The Phytophthora parasitica effector AVH195 interacts with ATG8, attenuates host autophagy, and promotes biotrophic infection.

BACKGROUND: Plant pathogens secrete effector proteins into host cells to suppress immune responses and manipulate fundamental cellular processes. One of these processes is autophagy, an essential recycling mechanism in eukaryotic cells that coordinates the turnover of cellular components and contributes to the decision on cell death or survival. RESULTS: We report the characterization of AVH195, an effector from the broad-spectrum oomycete plant pathogen, Phytophthora parasitica. We show that P. parasitica expresses AVH195 during the biotrophic phase of plant infection, i.e., the initial phase in which host cells are maintained alive. In tobacco, the effector prevents the initiation of cell death, which is caused by two pathogen-derived effectors and the proapoptotic BAX protein. AVH195 associates with the plant vacuolar membrane system and interacts with Autophagy-related protein 8 (ATG8) isoforms/paralogs. When expressed in cells from the green alga, Chlamydomonas reinhardtii, the effector delays vacuolar fusion and cargo turnover upon stimulation of autophagy, but does not affect algal viability. In Arabidopsis thaliana, AVH195 delays the turnover of ATG8 from endomembranes and promotes plant susceptibility to P. parasitica and the obligate biotrophic oomycete pathogen Hyaloperonospora arabidopsidis. CONCLUSIONS: Taken together, our observations suggest that AVH195 targets ATG8 to attenuate autophagy and prevent associated host cell death, thereby favoring biotrophy during the early stages of the infection process.

Prospective evaluation of patient-reported anxiety and experiences with adaptive radiation therapy on an MR-linac.

Purpose: An integrated magnetic resonance scanner and linear accelerator (MR-linac) was implemented with daily online adaptive radiation therapy (ART). This study evaluated patient-reported experiences with their overall hospital care as well as treatment in the MR-linac environment. Methods: Patients pre-screened for MR eligibility and claustrophobia were referred to simulation on a 1.5 T MR-linac. Patient-reported experience measures were captured using two validated surveys. The 15-item MR-anxiety questionnaire (MR-AQ) was administered immediately after the first treatment to rate MR-related anxiety and relaxation. The 40-item satisfaction with cancer care questionnaire rating doctors, radiation therapists, the services and care organization and their outpatient experience was administered immediately after the last treatment using five-point Likert responses. Results were analyzed using descriptive statistics. Results: 205 patients were included in this analysis. Multiple sites were treated across the pelvis and abdomen with a median treatment time per fraction of 46 and 66 min respectively. Patients rated MR-related anxiety as "not at all" (87%), "somewhat" (11%), "moderately" (1%) and "very much so" (1%). Positive satisfaction responses ranged from 78 to 100% (median 93%) across all items. All radiation therapist-specific items were rated positively as 96-100%. The five lowest rated items (range 78-85%) were related to general provision of information, coordination, and communication. Overall hospital care was rated positively at 99%. Conclusion: In this large, single-institution prospective cohort, all patients had low MR-related anxiety and completed treatment as planned despite lengthy ART treatments with the MR-linac. Patients overall were highly satisfied with their cancer care involving ART using an MR-linac.

A Prospective Study of Machine Learning-Assisted Radiation Therapy Planning for Patients Receiving 54 Gy to the Brain.

PURPOSE: The capacity for machine learning (ML) to facilitate radiation therapy (RT) planning for primary brain tumors has not been described. We evaluated ML-assisted RT planning with regard to clinical acceptability, dosimetric outcomes, and planning efficiency for adults and children with primary brain tumors. METHODS AND MATERIALS: In this prospective study, children and adults receiving 54 Gy fractionated RT for a primary brain tumor were enrolled. For each patient, one ML-assisted RT plan was created and compared with 1 or 2 plans created using standard ("manual") planning procedures. Plans were evaluated by the treating oncologist, who was blinded to the method of plan creation. The primary endpoint was the proportion of ML plans that were clinically acceptable for treatment. Secondary endpoints included the frequency with which ML plans were selected as preferable for treatment, and dosimetric differences between ML and manual plans. RESULTS: A total of 116 manual plans and 61 ML plans were evaluated across 61 patients. Ninety-four percent of ML plans and 93% of manual plans were judged to be clinically acceptable (P = 1.0). Overall, the quality of ML plans was similar to manual plans. ML plans comprised 34.5% of all plans evaluated and were selected for treatment in 36.1% of cases (P = .82). Similar tumor target coverage was achieved between both planning methods. Normal brain (brain minus planning target volume) received an average of 1 Gy less mean dose with ML plans (compared with manual plans, P < .001). ML plans required an average of 45.8 minutes less time to create, compared with manual plans (P < .001). CONCLUSIONS: ML-assisted automated planning creates high-quality plans for patients with brain tumors, including children. Plans created with ML assistance delivered slightly less dose to normal brain tissues and can be designed in less time.

