Reverse Transcriptase Reaction Research Articles

Interleukin-27-induced HIV-resistant dendritic cells suppress reveres transcription following virus entry in an SPTBN1, autophagy, and YB-1 independent manner.

Interleukin (IL)-27, a member of the IL-12 family of cytokines, induces human immunodeficiency virus (HIV)-resistant monocyte-derived macrophages and T cells. This resistance is mediated via the downregulation of spectrin beta, non-erythrocytic 1 (SPTBN1), induction of autophagy, or suppression of the acetylation of Y-box binding protein-1 (YB-1); however, the role of IL-27 administration during the induction of immature monocyte-derived dendritic cells (iDC) is poorly investigated. In the current study, we investigated the function of IL-27-induced iDC (27DC) on HIV infection. 27DC inhibited HIV infection by 95 ± 3% without significant changes in the expression of CD4, CCR5, and SPTBN1 expression, autophagy induction and acetylation of YB-1 compared to iDC. An HIV proviral DNA copy number assay displayed that 27DC suppressed reverse transcriptase (RT) reaction without influencing the virus entry. A DNA microarray analysis was performed to identify the differentially expressed genes between 27DC and iDC. Compared to iDC, 51 genes were differentially expressed in 27DC, with more than 3-fold changes in four independent donors. Cross-reference analysis with the reported 2,214 HIV regulatory host genes identified nine genes as potential interests: Ankyrin repeat domain 22, Guanylate binding protein (GBP)-1, -2, -4, -5, Stabilin 1, Serpin family G member 1 (SERPING1), Interferon alpha inducible protein 6, and Interferon-induced protein with tetratricopeptide repeats 3. A knock-down study using si-RNA failed to determine a key factor associated with the anti-HIV activity due to the induction of robust amounts of off-target effects. Overexpression of each protein in cells had no impact on HIV infection. Thus, we could not define the mechanism of the anti-HIV effect in 27DC. However, our findings indicated that IL-27 differentiates monocytes into HIV-resistant DC, and the inhibitory mechanism differs from IL-27-induced HIV-resistant macrophages and T cells.

Prime editing: Mechanism insight and recent applications in plants.

Prime editing (PE) technology utilizes an extended prime editing guide RNA (pegRNA) to direct a fusion peptide consisting of nCas9 (H840) and reverse transcriptase (RT) to a specific location in the genome. This enables the installation of base changes at the targeted site using the extended portion of the pegRNA through RT activity. The resulting product of the RT reaction forms a 3' flap, which can be incorporated into the genomic site through a series of biochemical steps involving DNA repair and synthesis pathways. PE has demonstrated its effectiveness in achieving almost all forms of precise gene editing, such as base conversions (all types), DNA sequence insertions and deletions, chromosomal translocation and inversion and long DNA sequence insertion at safe harbour sites within the genome. In plant science, PE could serve as a groundbreaking tool for precise gene editing, allowing the creation of desired alleles to improve crop varieties. Nevertheless, its application has encountered limitations due to efficiency constraints, particularly in dicotyledonous plants. In this review, we discuss the step-by-step mechanism of PE, shedding light on the critical aspects of each step while suggesting possible solutions to enhance its efficiency. Additionally, we present an overview of recent advancements and future perspectives in PE research specifically focused on plants, examining the key technical considerations of its applications.

Abstract #1406834: Study of Methylation Status and Expression of Vitamin D Receptor Gene in Polycystic Ovarian Syndrome Patients of Kashmiri Population

