| 1. |
- Fristedt, Rikard, et al.
(author)
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Photosystem II protein 33, a protein conserved in the plastid lineage, is associated with the chloroplast thylakoid membrane and provides stability to photosystem II supercomplexes in Arabidopsis
- 2015
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In: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 167:2, s. 481-492
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Journal article (peer-reviewed)abstract
- Photosystem II (PSII) is a multiprotein complex that catalyzes the light-driven water-splitting reactions of oxygenic photosynthesis. Light absorption by PSII leads to the production of excited states and reactive oxygen species that can cause damage to this complex. Here, we describe Arabidopsis (Arabidopsis thaliana) At1g71500, which encodes a previously uncharacterized protein that is a PSII auxiliary core protein and hence is named PHOTOSYSTEM II PROTEIN33 (PSB33). We present evidence that PSB33 functions in the maintenance of PSII-light-harvesting complex II (LHCII) supercomplex organization. PSB33 encodes a protein with a chloroplast transit peptide and one transmembrane segment. In silico analysis of PSB33 revealed a light-harvesting complex-binding motif within the transmembrane segment and a large surface-exposed head domain. Biochemical analysis of PSII complexes further indicates that PSB33 is an integral membrane protein located in the vicinity of LHCII and the PSII CP43 reaction center protein. Phenotypic characterization of mutants lacking PSB33 revealed reduced amounts of PSII-LHCII supercomplexes, very low state transition, and a lower capacity for nonphotochemical quenching, leading to increased photosensitivity in the mutant plants under light stress. Taken together, these results suggest a role for PSB33 in regulating and optimizing photosynthesis in response to changing light levels.
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| 2. |
- Ameur, Adam, et al.
(author)
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SweGen : a whole-genome data resource of genetic variability in a cross-section of the Swedish population
- 2017
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In: European Journal of Human Genetics. - : NATURE PUBLISHING GROUP. - 1018-4813 .- 1476-5438. ; 25:11, s. 1253-1260
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Journal article (peer-reviewed)abstract
- Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.
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| 3. |
- Linder, Nina, et al.
(author)
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Deep learning for detecting tumour-infiltrating lymphocytes in testicular germ cell tumours
- 2019
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In: Journal of Clinical Pathology. - : BMJ Publishing Group Ltd. - 0021-9746 .- 1472-4146. ; 72:2, s. 157-164
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Journal article (peer-reviewed)abstract
- AIMS: To evaluate if a deep learning algorithm can be trained to identify tumour-infiltrating lymphocytes (TILs) in tissue samples of testicular germ cell tumours and to assess whether the TIL counts correlate with relapse status of the patient.METHODS: TILs were manually annotated in 259 tumour regions from 28 whole-slide images (WSIs) of H&E-stained tissue samples. A deep learning algorithm was trained on half of the regions and tested on the other half. The algorithm was further applied to larger areas of tumour WSIs from 89 patients and correlated with clinicopathological data.RESULTS: A correlation coefficient of 0.89 was achieved when comparing the algorithm with the manual TIL count in the test set of images in which TILs were present (n=47). In the WSI regions from the 89 patient samples, the median TIL density was 1009/mm2. In seminomas, none of the relapsed patients belonged to the highest TIL density tertile (>2011/mm2). TIL quantifications performed visually by three pathologists on the same tumours were not significantly associated with outcome. The average interobserver agreement between the pathologists when assigning a patient into TIL tertiles was 0.32 (Kappa test) compared with 0.35 between the algorithm and the experts, respectively. A higher TIL density was associated with a lower clinical tumour stage, seminoma histology and lack of lymphovascular invasion.CONCLUSIONS: Deep learning-based image analysis can be used for detecting TILs in testicular germ cell cancer more objectively and it has potential for use as a prognostic marker for disease relapse.
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| 4. |
- Törneke, Krister, et al.
