| 1. |
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| 2. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 3. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 4. |
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| 5. |
- Naehrlich, L., et al.
(författare)
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Incidence of SARS-CoV-2 in people with cystic fibrosis in Europe between February and June 2020
- 2021
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Ingår i: Journal of Cystic Fibrosis. - : Elsevier BV. - 1569-1993. ; 20:4, s. 566-577
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Tidskriftsartikel (refereegranskat)abstract
- Background: Viral infections can cause significant morbidity in cystic fibrosis (CF). The current Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic could therefore have a serious impact on the health of people with CF (pwCF). Methods: We used the 38-country European Cystic Fibrosis Society Patient Registry (ECFSPR) to collect case data about pwCF and SARS-CoV-2 infection. Results: Up to 30 June 2020, 16 countries reported 130 SARS-CoV-2 cases in people with CF, yielding an incidence of 2.70/10 0 0 pwCF. Incidence was higher in lung-transplanted patients (n = 23) versus non transplanted patients (n = 107) (8.43 versus 2.36 cases/10 0 0). Incidence was higher in pwCF versus the age-matched general population in the age groups < 15, 15-24, and 25-49 years (p < 0.001), with similar trends for pwCF with and without lung transplant. Compared to the general population, pwCF (regardless of transplantation status) had significantly higher rates of admission to hospital for all age groups with available data, and higher rates of intensive care, although not statistically significant. Most pwCF recovered (96.2%), however 5 died, of whom 3 were lung transplant recipients. The case fatality rate for pwCF (3.85%, 95% CI: 1.26-8.75) was non-significantly lower than that of the general population (7.46%; p = 0.133). Conclusions: SARS-CoV-2 infection can result in severe illness and death for pwCF, even for younger patients and especially for lung transplant recipients. PwCF should continue to shield from infection and should be prioritized for vaccination. (c) 2021 The Authors. Published by Elsevier B.V. on behalf of European Cystic Fibrosis Society. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )
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| 6. |
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| 7. |
- Lewin, Harris A., et al.
(författare)
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The Earth BioGenome Project 2020 : Starting the clock
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:4
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 8. |
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| 9. |
- Margulies, Elliott H, et al.
(författare)
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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- 2007
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 17:6, s. 760-774
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Tidskriftsartikel (refereegranskat)abstract
- A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
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| 10. |
- Mikkelsen, Tarjei S, et al.
(författare)
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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7141, s. 167-177
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Tidskriftsartikel (refereegranskat)abstract
- We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.
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| 11. |
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| 12. |
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| 13. |
- Blaxter, Mark, et al.
(författare)
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Why sequence all eukaryotes?
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:4
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.
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| 14. |
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| 15. |
- Gretarsdottir, Solveig, et al.
(författare)
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Genome-wide association study identifies a sequence variant within the DAB2IP gene conferring susceptibility to abdominal aortic aneurysm
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 42:8, s. 71-692
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Tidskriftsartikel (refereegranskat)abstract
- We performed a genome-wide association study on 1,292 individuals with abdominal aortic aneurysms (AAAs) and 30,503 controls from Iceland and The Netherlands, with a follow-up of top markers in up to 3,267 individuals with AAAs and 7,451 controls. The A allele of rs7025486 on 9q33 was found to associate with AAA, with an odds ratio (OR) of 1.21 and P = 4.6 x 10(-10). In tests for association with other vascular diseases, we found that rs7025486[A] is associated with early onset myocardial infarction (OR = 1.18, P = 3.1 x 10(-5)), peripheral arterial disease (OR = 1.14, P = 3.9 x 10(-5)) and pulmonary embolism (OR = 1.20, P = 0.00030), but not with intracranial aneurysm or ischemic stroke. No association was observed between rs7025486[A] and common risk factors for arterial and venous diseases-that is, smoking, lipid levels, obesity, type 2 diabetes and hypertension. Rs7025486 is located within DAB2IP, which encodes an inhibitor of cell growth and survival.
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| 16. |
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| 17. |
- Christmas, Matthew, et al.
(författare)
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Evolutionary constraint and innovation across hundreds of placental mammals
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6643
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Tidskriftsartikel (refereegranskat)abstract
- Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (similar to 10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.
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| 18. |
- Grün, E., et al.