Downregulation of Vitamin D Receptor (VDR) gene expression resulting from epigenetics events, like methylation in promoter of VDR gene play an important role in pathogenesis, clinical and bio-chemical parameters of polycystic ovary syndrome, but the results from different studies are inconsistent. We aim to determine the methylation status of promoter of VDR gene and VDR gene expression analysis in addition to the co-relation between promoter methylation and expression profile of VDR genes in PCOS patients in Kashmiri Population. This study was a case control, comprising of 100 women with PCOS and 100 normal healthy control women aged between 15-45 years. PCOS patients were selected after proper diagnosis using Rotterdam criteria (2004) and obtaining written consent. DNA extraction was carried out by the non-enzymatic Salting out method and extracted DNA samples were subjected to bisulphite treatment using EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, California) to produces a chemical conversion of unmethylated cytosine to uracil, which is detected as a thymine after PCR. Methylation specific PCR (MS-PCR) was performed following the bisulfite conversion, using pre-designed sets of methylated and unmethylated primers to confirm the prominence of methylation in the promoter VDR region and to specially acknowledge methylated and unmethylated VDR fragments. The VDR expression analysis was carried out following RNA extraction from the blood sample and processed ahead for cDNA synthesis using reverse transcriptase reaction and then relative expression analysis by RT-PCR using SYBR Green fluorescent dye. We found that vitamin D level among test group was significantly lower compared to controls (13.95±9.60 VS. 16.63±7.46; p=0.026). Methylation was significantly higher in test group compared to controls (84% vs 62%; p<0.0001) with OR of 3.21. Furthermore, there exists a significant difference between the average cyclic threshold (CT) value of VDR gene among test and control groups (24.64 vs. 26.14;p <0.0001). The average CT value corresponding to GAPDH (glyceraldehyde phosphate dehydrogenase) is 29.76 in test group and 32.11 in control group. The expression of VDR gene was 0.55 times down regulated in test group in comparison to controls. In the present study, we have comprehensively shown that VDR hypermethylation is significantly associated with reduced vitamin D level and decreased expression level of VDR gene among PCOS women. Increased VDR methylation in response to decreased vitamin D levels could be involved in the impairment of VDR mediated effects resulting in the peculiar clinical and bio-chemical derangements in patients of polycystic ovary syndrome. However, the enhanced ligand availability results in decreased receptor expression to maintain homeostasis of vitamin D signalling. Hence, this, inverse association could have a significant role in the altered gene expression of VDR and thereby effecting the cell response in PCOS patients.

CPT1 and PyK Gene Expression Changes with Different Physiological Conditions between 2 Resistant to Starvation Fly Lines: A Basic Science Experiment

Background: Many organisms adapt to different physiological conditions by changing their gene expression to increase their chances of survival. Drosophila melanogaster fly line 765 show low resistance to starvation and line 362 show high resistance to starvation and were selected to examine how their gene expression would change based on a starved and refed environment. The genes selected were both metabolic genes CPT1 and PyK. CPT1 is responsible for fat breaking and PyK is responsible for the catalysis of the final stage in glycolysis. Methods: Specific Drosophila melanogaster fly lines were selected that showed either a high or low resistance to starvation. These lines were selected to examine how their gene expression would change based on a starved and re-fed environment. RNA was isolated from both sets of flies so that reverse transcriptase reactions could be performed using RT-PCR to generate complementary DNA using reverse transcriptase. The complementary DNA served as a template for amplification using endpoint and quantitative PCR to determine if gene expression would change between the two fly lines. A survival curve was also generated to illustrate the graphical differences among the various fly lines. Results: Quantitative PCR and gene expression data concluded that there was a difference between gene expression of CPT1 and PyK between the two lines. CPT1 quantitative PCR data did not match gene expression predictions, whereas, PyK did in both line 765 and 362. Conclusions: The finding that CPT1 was able to generate Ct values but was unable to adhere to the expected predictions of gene expression is indicative of line 765 having a problem sensing the nutrients and unlikely to be a problem in transcription. Future directions include to characterize both glycogen and triglyceride levels at time t=0 hrs, starved, and re-fed conditions and to investigate if there is a connection between enzyme efficiency and condition type between the two lines.

Predicting the effectiveness of methotrexate therapy based on basal expression of the AMP-activated protein kinase gene in the blood of patients with rheumatoid arthritis

Objective: to search for an association between basal expression of the AMP-activated protein kinase (adenosine monophosphate-activated protein kinase, AMPK) gene in the blood of patients with rheumatoid arthritis (RA) and disease activity, as well as joint destruction before and after 24 months of methotrexate (MT) therapy.Patients and methods. The study included 40 patients with RA who met the 1987 ACR classification criteria, with a disease duration of not more than 2 years, with a mean age of 47.5±15.5 years. All patients received 15 mg/week of MT. The number of swollen joints (SJC) out of 44, the number of tender joints (TSC) out of 53, the duration of morning stiffness (in minutes) and RA activity were assessed using the DAS28 index. The concentration of CRP and IgM rheumatoid factor (RF), antibodies to cyclic citrullinated peptide (ACCP) were assessed. To evaluate the radiological progression of RA, the Sharp method modified by van der Heijde was used. Gene expression in peripheral blood cells was determined by reverse transcriptase reaction and real-time polymerase chain reaction.Results and discussion. During MT therapy, there was a decrease in disease activity by DAS28 index, CRP level, duration of morning stiffness, SJC and TJC. After 2 years, there were no statistically significant changes in the number of erosions, while the number of joints with narrowing of the joint space increased by the end of the study (p=0.004). Treatment with MT resulted in a decrease in AMPK expression. At the same time, patients who achieved remission had the highest level of AMPK before therapy, as did seronegative patients compared to seropositive ones. Based on the ROC analysis, the threshold value of AMPK gene expression was determined, which makes it possible to predict a high probability of a positive effect of MT therapy.Conclusion. AMPK gene expression is associated with disease activity. Its high initial blood level in RA patients is associated with greater efficiency of MT and, possibly, plays a protective role. With an AMPK gene expression index greater than 3.83, the probability of a positive response to MT is high.

