| 1. |
- Bhattacharyya, Anirban, et al.
(author)
-
ESS RF Source and Spoke Cavity Test Plan
- 2015
-
Reports (other academic/artistic)abstract
- This report describes the test plan for the first high power RF source, ESS prototype double spoke cavity and ESS prototype cryomodule at the FREIA Laboratory.
|
|
| 2. |
- Cheng, Fang, et al.
(author)
-
Common traffic routes for imported spermine and endosomal glypican-1-derived heparan sulfate in fibroblasts
- 2018
-
In: Experimental Cell Research. - : Elsevier BV. - 0014-4827. ; 364:2, s. 133-142
-
Journal article (peer-reviewed)abstract
- Import of the polyamine spermine from the extracellular environment depends on the presence of cell surface heparan sulfate proteoglycans, such as glypican-1. This proteoglycan is internalized by endocytosis, releases its heparan sulfate chains in endosomes by a nitric oxide-, copper- and amyloid precursor protein-dependent mechanism, then penetrates the membrane and is transported to the nucleus and then to autophagosomes. This process is spontaneous or induced by ascorbate depending on the growth-state of the cell. Here, we have explored possible connections between the heparan sulfate traffic route and spermine uptake and delivery in wild-type and Tg2576 mouse fibroblasts. Cells were examined by deconvolution immunofluorescence microscopy. The antibodies used were specific for spermine, glypican-1-derived heparan sulfate, Rab7, nucleolin and a marker for autophagosomes. Endogenous immunostainable spermine was primarily associated with autophagosomes. When spermine synthesis was inhibited, imported spermine appeared in Rab7-positive endosomes. When ascorbate was added, heparan sulfate and spermine were transported to the nucleus where they colocalized with nucleolin. Spermine also appeared in autophagosomes. In a pulse-chase experiment, heparan sulfate and spermine were first arrested in late endosomes by actinomycin D treatment. During the chase, when arrest was abolished, heparan sulfate and spermine were both transported to the nucleus and targeted nucleolin. In amyloid precursor protein-/--fibroblasts, ascorbate failed to induce release of heparan sulfate and spermine remained in the endosomes. We propose that cell surface glypican-1 carries spermine to the endosomes and that the released heparan sulfate carries spermine across the membrane into the cytosol and then to the nucleus.
|
|
| 3. |
- Cheng, Fang, et al.
(author)
-
Cytochrome b561, copper, β-cleaved amyloid precursor protein and niemann-pick C1 protein are involved in ascorbate-induced release and membrane penetration of heparan sulfate from endosomal S-nitrosylated glypican-1
- 2017
-
In: Experimental Cell Research. - : Elsevier BV. - 0014-4827. ; 360:2, s. 171-179
-
Journal article (peer-reviewed)abstract
- Ascorbate-induced release of heparan sulfate from S-nitrosylated heparan sulfate proteoglycan glypican-1 takes place in endosomes. Heparan sulfate penetrates the membrane and is transported to the nucleus. This process is dependent on copper and on expression and processing of the amyloid precursor protein. It remains unclear how exogenously supplied ascorbate can generate HS-anMan in endosomes and how passage through the membrane is facilitated. Here we have examined wild-type, Alzheimer Tg2576 and amyloid precursor protein (-/-) mouse fibroblasts and human fetal and Niemann-Pick C1 fibroblasts by using deconvolution immunofluorescence microscopy, siRNA technology and [S35]sulfate-labeling, vesicle isolation and gel chromatography. We found that ascorbate-induced release of heparan sulfate was dependent on expression of endosomal cytochrome b561. Formation and nuclear transport of heparan sulfate was suppressed by inhibition of β-processing of the amyloid precursor protein and formation was restored by copper (I) ions. Membrane penetration was not dependent on amyloid beta channel formation. Inhibition of endosomal exit resulted in accumulation of heparan sulfate in vesicles that exposed the C-terminal of the amyloid precursor protein externally. Endosome-to-nucleus transport was also dependent on expression of the Niemann-Pick C1 protein. We propose that ascorbate is taken up from the medium and is oxidized by cytochrome b561 which, in turn, reduces copper (II) to copper (I) present in the N-terminal, β-cleaved domain of the amyloid precursor protein. Re-oxidation of copper (I) is coupled to reductive, deaminative release of heparan sulfate from glypican-1. Passage through the membrane may be facilitated by the C-terminal, β-cleaved fragment of the amyloid precursor protein and the Niemann-Pick C1 protein.
|
|
| 4. |
- Cheng, Fang, et al.