(author)
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Vägledning för kommunal VA-planering : för hållbar VA-försörjning och god vattenstatus
- 2014
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Reports (other academic/artistic)abstract
- Klimatförändringar och översvämningar, ökade miljökrav och en åldrad infrastruktur innebär ökade krav på kommunernas vatten- och avloppsverksamhet. Utanför verksamhetsområdet riskerar bristfälliga små avloppsanläggningar att sprida smittoämnen och bidra till att vattenförekomster inte uppnår god status. Kommunerna står inför stora investeringar för att nå en hållbar VAförsörjning. En strategisk och långsiktig VA-planering som omfattar både dricksvatten, spillvatten och dagvatten blir kommunens verktyg för att lyfta fram problem och prioritera åtgärder för att kostnadseffektivt möta de utmaningar som man står inför. Vägledningen är framtagen för att underlätta kommunernas planering för en trygg och hållbar VA-försörjning. Den ger konkreta råd för att komma igång och föreslår en stegvis planeringsprocess. Arbetssättet bygger på att börja med det som är tillgängligt, identifiera de strategiska frågorna och göra vägval inför den fortsatta planeringen. Vägledningen beskriver de olika stegen i planeringsprocessen och vilka styrdokument den bör omfatta. VA-planeringen bör initieras med ett tydligt uppdrag till en förvaltningsövergripande arbetsgrupp med tillräckliga resurser (steg 1). Steg 2 är att utarbeta en VA-översikt som beskriver omvärldsfaktorer, nuläge, förutsättningar och framtida behov. Steg 3 är att beskriva strategiska vägval för hantering av olika frågor, som fastställs i en VA-policy. Själva VAplanen (steg 4) tas fram utifrån VA-översikten och VA-policyn och innehåller en plan för såväl den allmänna anläggningen som för VA-försörjningen utanför verksamhetsområdet. VA-planen tillämpas sedan genom att åtgärderna förs in i kommunens löpande budgetprocess. Arbetet enligt VA-planen följs sedan upp regelbundet och planen revideras lämpligen varje mandatperiod (steg 5). En förutsättning för en lyckad VA-planering är att det finns en god kommunikation mellan politiker och tjänstemän från olika enheter inom kommunen. Det finns också ett stort värde i att samverka med länsstyrelser och grannkommuner för att utbyta erfarenheter. En väl genomförd VA-planering ger en beredskap och gör kommunen betydligt bättre rustad för att möta utmaningarna på VA-området och möjlighet att påverka utvecklingen i positiv riktning.
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| 5. |
- Ursby, Thomas, et al.
(author)
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BioMAX the first macromolecular crystallography beamline at MAX IV Laboratory
- 2020
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In: Journal of Synchrotron Radiation. - Chichester : Wiley-Blackwell. - 0909-0495 .- 1600-5775. ; 27, s. 1415-1429
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Journal article (peer-reviewed)abstract
- BioMAX is the first macromolecular crystallography beamline at the MAX IV Laboratory 3 GeV storage ring, which is the first operational multi-bend achromat storage ring. Due to the low-emittance storage ring, BioMAX has a parallel, high-intensity X-ray beam, even when focused down to 20 μm × 5 μm using the bendable focusing mirrors. The beam is tunable in the energy range 5-25 keV using the in-vacuum undulator and the horizontally deflecting double-crystal monochromator. BioMAX is equipped with an MD3 diffractometer, an ISARA high-capacity sample changer and an EIGER 16M hybrid pixel detector. Data collection at BioMAX is controlled using the newly developed MXCuBE3 graphical user interface, and sample tracking is handled by ISPyB. The computing infrastructure includes data storage and processing both at MAX IV and the Lund University supercomputing center LUNARC. With state-of-the-art instrumentation, a high degree of automation, a user-friendly control system interface and remote operation, BioMAX provides an excellent facility for most macromolecular crystallography experiments. Serial crystallography using either a high-viscosity extruder injector or the MD3 as a fixed-target scanner is already implemented. The serial crystallography activities at MAX IV Laboratory will be further developed at the microfocus beamline MicroMAX, when it comes into operation in 2022. MicroMAX will have a 1 μm × 1 μm beam focus and a flux up to 1015 photons s with main applications in serial crystallography, room-temperature structure determinations and time-resolved experiments.
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| 6. |
- Allen-Perkins, Alfonso, et al.
(author)
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CropPol : a dynamic, open and global database on crop pollination
- 2022
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In: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 103:3
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Journal article (peer-reviewed)abstract
- Seventy five percent of the world's food crops benefit from insect pollination. Hence, there has been increased interest in how global change drivers impact this critical ecosystem service. Because standardized data on crop pollination are rarely available, we are limited in our capacity to understand the variation in pollination benefits to crop yield, as well as to anticipate changes in this service, develop predictions, and inform management actions. Here, we present CropPol, a dynamic, open and global database on crop pollination. It contains measurements recorded from 202 crop studies, covering 3,394 field observations, 2,552 yield measurements (i.e. berry weight, number of fruits and kg per hectare, among others), and 47,752 insect records from 48 commercial crops distributed around the globe. CropPol comprises 32 of the 87 leading global crops and commodities that are pollinator dependent. Malus domestica is the most represented crop (32 studies), followed by Brassica napus (22 studies), Vaccinium corymbosum (13 studies), and Citrullus lanatus (12 studies). The most abundant pollinator guilds recorded are honey bees (34.22% counts), bumblebees (19.19%), flies other than Syrphidae and Bombyliidae (13.18%), other wild bees (13.13%), beetles (10.97%), Syrphidae (4.87%), and Bombyliidae (0.05%). Locations comprise 34 countries distributed among Europe (76 studies), Northern America (60), Latin America and the Caribbean (29), Asia (20), Oceania (10), and Africa (7). Sampling spans three decades and is concentrated on 2001-05 (21 studies), 2006-10 (40), 2011-15 (88), and 2016-20 (50). This is the most comprehensive open global data set on measurements of crop flower visitors, crop pollinators and pollination to date, and we encourage researchers to add more datasets to this database in the future. This data set is released for non-commercial use only. Credits should be given to this paper (i.e., proper citation), and the products generated with this database should be shared under the same license terms (CC BY-NC-SA). This article is protected by copyright. All rights reserved.