(författare)
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Dust measurements in the Jovian magnetosphere
- 1997
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Ingår i: Geophysical Research Letters. - 1944-8007. ; 24:17, s. 2171-2174
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Tidskriftsartikel (refereegranskat)abstract
- Dust measurements have been obtained with the dust detector onboard the Galileo spacecraft inside a distance of about 60RJ from Jupiter (Jupiter radius, RJ = 71,492 km) during two periods of about 8 days around Galileo's closest approaches to Ganymede on 27 June and on 6 Sept 1996. The impact rate of submicrometer-sized particles fluctuated by a factor of several hundred with a period of about 10 hours, implying that their trajectories are strongly affected by the interaction with the Jovian magnetic field. Concentrations of small dust impacts were detected at the times of Ganymede closest approaches that could be secondary ejecta particles generated upon impact of other particles onto Ganymede's surface. Micrometer-sized dust particles, which could be on bound orbits about Jupiter, are concentrated in the inner Jovian system inside about 20RJ from Jupiter.
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| 19. |
- Grün, E., et al.
(författare)
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Galileo observes electromagnetically coupled dust in the Jovian magnetosphere
- 1998
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Ingår i: Journal of Geophysical Research. - 2156-2202. ; 103:E9, s. 20011-20022
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Tidskriftsartikel (refereegranskat)abstract
- Measurements of dust coupled to the Jovian magnetosphere have been obtained with the dust detector on board the Galileo spacecraft. We report on data obtained during the first four orbits about Jupiter that had flybys of the Galilean satellites: Ganymede (orbits 1 and 2), Callisto (orbit 3), and Europa (orbit 4). The most prominent features observed are highly time variable dust streams recorded throughout the Jovian system. The impact rate varied by up to 2 orders of magnitude with a 5 and 10 hour periodicity, which shows a correlation with Galileo's position relative to the Jovian magnetic field. Around 20 RJ (Jupiter radius, RJ=71, 492 km) in bound a dip in the impact rate has been found consistently. At the same times, reversals by 180° in impact direction occurred. This behavior can be qualitatively explained by strong coupling of nanometer-sized dust to the Jovian magnetic field. At times of satellite flybys, enhanced rates of dust impacts have been observed, which suggests that all Galilean satellites are sources of ejecta particles. Inside about 20 RJ impacts of micrometer-sized particles have been recorded that could be particles on bound orbits about Jupiter.
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| 20. |
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| 21. |
- Adiels, Lars, 1952-, et al.
(författare)
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Test of CP violation with K0 and K‾0 at LEAR
- 1985
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Ingår i: Physics with antiprotons at LEAR in the ACOL era. - Gif sur Yvette : Editions Frontières. - 2863320351 ; , s. 467-482
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 22. |
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| 23. |
- Cornelissen, Johannes H C, et al.
(författare)
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Global negative vegetation feedback to climate warming responses of leaf litter decomposition rates in cold biomes
- 2007
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Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 10:7, s. 619-627
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Tidskriftsartikel (refereegranskat)abstract
- Whether climate change will turn cold biomes from large long-term carbon sinks into sources is hotly debated because of the great potential for ecosystem-mediated feedbacks to global climate. Critical are the direction, magnitude and generality of climate responses of plant litter decomposition. Here, we present the first quantitative analysis of the major climate-change-related drivers of litter decomposition rates in cold northern biomes worldwide.Leaf litters collected from the predominant species in 33 global change manipulation experiments in circum-arctic-alpine ecosystems were incubated simultaneously in two contrasting arctic life zones. We demonstrate that longer-term, large-scale changes to leaf litter decomposition will be driven primarily by both direct warming effects and concomitant shifts in plant growth form composition, with a much smaller role for changes in litter quality within species. Specifically, the ongoing warming-induced expansion of shrubs with recalcitrant leaf litter across cold biomes would constitute a negative feedback to global warming. Depending on the strength of other (previously reported) positive feedbacks of shrub expansion on soil carbon turnover, this may partly counteract direct warming enhancement of litter decomposition.
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| 24. |
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| 25. |
- Frantz, A M, et al.
(författare)
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Molecular Profiling Reveals Prognostically Significant Subtypes of Canine Lymphoma
- 2013
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Ingår i: Veterinary pathology. - : SAGE Publications. - 0300-9858 .- 1544-2217. ; 50:4, s. 693-703
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Tidskriftsartikel (refereegranskat)abstract
- We performed genomewide gene expression analysis of 35 samples representing 6 common histologic subtypes of canine lymphoma and bioinformatics analyses to define their molecular characteristics. Three major groups were defined on the basis of gene expression profiles: (1) low-grade T-cell lymphoma, composed entirely by T-zone lymphoma; (2) high-grade T-cell lymphoma, consisting of lymphoblastic T-cell lymphoma and peripheral T-cell lymphoma not otherwise specified; and (3) B-cell lymphoma, consisting of marginal B-cell lymphoma, diffuse large B-cell lymphoma, and Burkitt lymphoma. Interspecies comparative analyses of gene expression profiles also showed that marginal B-cell lymphoma and diffuse large B-cell lymphoma in dogs and humans might represent a continuum of disease with similar drivers. The classification of these diverse tumors into 3 subgroups was prognostically significant, as the groups were directly correlated with event-free survival. Finally, we developed a benchtop diagnostic test based on expression of 4 genes that can robustly classify canine lymphomas into one of these 3 subgroups, enabling a direct clinical application for our results.