The influence of social isolation on the incidence of positivity in covid-19 tests in a metropolitan region of São Paulo, Brazil

Introduction: With the arrival of the SARS-CoV-2 (Coronavirus 2 of severe acute respiratory syndrome) pandemic in Brazil, especially in the city of São Paulo, there was a need to apply social isolation policies associated with testing, covering all municipalities. The Clinical Analysis Laboratory of Centro Universitário FMABC was one of the first laboratories to receive certification and qualification to perform RT-PCR (reverse transcriptase reaction followed by polymerase chain reaction) tests in the metropolitan region of São Paulo.&#x0D; Objective: Aim to analyze the influence of adopting social isolation on the incidence of positivity in COVID-19 tests in the metropolitan region of São Paulo, Brazil.&#x0D; Methods: a descriptive study carried out from March to May 2020, epidemiological data were collected from each unit served and organized by the data controllership team of the Clinical Analysis Laboratory of FMABC. Epidemiological, demographic, and laboratory data were extracted from the Matrix® outpatient data management system. Clinically suspected cases and confirmed by laboratory tests (RT-PCR and serological tests) were entered. The tests were divided into serological tests using the RT-PCR molecular test, on samples of nasopharyngeal mucosal scrapings collected with sterile Swab.&#x0D; Results: It were evaluated PCR test and antibody presence (IgA, IgM and IgG) in blood samples of 16.297 patients. 22.718 tests were performed for the diagnosis of COVID-19, both RT-PCR (10.410 tests) and serological tests to detect anti-SARS-CoV-2 antibodies, IgA, IgM and IgG, a total of 16.297 patients were assessed, 63% women and 37% men. It was observed that the social isolation policies adopted during this period contained the massive expansion of contamination, at least while the social isolation rates were above 55%.&#x0D; Conclusion: The data of this study demonstrated the effectiveness of social isolation in containing the positive contamination of SARS-CoV-2 in the metropolitan region of São Paulo, at least for the first three months.

Systemic Antibiotic and Nonsteroidal Anti-Inflammatory Drug Treatment Decreases the Level of Endogenous Angiogenic Vascular Endothelial Growth Factor in Inflamed Human Periapical Tissues

Vascular endothelial growth factor (VEGF)-induced angiogenesis contributes to inflammatory bone resorption in humans. Widely documented antagonists to resorption include antibiotics and non-steroidal anti-inflammatory drugs (NSAIDs). The purpose of this study was to investigate the effect of these drugs on proangiogenic VEGF levels in periradicular lesions. Periapical tissue biopsies were obtained from 42 patients with chronic periapical periodontitis. VEGF levels were measured using a commercial ELISA kit in patients divided into groups according to treatment: no drugs (control group, n = 25), NSAIDs (n = 7), antibiotics (n = 5), and NSAIDs and antibiotics (n = 5). Reverse transcriptase (RT) reaction was performed in all the samples under analysis. Presence of VEGFA and VEGFB gene expression was assessed using reverse-transcription-polymerase chain reaction (RT-PCR). ELISA analysis indicated that average VEGF levels in tissue samples of patients treated with NSAIDs (6.097 ± 1.930 ng/mL), antibiotics (5.661 ± 2.395 ng/mL), and NSAIDs and antibiotics (7.142 ± 2.601 ng/mL) were significantly lower than in samples of control patients (10.432 ± 4.257 ng/mL, ANOVA p = 0.008). The RT-PCR did not reveal VEGFA gene expression in any of the 42 samples. VEGFB gene expression was found in 26 of 42 samples (69.1%). The use of NSAIDs or antibiotics in patients with exacerbated chronic periodontitis decreases VEGF levels in periapical tissues. Pharmacotherapy may minimize the effects of VEGF on apical periodontitis progression in that way.

