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- Baranasic, D, et al.
(författare)
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Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements
- 2022
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 54:7, s. 1037-
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Tidskriftsartikel (refereegranskat)abstract
- Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
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- Finegan, Donal P., et al.
(författare)
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Spatial dynamics of lithiation and lithium plating during high-rate operation of graphite electrodes
- 2020
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Ingår i: Energy and Environmental Science. - : Royal Society of Chemistry (RSC). - 1754-5692 .- 1754-5706. ; 13:8, s. 2570-2584
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Tidskriftsartikel (refereegranskat)abstract
- The principal inhibitor of fast charging lithium ion cells is the graphite negative electrode, where favorable conditions for lithium plating occur at high charge rates, causing accelerated degradation and safety concerns. The local response of graphite, both at the electrode and particle level, when exposed to fast charging conditions of around 6C is not well understood. Consequently, the conditions that lead to the onset of lithium plating, as well as the local dynamics of lithium plating and stripping, have also remained elusive. Here, we use high-speed (100 Hz) pencil-beam X-ray diffraction to repeatedly raster along the depth of a 101 µm thick graphite electrode in 3 µm steps during fast (up to 6C) charge and discharge conditions. Consecutive depth profiles from separator to current collector were each captured in 0.5 seconds, giving an unprecedented spatial and temporal description of the state of the electrode and graphite's staging dynamics during high rate conditions. The electrode is preferentially activated near the separator, and the non-uniformity increases with rate and is influenced by free-energy barriers between graphite's lithiation stages. The onset of lithium plating and stripping was quantified, occurring only within the first 15 µm from the separator. The presence of lithium plating changed the behavior of the underlying graphite, such as causing co-existence of LiC6 and graphite in the fully discharged state. Finally, the staging behavior of graphite at different rates was quantified, revealing a high dependency on rate and drastic hysteresis between lithiation and delithiation.
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- Meyer, Esther, et al.
(författare)
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Mutations in the histone methyltransferase gene KMT2B cause complex early-onset dystonia.
- 2017
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 49, s. 223-237
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Tidskriftsartikel (refereegranskat)abstract
- Histone lysine methylation, mediated by mixed-lineage leukemia (MLL) proteins, is now known to be critical in the regulation of gene expression, genomic stability, cell cycle and nuclear architecture. Despite MLL proteins being postulated as essential for normal development, little is known about the specific functions of the different MLL lysine methyltransferases. Here we report heterozygous variants in the gene KMT2B (also known as MLL4) in 27 unrelated individuals with a complex progressive childhood-onset dystonia, often associated with a typical facial appearance and characteristic brain magnetic resonance imaging findings. Over time, the majority of affected individuals developed prominent cervical, cranial and laryngeal dystonia. Marked clinical benefit, including the restoration of independent ambulation in some cases, was observed following deep brain stimulation (DBS). These findings highlight a clinically recognizable and potentially treatable form of genetic dystonia, demonstrating the crucial role of KMT2B in the physiological control of voluntary movement.
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- Henriques, Dora, et al.
(författare)
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Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)
- 2018
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Ingår i: Evolutionary Applications. - : WILEY. - 1752-4571. ; 11:8, s. 1270-1282
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Tidskriftsartikel (refereegranskat)abstract
- The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In western Europe, one such threat is large-scale introductions of commercial strains (C-lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M-lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C-lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (F-ST=1) is introduced when the sample size is small (N10) and when sampling only captures a small fraction of a population's genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training data set to design four independent SNP assays selected from pairwise F-ST between the Iberian and C-lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid data sets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A.m.iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia and South America, in a time- and cost-effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations.
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- Shepherd, J. W., et al.
(författare)
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Molecular crowding in single eukaryotic cells: Using cell environment biosensing and single-molecule optical microscopy to probe dependence on extracellular ionic strength, local glucose conditions, and sensor copy number
- 2021
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Ingår i: Methods. - : Elsevier BV. - 1046-2023. ; 193, s. 54-61
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Tidskriftsartikel (refereegranskat)abstract
- The physical and chemical environment inside cells is of fundamental importance to all life but has traditionally been difficult to determine on a subcellular basis. Here we combine cutting-edge genomically integrated FRET biosensing to readout localized molecular crowding in single live yeast cells. Confocal microscopy allows us to build subcellular crowding heatmaps using ratiometric FRET, while whole-cell analysis demonstrates crowding is reduced when yeast is grown in elevated glucose concentrations. Simulations indicate that the cell membrane is largely inaccessible to these sensors and that cytosolic crowding is broadly uniform across each cell over a timescale of seconds. Millisecond single-molecule optical microscopy was used to track molecules and obtain brightness estimates that enabled calculation of crowding sensor copy numbers. The quantification of diffusing molecule trajectories paves the way for correlating subcellular processes and the physicochemical environment of cells under stress. © 2020 Elsevier Inc.
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