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| 26. |
- Genereux, Diane P., et al.
(författare)
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A comparative genomics multitool for scientific discovery and conservation
- 2020
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Ingår i: Nature. - : NATURE RESEARCH. - 0028-0836 .- 1476-4687. ; 587:7833, s. 240-245
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Tidskriftsartikel (refereegranskat)abstract
- A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal-including 131 previously uncharacterized species-from the Zoonomia Project provides data that support biological discovery, medical research and conservation. The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.
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| 27. |
- Gruen, E., et al.
(författare)
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Ulysses Dust Detection System V3.1
- 2010
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Ingår i: NASA Planetary Data System. ; 140
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Tidskriftsartikel (refereegranskat)abstract
- This data set contains the data from the Ulysses dust detector system (UDDS) from start of mission through the end of mission, 1990-2007. (As the dust detector was turned off after Nov. 30, 2007, this is the last date for which UDDS data is recorded.) Included are the dust impact data, noise data, laboratory calibration data, and location and orientation of the spacecraft and instrument.
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| 28. |
- Grün, E., et al.
(författare)
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Dust Measurements During Galileo's Approach to Jupiter and Io Encounter
- 1996
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 274:5286, s. 399-401
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Tidskriftsartikel (refereegranskat)abstract
- About a hundred dust impacts per day were detected during the first week in December 1995 by Galileo during its approach to Jupiter. These impacts were caused by submicrometer-sized particles that were just above the detection limit. After the closest approach to Io on 7 December, impacts of these small particles ceased. This effect is expected for dust grains emitted from Io that exit the field of view of the instrument after the flyby. The impact rate of bigger micrometer-sized dust grains continued to increase toward Jupiter. These dust particles are in orbit about Jupiter or are interplanetary grains that are gravitationally concentrated near Jupiter.
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| 29. |
- Krueger, H., et al.
(författare)
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Five years of Ulysses dust data: 2000-2004
- 2006
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Ingår i: Planetary and Space Science. - : Elsevier BV. - 1873-5088 .- 0032-0633. ; 54:9-10, s. 932-956
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Tidskriftsartikel (refereegranskat)abstract
- The Ulysses spacecraft has been orbiting the Sun on a highly inclined ellipse (i = 79 degrees, perihelion distance 1.3 AU, aphelion distance 5.4 AU) since it encountered Jupiter in 1992. Between January 2000 and December 2004, the spacecraft completed almost an entire revolution about the Sun, passing through perihelion in May 2001 and aphelion in July 2004. In this five-year period the dust detector on board recorded 4415 dust impacts. We publish and analyse the complete data set of both raw and reduced data for particles with masses 10(-16) g <= M <= 10(-7) g. Together with. 1695 dust impacts recorded between launch of Ulysses and the end of 1999 published earlier (Grain, E., Baguhl, M., Divine, N., Fechtig, H., Hamilton, D.P, Harmer, M.S., Kissel, J., Lindblad, B.A., Linkert, D., Linkert, G., Mann, L, McDonnell, J.A.M., Morfill, G.E., Polanskey, C., Riemann, R., Schwehm, G.H., Siddique, N., Staubach, P., Zook, H.A., 1995a. Two years of Ulysses dust data. Planetary Space Sci. 43, 971-999, Paper III; Kruger, H., Grun, E., Landgraf, M., Baguhl, M., Dermott, S.F., Fechtig, H., Gustafson, B.A., Hamilton, D.P., Harmer, M.S., Horanyi, M., Kissel, J., Lindblad, B., Linkert, D., Linkert, G., Mann, L, McDonnell, J.A.M., Morfill, G.E., Polanskey, C., Schwehm, G.H., Srama, R., Zook, H.A., 1995. Three years of Ulysses dust data: 1993 to 1995. Planetary and Space Sci. 47, 363-383, Paper V; Kruger, H., Grun, E., Landgraf, M., Dermott, S.F., Fechtig, H., Gustafson, B.A., Hamilton, D.P., Harmer, M.S., Horanyi, M., Kissel, J., Lindblad, B., Linkert, D., Linkert, G., Mann, I., McDonnell, J.A.M., Morfill, G.E., Polanskey, C., Schwehm, G.H., Srama, R., Zook, H.A., 2001b. Four years of Ulysses dust data: 1996 to 1999. Planetary Space Sci. 49, 1303-1324, Paper VII), a data set of 6110 dust impacts detected with the Ulysses sensor between October 1990 and December 2004 is now available. The impact rate measured between 2000 and 2002 was relatively constant with about 0.3 impacts per day showing a maximum at 1.5 per day around ecliptic plane crossing in early-2001. The impact direction of the majority of impacts between 2000 and 2002 is compatible with particles of interstellar origin, the rest are most likely interplanetary particles. In 2003 and 2004 dust stream particles originating from the jovian system dominated the overall impact rate. Twenty-two individual dust streams were measured between November 2002 and December 2004. The observed impact rates are compared with models for interplanetary and interstellar dust. The dust measurements from the entire mission since Ulysses launch give good agreement with the interplanetary flux model of Staubach, P., Grun, E., Jehn, R., 1997. The meteoroid environment near Earth, Adv. Space Res. 19, 301-308. (c) 2006 Elsevier Ltd. All rights reserved.
