| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Li, Chen, et al.
(författare)
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Genome-wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length
- 2020
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Ingår i: American Journal of Human Genetics. - : CELL PRESS. - 0002-9297 .- 1537-6605. ; 106:3, s. 389-404
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Tidskriftsartikel (refereegranskat)abstract
- Leukocyte telomere length (LTL) is a heritable biomarker of genomic aging. In this study, we perform a genome-wide meta-analysis of LTL by pooling densely genotyped and imputed association results across large-scale European-descent studies including up to 78,592 individuals. We identify 49 genomic regions at a false dicovery rate (FDR) < 0.05 threshold and prioritize genes at 31, with five highlighting nucleotide metabolism as an important regulator of LTL. We report six genome-wide significant loci in or near SENP7, MOB1B, CARMIL1 , PRRC2A, TERF2, and RFWD3, and our results support recently identified PARP1, POT1, ATM, and MPHOSPH6 loci. Phenome-wide analyses in >350,000 UK Biobank participants suggest that genetically shorter telomere length increases the risk of hypothyroidism and decreases the risk of thyroid cancer, lymphoma, and a range of proliferative conditions. Our results replicate previously reported associations with increased risk of coronary artery disease and lower risk for multiple cancer types. Our findings substantially expand current knowledge on genes that regulate LTL and their impact on human health and disease.
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| 3. |
- Lotta, Luca A., et al.
(författare)
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Integrative genomic analysis implicates limited peripheral adipose storage capacity in the pathogenesis of human insulin resistance
- 2017
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 49:1, s. 17-26
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Tidskriftsartikel (refereegranskat)abstract
- Insulin resistance is a key mediator of obesity-related cardiometabolic disease, yet the mechanisms underlying this link remain obscure. Using an integrative genomic approach, we identify 53 genomic regions associated with insulin resistance phenotypes (higher fasting insulin levels adjusted for BMI, lower HDL cholesterol levels and higher triglyceride levels) and provide evidence that their link with higher cardiometabolic risk is underpinned by an association with lower adipose mass in peripheral compartments. Using these 53 loci, we show a polygenic contribution to familial partial lipodystrophy type 1, a severe form of insulin resistance, and highlight shared molecular mechanisms in common/mild and rare/severe insulin resistance. Population-level genetic analyses combined with experiments in cellular models implicate CCDC92, DNAH10 and L3MBTL3 as previously unrecognized molecules influencing adipocyte differentiation. Our findings support the notion that limited storage capacity of peripheral adipose tissue is an important etiological component in insulin-resistant cardiometabolic disease and highlight genes and mechanisms underpinning this link.
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| 4. |
- Scott, Robert A., et al.
(författare)
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Common Genetic Variants Highlight the Role of Insulin Resistance and Body Fat Distribution in Type 2 Diabetes, Independent of Obesity
- 2014
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Ingår i: Diabetes. - : American Diabetes Association. - 0012-1797 .- 1939-327X. ; 63:12, s. 4378-4387
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Tidskriftsartikel (refereegranskat)abstract
- We aimed to validate genetic variants as instruments for insulin resistance and secretion, to characterize their association with intermediate phenotypes, and to investigate their role in type 2 diabetes (T2D) risk among normal-weight, overweight, and obese individuals. We investigated the association of genetic scores with euglycemic-hyperinsulinemic clamp- and oral glucose tolerance test-based measures of insulin resistance and secretion and a range of metabolic measures in up to 18,565 individuals. We also studied their association with T2D risk among normal-weight, overweight, and obese individuals in up to 8,124 incident T2D cases. The insulin resistance score was associated with lower insulin sensitivity measured by M/I value (beta in SDs per allele [95% CI], -0.03 [-0.04, -0.01]; P = 0.004). This score was associated with lower BMI (-0.01 [-0.01, -0.0]; P = 0.02) and gluteofemoral fat mass (-0.03 [-0.05,-0.02; P = 1.4x10(-6) and with higher alanine transaminase (0.02 [0.01, 0.03]; P = 0.002) and gamma-glutamyl transferase (0.02 [0.01, 0.03]; P = 0.001). While the secretion score had a stronger association with T2D in leaner individuals (P-interaction = 0.001), we saw no difference in the association of the insulin resistance score with T2D among BMI or waist strata (P-interaction > 0.31). While insulin resistance is often considered secondary to obesity, the association of the insulin resistance score with lower BMI and adiposity and with incident T2D even among individuals of normal weight highlights the role of insulin resistance and ectopic fat distribution in T2D, independently of body size.
