Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control.

Aspergillus flavus is an agriculturally important fungus that causes ear rot of maize and produces aflatoxins, of which B1 is the most carcinogenic naturally-produced compound. In the US, the management of aflatoxins includes the deployment of biological control agents that comprise two nonaflatoxigenic A. flavus strains, either Afla-Guard (member of lineage IB) or AF36 (lineage IC). We used genotyping-by-sequencing to examine the influence of both biocontrol agents on native populations of A. flavus in cornfields in Texas, North Carolina, Arkansas, and Indiana. This study examined up to 27,529 single-nucleotide polymorphisms (SNPs) in a total of 815 A. flavus isolates, and 353 genome-wide haplotypes sampled before biocontrol application, three months after biocontrol application, and up to three years after initial application. Here, we report that the two distinct A. flavus evolutionary lineages IB and IC differ significantly in their frequency distributions across states. We provide evidence of increased unidirectional gene flow from lineage IB into IC, inferred to be due to the applied Afla-Guard biocontrol strain. Genetic exchange and recombination of biocontrol strains with native strains was detected in as little as three months after biocontrol application and up to one and three years later. There was limited inter-lineage migration in the untreated fields. These findings suggest that biocontrol products that include strains from lineage IB offer the greatest potential for sustained reductions in aflatoxin levels over several years. This knowledge has important implications for developing new biocontrol strategies.

T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees.

The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.

T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.

Motivation: High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades. Results: In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi-Pezizomycotina (Ascomycota)-based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2 ). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree. Availability and Implementation: T-BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu . Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources. Contact: icarbon@ncsu.edu. Supplementary information: Supplementary data are available at Bioinformatics online.

Detection of myocardial damage in patients with sarcoidosis.

BACKGROUND: In patients with sarcoidosis, sudden death is a leading cause of mortality, which may represent unrecognized cardiac involvement. Delayed-enhancement cardiovascular magnetic resonance (DE-CMR) can detect minute amounts of myocardial damage. We sought to compare DE-CMR with standard clinical evaluation for the identification of cardiac involvement. METHODS AND RESULTS: Eighty-one consecutive patients with biopsy-proven extracardiac sarcoidosis were prospectively recruited for a parallel and masked comparison of cardiac involvement between (1) DE-CMR and (2) standard clinical evaluation with the use of consensus criteria (modified Japanese Ministry of Health [JMH] guidelines). Standard evaluation included 12-lead ECG and at least 1 dedicated non-CMR cardiac study (echocardiography, radionuclide scintigraphy, or cardiac catheterization). Patients were followed for 21+/-8 months for major adverse events (death, defibrillator shock, or pacemaker requirement). Patients were predominantly middle-aged (46+/-11 years), female (62%), and black (73%) and had chronic sarcoidosis (median, 7 years) and preserved left ventricular ejection fraction (median, 56%). DE-CMR identified cardiac involvement in 21 patients (26%) and JMH criteria in 10 (12%, 8 overlapping), a >2-fold higher rate for DE-CMR (P=0.005). All patients with myocardial damage on DE-CMR had coronary disease excluded by x-ray angiography. Pathology evaluation in 15 patients (19%) identified 4 with cardiac sarcoidosis; all 4 were positive by DE-CMR, whereas 2 were JMH positive. On follow-up, 8 had adverse events, including 5 cardiac deaths. Patients with myocardial damage on DE-CMR had a 9-fold higher rate of adverse events and an 11.5-fold higher rate of cardiac death than patients without damage. CONCLUSIONS: In patients with sarcoidosis, DE-CMR is more than twice as sensitive for cardiac involvement as current consensus criteria. Myocardial damage detected by DE-CMR appears to be associated with future adverse events including cardiac death, but events were few, and this needs confirmation in a larger cohort.

Feasibility of magnetic resonance imaging in patients with an implantable loop recorder.

BACKGROUND: The implantable loop recorder (ILR) is a useful tool in the diagnosis of syncope. Our understanding of their functional and safety profile in interfering environments such as magnetic resonance imaging (MRI) becomes increasingly important as they become more prevalent. METHODS: We report four patients with an ILR who underwent MRI. The ILR memory was cleared before MRI and no changes were made to programmed settings. Device interrogation took place immediately after the scan. Patients were surveyed for device movement and heating, in addition to cardiopulmonary symptoms after their MRI. RESULTS: Following MRI scanning, all patients were asymptomatic and no device movement or heating was observed. In addition, the functionality of the device remained unaffected. Artifacts mimicking arrhythmias were seen in all ILR patients regardless of the type of MRI scan. CONCLUSIONS: MRI scanning of ILR patients can be performed without harm to patient or device, but artifacts that could be mistaken for a tachyarrhythmia are seen frequently.

Relative utility of magnetic resonance imaging and right ventricular angiography to diagnose arrhythmogenic right ventricular cardiomyopathy.

INTRODUCTION: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is characterized by fibrofatty replacement of the RV myocardium. Two imaging techniques used to assess patients suspected of having ARVC are magnetic resonance imaging (MRI) and right ventricular angiography (RVA). Traditionally, RVA has played a central role in the diagnosis of ARVC, but the non-invasive nature of MRI and its unique ability to detect fatty tissue infiltration has increased its popularity as a diagnostic tool. The objective of this study was to assess the relative diagnostic accuracy of MRI and RVA for ARVC. METHODS AND RESULTS: Seventeen patients (9 men, 8 women; ages 42 +/- 17 [range 16-78] years) with documented ventricular arrhythmias were investigated for ARVC. A positive diagnosis of ARVC was based on criteria set forth by the ISFC Working Group on Cardiomyopathies and Dysplasia. ECG-gated spin-echo and gradient-echo MR images in multiple planes and RAO/LAO RV angiograms were compared for diagnostic concordance. Based on working group criteria, 7 patients were diagnosed with ARVC. In ten patients, MRI suggested ARVC. The remaining 7 patients had no MRI findings suggestive of the disease. Four patients with MRI findings of ARVC were incorrectly diagnosed based on Task Force criteria. Conversely, 1 patient with a normal MRI met Task Force criteria for the diagnosis of ARVC. Based on RV angiograms, 7 patients had findings suggestive of ARVC. The 10 patients without AVRD (based on RVA) also did not meet the necessary criteria for diagnosis of ARVC using Task Force standards. RVA was 100% specific and 100% sensitive compared to MRI that was only 86% sensitive and 60% specific. MRI proved to be most reliable when the images demonstrated gross, lipomatous infiltration, evidenced by a large area of hyperintensity. When the results of MRI and RVA were congruent, the diagnosis was always accurate. CONCLUSION: RVA is more sensitive and specific to diagnose ARVC diagnosis than MRI, at least until MRI protocols are better developed. MRI results are most robust when indicators of ARVC are grossly apparent. False-positive diagnosis by MRI was primarily related to perceived motion abnormalities that were not seen by RVA. One of its greatest potential assets (fat detection) did not enhance diagnostic specificity.