| 1. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 2. |
- Evangelou, Evangelos, et al.
(författare)
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Meta-analysis of genome-wide association studies confirms a susceptibility locus for knee osteoarthritis on chromosome 7q22
- 2011
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Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 1468-2060 .- 0003-4967. ; 70:2, s. 349-355
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Tidskriftsartikel (refereegranskat)abstract
- Objectives Osteoarthritis (OA) is the most prevalent form of arthritis and accounts for substantial morbidity and disability, particularly in older people. It is characterised by changes in joint structure, including degeneration of the articular cartilage, and its aetiology is multifactorial with a strong postulated genetic component. Methods A meta-analysis was performed of four genome-wide association (GWA) studies of 2371 cases of knee OA and 35 909 controls in Caucasian populations. Replication of the top hits was attempted with data from 10 additional replication datasets. Results With a cumulative sample size of 6709 cases and 44 439 controls, one genome-wide significant locus was identified on chromosome 7q22 for knee OA (rs4730250, p = 9.2 x 10(-9)), thereby confirming its role as a susceptibility locus for OA. Conclusion The associated signal is located within a large (500 kb) linkage disequilibrium block that contains six genes: PRKAR2B (protein kinase, cAMP-dependent, regulatory, type II, beta), HPB1 (HMG-box transcription factor 1), COG5 (component of oligomeric golgi complex 5), GPR22 (G protein-coupled receptor 22), DUS4L (dihydrouridine synthase 4-like) and BCAP29 (B cell receptor-associated protein 29). Gene expression analyses of the (six) genes in primary cells derived from different joint tissues confirmed expression of all the genes in the joint environment.
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| 3. |
- Barrenäs, Fredrik, et al.
(författare)
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Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control
- 2019
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Natural hosts of simian immunodeficiency virus (SIV) avoid AIDS despite lifelong infection. Here, we examined how this outcome is achieved by comparing a natural SIV host, African green monkey (AGM) to an AIDS susceptible species, rhesus macaque (RM). To asses gene expression profiles from acutely SIV infected AGMs and RMs, we developed a systems biology approach termed Conserved Gene Signature Analysis (CGSA), which compared RNA sequencing data from rectal AGM and RM tissues to various other species. We found that AGMs rapidly activate, and then maintain, evolutionarily conserved regenerative wound healing mechanisms in mucosal tissue. The wound healing protein fibronectin shows distinct tissue distribution and abundance kinetics in AGMs. Furthermore, AGM monocytes exhibit an embryonic development and repair/regeneration signature featuring TGF-beta and concomitant reduced expression of inflammatory genes compared to RMs. This regenerative wound healing process likely preserves mucosal integrity and prevents inflammatory insults that underlie immune exhaustion in RMs.
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| 4. |
- Dong, Yan, et al.
(författare)
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Atom Probe Tomography Interlaboratory Study on Clustering Analysis in Experimental Data Using the Maximum Separation Distance Approach
- 2019
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Ingår i: Microscopy and Microanalysis. - 1435-8115 .- 1431-9276. ; 25:2, s. 356-366
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Tidskriftsartikel (refereegranskat)abstract
- We summarize the findings from an interlaboratory study conducted between ten international research groups and investigate the use of the commonly used maximum separation distance and local concentration thresholding methods for solute clustering quantification. The study objectives are: to bring clarity to the range of applicability of the methods; identify existing and/or needed modifications; and interpretation of past published data. Participants collected experimental data from a proton-irradiated 304 stainless steel and analyzed Cu-rich and Ni-Si rich clusters. The datasets were also analyzed by one researcher to clarify variability originating from different operators. The Cu distribution fulfills the ideal requirements of the maximum separation method (MSM), namely a dilute matrix Cu concentration and concentrated Cu clusters. This enabled a relatively tight distribution of the cluster number density among the participants. By contrast, the group analysis of the Ni-Si rich clusters by the MSM was complicated by a high Ni matrix concentration and by the presence of Si-decorated dislocations, leading to larger variability among researchers. While local concentration filtering could, in principle, tighten the results, the cluster identification step inevitably maintained a high scatter. Recommendations regarding reporting, selection of analysis method, and expected variability when interpreting published data are discussed.
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| 5. |
- Gray, Howard W. I., et al.
(författare)
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Comparative biogeography and the evolution of population structure for bottlenose and common dolphins in the Indian Ocean
- 2021
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 48:7, s. 1654-1668
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Tidskriftsartikel (refereegranskat)abstract
- Aim: In the marine environment, where there are few physical boundaries to gene flow, there is often nevertheless intraspecific diversity with consequences for effective conservation and management. Here, we compare two closely related dolphin species with a shared distribution in the Indian Ocean (IO) to better understand the biogeographic drivers of their population structure.Location: Global oceans and seas with a focus on the Indian OceanTaxon: Tursiops sp. and Delphinus sp.Methods: Bayesian, ordination, assignment, statistical and phylogenetic analyses to assess phylogeography, connectivity and population structure using microsatellite and mitochondrial DNA genetic markers.Results: Both Tursiops sp. and Delphinus sp. showed population structure across the western IO and, in each case, populations in the Arabian Sea (off India, Pakistan and Oman) were most differentiated. Comparisons with other populations worldwide revealed independent lineages in this geographic region for both genera. For T. aduncus, (for which multiple sites within the IO could be compared), Bayesian modelling best supported a scenario of expansion southwards following a bottleneck event resulting in differentiation between the northern and western IO. For Delphinus, the same pattern is even more pronounced. Populations in the Arabian Sea region of the north-western IO show genetic isolation for each of the two genera, consistent with other studies of cetacean species in this region.Main conclusions: We propose that changes in the intensity of the southwest monsoon during the climate cycles of the Pleistocene could have affected regional patterns of productivity and represent an important biogeographic driver promoting the observed patterns of differentiation and population dynamics seen in our focal species. Patterns of population genetic structure are consistent with phenotypic differences, suggesting an influence from distinct habitats and resources, and emphasising the need for effective conservation measures in this geographic region.
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| 7. |
- Marquis, Emmanuelle A., et al.
(författare)
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On the use of density-based algorithms for the analysis of solute clustering in atom probe tomography data
- 2019
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Ingår i: Minerals, Metals and Materials Series. - Cham : Springer International Publishing. - 2367-1696 .- 2367-1181. ; Part F11, s. 2097-2113
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Konferensbidrag (refereegranskat)abstract
- Because atom probe tomography (APT) provides three-dimensional reconstructions of small volumes by resolving atomic chemical identities and positions, it is uniquely suited to analyze solute clustering phenomena in materials. A number of approaches have been developed to extract clustering information from the 3D reconstructed dataset, and numerous reports can be found applying these methods to a wide variety of materials questions. However, results from clustering analyses can differ significantly from one report to another, even when performed on similar microstructures, raising questions about the reliability of APT to quantitatively describe solute clustering. In addition, analysis details are often not provided, preventing independent confirmation of the results. With the number of APT research groups growing quickly, the APT community recognizes the need for educating new users about common methods and artefacts, and for developing analysis and data reporting protocols that address issues of reproducibility, errors, and variability. To this end, a round robin experiment was organized among ten different international institutions. The goal is to provide a consistent framework for the analysis of irradiated stainless steels using APT. Through the development of more reliable and reproducible data analysis and through communication, this project also aims to advance the understanding between irradiated microstructure and materials performance by providing more complete quantitative microstructural input for modeling. The results, methods, and findings of this round robin will also apply to other clustering phenomena studied using APT, beyond the theme of radiation damage.
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