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- Sodergren, Erica, et al.
(author)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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In: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Journal article (peer-reviewed)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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| 4. |
- Roselli, Carolina, et al.
(author)
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Multi-ethnic genome-wide association study for atrial fibrillation
- 2018
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 50:9, s. 1225-1233
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Journal article (peer-reviewed)abstract
- Atrial fibrillation (AF) affects more than 33 million individuals worldwide(1) and has a complex heritability(2). We conducted the largest meta-analysis of genome-wide association studies (GWAS) for AF to date, consisting of more than half a million individuals, including 65,446 with AF. In total, we identified 97 loci significantly associated with AF, including 67 that were novel in a combined-ancestry analysis, and 3 that were novel in a European-specific analysis. We sought to identify AF-associated genes at the GWAS loci by performing RNA-sequencing and expression quantitative trait locus analyses in 101 left atrial samples, the most relevant tissue for AF. We also performed transcriptome-wide analyses that identified 57 AF-associated genes, 42 of which overlap with GWAS loci. The identified loci implicate genes enriched within cardiac developmental, electrophysiological, contractile and structural pathways. These results extend our understanding of the biological pathways underlying AF and may facilitate the development of therapeutics for AF.
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- Crespo, Ana, et al.
(author)
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Phylogenetic generic classification of parmelioid lichens (Parmeliaceae,Ascomycota) based on molecular, morphological and chemical evidence.
- 2010
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In: Taxon. - : John Wiley & Sons. - 0040-0262 .- 1996-8175. ; 59:6, s. 1735-1753
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Journal article (peer-reviewed)abstract
- Parmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were monophyletic, some were not, and others, previously believed to be unrelated, fell within single monophyletic groups, indicating the need for a revision of the generic delimitations. This study aims to give an overview of current knowledge of the major clades of all parmelioid lichens. For this, we assembled a dataset of 762 specimens, including 31 of 33 currently accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae). We performed maximum likelihood and Bayesian analyses of combined datasets including two, three and four loci. Based on these phylogenies and the correlation of morphological and chemical characters that characterize monophyletic groups, we accept 27 genera within nine main clades. We re-circumscribe several genera and reduce Parmelaria to synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic rank and 15 new combinations are proposed (in the genera Flavoparmelia, Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short discussion of the accepted genera is provided and remaining challenges and areas requiring additional taxon sampling are identified.
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- Sarri, Gianluca, et al.
(author)
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Laser-driven generation of collimated ultra-relativistic positron beams
- 2013
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In: Plasma Physics and Controlled Fusion. - London : Institute of Physics (IOP). - 0741-3335 .- 1361-6587. ; 55:12
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Journal article (peer-reviewed)abstract
- We report on recent experimental results concerning the generation of collimated (divergence of the order of a few mrad) ultra-relativistic positron beams using a fully optical system. The positron beams are generated exploiting a quantum-electrodynamic cascade initiated by the propagation of a laser-accelerated, ultra-relativistic electron beam through high-Z solid targets. As long as the target thickness is comparable to or smaller than the radiation length of the material, the divergence of the escaping positron beam is of the order of the inverse of its Lorentz factor. For thicker solid targets the divergence is seen to gradually increase, due to the increased number of fundamental steps in the cascade, but it is still kept of the order of few tens of mrad, depending on the spectral components in the beam. This high degree of collimation will be fundamental for further injection into plasma-wakefield afterburners.
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| 7. |
- Ercan, Ayse Bahar, et al.
(author)
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Clinical and biological landscape of constitutional mismatch-repair deficiency syndrome: an International Replication Repair Deficiency Consortium cohort study.
- 2024
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In: The Lancet. Oncology. - 1474-5488. ; 25:5, s. 668-682
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Journal article (peer-reviewed)abstract
- Constitutional mismatch repair deficiency (CMMRD) syndrome is a rare and aggressive cancer predisposition syndrome. Because a scarcity of data on this condition contributes to management challenges and poor outcomes, we aimed to describe the clinical spectrum, cancer biology, and impact of genetics on patient survival in CMMRD.In this cohort study, we collected cross-sectional and longitudinal data on all patients with CMMRD, with no age limits, registered with the International Replication Repair Deficiency Consortium (IRRDC) across more than 50 countries. Clinical data were extracted from the IRRDC database, medical records, and physician-completed case record forms. The primary objective was to describe the clinical features, cancer spectrum, and biology of the condition. Secondary objectives included estimations of cancer incidence and of the impact of the specific mismatch-repair gene and genotype on cancer onset and survival, including after cancer surveillance and immunotherapy interventions.We analysed data from 201 patients (103 males, 98 females) enrolled between June 5, 2007 and Sept 9, 2022. Median age at diagnosis of CMMRD or a related cancer was 8·9 years (IQR 5·9-12·6), and median follow-up from diagnosis was 7·2 years (3·6-14·8). Endogamy among minorities and closed communities contributed to high homozygosity within countries with low consanguinity. Frequent dermatological manifestations (117 [93%] of 126 patients with complete data) led to a clinical overlap with neurofibromatosis type 1 (35 [28%] of 126). 