Quantitative analysis of RNA by HPLC and evaluation of RT-dPCR for coronavirus RNA quantification

Nucleic acid detection and quantification have been known to be important at various fields, from genetically modified organisms and gene expression to virus detection. For DNA molecules, digital PCR has been developed as an absolute quantification method which is not dependent on external calibrators. While when it comes to RNA molecules, reverse transcription (RT) step must be taken before PCR amplification to obtain cDNA. With different kinds of reverse transcriptase (RTase) and RT reaction conditions being used in laboratory assays, the efficiency of RT process differs a lot which led variety in quantification results of RNA molecules. In this study, we developed HPLC method combined with enzymatic digestion of RNA to nucleotides for quantification of RNA without RT process. This method was metrologically traceable to four nuceloside monophosphate (NMP) Certification Reference Materials of National Institute of Metrology, China (NIMC) for insurance of accuracy. The established method was used to evaluate the reverse transcription digital polymerase chain reaction (RT-dPCR) of three target genes of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) RNA, including open reading frame 1ab (ORF1ab), nucleocapsid protein (N) and envelope protein (E) gene. Three available RT kits had been evaluated and disparities were observed for the RT efficiency varied from 9% to 182%. It is thus demonstrated that HPLC combined with enzymatic digestion could be a useful method to quantify RNA molecules and evaluate RT efficiency. It is suggested that RT process should be optimized and identified in RNA quantification assays.

Timeline analysis of IgA and IgG levels in Covid-19 hospitalized patients according to the clinical outcome

ABSTRACT Introduction: Studies suggest the association between antibody production and the severity of coronavirus disease 2019 (Covid-19). Objectives: To evaluate the concentrations of immunoglobulins class A (IgA) and class G (IgG) during the hospitalization period of Covid-19 patients according to the outcome (survival vs death). Materials and methods: Patients with severe acute respiratory syndrome of coronavirus 2 (Sars-CoV-2) infection confirmed by reverse transcriptase reaction followed by polymerase chain reaction (RT-PCR) were included in this prospective study. Samples were obtained weekly during the follow-up of individuals, considering symptom onset. Titers of anti-Sars-CoV-2 IgA and IgG were measured using a commercial immunoassay. Correlations between IgA/IgG and cycle threshold (Ct) values for N1 and N2 target genes were also assessed. Results: We studied 55 Covid-19 patients (59.7±16.2 years, 63.6% male), of which 28 (50.9%) died. We observed IgA and IgG positivity (IgA+ and IgG+) in 90.9% and 80% of patients, respectively. The highest IgA+ frequency was observed at weeks 2 and 3 and the highest IgG+ at weeks 3 and 4. It is important to note that patients who died presented lower IgA titers in the first two weeks (p < 0.05); however, a significant increase in IgA levels was observed in the subsequent weeks. Lastly, we identified that significant correlations between Ct values and immunoglobulins levels, both IgA and IgG were correlated with Ct N2 in patients who died. Conclusion: Our results suggest that lower IgA titers in early Covid-19, which is associated with lower Ct values, may indicate patients at higher risk for death.

Muscle gene expression of CGRP-α, CGRP receptor, nAchR-β, and GDNF in response to different endurance training protocols of Wistar rats.

The neuromuscular junction underwent adaptations to meet the demands of muscles following increased muscle activity. This study aimed to investigate the effects of high-intensity interval training (HIIT), endurance training (END), and mixed interval training (MIX) on the gene expression of the calcitonin gene-related peptide-α (CGRP-α), CGRP receptor, nicotinic acetylcholine receptors (nAchR)-β and glial-derived neurotrophic factor (GDNF) among different muscle types. Male Wistar rats were randomly divided into four groups: Control (n = 8), END (n = 8), HIIT (n = 8), and MIX (n = 8). The animals run each training protocol for 8weeks (five sessions/week). Forty-eight hours after the last training session, the muscles gastrocnemius and soleus were excised under the sterilized situation. After collection, the material was prepared for RNA extraction, Reverse Transcriptase reaction, and qPCR assay. The HIIT training up-regulated the CGRP-α (p < 0.01), CGRP-Rec (p < 0.01), and GDNF (p < 0.01) in soleus as well as the nAchR-β (p < 0.01) and GDNF (p < 0.01) in gastrocnemius muscles. END training down-regulated the gene expression of CGRP-α (p < 0.01), and nAchR-β (p < 0.01) in gastrocnemius but up-regulated nAchR-β (p = 0.037) in soleus and GDNF (p < 0.01) in gastrocnemius muscles. MIX training did not show any significant up or down-regulation. The endurance performance of HIIT and MIX groups was higher than the END group (p < 0.01). All studied genes up-regulated by HIIT training in a muscle type-specific manner. It seems that the improvement of some synaptic indices induced by HIIT resulted in the improvement of endurance performance.

Probing In Vivo Structure of Individual mRNA 3' Isoforms Using Dimethyl Sulfate.