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| 7. |
- Andersson, Anton, et al.
(author)
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Design of a Foiling Optimist
- 2018
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In: Journal of Sailboat Technology. ; 2018, s. 1-24
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Journal article (peer-reviewed)abstract
- Because of the successful application of hydrofoils on the America's Cup catamarans in the past two campaigns the interest in foiling sailing craft has boosted. Foils have been fitted to a large number of yachts with great success, ranging from dinghies to ocean racers. An interesting question is whether one of the slowest racing boats in the world, the Optimist dinghy, can foil, and if so, at what minimum wind speed. The present paper presents a comprehensive design campaign to answer the two questions. The campaign includes a newly developed Velocity Prediction Program (VPP) for foiling/non-foiling conditions, a wind tunnel test of sail aerodynamics, a towing tank test of hull hydrodynamics and a large number of numerical predictions of foil characteristics. An optimum foil configuration is developed and towing tank tested with satisfactory results. The final proof of the concept is a successful on the water test with stable foiling at a speed of 12 knots.
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| 8. |
- Austin, Christine, et al.
(author)
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Elemental Dynamics in Hair Accurately Predict Future Autism Spectrum Disorder Diagnosis : An International Multi-Center Study
- 2022
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In: Journal of Clinical Medicine. - : MDPI. - 2077-0383. ; 11:23
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Journal article (peer-reviewed)abstract
- Autism spectrum disorder (ASD) is a neurodevelopmental condition diagnosed in approximately 2% of children. Reliance on the emergence of clinically observable behavioral patterns only delays the mean age of diagnosis to approximately 4 years. However, neural pathways critical to language and social functions develop during infancy, and current diagnostic protocols miss the age when therapy would be most effective. We developed non-invasive ASD biomarkers using mass spectrometry analyses of elemental metabolism in single hair strands, coupled with machine learning. We undertook a national prospective study in Japan, where hair samples were collected at 1 month and clinical diagnosis was undertaken at 4 years. Next, we analyzed a national sample of Swedish twins and, in our third study, participants from a specialist ASD center in the US. In a blinded analysis, a predictive algorithm detected ASD risk as early as 1 month with 96.4% sensitivity, 75.4% specificity, and 81.4% accuracy (n = 486; 175 cases). These findings emphasize that the dynamics in elemental metabolism are systemically dysregulated in autism, and these signatures can be detected and leveraged in hair samples to predict the emergence of ASD as early as 1 month of age.
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| 9. |
- Bengtsson, Staffan, et al.
(author)
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Brandskyddsteknisk projektering
- 2005
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In: Brandskyddshandboken - En handbok för projektering av brandskydd i byggnader. - 1402-3504. ; , s. 21-49
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Book chapter (other academic/artistic)
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| 10. |
- Bestas, Burcu, et al.
(author)
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Splice-correcting oligonucleotides restore BTK function in X-linked agammaglobulinemia model
- 2014
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In: Journal of Clinical Investigation. - 0021-9738 .- 1558-8238. ; 124:9, s. 4067-4081
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Journal article (peer-reviewed)abstract
- X-linked agammaglobulinemia (XLA) is an inherited immunodeficiency that results from mutations within the gene encoding Bruton's tyrosine kinase (BTK). Many XLA-associated mutations affect splicing of BTK pre-mRNA and severely impair B cell development. Here, we assessed the potential of antisense, splice-correcting oligonucleotides (SCOs) targeting mutated BTKtranscripts for treating XLA. Both the SCO structural design and chemical properties were optimized using 2'-O-methyl, locked nucleic acid, or phosphorodiamidate morpholino backbones. In order to have access to an animal model of XLA, we engineered a transgenic mouse that harbors a BAC with an authentic, mutated, splice-defective human BTK gene. BTK transgenic mice were bred onto a Btk knockout background to avoid interference of the orthologous mouse protein. Using this model, we determined that BTK-specific SCOs are able to correct aberrantly spliced BTK in B lymphocytes, including pro-B cells. Correction of BTK mRNA restored expression of functional protein, as shown both by enhanced lymphocyte survival and reestablished BTK activation upon B cell receptor stimulation. Furthermore, SCO treatment corrected splicing and restored BTK expression in primary cells from patients with XLA. Together, our data demonstrate that SCOs can restore BTK function and that BTK-targeting SCOs have potential as personalized medicine in patients with XLA.
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