(author)
-
Hypoxia induces NO-dependent release of heparan sulfate in fibroblasts from the Alzheimer mouse Tg2576 by activation of nitrite reduction.
- 2016
-
In: Glycobiology. - : Oxford University Press (OUP). - 1460-2423 .- 0959-6658. ; 26:6, s. 623-634
-
Journal article (peer-reviewed)abstract
- There is a functional relationship between the heparan sulfate proteoglycan glypican-1 and the amyloid precursor protein of Alzheimer disease. In wild-type mouse embryonic fibroblasts, expression and processing of the amyloid precursor protein is required for endosome-to-nucleus translocation of anhydromannose-containing heparan sulfate released from S-nitrosylated glypican-1 by ascorbate-induced, nitrosothiol-catalyzed deaminative cleavage. In fibroblasts from the transgenic Alzheimer mouse Tg2576 there is increased processing of the amyloid precursor protein to amyloid-β peptides. Simultaneously, there is spontaneous formation of anhydromannose-containing heparan sulfate by an unknown mechanism. We have explored the effect of hypoxia on anhydromannose-containing heparan sulfate formation in wild-type and Tg2576 fibroblasts by deconvolution immunofluorescence microscopy and flow cytometry using an anhydromannose-specific monoclonal antibody and by (35)SO4-labeling experiments. Hypoxia prevented ascorbate-induced heparan sulfate release in wild-type fibroblasts, but induced an increased formation of anhydromannose-positive and (35)S-labeled heparan sulfate in Tg2576 fibroblasts. This appeared to be independent of glypican-1 S-nitrosylation as demonstrated by using a monoclonal antibody specific for S-nitrosylated glypican-1. In hypoxic wild-type fibroblasts, addition of nitrite to the medium restored anhydromannose-containing heparan sulfate formation. The increased release of anhydromannose-containing heparan sulfate in hypoxic Tg2576 fibroblasts did not require addition of nitrite. However, it was suppressed by inhibition of the nitrite reductase activity of xanthine oxidoreductase/aldehyde oxidase or by inhibition of p38 mitogen-activated protein kinase or by chelation of iron. We propose that normoxic Tg2576 fibroblasts maintain a high level of anhydromannose-containing heparan sulfate production by a stress-activated generation of nitric oxide from endogenous nitrite. This activation is enhanced by hypoxia.
|
|
| 5. |
- Cheng, Fang, et al.
(author)
-
Nucleolin is a nuclear target of heparan sulfate derived from glypican-1
- 2017
-
In: Experimental Cell Research. - : Elsevier BV. - 0014-4827. ; 354:1, s. 31-39
-
Journal article (peer-reviewed)abstract
- The recycling, S-nitrosylated heparan sulfate (HS) proteoglycan glypican-1 releases anhydromannose (anMan)-containing HS chains by a nitrosothiol-catalyzed cleavage in endosomes that can be constitutive or induced by ascorbate. The HS-anMan chains are then transported to the nucleus. A specific nuclear target for HS-anMan has not been identified. We have monitored endosome-to-nucleus trafficking of HS-anMan by deconvolution and confocal immunofluorescence microscopy using an anMan-specific monoclonal antibody in non-growing, ascorbate-treated, and growing, untreated, wild-type mouse embryonic fibroblasts and hypoxia-exposed Alzheimer mouse Tg2576 fibroblasts and human U87 glioblastoma cells. In all cells, nuclear HS-anMan targeted a limited number of sites of variable size where it colocalized with DNA and nucleolin, an established marker for nucleoli. HS-anMan also colocalized with ethynyl uridine-tagged nascent RNA and two acetylated forms of histone H3. Acute hypoxia increased the formation of HS-anMan in both Tg2576 and U87 cells. A portion of HS-anMan colocalized with nucleolin at small discrete sites, while most of the nucleolin and nascent RNA was dispersed. In U87 cells, HS-anMan, nucleolin and nascent RNA reassembled after prolonged hypoxia. Nucleolar HS may modulate synthesis and/or release of rRNA.
|
|
| 6. |
- Cheng, Fang, et al.
