| 1. |
- Ade, Peter, et al.
(författare)
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The Simons Observatory : science goals and forecasts
- 2019
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Ingår i: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :2
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Tidskriftsartikel (refereegranskat)abstract
- The Simons Observatory (SO) is a new cosmic microwave background experiment being built on Cerro Toco in Chile, due to begin observations in the early 2020s. We describe the scientific goals of the experiment, motivate the design, and forecast its performance. SO will measure the temperature and polarization anisotropy of the cosmic microwave background in six frequency bands centered at: 27, 39, 93, 145, 225 and 280 GHz. The initial con figuration of SO will have three small-aperture 0.5-m telescopes and one large-aperture 6-m telescope, with a total of 60,000 cryogenic bolometers. Our key science goals are to characterize the primordial perturbations, measure the number of relativistic species and the mass of neutrinos, test for deviations from a cosmological constant, improve our understanding of galaxy evolution, and constrain the duration of reionization. The small aperture telescopes will target the largest angular scales observable from Chile, mapping approximate to 10% of the sky to a white noise level of 2 mu K-arcmin in combined 93 and 145 GHz bands, to measure the primordial tensor-to-scalar ratio, r, at a target level of sigma(r) = 0.003. The large aperture telescope will map approximate to 40% of the sky at arcminute angular resolution to an expected white noise level of 6 mu K-arcmin in combined 93 and 145 GHz bands, overlapping with the majority of the Large Synoptic Survey Telescope sky region and partially with the Dark Energy Spectroscopic Instrument. With up to an order of magnitude lower polarization noise than maps from the Planck satellite, the high-resolution sky maps will constrain cosmological parameters derived from the damping tail, gravitational lensing of the microwave background, the primordial bispectrum, and the thermal and kinematic Sunyaev-Zel'dovich effects, and will aid in delensing the large-angle polarization signal to measure the tensor-to-scalar ratio. The survey will also provide a legacy catalog of 16,000 galaxy clusters and more than 20,000 extragalactic sources.
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| 2. |
- Aitomäki, Yvonne, et al.
(författare)
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Light scattering in cellulose nanofibre suspensions : Model and experiments
- 2016
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Ingår i: Computers in Chemistry Proceeding from ACS National Meeting San Diego. - : American Chemical Society (ACS). ; , s. 122-
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Here light scattering theory is used to assess the size distribution in a suspension of cellulose as it is fibrillated from micro-scaled to nano-scaled fibres. A model based on Monte carlo simulations of the scattering of photons by different sizes of cellulose fibres was used to predict the UV-IF spectrum of the suspensions. Bleached cellulose hardwood pulp was tested and compared to the visually transparent tempo-oxidised hardwood cellulose nanofibres (CNF) suspension. The theoretical results show that different diameter size classes exhibit very different scattering patterns. These classes could be identified in the experimental results and used to establish the size class dominating the suspension. A comparison to AFM/microscope size distribution was made and the results indicated that using the UV-IF light scattering spectrum maybe more reliable that size distribution measurement using AFM and microscopy on dried CNF samples. The UV-IF spectrum measurement combined with the theoretical prediction can be used even at this initial stage of development of this model to assess the degree of fibrillation when processing CNF.
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| 3. |
- Albaugh, Timothy J, et al.
(författare)
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Do biological expansion factors adequately estimate stand-scale aboveground component biomass for Norway spruce?
- 2009
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Ingår i: Forest Ecology and Management. - : Elsevier BV. - 0378-1127 .- 1872-7042. ; 258:12, s. 2628-2637
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Tidskriftsartikel (refereegranskat)abstract
- We developed site specific component (stem, branch, and foliage) biomass functions for two sites in Sweden (64° and 57° North latitude) where four treatments (control, irrigated, fertilized, irrigated plus fertilized) were applied in the existing Norway spruce stands (Picea abies L. Karst.) for 17 years. We tested for site effects in the component biomass equations and compared site specific biomass estimates to those generated using published functions ( Lehtonen et al., 2004 and Wirth et al., 2004). Site effects were significant for all components and indicated it would be unlikely to generate equations that well estimate biomass across the Norway spruce range as implicitly indicated in our efforts to generate species biomass expansion factors. We rejected our hypothesis that the published functions would well estimate component biomass for control plots. The published functions did not compare well with site specific component biomass estimates for the other treatments; both published functions well estimated stem mass up to stem mass of 25 Mg ha−1, beyond which stem mass was overestimated, and both functions over and under estimated foliage and branch mass. Nor did the published functions compare well with each other, with stem, foliage and branch mass estimate differences of 12, 55, −8% and 11, 77, and 59% for the southern and northern sites, respectively, when averaged over all treatments and years. Adding limiting resources through fertilization increased stem, foliage and branch mass 57, 11, 18% and 120, 37, and 69% at the southern and northern sites, respectively, which would increase carbon sequestration and available stemwood and bioenergy materials. We recommend that more effort is spent in process-based modeling to better predict mass at a given site and ultimately provide better estimates of carbon sequestration and bioenergy material production changes.
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| 4. |
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| 5. |
- Carlson, Johan, et al.
(författare)
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Projekt: SCOPE Norra
- 2011
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Annan publikation (populärvet., debatt m.m.)abstract
- SCOPE Norra är ett samarbetskonsortium för forskning och utveckling tillsammans med massa- och pappersindustrin i Norrbotten och Västerbotten. Projektet koordineras av centrumbildningen ProcessIT Innovations.Inom SCOPE Norra pågår ett flertal delprojekt, uppdelat på ett antal fokusområden.Huvudfinansiär för konsortiet är Tillväxtverket genom medel från EU:s strukturfonder.
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| 6. |
- Dalgard, Florence J., et al.
(författare)
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Itch and Mental Health in Dermatological Patients across Europe : A Cross-Sectional Study in 13 Countries
- 2020
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Ingår i: Journal of Investigative Dermatology. - : Elsevier BV. - 0022-202X. ; 140:3, s. 568-573
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Tidskriftsartikel (refereegranskat)abstract
- Itch is a highly prevalent and multidimensional symptom. We aimed to analyze the association between itch and mental health in dermatological patients. This multicenter study is observational and cross-sectional and was conducted in dermatological clinics across 13 European countries. A total of 3,530 patients and 1,094 healthy controls were included. Patients were examined clinically. Outcome measures were itch (presence, chronicity, and intensity), the Hospital Anxiety and Depression Scale, EQ-5D visual analogue scale, sociodemographics, suicidal ideation, and stress (negative life events and economic difficulties). Ethical approval was obtained. Results showed significant association between the presence of itch in patients and clinical depression (odds ratio, 1.53; 95% confidence interval, 1.15–2.02), suicidal ideation (odds ratio, 1.27; 95% confidence interval, 1.01–1.60), and economic difficulties (odds ratio, 1.24; 95% confidence interval, 1.10–1.50). The mean score of reported generic health status assessed by the EQ-5D visual analogue scale was 65.9 (standard deviation = 20.1) in patients with itch, compared with 74.7 (standard deviation = 18.0) in patients without itch (P < 0.001) and 74.9 (standard deviation = 15.7) in controls with itch compared with 82.9 (standard deviation = 15.6) in controls without itch (P < 0.001). Itch contributes substantially to the psychological disease burden in dermatological patients, and the management of patients should include access to multidisciplinary care.
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| 7. |
- Elmlund, Hans, et al.
(författare)
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Cryo-EM Reveals Promoter DNA Binding and Conformational Flexibility of the General Transcription Factor TFIID
- 2009
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 17:11, s. 1442-1452
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Tidskriftsartikel (refereegranskat)abstract
- The general transcription factor IID (TFIID) is required for initiation of RNA polymerase II-dependent transcription at many eukaryotic promoters. TFIID comprises the TATA-binding protein (TBP) and several conserved TBP-associated factors (TAFs). Recognition of the core promoter by TFIID assists assembly of the preinitiation complex. Using cryo-electron microscopy in combination with methods for ab initio single-particle reconstruction and heterogeneity analysis, we have produced density maps of two conformational states of Schizosaccharomyces pombe TFIID, containing and lacking TBP. We report that TBP-binding is coupled to a massive histone-fold domain rearrangement. Moreover, docking of the TBP-TAF1(N-terminus) atomic structure to the THID map and reconstruction of a TAF-promoter DNA complex helps to account for TAF-dependent regulation of promoter-TBP and promoter-TAF interactions.
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| 8. |
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| 9. |
- Hillarp, Andreas, et al.
