| 1. |
- Groenen, M. A., et al.
(author)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Journal article (peer-reviewed)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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| 2. |
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| 3. |
- Marcote, B., et al.
(author)
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A repeating fast radio burst source localized to a nearby spiral galaxy
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 577:7789, s. 190-194
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Journal article (peer-reviewed)abstract
- Fast radio bursts (FRBs) are brief, bright, extragalactic radio flashes1,2. Their physical origin remains unknown, but dozens of possible models have been postulated3. Some FRB sources exhibit repeat bursts4–7. Although over a hundred FRB sources have been discovered8, only four have been localized and associated with a host galaxy9–12, and just one of these four is known to emit repeating FRBs9. The properties of the host galaxies, and the local environments of FRBs, could provide important clues about their physical origins. The first known repeating FRB, however, was localized to a low-metallicity, irregular dwarf galaxy, and the apparently non-repeating sources were localized to higher-metallicity, massive elliptical or star-forming galaxies, suggesting that perhaps the repeating and apparently non-repeating sources could have distinct physical origins. Here we report the precise localization of a second repeating FRB source6, FRB 180916.J0158+65, to a star-forming region in a nearby (redshift 0.0337 ± 0.0002) massive spiral galaxy, whose properties and proximity distinguish it from all known hosts. The lack of both a comparably luminous persistent radio counterpart and a high Faraday rotation measure6 further distinguish the local environment of FRB 180916.J0158+65 from that of the single previously localized repeating FRB source, FRB 121102. This suggests that repeating FRBs may have a wide range of luminosities, and originate from diverse host galaxies and local environments.
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| 4. |
- Camilo, F., et al.
(author)
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Revival of the Magnetar PSR J1622-4950: Observations with MeerKAT, Parkes, XMM-Newton, Swift, Chandra, and NuSTAR
- 2018
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In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 856:2
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Journal article (peer-reviewed)abstract
- New radio (MeerKAT and Parkes) and X-ray (XMM-Newton, Swift, Chandra, and NuSTAR) observations of PSR J1622-4950 indicate that the magnetar, in a quiescent state since at least early 2015, reactivated between 2017 March 19 and April 5. The radio flux density, while variable, is approximately 100 larger than during its dormant state. The X-ray flux one month after reactivation was at least 800 larger than during quiescence, and has been decaying exponentially on a 111 19 day timescale. This high-flux state, together with a radio-derived rotational ephemeris, enabled for the first time the detection of X-ray pulsations for this magnetar. At 5%, the 0.3-6 keV pulsed fraction is comparable to the smallest observed for magnetars. The overall pulsar geometry inferred from polarized radio emission appears to be broadly consistent with that determined 6-8 years earlier. However, rotating vector model fits suggest that we are now seeing radio emission from a different location in the magnetosphere than previously. This indicates a novel way in which radio emission from magnetars can differ from that of ordinary pulsars. The torque on the neutron star is varying rapidly and unsteadily, as is common for magnetars following outburst, having changed by a factor of 7 within six months of reactivation.
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| 5. |
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| 6. |
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| 7. |
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| 8. |
- Gentekaki, Eleni, et al.
(author)
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Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis
- 2017
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In: PLoS biology. - : PUBLIC LIBRARY SCIENCE. - 1544-9173 .- 1545-7885. ; 15:9
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Journal article (peer-reviewed)abstract
- Blastocystis is the most prevalent eukaryotic microbe colonizing the human gut, infecting approximately 1 billion individuals worldwide. Although Blastocystis has been linked to intestinal disorders, its pathogenicity remains controversial because most carriers are asymptomatic. Here, the genome sequence of Blastocystis subtype (ST) 1 is presented and compared to previously published sequences for ST4 and ST7. Despite a conserved core of genes, there is unexpected diversity between these STs in terms of their genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content. ST1 has 6,544 protein-coding genes, which is several hundred more than reported for ST4 and ST7. The percentage of proteins unique to each ST ranges from 6.2% to 20.5%, greatly exceeding the differences observed within parasite genera. Orthologous proteins also display extreme divergence in amino acid sequence identity between STs (i.e., 59%-61% median identity), on par with observations of the most distantly related species pairs of parasite genera. The STs also display substantial variation in gene family distributions and sizes, especially for protein kinase and protease gene families, which could reflect differences in virulence. It remains to be seen to what extent these inter-ST differences persist at the intra-ST level. A full 26% of genes in ST1 have stop codons that are created on the mRNA level by a novel polyadenylation mechanism found only in Blastocystis. Reconstructions of pathways and organellar systems revealed that ST1 has a relatively complete membrane-trafficking system and a near-complete meiotic toolkit, possibly indicating a sexual cycle. Unlike some intestinal protistan parasites, Blastocystis ST1 has near-complete de novo pyrimidine, purine, and thiamine biosynthesis pathways and is unique amongst studied stramenopiles in being able to metabolize alpha-glucans rather than beta-glucans. It lacks all genes encoding heme-containing cytochrome P450 proteins. Predictions of the mitochondrion-related organelle (MRO) proteome reveal an expanded repertoire of functions, including lipid, cofactor, and vitamin biosynthesis, as well as proteins that may be involved in regulating mitochondrial morphology and MRO/endoplasmic reticulum (ER) interactions. In sharp contrast, genes for peroxisome-associated functions are absent, suggesting Blastocystis STs lack this organelle. Overall, this study provides an important window into the biology of Blastocystis, showcasing significant differences between STs that can guide future experimental investigations into differences in their virulence and clarifying the roles of these organisms in gut health and disease.