(author)
-
Rapid nuclear transit and impaired degradation of amyloid beta and glypican-1-derived heparan sulfate in Tg2576 mouse fibroblasts.
- 2015
-
In: Glycobiology. - : Oxford University Press (OUP). - 1460-2423 .- 0959-6658. ; 25:5, s. 548-556
-
Journal article (peer-reviewed)abstract
- Anhydromannose (anMan)-containing heparan sulfate (HS) derived from S-nitrosylated glypican-1 is generated in endosomes by an endogenously or ascorbate induced S-nitrosothiol-catalyzed reaction. Expression and processing of amyloid precursor protein (APP) is required to initiate formation and endosome-to-nucleus translocation of anMan-containing HS in wild-type mouse embryonic fibroblasts (WT MEF). HS is then transported to autophagosomes and finally degraded in lysosomes. To investigate how APP-derived amyloid beta peptide (Aβ) affects intracellular trafficking of HS we have studied nuclear transit as well as autophagosome/lysosome targeting and degradation in Tg2576 MEF which produce increased amounts of Aβ. Deconvolution immunofluorescence microscopy with an anMan-specific monoclonal antibody showed anMan-staining in the nuclei of Tg2576 MEF after 5 min of ascorbate treatment and after 15 min in WT MEF. There was also greater nuclear accumulation of HS in Tg2576 MEF as determined by (35)S-sulfate labeling experiments. Tg2576 MEF was less sensitive to inhibition of NO production and copper-chelation than WT MEF. By using APP- and Aβ-recognizing antibodies we observed nuclear translocation of Aβ peptide in Tg2576 MEF but not in WT MEF. HS remained in the nucleus of WT MEF for at least 8 h and was then transported to autophagosomes. By 8 h HS had disappeared from the nuclei of Tg2576 MEF but colocalized poorly with the autophagosome marker LC3. Aβ also disappeared rapidly from the nuclei of Tg2576 MEF. Initially it appeared in acidic vesicles and later it accumulated extracellularly. Thus, in Tg2576 MEF there is nuclear accumulation as well as secretion of Aβ and impaired degradation of HS.
|
|
| 7. |
- Cheng, Fang, et al.
(author)
-
Suppression of glypican-1 autodegradation by NO-deprivation correlates with nuclear accumulation of amyloid beta in normal fibroblasts.
- 2015
-
In: Glycoconjugate Journal. - : Springer Science and Business Media LLC. - 1573-4986 .- 0282-0080. ; 32:9, s. 675-684
-
Journal article (peer-reviewed)abstract
- Heparan sulfate (HS)-containing, S-nitrosylated (SNO) glypican-1 (Gpc-1) releases anhydromannose-containing HS (anMan-HS) by SNO-catalyzed autodegradation in endosomes. Transport of anMan-HS to the nucleus requires processing of the amyloid precursor protein (APP) to amyloid beta peptides (Aβ). To further examine the relationship between APP and Gpc-1 processing in normal fibroblasts we have suppressed Gpc-1 autodegradation by aminoguanidine inhibition of NO synthesis and prevented lysosomal degradation of anMan-HS by using chloroquine. Deconvolution immunofluorescence microscopy and SDS-PAGE using anMan- and APP/Aβ-specific antibodies and markers for nuclei and autophagosomes were used to identify subcellular localization of Aβ and its oligomeric state. Wild-type mouse embryonic fibroblasts (WT MEF) grown during NO-deprivation accumulated 95-98 % of Aβ as oligomers in the nucleus. WT MEF treated with chloroquine accumulated both anMan-HS and Aβ, first in the nucleus then in autophagosomes. Maximal nuclear anMan-HS and Aβ accumulation was obtained after 4 and 7 h of growth, respectively. Both yielded similar banding patterns on SDS-PAGE which were also similar to the Aβ oligomers obtained after NO-deprivation. Nuclear Aβ accumulation was marginally increased (from 54 to 58 %) by suppression of both release and degradation of anMan-HS. Nuclear exit of Aβ, accumulated during growth in aminoguanidine, was enhanced by ascorbate-induced reactivation of anMan-HS production. Transgenic Alzheimer disease mouse (Tg2576) MEF, which produces excess amount of Aβ was used for comparison. Overall, nuclear Aβ exit and lysosomal degradation was compromised by inhibition of the autophagosome-lysosome pathway in both WT and Tg2576 MEF, while only WT MEF was sensitive to suppression of Gpc-1 autodegradation.
