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Medulloblastoma (MB) comprises a group of heterogeneous paediatric embryonal neoplasms of the hindbrain with strong links to early development of the hindbrain 1–4. Mutations that activate Sonic hedgehog signalling lead to Sonic hedgehog MB in the upper rhombic lip (RL) granule cell lineage 5–8. By contrast, mutations that activate WNT signalling lead to WNT MB in the lower RL 9,10. However, little is known about the more commonly occurring group 4 (G4) MB, which is thought to arise in the unipolar brush cell lineage 3,4. Here we demonstrate that somatic mutations that cause G4 MB converge on the core binding factor alpha (CBFA) complex and mutually exclusive alterations that affect CBFA2T2, CBFA2T3, PRDM6, UTX and OTX2. CBFA2T2 is expressed early in the progenitor cells of the cerebellar RL subventricular zone in Homo sapiens, and G4 MB transcriptionally resembles these progenitors but are stalled in developmental time. Knockdown of OTX2 in model systems relieves this differentiation blockade, which allows MB cells to spontaneously proceed along normal developmental differentiation trajectories. The specific nature of the split human RL, which is destined to generate most of the neurons in the human brain, and its high level of susceptible EOMES +KI67 + unipolar brush cell progenitor cells probably predisposes our species to the development of G4 MB.

Here, we present an annotated, chromosome-anchored, genome assembly for Lake Trout (Salvelinus namaycush) - a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation. We leveraged Pacific Biosciences long-read sequencing, paired-end Illumina sequencing, proximity ligation (Hi-C) sequencing, and a previously published linkage map to produce a highly contiguous assembly composed of 7378 contigs (contig N50 = 1.8 Mb) assigned to 4120 scaffolds (scaffold N50 = 44.975 Mb). Long read sequencing data were generated using DNA from a female double haploid individual. 84.7% of the genome was assigned to 42 chromosome-sized scaffolds and 93.2% of Benchmarking Universal Single Copy Orthologues were recovered, putting this assembly on par with the best currently available salmonid genomes. Estimates of genome size based on k-mer frequency analysis were highly similar to the total size of the finished genome, suggesting that the entirety of the genome was recovered. A mitochondrial genome assembly was also produced. Self-versus-self synteny analysis allowed us to identify homeologs resulting from the salmonid specific autotetraploid event (Ss4R) as well as regions exhibiting delayed rediploidization. Alignment with three other salmonid genomes and the Northern Pike (Esox lucius) genome also allowed us to identify homologous chromosomes in related taxa. We also generated multiple resources useful for future genomic research on Lake Trout, including a repeat library and a sex-averaged recombination map. A novel RNA sequencing data set for liver tissue was also generated in order to produce a publicly available set of annotations for 49,668 genes and pseudogenes. Potential applications of these resources to population genetics and the conservation of native populations are discussed.

BACKGROUND Mobile health tools can support shared decision making. We developed a computer-based decision aid (DA) to help pregnant women and their partners make informed value-congruent decisions about prenatal screening for trisomy. OBJECTIVE We assessed the usability and usefulness of the computer-based DA among pregnant women and their partners, clinicians and policy makers. METHODS For this mixed-methods sequential explanatory study, we planned to recruit a convenient sample of 45 pregnant women with or without their partners and 45 clinicians in three clinical sites, and 15 policy makers identified in organigrams of organizations or institutions of interest. Eligible women were over 18 and more than 16 weeks pregnant or had given birth recently. Eligible clinicians and policy makers were involved in prenatal care. We asked participants to navigate the computer-based DA. Using validated tools, we collected data from pregnant women on its usefulness and their self-confidence about decision-making. From all participants, we collected data on usability, quality, acceptability, their satisfaction with its content and sociodemographic data. We also interviewed participants to explore their reactions to the computer-based DA and solicit suggestions. Our interview guide was based on the user version of the Mobile App Rating Scale. We performed descriptive analyses of quantitative data and thematic deductive and inductive analysis of qualitative data for each participant category. RESULTS Forty-five pregnant women (76% 25-34 years old, 93% Caucasian) with or without their partners (n=5) (51% 25-34 years old, 89% Caucasian), 14 clinicians (36% 35-44 years old, 79% female, all Caucasian) and eight policy makers (36% 45-54 years old, 62% female, all Caucasian) participated. Mean usefulness score for preparing for decision-making for women and their partners was 80/100 (SD 13), and mean self-efficacy score was 88 (SD 11). Mean usability score was 84 (SD 14) for pregnant women and their partners, 77 (SD 14) for clinicians and 79 (SD 23) for policy makers. Mean global score for quality was 80 (SD 9) for pregnant women and their partners, 72 (SD 12) for clinicians, and 80 (SD 9) for policy makers. Regarding acceptability, participants found the amount of information just right (79%), that it was balanced (88%), useful (50%) and sufficient (76%). Mean satisfaction score with content was 84 (SD 13) for pregnant women and their partners, 73 (SD 16) for clinicians, and 73 (SD 20) for policy makers. Participants thought the decision aid could be more engaging (e.g. more customizable), and suggested strategies for implementation such as incorporating it into clinical guidelines. CONCLUSIONS Pregnant women and their partners, clinicians and policy makers found the DA was usable and useful. Next steps are to incorporate users’ suggestions for improving engagement and implement the computer-based DA in clinical practice.