(författare)
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Effects of the oral, direct factor Xa inhibitor rivaroxaban on commonly used coagulation assays
- 2011
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Ingår i: JOURNAL OF THROMBOSIS AND HAEMOSTASIS. - : Blackwell Publishing. - 1538-7933 .- 1538-7836. ; 9:1, s. 133-139
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Rivaroxaban is an oral direct factor Xa inhibitor developed for prophylaxis and treatment of thromboembolic disorders. Laboratory monitoring is not necessary but the dose-dependent effects on common reagents and assay procedures are largely unknown. Objectives: To investigate the effect of rivaroxaban on commonly used coagulation assays. Materials and Methods: Rivaroxaban was added to plasma from healthy subjects in the concentration range 0-1000 mu g L-1 and analyzed using different reagents for activated partial thromboplastin time (APTT), prothrombin time (PT), antithrombin, fibrinogen and activated protein C (APC) resistance assays. Results: At an expected peak concentration of rivaroxaban in clinical use, the APTTs were almost invariably prolonged but at lower concentrations the effect was weak. The concentration needed to double the APTT varied between 389 +/- 106 and 617 +/- 149 mu g L-1 for different reagents. The PT assays showed a marked degree of difference. In general, the Quick PT type assays were more sensitive compared with the Owren type PT assays. The results from antithrombin assays were dependent on the type of reagent, with the Xa-based assay being sensitive for rivaroxaban with an estimated increase of 0.09 IU mL-1 per 100 mu g L-1 rivaroxaban. There were only minor effects on fibrinogen assays based on thrombin reagents. The APTT-based assay for APC resistance is affected in a dose-dependent manner whereas an assay based on the activation of coagulation at the prothrombinase level was unaffected. Conclusions: Different assays, and even different reagents within an assay group, display variable effects by therapeutic concentrations of rivaroxaban.
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| 10. |
- Hofmann, Robin, et al.
(författare)
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Oxygen therapy in ST-elevation myocardial infarction.
- 2018
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Ingår i: European Heart Journal. - : Oxford University Press (OUP). - 0195-668X .- 1522-9645. ; 39:29, s. 2730-2739
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Tidskriftsartikel (refereegranskat)abstract
- Aims: To determine whether supplemental oxygen in patients with ST-elevation myocardial infarction (STEMI) impacts on procedure-related and clinical outcomes.Methods and results: The DETermination of the role of Oxygen in suspected Acute Myocardial Infarction (DETO2X-AMI) trial randomized patients with suspected myocardial infarction (MI) to receive oxygen at 6 L/min for 6-12 h or ambient air. In this pre-specified analysis, we included only STEMI patients who underwent percutaneous coronary intervention (PCI). In total, 2807 patients were included, 1361 assigned to receive oxygen, and 1446 assigned to ambient air. The pre-specified primary composite endpoint of all-cause death, rehospitalization with MI, cardiogenic shock, or stent thrombosis at 1 year occurred in 6.3% (86 of 1361) of patients allocated to oxygen compared to 7.5% (108 of 1446) allocated to ambient air [hazard ratio (HR) 0.85, 95% confidence interval (95% CI) 0.64-1.13; P = 0.27]. There was no difference in the rate of death from any cause (HR 0.86, 95% CI 0.61-1.22; P = 0.41), rate of rehospitalization for MI (HR 0.92, 95% CI 0.57-1.48; P = 0.73), rehospitalization for cardiogenic shock (HR 1.05, 95% CI 0.21-5.22; P = 0.95), or stent thrombosis (HR 1.27, 95% CI 0.46-3.51; P = 0.64). The primary composite endpoint was consistent across all subgroups, as well as at different time points, such as during hospital stay, at 30 days and the total duration of follow-up up to 1356 days.Conclusions: Routine use of supplemental oxygen in normoxemic patients with STEMI undergoing primary PCI did not significantly affect 1-year all-cause death, rehospitalization with MI, cardiogenic shock, or stent thrombosis.
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| 11. |
- Hofmann, Robin, et al.
(författare)
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Oxygen therapy in suspected acute myocardial infarction
- 2017
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Ingår i: New England Journal of Medicine. - : MASSACHUSETTS MEDICAL SOC. - 0028-4793 .- 1533-4406. ; 377:13, s. 1240-1249
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The clinical effect of routine oxygen therapy in patients with suspected acute myocardial infarction who do not have hypoxemia at baseline is uncertain. METHODS: In this registry-based randomized clinical trial, we used nationwide Swedish registries for patient enrollment and data collection. Patients with suspected myocardial infarction and an oxygen saturation of 90% or higher were randomly assigned to receive either supplemental oxygen (6 liters per minute for 6 to 12 hours, delivered through an open face mask) or ambient air. RESULTS: A total of 6629 patients were enrolled. The median duration of oxygen therapy was 11.6 hours, and the median oxygen saturation at the end of the treatment period was 99% among patients assigned to oxygen and 97% among patients assigned to ambient air. Hypoxemia developed in 62 patients (1.9%) in the oxygen group, as compared with 254 patients (7.7%) in the ambient-air group. The median of the highest troponin level during hospitalization was 946.5 ng per liter in the oxygen group and 983.0 ng per liter in the ambient-air group. The primary end point of death from any cause within 1 year after randomization occurred in 5.0% of patients (166 of 3311) assigned to oxygen and in 5.1% of patients (168 of 3318) assigned to ambient air (hazard ratio, 0.97; 95% confidence interval [CI], 0.79 to 1.21; P=0.80). Rehospitalization with myocardial infarction within 1 year occurred in 126 patients (3.8%) assigned to oxygen and in 111 patients (3.3%) assigned to ambient air (hazard ratio, 1.13; 95% CI, 0.88 to 1.46; P=0.33). The results were consistent across all predefined subgroups. CONCLUSIONS: Routine use of supplemental oxygen in patients with suspected myocardial infarction who did not have hypoxemia was not found to reduce 1-year all-cause mortality. (Funded by the Swedish Heart–Lung Foundation and others; DETO2X-AMI ClinicalTrials.gov number, NCT01787110.)
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| 12. |
- Jocher, Georg, et al.
(författare)
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Apparent Winter CO2 uptake by a boreal forest due to decoupling
- 2017
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Ingår i: Agricultural and Forest Meteorology. - : Elsevier BV. - 0168-1923 .- 1873-2240. ; 232, s. 23-34
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Tidskriftsartikel (refereegranskat)abstract
- Net uptake of carbon dioxide (CO2) was observed during the winter when using the eddy covariance (EC) technique above a 90-year-old Scots pine (Pinus sylvestris L.) stand in northern Sweden. This uptake occurred despite photosynthetic dormancy. This discrepancy led us to investigate the potential impact of decoupling of below- and above-canopy air mass flow and accompanying below-canopy horizontal advection on these measurements. We used the correlation of above- and below-canopy standard deviation of vertical wind speed (sigma(w)), derived from EC measurements above and below the canopy, as the main mixing criterion. We identified 0.33 m s(-1) and 0.06 m s(-1) as site-specific o thresholds for above and below canopy, respectively, to reach the fully coupled state. Decoupling was observed in 45% of all cases during the measurement period (5.11.2014-25.2.2015). After filtering out decoupled periods the above-canopy mean winter NEE shifted from -0.52 mu mol m(-2) s(-1) to a more reasonable positive value of 0.31 mu mol m(-2) s(-1). None of the above-canopy data filtering criteria we tested (i.e., friction velocity threshold; horizontal wind speed threshold; single-level sigma(w) threshold) ensured sufficient mixing. All missed critical periods that were detected only by the two-level filtering approach. Tower-surrounding topography induced a predominant below-canopy wind direction and consequent wind shear between above- and below-canopy air masses. These processes may foster decoupling and below-canopy removal of CO2 rich air. To determine how broadly such a topographical influence might apply, we compared the topography surrounding our tower to that surrounding other forest flux sites worldwide. Medians of maximum elevation differences within 300m and 1000 m around 110 FLUXNET forest EC towers were 24 m and 66 m, respectively, compared to 24 m and 114 m, respectively, at our site. Consequently, below canopy flow may influence above-canopy NEE detections at many forested EC sites. Based on our findings we suggest below-canopy measurements as standard procedure at sites evaluating forest CO2 budgets.
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| 13. |
- Jocher, Georg, et al.
