| 1. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 2. |
- Curtis, Bruce A., et al.
(författare)
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Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 492:7427, s. 59-65
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Tidskriftsartikel (refereegranskat)abstract
- Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host-and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.
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| 3. |
- Hempel, Anders, et al.
(författare)
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Developmental perspectives on tutorial groups as projects groups
- 2001
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Ingår i: Studies of Groups and Change. Proceedings from a conference on group and social psychology, Lund University, May 2000. - 9163108992 ; , s. 112-124
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Konferensbidrag (refereegranskat)abstract
- A new system to categorize the content of group diaries is developed and tried out in 12 PBL groups. The theoretically derived and preformed main categories were Boundary manage¬ment, Transformational realms, Awareness of organizational contexts and temporal perspectives. After analysis it is concluded that it may be a more fruitful way to proceed through reading and analyzing the diaries as narratives, evaluating them a holistic perspec¬tive.
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| 4. |
- Zakhozhay, Olga, et al.
(författare)
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Radial Velocity Survey for Planets around Young stars (RVSPY) Target characterisation and high-cadence survey
- 2022
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 667
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Tidskriftsartikel (refereegranskat)abstract
- Context. The occurrence rate and period distribution of (giant) planets around young stars is still not as well constrained as for older main-sequence stars. This is mostly due to the intrinsic activity-related complications and the avoidance of young stars in many large planet search programmes. Yet, dynamical restructuring processes in planetary systems may last significantly longer than the actual planet formation phase and may well extend long into the debris disc phase, such that the planet populations around young stars may differ from those observed around main-sequence stars.Aims. We introduce our Radial Velocity Survey for Planets around Young stars (RVSPY), which is closely related to the NaCo-ISPY direct imaging survey, characterise our target stars, and search for substellar companions at orbital separations smaller than a few au from the host star.Methods. We used the FEROS spectrograph, mounted to the MPG/ESO 2.2 m telescope in Chile, to obtain high signal-to-noise spectra and time series of precise radial velocities (RVs) of 111 stars, most of which are surrounded by debris discs. Our target stars have spectral types between early F and late K, a median age of 400 Myr, and a median distance of 45 pc. During the initial reconnaissance phase of our survey, we determined stellar parameters and used high-cadence observations to characterise the intrinsic stellar activity, searched for hot companions with orbital periods of up to 10 days, and derived the detection thresholds for longer-period companions. In our analysis we, have included archival spectroscopic data, spectral energy distribution, and data for photometric time series from the TESS mission.Results. For all target stars we determined their basic stellar parameters and present the results of the high-cadence RV survey and activity characterisation. We have achieved a median single-measurement RV precision of 6 m s−1 and derived the short-term intrinsic RV scatter of our targets (median 23 m s−1), which is mostly caused by stellar activity and decays with an age from >100 m s−1 at <20 Myr to <20 m s−1 at >500 Myr. We analysed time series periodograms of the high-cadence RV data and the shape of the individual cross-correlation functions. We discovered six previously unknown close companions with orbital periods between 10 and 100 days, three of which are low-mass stars, and three are in the brown dwarf mass regime. We detected no hot companion with an orbital period <10 days down to a median mass limit of ~1 MJup for stars younger than 500 Myr, which is still compatible with the established occurrence rate of such companions around main-sequence stars. We found significant RV periodicities between 1.3 and 4.5 days for 14 stars, which are, however, all caused by rotational modulation due to starspots. We also analysed the data for TESS photometric time series and found significant periodicities for most of the stars. For 11 stars, the photometric periods are also clearly detected in the RV data. We also derived stellar rotation periods ranging from 1 to 10 days for 91 stars, mostly from the TESS data. From the intrinsic activity-related short-term RV jitter, we derived the expected mass-detection thresholds for longer-period companions, and selected 84 targets for the longer-term RV monitoring.
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| 5. |
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| 6. |
- Caruso, Tancredi, et al.
