Highlights of the 65th Annual Meeting of the American Association of Physicists in Medicine

The 65th annual meeting of the American Association of Physicists in Medicine took place in July 2023 with a theme of "The Art of Science, The Science of Care." We review a sample of the more than 1000 talks and 1600 posters, focusing on a few topics of interest. Recent legislative changes across the country regarding reproductive health care have led to questions about how these regulations may affect your practice. A fantastic multidisciplinary session addressed these issues with experts in the areas of legal, administration, physics, and medicine. Both the scientific sessions and vendor hall displayed a multitude of artificial intelligence-based solutions. Presenters from academia and industry discussed the latest technological advancements, along with the potential challenges of evaluating, implementing, and maintaining this new technology. Advancements in artificial intelligence have reduced the time required to contour and compute new plans, allowing adaptive radiation therapy (ART) to become mainstream. ART-specific treatment platforms, such as MR linacs and Ethos, streamline the ART workflow and make it accessible to most clinics. Presenters discussed the latest clinical applications of ART, and shared their experience with the workflows, commissioning, and training that has worked in their clinics. We hope this snapshot of American Association of Physicists in Medicine 2023 has piqued your interest and we will see you in Los Angeles in 2024.

Investigation of autosegmentation techniques on T2-weighted MRI for off-line dose reconstruction in MR-linac workflow for head and neck cancers

BACKGROUND

In order to accurately accumulate delivered dose for head and neck cancer patients treated with the Adapt to Position workflow on the 1.5T magnetic resonance imaging (MRI)-linear accelerator (MR-linac), the low-resolution T2-weighted MRIs used for daily setup must be segmented to enable reconstruction of the delivered dose at each fraction.

PURPOSE

In this pilot study, we evaluate various autosegmentation methods for head and neck organs at risk (OARs) on on-board setup MRIs from the MR-linac for off-line reconstruction of delivered dose.

METHODS

Seven OARs (parotid glands, submandibular glands, mandible, spinal cord, and brainstem) were contoured on 43 images by seven observers each. Ground truth contours were generated using a simultaneous truth and performance level estimation (STAPLE) algorithm. Twenty total autosegmentation methods were evaluated in ADMIRE: 1-9) atlas-based autosegmentation using a population atlas library (PAL) of 5/10/15 patients with STAPLE, patch fusion (PF), random forest (RF) for label fusion; 10-19) autosegmentation using images from a patient's 1-4 prior fractions (individualized patient prior [IPP]) using STAPLE/PF/RF; 20) deep learning (DL) (3D ResUNet trained on 43 ground truth structure sets plus 45 contoured by one observer). Execution time was measured for each method. Autosegmented structures were compared to ground truth structures using the Dice similarity coefficient, mean surface distance (MSD), Hausdorff distance (HD), and Jaccard index (JI). For each metric and OAR, performance was compared to the inter-observer variability using Dunn's test with control. Methods were compared pairwise using the Steel-Dwass test for each metric pooled across all OARs. Further dosimetric analysis was performed on three high-performing autosegmentation methods (DL, IPP with RF and 4 fractions [IPP_RF_4], IPP with 1 fraction [IPP_1]), and one low-performing (PAL with STAPLE and 5 atlases [PAL_ST_5]). For five patients, delivered doses from clinical plans were recalculated on setup images with ground truth and autosegmented structure sets. Differences in maximum and mean dose to each structure between the ground truth and autosegmented structures were calculated and correlated with geometric metrics.

RESULTS

DL and IPP methods performed best overall, all significantly outperforming inter-observer variability and with no significant difference between methods in pairwise comparison. PAL methods performed worst overall; most were not significantly different from the inter-observer variability or from each other. DL was the fastest method (33 s per case) and PAL methods the slowest (3.7-13.8 min per case). Execution time increased with a number of prior fractions/atlases for IPP and PAL. For DL, IPP_1, and IPP_RF_4, the majority (95%) of dose differences were within ± 250 cGy from ground truth, but outlier differences up to 785 cGy occurred. Dose differences were much higher for PAL_ST_5, with outlier differences up to 1920 cGy. Dose differences showed weak but significant correlations with all geometric metrics (R2 between 0.030 and 0.314).

CONCLUSIONS

The autosegmentation methods offering the best combination of performance and execution time are DL and IPP_1. Dose reconstruction on on-board T2-weighted MRIs is feasible with autosegmented structures with minimal dosimetric variation from ground truth, but contours should be visually inspected prior to dose reconstruction in an end-to-end dose accumulation workflow.

The Use of MR-Guided Radiation Therapy for Head and Neck Cancer and Recommended Reporting Guidance

Although magnetic resonance imaging (MRI) has become standard diagnostic workup for head and neck malignancies and is currently recommended by most radiological societies for pharyngeal and oral carcinomas, its utilization in radiotherapy has been heterogeneous during the last decades. However, few would argue that implementing MRI for annotation of target volumes and organs at risk provides several advantages, so that implementation of the modality for this purpose is widely accepted. Today, the term MR-guidance has received a much broader meaning, including MRI for adaptive treatments, MR-gating and tracking during radiotherapy application, MR-features as biomarkers and finally MR-only workflows. First studies on treatment of head and neck cancer on commercially available dedicated hybrid-platforms (MR-linacs), with distinct common features but also differences amongst them, have also been recently reported, as well as "biological adaptation" based on evaluation of early treatment response via functional MRI-sequences such as diffusion weighted ones. Yet, all of these approaches towards head and neck treatment remain at their infancy, especially when compared to other radiotherapy indications. Moreover, the lack of standardization for reporting MR-guided radiotherapy is a major obstacle both to further progress in the field and to conduct and compare clinical trials. Goals of this article is to present and explain all different aspects of MR-guidance for radiotherapy of head and neck cancer, summarize evidence, as well as possible advantages and challenges of the method and finally provide a comprehensive reporting guidance for use in clinical routine and trials.

Development and implementation of optimized endogenous contrast sequences for delineation in adaptive radiotherapy on a 1.5T MR-linear-accelerator: a prospective R-IDEAL stage 0-2a quantitative/qualitative evaluation of in vivo site-specific quality-assurance using a 3D T2 fat-suppressed platform for head and neck cancer

Purpose

To improve segmentation accuracy in head and neck cancer (HNC) radiotherapy treatment planning for the 1.5T hybrid magnetic resonance imaging/linear accelerator (MR-Linac), three-dimensional (3D), T2-weighted, fat-suppressed magnetic resonance imaging sequences were developed and optimized.

Approach

After initial testing, spectral attenuated inversion recovery (SPAIR) was chosen as the fat suppression technique. Five candidate SPAIR sequences and a nonsuppressed, T2-weighted sequence were acquired for five HNC patients using a 1.5T MR-Linac. MR physicists identified persistent artifacts in two of the SPAIR sequences, so the remaining three SPAIR sequences were further analyzed. The gross primary tumor volume, metastatic lymph nodes, parotid glands, and pterygoid muscles were delineated using five segmentors. A robust image quality analysis platform was developed to objectively score the SPAIR sequences on the basis of qualitative and quantitative metrics.

Results

Sequences were analyzed for the signal-to-noise ratio and the contrast-to-noise ratio and compared with fat and muscle, conspicuity, pairwise distance metrics, and segmentor assessments. In this analysis, the nonsuppressed sequence was inferior to each of the SPAIR sequences for the primary tumor, lymph nodes, and parotid glands, but it was superior for the pterygoid muscles. The SPAIR sequence that received the highest combined score among the analysis categories was recommended to Unity MR-Linac users for HNC radiotherapy treatment planning.

Conclusions

Our study led to two developments: an optimized, 3D, T2-weighted, fat-suppressed sequence that can be disseminated to Unity MR-Linac users and a robust image quality analysis pathway that can be used to objectively score SPAIR sequences and can be customized and generalized to any image quality optimization protocol. Improved segmentation accuracy with the proposed SPAIR sequence will potentially lead to improved treatment outcomes and reduced toxicity for patients by maximizing the target coverage and minimizing the radiation exposure of organs at risk.

Prospective evaluation of in vivo and phantom repeatability and reproducibility of diffusion-weighted MRI sequences on 1.5 T MRI-linear accelerator (MR-Linac) and MR simulator devices for head and neck cancers

INTRODUCTION

Diffusion-weighted imaging (DWI) on MRI-linear accelerator (MR-linac) systems can potentially be used for monitoring treatment response and adaptive radiotherapy in head and neck cancers (HNC) but requires extensive validation. We performed technical validation to compare six total DWI sequences on an MR-linac and MR simulator (MR sim) in patients, volunteers, and phantoms.

