SPORT: A new sub-nanosecond time-resolved instrument to study swift heavy ion-beam induced luminescence - Application to luminescence degradation of a fast plastic scintillator

We developed a new sub-nanosecond time-resolved instrument to study the dynamics of UV-visible luminescence under high stopping power heavy ion irradiation. We applied our instrument, called SPORT, on a fast plastic scintillator (BC-400) irradiated with 27-MeV Ar ions having high mean electronic stopping power of 2.6 MeV/\mu m. As a consequence of increasing permanent radiation damages with increasing ion fluence, our investigations reveal a degradation of scintillation intensity together with, thanks to the time-resolved measurement, a decrease in the decay constant of the scintillator. This combination indicates that luminescence degradation processes by both dynamic and static quenching, the latter mechanism being predominant. Under such high density excitation, the scintillation deterioration of BC-400 is significantly enhanced compared to that observed in previous investigations, mainly performed using light ions. The observed non-linear behaviour implies that the dose at which luminescence starts deteriorating is not independent on particles' stopping power, thus illustrating that the radiation hardness of plastic scintillators can be strongly weakened under high excitation density in heavy ion environments.Comment: 5 figures, accepted in Nucl. Instrum. Methods

More Filtering on SNP Calling Does Not Remove Evidence of Inter-Nucleus Recombination in Dikaryotic Arbuscular Mycorrhizal Fungi

Evidence for the existence of dikaryote-like strains, low nuclear sequence diversity and inter-nuclear recombination in arbuscular mycorrhizal fungi has been recently reported based on single nucleus sequencing data. Here, we aimed to support evidence of inter-nuclear recombination using an approach that filters SNP calls more conservatively, keeping only positions that are exclusively single copy and homozygous, and with at least five reads supporting a given SNP. This methodology recovers hundreds of putative inter-nucleus recombination events across publicly available sequence data from individual nuclei. Challenges related to the acquisition and analysis of sequence data from individual nuclei are highlighted and discussed, and ways to address these issues in future studies are presented

Satellite-Based Evidence for Shrub and Graminoid Tundra Expansion in Northern Quebec from 1986-2010

Global vegetation models predict rapid poleward migration of tundra and boreal forest vegetation in response to climate warming. Local plot and air-photo studies have documented recent changes in high-latitude vegetation composition and structure, consistent with warming trends. To bridge these two scales of inference, we analyzed a 24-year (1986-2010) Landsat time series in a latitudinal transect across the boreal forest-tundra biome boundary in northern Quebec province, Canada. This region has experienced rapid warming during both winter and summer months during the last forty years. Using a per-pixel (30 m) trend analysis, 30% of the observable (cloud-free) land area experienced a significant (p < 0.05) positive trend in the Normalized Difference Vegetation Index (NDVI). However, greening trends were not evenly split among cover types. Low shrub and graminoid tundra contributed preferentially to the greening trend, while forested areas were less likely to show significant trends in NDVI. These trends reflect increasing leaf area, rather than an increase in growing season length, because Landsat data were restricted to peak-summer conditions. The average NDVI trend (0.007/yr) corresponds to a leaf-area index (LAI) increase of ~0.6 based on the regional relationship between LAI and NDVI from the Moderate Resolution Spectroradiometer (MODIS). Across the entire transect, the area-averaged LAI increase was ~0.2 during 1986-2010. A higher area-averaged LAI change (~0.3) within the shrub-tundra portion of the transect represents a 20-60% relative increase in LAI during the last two decades. Our Landsat-based analysis subdivides the overall high-latitude greening trend into changes in peak-summer greenness by cover type. Different responses within and among shrub, graminoid, and tree-dominated cover types in this study indicate important fine-scale heterogeneity in vegetation growth. Although our findings are consistent with community shifts in low-biomass vegetation types over multi-decadal time scales, the response in tundra and forest ecosystems to recent warming was not uniform

Sex in Cheese: Evidence for Sexuality in the Fungus Penicillium roqueforti

Abstract Although most eukaryotes reproduce sexually at some moment of their life cycle, as much as a fifth of fungal species were thought to reproduce exclusively asexually. Nevertheless, recent studies have revealed the occurrence of sex in some of these supposedly asexual species. For industrially relevant fungi, for which inoculums are produced by clonal-subcultures since decades, the potentiality for sex is of great interest for strain improvement strategies. Here, we investigated the sexual capability of the fungus Penicillium roqueforti, used as starter for blue cheese production. We present indirect evidence suggesting that recombination could be occurring in this species. The screening of a large sample of strains isolated from diverse substrates throughout the world revealed the existence of individuals of both mating types, even in the very same cheese. The MAT genes, involved in fungal sexual compatibility, appeared to evolve under purifying selection, suggesting that they are still functional. The examination of the recently sequenced genome of the FM 164 cheese strain enabled the identification of the most important genes known to be involved in meiosis, which were found to be highly conserved. Linkage disequilibria were not significant among three of the six marker pairs and 11 out of the 16 possible allelic combinations were found in the dataset. Finally, the detection of signatures of repeat induced point mutations (RIP) in repeated sequences and transposable elements reinforces the conclusion that P. roqueforti underwent more or less recent sex events. In this species of high industrial importance, the induction of a sexual cycle would open the possibility of generating new genotypes that would be extremely useful to diversify cheese products