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| 30. |
- Krueger, H., et al.
(författare)
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Galileo dust data from the jovian system: 1997-1999
- 2006
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Ingår i: Planetary and Space Science. - : Elsevier BV. - 1873-5088 .- 0032-0633. ; 54:9-10, s. 879-910
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Tidskriftsartikel (refereegranskat)abstract
- The dust detector system on board the Galileo spacecraft recorded dust impacts in circumjovian space during the craft's orbital mission about Jupiter. This is the eighth in a series of papers dedicated to presenting Galileo and Ulysses dust data. We present data from the Galileo dust instrument for the period January 1997-December 1999 when the spacecraft completed 21 revolutions about Jupiter. In this time interval data were obtained as high resolution realtime science data or recorded data during 449 days (representing 41% of the entire period), or via memory readouts during the remaining times. Because the data transmission rate of the spacecraft was very low, the complete data set (i.e. all parameters measured by the instrument during impact of a dust particle) of only 3% (7625) of all particles detected could be transmitted to Earth; the other particles were only counted. Together with the data of 2883 particles detected during, Galileo's interplanetary cruise and 53 53 particles detected in the jovian system in 1996, complete data of 15 861 particles detected by the Galileo dust instrument from 1989 to 1999 are now available. The majority of the detected particles were tiny grains (about 10 nm in radius), most of them originating from Jupiter's innermost Galilean moon Io. They were detected throughout the jovian system and the highest impact rates exceeded 100 min(-1) (C21 orbit; 01 July 1999). With the new data set the times of onset, cessation and a 180 degrees shift in the impact direction of the grains measured during 19 Galileo orbits about Jupiter are well reproduced by simulated 9 nm particles charged up to a potential of +3 V, confirming earlier results obtained for only two Galileo orbits (Horanyi, M., Grun, E., Heck, A., 1997. Modeling the Galileo dust measurements at Jupiter. Geophys. Res. Lett. 24, 2175-2178). Galileo has detected a large number of bigger particles mostly in the region between the Galilean moons. The average radius of 370 of these grains measured in the 1996-1999 period is about 2 mu m (assuming spherical grains with density 1 g cm(-3)) and the size distribution rises steeply towards smaller grains. The biggest detected particles have a radius of about 10 mu m. (c) 2006 Elsevier Ltd. All rights reserved.
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| 31. |
- Krüger, H., et al.
(författare)
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One year of Galileo dust data from the Jovian system: 1996
- 2001
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Ingår i: Planetary and Space Science. - 1873-5088. ; 49:13, s. 1285-1301
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Tidskriftsartikel (refereegranskat)abstract
- The dust detector system onboard Galileo has recoding dust impacts incircumjovian space since the spacecraft was injected into a bound orbitabout Jupiter in December 1995. This is the sixth in a series of papersdedicated to presenting Galileo and Ulysses dust data. We present datafrom the Galileo dust instrument for the period January to December 1996when the spacecraft completed four orbits about Jupiter (G1, G2, C3 andE4). Data were obtained as high-resolution realtime science data orrecorded data during a time period of 100 days, or via memory read-outsduring the remaining times. Because the data transmission rate of thespacecraft is very low, the complete data set (i.e. all parametersmeasured by the instrument during impact of a dust particle) for only 2%(5353) of all particles detected could be transmitted to Earth; theother particles were only counted. Together with the data for 2883particles detected during Galileo's interplanetary cruise and publishedearlier, complete data of 8236 particles detected by the Galileo dustinstrument from 1989 to 1996 are now available. The majority ofparticles detected are tiny grains (about 10nm in radius) originatingfrom Jupiter's innermost Galilean moon Io. These grains have beendetected throughout the Jovian system and the highest impact ratesexceeded 100min-1. A small number of grains has been detectedin the close vicinity of the Galilean moons Europa, Ganymede andCallisto which belong to impact-generated dust clouds formed by (mostlysubmicrometer sized) ejecta from the surfaces of the moons (Krügeret al., /1999e. Nature 399, 558). Impacts of submicrometer to micrometersized grains have been detected throughout the Jovian system andespecially in the region between the Galilean moons.