METHODS

Ten human papillomavirus-positive oropharyngeal cancer patients and ten healthy volunteers underwent DWI on a 1.5 T MR-linac with three DWI sequences: echo planar imaging (EPI), split acquisition of fast spin echo signals (SPLICE), and turbo spin echo (TSE). Volunteers were also imaged on a 1.5 T MR sim with three sequences: EPI, BLADE (vendor tradename), and readout segmentation of long variable echo trains (RESOLVE). Participants underwent two scan sessions per device and two repeats of each sequence per session. Repeatability and reproducibility within-subject coefficient of variation (wCV) of mean ADC were calculated for tumors and lymph nodes (patients) and parotid glands (volunteers). ADC bias, repeatability/reproducibility metrics, SNR, and geometric distortion were quantified using a phantom.

RESULTS

In vivo repeatability/reproducibility wCV for parotids were 5.41%/6.72%, 3.83%/8.80%, 5.66%/10.03%, 3.44%/5.70%, 5.04%/5.66%, 4.23%/7.36% for EPIMR-linac, SPLICE, TSE, EPIMR sim, BLADE, RESOLVE. Repeatability/reproducibility wCV for EPIMR-linac, SPLICE, TSE were 9.64%/10.28%, 7.84%/8.96%, 7.60%/11.68% for tumors and 7.80%/9.95%, 7.23%/8.48%, 10.82%/10.44% for nodes. All sequences except TSE had phantom ADC biases within ± 0.1x10-3 mm2/s for most vials (EPIMR-linac, SPLICE, and BLADE had 2, 3, and 1 vials out of 13 with larger biases, respectively). SNR of b = 0 images was 87.3, 180.5, 161.3, 171.0, 171.9, 130.2 for EPIMR-linac, SPLICE, TSE, EPIMR sim, BLADE, RESOLVE.

CONCLUSION

MR-linac DWI sequences demonstrated near-comparable performance to MR sim sequences and warrant further clinical validation for treatment response assessment in HNC.

Prospective validation of diffusion-weighted MRI as a biomarker of tumor response and oncologic outcomes in head and neck cancer: Results from an observational biomarker pre-qualification study

PURPOSE

To determine DWI parameters associated with tumor response and oncologic outcomes in head and neck (HNC) patients treated with radiotherapy (RT).

METHODS

HNC patients in a prospective study were included. Patients had MRIs pre-, mid-, and post-RT completion. We used T2-weighted sequences for tumor segmentation which were co-registered to respective DWIs for extraction of apparent diffusion coefficient (ADC) measurements. Treatment response was assessed at mid- and post-RT and was defined as: complete response (CR) vs. non-complete response (non-CR). The Mann-Whitney U test was used to compare ADC between CR and non-CR. Recursive partitioning analysis (RPA) was performed to identify ADC threshold associated with relapse. Cox proportional hazards models were done for clinical vs. clinical and imaging parameters and internal validation was done using bootstrapping technique.

RESULTS

Eighty-one patients were included. Median follow-up was 31 months. For patients with post-RT CR, there was a significant increase in mean ADC at mid-RT compared to baseline ((1.8 ± 0.29) × 10-3 mm2/s vs. (1.37 ± 0.22) × 10-3 mm2/s, p < 0.0001), while patients with non-CR had no significant increase (p > 0.05). RPA identified GTV-P delta (Δ)ADCmean < 7% at mid-RT as the most significant parameter associated with worse LC and RFS (p = 0.01). Uni- and multi-variable analysis showed that GTV-P ΔADCmean at mid-RT ≥ 7% was significantly associated with better LC and RFS. The addition of ΔADCmean significantly improved the c-indices of LC and RFS models compared with standard clinical variables (0.85 vs. 0.77 and 0.74 vs. 0.68 for LC and RFS, respectively, p < 0.0001 for both).

CONCLUSION

ΔADCmean at mid-RT is a strong predictor of oncologic outcomes in HNC. Patients with no significant increase of primary tumor ADC at mid-RT are at high risk of disease relapse.

Dose accumulation for MR-guided adaptive radiotherapy: From practical considerations to state-of-the-art clinical implementation

MRI-linear accelerator (MR-linac) devices have been introduced into clinical practice in recent years and have enabled MR-guided adaptive radiation therapy (MRgART). However, by accounting for anatomical changes throughout radiation therapy (RT) and delivering different treatment plans at each fraction, adaptive radiation therapy (ART) highlights several challenges in terms of calculating the total delivered dose. Dose accumulation strategies-which typically involve deformable image registration between planning images, deformable dose mapping, and voxel-wise dose summation-can be employed for ART to estimate the delivered dose. In MRgART, plan adaptation on MRI instead of CT necessitates additional considerations in the dose accumulation process because MRI pixel values do not contain the quantitative information used for dose calculation. In this review, we discuss considerations for dose accumulation specific to MRgART and in relation to current MR-linac clinical workflows. We present a general dose accumulation framework for MRgART and discuss relevant quality assurance criteria. Finally, we highlight the clinical importance of dose accumulation in the ART era as well as the possible ways in which dose accumulation can transform clinical practice and improve our ability to deliver personalized RT.

Comprehensive Quantitative Evaluation of Variability in MR-guided Delineation of Oropharyngeal Gross Tumor Volumes and High-risk Clinical Target Volumes: An R-IDEAL Stage 0 Prospective Study

PURPOSE

Tumor and target volume manual delineation remains a challenging task in head-and-neck cancer radiotherapy. The purpose of this study was to conduct a multi-institutional evaluation of manual delineations of gross tumor volume (GTV), high-risk clinical target volume (CTV), parotids, and submandibular glands on treatment simulation MR scans of oropharyngeal cancer (OPC) patients.

METHODS

Pre-treatment T1-weighted (T1w), T1-weighted with gadolinium contrast (T1w+C) and T2-weighted (T2w) MRI scans were retrospectively collected for 4 OPC patients under an IRB-approved protocol. The scans were provided to twenty-six radiation oncologists from seven international cancer centers who participated in this delineation study. In addition, patients' clinical history and physical examination findings, along with a medical photographic image and radiological results, were provided. The contours were compared using overlap/distance metrics using both STAPLE and pair-wise comparisons. Lastly, participants completed a brief questionnaire to assess participants' experience and CTV delineation institutional practices.

RESULTS

Large variability was measured between observers' delineations for GTVs and CTVs. The mean Dice Similarity Coefficient values across all physicians' delineations for GTVp, GTVn, CTVp, and CTVn were 0.77, 0.67, 0.77, and 0.69, respectively, for STAPLE comparison and 0.67, 0.60, 0.67, and 0.58, respectively, for pair-wise analysis. Normal tissue contours were defined more consistently when considering overlap/distance metrics. The median radiation oncology clinical experience was 7 years. The median experience delineating on MRI was 3.5 years. The GTV-to-CTV margin used was 10 mm for six of seven participant institutions. One institution used 8 mm and three participants (from three different institutions) used a margin of 5 mm.

CONCLUSION

The data from this study suggests that appropriate guidelines, contouring quality assurance sessions, and training are still needed for the adoption of MR-based treatment planning for head-and-neck cancers. Such efforts should play a critical role in reducing delineation variation and ensure standardization of target design across clinical practices.

Evaluation of deep learning-based multiparametric MRI oropharyngeal primary tumor auto-segmentation and investigation of input channel effects: Results from a prospective imaging registry

BACKGROUND/PURPOSE

Oropharyngeal cancer (OPC) primary gross tumor volume (GTVp) segmentation is crucial for radiotherapy. Multiparametric MRI (mpMRI) is increasingly used for OPC adaptive radiotherapy but relies on manual segmentation. Therefore, we constructed mpMRI deep learning (DL) OPC GTVp auto-segmentation models and determined the impact of input channels on segmentation performance.

MATERIALS/METHODS

GTVp ground truth segmentations were manually generated for 30 OPC patients from a clinical trial. We evaluated five mpMRI input channels (T2, T1, ADC, Ktrans, Ve). 3D Residual U-net models were developed and assessed using leave-one-out cross-validation. A baseline T2 model was compared to mpMRI models (T2 + T1, T2 + ADC, T2 + Ktrans, T2 + Ve, all five channels [ALL]) primarily using the Dice similarity coefficient (DSC). False-negative DSC (FND), false-positive DSC, sensitivity, positive predictive value, surface DSC, Hausdorff distance (HD), 95% HD, and mean surface distance were also assessed. For the best model, ground truth and DL-generated segmentations were compared through a blinded Turing test using three physician observers.

RESULTS

Models yielded mean DSCs from 0.71 ± 0.12 (ALL) to 0.73 ± 0.12 (T2 + T1). Compared to the T2 model, performance was significantly improved for FND, sensitivity, surface DSC, HD, and 95% HD for the T2 + T1 model (p < 0.05) and for FND for the T2 + Ve and ALL models (p < 0.05). No model demonstrated significant correlations between tumor size and DSC (p > 0.05). Most models demonstrated significant correlations between tumor size and HD or Surface DSC (p < 0.05), except those that included ADC or Ve as input channels (p > 0.05). On average, there were no significant differences between ground truth and DL-generated segmentations for all observers (p > 0.05).