339 cancers were reported in 194 (97%) of 201 patients. The cumulative cancer incidence by age 18 years was 90% (95% CI 80-99). Median time between cancer diagnoses for patients with more than one cancer was 1·9 years (IQR 0·8-3·9). Neoplasms developed in 15 organs and included early-onset adult cancers. CNS tumours were the most frequent (173 [51%] cancers), followed by gastrointestinal (75 [22%]), haematological (61 [18%]), and other cancer types (30 [9%]). Patients with CNS tumours had the poorest overall survival rates (39% [95% CI 30-52] at 10 years from diagnosis; log-rank p<0·0001 across four cancer types), followed by those with haematological cancers (67% [55-82]), gastrointestinal cancers (89% [81-97]), and other solid tumours (96% [88-100]). All cancers showed high mutation and microsatellite indel burdens, and pathognomonic mutational signatures. MLH1 or MSH2 variants caused earlier cancer onset than PMS2 or MSH6 variants, and inferior survival (overall survival at age 15 years 63% [95% CI 55-73] for PMS2, 49% [35-68] for MSH6, 19% [6-66] for MLH1, and 0% for MSH2; p<0·0001). Frameshift or truncating variants within the same gene caused earlier cancers and inferior outcomes compared with missense variants (p<0·0001). The greater deleterious effects of MLH1 and MSH2 variants as compared with PMS2 and MSH6 variants persisted despite overall improvements in survival after surveillance or immune checkpoint inhibitor interventions.The very high cancer burden and unique genomic landscape of CMMRD highlight the benefit of comprehensive assays in timely diagnosis and precision approaches toward surveillance and immunotherapy. These data will guide the clinical management of children and patients who survive into adulthood with CMMRD.The Canadian Institutes for Health Research, Stand Up to Cancer, Children's Oncology Group National Cancer Institute Community Oncology Research Program, Canadian Cancer Society, Brain Canada, The V Foundation for Cancer Research, BioCanRx, Harry and Agnieszka Hall, Meagan's Walk, BRAINchild Canada, The LivWise Foundation, St Baldrick Foundation, Hold'em for Life, and Garron Family Cancer Center.
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| 8. |
- Flores, Alexandra, et al.
(author)
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Politicians polarize and experts depolarize public support for COVID-19 management policies across countries
- 2022
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In: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:3
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Journal article (peer-reviewed)abstract
- Political polarization impeded public support for policies to reduce the spread of COVID-19, much as polarization hinders responses to other contemporary challenges. Unlike previous theory and research that focused on the United States, the present research examined the effects of political elite cues and affective polarization on support for policies to manage the COVID-19 pandemic in seven countries (n = 12,955): Brazil, Israel, Italy, South Korea, Sweden, the United Kingdom, and the United States. Across countries, cues from political elites polarized public attitudes toward COVID-19 policies. Liberal and conservative respondents supported policies proposed by ingroup politicians and parties more than the same policies from outgroup politicians and parties. Respondents disliked, distrusted, and felt cold toward outgroup political elites, whereas they liked, trusted, and felt warm toward both ingroup political elites and nonpartisan experts. This affective polarization was correlated with policy support. These findings imply that policies from bipartisan coalitions and nonpartisan experts would be less polarizing, enjoying broader public support. Indeed, across countries, policies from bipartisan coalitions and experts were more widely supported. A follow-up experiment replicated these findings among US respondents considering international vaccine distribution policies. The polarizing effects of partisan elites and affective polarization emerged across nations that vary in cultures, ideologies, and political systems. Contrary to some propositions, the United States was not exceptionally polarized. Rather, these results suggest that polarizing processes emerged simply from categorizing people into political ingroups and outgroups. Political elites drive polarization globally, but nonpartisan experts can help resolve the conflicts that arise from it.
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| 9. |
- Mumme, Steffen, et al.
(author)
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Wherever I may roam—Human activity alters movements of red deer (Cervus elaphus) and elk (Cervus canadensis) across two continents
- 2023
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In: Global Change Biology. - Chichester : Wiley-Blackwell Publishing Inc.. - 1354-1013 .- 1365-2486. ; 29:20, s. 5788-5801
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Journal article (peer-reviewed)abstract
- Human activity and associated landscape modifications alter the movements of animals with consequences for populations and ecosystems worldwide. Species performing long-distance movements are thought to be particularly sensitive to human impact. Despite the increasing anthropogenic pressure, it remains challenging to understand and predict animals' responses to human activity. Here we address this knowledge gap using 1206 Global Positioning System movement trajectories of 815 individuals from 14 red deer (Cervus elaphus) and 14 elk (Cervus canadensis) populations spanning wide environmental gradients, namely the latitudinal range from the Alps to Scandinavia in Europe, and the Greater Yellowstone Ecosystem in North America. We measured individual-level movements relative to the environmental context, or movement expression, using the standardized metric Intensity of Use, reflecting both the directionality and extent of movements. We expected movement expression to be affected by resource (Normalized Difference Vegetation Index, NDVI) predictability and topography, but those factors to be superseded by human impact. Red deer and elk movement expression varied along a continuum, from highly segmented trajectories over relatively small areas (high intensity of use), to directed transitions through restricted corridors (low intensity of use). Human activity (Human Footprint Index, HFI) was the strongest driver of movement expression, with a steep increase in Intensity of Use as HFI increased, but only until a threshold was reached. After exceeding this level of impact, the Intensity of Use remained unchanged. These results indicate the overall sensitivity of Cervus movement expression to human activity and suggest a limitation of plastic responses under high human pressure, despite the species also occurring in human-dominated landscapes. Our work represents the first comparison of metric-based movement expression across widely distributed populations of a deer genus, contributing to the understanding and prediction of animals' responses to human activity. Global Change Biology© 2023 The Authors. Global Change Biology published by John Wiley & Sons Ltd.
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