MIF-like domain containing protein orchestrates cellular differentiation and virulence in the fungal pathogen Magnaporthe oryzae.

Macrophage migration inhibitory factor (MIF) is a pleiotropic protein with chemotactic, pro-inflammatory, and growth-promoting activities first discovered in mammals. In parasites, MIF homologs are involved in immune evasion and pathogenesis. Here, we present the first comprehensive analysis of an MIF protein from the devastating plant pathogen Magnaporthe oryzae (Mo). The fungal genome encodes a single MIF protein (MoMIF1) that, unlike the human homolog, harbors multiple low-complexity regions (LCRs) and is unique to Ascomycota. Following infection, MoMIF1 is expressed in the biotrophic phase of the fungus, and is strongly down-regulated during subsequent necrotrophic growth in leaves and roots. We show that MoMIF1 is secreted during plant infection, affects the production of the mycotoxin tenuazonic acid and inhibits plant cell death. Our results suggest that MoMIF1 is a novel key regulator of fungal virulence that maintains the balance between biotrophy and necrotrophy during the different phases of fungal infection.

Superhydrophobicity mechanism of refoliated quaking aspen leaves after complete defoliation by LDD (gypsy, spongy) moth caterpillars.

Complete defoliation of trees due to periodic LDD (Lymantria dispar dispar) moth outbreaks in many parts of the world is a significant stress factor for the survival of individual trees and entire forests over vast areas. This study addresses such a mid-summer defoliation event in Ontario, Canada for quaking aspen trees during 2021. It is shown that complete refoliation in the same year is possible for these trees, albeit with significantly smaller leaf size. Regrown leaves showed the well-known non-wetting behaviour typically observed for the quaking aspen tree without a defoliation event. These leaves have the same hierarchical dual-scale surface structure consisting of nanometre-size epicuticular wax (ECW) crystals superimposed on micrometre-sized papillae. This structure provides for the Cassie-Baxter non-wetting state with a very high water contact angle on the adaxial surface of the leaves. Subtle differences in the leaf surface morphology of the refoliation leaves compared with the regular growth leaves are likely due to environmental factors such as seasonal temperature during the leaf growth period after budbreak.

Evaluating the Short-term Environmental and Clinical Effects of a Radiation Oncology Department's Response to the COVID-19 Pandemic.

PURPOSE: During the COVID-19 pandemic, many radiation oncology departments worldwide adopted the use of shorter and more intense hypofractionated regimens. Hospital foot traffic was reduced through virtual care. This study's primary objective was to assess the collective environmental effect of these strategic changes by identifying sources of carbon dioxide equivalents (CO2e). The rate of radiation-related adverse events from the increased use of hypofractionated treatments was assessed. METHODS AND MATERIALS: All patients treated with external beam radiation therapy from April 1, 2019, to March 31, 2021, at our single institution were identified (n = 10,175) along with their radiation therapy visits (176,423 fractions) and unplanned visits to the radiation nursing clinic or emergency department. Out-patient hospital and virtual visits (n = 75,853) during this same period were also analyzed. Environmental effect measures, including linear accelerator power usage, patient travel distances, and personal protection equipment consumption were all converted into CO2e. RESULTS: The use of curative hypofractionated regimens increased from 17% to 27% during the pandemic year. Carbon footprint was reduced by 39% during the pandemic year (1,332,388 kg CO2e) compared with the prepandemic year (2,024,823 kg CO2e). Comparing patients in the prepandemic versus pandemic year, there was a significant reduction in the proportion of hypofractionated patients who needed a visit to either the radiation nursing clinic (39% vs 25%; P < .001) or emergency department (6% vs 2%; P < .001) during and within 90 days of radiation therapy. CONCLUSIONS: This is the first study to demonstrate the environmental benefits of increased use of hypofractionated regimens and virtual care, while assuring that there was no added acute radiation-related adverse event. Our findings support their continued use as one of many long-term strategies to reduce the environmental footprint of health care delivery.

