Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi.

Studying the signatures of evolution can help to understand genetic processes. Here, we demonstrate how the existence of balancing selection can be used to identify the breeding systems of fungi from genomic data. The breeding systems of fungi are controlled by self-incompatibility loci that determine mating types between potential mating partners, resulting in strong balancing selection at the loci. Within the fungal phylum Basidiomycota, two such self-incompatibility loci, namely HD MAT locus and P/R MAT locus, control mating types of gametes. Loss of function at one or both MAT loci results in different breeding systems and relaxes the MAT locus from balancing selection. By investigating the signatures of balancing selection at MAT loci, one can infer a species' breeding system without culture-based studies. Nevertheless, the extreme sequence divergence among MAT alleles imposes challenges for retrieving full variants from both alleles when using the conventional read-mapping method. Therefore, we employed a combination of read-mapping and local de novo assembly to construct haplotypes of HD MAT alleles from genomes in suilloid fungi (genera Suillus and Rhizopogon). Genealogy and pairwise divergence of HD MAT alleles showed that the origins of mating types predate the split between these two closely related genera. High sequence divergence, trans-specific polymorphism, and the deeply diverging genealogy confirm the long-term functionality and multiallelic status of HD MAT locus in suilloid fungi. This work highlights a genomics approach to studying breeding systems regardless of the culturability of organisms based on the interplay between evolution and genetics.

Diversity of genomic adaptations to the post-fire environment in Pezizales fungi points to crosstalk between charcoal tolerance and sexual development.

Wildfires drastically impact the soil environment, altering the soil organic matter, forming pyrolyzed compounds, and markedly reducing the diversity of microorganisms. Pyrophilous fungi, especially the species from the orders Pezizales and Agaricales, are fire-responsive fungal colonizers of post-fire soil that have historically been found fruiting on burned soil and thus may encode mechanisms of processing these compounds in their genomes. Pyrophilous fungi are diverse. In this work, we explored this diversity and sequenced six new genomes of pyrophilous Pezizales fungi isolated after the 2013 Rim Fire near Yosemite Park in California, USA: Pyronema domesticum, Pyronema omphalodes, Tricharina praecox, Geopyxis carbonaria, Morchella snyderi, and Peziza echinospora. A comparative genomics analysis revealed the enrichment of gene families involved in responses to stress and the degradation of pyrolyzed organic matter. In addition, we found that both protein sequence lengths and G + C content in the third base of codons (GC3) in pyrophilous fungi fall between those in mesophilic/nonpyrophilous and thermophilic fungi. A comparative transcriptome analysis of P. domesticum under two conditions - growing on charcoal, and during sexual development - identified modules of genes that are co-expressed in the charcoal and light-induced sexual development conditions. In addition, environmental sensors such as transcription factors STE12, LreA, LreB, VosA, and EsdC were upregulated in the charcoal condition. Taken together, these results highlight genomic adaptations of pyrophilous fungi and indicate a potential connection between charcoal tolerance and fruiting body formation in P. domesticum.

The influence of stereoscopic vision on surgical performance in minimal invasive surgery-a substudy of the IDOSP-Study (Influence of 3D- vs. 4 K-Display Systems on Surgical Performance in minimal invasive surgery).