(författare)
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Impact of Canopy Decoupling and Subcanopy Advection on the Annual Carbon Balance of a Boreal Scots Pine Forest as Derived From Eddy Covariance
- 2018
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Ingår i: Journal of Geophysical Research: Biogeosciences. - 2169-8953 .- 2169-8961. ; 123:2, s. 303-325
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Tidskriftsartikel (refereegranskat)abstract
- Apparent net uptake of carbon dioxide (CO 2 ) during wintertime by an ∼ 90 year old Scots pine stand in northern Sweden led us to conduct canopy decoupling and subcanopy advection investigations over an entire year. Eddy covariance (EC) measurements ran simultaneously above and within the forest canopy for that purpose. We used the correlation of above- and below-canopy standard deviation of vertical wind speed (σ w ) as decoupling indicator. We identified 0.33 m s -1 and 0.06 m s -1 as site-specific σ w thresholds for above- and below-canopy coupling during nighttime (global radiation < 20 W m -2 ) and 0.23 m s -1 and 0.06 m s -1 as daytime (global radiation > 20 W m -2 ) σ w thresholds. Decoupling occurred in 53% of the annual nighttime and 14% of the annual daytime. The annual net ecosystem exchange (NEE), gross ecosystem exchange (GEE), and ecosystem respiration (R eco ) derived via two-level filtered EC data were -357 g C m -2 , -1,138 g C m -2 , and 781 g C m -2 , respectively. In comparison, both single-level friction velocity (u * ) and quality filtering resulted in ~ 22% higher NEE, mainly caused by ~ 16% lower R eco . GEE remained similar among filtering regimes. Accounting for changes of CO 2 storage across the canopy in the single-level filtered data could only marginally decrease these discrepancies. Consequently, advection appears to be responsible for the major part of this divergence. We conclude that the two-level filter is necessary to adequately address decoupling and subcanopy advection at our site, and we recommend this filter for all forested EC sites.
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| 14. |
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| 15. |
- Kvernby, Sofia, et al.
(författare)
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Quantitative comparison of data-driven gating and external hardware gating for 18F-FDG PET-MRI in patients with esophageal tumors
- 2021
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Ingår i: European Journal of Hybrid Imaging. - : Springer Nature. - 2510-3636. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundRespiratory motion during PET imaging reduces image quality. Data-driven gating (DDG) based on principal component analysis (PCA) can be used to identify respiratory signals. The use of DDG, without need for external devices, would greatly increase the feasibility of using respiratory gating in a routine clinical setting. The objective of this study was to evaluate data-driven gating in relation to external hardware gating and regular static image acquisition on PET-MRI data with respect to SUVmax and lesion volumes.MethodsSixteen patients with esophageal or gastroesophageal cancer (Siewert I and II) underwent a 6-min PET scan on a Signa PET-MRI system (GE Healthcare) 1.5-2 h after injection of 4 MBq/kg F-18-FDG. External hardware gating was done using a respiratory bellow device, and DDG was performed using MotionFree (GE Healthcare). The DDG raw data files and the external hardware-gating raw files were created on a Matlab-based toolbox from the whole 6-min scan LIST-file. For comparison, two 3-min static raw files were created for each patient. Images were reconstructed using TF-OSEM with resolution recovery with 2 iterations, 28 subsets, and 3-mm post filter. SUVmax and lesion volume were measured in all visible lesions, and noise level was measured in the liver. Paired t-test, linear regression, Pearson correlation, and Bland-Altman analysis were used to investigate difference, correlation, and agreement between the methods.ResultsA total number of 30 lesions were included in the study. No significant differences between DDG and external hardware-gating SUVmax or lesion volumes were found, but the noise level was significantly reduced in the DDG images. Both DDG and external hardware gating demonstrated significantly higher SUVmax (9.4% for DDG, 10.3% for external hardware gating) and smaller lesion volume (- 5.4% for DDG, - 6.6% for external gating) in comparison with non-gated static images.ConclusionsData-driven gating with MotionFree for PET-MRI performed similar to external device gating for esophageal lesions with respect to SUVmax and lesion volume. Both gating methods significantly increased the SUVmax and reduced the lesion volume in comparison with non-gated static acquisition. DDG resulted in reduced image noise compared to external device gating and static images.
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| 16. |
- Lim, Hyungwoo, et al.
(författare)
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Annual climate variation modifies nitrogen induced carbon accumulation of Pinus sylvestris forests
- 2017
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Ingår i: Ecological Applications. - : Wiley. - 1051-0761 .- 1939-5582. ; 27, s. 1838-1851
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Tidskriftsartikel (refereegranskat)abstract
- We report results from long-term simulated external nitrogen (N) input experiments in three northern Pinus sylvestris forests, two of moderately high and one of moderately low productivity, assessing effects on annual net primary production (NPP) of woody mass and its interannual variation in response to variability in weather conditions. A sigmoidal response of wood NPP to external N inputs was observed in the both higher and lower productivity stands, reaching a maximum of similar to 65% enhancement regardless of the native site productivity, saturating at an external N input of 4-5 g N . m(-2) . yr(-1). The rate of increase in wood NPP and the N response efficiency (REN, increase in wood NPP per external N input) were maximized at an external N input of similar to 3 gN . m(-2) (.) yr(-1), regardless of site productivity. The maximum REN was greater in the higher productivity than the lower productivity stand (similar to 20 vs. similar to 14 g C/g N). The N-induced enhancement of wood NPP and its REN were, however, markedly contingent on climatic variables. In both of the higher and lower productivity stands, wood NPP increased with growing season precipitation (P), but only up to similar to 400 mm. The sensitivity of the response to P increased with increasing external N inputs. Increasing growing season temperature (T) somewhat increased the N-induced drought effect, whereas decreasing T reduced the drought effect. These responses of wood NPP infused a large temporal variation to REN, making the use of a fixed value unadvisable. Based on these results, we suggest that regional climate conditions and future climate scenarios should be considered when modeling carbon sequestration in response to N deposition in boreal P. sylvestris, and possibly other forests.
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| 17. |
- Lim, Hyungwoo, et al.
(författare)
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Boreal forest biomass accumulation is not increased by two decades of soil warming
- 2019
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Ingår i: Nature Climate Change. - : Springer Science and Business Media LLC. - 1758-678X .- 1758-6798. ; 9, s. 49-52
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Tidskriftsartikel (refereegranskat)abstract
- Increased soil organic matter decomposition with increasing temperature has been hypothesized to enhance soil nitrogen availability, consequently stimulating forest biomass production and offsetting decomposition-induced soil carbon losses(1-5). This projection, however, is based on evidence gathered from short-term studies (<= 10 years)(2,3,5). The key question for carbon sequestration is whether such responses are transient or persist over long forest rotation periods. Here we report on biomass production in a typical nitrogen-limited boreal Picea abies forest, exposed to 18 years of soil warming manipulation (+ 5 degrees C) at a plot scale (100 m(2)). We show that two decades of soil warming elicited only short-duration growth responses, thus not significantly increasing aboveground biomass accumulation. Furthermore, in combination with published work from this forest, our results suggest that increased decomposition is slight and ephemeral, and increased fine root production and turnover in deeper soil may be greater than increased decomposition, netting slightly more biomass, perhaps conserving the soil carbon stock. Thus, this long-term study does not support the notion that the projected increase in soil temperatures will cause either an increased carbon loss with decomposition or a compensatory growth increase from nitrogen mineralization.
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| 18. |
- Lim, Hyungwoo, et al.
