Comparative procedures for sample processing and quantitative PCR detection of grapevine viruses

In this study different instruments and methods used for tissue homogenization, RNA extraction and quantitative PCR (qPCR) based detection of grapevine RNA viruses were evaluated. Semi-automated and automated homogenization techniques were compared to process samples from grapevine petioles and cambial tissue. Four different high throughput automated nucleic acid extraction platforms were compared with the RNeasy plant extraction kit for their capacity and efficiency of extracting viral RNA from grapevine infected tissues. The RNA prepared from each extraction platform was then used as template for a comparative analysis of qPCR by One Step RT-qPCR, Two Step RT-qPCR and low density array (LDA) detection. This study showed that a thorough homogenization of grapevine tissues using the Tissue Lyser as well as DNase digestion of the purified RNA prior to cDNA synthesis improved the virus detection and yielded the lowest quantitation cycle (Cq) values in RT-qPCR. Comparison of different RNA extraction methods showed that methods implementing the magnetic bead-based technology were superior to other methods used. Comparing different qPCR detection methods, One Step RT-qPCR showed the lowest Cq values for the same sample tested compared to Two Step RT-qPCR and LDA.     

Exploiting MYC-induced PARPness to target genomic instability in multiple myeloma

Multiple myeloma (MM) is a hematologic malignancy strongly characterized by genomic instability, which promotes disease progression and drug resistance. Since we previously demonstrated that LIG3-dependent repair is involved in the genomic instability, drug resistance and survival of MM cells, we here investigated the biological relevance of PARP1, a driver component of the alternative nonhomologous end joining pathway, in MM. We found a significant correlation between higher PARP1 mRNA expression and poor prognosis of MM patients. PARP1 knockdown or its pharmacological inhibition by olaparib impaired MM cell viability in vitro and was effective against in vivo xenografts of human MM. Anti-proliferative effects induced by PARP1 inhibition were correlated with an increase of DNA double-strand breaks, activation of the DNA damage response and apoptosis. Importantly, by comparing a gene expression signature of PARP-inhibitor sensitivity to our plasma cell dyscrasia gene expression profiling, we identified a subset of MM patients who could benefit from PARP inhibitors. In particular, gene set enrichment analysis suggested that high MYC expression correlates with sensitivity to PARP inhibitors in MM. Indeed, we identified MYC as a promoter of PARP1-mediated repair in MM and, consistently, we demonstrated that cytotoxic effects induced by PARP inhibition are mostly detectable in MYC-proficient MM cells. Taken together, our findings indicate that MYC-driven MM cells are addicted to PARP1 alternative non-homologous end joining repair, which therefore represents a druggable target in this still incurable disease.     

Low dose dobutamine echocardiography for predicting functional recovery after coronary revascularisation

OBJECTIVE—To evaluate the effects of chronic coronary occlusion on the accuracy of low dose dobutamine echocardiography in predicting recovery of dysfunctional myocardium after revascularisation.
DESIGN—Retrospective study.
SETTING—Tertiary referral centre.
PATIENTS—53 consecutive patients with  70% stenosis of the left anterior descending coronary artery (LAD) and regional ventricular dysfunction (group 1, non-occluded LAD; group 2, occluded LAD) who underwent dobutamine echocardiography.
INTERVENTIONS—26 patients underwent coronary artery bypass grafting and 27 had percutaneous transluminal coronary angioplasty.
MAIN OUTCOME MEASURES—Baseline studies before revascularisation included cross sectional echocardiography at rest and during dobutamine infusion (5-10 µg/kg/min), and coronary angiography. The dobutamine study was performed mean (SD) 35 (28) days before revascularisation. Echocardiography at rest was repeated 90 (48) days after revascularisation.
RESULTS—Of 296 dysfunctional segments, 63 in group 1 (43%; 63/146) and 69 in group 2 (46%; 69/150) (NS) improved at follow up. Mean (SD) regional wall motion score index decreased from 1.97 (0.48) (95% confidence interval (CI) 1.01 to 2.93) before revascularisation to 1.74 (0.52) (95% CI 0.70 to 2.78) at follow up in group 1 (p = 0.001), and from 2.12 (0.41) (95% CI 1.30 to 2.98) to 1.88 (0.36) (95% CI 1.16 to 2.60) in group 2 (p = 0.0006). In group 1, sensitivity (87% v 52%; p < 0.0001), negative predictive value (88% v 65%; p = 0.001), and accuracy (77% v 64%; p = 0.01) were all significantly higher than in group 2, despite the angiographic evidence of collaterals in patients with occluded vessels.
CONCLUSIONS—Dobutamine echocardiography shows reduced sensitivity in predicting recovery of dysfunctional myocardium supplied by totally occluded vessels. Thus caution should be used in selecting such patients for revascularisation on the basis of a viability assessment made in this way.