PURPOSE: This study is a secondary analysis of the IDOSP trial published in the Annals of Surgery 2020. The aim of this study was to examine the influence of stereo acuity on surgical performance in a laparoscopic training parkour with 3D- versus 4 K-2D-display technique. METHODS: The surgical performance of medical students (MS), non-board-certified surgeons (NBC), and board-certified surgeons (BC) was compared using 3D- versus 4 K-2D-display technique at a training parkour in a randomized cross-over trial. Stereo acuity was tested by TNO and Titmus Stereo tests. RESULTS: Eighty-nine participants were included in this sub-trial. The median stereo acuity for all participants, measured with the Titmus test, was 25 s arc, with TNO test 30 s arc. Higher quality stereo vision, measured with the Titmus test, correlated significantly with a reduced parkour time (r = 0.26, p = 0.02) and error (r = 0.21, p = 0.048) with the 3D screen. The TNO test did not correlate significantly with parkour performance. There was no statistically significant correlation between parkour time nor error and stereo acuity using the 4 K system (p > 0.457 respectively). Higher age showed a significant correlation with lower stereo acuity measured with TNO (r = 0.21, p = 0.014), but not with the Titmus test (r = - 0.7, p = 0.39). Seven percent of the group "NBC and BC" showed reduced stereo acuity > 120 s arc with the Titmus test and 3% with the TNO test. CONCLUSION: High-quality stereo vision is of utmost importance for surgical skills using a 3D-display system. This was most obvious for MS and for tasks that place particularly high demands on hand-eye coordination. The Titmus test was more precise than the TNO test to predict the benefit of a 3D monitor system. Experience and fine motor skills could partly compensate for a poorer stereo acuity. TRIAL REGISTRATION: This trial was registered at clinicaltrials.gov (trial number: NCT03445429, registered February 26, 2018).

Gender benefit in laparoscopic surgical performance using a 3D-display system: data from a randomized cross-over trial.

BACKGROUND: The use of 3D technique compared to high-resolution 2D-4K-display technique has been shown to optimize spatial orientation and surgical performance in laparoscopic surgery. Since women make up an increasing amount of medical students and surgeons, this study was designed to investigate whether one gender has a greater benefit from using a 3D compared to a 4K-display system. METHODS: In a randomized cross-over trial, the surgical performance of male and female medical students (MS), non-board certified surgeons (NBCS), and board certified surgeons (BCS) was compared using 3D- vs. 4K-display technique at a minimally invasive training parkour with multiple surgical tasks and repetitions. RESULTS: 128 participants (56 women, 72 men) were included. Overall parkour time in seconds was 3D vs. 4K for all women 770.7 ± 31.9 vs. 1068.1 ± 50.0 (p < 0.001) and all men 664.5 ± 19.9 vs. 889.7 ± 31.2 (p < 0.001). Regarding overall mistakes, participants tend to commit less mistakes while using the 3D-vision system, showing 10.2 ± 1.1 vs. 13.3 ± 1.3 (p = 0.005) for all women and 9.6 ± 0.7 vs. 12.2 ± 1.0 (p = 0.001) for all men. The benefit of using a 3D system, measured by the difference in seconds, was for women 297.3 ± 41.8 (27.84%) vs. 225.2 ± 23.3 (25.31%) for men (p = 0.005). This can be confirmed in the MS group with 327.6 ± 65.5 (35.82%) vs. 249.8 ± 33.7 (32.12%), p = 0.041 and in the NBCS group 359 ± 52.4 (28.25%) vs. 198.2 ± 54.2 (18.62%), p = 0.003. There was no significant difference in the BCS group. CONCLUSION: 3D laparoscopic display technique optimizes surgical performance compared to the 2D-4K technique for both women and men. The greatest 3D benefit was found for women with less surgical experience. As a possible result of surgical education, this gender specific difference disappears with higher grade of experience. Using a 3D-vision system could facilitate surgical apprenticeship, especially for women.

Toward Smart Traceability for Digital Sensors and the Industrial Internet of Things.

The Internet of Things (IoT) is characterized by a large number of interconnected devices or assets. Measurement instruments in the IoT are typically digital in the sense that their indications are available only as digital output. Moreover, a growing number of IoT sensors contain a built-in pre-processing system, e.g., for compensating unwanted effects. This paper considers the application of metrological principles to such so-called "smart sensors" in the IoT. It addresses the calibration of digital sensors, mathematical and semantic approaches, the communication of data quality and the meaning of traceability for the IoT in general.

A non-linear effect of the spatial structure of the soil ectomycorrhizal spore bank on the performance of pine seedlings.