The exodomain of the impaired oomycete susceptibility 1 receptor mediates both endoplasmic reticulum stress responses and abscisic acid signalling during downy mildew infection of Arabidopsis.

The phytohormone abscisic acid (ABA) regulates cell growth and plant development, and contributes to defence responses to pathogens. We previously showed that the Arabidopsis malectin-like domain leucine-rich repeat receptor-like kinase (MLD-LRR-RLK) impaired oomycete susceptibility 1 (IOS1) attenuates ABA signalling during infection with the oomycete downy mildew pathogen Hyaloperonospora arabidopsidis. The exodomain of IOS1 with its MLD retains the receptor in the endoplasmic reticulum (ER), where it interacts with the ribophorin HAP6 to dampen a pathogen-induced ER stress response called the unfolded protein response (UPR). The down-regulation of both ABA and UPR signalling probably provides the pathogen with an advantage for infection. Here, we show that ABA-related phenotypes of the ios1-1 mutant, such as up-regulated expression of ABA-responsive genes and hypersensitivity to exogenous ABA application, were reverted by expression of the IOS1 exodomain in the mutant background. Furthermore, knockdown mutants for ER-resident HAP6 showed similarly reduced UPR and ABA signalling, indicating that HAP6 positively regulates both pathways. Our data suggest that the IOS1 exodomain and HAP6 contribute in the ER to the IOS1-mediated interference with ABA and UPR signalling.

Noise-Based Image Harmonization Significantly Increases Repeatability and Reproducibility of Radiomics Features in PET Images: A Phantom Study.

For multicenter clinical studies, characterizing the robustness of image-derived radiomics features is essential. Features calculated on PET images have been shown to be very sensitive to image noise. The purpose of this work was to investigate the efficacy of a relatively simple harmonization strategy on feature robustness and agreement. A purpose-built texture pattern phantom was scanned on 10 different PET scanners in 7 institutions with various different image acquisition and reconstruction protocols. An image harmonization technique based on equalizing a contrast-to-noise ratio was employed to generate a "harmonized" alongside a "standard" dataset for a reproducibility study. In addition, a repeatability study was performed with images from a single PET scanner of variable image noise, varying the binning time of the reconstruction. Feature agreement was measured using the intraclass correlation coefficient (ICC). In the repeatability study, 81/93 features had a lower ICC on the images with the highest image noise as compared to the images with the lowest image noise. Using the harmonized dataset significantly improved the feature agreement for five of the six investigated feature classes over the standard dataset. For three feature classes, high feature agreement corresponded with higher sensitivity to the different patterns, suggesting a way to select suitable features for predictive models.

A plant receptor domain with functional analogies to animal malectin disables ER stress responses upon infection.

Malectins from the oligosaccharyltransferase (OST) complex in the endoplasmic reticulum (ER) of animal cells are involved in ER quality control and contribute to the Unfolded Protein Response (UPR). Malectins are not found in plant cells, but malectin-like domains (MLDs) are constituents of many membrane-bound receptors. In Arabidopsis thaliana, the MLD-containing receptor IOS1 promotes successful infection by filamentous plant pathogens. We show that the MLD of its exodomain retains IOS1 in the ER of plant cells and attenuates the infection-induced UPR. Expression of the MLD in the ios1-1 knockout background is sufficient to complement infection-related phenotypes of the mutant, such as increased UPR and reduced disease susceptibility. IOS1 interacts with the ER membrane-associated ribophorin HAP6 from the OST complex, and hap6 mutants show decreased pathogen-responsive UPR and increased disease susceptibility. Altogether, this study revealed a previously uncharacterized role of a plant receptor domain in the regulation of ER stress during infection.