(författare)
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Assessing soil ecosystem processes – biodiversity relationships in a nature reserve in Central Europe
- 2018
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Ingår i: Plant and Soil. - : Springer Science and Business Media LLC. - 0032-079X .- 1573-5036. ; 424:1-2, s. 491-501
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Tidskriftsartikel (refereegranskat)abstract
- Background and aims: Plant diversity – ecosystem processes relationships are essential to our understanding of ecosystem functioning. We aimed at disentangling the nature of such relationships in a mesotrophic grassland that was highly heterogeneous with regards to nutrient availability. Methods: Rather than targeting primary productivity, like most existing reports do, we focused our study on belowground ecosystem processes. We tested three, largely mutually exclusive, hypotheses of ecosystem processes relationships: the redundancy hypothesis, the insurance hypothesis and the centrifugal model hypothesis. We sampled the grassland twice within a single plant growing season in a spatially explicit way and assayed the soil for nitrification, urease activity, relative bacterial activity and a microbial community profile based on respiration while we simultaneously assessed plant diversity. Results: Results supported the centrifugal model. We justify the lack of support for the other two hypotheses on the basis of having conducted an observational study in an environmentally heterogeneous site. Conclusions: The centrifugal model hypothesis appears to be a very good predictive model for explaining diversity in observational, heterogeneous studies. The specific study represents one of the few observational studies that consider measures of ecosystem functioning other than primary productivity.
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| 7. |
- Fischer, Tobias, et al.
(författare)
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Core collapse supernovae in the QCD phase diagram
- 2012
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Ingår i: Physics of Atomic Nuclei. - 1063-7788 .- 1562-692X. ; 75:5, s. 613-620
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Tidskriftsartikel (refereegranskat)abstract
- We compare two classes of hybrid equations of state with a hadron-to-quark matter phase transition in their application to core collapse supernova simulations. The first one uses the quark bag model and describes the transition to three-flavor quark matter at low critical densities. The second one employs a Polyakov-loop extended Nambu-Jona-Lasinio (PNJL) model with parameters describing a phase transition to two-flavor quark matter at higher critical densities. These models possess a distinctly different temperature dependence of their transition densities which turns out to be crucial for the possible appearance of quark matter in supernova cores. During the early post-bounce accretion phase quark matter is found only if the phase transition takes place at sufficiently low densities as in the study based on the bag model. The increase critical density with increasing temperature, as obtained for our PNJL parametrization, prevents the formation of quark matter. The further evolution of the core collapse supernova as obtained applying the quark bag model leads to a structural reconfiguration of the central protoneutron star where, in addition to a massive pure quark matter core, a strong hydrodynamic shock wave forms and a second neutrino burst is released during the shock propagation across the neutrinospheres. We discuss the severe constraints in the freedom of choice of quark matter models and their parametrization due to the recently observed 2M ⊙ pulsar and their implications for further studies of core collapse supernovae in the QCD phase diagram.
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| 8. |
- Granström, Kjell, et al.
(författare)
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Smågruppsprocesser
- 1999
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Bok (refereegranskat)abstract
- Innehåll: Fångad i gruppen : om gruppen som socialt system / Gunnel Colnerud. The rise and decline of groups / Stefan Jern & Anders Hempel. Om konstruktiva och destruktiva krafter i grupper : eller har ni sett katten som inte har någon svans / Gunilla Guvå Irrationella fenomen i grupper / Anders Hempel. Destruktivt grupptänkande (groupthink) : i teori pch praktik / Michael Rosander & Kjell Granström
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| 9. |
- Hempel, Tim, et al.