The DMS region extraction and deep sequencing (DREADS) procedure was designed to probe RNA structure in vivo and to link this structural information to specific 3' isoforms. Growing cells are treated with the alkylating agent dimethyl sulfate (DMS), which enters easily into cells and modifies RNA molecules at solvent-exposed A and C residues. RNA is isolated, and sequencing libraries are constructed in a manner that preserves the identities of individual mRNA isoforms arising from alternative cleavage/polyadenylation sites. During the cDNA synthesis step of library construction, the progress of reverse transcriptase (RT) is blocked when it encounters a DMS modification on the RNA, leading to disproportionate cDNA termination adjacent to DMS-modified positions. After paired-end deep sequencing, the downstream end of each sequenced fragment is mapped to a specific cleavage/poly(A) site representing an individual mRNA 3' isoform. The upstream mapped end of the sequenced fragment defines where the RT reaction stopped. Over the population of all sequenced fragments derived from a particular isoform, A and C positions that are overrepresented next to the upstream endpoints in the DMS sample (relative to a parallel untreated control) are inferred to have been DMS modified, and hence solvent exposed. This method thus allows in vivo structural information obtained using DMS to be linked to individual mRNA 3' isoforms. © 2019 by John Wiley & Sons, Inc.

Abolishment of proximal tubule albumin endocytosis does not affect plasma albumin during nephrotic syndrome in mice

The megalin/cubilin receptor complex is required for proximal tubular endocytosis and degradation of filtered albumin. An additional high-capacity retrieval pathway of intact albumin for the recovery of large amounts of filtered albumin has been proposed, possibly involving cooperation between megalin/cubilin and the neonatal Fc receptor. To clarify the potential role of such a pathway, we examined the effects of megalin/cubilin gene inactivation on tubular albumin uptake and plasma albumin levels in nephrotic, podocin knockout mice. Immunofluorescence microscopy of megalin/cubilin/podocin knockout mouse kidneys demonstrated abolishment of proximal tubule albumin uptake, in contrast to the excessive albumin accumulation observed in podocin knockout mice compared to controls. Correspondingly, urinary albumin excretion was increased 1.4 fold in megalin/cubilin/podocin compared to podocin knockout mice (albumin/creatinine: 226 vs. 157 mg/mg). However, no difference in plasma albumin levels was observed between megalin/cubilin/podocin and podocin knockout mice, as both were reduced to approximately 40% of controls. There were no differences in liver albumin synthesis by mRNA levels and protein abundance. Thus, megalin/cubilin knockout efficiently blocks proximal tubular albumin uptake in nephrotic mice but plasma albumin levels did not differ as a result of megalin/cubilin-deficiency, suggesting no significance of the megalin/cubilin-pathway for albumin homeostasis by retrieval of intact albumin.

Multiplex polymerase chain reaction: Could change diagnosis of Ventilator-associated pneumonia in pediatric critical care units to the fast track?

BackgroundVentilator-associated pneumonia (VAP) is a frequent hospital-acquired infection in critically ill children. The increasing incidence of infections by antibiotic-resistant pathogens adds significantly to the cost of hospital care and to the length of hospital stays. Besides clinical prerequisites for presumptive diagnosis of VAP, rapid identification of the causative pathogen is essential for appropriate treatment. Aim of studyTo identify the causative bacterial pathogens of VAP by both conventional microbiological cultures and multiplex reverse transcriptase reaction (m-PCR) methods with assessment of turnaround time for both diagnostic modalities together with their diagnostic accuracy. MethodsPatients were diagnosed to have VAP when their Clinical Pulmonary Infection Score (CPIS) index was more than 6. Endotracheal aspirate was subjected to both microbiological cultures and multiplex PCR for bacterial pathogens. ResultsMultiplex-PCR showed better sensitivity and positive predictive value than bacterial culture for etiological diagnosis of VAP. Acinetobacter and Klebsiella pneumoniae were the most common identified pathogens. Mean turnaround times were 6h for multiplex PCR and 72h for conventional microbiology. Significant shorter turnaround time was recorded with m PCR compared to microbiological culture. ConclusionMultiplex-PCR permits simultaneous detection of several bacterial pathogens in a single reaction with best turnaround time that permit optimization of emergency diagnosis of VAP and subsequently improve early management of selective bacterial pathogens.