The spatial structure of the environment is known to affect ecological processes. Unlike the spatial structure of negative interactions, such as competition and predation, the role of spatial structure in positive interaction has received less attention. We tested how the spatial structure of spores of ectomycorrhizal fungi (EMF) in the soil affects the growth of Aleppo pine (Pinus halepensis) seedlings. Spores were spatially distributed at four different levels of patchiness (1 patch, 4 patches, 8 patches and complete mixing) in 4 L pots (all pots received the same total amount of spores). Based on previous findings, we hypothesized that plant performance would gradually increase from the single patch treatment to the complete mixing. However, we found a non-linear response to patchiness. Specifically, plants were largest in the single patch and complete mixing while those in the 4 and 8 patch treatments were the smallest. This non-monotonic response, which might be the result of spatially determined colonization timing or community composition, suggests that the spatial structure of EMF spores has a complex effect on seedling growth.

High resilience of the mycorrhizal community to prescribed seasonal burnings in eastern Mediterranean woodlands.

Fire effects on ecosystems range from destruction of aboveground vegetation to direct and indirect effects on belowground microorganisms. Although variation in such effects is expected to be related to fire severity, another potentially important and poorly understood factor is the effect of fire seasonality on soil microorganisms. We carried out a large-scale field experiment examining the effects of spring (early-dry season) versus autumn (late-dry- season) burns on the community composition of soil fungi in a typical Mediterranean woodland. Although the intensity and severity of our prescribed burns were largely consistent between the two burning seasons, we detected differential fire season effects on the composition of the soil fungal community, driven by changes in the saprotrophic fungal guild. The community composition of ectomycorrhizal fungi, assayed both in pine seedling bioassays and from soil sequencing, appeared to be resilient to the variation inflicted by seasonal fires. Since changes in the soil saprotrophic fungal community can directly influence carbon emission and decomposition rates, we suggest that regardless of their intensity and severity, seasonal fires may cause changes in ecosystem functioning.

Comparative genomics of pyrophilous fungi reveals a link between fire events and developmental genes.

Forest fires generate a large amount of carbon that remains resident on the site as dead and partially 'pyrolysed' (i.e. burnt) material that has long residency times and constitutes a significant pool in fire-prone ecosystems. In addition, fire-induced hydrophobic soil layers, caused by condensation of pyrolysed waxes and lipids, increase post-fire erosion and can lead to long-term productivity losses. A small set of pyrophilous fungi dominate post-fire soils and are likely to be involved with the degradation of all these compounds, yet almost nothing is currently known about what these fungi do or the metabolic processes they employ. In this study, we sequenced and analysed genomes from fungi isolated after Rim fire near Yosemite National Park in 2013 and showed the enrichment/expansion of CAZymes and families known to be involved in fruiting body initiation when compared to other basidiomycete fungi. We found gene families potentially involved in the degradation of the hydrophobic layer and pyrolysed organic matter, such as hydrophobic surface binding proteins, laccases (AA1_1), xylanases (GH10, GH11), fatty acid desaturases and tannases. Thus, pyrophilous fungi are important actors to restate the soil's functional capabilities.

3D Versus 4K Display System - Influence of "State-of-the-art"-Display Technique on Surgical Performance (IDOSP-study) in Minimally Invasive Surgery: A Randomized Cross-over Trial.