CONCLUSION

DL using mpMRI provides reasonably accurate segmentations of OPC GTVp that may be comparable to ground truth segmentations generated by clinical experts. Incorporating additional mpMRI channels may increase the performance of FND, sensitivity, surface DSC, HD, and 95% HD, and improve model robustness to tumor size.

Magnetic resonance linear accelerator technology and adaptive radiation therapy: An overview for clinicians

Radiation therapy (RT) continues to play an important role in the treatment of cancer. Adaptive RT (ART) is a novel method through which RT treatments are evolving. With the ART approach, computed tomography or magnetic resonance (MR) images are obtained as part of the treatment delivery process. This enables the adaptation of the irradiated volume to account for changes in organ and/or tumor position, movement, size, or shape that may occur over the course of treatment. The advantages and challenges of ART maybe somewhat abstract to oncologists and clinicians outside of the specialty of radiation oncology. ART is positioned to affect many different types of cancer. There is a wide spectrum of hypothesized benefits, from small toxicity improvements to meaningful gains in overall survival. The use and application of this novel technology should be understood by the oncologic community at large, such that it can be appropriately contextualized within the landscape of cancer therapies. Likewise, the need to test these advances is pressing. MR-guided ART (MRgART) is an emerging, extended modality of ART that expands upon and further advances the capabilities of ART. MRgART presents unique opportunities to iteratively improve adaptive image guidance. However, although the MRgART adaptive process advances ART to previously unattained levels, it can be more expensive, time-consuming, and complex. In this review, the authors present an overview for clinicians describing the process of ART and specifically MRgART.

Intensity standardization methods in magnetic resonance imaging of head and neck cancer

Background and Purpose

Conventional magnetic resonance imaging (MRI) poses challenges in quantitative analysis because voxel intensity values lack physical meaning. While intensity standardization methods exist, their effects on head and neck MRI have not been investigated. We developed a workflow based on healthy tissue region of interest (ROI) analysis to determine intensity consistency within a patient cohort. Through this workflow, we systematically evaluated intensity standardization methods for MRI of head and neck cancer (HNC) patients.

Materials and Methods

Two HNC cohorts (30 patients total) were retrospectively analyzed. One cohort was imaged with heterogenous acquisition parameters (HET cohort), whereas the other was imaged with homogenous acquisition parameters (HOM cohort). The standard deviation of cohort-level normalized mean intensity (SD NMI_c), a metric of intensity consistency, was calculated across ROIs to determine the effect of five intensity standardization methods on T2-weighted images. For each cohort, a Friedman test followed by a post-hoc Bonferroni-corrected Wilcoxon signed-rank test was conducted to compare SD NMI_c among methods.

Results

Consistency (SD NMI_c across ROIs) between unstandardized images was substantially more impaired in the HET cohort (0.29 ± 0.08) than in the HOM cohort (0.15 ± 0.03). Consequently, corrected p-values for intensity standardization methods with lower SD NMI_c compared to unstandardized images were significant in the HET cohort (p < 0.05) but not significant in the HOM cohort (p > 0.05). In both cohorts, differences between methods were often minimal and nonsignificant.

Conclusions

Our findings stress the importance of intensity standardization, either through the utilization of uniform acquisition parameters or specific intensity standardization methods, and the need for testing intensity consistency before performing quantitative analysis of HNC MRI.

Advances in Imaging for HPV-Related Oropharyngeal Cancer: Applications to Radiation Oncology

While there has been an overall decline of tobacco and alcohol-related head and neck cancer in recent decades, there has been an increased incidence of HPV-associated oropharyngeal cancer (OPC). Recent research studies and clinical trials have revealed that the cancer biology and clinical progression of HPV-positive OPC is unique relative to its HPV-negative counterparts. HPV-positive OPC is associated with higher rates of disease control following definitive treatment when compared to HPV-negative OPC. Thus, these conditions should be considered unique diseases with regards to treatment strategies and survival. In order to sufficiently characterize HPV-positive OPC and guide treatment strategies, there has been a considerable effort to diagnose, prognose, and track the treatment response of HPV-associated OPC through advanced imaging research. Furthermore, HPV-positive OPC patients are prime candidates for radiation de-escalation protocols, which will ideally reduce toxicities associated with radiation therapy and has prompted additional imaging research to detect radiation-induced changes in organs at risk. This manuscript reviews the various imaging modalities and current strategies for tackling these challenges as well as provides commentary on the potential successes and suggested improvements for the optimal treatment of these tumors.

Integration of quantitative imaging biomarkers in clinical trials for MR-guided radiotherapy: Conceptual guidance for multicentre studies from the MR-Linac Consortium Imaging Biomarker Working Group

Quantitative imaging biomarkers (QIBs) derived from MRI techniques have the potential to be used for the personalised treatment of cancer patients. However, large-scale data are missing to validate their added value in clinical practice. Integrated MRI-guided radiotherapy (MRIgRT) systems, such as hybrid MRI-linear accelerators, have the unique advantage that MR images can be acquired during every treatment session. This means that high-frequency imaging of QIBs becomes feasible with reduced patient burden, logistical challenges, and costs compared to extra scan sessions. A wealth of valuable data will be collected before and during treatment, creating new opportunities to advance QIB research at large. The aim of this paper is to present a roadmap towards the clinical use of QIBs on MRIgRT systems. The most important need is to gather and understand how the QIBs collected during MRIgRT correlate with clinical outcomes. As the integrated MRI scanner differs from traditional MRI scanners, technical validation is an important aspect of this roadmap. We propose to integrate technical validation with clinical trials by the addition of a quality assurance procedure at the start of a trial, the acquisition of in vivo test-retest data to assess the repeatability, as well as a comparison between QIBs from MRIgRT systems and diagnostic MRI systems to assess the reproducibility. These data can be collected with limited extra time for the patient. With integration of technical validation in clinical trials, the results of these trials derived on MRIgRT systems will also be applicable for measurements on other MRI systems.

Initial Feasibility and Clinical Implementation of Daily MR-Guided Adaptive Head and Neck Cancer Radiation Therapy on a 1.5T MR-Linac System: Prospective R-IDEAL 2a/2b Systematic Clinical Evaluation of Technical Innovation

PURPOSE

This prospective study is, to our knowledge, the first report of daily adaptive radiation therapy (ART) for head and neck cancer (HNC) using a 1.5T magnetic resonance imaging-linear accelerator (MR-linac) with particular focus on safety and feasibility and dosimetric results of an online rigid registration-based adapt to position (ATP) workflow.

METHODS AND MATERIALS

Ten patients with HNC received daily ART on a 1.5T/7MV MR-linac, 6 using ATP only and 4 using ATP with 1 offline adapt-to-shape replan. Setup variability with custom immobilization masks was assessed by calculating the mean systematic error (M), standard deviation of the systematic error (Σ), and standard deviation of the random error (σ) of the isocenter shifts. Quality assurance was performed with a cylindrical diode array using 3%/3 mm γ criteria. Adaptive treatment plans were summed for each patient to compare the delivered dose with the planned dose from the reference plan. The impact of dosimetric variability between adaptive fractions on the summation plan doses was assessed by tracking the number of optimization constraint violations at each individual fraction.

RESULTS

The random errors (mm) for the x, y, and z isocenter shifts, respectively, were M = -0.3, 0.7, 0.1; Σ = 3.3, 2.6, 1.4; and σ = 1.7, 2.9, 1.0. The median (range) γ pass rate was 99.9% (90.9%-100%). The differences between the reference and summation plan doses were -0.61% to 1.78% for the clinical target volume and -11.74% to 8.11% for organs at risk (OARs), although an increase greater than 2% in OAR dose only occurred in 3 cases, each for a single OAR. All cases had at least 2 fractions with 1 or more constraint violations. However, in nearly all instances, constraints were still met in the summation plan despite multiple single-fraction violations.

CONCLUSIONS

Daily ART on a 1.5T MR-linac using an online ATP workflow is safe and clinically feasible for HNC and results in delivered doses consistent with planned doses.

Redefining genera of cereal pathogens: Oculimacula, Rhynchosporium and Spermospora

The taxonomy of Oculimacula, Rhynchosporium and Spermospora is re-evaluated, along with that of phylogenetically related genera. Isolates are identified using comparisons of DNA sequences of the internal transcribed spacer ribosomal RNA locus (ITS), partial translation elongation factor 1-alpha (tef1), actin (act), DNA-directed RNA polymerase II largest (rpb1) and second largest subunit (rpb2) genes, and the nuclear ribosomal large subunit (LSU), combined with their morphological characteristics. Oculimacula is restricted to two species, O. acuformis and O. yallundae, with O. aestiva placed in Cyphellophora, and O. anguioides accommodated in a new genus, Helgardiomyces. Rhynchosporium s. str. is restricted to species with 1-septate conidia and hooked apical beaks, while Rhynchobrunnera is introduced for species with 1–3-septate, straight conidia, lacking any apical beak. Rhynchosporium graminicola is proposed to replace the name R. commune applied to the barley scald pathogen based on nomenclatural priority. Spermospora is shown to be paraphyletic, representing Spermospora (type: S. subulata), with three new species, S. arrhenatheri, S. loliiphila and S. zeae, and Neospermospora gen. nov. (type: N. avenae). Ypsilina (type: Y. graminea), is shown to be monophyletic, but appears to be of minor importance on cereals. Finally, Vanderaaea gen. nov. (type: V. ammophilae), is introduced as a new coelomycetous fungus occurring on dead leaves of Ammophila arenaria.

