| 1. |
- Gao, Hong, et al.
(författare)
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The landscape of tolerated genetic variation in humans and primates
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6648
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Tidskriftsartikel (refereegranskat)abstract
- Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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| 2. |
- Kuderna, Lukas F. K., et al.
(författare)
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A global catalog of whole-genome diversity from 233 primate species
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6648, s. 906-913
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Tidskriftsartikel (refereegranskat)abstract
- The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage wholegenome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
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| 3. |
- Kuderna, Lukas F. K., et al.
(författare)
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Identification of constrained sequence elements across 239 primate genomes
- 2024
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 625:7996, s. 735-742
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Tidskriftsartikel (refereegranskat)abstract
- Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3,4,5,6,7,8,9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
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| 4. |
- Andersson, Christian H., et al.
(författare)
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Mathematics curriculum discourses on democracy : Critical thinking in the age of digital traces
- 2022
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Ingår i: Proceeding of the twelfth Congress of the European Society for Research in Mathematics Education. - 9791221025378
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Konferensbidrag (refereegranskat)abstract
- The use of people’s online digital traces has given rise to concerns for democracy. The digital traces may affect the individual’s life in unexpected and negative ways. Such traces may also be of importance for understanding the spread of disinformation and the like. This paper reports on a Foucault inspired discourse analysis of the Swedish upper secondary mathematics curriculum. Two discourses are construed in the intersection of critical thinking, democracy, and this new technology. Skovsmose’s concept of mathemacy is used to identify what is critical knowledge and what is not. The first construed discourse is, “With knowledge in formal mathematics, critical thinking on democracy will follow.” The second is, “Rather a personal career than a critical citizenship.” Neither of the discourses promotes a need for mathematics education to change due to new technology with regards to critical thinking.
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| 5. |
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| 6. |
- de Wit, Cynthia A., et al.
(författare)
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Organohalogen compounds of emerging concern in Baltic Sea biota : Levels, biomagnification potential and comparisons with legacy contaminants
- 2020
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Ingår i: Environment International. - : Elsevier BV. - 0160-4120 .- 1873-6750. ; 144
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Tidskriftsartikel (refereegranskat)abstract
- While new chemicals have replaced major toxic legacy contaminants such as polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane (DDT), knowledge of their current levels and biomagnification potential in Baltic Sea biota is lacking. Therefore, a suite of chemicals of emerging concern, including organophosphate esters (OPEs), short-chain, medium-chain and long-chain chlorinated paraffins (SCCPs, MCCPs, LCCPs), halogenated flame retardants (HFRs), and per- and polyfluoroalkyl substances (PFAS), were analysed in blue mussel (Mytilus edulis), viviparous eelpout (Zoarces viviparus), Atlantic herring (Clupea harengus), grey seal (Halichoerus grypus), harbor seal (Phoca vitulina), harbor porpoise (Phocoena phocoena), common eider (Somateria mollissima), common guillemot (Uria aalge) and white-tailed eagle (Haliaeetus albicilla) from the Baltic Proper, sampled between 2006 and 2016. Results were benchmarked with existing data for legacy contaminants. The mean concentrations for Sigma OPEs ranged from 57 to 550 ng g(-1) lipid weight (lw), for Sigma CPs from 110 to 640 ng g(-1) lw for Sigma HFRs from 0.42 to 80 ng g(-1) lw, and for Sigma PFAS from 1.1 to 450 ng g(-1) wet weight. Perfluoro-4-ethyl-cyclohexanesulfonate (PFECHS) was detected in most species. Levels of OPEs, CPs and HFRs were generally similar or higher than those of polybrominated diphenyl ethers (PBDEs) and/or hexabromocyclododecane (HBCDD). OPE, CP and HFR concentrations were also similar to PCBs and DDTs in blue mussel, viviparous eelpout and Atlantic herring. In marine mammals and birds, PCB and DDT concentrations remained orders of magnitude higher than those of OPEs, CPs, HFRs and PFAS. Predator-prey ratios for individual OPEs (0.28-3.9) and CPs (0.40-5.0) were similar or somewhat lower than those seen for BDE-47 (5.0-29) and HBCDD (2.4-13). Ratios for individual HFRs (0.010-37) and PFAS (0.15-47) were, however, of the same order of magnitude as seen for p,p'-DDE (4.7-66) and CB-153 (31-190), indicating biomagnification potential for many of the emerging contaminants. Lack of toxicity data, including for complex mixtures, makes it difficult to assess the risks emerging contaminants pose. Their occurence and biomagnification potential should trigger risk management measures, particularly for MCCPs, HFRs and PFAS.
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| 7. |
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| 8. |
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| 9. |
- Jensen, Axel, et al.
(författare)
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Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation
- 2023
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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 40:12
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.
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| 10. |
- Olsson, Sylvia, Phd student in social work, 1972-
(författare)
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Longing to belong : deaf and hard of hearing young adults’ social interaction, social relationships, and identity
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis gives an insight about the impact of hearing loss on young adults as they function in daily life. Young adults with hearing loss included in the thesis can convey a very central perspective that can have an impact on a change in interventions and treatment in school life, working life and even in their leisure time. The overall aim of the thesis is to study the living conditions and life experiences of young men and women who are deaf or hard of hearing (DHH). Despite the increased proportion of people with hearing loss, there still seem to be challenges in the face of inclusive environments for people with hearing loss. This thesis hopes to shed some light on the experiences of people with hearing loss and also to explain the link between hearing loss, social inclusion and social exclusion.The thesis is based on four different sub-studies. In Studies I and IV, a survey study with material collected from the web-based survey Liv och Hälsa Ung (Life and Health of Young People) was used. Pupils attending grades 7 and 9 in compulsory schools and year 2 in upper-secondary schools in all municipalities of the county of Örebro in Sweden. Life and Health of Young People survey examines young people's living conditions, lifestyles and health. The results of Study I showed that people with (DHH) experienced lower levels of well-being than those who had no disability. The results also showed that those who went to special school felt that they had more friends and were more socially included than those who went to mainstream schools. The results of Study IV showed that adolescents without disabilities rate their well-being higher, have lower mental ill-health and have fewer somatic problems than adolescents with DHH. The results also showed that boys rate their well-being, lower mental ill-health and somatic problems higher than girls. These patterns were the same regardless of whether the adolescents had a disability and regardless of their year in school.In Studies II and III, interviews were conducted with 16 participants (10 male, 6 female), aged 24 to 31 years, and all had severe-to-profound hearing loss. The results of that analysis in Study II showed that they longed to be included, to be accepted, to create an inclusive social environment, to find friends and partners, and to communicate effectively so that they could be understood. In other words, they desired to feel a sense of belonging. Study III showed that most HH people experience communication barriers in higher education, at work and in leisure time. These barriers lead to feelings of loneliness and make it difficult to achieve social inclusion. Another result in study III revealed how important technology is for social interactions and social relationships. The technology has helped reduce several barriers when it comes to communicating with others. Both Assistant Technology (AT) and Information and Communication Technology (ICT) are important tools for facilitate social interaction and maintaining social activities with friends and partner and creating inclusive arenas.
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