Divergence of Arctic shrub growth associated with sea ice decline

Arctic sea ice extent (SIE) is declining at an accelerating rate with a wide range of ecological consequences. However, determining sea ice effects on tundra vegetation remains a challenge. In this study, we examined the universality or lack thereof in tundra shrub growth responses to changes in SIE and summer climate across the Pan-Arctic, taking advantage of 23 tundra shrub-ring chronologies from 19 widely distributed sites (56°N to 83°N). We show a clear divergence in shrub growth responses to SIE that began in the mid-1990s, with 39% of the chronologies showing declines and 57% showing increases in radial growth (decreasers and increasers, respectively). Structural equation models revealed that declining SIE was associated with rising air temperature and precipitation for increasers and with increasingly dry conditions for decreasers. Decreasers tended to be from areas of the Arctic with lower summer precipitation and their growth decline was related to decreases in the standardized precipitation evapotranspiration index. Our findings suggest that moisture limitation, associated with declining SIE, might inhibit the positive effects of warming on shrub growth over a considerable part of the terrestrial Arctic, thereby complicating predictions of vegetation change and future tundra productivity

Time to revise classification of phyllodes tumors of breast? Results of a French multicentric study

OBJECTIVE: To assess prognostic factors of recurrence of phyllodes tumors (PT) of the breast. METHODS: We performed a retrospective, multicentric cohort study, including all patients who underwent breast surgery for grade 1 (benign), 2 (borderline) or 3 (malignant) PT between 2000 and 2016 in five tertiary University hospitals, diagnosed according to World Health Organisation classification. RESULTS: 230 patients were included: 144 (63%), 60 (26%) and 26 (11%) with grade 1, 2 and 3 PT, respectively. Recurrence occurred in 10 (7%), 7 (12%) and 5 (19%) patients with grade 1, 2 and 3 PT, respectively. In univariate analysis, moderate to severe nuclear stromal pleomorphism (HR 8.00 [95% CI: 1.65-38.73], p &lt; 0.009) was correlated with recurrence in all groups including grade 1 (HR 14.3 [95% CI: 1.29-160], p = 0.031). In multivariate analysis, surgical margin &gt;5 mm, (HR 0.20 [95% CI: 0.06-0.63], p = 0.013) were significantly correlated with less recurrence in all PT grades. For grade 1 PT, there was also significantly less recurrence with surgical margin &gt;5 mm, (HR 0.09 [95% CI: 0.01-0.85], p = 0.047) in multivariate analysis. CONCLUSION: The surgical margin should be at least 5 mm whatever the grade of PT. Moderate to severe nuclear stromal pleomorphism identified a subgroup of grade 1 PT with a higher rate of recurrence. This suggests that the WHO classification could be revised with the introduction of nuclear stromal pleomorphism to tailor PT management

Domestication of different varieties in the cheese-making fungus Geotrichum candidum

Domestication is an excellent model for studying adaptation processes, involving recent adaptation and diversification, convergence following adaptation to similar conditions, as well as degeneration of unused functions. Geotrichum candidum is a fungus used for cheese making and is also found in other environments such as soil and plants. By analyzing whole-genome data from 98 strains, we found that all strains isolated from cheese formed a monophyletic clade. Within the cheese clade, we identified three genetically differentiated populations and we detected footprints of recombination and admixture. The genetic diversity in the cheese clade was similar as that in the wild clade, suggesting the lack of strong bottlenecks. Commercial starter strains were scattered across the cheese clade, thus not constituting a single clonal lineage. The cheese populations were phenotypically differentiated from other populations, with a slower growth on all media, even cheese, a prominent production of typical cheese volatiles and a lower proteolytic activity. One of the cheese clusters encompassed all soft goat cheese strains, suggesting an effect of cheese-making practices on differentiation. Another of the cheese populations seemed to represent a more advanced stage of domestication, with stronger phenotypic differentiation from the wild clade, harboring much lower genetic diversity, and phenotypes more typical of cheese fungi, with denser and fluffier colonies and a greater ability of excluding cheese spoiler fungi. Cheese populations lacked two beta lactamase-like genes present in the wild clade, involved in xenobiotic clearance, and displayed higher contents of transposable elements, likely due to relaxed selection. Our findings suggest the existence of genuine domestication in G. candidum, which led to diversification into different varieties with contrasted phenotypes. Some of the traits acquired by cheese strains indicate convergence with other, distantly related fungi used for cheese maturation

Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis.

Arbuscular mycorrhizal (AM) fungi are symbionts of most plants, increasing plant growth and diversity. The model AM fungus Rhizophagus irregularis (isolate DAOM 197198) exhibits low within-fungus polymorphism. In contrast, another study reported high within-fungus variability. Experiments with other R. irregularis isolates suggest that within-fungus genetic variation can affect the fungal phenotype and plant growth, highlighting the biological importance of such variation. We investigated whether there is evidence of differing levels of within-fungus polymorphism in an R. irregularis population. We genotyped 20 isolates using restriction site-associated DNA sequencing and developed novel approaches for characterizing polymorphism among haploid nuclei. All isolates exhibited higher within-isolate poly-allelic single-nucleotide polymorphism (SNP) densities than DAOM 197198 in repeated and non-repeated sites mapped to the reference genome. Poly-allelic SNPs were independently confirmed. Allele frequencies within isolates deviated from diploids or tetraploids, or that expected for a strict dikaryote. Phylogeny based on poly-allelic sites was robust and mirrored the standard phylogeny. This indicates that within-fungus genetic variation is maintained in AM fungal populations. Our results predict a heterokaryotic state in the population, considerable differences in copy number variation among isolates and divergence among the copies, or aneuploidy in some isolates. The variation may be a combination of all of these hypotheses. Within-isolate genetic variation in R. irregularis leads to large differences in plant growth. Therefore, characterizing genomic variation within AM fungal populations is of major ecological importance