Keywords: dobutamine; coronary artery disease; viability; chronic occlusion     

Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics

Development of High-Throughput Sequencing (HTS), also known as next generation sequencing, revolutionized diagnostic research of plant viruses. HTS outperforms bioassays and molecular diagnostic assays that are used to screen domestic and quarantine grapevine materials in data throughput, cost, scalability, and detection of novel and highly variant virus species. However, before HTS-based assays can be routinely used for plant virus diagnostics, performance specifications need to be developed and assessed. In this study, we selected 18 virus-infected grapevines as a test panel for measuring performance characteristics of an HTS-based diagnostic assay. Total nucleic acid (TNA) was extracted from petioles and dormant canes of individual samples and constructed libraries were run on Illumina NextSeq 500 instrument using a 75-bp single-end read platform. Sensitivity was 98% measured over 264 distinct virus and viroid infections with a false discovery rate (FDR) of approximately 1 in 5 positives. The results also showed that combining a spring petiole test with a fall cane test increased sensitivity to 100% for this TNA HTS assay. To evaluate extraction methodology, these results were compared to parallel dsRNA extractions. In addition, in a more detailed dilution study, the TNA HTS assay described here consistently performed well down to a dilution of 5%. In that range, sensitivity was 98% with a corresponding FDR of approximately 1 in 5. Repeatability and reproducibility were assessed at 99% and 93%, respectively. The protocol, criteria, and performance levels described here may help to standardize HTS for quality assurance and accreditation purposes in plant quarantine or certification programs.     

Effect of thromboxane and serotonin receptor antagonists on intracoronary platelet deposition in dogs with experimentally stenosed coronary arteries

We have reported previously that thromboxane A2 (TXA2) and serotonin (5-HT, 5-hydroxytryptamine) are important mediators of cyclic flow variations (CFVs) in a canine model of coronary artery stenosis and endothelial injury. The present study tested the hypothesis that a TXA2 receptor antagonist is more effective in reducing intracoronary platelet deposition at sites of endothelial injury and severe stenosis than a 5-HT2 receptor antagonist. CFVs developed after placing a plastic constrictor around the left anterior descending coronary artery (LAD) in 51 of 56 dogs. Autologous platelets labeled with 111In were injected in 48 animals. Ten control dogs (group 1A) were killed after CFVs were observed for 1 hour at the nadir of coronary blood flow. Five dogs (group 1B) did not develop CFVs after placement of the constrictor. CFVs were abolished with SQ 28668 (2.75 +/- 0.36 mg/kg, group 2) and SQ 29548 (0.45 +/- 0.1 mg/kg, group 3), two different TXA2 and PGH2 receptor antagonists, in eight of 10 and six of seven dogs, respectively. In eight of 10 dogs (group 4), CFVs were abolished with ketanserin (0.66 +/- 0.12 mg/kg), a 5-HT2 receptor antagonist. In group 2, 3, and 4 dogs, the respective drugs were given so that the minimal dose required to abolished CFVs was administered. In six of six dogs (group 5), a higher dose of ketanserin (i.e., 1.5 mg/kg) was used to abolish CFVs. At death, intracoronary platelet deposition was evaluated by calculating the LAD platelet accumulation ratio (111In activity in the LAD/111In activity in the circumflex coronary artery) in 43 dogs and, in 22 dogs, by microscopic examination of the LAD. A marked LAD platelet accumulation ratio was found in group 1A dogs at the stenotic site and in segments immediately distal to it. The LAD platelet accumulation ratio was significantly reduced by both the low and the high doses of ketanserin compared with group 1A dogs (p less than 0.001). However, the two TXA2 receptor antagonists further reduced the LAD platelet accumulation ratio compared with ketanserin-treated animals (p less than 0.01). Microscopic examination confirmed these findings. We conclude that SQ 28668 and SQ 29548, two different TXA2 receptor antagonists, reduce residual intracoronary platelet deposition associated with CFVs in this canine model more effectively than ketanserin, a 5-HT2 receptor antagonist.     