Polymer-Conjugated Carbon Nanotubes for Biomolecule Loading.

Nanomaterials have emerged as an invaluable tool for the delivery of biomolecules such as DNA and RNA, with various applications in genetic engineering and post-transcriptional genetic manipulation. Alongside this development, there has been an increasing use of polymer-based techniques, such as polyethylenimine (PEI), to electrostatically load polynucleotide cargoes onto nanomaterial carriers. However, there remains a need to assess nanomaterial properties, conjugation conditions, and biocompatibility of these nanomaterial-polymer constructs, particularly for use in plant systems. In this work, we develop mechanisms to optimize DNA loading on single-walled carbon nanotubes (SWNTs) with a library of polymer-SWNT constructs and assess DNA loading ability, polydispersity, and both chemical and colloidal stability. Counterintuitively, we demonstrate that polymer hydrolysis from nanomaterial surfaces can occur depending on polymer properties and attachment chemistries, and we describe mitigation strategies against construct degradation. Given the growing interest in delivery applications in plant systems, we also assess the stress response of plants to polymer-based nanomaterials and provide recommendations for future design of nanomaterial-based polynucleotide delivery strategies.

Carbon nanotube biocompatibility in plants is determined by their surface chemistry.

BACKGROUND: Agriculture faces significant global challenges including climate change and an increasing food demand due to a growing population. Addressing these challenges will require the adoption of transformative innovations into biotechnology practice, such as nanotechnology. Recently, nanomaterials have emerged as unmatched tools for their use as biosensors, or as biomolecule delivery vehicles. Despite their increasingly prolific use, plant-nanomaterial interactions remain poorly characterized, drawing into question the breadth of their utility and their broader environmental compatibility. RESULTS: Herein, we characterize the response of Arabidopsis thaliana to single walled carbon nanotube (SWNT) exposure with two different surface chemistries commonly used for biosensing and nucleic acid delivery: oligonucleotide adsorbed-pristine SWNTs, and polyethyleneimine-SWNTs loaded with plasmid DNA (PEI-SWNTs), both introduced by leaf infiltration. We observed that pristine SWNTs elicit a mild stress response almost undistinguishable from the infiltration process, indicating that these nanomaterials are well-tolerated by the plant. However, PEI-SWNTs induce a much larger transcriptional reprogramming that involves stress, immunity, and senescence responses. PEI-SWNT-induced transcriptional profile is very similar to that of mutant plants displaying a constitutive immune response or treated with stress-priming agrochemicals. We selected molecular markers from our transcriptomic analysis and identified PEI as the main cause of this adverse reaction. We show that PEI-SWNT response is concentration-dependent and, when persistent over time, leads to cell death. We probed a panel of PEI variant-functionalized SWNTs across two plant species and identified biocompatible SWNT surface functionalizations. CONCLUSIONS: While SWNTs themselves are well tolerated by plants, SWNTs surface-functionalized with positively charged polymers become toxic and produce cell death. We use molecular markers to identify more biocompatible SWNT formulations. Our results highlight the importance of nanoparticle surface chemistry on their biocompatibility and will facilitate the use of functionalized nanomaterials for agricultural improvement.

Medical physics external beam plan review: What contributes to the variability?

PURPOSE: In this article we report on the results of a survey of physics plan review practices conducted by the Cancer Care Ontario Communities of Practice and the variations in practice between and within centers. METHODS: The medical physicists at each center worked together to complete the survey and submit a single response for that center. A 4-point Likert scale, used to report the variation in practice at each center, was quantified into two parameters: "Intra-center variation", the distribution of responses within the center, and "Variation between centers", the difference between the center's response and the provincial mean. These metrics were correlated with center characteristics to identify factors that impacted on variations in practice. RESULTS: Bolus and heterogeneity correction were the only two items checked by all physicists in all centers. In more than half of the centers, image registration and DVH binning are not likely checked by physics. A significant difference in the variation between centers is observed for centers that used a single vendor's products. Centers that used an official checklist indicated higher levels and a wider range of Intra-center variation. Higher workload did not affect the variation in checking patterns between physicists in the same center. CONCLUSIONS: The effect of a center's resources on their checking practice suggest that local environment and workflow be accounted for when implementing TG275 guidelines. The observation that standardized checklists did not reduce checking variability point to the importance of following the checklist development guidelines in MPPG4 to avoid ineffective checklists.