(författare)
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Inter-annual variability of precipitation constrains the production response of boreal Pinus sylvestris to nitrogen fertilization
- 2015
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Ingår i: Forest Ecology and Management. - : Elsevier BV. - 0378-1127 .- 1872-7042. ; 348, s. 31-45
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Tidskriftsartikel (refereegranskat)abstract
- Tree growth resources and the efficiency of resource-use for biomass production determine the productivity of forest ecosystems. In nutrient-limited forests, nitrogen (N)-fertilization increases foliage [NI, which may increase photosynthetic rates, leaf area index (L), and thus light interception (I-C). The product of such changes is a higher gross primary production and higher net primary production (NPP). However, fertilization may also alter carbohydrate partitioning from below- to aboveground, increasing aboveground NPP (ANPP). We analyzed effects of long-term N-fertilization on NPP, and that of long-term carbon storing organs (NPPs) in a Pinus sylvestris forest on sandy soil, a wide-ranging forest type in the boreal region. We based our analyses on a combination of destructive harvesting, consecutive mensuration, and optical measurements of canopy openness. After eight-year fertilization with a total of 70 g N m(-2), ANPP was 27 +/- 7% higher in the fertilized (F) relative to the reference (R) stand, but although L increased relative to its pre-fertilization values, I-C was not greater than in R. On the seventh year after the treatment initiation, the increase of ANPP was matched by the decrease of belowground NPP (78 vs. 92 g C m(-2) yr(-1); similar to 17% of NPP) and, given the similarity of I-C, suggests that the main effect of N-fertilization was changed carbon partitioning rather than increased canopy photosynthesis. Annual NPPs increased linearly with growing season temperature (T) in both treatments, with an upward shift of 70.2 g C m(-2) yr(-1) by fertilization, which also caused greater amount of unexplained variation (r(2) = 0.53 in R, 0.21 in F). Residuals of the NPPs-T relationship of F were related to growing season precipitation (P, r(2) = 0.48), indicating that T constrains productivity at this site regardless of fertility, while P is important in determining productivity where N-limitation is alleviated. We estimated that, in a growing season average T (11.5 +/- 1.0 degrees C; 33-year-mean), NPPs response to N-fertilization will be nullified with P 31 mm less than the mean (325 +/- 85 mm), and would double with P '109 mm greater than the mean. These results suggest that inter-annual variation in climate, particularly in P, may help explaining the reported large variability in growth responses to fertilization of pine stands on sandy soils. Furthermore, forest management of long-rotation systems, such as those of boreal and northern temperate forests, must consider the efficiency of fertilization in terms of wood production in the context of changes in climate predicted for the region. (C) 2015 Elsevier B.V. All rights reserved.
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| 19. |
- Lindahl, Bertil, et al.
(författare)
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An algorithm for rule-in and rule-out of acute myocardial infarction using a novel troponin I assay
- 2017
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Ingår i: Heart. - : BMJ. - 1355-6037 .- 1468-201X. ; 103:2, s. 125-131
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Tidskriftsartikel (refereegranskat)abstract
- Objective To derive and validate a hybrid algorithm for rule-out and rule-in of acute myocardial infarction based on measurements at presentation and after 2 hours with a novel cardiac troponin I (cTnI) assay. Methods The algorithm was derived and validated in two cohorts (605 and 592 patients) from multicentre studies enrolling chest pain patients presenting to the emergency department (ED) with onset of last episode within 12 hours. The index diagnosis and cardiovascular events up to 30 days were adjudicated by independent reviewers. Results In the validation cohort, 32.6% of the patients were ruled out on ED presentation, 6.1% were ruled in and 61.3% remained undetermined. A further 22% could be ruled out and 9.8% ruled in, after 2 hours. In total, 54.6% of the patients were ruled out with a negative predictive value (NPV) of 99.4% (95% CI 97.8% to 99.9%) and a sensitivity of 97.7% (95% CI 91.9% to 99.7%); 15.8% were ruled in with a positive predictive value (PPV) of 74.5% (95% CI 64.8% to 82.2%) and a specificity of 95.2% (95% CI 93.0% to 96.9%); and 29.6% remained undetermined after 2 hours. No patient in the rule-out group died during the 30-day follow-up in the two cohorts. Conclusions This novel two-step algorithm based on cTnI measurements enabled just over a third of the patients with acute chest pain to be ruled in or ruled out already at presentation and an additional third after 2 hours. This strategy maximises the speed of rule-out and rule-in while maintaining a high NPV and PPV, respectively.
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| 20. |
- Lindahl, Tomas, et al.
(författare)
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Effects of the oral, direct thrombin inhibitor dabigatran on five common coagulation assays
- 2011
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Ingår i: Thrombosis and Haemostasis. - : F K Schattauer Verlagsgesellschaft MBH. - 0340-6245 .- 2567-689X. ; 105:2, s. 371-378
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Tidskriftsartikel (refereegranskat)abstract
- Dabigatran is an oral, reversible thrombin inhibitor that has shown promising results in large clinical trials. Laboratory monitoring is not needed but the effects on common coagulation assays are incompletely known. Dabigatran was added to plasma from healthy subjects in the concentration range 0-1,000 μg/l and analysed using several reagents for activated thromboplastin time (APTT), prothrombin time (PT), fibrinogen, antithrombin, and activated protein C resistance. Typical trough concentrations are about 50 μg/l, peak concentrations 100-300 μg/l. At 100 μg/l all APTT-results were prolonged. The concentration required to double APTT ranged between 227 and 286 μg/l, the responses for all five reagents were similar. PT-reagents were much less affected with almost no samples above INR 1.2 at 100 μg/l. The effect was sample dilution dependent with PT Quick type more sensitive than PT Owren type methods. If a patient on dabigatran has prolonged APTT, >90 seconds, and Quick PT INR>2 or Owren PT INR>1.5 over-dosing or accumulation of dabigatran should be considered. Two of four fibrinogen reagents underestimated the fibrinogen concentration considerably at expected peak concentration. Methods based on inhibition of thrombin over-estimated the antithrombin concentration, but not Xa-based. The APC-resistance methods over-estimated the APC-ratio, which may lead to miss-classification of factor V Leiden patients as being normal. Different coagulation assays, and even different reagents within an assay group, display variable effects at therapeutic concentrations of dabigatran. Some of these assay variations are of clinical importance, thus knowledge is needed for a correct interpretation of results.
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| 21. |
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| 22. |
- Linder, Gustav, et al.
(författare)
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F-18-FDG-PET/MRI in preoperative staging of oesophageal and gastroesophageal junctional cancer
- 2019
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Ingår i: Clinical Radiology. - : W B SAUNDERS CO LTD. - 0009-9260 .- 1365-229X. ; 74:9, s. 718-725
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Tidskriftsartikel (refereegranskat)abstract
- AIM: To evaluate integrated 2-[F-18]-fluoro-2-deoxy-D-glucose (F-18-FDG) positron-emission tomography (PET)/magnetic resonance imaging (MRI), in comparison with the standard technique, integrated F-18-FDG-PET/computed tomography (CT), in preoperative staging of oesophageal or gastroesophageal junctional cancer.MATERIALS AND METHODS: In the preoperative staging of 16 patients with oesophageal or gastroesophageal junctional cancer, F-18-FDG-PET/MRI was performed immediately following the clinically indicated F-18-FDG-PET/CT. MRI-sequences included T1-weighted fat-water separation (Dixon's technique), T2-weighted, diffusion-weighted imaging (DWI), and gadolinium contrast-enhanced T1-weighted three-dimensional (3D) imaging. PET was performed with F-18-FDG. Two separate teams of radiologists conducted structured blinded readings of F-18-FDG-PET/MRI or F-18-FDG-PET/CT, which were then compared regarding tumour measurements and characteristics as well as assessment of inter-rater agreement (Cohen's kappa) for the clinical tumour, nodal and metastatic (TNM) stage.RESULTS: There were no medical complications. Comparison of tumour measurements revealed high correlations without significant differences between modalities. The maximum standardised uptake value (SUVmax) values of the primary tumour with F-18-FDG-PET/MRI had excellent correlation to those of F-18-FDG-PET/CT (0.912, Spearman's rho). Inter-rater agreement between the techniques regarding T-stage was only fair (Cohen's kappa, 0.333), arguably owing to relative over-classification of the T-stage using F-18-FDG-PET/CT. Agreements in the assessment of N- and M-stage were substantial (Cohen's kappa, 0.849 and 0.871 respectively).CONCLUSION: Preoperative staging with F-18-FDG-PET/MRI is safe and promising with the potential to enhance tissue resolution in the area of interest. F-18-FDG-PET/MRI and F-18-FDG-PET/CT correlated well for most of the measured values and discrepancies were seen mainly in the assessment of the T-stage. These results facilitate further studies investigating the role of F-18-FDG-PET/MRI in, e.g., predicting or determining the response to neoadjuvant therapy.
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| 23. |
- Linder, Tomas, et al.
(författare)
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A family of putative transcription termination factors shared amongst metazoans and plants.
- 2005
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Ingår i: Current genetics. - : Springer Science and Business Media LLC. - 0172-8083 .- 1432-0983. ; 48:4, s. 265-9
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Tidskriftsartikel (refereegranskat)abstract
- The human mitochondrial transcription termination factor (mTERF) is involved in the regulation of transcription of the mitochondrial genome. Similarity searches and phylogenetic analysis demonstrate that mTERF is a member of large and complex protein family (the MTERF family) shared amongst metazoans and plants. Interestingly, we identify three novel MTERF genes in vertebrates, which all encode proteins with predicted mitochondrial localization. Members of the MTERF family have so far not been detected in fungi, supporting the notion that mitochondrial transcription regulation may have evolved separately in yeast and animal cells.