|
|
| 8. |
- Cheng, Fang, et al.
(author)
-
The cyanobacterial neurotoxin β-N-methylamino-L-alanine prevents addition of heparan sulfate to glypican-1 and increases processing of amyloid precursor protein in dividing neuronal cells
- 2019
-
In: Experimental Cell Research. - : Elsevier BV. - 0014-4827. ; 379:2, s. 172-181
-
Journal article (peer-reviewed)abstract
- The neurotoxin β-N-methylamino-L-alanine replaces L-serine in proteins and produces Alzheimer-like pathology. In proteoglycans, e.g. glypican-1, this should preclude substitution with heparan sulfate chains. Reduced release of heparan sulfate should increase β-secretase activity and processing of amyloid precursor protein. Cultured cells were treated with β-N-methylamino-L-alanine during the growth-phase and the effect on heparan sulfate substitution and amyloid precursor protein processing was evaluated using antibodies specific for heparan sulfate, the N- and C-termini of the C-terminal fragment of β-cleaved amyloid precursor protein, and amyloid beta followed by immunofluorescence microscopy, flow cytometry or SDS-PAGE. Mouse fibroblasts, N2a neuroblastoma cells and human neural stem cells released less heparan sulfate when grown in the presence of β-N-methylamino-L-alanine. Cells expressing a recombinant, anchor-less glypican-1 secreted heparan sulfate-deficient glypican-1. There was increased processing of amyloid precursor protein in N2a cells when grown in the presence of the neurotoxin. The degradation products accumulated in cytoplasmic clusters. Secretion of amyloid beta increased approx. 3-fold. Human neural stem cells also developed cytoplasmic clusters containing degradation products of amyloid precursor protein. When non-dividing mouse N2a cells or cortical neurons were exposed to β-N-methylamino-L-alanine there was no effect on heparan sulfate substitution in glypican-1 or on amyloid precursor protein processing.
|
|
| 9. |
- Fransson, Peter, 1988-, et al.
(author)
-
Model-based investigation on the effects of spatial evenness, and size selection in thinning of Picea abies stands
- 2019
-
In: Scandinavian Journal of Forest Research. - : Taylor & Francis. - 0282-7581 .- 1651-1891. ; 34:3, s. 189-199
-
Journal article (peer-reviewed)abstract
- Size and spatial distribution of trees are important for forest stand growth, but the extent to which itmatters in thinning operations, in terms of wood production and stand economy, has rarely beendocumented. Here we investigate how the choice of spatial evenness and tree-size distribution ofresidual trees impacts wood production and stand economy. A spatially explicit individual-basedgrowth model was used, in conjunction with empirical cost functions for harvesting andforwarding, to calculate net production and net present value for different thinning operations inNorway spruce stands in Northern Sweden. The in silico thinning operations were defined by threevariables: (1) spatial evenness after thinning, (2) tree size preference for harvesting, and (3) basalarea reduction. We found that thinning that increases spatial evenness increases net productionand net present value by around 2.0%, compared to the worst case. When changing the spatialevenness in conjunction with size preference we could observe an improvement of the netproduction and net present value up to 8.0%. The magnitude of impact differed greatly betweenthe stands (from 1.7% to 8.0%) and was highest in the stand with the lowest stem density.