MOLECULAR MECHANISMS OF INHIBITION OF COLLAGEN CLEAVAGE ACTIVITY BY DEFEROXAMINE IN THE CARTILAGE OF PATIENTS WITH OSTEOARTHRITIS

Objective : to study the molecular mechanisms underlying the suppression of collagenase activity in the presence of deferoxamine (DFO) in articular cartilage explants from patients with osteoarthritis (OA). Subjects and methods. The knee joint cartilage obtained during arthroplasty from 33 patients (mean age, 61.8±10.3 years) with OA, and that derived at autopsy from 25 people (mean age 40±6.1 years) without this disease were investigated. The cartilage was cultured in the presence of 10 μm DFO. The gene expression in the cartilage explants was determined by real-time reverse transcriptase and polymerase chain reaction. Results and discussion. The reduced collagenase activity in the presence of DFO in the articular cartilage explants from patients with OA, which had been shown earlier, was accompanied by the significantly inhibited expression of matrix metalloproteinases 1 and 13 and cathepsin K, which had collagenase activity, as well as the marker of hypertrophic chondrocytes, such as X type collagen, and the proinflammatory cytokines interleukin-1β and tumor necrosis factor-α. DFO did not change the expression levels of the phosphoglucomutase and pyruvate kinase genes responsible for the production of adenosine triphosphate (ATP) during glycolysis and the glucose transporter Glut 1. On the contrary, the expression of the genes associated with ATP generation in the tricarboxylic acid cycle: isocitrate dehydrogenase, succinate dehydrogenase, α-ketoglutarate dehydrogenase, malate dehydrogenase, and adenosine monophosphate- activated protein kinase (AMPK) significantly increased. The expression of AMPK in the articular cartilage of patients with OA was significantly lower than that in healthy individuals. Conclusion. Inhibition of collagen cleavage in the presence of DFO in the articular cartilage explants from OA patients, which was accompanied by a considerable decrease in the expression of the proteases responsible for degradation of the extracellular matrix, proinflammatory cytokines and chondrocytes hypertrophy, was due to the enhanced activity of mitochondrial oxidative phosphorylation in the chondrocytes.

Increasing the Sensitivity of BCR-ABL Monitoring By Digital PCR By Reducing the Background Noise

BackgroundDroplet digital PCR (dPCR) is a potentially appealing technology for quantitative detection of specific mutations with simultaneous measurement of the reference gene and without the need for standard curves. This makes dPCR particularly suitable for minimal residual disease (MRD) diagnostics in chronic myeloid leukaemia. However, a limitation of the dPCR assays compared to standard quantitative PCR (qPCR) is the background (termed lower limit of blank, LoB) of 1 or 2 positive droplets for BCR-ABL (Franke et al, ASH 2015, Cross et al, Leukemia 2016). The resulting false positive rate (FPR) limits the sensitivity and the ability of the test to detect deep molecular remissions.AimsThe aim was to establish BCR-ABL (b2/a2 and/or b3/a2 transcript) dPCR assays with a sensitivity at least equivalent to that of qPCR, in which <5% of negative controls generate a single positive drop (FPR<5%, LoB=0).MethodsOne assay (Assay 1) was developed in Leipzig and another (Assay 2) by Bio-Rad laboratories. Sample preparation was identical for both assays up to the stage of reverse transcription (RT). Assay 1 used routine local RT procedure followed by a duplex BCR-ABL / ABL dPCR reaction modified from the M-BCR-ABL PCR published by Jennings et al. 2014. We tested ABL primer combinations from exons 4, 8, 10, and 11 generating a range of product lengths and optimised quenchers and PCR conditions to maximise the separation between positive and negative droplets. Assay 2 consisted of a reverse transcriptase reaction followed by a duplex PCR specific for ABL and both the b2/a2 and b3/a2 transcripts of BCR-ABL. Digital droplet PCR was performed in both cases using the Bio-Rad QX200 system.Background noise and cross hybridisation were assessed in non-template controls (NTC), BCR-ABL negative cell lines and healthy wild-type donor samples. In addition, assay 2 was tested on 40 CML patient samples with MRD levels ranging from BCR-ABL negative to 1% BCR-ABL/ABL as defined by standard qPCR.ResultsAssay 1 yielded a FPR of 4% (4/94) in NTC with 1 positive droplet for BCR-ABL and a FPR of 3% for ABL (n = 3/94), resulting in a specificity of >95% and a LOB of 0. The BCR-ABL FPR using wild type target (HEK 293T cell line and healthy donors) was 5% (5/92 and 2/37, respectively).Assay2: The specificity was >95% for both BCR-ABL and ABL in NTC and wild type samples. Extensive NTC analysis yielded no false positives for BCR-ABL PCR (n = 0/176; LoB = 0) and 1% false positives in ABL PCR (n = 2/176; 1-2 positive droplets, LoB = 0). The BCR-ABL negative cell line was confirmed negative for BCR-ABL PCR (n = 44), while the BCR-ABL assays of healthy donors were positive in 2% (n = 5/234) with 1 positive droplet per positive sample. The BCR-ABL copy numbers of the 40 CML samples were lower by dPCR than by RT-PCR (median 3/6) with similar ABL transcripts (median 55500/54949). This resulted in lower ratios by dPCR (mean 0.0313 vs. 0.0461 by qPCR). However, after conversion of the qPCR results with our lab specific conversion factor (CF) <1, the dPCR ratios were higher (mean 0.0313 vs. 0.0134). The MR classes were concordant in 60% of the samples, but 30% had more MRD while 10% had less MRD by dPCR than by qPCR, confirming our previous results using the EAC protocol (Franke, ASH 2015). More samples were MRD positive by dPCR than by qPCR (58% vs 50%).ConclusionsAn assay with a FPR of <5% and a LoB = 0 for the detection of BCR-ABL was developed. The BIO-RAD QX 200-Dx BCR-ABL Kit is fully functional and has a high specificity for BCR-ABL and ABL with a LoB of 0. The high specificity and low FPR/LoB of both assays enables sensitive and accurate monitoring of deep molecular remissions in CML. DisclosuresFranke:Novartis: Honoraria, Research Funding. Tzonev:Bio-Rad: Employment, Equity Ownership. Shelton:Bio-Rad: Employment. Niederwieser:Amgen: Speakers Bureau; Novartis Oncology Europe: Research Funding, Speakers Bureau. Lange:Novartis: Research Funding.