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| 24. |
- Linder, Tomas
(författare)
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A genomic survey of nitrogen assimilation pathways in budding yeasts (sub-phylum Saccharomycotina)
- 2019
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Ingår i: Yeast. - : Wiley. - 0749-503X .- 1097-0061. ; 36, s. 259-273
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Tidskriftsartikel (refereegranskat)abstract
- Sequenced genomes of 149 species of budding yeast (including 62 species with draft genomes that currently lack gene annotations) were surveyed for the presence of 24 genes associated with the assimilation of amines, uracil, dihydropyrimidines, purines, uric acid, allantoin, and nitrate as nitrogen sources. Genes for the assimilation of primary amines were distributed broadly across the Saccharomycotina while choline assimilation appeared to be mostly restricted to the families Debaryomycetaceae, Metschnikowiaceae, and Pichiaceae. Conversely, the uracil catabolic pathway was completely absent in Debaryomycetaceae and Metschnikowiaceae but present in the majority of the remaining Saccharomycotina. The super-pathway for assimilation of purines, uric acid, and allantoin was present in the majority of surveyed species. Genes for the assimilation of nitrate were restricted to a minority of species in families Phaffomycetaceae, Pichiaceae, and Trichomonascaceae as well as some currently unassigned genera. This study also successfully identified yeast homologs of all six previously known eukaryotic genes involved in the biosynthesis of the molybdenum cofactor, which is required for the activity of the nitrogen assimilation-associated enzymes nitrate reductase and xanthine oxidoreductase. Analysis of 1,187 upstream intergenic regions identified three novel putative regulatory motifs for the assimilation of uracil, purines, and uric acid as well as a possible role for the MADS-box transcription factor Mcm1 in the regulation of amine assimilation genes.
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| 25. |
- Linder, Tomas
(författare)
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A standardized toolkit for genetic engineering of CTG Glade yeasts
- 2018
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Ingår i: Journal of Microbiological Methods. - : Elsevier BV. - 0167-7012 .- 1872-8359. ; 144, s. 152-156
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a series of synthetic constructs suitable to genetically manipulate a broad range of yeast species belonging to the fungal CTG Glade. This molecular toolbox notably allows heterologous gene expression, single or dual fluorescence labeling and construction of luciferase-expressing strains for bioluminescence imaging.
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| 26. |
- Linder, Tomas
(författare)
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An additional Meyerozyma guilliermondii IMH3 gene confers mycophenolic acid resistance in fungal CTG clade species
- 2016
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Ingår i: FEMS Yeast Research. - : Oxford University Press (OUP). - 1567-1356 .- 1567-1364. ; 16
-
Tidskriftsartikel (refereegranskat)abstract
- The fungal CTG clade comprises a number of well-known yeasts that impact human health or with high biotechnological potential. To further extend the set of molecular tools dedicated to these microorganisms, the initial focus of this study was to develop a mycophenolic acid (MPA) resistance cassette. Surprisingly, while we were carrying out preliminary susceptibility testing experiments in a set of yeast species, Meyerozyma guilliermondii, although not being a MPA producer, was found to be primarily resistant toward this drug, whereas a series of nine related species were susceptible to MPA. Using comparative and functional genomic approaches, we demonstrated that all MPA-susceptible CTG clade species display a single gene, referred to as IMH3.1, encoding the MPA target inosine monophosphate dehydrogenase (IMPDH) and that MPA resistance relies on the presence in the M. guilliermondii genome of an additional IMPDH-encoding gene (IMH3.2). The M. guilliermondii IMH3.2 gene displays marked differences compared to IMH3.1 including the lack of intron, a roughly 160-fold higher transcription level and a serine residue at position 251. Placed under the control of the M. guilliermondii actin 1 gene promoter, IMH3.2 was successfully used to transform Lodderomyces elongisporus, Clavispora lusitaniae, Scheffersomyces stipitis and Candida parapsilosis.Deciphering molecular mechanisms underlying mycophenolic acid resistance in Meyerozyma guilliermondii shed light on a new selectable marker for fungal CTG clade yeasts genetics.Deciphering molecular mechanisms underlying mycophenolic acid resistance in Meyerozyma guilliermondii shed light on a new selectable marker for fungal CTG clade yeasts genetics.
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| 27. |
- Linder, Tomas, et al.
(författare)
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Anisotropic light propagation in paper
- 2012
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Ingår i: Nordic Pulp & Paper Research Journal. - 0283-2631 .- 2000-0669. ; 27:2, s. 500-506
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Tidskriftsartikel (refereegranskat)abstract
- We investigate anisotropic light propagation in paper using both a theoretical model and experiments. The theoretical model utilizes the Monte Carlo method to solve the photon transport equation numerically. It is assumed that wood fibres are represented by infinitely long, homogeneous and straight cylinders. The layer-like microstructure and anisotropic orientation of the fibres is considered in the model. The conical scattering by cylindrical objects, the wood fibres, is argued as the main source of anisotropic scattering. Simulations revealed that laterally resolved transmittance exhibits directional dependence. Experiments on light transmitted through a standard kraft liner product confirmed that light in fact do propagate more in the machine direction than in the cross direction. Reasonably good agreement was obtained between experimentally and numerically obtained iso-intensity patterns.
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| 28. |
- Linder, Tomas
(författare)
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Assimilation of alternative sulfur sources in fungi
- 2018
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Ingår i: World Journal of Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0959-3993 .- 1573-0972. ; 34
-
Forskningsöversikt (refereegranskat)abstract
- Fungi are well known for their metabolic versatility, whether it is the degradation of complex organic substrates or the biosynthesis of intricate secondary metabolites. The vast majority of studies concerning fungal metabolic pathways for sulfur assimilation have focused on conventional sources of sulfur such as inorganic sulfur ions and sulfur-containing biomolecules. Less is known about the metabolic pathways involved in the assimilation of so-called "alternative" sulfur sources such as sulfides, sulfoxides, sulfones, sulfonates, sulfate esters and sulfamates. This review summarizes our current knowledge regarding the structural diversity of sulfur compounds assimilated by fungi as well as the biochemistry and genetics of metabolic pathways involved in this process. Shared sequence homology between bacterial and fungal sulfur assimilation genes have lead to the identification of several candidate genes in fungi while other enzyme activities and pathways so far appear to be specific to the fungal kingdom. Increased knowledge of how fungi catabolize this group of compounds will ultimately contribute to a more complete understanding of sulfur cycling in nature as well as the environmental fate of sulfur-containing xenobiotics.
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| 29. |
- Linder, Tomas
(författare)
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ATP Sulfurylase is Essential for the Utilization of Sulfamate as a Sulfur Source in the Yeast Komagataella pastoris (syn. Pichia pastoris)
- 2017
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Ingår i: Current Microbiology. - : Springer Science and Business Media LLC. - 0343-8651 .- 1432-0991. ; 74, s. 1021-1025
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Tidskriftsartikel (refereegranskat)abstract
- The methylotrophic yeast Komagataella pastoris (syn. Pichia pastoris) is one of the few known yeasts that can utilize sulfamate (NH2SO3-) as a sulfur source. The biochemical pathway responsible for the catabolism of sulfamate has yet to be identified. The present study sought to investigate whether sulfamate catabolism proceeds through either of the inorganic sulfur intermediates sulfate (SO42-) or sulfite (SO32-) before its assimilation and subsequent incorporation into sulfur-containing amino acids and their derivatives. Two key genes in the K. pastoris inorganic sulfur assimilation pathway were deleted separately and the ability of each deletion mutant to utilize sulfamate and other selected sulfur sources was studied. Deletion of the MET3 gene (which encodes the enzyme ATP sulfurylase) did not affect growth on L-methionine, sulfite, methanesulfonate, or taurine but completely abolished growth on sulfate, methyl sulfate and sulfamate. Deletion of the MET5 gene (which encodes the beta subunit of the enzyme sulfite reductase) abolished growth on all tested sulfur sources except L-methionine. These results suggest that the catabolism of sulfamate proceeds through a sulfate intermediate before its assimilation.
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| 30. |
- Linder, Tomas
(författare)
-
Can we feed humanity and save the planet with edible microbes?
- 2021
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Annan publikation (populärvet., debatt m.m.)abstract
- Edible microbes such as bacteria, yeasts, filamentous fungi, and microscopic algae are emerging as a potentially more sustainable and resilient option for food and food production for a warmer and more crowded planet. In this buildup, conventional agriculture not only underperforms; it also aggravates the problem.