OBJECTIVE: To evaluate if "state-of-the-art" 3D- versus 4K-display techniques could influence surgical performance. BACKGROUND: High quality minimally invasive surgery is challenging. Therefore excellent vision is crucial. 3D display technique (3D) and 2D-4K technique (4K) are designed to facilitate surgical performance, either due to spatial resolution (3D) or due to very high resolution (4K). METHODS: In randomized cross-over trial the surgical performance of medical students (MS), non-board certified surgeons (NBC), and board certified surgeons (BC) was compared using 3D versus 4K display technique at a minimally invasive training Parkour. RESULTS: One hundred twenty-eight participants were included (February 2018 through October 2019, 49 MS, 39 NBC, 40 BC). The overall Parkour time (s) 3D versus 4K was 712.5 s ± 17.5 s versus 999.5 s ±â€Š25.1 s (P < 0.001) for all levels of experience. It was (3D vs 4K) for MS (30 tasks) 555.4 s ±â€Š28.9 s versus 858.7 s ±â€Š41.6 s, (P < 0.0001), for NBC (42 tasks) 935.9 s ±â€Š31.5 s versus 1274.1 s ±â€Š45.1 s (P =< 0.001) and for BC (42 task) 646.3 s ±â€Š30.9 s versus 865.7 s ±â€Š43.7 s (P < 0.001). The overall number of mistakes was (3D vs 4K) 10.0 ±â€Š0.5 versus 13.3 ±â€Š0.7 (P < 0.001), for MS 8.9 ±â€Š0.9 versus 13.1 ±â€Š1.1 (P < 0.001), for NBC 12.45 ±â€Š1.0 versus 16.7 ±â€Š1.2 (P < 0.001) and for BC 8.8 ±â€Š1.0 versus 10.0 ±â€Š1.2 (P = 0.18). MS, BC, and NBC showed shorter performance time in 100% of the task with 3D (significantly in 6/7 tasks). For number of mistakes the effect was less pronounced for more experienced surgeons. The National Aeronautics and Space Administration-task load index was lower with 3D. CONCLUSION: 3D laparoscopic display technique optimizes surgical performance compared to the 4K technique. Surgeons benefit from the improved visualization regardless of their individual surgical expertise.

Soil microbial communities associated with giant sequoia: How does the world's largest tree affect some of the world's smallest organisms?

Giant sequoia (Sequoiadendron giganteum) is an iconic conifer that lives in relict populations on the western slopes of the California Sierra Nevada. In these settings, it is unusual among the dominant trees in that it associates with arbuscular mycorrhizal fungi rather than ectomycorrhizal fungi. However, it is unclear whether differences in microbial associations extend more broadly to nonmycorrhizal components of the soil microbial community. To address this question, we used next-generation amplicon sequencing to characterize bacterial/archaeal and fungal microbiomes in bulk soil (0-5 cm) beneath giant sequoia and co-occurring sugar pine (Pinus lambertiana) individuals. We did this across two groves with distinct parent material in Yosemite National Park, USA. We found tree-associated differences were apparent despite a strong grove effect. Bacterial/archaeal richness was greater beneath giant sequoia than sugar pine, with a core community double the size. The tree species also harbored compositionally distinct fungal communities. This pattern depended on grove but was associated with a consistently elevated relative abundance of Hygrocybe species beneath giant sequoia. Compositional differences between host trees correlated with soil pH and soil moisture. We conclude that the effects of giant sequoia extend beyond mycorrhizal mutualists to include the broader community and that some but not all host tree differences are grove-dependent.

Pyrophilous fungi detected after wildfires in the Great Smoky Mountains National Park expand known species ranges and biodiversity estimates.

Following a late fall wildfire in 2016 in the Great Smoky Mountains National Park, pyrophilous fungi in burn zones were documented over a 2-y period with respect to burn severity and phenology. Nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) barcodes were obtained to confirm morphological evaluations. Forty-one taxa of Ascomycota and Basidiomycota were identified from burn sites and categorized as fruiting only in response to fire or fruiting enhanced by fire. Twenty-two species of Pezizales (Ascomycota) were among the earliest to form ascomata in severe burn zones, only one of which had previously been documented in the Great Smoky Mountains National Park. Nineteen species of Basidiomycota, primarily Agaricales, were also documented. Among these, only five species (Coprinellus angulatus, Gymnopilus decipiens, Lyophyllum anthracophilum, Pholiota carbonicola, and Psathyrella pennata) were considered to be obligate pyrophilous taxa, but fruiting of two additional taxa (Hygrocybe conica and Mycena galericulata) was clearly enhanced by fire. Laccaria trichodermophora was an early colonizer of severe burn sites and persisted through the winter of 2017 and into spring and summer of 2018, often appearing in close association with Pinus pungens seedlings. Fruiting of pyrophilous fungi peaked 4-6 mo post fire then diminished, but some continued to fruit up to 2.5 y after the fire. In all, a total of 27 previously unrecorded taxa were added to the All Taxa Biodiversity Inventory (ATBI) database (~0.9%). Most pyrophilous fungi identified in this study are either cosmopolitan or have a Northern Hemisphere distribution, but cryptic endemic lineages were detected in Anthracobia and Sphaerosporella. One new combination, Hygrocybe spadicea var. spadicea f. odora, is proposed.