Citation: Crous PW, Braun U, McDonald BA, Lennox CL, Edwards J, Mann RC, Zaveri A, Linde CC, Dyer PS, Groenewald JZ (2020). Redefining genera of cereal pathogens: Oculimacula, Rhynchosporium and Spermospora. Fungal Systematics and Evolution7: 67–98. doi: 10.3114/fuse.2021.07.04

Development and validation of a contouring guideline for the taste bud bearing tongue mucosa

PURPOSE

To introduce a contouring guideline for the taste bud bearing tongue mucosa for head and neck cancer patients receiving radiotherapy.

METHODS AND MATERIALS

CT simulation images of oropharyngeal cancer patients were used to delineate both the whole tongue (extrinsic/intrinsic tongue muscles, floor of mouth) and the taste bud bearing tongue mucosa (method A: adaptation of the whole tongue structure; method B: axial adaptation of a mid-sagittal contour). Volumetric and dosimetric parameters of the whole tongue and the two methods of mucosal delineation, spatial overlap between methods A and B, and inter-observer variability for method B were calculated.

RESULTS

The study cohort was comprised of 70 patients with T1-4 N0-1 tonsillar (83%) and base of tongue (17%) cancers. Most of the comparative parameters between the whole tongue and mucosa (method A) significantly differed (mean, minimum, and maximum dose, V5-V70, D40-D90). The mean dose calculated for the whole tongue deviated on average 3.77 Gy compared to method A. No significant differences were found between methods A and B of the taste bud bearing tongue mucosa structure, and none of the dosimetric parameters differed more than 1.03 Gy on average. The mean Dice similarity coefficient for both mucosal structures was 0.79 ± 0.05, and 0.63 ± 0.12 for the inter-observer analysis of method B.

CONCLUSIONS

We defined two methods for delineating the taste bud bearing mucosa and both are equally satisfactory procedures. Either method is preferable over delineation of the whole tongue as organ at risk for taste impairment.

Accuracy of deformable image registration techniques for alignment of longitudinal cholangiocarcinoma CT images

PURPOSE

Response assessment of radiotherapy for the treatment of intrahepatic cholangiocarcinoma (IHCC) across longitudinal images is challenging due to anatomical changes. Advanced deformable image registration (DIR) techniques are required to correlate corresponding tissues across time. In this study, the accuracy of five commercially available DIR algorithms in four treatment planning systems (TPS) was investigated for the registration of planning images with posttreatment follow-up images for response assessment or re-treatment purposes.

METHODS

Twenty-nine IHCC patients treated with hypofractionated radiotherapy and with pretreatment and posttreatment contrast-enhanced computed tomography (CT) images were analyzed. Liver segmentations were semiautomatically generated on all CTs and the posttreatment CT was then registered to the pretreatment CT using five commercially available algorithms (Demons, B-splines, salient feature-based, anatomically constrained and finite element-based) in four TPSs. This was followed by an in-depth analysis of 10 DIR strategies (plus global and liver-focused rigid registration) in one of the TPSs. Eight of the strategies were variants of the anatomically constrained DIR while the two were based on a finite element-based biomechanical registration. The anatomically constrained techniques were combinations of: (a) initializations with the two rigid registrations; (b) two similarity metrics - correlation coefficient (CC) and mutual information (MI); and (c) with and without a controlling region of interest (ROI) - the liver. The finite element-based techniques were initialized by the two rigid registrations. The accuracy of each registration was evaluated using target registration error (TRE) based on identified vessel bifurcations. The results were statistically analyzed with a one-way analysis of variance (ANOVA) and pairwise comparison tests. Stratified analysis was conducted on the inter-TPS data (plus the liver-focused rigid registration) using treatment volume changes, slice thickness, time between scans, and abnormal lab values as stratifying factors.

RESULTS

The complex deformation observed following treatment resulted in average TRE exceeding the image voxel size for all techniques. For the inter-TPS comparison, the Demons algorithm had the lowest TRE, which was significantly superior to all the other algorithms. The respective mean (standard deviation) TRE (in mm) for the Demons, B-splines, salient feature-based, anatomically constrained, and finite element-based algorithms were 4.6 (2.0), 7.4 (2.7), 7.2 (2.6), 6.3 (2.3), and 7.5 (4.0). In the follow-up comparison of the anatomically constrained DIR, the strategy with liver-focused rigid registration initialization, CC as similarity metric and liver as a controlling ROI had the lowest mean TRE - 6.0 (2.0). The maximum TRE for all techniques exceeded 10 mm. Selection of DIR strategy was found to be a statistically significant factor for registration accuracy. Tumor volume change had a significant effect on TRE for finite element-based registration and B-splines DIR. Time between scans had a substantial effect on TRE for all registrations but was only significant for liver-focused rigid, finite element-based and salient feature-based DIRs.

CONCLUSIONS

This study demonstrates the limitations of commercially available DIR techniques in TPSs for alignment of longitudinal images of liver cancer presenting complex anatomical changes including local hypertrophy and fibrosis/necrosis. DIR in this setting should be used with caution and careful evaluation.

Low-density gel dosimeter for measurement of the electron return effect in an MR-linac

Radiation therapy in the presence of a strong magnetic field is known to cause regions of enhanced and reduced dose at interfaces of materials with varying densities, in a phenomenon known as the electron return effect (ERE). In this study, a novel low-density gel dosimeter was developed to simulate lung tissue and was used to measure the ERE at the lung-soft tissue interface. Low-density gel dosimeters were developed with Fricke xylenol orange gelatin (FXG) and ferrous oxide xylenol orange (FOX) gels mixed with polystyrene foam beads of various sizes. The gels were characterized based on CT number, MR signal intensity, and uniformity. All low-density gels had CT numbers roughly equivalent to lung tissue. The optimal lung-equivalent gel formulation was determined to be FXG with  <1 mm polystyrene beads due to the higher signal intensity of FXG compared to FOX and the higher uniformity with the small beads. Dose response curves were generated for the optimal low-density gel and conventional FXG. The change in spin-lattice relaxation rate (R1) before and after irradiation was linear with dose for both gels. Next, phantoms consisting of concentric cylinders with low-density and conventional FXG were created to simulate the lung-soft tissue interface. The phantoms were irradiated in a conventional linear accelerator (linac) and in a linac combined with a 1.5 T magnetic resonance imaging (MRI) unit (MR-linac) to measure the effects of the magnetic field on the dose distribution. Hot and cold spots were observed in the dose distribution at the boundaries between the gels for the phantom irradiated in the MR-linac but not the conventional linac, consistent with the ERE.

First Report of Resistance to QoI Fungicides in North American Populations of Zymoseptoria tritici, Causal Agent of Septoria Tritici Blotch of Wheat

