-, and 60-minute time points contralaterally (P < 0.001).ConclusionUnilateral masseter inflammation can induce bilateral allodynia in rats. The study provided evidence that P2X3 receptors can functionally influence masseter muscle allodynia and suggested that P2X3 receptors expressed in TRG neurons are involved in masseter inflammatory pain conditions.