The Effect of Stem Cells as an Adjuvant on the Immunogenicity of a Potential Anti-Schistosomal Vaccine in Mice

Vaccination against schistosomes can be targeted towards the prevention of infection and/or to the reduction of parasite fecundity and pathology. However, as eggs are responsible mainly for schistosomiasis pathology, so crude soluble egg antigen (SEA) seems suitable to be used as a potential vaccine. Many studies have provided new insights establishing a role for mesenchymal stem cells (MSCs) in liver regeneration and improvement of schistosomiasis hepatic fibrosis, in addition to the need for standardized and effective adjuvant-vaccine formulations. So, the aim of this work is to evaluate the effect of stem cells when used as an adjuvant of a potential anti-schistosomal vaccine (crude SEA) in murine models. The current work was carried out on 100 mice (30 males for harvesting MSCs + 70 females for seven study groups, each of 10). A schedule of vaccination and challenge infection was followed so, GI (control healthy), G2 (control infected only) infected subcutaneously with S. mansoni cercaria (80-90 Schistosoma mansoni cercariae suspended in 0.2 ml distilled Water), G 3 (FCA then infected) received Freund's complete adjuvant (FCA) then infected, G4 (MSCs then infected) received MSCs then infected, G5 (SEA then infected) received SEA vaccine then infected, G6 (SEA+FCA then infected) received SEA vaccine and FCA then infected, G7 (SEA+MSCs then infected) received SEA vaccine and MSCs then infected. The current work was assessed by histopathological study and morphometric analysis (using H&E and Masson's Trichrome stains) to highlight number, size and type of liver granulomas and percentage of liver fibrosis, immunological and molecular studies (RNA extraction, Re- verse Transcriptase and PCR technique) for detection of interleukin-10 mRNA gene expression in liver tissue by reverse transcriptase & polymerase chain reaction (RT & PCR). The results showed that a- SEA alone as a potential anti-schistosomal vaccine was more or less moderately protective, b- MSCs alone before the infection had mild prophylactic effects, c- MSCs as an adjuvant of the crude SEA increased its capabilities with highly significant results regarding the decrease in granuloma number, size, percentage and density of hepatic fi- brosis, and d-There was significant increase in IL-10 mRNA gene expression on using (SEA+MSCs) (G7) if compared to other tested groups.

Comparison of RNA Extraction Methods for Molecular Analysis of Oral Cytology.