The G143A mutation in cytb (cytochrome b gene) is associated with high levels of resistance to quinone outside inhibitor (QoI or strobilurin) fungicides that disrupt electron transport during cellular respiration (1). The G143A mutation in Zymoseptoria tritici (synonyms: Mycosphaerella graminicola and Septoria tritici), the causal agent of septoria tritici blotch of wheat (Triticum aestivum), was first reported in Europe in 2001 (1). Although Z. tritici has a global distribution (3), G143A mutants of Z. tritici have not been reported outside of Europe. We used PCR-RFLP (4) to estimate the frequencies of G143A mutants in Z. tritici populations at two locations in the Willamette Valley of western Oregon: the Hyslop Crop Science Field Research Laboratory (Hyslop Farm, HF), Benton County (44°37'52.85″ N, 123°11'55.19″ W) and research plots planted in a commercial wheat field in Washington County (45°33'58.53″ N, 123°00'11.78″ W) (North Valley Farm, NVF). Isolates originated from flag leaf collections from two cultivars ('Bobtail' and 'Tubbs 06') made in April and June of 2012 from plants in a replicated fungicide-treatment experiment, with isolates collected from both sprayed and unsprayed plots. Sixteen of the 169 isolates (9.5%) from HF possessed the G143A mutation (7 of 132 isolates from plots not receiving a QoI fungicide and 9 of 37 isolates collected from plots receiving two applications of the QoI azoxystrobin). One hundred forty six of the 175 isolates (83.4%) from NVF were G143A mutants (101 of 129 isolates from plots receiving no QoI fungicide and 45 of 46 isolates from plots receiving two applications of azoxystrobin). Results of phenotypic assays of a subset of 10 isolates from each location (5 mutants, 5 wild types from each location; 20 isolates altogether) supported a high level of resistance to azoxystrobin only in the G143A mutants. All 10 G143A mutants developed colonies after 8 days of growth on YMA plates amended with SHAM (2) and 1 ppm or 10 ppm azoxystrobin, with nine and eight G143A mutant isolates developing colonies on plates amended with 1 ppm and 10 ppm azoxystrobin, respectively. None of the wild-type isolates developed colonies on plates amended with SHAM and 1 ppm azoxystrobin, nor on plates amended with SHAM and 10 ppm azoxystrobin. All 20 isolates developed colonies on YMA plates lacking azoxystrobin, and treatments produced identical results across three replicates. These results are consistent with findings of higher levels of azoxystrobin resistance in G143A mutants compared to wild types in European populations (1). Isolates from HF and NVF differ in their previous exposure to QoI fungicides. The majority of the wheat area at HF is planted to breeding plots that are not sprayed with fungicide. Plots at NVF were planted in a commercial wheat field in a county where most wheat fields were treated with two to three applications of strobilurins each year over the past 4 years. Future monitoring for G143A mutants of Z. tritici throughout its range in North America will be necessary to assess whether strobilurin resistance will spread via wind-dispersal of ascospores or emerge de novo in treated fields. In Europe, stobilurins were first applied to wheat in 1996. G143A mutants of Z. tritici emerged de novo several times (4) and were widespread by 2007. References: (1) B. A. Fraaje et al. Phytopathology 95:933, 2005. (2) J. A. LaMondia. Tob. Sci. 49:1, 2012. (3) E. S. Orton et al. Mol. Plant Pathol. 12:413, 2011. (4) S. F. F. Torriani et al. Pest Manag. Sci. 65:155, 2008.

Divergence between sympatric rice- and maize-infecting populations of Rhizoctonia solani AG-1 IA from Latin America

ABSTRACT The basidiomycetous fungus Rhizoctonia solani anastomosis group (AG)-1 IA is a major pathogen in Latin America causing sheath blight (SB) of rice. Particularly in Venezuela, the fungus also causes banded leaf and sheath blight (BLSB) on maize, which is considered an emerging disease problem where maize replaced traditional rice-cropping areas or is now planted in adjacent fields. Our goals in this study were to elucidate (i) the effects of host specialization on gene flow between sympatric and allopatric rice and maize-infecting fungal populations and (ii) the reproductive mode of the fungus, looking for evidence of recombination. In total, 375 isolates of R. solani AG1 IA sampled from three sympatric rice and maize fields in Venezuela (Portuguesa State) and two allopatric rice fields from Colombia (Meta State) and Panama (Chiriquí State) were genotyped using 10 microsatellite loci. Allopatric populations from Venezuela, Colombia, and Panama were significantly differentiated (Phi(ST) of 0.16 to 0.34). Partitioning of the genetic diversity indicated differentiation between sympatric populations from different host species, with 17% of the total genetic variation distributed between hosts while only 3 to 6% was distributed geographically among the sympatric Venezuelan fields. We detected symmetrical historical migration between the rice- and the maize-infecting populations from Venezuela. Rice- and maize-derived isolates were able to infect both rice and maize but were more aggressive on their original hosts, consistent with host specialization. Because the maize- and rice-infecting populations are still cross-pathogenic, we postulate that the genetic differentiation was relatively recent and mediated via a host shift. An isolation with migration analysis indicated that the maize-infecting population diverged from the rice-infecting population between 40 and 240 years ago. Our findings also suggest that maize-infecting populations have a mainly recombining reproductive system whereas the rice-infecting populations have a mixed reproductive system in Latin America.

Genetic structure of populations of Rhizoctonia solani anastomosis group-1 IA from soybean in Brazil

The Basidiomycete fungus Rhizoctonia solani anastomosis group (AG)-1 IA is a major pathogen of soybean in Brazil, where the average yield losses have reached 30 to 60% in some states in Northern Brazil. No information is currently available concerning levels of genetic diversity and population structure for this pathogen in Brazil. A total of 232 isolates of R. solani AG1 IA were collected from five soybean fields in the most important soybean production areas in central-western, northern, and northeastern Brazil. These isolates were genotyped using 10 microsatellite loci. Most of the multilocus genotypes (MLGTs) were site-specific, with few MLGTs shared among populations. Significant population subdivision was evident. High levels of admixture were observed for populations from Mato Grosso and Tocantins. After removing admixed genotypes, three out of five field populations (Maranhao, Mato Grosso, and Tocantins), were in Hardy-Weinberg (HW) equilibrium, consistent with sexual recombination. HW and gametic disequilibrium were found for the remaining soybean-infecting populations. The findings of low genotypic diversity, departures from HW equilibrium, gametic disequilibrium, and high degree of population subdivision in these R. solani AG-1 IA populations from Brazil are consistent with predominantly asexual reproduction, short-distance dispersal of vegetative propagules (mycelium or sclerotia), and limited long-distance dispersal, possibly via contaminated seed. None of the soybean-infecting populations showed a reduction in population size (bottleneck effect). We detected asymmetric historical migration among the soybean-infecting populations, which could explain the observed levels of subdivision.

Evolution of the CYP51 gene in Mycosphaerella graminicola: evidence for intragenic recombination and selective replacement

Recent findings are consistent with a slow but constant shift towards reduced sensitivity of Mycosphaerella graminicola to azole fungicides, which target the CYP51 gene. The goal of this study was to elucidate the evolutionary mechanisms through which CYP51-based mutations associated with altered sensitivity have evolved in M. graminicola over space and time. To accomplish this, we sequenced and compared a portion of the CYP51 gene encompassing the main mutations associated with altered sensitivity towards demethylation inhibitor fungicides. The CYP51 gene showed an extraordinary dynamic shift consistent with a selective haplotype replacement both in space and in time. No mutations associated with increased resistance to azoles were found in non-European populations. These mutations were also absent in the oldest collections from Europe, whereas they dominated in the recent European populations. Intragenic recombination was identified as an important evolutionary process in populations affected by high fungicide selection, suggesting the creation of novel alleles among existing mutations as a potential source of novel resistance alleles. We propose that CYP51 mutations giving resistance in M. graminicola arose only locally (perhaps in Denmark or the UK) and were then spread eastward across Europe through wind-dispersed ascospores. We conclude that recurring cycles of recombination coupled with selection due to the widespread use of azole fungicides will increase the frequency of novel mutants or recombinants with higher resistance. Long-distance gene flow due to wind dispersal of ascospores will move the resulting new alleles to new areas following the prevailing wind directions. A selective replacement favouring haplotypes with various coding mutations at the target site for azole fungicides during the last 5-10 years is the most likely cause of the decrease in sensitivity reported for many azole fungicides in the same period.

The origin and colonization history of the barley scald pathogen Rhynchosporium secalis

The origins of pathogens and their past and present migration patterns are often unknown. We used phylogenetic haplotype clustering in conjunction with model-based coalescent approaches to reconstruct the genetic history of the barley leaf pathogen Rhynchosporium secalis using the avirulence gene NIP1 and its flanking regions. Our results falsify the hypothesis that R. secalis emerged in association with its host during the domestication of barley 10,000 to 15,000 years ago in the Fertile Crescent and was introduced into Europe through the migration of Neolithic farmers. Estimates of time since most recent common ancestor (2500-5000 BP) placed the emergence of R. secalis clearly after the domestication of barley. We propose that modern populations of R. secalis originated in northern Europe following a host switch, most probably from a wild grass onto cultivated barley shortly after barley was introduced into northern Europe. R. secalis subsequently spread southwards into already established European barley-growing areas.

Sexual reproduction facilitates the adaptation of parasites to antagonistic host environments: Evidence from empirical study in the wheat-Mycosphaerella graminicola system

Most eukaryotes use sexual reproduction to transmit genetic information from generation to generation despite the advantages offered by asexual reproduction. One theory to explain the origin and maintenance of sexual reproduction hypothesises that sexual recombination generates genetic variation that allows faster adaptation to fluctuating and/or stressful environments. We used a combination of ecological, molecular genetic, statistical and experimental evolution approaches to test this hypothesis in an agricultural plant-pathogen system. We inoculated wheat hosts with 10 strains of the fungal pathogen Mycosphaerella graminicola in a field experiment and estimated the contributions of sexual reproduction, asexual reproduction and immigration to the genetic composition of fungal populations sampled from moderately resistant and susceptible hosts through the course of an epidemic cycle. We found that a significant proportion of the M. graminicola population in the late phase of the epidemic originated from sexual reproduction among isolates that had been introduced into the field plots at the beginning of the epidemic. Recombinants were recovered at a higher frequency on the moderately resistant plant host Madsen than on the susceptible host Stephens. By the end of the growing season, we estimated that approximately 13% of the strains sampled from the resistant host were recombinants, compared with 9% in the samples collected from the susceptible host. We also found that pathogen strains originating from the resistant cultivar displayed higher levels of fitness, virulence and fungicide tolerance than those originating from the susceptible cultivar. Our results provide empirical support for the hypothesis that sexual reproduction facilitates the evolution of parasites to overcome host resistance.