Chemokine-like MDL proteins modulate flowering time and innate immunity in plants.

Human macrophage migration inhibitory factor (MIF) is an atypical chemokine implicated in intercellular signaling and innate immunity. MIF orthologs (MIF/D-DT-like proteins, MDLs) are present throughout the plant kingdom, but remain experimentally unexplored in these organisms. Here, we provide an in planta characterization and functional analysis of the three-member gene/protein MDL family in Arabidopsis thaliana. Subcellular localization experiments indicated a nucleo-cytoplasmic distribution of MDL1 and MDL2, while MDL3 is localized to peroxisomes. Protein-protein interaction assays revealed the in vivo formation of MDL1, MDL2, and MDL3 homo-oligomers, as well as the formation of MDL1-MDL2 hetero-oligomers. Functionally, Arabidopsismdl mutants exhibited a delayed transition from vegetative to reproductive growth (flowering) under long-day conditions, but not in a short-day environment. In addition, mdl mutants were more resistant to colonization by the bacterial pathogen Pseudomonas syringae pv. maculicola. The latter phenotype was compromised by the additional mutation of SALICYLIC ACID INDUCTION DEFICIENT 2 (SID2), a gene implicated in the defense-induced biosynthesis of the key signaling molecule salicylic acid. However, the enhanced antibacterial immunity was not associated with any constitutive or pathogen-induced alterations in the levels of characteristic phytohormones or defense-associated metabolites. Interestingly, bacterial infection triggered relocalization and accumulation of MDL1 and MDL2 at the peripheral lobes of leaf epidermal cells. Collectively, our data indicate redundant functionality and a complex interplay between the three chemokine-like Arabidopsis MDL proteins in the regulation of both developmental and immune-related processes. These insights expand the comparative cross-kingdom analysis of MIF/MDL signaling in human and plant systems.

Atypical Membrane-Anchored Cytokine MIF in a Marine Dinoflagellate.

Macrophage Migration Inhibitory Factors (MIF) are pivotal cytokines/chemokines for vertebrate immune systems. MIFs are typically soluble single-domain proteins that are conserved across plant, fungal, protist, and metazoan kingdoms, but their functions have not been determined in most phylogenetic groups. Here, we describe an atypical multidomain MIF protein. The marine dinoflagellate Lingulodinium polyedra produces a transmembrane protein with an extra-cytoplasmic MIF domain, which localizes to cell-wall-associated membranes and vesicular bodies. This protein is also present in the membranes of extracellular vesicles accumulating at the secretory pores of the cells. Upon exposure to biotic stress, L. polyedra exhibits reduced expression of the MIF gene and reduced abundance of the surface-associated protein. The presence of LpMIF in the membranes of secreted extracellular vesicles evokes the fascinating possibility that LpMIF may participate in intercellular communication and/or interactions between free-living organisms in multispecies planktonic communities.

A Multidisciplinary Approach to Implement Image-Guided Craniospinal Irradiation.

PURPOSE: Practical considerations dictated a change in the craniospinal irradiation (CSI) technique. We report our experience in developing and refining CSI planning and treatment parameters, using a 3-isocenter image-guided intensity-modulated radiation therapy (IG-IMRT) technique. METHODS AND MATERIALS: Two institutional values guided development: multidisciplinary decision-making and coordinated considerations throughout simulation, planning, and delivery. Patient immobilization and simulation parameters were selected based on treatment delivery system limitations. Commissioning fluence verification maps were acquired to verify dose in regions of overlapping fields. Robustness analysis was performed to assess impact of potential setup errors measured through IGRT verification. Treatment considerations included order of isocenter imaging and treatment and respective IGRT frequency, modality, and image registration thresholds. RESULTS: Overall film measurements were within 3% of planned dose, confirmed by phantom composite measurements showing all points were within 97% of planned dose. Setup sensitivity analysis suggested a 3-mm setup tolerance was sufficient to ensure confidence in the delivered plan. As the most critical organs at risk were in the superior isocenter, the daily isocenter treatment order was confirmed as superior, middle, and inferior. Daily cone beam computed tomography guidance was chosen for all isocenters (3° rotational threshold). Except for the superior/inferior direction of the middle and inferior isocenters, which were adjusted to 3 mm based on sensitivity analysis, a 1-mm translational threshold was used. CONCLUSIONS: An IG-IMRT CSI technique has been developed and implemented in our institution through a multidisciplinary approach. This process highlights the collaborative, iterative approach used to successfully integrate a new treatment technique in an image-guidance era.