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| 32. |
- Lawniczak, Mara K. N., et al.
(författare)
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Standards recommendations for the Earth BioGenome Project
- 2022
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:4
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Tidskriftsartikel (refereegranskat)abstract
- A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
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| 33. |
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| 34. |
- Lindehammer, Sabina, et al.
(författare)
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Temporal trends of HLA genotype frequencies of type 1 diabetes patients in Sweden from 1986 to 2005 suggest altered risk
- 2008
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Ingår i: Acta Diabetologica. - : Springer Science and Business Media LLC. - 0940-5429 .- 1432-5233. ; 45:4, s. 231-5
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to compare the frequency of human leukocyte antigen (HLA) genotypes in 1-18-year-old patients with type 1 diabetes newly diagnosed in 1986-1987 (n = 430), 1996-2000 (n = 342) and in 2003-2005 (n = 171). We tested the hypothesis that the HLA DQ genotype distribution changes over time. Swedish type 1 diabetes patients and controls were typed for HLA using polymerase chain reaction amplification and allele specific probes for DQ A1* and B1* alleles. The most common type 1 diabetes HLA DQA1*-B1*genotype 0501-0201/0301-0302 was 36% (153/430) in 1986-1987 and 37% (127/342) in 1996-2000, but decreased to 19% (33/171) in 2003-2005 (P \ 0.0001). The 0501-0201/0501-0201 genotype increased from 1% in 1986-1987 to 7% in 1996-2000 (P = 0.0047) and to 5% in 2003-2005 (P > 0.05). This study in 1-18-year-old Swedish type 1 diabetes patients supports the notion that there is a temporal change in HLA risk.
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| 35. |
- Lundtoft, Christian, et al.
(författare)
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Strong Association of Combined Genetic Deficiencies in the Classical Complement Pathway With Risk of Systemic Lupus Erythematosus and Primary Sjogren's Syndrome
- 2022
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Ingår i: Arthritis & Rheumatology. - : Wiley. - 2326-5191 .- 2326-5205. ; 74:11, s. 1842-1850
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Tidskriftsartikel (refereegranskat)abstract
- Objective Complete genetic deficiency of the complement component C2 is a strong risk factor for monogenic systemic lupus erythematosus (SLE), but whether heterozygous C2 deficiency adds to the risk of SLE or primary Sjogren's syndrome (SS) has not been studied systematically. This study was undertaken to investigate potential associations of heterozygous C2 deficiency and C4 copy number variation with clinical manifestations in patients with SLE and patients with primary SS. Methods The presence of the common 28-bp C2 deletion rs9332736 and C4 copy number variation was examined in Scandinavian patients who had received a diagnosis of SLE (n = 958) or primary SS (n = 911) and in 2,262 healthy controls through the use of DNA sequencing. The concentration of complement proteins in plasma and classical complement function were analyzed in a subgroup of SLE patients. Results Heterozygous C2 deficiency-when present in combination with a low C4A copy number-substantially increased the risk of SLE (odds ratio [OR] 10.2 [95% confidence interval (95% CI) 3.5-37.0]) and the risk of primary SS (OR 13.0 [95% CI 4.5-48.4]) when compared to individuals with 2 C4A copies and normal C2. For patients heterozygous for rs9332736 with 1 C4A copy, the median age at diagnosis was 7 years earlier in patients with SLE and 12 years earlier in patients with primary SS when compared to patients with normal C2. Reduced C2 levels in plasma (P = 2 x 10(-9)) and impaired function of the classical complement pathway (P = 0.03) were detected in SLE patients with heterozygous C2 deficiency. Finally, in a primary SS patient homozygous for C2 deficiency, we observed low levels of anti-Scl-70, which suggests a risk of developing systemic sclerosis or potential overlap between primary SS and other systemic autoimmune diseases. Conclusion We demonstrate that a genetic pattern involving partial deficiencies of C2 and C4A in the classical complement pathway is a strong risk factor for SLE and for primary SS. Our results emphasize the central role of the complement system in the pathogenesis of both SLE and primary SS.