Selection for increased cyproconazole tolerance in Mycosphaerella graminicola through local adaptation and in response to host resistance

SUMMARY Sterol demethylation inhibitors (DMIs) represent one of the largest groups of systemic fungicides that have been used to control agriculturally important fungal pathogens. Knowledge regarding the evolution of fungicide resistance in agricultural ecosystems is fragmentary and a better understanding of the processes driving the development of DMI resistance in populations of fungal pathogens is needed by plant pathologists and the agrochemical industry. We considered some of these processes using approaches based on molecular population and quantitative genetics. Five Mycosphaerella graminicola populations sampled from unsprayed wheat fields on four continents were assayed for eight restriction fragment length polymorphism (RFLP) markers and their level of tolerance to cyproconazole. DMI fungicides such as cyproconazole inhibit the enzyme eburicol 14-alpha-demethylase. The gene encoding this target, CYP51, was sequenced for all isolates. We found unimodal, continuous variations in cyproconazole tolerance among the M. graminicola isolates sampled from individual fields, consistent with a polygenic mode of inheritance. We also found that population differentiation for cyproconazole tolerance (Q(ST)) among the five M. graminicola populations was significantly higher than the corresponding population differentiation for neutral RFLP markers (G(ST)), suggesting that selection for cyproconazole tolerance in the Swiss population has already led to local adaptation that can be seen even in an unsprayed population. The Swiss population displayed the highest level of tolerance to cyproconazole, in addition to a lower than expected quantitative variation in fungicide tolerance and a skewed distribution, indicating that selection had increased the overall tolerance of this population. Further analysis with DNA sequencing showed that the population from Switzerland was dominated by isolates with several point mutations and a 6-bp deletion in CYP51. This deletion and one of the point mutations were previously related to increased resistance in field isolates. The fungal population from Oregon sampled from an unsprayed resistant host cultivar displayed the same gene diversity in RFLP loci but higher cyproconazole tolerance and quantitative variation in tolerance than the fungal population from the same field sampled from an unsprayed susceptible host cultivar.

Variation for neutral markers is correlated with variation for quantitative traits in the plant pathogenic fungus Mycosphaerella graminicola

We compared genetic variation and population differentiation at RFLP marker loci with seven quantitative characters including fungicide resistance, temperature sensitivity, pycnidial size, pycnidial density, colony size, percentage of leaves covered by pycnidia (PLACP) and percentage of leaves covered by lesions (PLACL) in Mycosphaerella graminicola populations sampled from four regions. Wide variation in population differentiation was found across the quantitative traits assayed. Fungicide resistance, temperature sensitivity, and PLACP displayed a significantly higher Q(ST) than G(ST), consistent with selection for local adaptation, while pycnidial size, pycnidial density and colony size displayed a lower or significantly lower Q(ST) than G(ST), consistent with constraining selection. There was not a statistical difference between Q(ST) and G(ST) in PLACL. We also found a positive and significant correlation between genetic variation in molecular marker loci and quantitative traits at the multitrait scale, suggesting that estimates of overall genetic variation for quantitative traits in M. graminicola could be derived from analysis of the molecular genetic markers.

Migration patterns among global populations of the pathogenic fungus Mycosphaerella graminicola

DNA sequences from five nuclear loci and data from three microsatellites were collected from 360 isolates representing 14 globally distributed populations of the plant pathogenic fungus Mycosphaerella graminicola. Haplotype networks were constructed for the five sequence loci and population subdivision was assessed using Hudson's permutation test. Migration estimates were calculated using six regional populations for both the sequence and microsatellite loci. While subdivision was detected among the six regional populations, significant gene flow was indicated among some of the populations. The European and Israeli populations contributed the majority of historical immigrants to the New World. Migration estimates for microsatellite loci were used to infer more recent migration events among specific New World populations. We conclude that gene flow was an important factor in determining the demographic history of Mycosphaerella graminicola.

The interaction among evolutionary forces in the pathogenic fungus Mycosphaerella graminicola

The population genetic dynamic of a species is driven by interactions among mutation, migration, drift, mating system, and selection, but it is rare to have sufficient empirical data to estimate values for all of these forces and to allow comparison of the relative magnitudes of these evolutionary forces. We combined data from a mark-release-recapture experiment, extensive population surveys, and computer simulations to evaluate interactions among these evolutionary forces in the pathogenic fungus Mycosphaerella graminicola. The results from these studies showed that, on average, the immigration rate was 0.027, the fraction of outcrossing individuals was 0.035, and the selection coefficient associated with immigrants was 0.106 each generation. We also estimated that effective population sizes for this fungus were larger than 24,000 and the mutation rate for the RFLP markers used in surveys and field experiments was approximately 4 x 10(-5). Computer simulations based on these estimates indicate that, on average, the global population of M. graminicola has reached equilibrium. Population genetic parameters including number of alleles, gene diversity, and population subdivision estimated from the computer simulations were surprisingly close to empirical estimates. Simulations also revealed that random drift is the major evolutionary force decreasing genetic variation in this fungus, followed by natural selection. The major force adding to genetic variation was mutation, followed by gene flow and sexual recombination. Gene flow played the leading role in decreasing population subdivision while natural selection was the major factor increasing population subdivision.

Evidence for Natural Selection in the Mitochondrial Genome of Mycosphaerella graminicola

ABSTRACT Pathogenicity assays were combined with restriction fragment length polymorphism (RFLP) markers in the mitochondrial and nuclear genomes to compare Mycosphaerella graminicola populations adapted to bread wheat (Triticum aestivum) and durum wheat (T. turgidum) in the Mediterranean Basin. The majority of isolates had unique nuclear DNA fingerprints and multilocus haplotypes. Only six mitochondrial DNA (mtDNA) haplotypes were identified among 108 isolates assayed. There were minor differences in frequencies of alleles at nuclear RFLP loci between the two host-adapted populations, but differences in the frequencies of mtDNA haplotypes were highly significant (P < 0.0001). mtDNA haplotype 1 dominated on the isolates adapted to bread wheat, and its frequency was twice as high as for the isolates adapted to durum wheat. mtDNA haplotype 4, which contained a unique approximately 3-kb insertion, was detected only in isolates showing specificity toward durum wheat and was the dominant haplotype on this species. We propose that the low mitochondrial diversity in this pathogenic fungus is due to a selective sweep and that differences in the frequencies of mtDNA haplotypes between the two host-adapted populations were due to natural selection according to host species.

Phylogenetic analysis of globally distributed Mycosphaerella graminicola populations based on three DNA sequence loci

DNA sequence data from three nuclear loci were collected from 384 isolates representing fourteen globally distributed populations of the plant pathogenic fungus Mycosphaerella graminicola. Gene genealogies were constructed for the actin and beta-tubulin loci as well as for the previously characterized RFLP locus STS2. The STS2 and beta-tubulin loci showed greater potential for phylogenetic studies than the actin locus. Greater sequence diversity was found in the "Old World" populations (Middle East and Europe) than in the "New World" populations (North and South America and Australia). The gene trees were rooted using homologous DNA sequences of Septoria passerinii, the closest known relative to M. graminicola, as well as coalescent rooting. Based on the rooted trees, a tentative phylogenetic history of these populations was inferred. The Middle East appears to be the most likely center of origin, while European populations are more ancient than New World populations. A test for neutrality indicated that the intron in the actin locus could be under selection, while the other two sequence loci were neutral.

The global genetic structure of the wheat pathogen Mycosphaerella graminicola is characterized by high nuclear diversity, low mitochondrial diversity, regular recombination, and gene flow

A total of 1673 Mycosphaerella graminicola strains were assayed for DNA fingerprints and restriction fragment length polymorphism (RFLP) markers in the nuclear and mitochondrial genomes. The isolates were collected from 17 wheat fields located in 11 countries on five continents over a six year period (1989-1995). Our results indicate that genetic diversity in the nuclear genome of this fungus was high for all but three of the field populations surveyed and that populations sampled from different continents had similar frequencies for the most common RFLP alleles. Hierarchical analysis revealed that more than 90% of global gene diversity was distributed within a wheat field, while approximately 5% of gene diversity was distributed among fields within regions and approximately 3% was distributed among regions on different continents. These findings suggest that gene flow has occurred on a global scale. On average, each leaf was colonized by a different nuclear genotype. In contrast, only seven mtDNA haplotypes were detected among the 1673 isolates and the two most common mtDNA haplotypes represented approximately 93% of the world population, consistent with a selective sweep. Analysis of multilocus associations indicated that all field populations were in gametic equilibrium, suggesting that sexual recombination is a regular occurrence globally.