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| 9. |
- Jacobsen, M, et al.
(author)
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Refined candidate region specified by haplotype sharing for Escherichia coli F4ab/F4ac susceptibility alleles in pigs
- 2010
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In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 41:1, s. 21-25
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Journal article (peer-reviewed)abstract
- Infection of the small intestine by enterotoxigenic Escherichia coli F4ab/ac is a major welfare problem and financial burden for the pig industry. Natural resistance to this infection is inherited as a Mendelian recessive trait, and a polymorphism in the MUC4 gene segregating for susceptibility/resistance is presently used in a selection programme by the Danish pig breeding industry. To elucidate the genetic background involved in E. coli F4ab/ac susceptibility in pigs, a detailed haplotype map of the porcine candidate region was established. This region covers approximately 3.7 Mb. The material used for the study is a three generation family, where the founders are two Wild boars and eight Large White sows. All pigs have been phenotyped for susceptibility to F4ab/ac using an adhesion assay. Their haplotypes are known from segregation analysis using flanking markers. By a targeted approach, the candidate region was subjected to screening for polymorphisms, mainly focusing on intronic sequences. A total of 18 genes were partially sequenced, and polymorphisms were identified in GP5, CENTB2, APOD, PCYT1A, OSTalpha, ZDHHC19, TFRC, ACK1, MUC4, MUC20, KIAA0226, LRCH3 and MUC13. Overall, 227 polymorphisms were discovered in the founder generation. The analysis revealed a large haplotype block, spanning at least 1.5 Mb around MUC4, to be associated with F4ab/ac susceptibility.
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| 10. |
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| 11. |
- Nimmo, K., et al.
(author)
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Burst timescales and luminosities as links between young pulsars and fast radio bursts
- 2022
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In: Nature Astronomy. - : Springer Science and Business Media LLC. - 2397-3366. ; 6:3, s. 393-401
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Journal article (peer-reviewed)abstract
- Fast radio bursts (FRBs) are extragalactic radio flashes of unknown physical origin. Their high luminosities and short durations require extreme energy densities, such as those found in the vicinity of neutron stars and black holes. Studying the burst intensities and polarimetric properties on a wide range of timescales, from milliseconds down to nanoseconds, is key to understanding the emission mechanism. However, high-time-resolution studies of FRBs are limited by their unpredictable activity levels, available instrumentation and temporal broadening in the intervening ionized medium. Here we show that the repeating FRB 20200120E can produce isolated shots of emission as short as about 60 nanoseconds in duration, with brightness temperatures as high as 3 × 1041 K (excluding relativistic effects), comparable with ‘nano-shots’ from the Crab pulsar. Comparing both the range of timescales and luminosities, we find that FRB 20200120E observationally bridges the gap between known Galactic young pulsars and magnetars and the much more distant extragalactic FRBs. This suggests a common magnetically powered emission mechanism spanning many orders of magnitude in timescale and luminosity. In this Article, we probe a relatively unexplored region of the short-duration transient phase space; we highlight that there probably exists a population of ultrafast radio transients at nanosecond to microsecond timescales, which current FRB searches are insensitive to.
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| 12. |
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| 13. |
- Bard-Chapeau, Emilie A, et al.