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| 36. |
- Noh, Hyun Ji, et al.
(författare)
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Integrating evolutionary and regulatory information with multispecies approach implicates genes and pathways in obsessive-compulsive disorder
- 2017
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Obsessive-compulsive disorder is a severe psychiatric disorder linked to abnormalities in glutamate signaling and the cortico-striatal circuit. We sequenced coding and regulatory elements for 608 genes potentially involved in obsessive-compulsive disorder in human, dog, and mouse. Using a new method that prioritizes likely functional variants, we compared 592 cases to 560 controls and found four strongly associated genes, validated in a larger cohort. NRXN1 and HTR2A are enriched for coding variants altering postsynaptic protein-binding domains. CTTNBP2 (synapse maintenance) and REEP3 (vesicle trafficking) are enriched for regulatory variants, of which at least six (35%) alter transcription factor-DNA binding in neuroblastoma cells. NRXN1 achieves genome-wide significance (p = 6.37 x 10(-11)) when we include 33,370 population-matched controls. Our findings suggest synaptic adhesion as a key component in compulsive behaviors, and show that targeted sequencing plus functional annotation can identify potentially causative variants, even when genomic data are limited.
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| 37. |
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| 38. |
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| 39. |
- van den Berg, L, et al.
(författare)
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Evaluation of the serotonergic genes htr1A, htr1B, htr2A, and slc6A4 in aggressive behavior of golden retriever dogs
- 2008
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Ingår i: Behavior Genetics. - : Springer Science and Business Media LLC. - 0001-8244 .- 1573-3297. ; 38:1, s. 55-66
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Tidskriftsartikel (refereegranskat)abstract
- Aggressive behavior displays a high heritability in our study group of Golden Retriever dogs. Alterations in brain serotonin metabolism have been described in aggressive dogs before. Here, we evaluate whether four genes of the canine serotonergic system, coding for the serotonin receptors 1A, 1B, and 2A, and the serotonin transporter, could play a major role in aggression in Golden Retrievers. We performed mutation screens, linkage analysis, an association study, and a quantitative genetic analysis. There was no systematic difference between the coding DNA sequence of the candidate genes in aggressive and non-aggressive Golden Retrievers. An affecteds-only parametric linkage analysis revealed no strong major locus effect on human-directed aggression related to the candidate genes. An analysis of 41 single nucleotide polymorphisms (SNPs) in the 1 Mb regions flanking the genes in 49 unrelated human-directed aggressive and 49 unrelated non-aggressive dogs did not show association of SNP alleles, genotypes, or haplotypes with aggression at the candidate loci. We completed our analyses with a study of the effect of variation in the candidate genes on a collection of aggression-related phenotypic measures. The effects of the candidate gene haplotypes were estimated using the Restricted Maximum Likelihood method, with the haplotypes included as fixed effects in a linear animal model. We observed no effect of the candidate gene haplotypes on a range of aggression-related phenotypes, thus extending our conclusions to several types of aggressive behavior. We conclude that it is unlikely that these genes play a major role in the variation in aggression in the Golden Retrievers that we studied. Smaller phenotypic effects of these loci could not be ruled out with our sample size.
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| 40. |
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| 41. |
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| 42. |
- Alfoeldi, Jessica, et al.
(författare)
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The genome of the green anole lizard and a comparative analysis with birds and mammals
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 477:7366, s. 587-591
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Tidskriftsartikel (refereegranskat)abstract
- The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments(1). Among amniotes, genome sequences are available for mammals and birds(2-4), but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes(2). Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds(5). We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
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| 43. |
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| 44. |
- Bergström, A., et al.
(författare)
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Physical activity and risk of renal cell cancer
- 2001
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Ingår i: International Journal of Cancer. - New York, USA : John Wiley & Sons. - 0020-7136 .- 1097-0215. ; 92:1, s. 155-157
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Tidskriftsartikel (refereegranskat)abstract
- The relation between physical activity and renal cell cancer is unclear. High occupational physical activity has been associated with a decreased risk of renal cell cancer among men-but not among women-in two previous studies, while no association has been found for leisure time physical activity. Our aim was to investigate the association between occupational and leisure time physical activity in a prospective cohort of 17,241 Swedish twins. Information on physical activity and a wide range of potential confounding factors was obtained through a mailed questionnaire. During follow-up from 1967 through 1997 we identified 102 cases of renal cell cancer. We found no evidence of an inverse association between either occupational or leisure time physical activity and risk of renal cell cancer in this prospective cohort.