Population Structure of Mycosphaerella graminicola: From Lesions to Continents

ABSTRACT The genetic structure of field populations of Mycosphaerella graminicola was determined across a hierarchy of spatial scales using restriction fragment length polymorphism markers. The hierarchical gene diversity analysis included 1,098 isolates from seven field populations. Spatial scales ranged from millimeters to thousands of kilometers, including comparisons within and among lesions, within and among fields, and within and among regions and continents. At the smallest spatial scale, microtransect sampling was used to determine the spatial distribution of 15 genotypes found among 158 isolates sampled from five individual lesions. Each lesion had two to six different genotypes including both mating types in four of the five lesions, but in most cases a lesion was composed of one or two genotypes that occupied the majority of the lesion, with other rare genotypes interspersed among the common genotypes. The majority (77%) of gene diversity was distributed within plots ranging from approximately 1 to 9 m(2) in size. Genotype diversity (G / N) within fields for the Swiss, Texas, and Israeli fields was high, ranging from 79 to 100% of maximum possible values. Low population differentiation was indicated by the low G(ST) values among populations, suggesting a corresponding high degree of gene flow among these populations. At the largest spatial scale, populations from Switzerland, Israel, Oregon, and Texas were compared. Population differentiation among these populations was low (G(ST) = 0.05), and genetic identity between populations was high. A low but significant correlation between genetic and geographic distance among populations was found (r = -0.47, P = 0.012), suggesting that these populations probably have not reached an equilibrium between gene flow and genetic drift. Gene flow on a regional level can be reduced by implementing strategies, such as improved stubble management that minimize the production of ascospores. The possibility of high levels of gene flow on a regional level indicates a significant potential risk for the regional spread of mutant alleles that enable fungicide resistance or the breakdown of resistance genes.

Distribution of mating type alleles in the wheat pathogen Mycosphaerella graminicola over spatial scales from lesions to continents

A total of 2035 Mycosphaerella graminicola strains collected from 16 geographic locations on four continents were assayed for the mating type locus. RFLP fingerprints were used to identify clones in each population. At the smallest spatial scale analyzed, both mating types were found among fungal strains sampled from different lesions of the same leaf as well as from different pycnidia in the same lesion. At larger spatial scales, the two mating types were found at equal frequencies across spatial scales ranging from several square meters to several thousand square kilometers. Though the absolute frequencies of the two mating types sometimes varied for different sampling units within the same spatial scale in the hierarchy (plots within a field, fields within a country, or different continents of the world), none of the differences were statistically significant from the null hypothesis of equal frequencies for the two mating types. The evolutionary forces likely to maintain the even distribution of the two mating types in this pathogen were discussed.

Uncoupling and recoupling of autonomic regulation of the heart beat in pediatric septic shock

Healthy physiological systems exhibit marked signal variability and complexity, whereas diseased systems generally show a loss of variability, decreased complexity ("decomplexification"), and increased regularity. The goal of this study was to evaluate the uncoupling and recoupling phenomenon in children with septic shock by observing serial changes in heart rate variability metrics. Data were collected from 7 children with septic shock by using the computer system in the Complex Systems Laboratory at Oregon Health Sciences University. Heart rate time series were constructed and analyzed by using the Hales Research System at intervals of 6 h during pediatric intensive care unit (PICU) hospitalization. These power spectral values were then plotted vs. time. Six of seven patients showed an increase over time in low-frequency heart rate power and the low-/high-frequency ratio, whereas high-frequency heart rate power decreased. We also compared the change in mean heart rate, heart rate standard deviation, and power spectral values during the first 24 h of PICU hospitalization vs. the remainder of the PICU stay (for the 5 patients with a PICU length of stay > 48 h). Compared to the initial 24 h in the PICU, low-frequency power and the low-/high-frequency ratio increased, whereas high-frequency power decreased over the course of the illness. This report shows the potential value of monitoring the uncoupling and recoupling phenomenon in patients with septic shock. Our results are in agreement with other investigators who report evidence of decomplexification both in experimental models of sepsis and in clinical studies and provide direction for further work.

Using Restriction Fragment Length Polymorphisms to Assess Temporal Variation and Estimate the Number of Ascospores that Initiate Epidemics in Field Populations of Mycosphaerella graminicola

ABSTRACT Restriction fragment length polymorphisms (RFLPs) and DNA fingerprints were used to assess temporal variation and estimate the effective population size of the wheat pathogen Mycosphaerella graminicola over a 6-year period. In each year, the fungal population was founded by ascospores originating from outside the sampled fields. A total of 605 fungal isolates were included in this study. Our results indicate that the genetic structure of these M. graminicola populations were stable over the 6-year period. The common alleles at each RFLP locus were present at similar frequencies each year. More than 99% of gene diversity was distributed within populations sampled from the same year and less than 1% was attributed to differences among years. The lack of population differentiation among collections taken in different years indicated that the effective size of the source population was sufficiently large that genetic drift was insignificant in this location. It also suggests that the initial colonists from ascospore founder populations were a fair reflection of the source population. We estimate that the effective sizes of these field populations ranged from 3,400 to 700,000 individuals, depending on the size of the field sampled and assumptions about mutation rates. Estimates of the number of ascospores initiating epidemics of leaf blotch disease in each field plot and factors that contribute to the large effective population size of M. graminicola are discussed.

The Genetic Structure of Field Populations of Rhynchosporium secalis from Three Continents Suggests Moderate Gene Flow and Regular Recombination

ABSTRACT Restriction fragment length polymorphism (RFLP) markers were used to compare the genetic structure of field populations of Rhynchosporium secalis from barley. A total of 543 isolates representing 8 field populations were sampled from Australia, California, Finland, and Norway. Gene and genotype diversity were high in all populations. Nei's average gene diversity across seven RFLP loci was 0.513. Hierarchical gene diversity analysis showed that 9% of the total genetic variability was distributed among continents, 4% was distributed among fields within continents, and 13% was distributed among collection stations within a field. The majority (74%) of genetic variability was distributed within collection areas of approximately 1 m(2) within fields. Gene flow appears to be significant on a regional scale but more restricted among continents. Allele frequencies were significantly different at several RFLP loci. Genetic distances were small among populations within regions and large between regions. Pairwise comparisons of genotype diversity in the populations revealed significant differences among populations that were related mainly to differences in sampling strategies. Isolates from Norway and Finland showed a lower copy hybridization pattern with probe pRS26. This probe functioned as a fingerprint probe for the California and Australian isolates. Seven out of the eight populations studied were at gametic equilibrium for RFLP loci, suggesting that R. secalis populations in Norway, Finland, and Australia undergo regular recombination, although a teleomorph has not yet been recognized.

Estimation of rates of recombination and migration in populations of plant pathogens-a reply

ABSTRACT We find that the maximum likelihood method proposed by J. K. M. Brown has deficiencies that limit its usefulness for actual data sets. We propose two alternative statistical methods based on maximum likelihood that could be used to quantify rates of recombination and immigration in fungal populations. We also show that minor modification of our original method, which was based upon posterior probabilities, leads to a result that is identical to one of the maximum likelihood methods. Our previous estimates of the relative contributions of sexual reproduction, asexual reproduction, and immigration to the genetic structure of a Mycosphaerella graminicola population did not change significantly following reanalysis of our data with these new methods.

High levels of gene flow and heterozygote excess characterize Rhizoctonia solani AG-1 IA (Thanatephorus cucumeris) from Texas

To date, much of the genetics of the basidiomycete Thanatephorus cucumeris (anamorph = Rhizoctonia solani) remains unknown. Here, we present a population genetics study using codominant markers to augment laboratory analyses. Seven single-copy nuclear RFLP markers were used to examine 182 isolates of Rhizoctonia solani AG-1 IA collected from six commercial rice fields in Texas. Thirty-six multilocus RFLP genotypes were identified. Population subdivision analyses indicated a high degree of gene flow/migration between the six geographic populations. Tests for Hardy-Weinberg equilibrium (HWE) among the 36 multilocus RFLP genotypes revealed that four of the seven loci did not significantly differ from HWE. Subsequent analysis demonstrated that departures from HWE at the three remaining loci were due to an excess of heterozygotes. Data presented here suggest that R. solani AG-1 IA is actively outbreeding (heterothallic). Possible explanations for heterozygote excess, which was observed at all seven RFLP loci, are discussed.