This paper presents the first study to quantify and demonstrate the interactions between SBR operating conditions (hydraulic retention time (HRT) and temperature) and soluble microbial product (SMP) generation, as well as the impact of SBR operating conditions and filtration temperature on fouling of membranes used in tertiary treatment. Reducing SBR operating HRT from 20 to 10 h resulted in an increase in SMP concentrations, however, the extent of the increase in high and low molecular weight (MW) organics was different for the effluents from SBRs operated at 8 and 20 °C. Results of SMP modelling demonstrated that a reduction in SBR operating HRT induced decreased utilization associated product (UAP) yields and the influence was greater at the SBR operating temperature of 8 °C. In contrast, biomass associated product (BAP) yields were relatively stable with SBR operating HRT but greater at lower SBR operating temperature. The effects of SBR operating HRT and temperature on fouling indices were also interactive. Reducing SBR operating HRT led to a lower increase in hydraulically reversible resistances and a greater increase in hydraulically irreversible resistances for the effluent from the SBR operated at 8 °C. Reducing the filtration temperature resulted in additional increase in membrane resistances, and the increase was greater at lower SBR operating HRT. The contribution of filtration temperature was observed to have the greatest impact on membrane resistances, followed in importance by SBR operating HRT and temperature. The comprehensive analysis undertaken in the present study provides insights into the interaction between secondary and tertiary operations on fouling development. The results can be employed to understand the limits of fouling control for tertiary treatment under challenging conditions.

Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. In this study, we combined single molecule sequencing of long reads (Pacific Sciences) with Chromatin Conformation Capture sequencing (Hi-C) data to provide the first chromosome-level genome reference for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1 594 scaffolds (scaffold N50 = 25 Mb) with 96 % of its total length distributed among 24 chromosomes. The investigation of its syntenic relationships with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that flatfishes do not escape the rule applied to other teleost fish and exhibit a high level of plasticity and turnover in sex-determination mechanisms. A whole-genome sequence analysis of 198 individuals allowed us to draw a full picture of the molecular sex determination (SD) system for Greenland Halibut, revealing that this species possesses a very nascent male heterogametic XY system, with a putative major effect of the sox2 gene, also described as the main SD driver in two other flatfishes. Interestingly, our study also suggested for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of early steps of sex chromosome evolution.

Sonic hedgehog medulloblastoma encompasses a clinically and molecularly diverse group of cancers of the developing central nervous system. Here, we use unbiased sequencing of the transcriptome across a large cohort of 250 tumors to reveal differences among molecular subtypes of the disease, and demonstrate the previously unappreciated importance of non-coding RNA transcripts. We identify alterations within the cAMP dependent pathway (GNAS, PRKAR1A) which converge on GLI2 activity and show that 18% of tumors have a genetic event that directly targets the abundance and/or stability of MYCN. Furthermore, we discover an extensive network of fusions in focally amplified regions encompassing GLI2, and several loss-of-function fusions in tumor suppressor genes PTCH1, SUFU and NCOR1. Molecular convergence on a subset of genes by nucleotide variants, copy number aberrations, and gene fusions highlight the key roles of specific pathways in the pathogenesis of Sonic hedgehog medulloblastoma and open up opportunities for therapeutic intervention., Sonic Hedgehog medulloblastoma (Shh-MB) comprises four subtypes each with distinct clinical traits. Here the authors characterize the genome, transcriptome, and methylome of Shh-MB subtypes, revealing a complex fusion landscape and the molecular convergence of MYCN and cAMP signaling pathways.