(författare)
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Molecular mechanism of inhibiting the SARS-CoV-2 cell entry facilitator TMPRSS2 with camostat and nafamostat
- 2021
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Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6539 .- 2041-6520. ; 12:3, s. 983-992
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Tidskriftsartikel (refereegranskat)abstract
- The entry of the coronavirus SARS-CoV-2 into human lung cells can be inhibited by the approved drugs camostat and nafamostat. Here we elucidate the molecular mechanism of these drugs by combining experiments and simulations. In vitro assays confirm that both drugs inhibit the human protein TMPRSS2, a SARS-Cov-2 spike protein activator. As no experimental structure is available, we provide a model of the TMPRSS2 equilibrium structure and its fluctuations by relaxing an initial homology structure with extensive 330 microseconds of all-atom molecular dynamics (MD) and Markov modeling. Through Markov modeling, we describe the binding process of both drugs and a metabolic product of camostat (GBPA) to TMPRSS2, reaching a Michaelis complex (MC) state, which precedes the formation of a long-lived covalent inhibitory state. We find that nafamostat has a higher MC population than camostat and GBPA, suggesting that nafamostat is more readily available to form the stable covalent enzyme-substrate intermediate, effectively explaining its high potency. This model is backed by our in vitro experiments and consistent with previous virus cell entry assays. Our TMPRSS2-drug structures are made public to guide the design of more potent and specific inhibitors.
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| 10. |
- Hoffmann, Markus, et al.
(författare)
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Camostat mesylate inhibits SARS-CoV-2 activation by TMPRSS2-related proteases and its metabolite GBPA exerts antiviral activity
- 2021
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Ingår i: EBioMedicine. - : Elsevier BV. - 2352-3964. ; 65
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Tidskriftsartikel (refereegranskat)abstract
- Background: Antivirals are needed to combat the COVID-19 pandemic, which is caused by SARS-CoV-2. The clinically-proven protease inhibitor Camostat mesylate inhibits SARS-CoV-2 infection by blocking the virus-activating host cell protease TMPRSS2. However, antiviral activity of Camostat mesylate metabolites and potential viral resistance have not been analyzed. Moreover, antiviral activity of Camostat mesylate in human lung tissue remains to be demonstrated. Methods: We used recombinant TMPRSS2, reporter particles bearing the spike protein of SARS-CoV-2 or authentic SARS-CoV-2 to assess inhibition of TMPRSS2 and viral entry, respectively, by Camostat mesylate and its metabolite GBPA. Findings: We show that several TMPRSS2-related proteases activate SARS-CoV-2 and that two, TMPRSS11D and TMPRSS13, are robustly expressed in the upper respiratory tract. However, entry mediated by these proteases was blocked by Camostat mesylate. The Camostat metabolite GBPA inhibited recombinant TMPRSS2 with reduced efficiency as compared to Camostat mesylate. In contrast, both inhibitors exhibited similar antiviral activity and this correlated with the rapid conversion of Camostat mesylate into GBPA in the presence of serum. Finally, Camostat mesylate and GBPA blocked SARS-CoV-2 spread in human lung tissue ex vivo and the related protease inhibitor Nafamostat mesylate exerted augmented antiviral activity. Interpretation: Our results suggest that SARS-CoV-2 can use TMPRSS2 and closely related proteases for spread in the upper respiratory tract and that spread in the human lung can be blocked by Camostat mesylate and its metabolite GBPA. Funding: NIH, Damon Runyon Foundation, ACS, NYCT, DFG, EU, Berlin Mathematics center MATH+, BMBF, Lower Saxony, Lundbeck Foundation, Novo Nordisk Foundation.
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| 11. |
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| 12. |
- Jern, Stefan, et al.
(författare)
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Gruppdagbok i forskning och praktik : en metod för gruppstudier
- 2002
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This paper describes a new method for collection of group data called Group Diary. Document studies in psychology are presented as a background to the new method, which was developed in the educational setting of Problem Based Learning. Examples of related research methods in organisational and gender psychology form a setting for the introduction to the procedures of the Group Diary. This is based on the idea that group members themselves collect data acting as recorders and subsequently discuss and synthesise the notes. Data are supplied in the form of results of this work - reports - and the notes taken by the recorders. The method is presented as a tool for learning, research and consultation. Furthermore methodological issues such as the degree of control and supervision required in data collection, the relation between individual and collective diaries, the diary as product and process, analysis and data processing are elucidated. The pros and cons of the Group Diary in research, the epistemology of the method, ethics and the precision and quality of data are critically discussed, after presentation of five studies, done by the authors, on group formation and development. The method is considered a valid and economical alternative to traditional observation methods, especially for studies that require collection of data over time as in e.g. research on group development. Finally, future measures for validation of the method are pointed out.