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| 31. |
- Linder, Tomas
(författare)
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CMO1 encodes a putative choline monooxygenase and is required for the utilization of choline as the sole nitrogen source in the yeast Scheffersomyces stipitis (syn. Pichia stipitis)
- 2014
-
Ingår i: Microbiology. - : Microbiology Society. - 1350-0872 .- 1465-2080. ; 160, s. 929-940
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Tidskriftsartikel (refereegranskat)abstract
- Sixteen yeasts with sequenced genomes belonging to the ascomycete subphyla Saccharomycotina and Taphrinomycotina were assayed for their ability to utilize a variety of primary, secondary, tertiary and quartenary aliphatic amines as nitrogen sources. The results support a previously proposed pathway of quaternary amine catabolism whereby glycine betaine is first converted into choline, which is then cleaved to release trimethylamine, followed by stepwise demethylation of trimethylamine to release free ammonia. There were only a few instances of utilization of N-methylated glycine species (sarcosine and N,N-dimethylglycine), which suggests that this pathway is not intact in any of the species tested. The ability to utilize choline as a sole nitrogen source correlated strongly with the presence of a putative Rieske non-haem iron protein homologous to bacterial ring-hydroxylating oxygenases and plant choline monooxygenases. Deletion of the gene encoding the Rieske non-haem iron protein in the yeast Scheffersomyces stipitis abolished its ability to utilize choline as the sole nitrogen source, but did not affect its ability to use methylamine, dimethylamine, trimethylamine, ethylamine, diethylamine, ethanolamine or glycine as nitrogen sources. The gene was named CMO1 for putative choline monooxygenase 1. A bioinformatic survey of eukaryotic genomes showed that CMO1 homologues are found throughout the eukaryotic domain.
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| 32. |
- Linder, Tomas
(författare)
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Conserved structure-function relationships in the mediator complex
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The Mediator complex is an essential multiprotein coregulator of RNA polymerase II (pol II)- dependent transcription in fungi and metazoans. Mediator interacts directly with both pol II and sequence-specific transcriptional regulators and thus acting as a bridge between the two. We have performed a comparative biochemical and functional characterisation the Mediator in the two ascomycete yeasts S. cerevisiae and S. pombe to address to what degree subunit architecture and specific regulatory functions have been conserved between these two species. In Paper I we identified the Med31 protein as a stable subunit of Mediator in S. cerevisiae and S. pombe. We defined a highly conserved central motif in the Med31 protein that appeared to be required but not sufficient for the association of Med31 with the rest of the Mediator complex. In Paper II we investigated the structural basis for the global shutdown of pol II-dependent transcription in the S. cerevisiae MED17 temperature sensitive allele srb4-138. We found that the srb4-138 allele disrupts the interaction between the head and middle domains both in vitro and in vivo. This suggested that the global shutdown of transcription in srb4-138 cells at the non-permissive temperature is caused by destabilisation of the core Mediator complex. In Paper III we characterised the architecture of the S. pombe Cdk8 module by biochemical means and addressed its relationship to the non-essential Med1 subunit. We found that the Med1 subunit is closely linked both structurally and functionally with the Cdk8 module. Electron microscopy of wildtype and Δmed1 Mediator resolved the position of the Med1 subunit as proximal to the Cdk8 module within the pol II-binding cleft of the core Mediator complex. Expression profiling of Δmed1 cells showed significant overlap with the changes seen in cells lacking either Med12 or Med13. In Paper IV we carried out a comprehensive functional characterisation of the S. pombe Mediator complex and identified two distinct morphological pathways that require different parts of the Mediator for their proper regulation. Head domain-linked mutants tended to grow as hyphae due to their inability to express genes required for proper cell separation after mitosis. Mutants of the Cdk8 module aggregated into large clumps due to impaired repression of genes that code for cell surface agglutinins. Comparison with similar studies done in S. cerevisiae revealed that both regulatory roles for these subcomplexes are conserved.
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| 33. |
- Linder, Tomas
(författare)
-
Cyanase-independent utilization of cyanate as a nitrogen source in ascomycete yeasts
- 2019
-
Ingår i: World Journal of Microbiology and Biotechnology. - : Springer Science and Business Media LLC. - 0959-3993 .- 1573-0972. ; 35
-
Tidskriftsartikel (refereegranskat)abstract
- The occurrence of putative cyanases (EC 4.2.1.104) in the genomes of yeasts belonging to the ascomycete sub-phyla Saccharomycotina (budding yeasts) and Taphrinomycotina (fission yeasts) was investigated. Predicted gene products displaying significant sequence similarity to previously characterized cyanases were identified in the genomes of the budding yeast Lipomyces starkeyi and the fission yeasts Protomyces lactucaedebilis, Saitoella complicata and Taphrina deformans. Li. starkeyi and Sai. complicata were further tested for their ability to utilize cyanate as a nitrogen source. However, neither species displayed significant growth when cyanate was provided as the sole nitrogen source. Cyanate utilization assays of 15 yeast species whose genomes lack detectable cyanase homologs unexpectedly resulted in consistently strong growth in six species as well as variable growth in an additional three species. The present study represents the first known report of cyanase-independent utilization of cyanate as a nitrogen source in ascomycete yeasts. Implications of cyanate utilization for the ecological niches occupied by ascomycete yeasts are discussed.
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| 34. |
- Linder, Tomas
(författare)
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Development of a yeast heterologous expression cassette based on the promoter and terminator elements of the Eremothecium cymbalariae translational elongation factor 1α (EcTEF1) gene
- 2018
-
Ingår i: 3 BIOTECH. - : Springer Science and Business Media LLC. - 2190-572X .- 2190-5738. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- A new expression cassette (EC0) consisting of the fused 5′ and 3′ intergenic regions (IGRs) of the Eremothecium cymbalariae translational elongation factor 1α (EcTEF1) gene was evaluated through expression of the bacterial hygromycin B phosphotransferase (hph) resistance gene in the common baker’s yeast Saccharomyces cerevisiae. Progressively shorter versions of the hph-containing EC cassette (hphEC1 though hphEC6) with trimmed 5′ and 3′ EcTEF1 IGRs were tested for their ability to confer resistance to hygromycin B in S. cerevisiae. Hygromycin B resistance was retained in all six generated hphEC variants up to a concentration of 400 mg/L. The hphEC6 cassette was the shortest cassette to be assayed in this study with 366 and 155 bp of the EcTEF1 5′ and 3′ IGRs, respectively. When tested for deletion of the S. cerevisiae proline oxidase gene PUT1, the hphEC6 cassette was shown to successfully act as a selection marker on hygromycin B-containing medium. The hphEC6 cassette could be placed immediately adjacent to a kanMX4 G418 disulfate resistance marker without any discernable efect on the ability of the yeast to grow in the presence of both hygromycin B and G418 disulfate. Co-cultivation experiments under non-selective conditions demonstrated that a PUT1 deletion strain carrying the hphEC6 cassette displayed equivalent ftness to an otherwise isogenic PUT1 deletion strain carrying the kanMX4 cassette.
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| 35. |
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| 36. |
- Linder, Tomas
(författare)
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Evaluation of the chitin-binding dye Congo red as a selection agent for the isolation, classification, and enumeration of ascomycete yeasts
- 2018
-
Ingår i: Archives of Microbiology. - : Springer Science and Business Media LLC. - 0302-8933 .- 1432-072X. ; 200, s. 671-675
-
Tidskriftsartikel (refereegranskat)abstract
- Thirty-nine strains of ascomycete yeasts representing 35 species and 33 genera were tested for their ability to grow on solid agar medium containing increasing concentrations of the chitin-binding dye Congo red. Six strains were classified as hypersensitive (weak or no growth at 10 mg/l Congo red), five were moderately sensitive (weak or no growth at 50 mg/l), three were moderately tolerant (weak or no growth at 100 mg/l), while the remaining 25 strains were classified as resistant (robust growth at >= 100 mg/l) with 20 of these strains classified as hyper-resistant (robust growth at 200 mg/l). Congo red growth phenotypes were consistent within some families but not others. The frequency of Congo red resistance among ascomycete yeasts was deemed too high for the practical use of Congo red as a selection agent for targeted isolation, but can be useful for identification and enumeration of yeasts.