The opioid receptor (OPR) family comprises the mu-, delta-, and kappa-opioid, and nociceptin receptors that belong to the superfamily of 7-transmembrane spanning G protein-coupled receptors (GPCRs). The mu-opioid receptor is the main target for clinically used opioid analgesics, and its biology has been extensively studied. The N-terminally truncated 6TM receptors isoform produced through alternative splicing of the OPRM1 gene displays unique signaling and analgesic properties, but it is unclear if other OPRs have the same ability. In this study, we have built a comprehensive map of alternative splicing events that produce 6TM receptor variants in all the OPRs and demonstrated their evolutionary conservation. We then obtained evidence for their translation through ribosomal footprint analysis. We discovered that N-terminally truncated 6TM GPCRs are rare in the human genome and OPRs are overrepresented in this group. Finally, we also observed a significant enrichment of 6TM GPCR genes among genes associated with pain, psychiatric disorders, and addiction. Understanding the biology of 6TM receptors and leveraging this knowledge for drug development should pave the way for novel therapies. Electronic supplementary material The online version of this article (10.1007/s10571-020-00971-7) contains supplementary material, which is available to authorized users.

The article “Alternative Splicing of Opioid Receptor Genes Shows a Conserved Pattern for 6TM Receptor Variants”, written by Marjo Piltonen, Andrey Krokhotin, Marc Parisien, Pierre Berube, Haig Djambazian, Rob Sladek, Nikolay V. Dokholyan, Svetlana A. Shabalina and Luda Diatchenko was originally published electronically on the publisher’s internet portal on October 3, 2020 without open access. With the author(s)’ decision to opt for Open Choice the copyright of the article changed on October 27, 2020 to © The Author(s) 2020 and the article is forthwith distributed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, https://creativecommons.org/licenses/by/4.0/ .

The delta-opioid receptor (DOPr) participates in mediating the effects of opioid analgesics. However, no selective agonists have entered clinical care despite potential to ameliorate many neurological and psychiatric disorders. In an effort to address the drug development challenges, the functional contribution of receptor isoforms created by alternative splicing of the three-exonic coding gene, OPRD1, has been overlooked. We report that the gene is transcriptionally more diverse than previously demonstrated, producing novel protein isoforms in humans and mice. We provide support for the functional relevance of splice variants through context-dependent expression profiling (tissues, disease model) and conservation of the transcriptional landscape in closely related vertebrates. The conserved alternative transcriptional events have two distinct patterns. First, cassette exon inclusions between exons 1 and 2 interrupt the reading frame, producing truncated receptor fragments comprising only the first transmembrane (TM) domain, despite the lack of exact exon orthologues between distant species. Second, a novel promoter and transcriptional start site upstream of exon 2 produces a transcript of an N-terminally truncated 6TM isoform. However, a fundamental difference in the exonic landscaping as well as translation and translation products poses limits for modelling the human DOPr receptor system in mice.

Nontoxic multinodular goiter (MNG) occurs frequently, but its genetic etiology is not well established. Familial MNG and MNG occurring with ovarian Sertoli-Leydig cell tumor are associated with germline DICER1 mutations. We recently identified second somatic DICER1 ribonuclease (RNase) IIIb mutations in two MNGs.The objective of the study was to investigate the occurrence of somatic DICER1 mutations and mutational clonality in MNG.MNGs from 15 patients (10 with and five without germline DICER1 mutations) were selected based on tissue availability.Core biopsies/scrapings (n = 70) were obtained, sampling areas of follicular hyperplasia, hyperplasia within colloid pools, unremarkable thyroid parenchyma, and areas of thyroid parenchyma, not classified. After capture with a Fluidigm access array, the coding sequence of DICER1 was deep sequenced using DNA from each core/scraping.All germline DICER1-mutated cases were found to harbor at least one RNase III mutation. Specifically, we identified 12 individually distinct DICER1 RNase IIIb hot spot mutations in 32 of the follicular hyperplasia or hyperplasia within colloid pools cores/scrapings. These mutations are predicted to affect the metal-ion binding residues at positions p.Glu1705, p.Asp1709, p.Gly1809, p.Asp1810, and p.Glu1813. Somatic RNase IIIb mutations were identified in the 10 DICER1 germline mutated MNGs as follows: two cases contained one somatic mutation, five cases contained two mutations, and three cases contained three distinct somatic hot spot mutations. No RNase IIIb mutations were identified in the MNGs from individuals without germline DICER1 mutations.This study demonstrates that nodules within MNG occurring in DICER1 syndrome are associated with spatially distributed somatic DICER1 RNase IIIb mutations.