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| 13. |
- Jern, Stefan, et al.
(författare)
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Gruppdagbok i forskning och praktik – en metod för gruppstudier
- 2002
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- A new method for collection of group data is described— Group Diary. Document studies in psychology are a background. Group members collect data as recorders and synthesize their notes. The method is a tool for learning, research and consultation. Methodological issues are elucidated. After presentation of five studies on group formation and development done by the authors, the pros and cons of the method in research, epistemology, ethics, precision and quality of data are critically discussed. The method is a valid alternative to traditional observation, especially for studies that require collection of data over time. Future measures for validation are pointed out.
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| 14. |
- Jern, Stefan, et al.
(författare)
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PBL-grupper som grupper: gruppdynamiken en förbisedd faktor?
- 2001
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This paper questions assumptions about the importance of group processes for the learning outcome in PBL groups. It is argued that previous research has downplayed the occurrence and importance of such processes. Through an empirical study with collective Group Diaries in 12 PBL group of approx. 70 students over one term., the occurrence of 67 hindering incidents is demonstrated. The most frequent were: leadership problems, conflict avoidance, task indistinctness and influence of disturbing contextual factors. The implications for future research and praxis are discussed.
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| 15. |
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| 16. |
- Jern, Stefan, et al.
(författare)
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Rollernas roll i grupparbete
- 2020
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Ingår i: Handbok för grupparbete – att skapa fungerande grupparbeten i undervisning. - 9789144132556 ; , s. 159-184
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Bokkapitel (refereegranskat)abstract
- Types and functions of roles in work groups are presented in overview followed by a discussion of relations between roles, personality and team roles. Role conflicts, role stress and problems in roles are discussed and advice is given on how to apply small group role theory to group work in higher education and the chapter ends with suggestions for exercises and a few role related instruments.
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| 17. |
- Jern, Stefan, et al.
(författare)
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Slump, sammanträffanden och spår: Om en lärares inflytande
- 2007
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Ingår i: Det enkla är det sköna - en vänbok till Kjell Granström. - 0284-1266. - 9789185831289 ; 53, s. 343-356
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Bokkapitel (refereegranskat)abstract
- The paper describes the influence exercised by professor Kjell Granström in the teaching of psychology. Among pedagogical inventions inspired by Granström are to be found training in small group obesrvation in a laboratory format the use of group diaries, training in consultation. The importance of a close connection between research and teaching is discussed.
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| 18. |
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| 19. |
- Jern, Stefan, et al.
(författare)
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Vid grupparbete spelar rollerna roll.
- 2005
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Ingår i: Handbok för grupparbete – att skapa fungerande grupparbeten i undervisning. - 9789144039442 ; , s. 93-120
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Bokkapitel (refereegranskat)abstract
- In group work roles play a role. (Swedish: Vid grupparbete spelar rollerna roll) In Handbook for group work – how to form functioning group work in education (Swedish: Handbok för grupparbete – att skapa fungerande grupparbeten i undervisning) Types and functions of roles in work groups are presented in overview followed by a discussion of relations between roles, personality and team roles. Role conflicts, role stress and problems in roles are discussed and advice is given on how to apply small group role theory to group work in higher education and the chapter ends with suggestions for exercises and a few role related instruments.
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| 20. |
- Paeschke, Katrin, et al.
(författare)
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Telomerase recruitment by the telomere end binding protein-beta facilitates G-quadruplex DNA unfolding in ciliates.