|
|
| 10. |
- Fransson, Peter, 1988-
(author)
-
Optimal thinning : a theoretical investigation on individual-tree level
- 2019
-
Doctoral thesis (other academic/artistic)abstract
- Paper I: In paper I, we asked how a tree should optimally allocate its resources to maximize its fitness. We let a subject tree grow in an environment shaded by nearby competing trees. The competitors were assumed to have reached maturity and had stopped growing, thus creating a static light environment for the subject tree to grow in. The light environment was modeled as a logistic function. For the growth model we used the pipe model as a foundation, linking tree width and leaf mass. This allowed us to construct a dynamic tree-growth model where the tree can allocate biomass from photosynthesis (net productivity) to either stem-height growth, crown-size growth, or reproduction (seed production). Using Pontryagin's maximum principle we derived necessary conditions for optimal biomass allocation, and on that built a heuristic allocation model. The heuristic model states that the tree should first invest into crown-size and then switch to tree height-growth, and lastly invest into crown-size before the growth investments stop and all investments are allocated to reproduction. To test our heuristic method, we used it to determine the growth in several different light environments. The results were then compared to the optimal growth trajectories. The optimal growth was determined by applying dynamic programming. Our less computationally demanding heuristic performed very well in comparison. We also found there exist a critical crown-size: if the subject tree possessed a larger crown-size, the tree would be unable to reach up to the canopy height.Paper II: One of the most important aspects of modelling forest growth, and modelling growth of individual trees in general, is the competition between trees. A high level of competition pressure has a negative impact on the growth of individual trees. There are many ways of modelling competition, the most common one is by using a competition index. In this paper we tested 16 competition indices, in conjunction with a log-linear growth model, in terms of the mean squared error and the coefficient of determination. 5 competition indices are distance-independent (i.e. distance between the competitors are not taken into consideration) and 11 are distance-dependent. The data we used to fit our growth model, with accompanying competition index, was taken from an experimental site, in northern Sweden, of Norway spruce. The growth data for the Norway spruce comes from stands which were treated with one of two treatments, solid fertilization, liquid fertilization, or no treatment (control stand). We found that the distance-dependent indices perform better than the distance-independent. However, both the best distance-dependent and independent index performed overall well. We also found that the ranking of the indices was unaffected by the stand treatment, i.e. indices that work well for one treatment will work well for the others.Paper III: In this paper we studied how spatial distribution and size selection affect the residual trees, after a thinning operation, in terms of merchantable wood production and stand economy. We constructed a spatially explicit individual-based forest-growth model and fitted and validated the model against empirical data for Norway spruce stands in northern Sweden. To determine the cost for the forest operation we employed empirical cost functions for harvesting and forwarding. The income from the harvested timber is calculated from volume-price lists. The thinnings were determined by three parameters: the spatial evenness of residual trees, the size selection of removed trees, and the basal area reduction. In order to find tree selections fulfilling these constraints we used the metropolis algorithm. We varied these three constrains and applied them for thinning of different initial configurations of Norway spruce stands. The initial configurations for the stands where collected from empirical data. We found that changing the spatial evenness and size selection improved the net wood production and net present value of the stand up to 8%. However, the magnitude of improvement was dependent on the initial configuration (the magnitude of improvement varied between 1.7%—8%).Paper IV: With new technology and methods from remote sensing, such as LIDAR, becoming more prevalent in forestry, the ability to assess information on a detailed scale has become more available. Measurements for each individual tree can be more easily gathered on a larger scale. This type of data opens up for using individual-based model for practical precision forestry planning. In paper IV we used the individual-based model constructed in paper III to find the optimal harvesting time for each individual tree, such that the land expectation value is maximized. We employed a genetic algorithm to find a near optimal solution to our optimization. We optimized a number of initial Norway spruce stands (data obtained from field measurements). The optimal management strategy was to apply thinning from above. We also found that increasing the discount rate will decrease the time for final felling and increase basal area reduction for the optimal strategy. Decreasing relocation costs (the cost to bring machines to the stand) led to an increase in the number of optimal thinnings and postponed the first thinning. Our strategy was superior to both the unthinned strategy and a conventional thinning strategy, both in terms of land expectation value (>20% higher) and merchantable wood production.
|
|