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| 37. |
- Linder, Tomas
(författare)
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Genetic redundancy in the catabolism of methylated amines in the yeast Scheffersomyces stipitis
- 2018
-
Ingår i: Antonie van Leeuwenhoek. - : Springer Science and Business Media LLC. - 0003-6072 .- 1572-9699. ; 111, s. 401-411
-
Tidskriftsartikel (refereegranskat)abstract
- The catabolism of choline as a source of nitrogen in budding yeasts is thought to proceed via the intermediates trimethylamine, dimethylamine and methylamine before the release of ammonia. The present study investigated the utilisation of choline and its downstream intermediates as nitrogen sources in the yeast Scheffersomyces stipitis using a reverse genetics approach. Six genes (AMO1, AMO2, SFA1, FGH1, PICST_49761, PICST_63000) that have previously been predicted to be directly or indirectly involved in the catabolism of methylated amines were individually deleted. The growth of each deletion mutant was assayed on minimal media with methylamine, dimethylamine, trimethylamine or choline as the sole nitrogen source. The two amine oxidase-encoding genes AMO1 and AMO2 appeared to be functionally redundant for growth on methylated amines as both deletion mutants displayed growth on all nitrogen sources tested. However, deletion of AMO1 resulted in a pronounced growth lag on all four methylated amines while deletion of AMO2 only caused a growth lag when methylamine was the sole nitrogen source. The glutathione-dependent formaldehyde dehydrogenase-encoding gene SFA1 was found to be absolutely essential for growth on all methylated amines tested while deletion of the S-formylglutathione hydrolase gene FGH1 caused a pronounced growth lag on dimethylamine, trimethylamine and choline. The putative cytochrome P450 monooxygenase-encoding genes PICST_49761 and PICST_63000 were considered likely candidates for demethylation of di- and trimethylamine but produced no discernable phenotype on any of the tested nitrogen sources when deleted. This study revealed notable instances of genetic redundancies in the choline catabolic pathway, which are discussed.
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| 38. |
- Linder, Tomas
(författare)
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Genomics of alternative sulfur utilization in ascomycetous yeasts
- 2012
-
Ingår i: Microbiology. - : Microbiology Society. - 1350-0872 .- 1465-2080. ; 158, s. 2585-2597
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Tidskriftsartikel (refereegranskat)abstract
- Thirteen ascomycetous yeast strains with sequenced genomes were assayed for their ability to grow on chemically defined medium with 16 different sulfur compounds as the only significant source of sulfur. These compounds included sulfoxides, sulfones, sulfonates, sulfamates and sulfate esters. Broad utilization of alternative sulfur sources was observed in Komagataella pastoris (syn. Pichia pastoris), Lodderomyces elongisporus, Millerozyma farinosa (syn. Pichia sorbitophila), Pachysolen tannophilus, Scheffersomyces stipitis (syn. Pichia stipitis), Spathaspora passalidarum, Yamadazyma tenuis (syn. Candida tenuis) and Yarrowia lipolytica. Kluyveromyces lactis, Saccharomyces cerevisiae and Zygosaccharomyces rouxii were mainly able to utilize sulfonates and sulfate esters, while Lachancea thermotolerans and Schizosaccharomyces pombe were limited to aromatic sulfate esters. Genome analysis identified several candidate genes with bacterial homologues that had been previously shown to be involved in the utilization of alternative sulfur sources. Analysis of candidate gene promoter sequences revealed a significant overrepresentation of DNA motifs that have been shown to regulate sulfur metabolism in Sacc. cerevisiae.
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| 39. |
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| 40. |
- Linder, Tomas, et al.
(författare)
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Lateral light scattering in fibrous media
- 2013
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Ingår i: Optics Express. - 1094-4087. ; 21:6, s. 7835-7840
-
Tidskriftsartikel (refereegranskat)abstract
- Lateral light scattering in fibrous media is investigated by computing the modulation transfer function (MTF) of 22 paper samples using a Monte Carlo model. The simulation tool uses phase functions from infinitely long homogenous cylinders and the directional inhomogeneity of paper is achieved by aligning the cylinders in the plane. The inverse frequency at half maximum of the MTF is compared to both measurements and previous simulations with isotropic and strongly forward single scattering phase functions. It is found that the conical scattering by cylinders enhances the lateral scattering and therefore predicts a larger extent of lateral light scattering than models using rotationally invariant single scattering phase functions. However, it does not fully reach the levels of lateral scattering observed in measurements. It is argued that the hollow lumen of a wood fiber or dependent scattering effects must be considered for a complete description of lateral light scattering in paper.
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| 41. |
- Linder, Tomas
(författare)
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Light Scattering in Fiber-based Materials : a foundation for characterization of structural properties
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Deeper knowledge of light propagation in fiber-based materials is fundamental in order to understand their optical appearance as well as for industrial applications. Light scattering measurements are appropriate in handling dynamic industrial environments and can provide information regarding structural properties. In general, on-line property measurements are best utilized by establishing an understanding of the underlying physics and using that knowledge in an optimal way to determine the parameters or properties sought after. Light scattering is affected by numerous parameters such as size, shape, concentration and refractive index of the scattering particles as well as the waveleng th of the incident source. In addition, anisotropic light diffusion in media which have a directional-dependency, such as structured fiber-based materials, are neither well understood nor well investigated.By approximating cellulose fibers as infinitely long, straigth cylinders it is possible to use an analytical solution to Maxwell’s equations to describe the scattering characteristics such as phase functions and scattering efficiency. This makes it possible to utilize both the wave nature of light and structural properties of the fiber network when modelling multiple light scattering. The developed model solves the radiative transfer equation numerically using theMonte Carlo method resulting in a description of multiple scattering in a sphere-cylinder media.The results show that scattering media consisting of infinite long, straigth, homogeneous or hollow cylinders scatter light very differently as compared with a media consisting of spherical particles. Both scattered intensity and the degree of depolarization are affected by a strong forward scattering behavior observed for cylindrical particles. This strong forward scattering behavior was also found to enhance lateral scattering in paper, and therefore predicts a larger extent of lateral light scattering than models using rotationally invariant single scattering phase functions. A strong relationship between anisotropic diffusion and to degree of in-plane fiber orientation was also observed using both measurements and simulations. In conclusion, it was found that the approximation of cellulose fibers as infinitely long, straigth cylinders is reasonable when modelling scattering in paper. The findings indicate that parameters such as geometrical properties, particle composition, fiber orientation and fiber orientation variations can be measured by monitoring scattered light intensity. The obtained knowledge provides a base for further development of on-line sensing techniques that meet industrial requirements. Since the theory is general, it is likewise relevant and applicable to other areas of material science where imaging or remote sensing techniques are of interest.
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| 42. |
- Linder, Tomas, et al.
(författare)
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Light scattering in fibrous media with different degrees of in-plane fiber alignment
- 2014
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Ingår i: Optics Express. - 1094-4087. ; 22:14, s. 16829-16840
-
Tidskriftsartikel (refereegranskat)abstract
- Fiber orientation is an important structural property in paper and other fibrous materials. In this study we explore the relation between light scattering and in-plane fiber orientation in paper sheets. Light diffusion from a focused light source is simulated using a Monte Carlo technique where parameters describing the paper micro-structure were determined from 3D x-ray computed tomography images. Measurements and simulations on both spatially resolved reflectance and transmittance light scattering patterns show an elliptical shape where the main axis is aligned towards the fiber orientation. Good qualitative agreement was found at low intensities and the results indicate that fiber orientation in thin fiber-based materials can be determined using spatially resolved reflectance or transmittance.
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| 43. |
- Linder, Tomas
(författare)
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Light scattering in pulp and paper
- 2012
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The pulp and paper industry of today is facing a highly competitive market where manufacturers are constantly seeking ways to reduce costs as well as to improve product specifications and quality. On-line quality control is one of many areas being actively developed, from the wood delivered to the plant to the fibers in the finished product. In general, on-line property measurements are best utilized by establishing an understanding of the underlying physics and using that knowledge in an optimal way to determine the parameter or property sought for. One specific area of development is to determine fiber orientation in a paper sheet. The fiber orientation is set by the production Process and is an important parameter since it defines e.g. strength and Optical properties of the paper. In the paper mill today, improvements can be made if the fiber orientation could be determined on-line and in real time. One way of doing this is to use non-contact, full-optical techniques to determine the light scattering pattern in a paper sheet. The objective of this work is to determine the properties of light scattering in paper and how this knowledge could be utilized in extracting information on the properties of paper.A numerical model utilizing light scattering in a sphere-cylinder medium is presented. The simulated medium can represent scattering in both wood pulp and paper. Wood fibers are represented as long, straight cylinders and smaller particles, like fines, are represented as small spherical particles. Scattering from fibers are determined by an analytical solution of Maxwell’s equations for scattering on infinitely long cylinders. The small spherical particles are described by Mie theory. Fibers can have random orientation as in the case of pulp, or aligned orientation as in paper. The layer-like anisotropic microstructure in paper is considered in the model. The model also employ the Stokes-Mueller formalism for the scattering particles, making the state of polarization possible to track.The effects of varying volume concentration and size of the scattering components on reflection, transmission and polarization of the incident light are investigated. The findings on the differences in depolarization and its spatial distribution opens for techniques that enables the relative proportions of fibers and fines in pulp to be determined.For aligned fiber structures it is shown both theoretically and experimentally that spatially resolved reflectance and transmittance exhibits directional dependence. This information could possibly be used in a robust, rapid and cheap device for on-line characterization in the paper production process.