Role of Tissue Factor Pathway Inhibitor in the Regulation of Tissue Factor‐Dependent Blood Coagulation

Tissue factor pathway inhibitor (TFPI) is a multivalent, Kunitz‐type plasma proteinase inhibitor that modulates tissue factor‐dependent coagulation in vivo. TFPI possesses a peculiar two‐step mechanism of action; it directly inhibits activated factor X and subsequently produces feedback inhibition of the factor VIIa/tissue factor catalytic complex in a factor Xa‐dependent fashion. TFPI biochemistry and physiology have been extensively studied during the last decade. Its pathophysiologic role in thrombotic disorders has, however, only recently started to be unraveled. In particular, circulating plasma TFPI levels have been found to modulate the activity of the tissue factor‐dependent coagulation cascade. In animal models, neutralization of circulating TFPI activity results in restoration of intravascular thrombus formation previously abolished by aspirin. In patients with acute myocardial infarction, TFPI plasma levels measured in blood samples obtained from the coronary sinus were significantly lower than those measured in blood obtained from the ascending aorta, indicating acute consumption of TFPI within the coronary circulation of patients with intracoronary thrombosis. Finally, recent data indicate that transfection of the arterial wall with the gene coding for TFPI is an effective therapeutic intervention to prevent intravascular thrombus formation. Taken together, these observations underline the pathophysiologic importance of TFPI in regulating the procoagulant activity of tissue factor and open new potential therapeutic approaches for the treatment of thrombotic disorders.     

Myocardial revascularization in women

To compare the results of coronary artery bypass in women and men, we reviewed our experience from January 1976 through June 1989. During this period, 170 women with coronary artery disease but with no other cardiac abnormalities underwent coronary artery bypass. We compared this group with a group of 150 men, matching them according to age, presence of angina, extent of disease, and surgical treatment. Preoperative clinical features, surgical data, and early and late results were analyzed. The operative mortality was similar between groups (2.9% for women vs 2.6% for men). The women, however, were more frequently overweight (54% vs 15%; p <0.001) and more often had the following: diabetes mellitus (34% vs 20%; p <0.01), a coronary artery diameter of <1.8 mm (64% vs 29%; p <0.001), poor saphenous vein quality (50% vs 16%; p <0.001), and incomplete revascularization (20% vs 4%; p <0.001). After a mean follow-up of 6 years, the women also had a higher incidence of recent-onset myocardial infarction (31% vs 12%; p <0.001) and a greater tendency to be symptomatic (48% vs 19%; p <0.001). The 12-year cumulative survival rates were similar in both groups (76.2% for women vs 77.1% for men). According to logistic regression analysis of the significantly different variables, the only independent determinants of postoperative asymptomatic status were satisfactory coronary artery caliber, good saphenous vein quality, and complete revascularization. We conclude that poorer functional results after coronary artery bypass surgery in women may be caused by a poorer quality of revascularization, which in turn is a result of smaller coronary artery diameter, worse distal runoff, and less satisfactory vein quality.     

Clinical profile of direct oral anticoagulants versus vitamin K anticoagulants in octogenarians with atrial fibrillation: a multicentre propensity score matched real-world cohort study

Journal of Thrombosis and Thrombolysis - Atrial fibrillation (AF) is the most common arrhythmia in clinical practice and its prevalence increases with age. Few data are available about the clinical...     

Molecular analysis of a California strain of Rupestris stem pitting-associated virus isolated from declining Syrah grapevines

Summary. The sequence of the genome of a Rupestris stem pitting-associated virus (RSPaV) isolated from a declining Syrah grapevine in California, designated the Syrah strain (RSPaV-SY) was determined. The genome of this strain had an overall nucleotide identity of 77% in comparison with RSPaV sequences in GenBank; the coat protein was the most conserved gene among RSPaV sequences and the replicase was the least conserved gene. Phylogenetic analysis of partial coat protein and replicase gene sequences showed RSPaV-SY clustered independently from the majority of RSPaV isolates.     

Comparison of low-density arrays, RT-PCR and real-time TaqMan RT-PCR in detection of grapevine viruses

Low-density arrays (LDA) have been designed based on the real-time RT-PCR (TaqMan) assays for the specific detection of 13 viruses that infect Grapevines in addition to the housekeeping gene 18S rRNA. The viruses included in the study are Grapevine leafroll associated viruses 1, 2, 3, 4, 5, and 9, Grapevine leafroll associated virus-2 Redglobe (GLRaV-2RG) strain, Ruspestris stem pitting associated virus, Grapevine vitivirus A, Grapevine vitivirus B, Grapevine fanleaf virus, Tomato ringspot virus (ToRSV), and Grapevine fleck virus (GFkV). This study includes three new TaqMan RT-PCR assays that have been developed for GLRaV-2RG, GFkV and ToRSV and have been included in the TaqMan RT-PCR and LDA detection. The LDAs were evaluated against a wide range of isolates distributed geographically. Geographical locations included Africa, Europe, Australia, Asia, Latin America and the United States. High-throughput detection of these viruses using LDAs was compared to RT-PCR and real-time TaqMan RT-PCR. The efficiency of different RNA extraction methodologies and buffers were compared for use in low-density array detection. In addition improving the RNA extraction technique and testing the quality of the RNA using the 18S ribosomal RNA TaqMan assay as an RNA specific internal control proved to generate better diagnostic assays. This is the first report on the use of LDA for the detection of plant viruses.