We quantified fine-sediment accumulation annually from 2000 to 2003 after culvert construction in five Laurentian Shield streams containing brook trout Salvelinus fontinalis. A significant spatial pattern (section effect) was observed in which the accumulation was lowest upstream of the culvert (section 1), peaked in the section directly below the culvert (section 2), and slightly decreased in sections further downstream (sections 3-5) without returning to upstream levels. The accumulation was always significantly higher downstream of the culvert than in section 1. The temporal pattern (period effect) was also significant; accumulation was lowest several weeks after construction, peaked at one full year after construction, and decreased at 2-3 years postconstruction. Fine-sediment accumulation differed significantly among all periods. The downstream distance at which sediment accumulation returned to upstream levels varied from 358 and 1,442 m below the culvert. Owing to the accumulated sediment,...

We used classification trees and regression trees to relate the incidence and density of juvenile Atlantic salmon (Salmo salar) to forestry activities measured at four spatial scales (subbasin and 8, 2, and 0.5 km radii up- stream of study sites) and environmental features in 120 stream reaches of the Cascapedia River basin, Quebec, Can- ada. At all scales, incidence increased with reach size and accessibility to the reach from the river mainstem. Incidence declined with areal coverage of logging at all scales, but only in larger reaches. The time horizon over which logging effects were detected increased with spatial scale. At all scales, density in salmon-bearing reaches increased with acces- sibility. Density in more accessible reaches was negatively related to logging over the preceding 9 years at the subbasin and 8 km scales, but no effects of logging on density were detected at the 2 and 0.5 km scales. Overall, apparent ef- fects of logging activities on salmon incidence and density were mostly negative and strong, but were both markedly scale-dependent and conditional on environmental context. Resume : Nous avons utilise les arbres de classification et de regression pour relier l'incidence et la densite de sau- mons de l'Atlantique (Salmo salar) a l'environnement et aux activites forestieres quantifiees a quatre echelles spatiales (le sous-bassin et des rayons de 8, 2 et 0,5 km en amont de chaque troncon) dans 120 troncons du bassin versant de la riviere Cascapedia, Quebec, Canada. A toutes les echelles, l'incidence du saumon augmentait avec la taille des troncons et l'accessibilite depuis la riviere principale et diminuait avec une augmentation du pourcentage de superficie coupee. Les effets des coupes etaient detectables sur des horizons temporels croissants avec l'augmentation de l'echelle spa- tiale. La densite de saumons augmentait avec l'accessibilite a toutes les echelles. Dans les troncons plus accessibles, la densite diminuait avec une augmentation du pourcentage de superficie coupe au cours des 9 annees precedentes aux deux plus grandes echelles du sous-bassin et de 8 km. Aucun effet des coupes sur la densite de saumons n'etait detec- table aux deux plus petites echelles de 2 et 0,5 km. Les effets apparents des coupes sur l'incidence et la densite de saumons juveniles etaient forts et negatifs, mais dependant de l'echelle spatiale et du contexte environnemental.

SUMMARY 1. Forestry activities can greatly modify the structure and function of invertebrate communities in streams, but the ability to detect effects of forestry may depend on the spatial scale considered, the choice of response metric and the environmental context. In this study, a multi-scale, multi-metric approach was used to compare the usefulness of proximate and larger-scale measurements of forestry activity for understanding the impacts of forestry on stream macrobenthos. 2. Site-specific responses of macrobenthic communities to forestry activities measured at four spatial scales (sub-basin and 8-, 2- and 0.5-km radii upstream of study sites) were examined for 90 riffle sites distributed among 22 tributary streams (Strahler order 1–5) of the Cascapedia River basin, Quebec, Canada. 3. Multiple regression models and canonical correspondence analysis were used to relate six biological metrics (taxonomic richness, numerical density, biomass density, normalised biomass spectrum, individual body mass and community structure) to variables quantifying logging 1–19 years prior to the study and road density. Environmental predictors (variables quantifying local habitat or landscape features) were included in all analyses to statistically account for environmental context and increase the likelihood of detecting potentially subtle forestry impacts. 4. Forestry activities measured at the larger (sub-basin and 8 km) scales were linked to decline in taxonomic richness, increase in numerical and biomass densities and shift in size structure of benthic macroinvertebrates, indicating that analyses encompassing larger areas, up to the full basin, may allow for more sensitive detection of effects than those of more limited span. 5. These responses primarily reflected marked increases in the abundance of chironomids and decline in the number of trichopteran taxa with increasing areal coverage of recent (£2–4 years) cuts, suggesting that larger, longer-lived and possibly more specialised taxa were more vulnerable to forestry impacts than smaller, multivoltine, generalist invertebrates. After partialling out the influence of other variables, rapid decline in richness occurred even when