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| 44. |
- Linder, Tomas
(författare)
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Making the case for edible microorganisms as an integral part of a more sustainable and resilient food production system
- 2019
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Ingår i: Food Security. - : Springer Science and Business Media LLC. - 1876-4517 .- 1876-4525. ; 11, s. 265-278
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Forskningsöversikt (refereegranskat)abstract
- Edible microbial biomass derived from bacteria, yeasts, filamentous fungi or microalgae is a promising alternative to conventional sources of food and feed. Microorganisms are a good source of protein, vitamins and, in some cases, also contain beneficial lipids. The ability of microorganisms to use simple organic substrates for growth permits industrial-scale cultivation of edible microbial biomass in geographical locations that would not compete with agricultural production. Only a handful of microbial products are currently available for human consumption. The use of microbial biomass for animal feed is limited by access to low-cost growth substrates and competition from conventional feed sources such as soy and fishmeal. At a time when the global food production system is threatened by the effects of climate change, the production of edible microorganisms has the potential to circumvent many of the current environmental boundaries of food production as well as reducing its environmental impact. Photosynthetic microorganisms such as cyanobacteria and microalgae can be cultivated for food and feed independently of arable land. In addition, recent technological developments in atmospheric carbon dioxide (CO2) capture, extraction and catalytic conversion into simple organic compounds can be used for cultivation of edible microbial biomass for food and feed in a manner that is wholly independent of photosynthesis. The future possibilities, challenges and risks of scaled-up production of edible microbial biomass in relation to the global food system and the environment are discussed.
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| 45. |
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| 46. |
- Linder, Tomas, et al.
(författare)
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Monte Carlo simulation of photon transport in a randomly oriented sphere-cylinder scattering medium
- 2011
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Ingår i: Applied physics. B, Lasers and optics (Print). - : Springer Science and Business Media LLC. - 0946-2171 .- 1432-0649. ; 105:3, s. 659-664
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Tidskriftsartikel (refereegranskat)abstract
- A Monte Carlo simulation tool for simulating photon transport in a randomly oriented sphere-cylinder medium has been developed. The simulated medium represents a paper pulp suspension where the constituents are assumed to be mono-disperse micro-spheres, representing dispersed fiber fragments, and infinitely long, straight, randomly oriented cylinders representing fibers. The diameter of the micro-spheres is considered to be about the order of the wavelength and is described by Mie scattering theory. The fiber diameter is considerably larger than the wavelength and the photon scattering is therefore determined by an analytical solution ofMaxwell’s equation for scattering at an infinitely long cylinder. By employing a Stokes–Mueller formalism, the software tracks the polarization of the light while propagating through the medium. The effects of varying volume concentrations and sizes of the scattering components on reflection, transmission and polarization of the incident light are investigated. It is shown that not only the size but also the shape of the particles has a big impact on the depolarization.
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| 47. |
- Linder, Tomas
(författare)
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Nitrogen Assimilation Pathways in Budding Yeasts
- 2019
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Ingår i: Non-conventional Yeasts: from Basic Research to Application. - Cham : Springer International Publishing. - 9783030211097 ; , s. 197-236
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 48. |
- Linder, Tomas
(författare)
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Nitrogen source-dependent inhibition of yeast growth by glycine and its N-methylated derivatives
- 2020
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Ingår i: Antonie van Leeuwenhoek. - : Springer Science and Business Media LLC. - 0003-6072 .- 1572-9699. ; 113, s. 437-445
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Tidskriftsartikel (refereegranskat)abstract
- The effect of nitrogen source on the inhibitory properties of glycine and its N-methylated derivatives N-methylglycine (sarcosine), N,N-dimethylglycine, N,N,N-trimethylglycine (glycine betaine) on yeast growth was investigated. On solid minimal medium, all four glycine species completely or partially inhibited growth of Kluyveromyces lactis, Komagataella pastoris, Ogataea arabinofermentans, Spathaspora passalidarum and Yamadazyma tenuis at concentrations 5-10 mM when 10 mM NH4Cl was the sole source of nitrogen. If NH4Cl was substituted by sodium L-glutamate as the sole source of nitrogen, obvious growth inhibition by glycine and its N-methylated derivatives was generally not observed in any of these species. No obvious growth inhibition by any of the glycine species at a concentration of 10 mM was observed in Cyberlindnera jadinii, Lipomyces starkeyi, Lodderomyces elongisporus, Scheffersomyces stipitis or Yarrowia lipolytica on solid minimal medium irrespective of whether the nitrogen source was NH4Cl or sodium L-glutamate. Growth inhibition assays of K. pastoris in liquid minimal medium supplemented with increasing concentrations of N,N-dimethylglycine demonstrated inhibitory effects for nine tested nitrogen sources. In most cases, N,N-dimethylglycine supplementation caused a decrease in growth efficiency that appeared to be proportional to the concentration of N,N-dimethylglycine. The biological relevance of these results is discussed.
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| 49. |
- Linder, Tomas
(författare)
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Phenotypical characterisation of a putative -amino acid transaminase in the yeast Scheffersomyces stipitis
- 2019
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Ingår i: Archives of Microbiology. - : Springer Science and Business Media LLC. - 0302-8933 .- 1432-072X. ; 201, s. 185-192
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic analysis of class III transaminases in the budding yeasts Lachancea kluyveri, Saccharomyces cerevisiae and Scheffersomyces stipitis identified a hitherto uncharacterised Sch. stipitis transaminase encoded by the PICST_54153 gene, which clustered with previously described -amino butyric acid (GABA) and -alanine transaminases. Deletion of the PICST_54153 gene in Sch. stipitis resulted in a complete loss in the utilisation of -alanine and -ureidopropionic acid as nitrogen sources, while growth on 1,3-diaminopropane displayed a significant lag phase compared to the wild-type control. It was therefore concluded that the Sch. stipitis PICST_54153 gene likely encodes a -alanine transaminase. However, minor growth defects when 1,4-diaminobutane or 1,5-diaminopentane was provided as the nitrogen source suggested that the Picst_54153 transaminase may also participate in the catabolism of other diamine-derived -amino acids. Unexpectedly, the picst_54153 deletion mutant failed to grow on solid minimal medium in the presence of 5mM -alanine even if a preferred nitrogen source was provided.
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| 50. |
- Linder, Tomas
(författare)
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Projected environmental benefits of replacing beef with microbial protein
- 2022
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 605, s. 90-96
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Tidskriftsartikel (refereegranskat)abstract
- Ruminant meat provides valuable protein to humans, but livestock production has many negative environmental impacts, especially in terms of deforestation, greenhouse gas emissions, water use and eutrophication(1). In addition to a dietary shift towards plant-based diets(2), imitation products, including plant-based meat, cultured meat and fermentation-derived microbial protein (MP), have been proposed as means to reduce the externalities of livestock production(3-7). Life cycle assessment (LCA) studies have estimated substantial environmental benefits of MP, produced in bioreactors using sugar as feedstock, especially compared to ruminant meat(3,7). Here we present an analysis of MP as substitute for ruminant meat in forward-looking global land-use scenarios towards 2050. Our study complements LCA studies by estimating the environmental benefits of MP within a future socio-economic pathway. Our model projections show that substituting 20% of per-capita ruminant meat consumption with MP globally by 2050 (on a protein basis) offsets future increases in global pasture area, cutting annual deforestation and related CO2 emissions roughly in half, while also lowering methane emissions. However, further upscaling of MP, under the assumption of given consumer acceptance, results in a non-linear saturation effect on reduced deforestation and related CO2 emissions-an effect that cannot be captured with the method of static LCA.
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