COVID-19: Facts, Cultural Considerations, and Risk of Stigmatization.

Data on COVID-19 supports targeted social distancing could be an effective way to reduce morbidity and mortality, but could inadvertently increase stigma for affected populations. As health care providers we must be aware of the facts of COVID-19, cultural implications, and potential for stigmatization of populations affected by COVID-2019. It is important to consider the real economic impact related to lost workdays due to quarantine and social isolation efforts as well as travel restrictions that may negatively impact access to care and ability to pay for care. Efforts geared towards general education about the disease and the rationale for quarantine and public health information provided to the general public can reduce stigmatization. Countries who are successful at aggressive screening, early identification, patient isolation, contact tracing, quarantine, and infection control methods should also address the risk of stigmatization among populations and the negative effects which could occur. The cases of COVID-19 will continue to rise and the virus will be sustainable for future infections. Timely and appropriate public health interventions addressing cultural impact and risk for stigmatization along with proper screening, treatment, and follow up for affected individuals and close contacts can reduce the number of infections, serious illness, and deaths.

Correction to: 3D vs. 4 K Display System - Influence of "State-of-the-art"-Display Technique On Surgical Performance (IDOSP-Study) in minimally invasive surgery: protocol for a randomized cross-over trial.

After publication of our article [1] the authors have notified us that one of the names has been incorrectly spelled.

A simple pyrocosm for studying soil microbial response to fire reveals a rapid, massive response by Pyronema species.

We have designed a pyrocosm to enable fine-scale dissection of post-fire soil microbial communities. Using it we show that the peak soil temperature achieved at a given depth occurs hours after the fire is out, lingers near this peak for a significant time, and is accurately predicted by soil depth and the mass of charcoal burned. Flash fuels that produce no large coals were found to have a negligible soil heating effect. Coupling this system with Illumina MiSeq sequencing of the control and post-fire soil we show that we can stimulate a rapid, massive response by Pyronema, a well-known genus of pyrophilous fungus, within two weeks of a test fire. This specific stimulation occurs in a background of many other fungal taxa that do not change noticeably with the fire, although there is an overall reduction in richness and evenness. We introduce a thermo-chemical gradient model to summarize the way that heat, soil depth and altered soil chemistry interact to create a predictable, depth-structured habitat for microbes in post-fire soils. Coupling this model with the temperature relationships found in the pyrocosms, we predict that the width of a survivable "goldilocks zone", which achieves temperatures that select for postfire-adapted microbes, will stay relatively constant across a range of fuel loads. In addition we predict that a larger necromass zone, containing labile carbon and nutrients from recently heat-killed organisms, will increase in size rapidly with addition of fuel and then remain nearly constant in size over a broad range of fuel loads. The simplicity of this experimental system, coupled with the availability of a set of sequenced, assembled and annotated genomes of pyrophilous fungi, offers a powerful tool for dissecting the ecology of post-fire microbial communities.

Rhizopogon olivaceotinctus increases its inoculum potential in heated soil independent of competitive release from other ectomycorrhizal fungi.