(author)
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Mice carrying a hypomorphic Evi1 allele are embryonic viable but exhibit severe congenital heart defects
- 2014
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:2
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Journal article (peer-reviewed)abstract
- The ecotropic viral integration site 1 (Evi1) oncogenic transcription factor is one of a number of alternative transcripts encoded by the Mds1 and Evi1 complex locus (Mecom). Overexpression of Evi1 has been observed in a number of myeloid disorders and is associated with poor patient survival. It is also amplified and/or overexpressed in many epithelial cancers including nasopharyngeal carcinoma, ovarian carcinoma, ependymomas, and lung and colorectal cancers. Two murine knockout models have also demonstrated Evi1's critical role in the maintenance of hematopoietic stem cell renewal with its absence resulting in the death of mutant embryos due to hematopoietic failure. Here we characterize a novel mouse model (designated Evi1(fl3)) in which Evi1 exon 3, which carries the ATG start, is flanked by loxP sites. Unexpectedly, we found that germline deletion of exon3 produces a hypomorphic allele due to the use of an alternative ATG start site located in exon 4, resulting in a minor Evi1 N-terminal truncation and a block in expression of the Mds1-Evi1 fusion transcript. Evi1(δex3/δex3) mutant embryos showed only a mild non-lethal hematopoietic phenotype and bone marrow failure was only observed in adult Vav-iCre/+, Evi1(fl3/fl3) mice in which exon 3 was specifically deleted in the hematopoietic system. Evi1(δex3/δex3) knockout pups are born in normal numbers but die during the perinatal period from congenital heart defects. Database searches identified 143 genes with similar mutant heart phenotypes as those observed in Evi1(δex3/δex3) mutant pups. Interestingly, 42 of these congenital heart defect genes contain known Evi1-binding sites, and expression of 18 of these genes are also effected by Evi1 siRNA knockdown. These results show a potential functional involvement of Evi1 target genes in heart development and indicate that Evi1 is part of a transcriptional program that regulates cardiac development in addition to the development of blood.
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| 14. |
- Curtis, Bruce A., et al.
(author)
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Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
- 2012
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 492:7427, s. 59-65
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Journal article (peer-reviewed)abstract
- Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host-and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.
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| 15. |
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| 16. |
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| 17. |
- Joller, D, et al.
(author)
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Refined localization of the Escherichia coli F4ab/F4ac receptor locus on pig chromosome 13
- 2009
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In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 40:5, s. 749-752
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Journal article (peer-reviewed)abstract
- Diarrhoea in newborn and weaned pigs caused by enterotoxigenic Escherichia coli (ETEC) expressing F4 fimbriae leads to considerable losses in pig production. In this study, we refined the mapping of the receptor locus for ETEC F4ab/F4ac adhesion (F4bcR) by joint analysis of Nordic and Swiss data. A total of 236 pigs from a Nordic experimental herd, 331 pigs from a Swiss experimental herd and 143 pigs from the Swiss performing station were used for linkage analysis. Genotyping data of six known microsatellite markers, two newly developed markers (MUC4gt and HSA125gt) and an intronic SNP in MUC4 (MUC4-8227) were used to create the linkage map. The region for F4bcR was refined to the interval SW207-S0075 on pig chromosome 13. The most probable position of F4bcR was in the SW207-MUC4 region. The order of six markers was supported by physical mapping on the BAC fingerprint contig from the Wellcome Trust Sanger Institute. Thus, the region for F4bcR could be reduced from 26 to 14 Mb.
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| 18. |
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| 19. |
- Merbold, L., et al.
(author)
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Precipitation as driver of carbon fluxes in 11 African ecosystems
- 2009
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In: Biogeosciences. - 1726-4189. ; 6:6, s. 1027-1041
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Journal article (peer-reviewed)abstract
- This study reports carbon and water fluxes between the land surface and atmosphere in eleven different ecosystems types in Sub-Saharan Africa, as measured using eddy covariance (EC) technology in the first two years of the CarboAfrica network operation. The ecosystems for which data were available ranged in mean annual rainfall from 320 mm (Sudan) to 1150 mm (Republic of Congo) and include a spectrum of vegetation types (or land cover) (open savannas, woodlands, croplands and grasslands). Given the shortness of the record, the EC data were analysed across the network rather than longitudinally at sites, in order to understand the driving factors for ecosystem respiration and carbon assimilation, and to reveal the different water use strategies in these highly seasonal environments. Values for maximum net carbon assimilation rates (photosynthesis) ranged from -12.5 mu mol CO2 m(-2) s(-1) in a dry, open Millet cropland (C-4-plants) up to -48 mu mol CO2 m(-2) s(-1) for a tropical moist grassland. Maximum carbon assimilation rates were highly correlated with mean annual rainfall (r(2)=0.74). Maximum photosynthetic uptake rates (Fp(max)) were positively related to satellite-derived f(APAR). Ecosystem respiration was dependent on temperature at all sites, and was additionally dependent on soil water content at sites receiving less than 1000 mm of rain per year. All included ecosystems dominated by C-3-plants, showed a strong decrease in 30-min assimilation rates with increasing water vapour pressure deficit above 2.0 kPa.