The aim of this study was to compare three methods of RNA extraction for molecular analysis of oral cytology to establish the best technique, considering its concentration and purity for molecular tests of oral lesions such as real-time reverse transcriptase reaction. The sample included exfoliative cytology from the oral cavity mucosa of patients with no visible clinical changes, using Orcellex Rovers Brush®. The extraction of total RNA was performed using the following three techniques: 30 samples were extracted by Trizol® technique, 30 by the Direct-zolTM RNA Miniprep system and 30 by the RNeasy mini Kit. The absorbance was measured by spectrophotometer to estimate the purity. The estimated RNA concentration was obtained by multiplying the value of A260 (ng/mL) by 40. Statistical analysis of the obtained data was performed using GraphPad Prism 5.03 software with Student t, analysis of variance and Bonferroni tests, considering p ≤0.05. Trizol® group revealed higher average concentration, followed by Direct-zolTM and Rneasy group. It was observed that the RNA Direct-zolTM group had the highest purity, followed by RNeasy and Trizol® groups, allowing for the two ratios. Considering all aspects, concentration, purity and time spent in the procedures, the Direct-zolTM group showed the best results.

Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR

Real Time Polymerase Chain Reaction also known as quantitative PCR (q-PCR) is a widely used tool in microbial ecology to quantify gene abundances of taxonomic and functional groups in environmental samples. Used in combination with a reverse transcriptase reaction (RT-q-PCR), it can also be employed to quantify gene transcripts. q-PCR makes use of highly sensitive fluorescent detection chemistries that allow quantification of PCR amplicons during the exponential phase of the reaction. Therefore, the biases associated with 'end-point' PCR detected in the plateau phase of the PCR reaction are avoided. A protocol to quantify bacterial 16S rRNA genes and transcripts from coastal sediments via real-time PCR is provided. First, a method for the co-extraction of DNA and RNA from coastal sediments, including the additional steps required for the preparation of DNA-free RNA, is outlined. Second, a step-by-step guide for the quantification of 16S rRNA genes and transcripts from the extracted nucleic acids via q-PCR and RT-q-PCR is outlined. This includes details for the construction of DNA and RNA standard curves. Key considerations for the use of RT-q-PCR assays in microbial ecology are included.

Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR

Real Time Polymerase Chain Reaction also known as quantitative PCR (q-PCR) is a widely used tool in microbial ecology to quantify gene abundances of taxonomic and functional groups in environmental samples. Used in combination with a reverse transcriptase reaction (RT-q-PCR), it can also be employed to quantify gene transcripts. q-PCR makes use of highly sensitive fluorescent detection chemistries that allow quantification of PCR amplicons during the exponential phase of the reaction. Therefore, the biases associated with 'end-point' PCR detected in the plateau phase of the PCR reaction are avoided. A protocol to quantify bacterial 16S rRNA genes and transcripts from coastal sediments via real-time PCR is provided. First, a method for the co-extraction of DNA and RNA from coastal sediments, including the additional steps required for the preparation of DNA-free RNA, is outlined. Second, a step-by-step guide for the quantification of 16S rRNA genes and transcripts from the extracted nucleic acids via q-PCR and RT-q-PCR is outlined. This includes details for the construction of DNA and RNA standard curves. Key considerations for the use of RT-q-PCR assays in microbial ecology are included.

Generation of Recombinant Monoclonal Antibodies from Immunised Mice and Rabbits via Flow Cytometry and Sorting of Antigen-Specific IgG+ Memory B Cells.

Single B cell screening strategies, which avoid both hybridoma fusion and combinatorial display, have emerged as important technologies for efficiently sampling the natural antibody repertoire of immunized animals and humans. Having access to a range of methods to interrogate different B cell subsets provides an attractive option to ensure large and diverse panels of high quality antibody are produced. The generation of multiple antibodies and having the ability to find rare B cell clones producing IgG with unique and desirable characteristics facilitates the identification of fit-for-purpose molecules that can be developed into therapeutic agents or research reagents. Here, we describe a multi-parameter flow cytometry single-cell sorting technique for the generation of antigen-specific recombinant monoclonal antibodies from single IgG+ memory B cells. Both mouse splenocytes and rabbit PBMC from immunised animals were used as a source of B cells. Reagents staining both B cells and other unwanted cell types enabled efficient identification of class-switched IgG+ memory B cells. Concurrent staining with antigen labelled separately with two spectrally-distinct fluorophores enabled antigen-specific B cells to be identified, i.e. those which bind to both antigen conjugates (double-positive). These cells were then typically sorted at one cell per well using FACS directly into a 96-well plate containing reverse transcriptase reaction mix. Following production of cDNA, PCR was performed to amplify cognate heavy and light chain variable region genes and generate transcriptionally-active PCR (TAP) fragments. These linear expression cassettes were then used directly in a mammalian cell transfection to generate recombinant antibody for further testing. We were able to successfully generate antigen-specific recombinant antibodies from both the rabbit and mouse IgG+ memory B cell subset within one week. This included the generation of an anti-TNFR2 blocking antibody from mice with an affinity of 90 pM.