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| 45. |
- Brawand, David, et al.
(författare)
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The genomic substrate for adaptive radiation in African cichlid fish
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 513:7518, s. 375-381
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Tidskriftsartikel (refereegranskat)abstract
- Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand themolecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
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| 46. |
- Carlsson, Annelie, et al.
(författare)
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Low risk HLA-DQ and increased body mass index in newly diagnosed type 1 diabetes children in the Better Diabetes Diagnosis study in Sweden
- 2012
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Ingår i: International Journal of Obesity. - : Nature Publishing Group. - 0307-0565 .- 1476-5497. ; 36:5, s. 718-724
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Tidskriftsartikel (refereegranskat)abstract
- Objective: Type 1 diabetes and obesity has increased in childhood. We therefore tested the hypothesis that type 1 diabetes human leukocyte antigen DQ (HLA-DQ) risk genotypes may be associated with increased body mass index (BMI). less thanbrgreater than less thanbrgreater thanDesign: The type 1 diabetes high-risk HLA-DQ A1*05:01-B1*02:01/A1*03:01-B1*03:02 genotype along with lower risk DQ genotypes were determined at the time of clinical onset by PCR and hybridization with allele-specific probes. BMI was determined after diabetes was stabilized. less thanbrgreater than less thanbrgreater thanSubjects: A total of 2403 incident type 1 diabetes children below 18 years of age were ascertained in the Swedish national Better Diabetes Diagnosis (BDD) study between May 2005 to September 2009. All children classified with type 1 diabetes, including positivity for at least one islet autoantibody, were investigated. less thanbrgreater than less thanbrgreater thanResults: Overall, type 1 diabetes HLA-DQ risk was negatively associated with BMI (Pandlt;0.0008). The proportion of the highest risk A1*05:01-B1*02:01/A1*03:01-B1*03:02 genotype decreased with increasing BMI (Pandlt;0.0004). However, lower risk type 1 diabetes DQ genotypes were associated with an increased proportion of patients who were overweight or obese (Pandlt;0.0001). Indeed, the proportion of patients with the low-risk A1*05:01-B1*02:01/A1*05:01-B1*02:01 genotype increased with increasing BMI (Pandlt;0.003). The magnitude of association on the multiplicative scale between the A1*05:01-B1*02:01/A1*05:01-B1*02:01 genotype and increased BMI was significant (Pandlt;0.006). The odds ratio in patients with this genotype of being obese was 1.80 (95% confidence interval 1.21-2.61; Pandlt;0.006). The increased proportion of overweight type 1 diabetes children with the A1*05:01-B1*02:01 haplotype was most pronounced in children diagnosed between 5 and 9 years of age. less thanbrgreater than less thanbrgreater thanConclusions: Susceptibility for childhood type 1 diabetes was unexpectedly found to be associated with the A1*05:01-B1*02:01/A1*05:01-B1*02:01 genotype and an increased BMI. These results support the hypothesis that overweight may contribute to the risk of type 1 diabetes in children positive for HLA-DQ A1*05:01-B1*02:01.
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| 47. |
- Casewell, Nicholas R, et al.
(författare)
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Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals.
- 2019
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:51, s. 25745-25755
-
Tidskriftsartikel (refereegranskat)abstract
- Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan solenodon (Solenodon paradoxus). We constructed a genome to underpin proteomic identifications of solenodon venom toxins, before undertaking evolutionary analyses of those constituents, and functional assessments of the secreted venom. Our findings show that solenodon venom consists of multiple paralogous kallikrein 1 (KLK1) serine proteases, which cause hypotensive effects in vivo, and seem likely to have evolved to facilitate vertebrate prey capture. Comparative analyses provide convincing evidence that the oral venom systems of solenodons and shrews have evolved convergently, with the 4 independent origins of venom in eulipotyphlans outnumbering all other venom origins in mammals. We find that KLK1s have been independently coopted into the venom of shrews and solenodons following their divergence during the late Cretaceous, suggesting that evolutionary constraints may be acting on these genes. Consequently, our findings represent a striking example of convergent molecular evolution and demonstrate that distinct structural backgrounds can yield equivalent functions.
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| 48. |
- Damas, Joana, et al.
(författare)
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Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates
- 2020
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 117:36, s. 22311-22322
-
Tidskriftsartikel (refereegranskat)abstract
- The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. We designed a five-category binding score based on the conservation properties of 25 amino acids important for the binding between ACE2 and the SARS-CoV-2 spike protein. Only mammals fell into the medium to very high categories and only catarrhine primates into the very high category, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 spike protein binding and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (frequency <0.001) variants in 10/25 binding sites. In addition, we found significant signals of selection and accelerated evolution in the ACE2 coding sequence across all mammals, and specific to the bat lineage. Our results, if confirmed by additional experimental data, may lead to the identification of intermediate host species for SARS-CoV-2, guide the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.