We demonstrate a new platform, convex lens-induced nanoscale templating (CLINT), for dynamic manipulation and trapping of single DNA molecules. In the CLINT technique, the curved surface of a convex lens is used to deform a flexible coverslip above a substrate containing embedded nanotopography, creating a nanoscale gap that can be adjusted during an experiment to confine molecules within the embedded nanostructures. Critically, CLINT has the capability of transforming a macroscale flow cell into a nanofluidic device without the need for permanent direct bonding, thus simplifying sample loading, providing greater accessibility of the surface for functionalization, and enabling dynamic manipulation of confinement during device operation. Moreover, as DNA molecules present in the gap are driven into the embedded topography from above, CLINT eliminates the need for the high pressures or electric fields required to load DNA into direct-bonded nanofluidic devices. To demonstrate the versatility of CLINT, we confine DNA to nanogroove and nanopit structures, demonstrating DNA nanochannel-based stretching, denaturation mapping, and partitioning/trapping of single molecules in multiple embedded cavities. In particular, using ionic strengths that are in line with typical biological buffers, we have successfully extended DNA in sub-30-nm nanochannels, achieving high stretching (90%) that is in good agreement with Odijk deflection theory, and we have mapped genomic features using denaturation analysis.

Tolerance to naturally acidic conditions of a Côte-Nord brook trout (Salvelinus fontinalis) strain (Arseneault strain, presumed acid tolerant) does not appear completely genetically mediated, since this tolerance was not evident when the fish were subject to acid conditions of anthropogenic origin. Three wild brook trout strains, at the egg and fingerling stages, were exposed in the field to waters acidified by atmospheric deposition of anthropogenic origin as well as to natural waters typical of the region. Although egg mortality was significantly higher in acid (61.0-85.6%) than in reference (6.3-20.8%) conditions, no differences between strains were noted. Residual density 1 year after stocking with fingerlings was significantly higher (by 56%) in the reference lake than in the acid lake, but differences between strains did not follow any clear tendency. While overall growth was greater in the acid environment, weight yield was lower except for the Arseneault strain. Variations pertaining to gonadosomatic index and percent mature individuals in both males and females seemed linked more to differences in growth than to chemical conditions. Developing a permanent reintroduction program with the Arseneault strain to counter losses of brook trout populations due to acid precipitation in Québec does not appear justified at this time.

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS or SACS) is an early onset neurodegenerative disease with high prevalence (carrier frequency 1/22) in the Charlevoix-Saguenay-Lac-Saint-Jean (CSLSJ) region of Quebec. We previously mapped the gene responsible for ARSACS to chromosome 13q11 and identified two ancestral haplotypes. Here we report the cloning of this gene, SACS, which encodes the protein sacsin. The ORF of SACS is 11,487 bp and is encoded by a single gigantic exon spanning 12,794 bp. This exon is the largest to be identified in any vertebrate organism. The ORF is conserved in human and mouse. The putative protein contains three large segments with sequence similarity to each other and to the predicted protein of an Arabidopsis thaliana ORF. The presence of heat-shock domains suggests a function for sacsin in chaperone-mediated protein folding. SACS is expressed in a variety of tissues, including the central nervous system. We identified two SACSmutations in ARSACS families that lead to protein truncation, consistent with haplotype analysis.

Autosomal recessive spastic ataxia of Charlevoix–Saguenay (ARSACS or SACS) is a neurodegenerative disease frequent in northeastern Quebec. In a previous study, we localized the disease gene to chromosome region 13q11 by identifying excess sharing of a marker allele in patients followed by linkage analysis and haplotyping. To create a detailed physical map of this region, we screened CEPH mega-YACs with 41 chromosome 13 sequence-tagged-sites (STSs) known to map to 13q11–q12. The YAC contig, composed of 27 clones, extends on the genetic map from D13S175 to D13S221, an estimated distance of at least 19.3 cM. A high-resolution BAC and PAC map that includes the ARSACS critical region flanked by D13S1275 and D13S292 was constructed. These YAC and BAC/PAC maps allowed the accurate placement of 29 genes and ESTs previously mapped to the proximal region of chromosome 13q. We confirmed the position of two candidate genes within the critical region and mapped the other 27 genes and ESTs to nearby intervals. Six BAC/PAC clones form a contig between D13S232 and D13S787 for sequencing within the ARSACS critical region.