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| 20. |
- Percival, Carl J., et al.
(author)
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Regional and global impacts of Criegee intermediates on atmospheric sulphuric acid concentrations and first steps of aerosol formation
- 2013
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In: Faraday discussions. - : Royal Society of Chemistry (RSC). - 1359-6640 .- 1364-5498. ; 165, s. 45-73
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Journal article (peer-reviewed)abstract
- Carbonyl oxides (Criegee intermediates), formed in the ozonolysis of alkenes, are key species in tropospheric oxidation of organic molecules and their decomposition provides a non-photolytic source of OH in the atmosphere (Johnson and Marston, Chem. Soc. Rev., 2008, 37, 699, Harrison et al., Sci. Total Environ., 2006, 360, 5, Gab et al., Nature, 1985, 316, 535, ref. 1-3). Recently it was shown that small Criegee intermediates, C.I.'s, react far more rapidly with SO2 than typically represented in tropospheric models, (Welz, Science, 2012, 335, 204, ref. 4) which suggested that carbonyl oxides could have a substantial influence on the atmospheric oxidation of SO2. Oxidation of SO2 is the main atmospheric source of sulphuric acid (H2SO4), which is a critical contributor to aerosol formation, although questions remain about the fundamental nucleation mechanism (Sipila et al., Science, 2010, 327, 1243, Metzger et al., Proc. Natl. Acad. Sci. U. S. A., 2010 107, 6646, Kirkby et al., Nature, 2011, 476, 429, ref. 5-7). Non-absorbing atmospheric aerosols, by scattering incoming solar radiation and acting as cloud condensation nuclei, have a cooling effect on climate (Intergovernmental Panel on Climate Change (IPCC), Climate Change 2007: The Physical Science Basis, Cambridge University Press, 2007, ref. 8). Here we explore the effect of the Criegees on atmospheric chemistry, and demonstrate that ozonolysis of alkenes via the reaction of Criegee intermediates potentially has a large impact on atmospheric sulphuric acid concentrations and consequently the first steps in aerosol production. Reactions of Criegee intermediates with SO2 will compete with and in places dominate over the reaction of OH with SO2 (the only other known gas-phase source of H2SO4) in many areas of the Earth's surface. In the case that the products of Criegee intermediate reactions predominantly result in H2SO4 formation, modelled particle nucleation rates can be substantially increased by the improved experimentally obtained estimates of the rate coefficients of Criegee intermediate reactions. Using both regional and global scale modelling, we show that this enhancement is likely to be highly variable spatially with local hot-spots in e. g. urban outflows. This conclusion is however contingent on a number of remaining uncertainties in Criegee intermediate chemistry.
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| 21. |
- Probert, James R., et al.
(author)
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Anthropogenic modifications to fire regimes in the wider Serengeti-Mara ecosystem
- 2019
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In: Global Change Biology. - : WILEY. - 1354-1013 .- 1365-2486. ; 25:10, s. 3406-3423
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Journal article (peer-reviewed)abstract
- Fire is a key driver in savannah systems and widely used as a land management tool. Intensifying human land uses are leading to rapid changes in the fire regimes, with consequences for ecosystem functioning and composition. We undertake a novel analysis describing spatial patterns in the fire regime of the Serengeti-Mara ecosystem, document multidecadal temporal changes and investigate the factors underlying these patterns. We used MODIS active fire and burned area products from 2001 to 2014 to identify individual fires; summarizing four characteristics for each detected fire: size, ignition date, time since last fire and radiative power. Using satellite imagery, we estimated the rate of change in the density of livestock bomas as a proxy for livestock density. We used these metrics to model drivers of variation in the four fire characteristics, as well as total number of fires and total area burned. Fires in the Serengeti-Mara show high spatial variability-with number of fires and ignition date mirroring mean annual precipitation. The short-term effect of rainfall decreases fire size and intensity but cumulative rainfall over several years leads to increased standing grass biomass and fuel loads, and, therefore, in larger and hotter fires. Our study reveals dramatic changes over time, with a reduction in total number of fires and total area burned, to the point where some areas now experience virtually no fire. We suggest that increasing livestock numbers are driving this decline, presumably by inhibiting fire spread. These temporal patterns are part of a global decline in total area burned, especially in savannahs, and we caution that ecosystem functioning may have been compromised. Land managers and policy formulators need to factor in rapid fire regime modifications to achieve management objectives and maintain the ecological function of savannah ecosystems.
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| 22. |
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| 23. |
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| 24. |
- Salas-Leiva, Dayana E., et al.
(author)
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Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist
- 2021
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Journal article (peer-reviewed)abstract
- Cells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.
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