- 2008
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Ingår i: Nature structural & molecular biology. - : Springer Science and Business Media LLC. - 1545-9985 .- 1545-9993. ; 15:6, s. 598-604
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Tidskriftsartikel (refereegranskat)abstract
- The telomeric G-overhangs of the ciliate Stylonychia lemnae fold into a G-quadruplex DNA structure in vivo. Telomeric G-quadruplex formation requires the presence of two telomere end binding proteins, TEBPalpha and TEBPbeta, and is regulated in a cell-cycle dependent manner. Unfolding of this structure in S phase is dependent on the phosphorylation of TEBPbeta. Here we show that TEBPbeta phosphorylation is necessary but not sufficient for a G-quadruplex unfolding rate compatible with telomere synthesis. The telomerase seems to be actively involved in telomeric G-quadruplex DNA structure unfolding in vivo. Significantly, the telomerase is recruited to telomeres by phosphorylated TEBPbeta, and hence telomerase recruitment is cell-cycle regulated through phosphorylation. These observations allow us to propose a model for the regulation of G-quadruplex unfolding and telomere synthesis during the cell cycle.
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| 21. |
- Park, Julien H., et al.
(författare)
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The motor system is exceptionally vulnerable to absence of the ubiquitously expressed superoxide dismutase-1
- 2023
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Ingår i: Brain Communications. - : Oxford University Press. - 2632-1297. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Superoxide dismutase-1 is a ubiquitously expressed antioxidant enzyme. Mutations in SOD1 can cause amyotrophic lateral sclerosis, probably via a toxic gain-of-function involving protein aggregation and prion-like mechanisms. Recently, homozygosity for loss-of-function mutations in SOD1 has been reported in patients presenting with infantile-onset motor neuron disease. We explored the bodily effects of superoxide dismutase-1 enzymatic deficiency in eight children homozygous for the p.C112Wfs∗11 truncating mutation. In addition to physical and imaging examinations, we collected blood, urine and skin fibroblast samples. We used a comprehensive panel of clinically established analyses to assess organ function and analysed oxidative stress markers, antioxidant compounds, and the characteristics of the mutant Superoxide dismutase-1. From around 8 months of age, all patients exhibited progressive signs of both upper and lower motor neuron dysfunction, cerebellar, brain stem, and frontal lobe atrophy and elevated plasma neurofilament concentration indicating ongoing axonal damage. The disease progression seemed to slow down over the following years. The p.C112Wfs∗11 gene product is unstable, rapidly degraded and no aggregates were found in fibroblast. Most laboratory tests indicated normal organ integrity and only a few modest deviations were found. The patients displayed anaemia with shortened survival of erythrocytes containing decreased levels of reduced glutathione. A variety of other antioxidants and oxidant damage markers were within normal range. In conclusion, non-neuronal organs in humans show a remarkable tolerance to absence of Superoxide dismutase-1 enzymatic activity. The study highlights the enigmatic specific vulnerability of the motor system to both gain-of-function mutations in SOD1 and loss of the enzyme as in the here depicted infantile superoxide dismutase-1 deficiency syndrome.
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| 22. |
- Ried, Janina S., et al.
(författare)
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A principal component meta-analysis on multiple anthropometric traits identifies novel loci for body shape
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Large consortia have revealed hundreds of genetic loci associated with anthropometric traits, one trait at a time. We examined whether genetic variants affect body shape as a composite phenotype that is represented by a combination of anthropometric traits. We developed an approach that calculates averaged PCs (AvPCs) representing body shape derived from six anthropometric traits (body mass index, height, weight, waist and hip circumference, waist-to-hip ratio). The first four AvPCs explain >99% of the variability, are heritable, and associate with cardiometabolic outcomes. We performed genome-wide association analyses for each body shape composite phenotype across 65 studies and meta-analysed summary statistics. We identify six novel loci: LEMD2 and CD47 for AvPC1, RPS6KA5/C14orf159 and GANAB for AvPC3, and ARL15 and ANP32 for AvPC4. Our findings highlight the value of using multiple traits to define complex phenotypes for discovery, which are not captured by single-trait analyses, and may shed light onto new pathways.
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