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| 2. |
- 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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| 3. |
- Kupitz, Christopher, et al.
(författare)
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Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 513:7517, s. 261-265
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Tidskriftsartikel (refereegranskat)abstract
- Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.
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| 4. |
- Foster, James J., et al.
(författare)
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Polarisation vision : overcoming challenges of working with a property of light we barely see
- 2018
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Ingår i: Science of Nature. - : Springer Science and Business Media LLC. - 0028-1042 .- 1432-1904. ; 105:3-4
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Forskningsöversikt (refereegranskat)abstract
- In recent years, the study of polarisation vision in animals has seen numerous breakthroughs, not just in terms of what is known about the function of this sensory ability, but also in the experimental methods by which polarisation can be controlled, presented and measured. Once thought to be limited to only a few animal species, polarisation sensitivity is now known to be widespread across many taxonomic groups, and advances in experimental techniques are, in part, responsible for these discoveries. Nevertheless, its study remains challenging, perhaps because of our own poor sensitivity to the polarisation of light, but equally as a result of the slow spread of new practices and methodological innovations within the field. In this review, we introduce the most important steps in designing and calibrating polarised stimuli, within the broader context of areas of current research and the applications of new techniques to key questions. Our aim is to provide a constructive guide to help researchers, particularly those with no background in the physics of polarisation, to design robust experiments that are free from confounding factors.
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| 5. |
- 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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| 6. |
- 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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| 7. |
- Drerup, Christian, et al.
(författare)
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Dynamic visual noise has limited influence on the habitat selection and behavioural activity of crustaceans and cephalopods
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Ingår i: Ethology. - 0179-1613. ; 130:3
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Tidskriftsartikel (refereegranskat)abstract
- Environments contain various forms of noise that can interfere with the ability of animal sensory systems to perceive information. One ubiquitous type of visual noise in shallow aquatic habitats is caustic flicker (or caustics), consisting of dynamically moving light patterns caused by the refraction of light when passing through the water's rippling surface. While some teleost fish avoid environments with caustic noise (where their prey can be more difficult to detect), it remains untested whether caustics affect the habitat selection of invertebrates. In the present study, we ask whether three invertebrate species, the shore crab Carcinus maenas, the brown shrimp Crangon crangon, and the common cuttlefish Sepia officinalis, prefer or avoid associating with environments with caustic noise, and whether caustics affect their behavioural activity and habitat exploration. To do this, we exposed the three species in binary choice experiments to different simulated caustic noise levels varying in their temporal (speed) and spatial (definition) components. Neither of the three tested invertebrate species spent more or less time in environments with higher caustic noise levels. While we also found no evidence that caustics affected the behavioural activity and exploration of Ca. maenas and S. officinalis, the brown shrimp Cr. crangon reduced its activity with increasing spatial caustic noise. However, all obtained effect sizes in this study were small, suggesting that caustic noise only minimally affects invertebrate behaviour. Overall, our results show that, unlike in teleost fish, caustics have limited influence on the habitat selection, exploration, and activity of crustaceans and cephalopods.
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| 8. |
- Drerup, Christian, et al.
(författare)
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Visual noise from caustic flicker does not affect the hunting success of cuttlefish
- 2023
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Ingår i: Animal Behaviour. - 0003-3472. ; 202, s. 59-72
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Tidskriftsartikel (refereegranskat)abstract
- Many animals rely on their visual systems to detect, locate or discriminate information in their environment. Environmental ‘visual noise’, however, may interfere with an animal's ability to detect visual information, affecting decision-making processes. A ubiquitous form of visual noise in aquatic environments is caustic flicker: moving light patterns caused by the refraction of light through surface waves. While caustics impair the ability of fishes to detect prey, the impacts of caustics on the ability of nonvertebrates to target prey remains untested. In the present study, we asked whether the hunting success of the common cuttlefish, Sepia officinalis, is affected by the presence of caustic flicker. To do this, we tested whether both the spatial (definition) and temporal (speed) components of caustic flicker affected the ability of cuttlefish to detect and catch a common prey, the brown shrimp, Crangon crangon. Neither the spatial nor temporal components of caustic flicker affected the detection latency or the capture time of prey. Moreover, cuttlefish did not adapt their hunting behaviour, including their approach speed, movement bouts, attack distance or angle, as a function of caustic flicker. Our results show that visual noise from caustic flicker does not affect the ability of cuttlefish to hunt their prey or their hunting behaviour. We provide multiple explanations, including the role of polarization vision, for why dynamic illumination does not appear to impact the visual sensory processing of cuttlefish.
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| 9. |
- Venables, Siân Vincent, et al.
(författare)
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Polarization vision mitigates visual noise from flickering light underwater
- 2022
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:36
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Tidskriftsartikel (refereegranskat)abstract
- In shallow water, downwelling light is refracted from surface waves onto the substrate creating bands of light that fluctuate in both time and space, known as caustics. This dynamic illumination can be a visual hindrance for animals in shallow underwater environments. Animals in such habitats may have evolved to use polarization vision for discriminating objects while ignoring the variations in illumination caused by caustics. To explore this possibility, crabs (Carcinus maenas) and cuttlefish (Sepia officinalis), both of which have polarization vision, were presented with moving stimuli overlaid with caustics. Dynamic caustics inhibited the detection of an intensity-based stimulus but not when these stimuli were polarized. This study is the first to demonstrate that polarization vision reduces the negative impacts that dynamic illumination can have on visual perception.
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