Genetic Structure of Rhynchosporium secalis in Australia

ABSTRACT Restriction fragment length polymorphism (RFLP) markers were used to determine the genetic structure of Australian field populations of the barley scald pathogen Rhynchosporium secalis. Fungal isolates were collected by hierarchical sampling from five naturally infected barley fields in different geographic locations during a single growing season. Genetic variation was high in Australian R. secalis populations. Among the 265 fungal isolates analyzed, 214 distinct genotypes were identified. Average genotype diversity within a field population was 65% of its theoretical maximum. Nei's average gene diversity across seven RFLP loci was 0.54. The majority (76%) of gene diversity was distributed within sampling site areas measuring 1 m(2); 19% of gene diversity was distributed among sampling sites within fields; and 5% of gene diversity was distributed among fields. Fungal populations from different locations differed significantly both in allele frequencies and genotype diversities. The degree of genetic differentiation was significantly correlated with geographic distance between populations. Our results suggest that the R. secalis population in Western Australia has a different genetic structure than populations in Victoria and South Australia.

Measuring Immigration and Sexual Reproduction in Field Populations of Mycosphaerella graminicola

ABSTRACT A field experiment was conducted to determine the relative contributions of immigration and sexual reproduction to the genetic structure of Mycosphaerella graminicola populations during the course of an epidemic. The genetic structure of M. graminicola populations sampled from wheat plots inoculated artificially with 10 isolates was compared with control plots infected naturally by airborne ascospores. Restriction fragment length polymorphisms (RFLPs) were used to test the randomness of associations among loci, and DNA fingerprints were used to identify clones. All isolates in the control plots had unique genotypes and RFLP loci were at gametic equilibrium, findings consistent with random mating. The proportion of isolates in the inoculated plots with DNA fingerprints that differed from the 10 inoculated isolates increased from 3% in the early to 39 and 34% in the mid- and late season, respectively. The degree of gametic disequilibrium was higher in the mid-season than in the late-season population. By the end of the growing season, we estimate that 66% of the isolates in the inoculated plots were asexual progeny of the 10 inoculated isolates, 10% were immigrants, and 24% were sexual recombinants. The proportion of infections caused by ascospores increased over the growing season.

Genetic Structure and Temporal Dynamics of a Colletotrichum graminicola Population in a Sorghum Disease Nursery

ABSTRACT Restriction fragment length polymorphisms (RFLPs) were used to study the population genetics of Colletotrichum graminicola (= C. sublineolum), the causal agent of sorghum anthracnose. Screening of 80 anonymous probes from a genomic library detected polymorphisms in 81% of 299 probe-enzyme combinations among nine international isolates. Seven single- or low-copy probes were used to study a collection of 411 isolates sampled during 1991 to 1993 from a sorghum disease nursery in Georgia. Nei's gene diversity was moderately high, with = 0.215 on average, while genotypic diversity was extremely low with an average genotypic diversity value of G = 1.513. Only nine multilocus haplotypes were identified, with one haplotype being present at a frequency of approximately 80% each year. Two other haplotypes were found at significant frequencies (4 to 10%). Allele and haplotype frequencies did not differ over the 3 years, indicating that this population was stable. Our findings suggest that genetic drift and gene flow were not major contributors to genetic structure, while asexual reproduction had a significant effect.

High Genetic Similarity Among Populations of Phaeosphaeria nodorum Across Wheat Cultivars and Regions in Switzerland

ABSTRACT Phaeosphaeria nodorum was sampled from nine wheat fields across a 30-km transect representing three geographical regions in Switzerland to determine the scale of genetic differentiation among subpopulations. Three different wheat cultivars were sampled three times to determine whether differences in host genotype correlated with differences among corresponding pathogen populations. Seven restriction fragment length polymorphism (RFLP) loci and one DNA fingerprint were assayed for each of the 432 isolates in the collection. DNA fingerprints differentiated 426 unique genotypes. Though absolute differences were small, five RFLP loci exhibited significant differences in allele frequencies across the nine sub-populations. Gene diversity within all subpopulations was high (H(T) = 0.51), but only 3% of the total genetic variation was distributed among the nine subpopulations. When subpopulations were grouped according to geographical region or host cultivar, less than 1% of the genetic variation was distributed among groups, suggesting widespread gene flow and the absence of pathogen adaptation to specific wheat cultivars. Tests for gametic equilibrium within subpopulations and across the entire Swiss population supported the hypothesis of random mating.

Gene Flow and Sexual Reproduction in the Wheat Glume Blotch Pathogen Phaeosphaeria nodorum (Anamorph Stagonospora nodorum)

ABSTRACT Restriction fragment length polymorphisms (RFLPs) were used to characterize the genetic structures of three field populations of Phaeosphaeria nodorum from Texas, Oregon, and Switzerland. Data from seven nuclear RFLP loci were used to estimate gene diversity and genetic distances and to make indirect measures of gene flow between populations. Three of the seven RFLP loci differed significantly in allele frequencies across populations. On average, 96% of the total gene diversity was found within populations. There was little evidence for population subdivision, suggesting that gene flow was not restricted among populations. Based on an average population differentiation of 0.04, we estimated that the exchange of 11 migrants among populations per generation would be needed to account for the present level of population subdivision. Genotype diversity based on DNA fingerprints was at a maximum for the Swiss population, whereas populations in Texas and Oregon had lower genotype diversities. Many multilocus haplotypes were found in each population. Ninety-five percent of RFLP allele pairs were in gametic equilibrium. The data were consistent with random mating within each population.

Sexual reproduction plays a major role in the genetic structure of populations of the fungus Mycosphaerella graminicola

The relative contributions of sexual and asexual reproduction to the genetic structure of populations can be difficult to determine for fungi that use a mixture of both types of propagation. Nuclear RFLPs and DNA fingerprints were used to make indirect and direct measures of departures from random mating in a population of the plant pathogenic fungus Mycosphaerella graminicola during the course of an epidemic cycle. DNA fingerprints resolved 617 different genotypes among 673 isolates sampled from a single field over a 3-month period. Only 7% of the isolates represented asexual clones that were found more than once in the sample. The most common clone was found four times. Genotypic diversity averaged 85% of its maximum possible value during the course of the epidemic. Analyses of multilocus structure showed that allelic distributions among RFLP loci were independent. Pairwise comparisons between individual RFLP loci showed that the majority of alleles at these loci were in gametic equilibrium. Though this fungus has the capacity for a significant level of asexual reproduction, each analysis suggested that M. graminicola populations maintain a genetic structure more consistent with random-mating over the course of an epidemic cycle.

RFLPs in mitochondrial and nuclear DNA indicate low levels of genetic diversity in the oak wilt pathogen Ceratocystis fagacearum

Genetic diversity in the oak wilt pathogen Ceratocystis fagacearum was assessed using restriction fragment length polymorphisms (RFLPs) of the mitochondrial DNA (mtDNA) and anonymous RFLP loci in the nuclear DNA (nuDNA). No genetic variation was detected in the mtDNA among 27 isolates sampled from a broad geographical area. Southern hybridization to 100 anonymous, random, nuDNA probes detected a low level of variation among nine of the isolates. Only 35 out of 437 probe-enzyme combinations detected RFLPs. Most of the RFLPs appeared to result from insertions and deletions of less than 200 bp. A composite multilocus haplotype based on hybridization to six anonymous probes could differentiate each of the nine isolates tested, suggesting that these probes may be useful for further studies of the population biology and epidemiology of this pathogen. Hypotheses are presented to account for the low level of genetic variation.

Genetic variability for pathogenicity, isozyme, ribosomal DNA and colony color variants in populations of Rhynchosporium secalis

Samples of Rhynchosporium secalis were collected from two experimental barley populations known to carry a diverse array of alleles for resistance to this fungal pathogen. Classification of 163 isolates for four putative isozyme systems, a colony color dimorphism and 20 ribosomal DNA restriction fragment length variants revealed 49 different multilocus phenotypes (haplotypes). The six most common haplotypes differed significantly in pathogenicity. Genetic analyses of the data indicated that effective population sizes of the fungus were very large, that the effects of genetic drift were small, and that negligible recombination occurred in the populations studied. Frequency dependent selection was suggested as an explanation for the maintenance of variation in pathogenicity in the fungus.

Coevolution of host and pathogen populations in the Hordeum vulgare-Rhynchosporium secalis pathosystem

Isolates of Rhynchosporium secalis collected from two experimental barley populations were scored for putative isozyme, colony color, and virulence loci. Allelic frequencies, multilocus haplotype frequencies, and multilocus genetic structure differed in the two populations of R. secalis; haplotypes also differed widely from each other in virulence. The average virulence of isolates collected from the more resistant host population was greater than the average virulence of the isolates collected from the less resistant host population; also the least virulent haplotype, which made up 19% of the pathogen population collected from the less resistant host population, accounted for only 0.3% of the isolates collected from the more resistant host population. It was concluded that the genetic systems of the barley host and fungal pathogen interacted in a complementary fashion and that the genetic structures of both the host and pathogen populations were shaped by coevolutionary processes featuring interactions among loci affecting many different traits, including interactions among host resistance genes and pathogen virulence genes.