Rhizopogon olivaceotinctus is a rarely collected ectomycorrhizal fungus that has been found primarily in California and southern Oregon. Prior work has shown that it (i) is common in soil spore banks associated with pine forests from these areas; (ii) is rare or absent on trees in undisturbed forests in these same areas; (iii) exhibits an increased abundance on pine seedlings following fire or experimental soil heating; and (iv) has spores that are more resistant to heat than those of several other ectomycorrhizal species tested to date. Here, we reject the hypothesis that the increased abundance of the species following soil heating is caused only by reduced competition with other ectomycorrnizal fungi and show instead that heating alone significantly increases the inoculum potential of its spores. We argue that this is likely caused by heat stimulation of the spores, a process that has precedent in saprotrophic fungi and plant seeds. This result, in combination with those of previous studies, shows that Rhizopogon olivaceotinctus is well adapted to fire.

3D vs. 4K Display System - Influence of "State-of-the-art"-Display Technique On Surgical Performance (IDOSP-Study) in minimally invasive surgery: protocol for a randomized cross-over trial.

BACKGROUND: Three-dimensional (3D) stereoscopic vision is crucial to perform any kind of manual task. The reduction from real life 3D to virtual two-dimensional (2D) sight is a major challenge in minimally invasive surgery (MIS). A 3D display technique has been shown to reduce operation time and mistakes and to improve the learning curve. Therefore, the use of a3D display technique seems to optimize surgical performance for novice and experienced surgeons. Inspired by consumer electronics, a 4K display technique was recently introduced to MIS. Due to its high resolution and zoom effect, surgeons should benefit from it. The aim of this study is to evaluate if "state-of-the-art" 3D- vs. 4K-display techniques could influence surgical performance. METHODS: A randomized, cross-over, single-institution, single-blinded trial is designed. It compares the primary outcome parameter "surgical performance", represented by "performance time "and "number of mistakes", using a passive polarizing 3D and a 4K display system (two arms) to perform different tasks in a minimally invasive/laparoscopic training parkour. Secondary outcome parameters are the mental stress load (National Aeronautics and Space Administration (NASA) Task Load Index) and the learning curve. Unexperienced novices (medical students), non-board-certified, and board-certified abdominal surgeons participate in the trial (i.e., level of experience, 3 strata). The parkour consists of seven tasks (for novices, five tasks), which will be repeated three times. The 1st run of the parkour will be performed with the randomized display system, the 2nd run with the other one. After each run, the mental stress load is measured. After completion of the parkour, all participants are evaluated by an ophthalmologist for visual acuity and stereoscopic vision with five tests. Assuming a correlation of 0.5 between measurements per subject, a sample size of 36 per stratum is required to detect a standardized effect of 0.5 (including an additional 5% for a non-parametric approach) with a power of 80% at a two-sided type I error of 5%. Thus, altogether 108 subjects need to be enrolled. DISCUSSION: Complex surgical procedures are performed in a minimally invasive/laparoscopic technique. This study should provide some evidence to decide which display technique a surgeon could choose to optimize his performance. TRIAL REGISTRATION: ClinicalTrials.gov, NCT03445429 . Registered on 7 February 2018.

Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles.

Ribosomal DNA (rDNA) copy number variation (CNV) has major physiological implications for all organisms, but how it varies for fungi, an ecologically ubiquitous and important group of microorganisms, has yet to be systemically investigated. Here, we examine rDNA CNV using an in silico read depth approach for 91 fungal taxa with sequenced genomes and assess copy number conservation across phylogenetic scales and ecological lifestyles. rDNA copy number varied considerably across fungi, ranging from an estimated 14 to 1,442 copies (mean = 113, median = 82), and copy number similarity was inversely correlated with phylogenetic distance. No correlations were found between rDNA CNV and fungal trophic mode, ecological guild or genome size. Taken together, these results show that like other microorganisms, fungi exhibit substantial variation in rDNA copy number, which is linked to their phylogeny in a scale-dependent manner.