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| 49. |
- Grun, E., et al.
(författare)
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South-North and Radial Traverses through the Interplanetary Dust Cloud
- 1997
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Ingår i: Icarus. - : Elsevier BV. - 0019-1035. ; 129:2, s. 270-288
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Tidskriftsartikel (refereegranskat)abstract
- Identical in situ dust detectors are flown on board the Galileo and Ulysses spacecraft. They record impacts of micrometeoroids in the ecliptic plane at heliocentric distances from 0.7 to 5.4 AU and in a plane almost perpendicular to the ecliptic from -79 deg to +79 deg ecliptic latitude. The combination of both Ulysses and Galileo measurements yields information about the radial and latitudinal distributions of micron- and sub-micron-sized dust in the Solar System. Two types of dust particles were found to dominate the dust flux in interplanetary space. Interplanetary micrometeoroids covering a wide mass range from 10^-16 to 10^-6 g are recorded mostly inside 3 AU and at latitudes below 30 deg. Interstellar grains with masses between 10^-14 and 10^-12 g have been positively identified outside 3 AU near the ecliptic plane and outside 1.8 AU at high ecliptic latitudes (>50 deg). Interstellar grains move on hyperbolic trajectories through the planetary system and constitute the dominant dust flux (1.5 x 10^-4 m^-2 sec^-1) in the outer Solar System and at high ecliptic latitudes. To compare and analyze the Galileo and Ulysses data sets, a new model is developed based on J. Geophys. Res. 98, 17029-17048, Divine's (1993, ``five populations of interplanetary meteoroids'' model. Both models describe the interplanetary meteoroid environment in terms of dust populations on distinct orbits. Taking into account the measured velocities and the effect of radiation pressure on small particles (described by the ratio of radiation pressure force to gravity, beta), we define four populations of meteoroids on elliptical orbits and one population on hyperbolic orbit that can fit the micrometeoroid flux observed by Galileo and Ulysses. Micrometeoroids with masses greater than 10^-10 g and negligible radiation pressure (beta = 0) orbit the Sun on low to moderately eccentric orbits and with low inclinations (<=30 deg). Populations of smaller particles with mean masses of 10^-11 g (beta = 0.3), 10^-13 g (beta = 0.8), and 5 x 10^-15 g (beta = 0.3), respectively, have components with high eccentricities and have increasingly wider inclination distributions with decreasing mass. Similarities among the orbit distributions of the small particle populations on bound orbits suggest that all are genetically related and are part of an overall micrometeoroid complex that prevails in the inner Solar System. The high-eccentricity component of the small particle populations may actually be beta-meteoroids which are not well characterized by our measurements. Our modeling suggests further that the interstellar dust flux is not reduced at Ulysses' perihelion distance (1.3 AU) and that it contributes about 30% of the total dust flux observed there.
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| 50. |
- Gyllenberg, A, et al.
(författare)
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Age-dependent variation of genotypes in MHC II transactivator gene (CIITA) in controls and association to type 1 diabetes
- 2012
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Ingår i: Genes and Immunity. - Stockholm : Springer Science and Business Media LLC. - 1476-5470 .- 1466-4879. ; 76:2, s. 202-203
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Tidskriftsartikel (refereegranskat)abstract
- The major histocompatibility complex class II transactivator (CIITA) gene (16p13) has been reported to associate with susceptibility to multiple sclerosis, rheumatoid arthritis and myocardial infarction, recently also to celiac disease at genome-wide level. However, attempts to replicate association have been inconclusive. Previously, we have observed linkage to the CIITA region in Scandinavian type 1 diabetes (T1D) families. Here we analyze five Swedish T1D cohorts and a combined control material from previous studies of CIITA. We investigate how the genotype distribution within the CIITA gene varies depending on age, and the association to T1D. Unexpectedly, we find a significant difference in the genotype distribution for markers in CIITA (rs11074932, P=4 × 10(-5) and rs3087456, P=0.05) with respect to age, in the collected control material. This observation is replicated in an independent cohort material of about 2000 individuals (P=0.006, P=0.007). We also detect association to T1D for both markers, rs11074932 (P=0.004) and rs3087456 (P=0.001), after adjusting for age at sampling. The association remains independent of the adjacent T1D risk gene CLEC16A. Our results indicate an age-dependent variation in CIITA allele frequencies, a finding of relevance for the contrasting outcomes of previously published association studies.
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