Impact of Intraoperative Cell Salvage on Blood Coagulation Factor Concentrations in Patients Undergoing Cardiac Surgery.

BACKGROUND: Cardiothoracic surgery is associated with major blood loss and allogeneic transfusion of red blood cell concentrates. To minimize allogeneic red blood cell (RBC) transfusion, intraoperative cell salvage has been effectively used for years. The objective of this study was to evaluate the impact of cell salvage on blood coagulation factors. METHODS: We enrolled 30 patients scheduled for cardiac surgery in a prospective single-center observational cohort study at an academic hospital. Blood samples from the cell salvage system were obtained from both the reservoir and the processed red blood cell concentrate. Coagulation factors, fibrinogen, antithrombin and von Willebrand activity, and antigen were assessed before and after cell salvage. Statistical analysis was performed using Wilcoxon matched-pairs signed rank test. RESULTS: Our results revealed a significant decrease of fibrinogen (P < .001), coagulation factors II (P = .004), factors VII, X, and XIII (P < .001), and all other measured coagulation factor concentrations/activities in the processed red blood cell concentrate, when compared to the concentrations/activities of the reservoir. CONCLUSIONS: The results of the present study revealed a significant reduction of coagulation factor concentrations/activities by the washing process. Therefore, physicians need to consider adequate management of coagulation in patients with major blood loss and the need of large volumes of RBC transfusion.

BAX inhibitor-1: between stress and survival.

Cellular gatekeepers are essential to maintain order within a cell and anticipate signals of stress to promote survival. BCL2 associated X, apoptosis regulator (BAX) inhibitor-1 (BI-1), also named transmembrane BAX inhibitor motif containing-6, is a highly conserved endoplasmic reticulum (ER) transmembrane protein. Originally identified as an inhibitor of BAX-induced apoptosis, its pro-survival properties have been expanded to include functions targeted against ER stress, calcium imbalance, reactive oxygen species accumulation, and metabolic dysregulation. Nevertheless, the structural biology and biochemical mechanism of action of BI-1 are still under debate. BI-1 has been implicated in several diseases, including chronic liver disease, diabetes, ischemia/reperfusion injury, neurodegeneration, and cancer. While most studies have demonstrated a beneficial role for BI-1 in the ubiquitous maintenance of cellular homeostasis, its expression in cancer cells seems most often to contribute to tumorigenesis and metastasis. Here, we summarize what is known about BI-1 and encourage future studies on BI-1's contribution to cellular life and death decisions to advocate its potential as a target for drug development and other therapeutic strategies.

Cross-Kingdom Analysis of Diversity, Evolutionary History, and Site Selection within the Eukaryotic Macrophage Migration Inhibitory Factor Superfamily.

Macrophage migration inhibitory factors (MIF) are multifunctional proteins regulating major processes in mammals, including activation of innate immune responses. MIF proteins also play a role in innate immunity of invertebrate organisms or serve as virulence factors in parasitic organisms, raising the question of their evolutionary history. We performed a broad survey of MIF presence or absence and evolutionary relationships across 803 species of plants, fungi, protists, and animals, and explored a potential relation with the taxonomic status, the ecology, and the lifestyle of individual species. We show that MIF evolutionary history in eukaryotes is complex, involving probable ancestral duplications, multiple gene losses and recent clade-specific re-duplications. Intriguingly, MIFs seem to be essential and highly conserved with many sites under purifying selection in some kingdoms (e.g., plants), while in other kingdoms they appear more dispensable (e.g., in fungi) or present in several diverged variants (e.g., insects, nematodes), suggesting potential neofunctionalizations within the protein superfamily.