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| 5. |
- Angelstam, Per, et al.
(författare)
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Learning about the history of landscape use for the future : consequences for ecological and social systems in Swedish Bergslagen
- 2013
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Ingår i: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 42:2, s. 146-159
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Tidskriftsartikel (refereegranskat)abstract
- Barriers and bridges to implement policies about sustainable development and sustainability commonly depend on the past development of social-ecological systems. Production of metals required integration of use of ore, streams for energy, and wood for bioenergy and construction, as well as of multiple societal actors. Focusing on the Swedish Bergslagen region as a case study we (1) describe the phases of natural resource use triggered by metallurgy, (2) the location and spatial extent of 22 definitions of Bergslagen divided into four zones as a proxy of cumulative pressure on landscapes, and (3) analyze the consequences for natural capital and society. We found clear gradients in industrial activity, stream alteration, and amount of natural forest from the core to the periphery of Bergslagen. Additionally, the legacy of top-down governance is linked to today's poorly diversified business sector and thus municipal vulnerability. Comparing the Bergslagen case study with other similar regions in Russia and Germany, we discuss the usefulness of multiple case studies.
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| 6. |
- Bahnan, Wael, et al.
(författare)
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Spike-Dependent Opsonization Indicates Both Dose-Dependent Inhibition of Phagocytosis and That Non-Neutralizing Antibodies Can Confer Protection to SARS-CoV-2
- 2022
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Ingår i: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Spike-specific antibodies are central to effective COVID19 immunity. Research efforts have focused on antibodies that neutralize the ACE2-Spike interaction but not on non-neutralizing antibodies. Antibody-dependent phagocytosis is an immune mechanism enhanced by opsonization, where typically, more bound antibodies trigger a stronger phagocyte response. Here, we show that Spike-specific antibodies, dependent on concentration, can either enhance or reduce Spike-bead phagocytosis by monocytes independently of the antibody neutralization potential. Surprisingly, we find that both convalescent patient plasma and patient-derived monoclonal antibodies lead to maximum opsonization already at low levels of bound antibodies and is reduced as antibody binding to Spike protein increases. Moreover, we show that this Spike-dependent modulation of opsonization correlate with the outcome in an experimental SARS-CoV-2 infection model. These results suggest that the levels of anti-Spike antibodies could influence monocyte-mediated immune functions and propose that non-neutralizing antibodies could confer protection to SARS-CoV-2 infection by mediating phagocytosis.
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| 7. |
- Bergman Bruhn, Åsa, 1972-
(författare)
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The double-sided nature of lifestyle-oriented work within the Swedish equine sector : Characteristics and consequences for employee health and well-being
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis considers the nature of lifestyle-oriented work, i.e. making a livelihood based on leisure interest or personal lifestyle, and focuses on the perspective of employees within the Swedish equine sector. The purpose was to gain an increased understanding of the characteristics of lifestyle-oriented work and the consequences for health and well-being. The thesis has a case study research design with two embedded units, riding schools and trotting stables, and a mixed methodological approach based on questionnaires and interviews. The findings show that employees experienced their work as both important and attractive with loyalty, relations, and stimulation being important factors for work attractiveness (Paper I). The employees found their work meaningful and worked primarily to achieve self-realization and quality of life. Person–environment fit, task significance, and occupational culture emerged as important factors for meaningfulness. However, the work had an inherent duality as the same factors both promoted and challenged the experiences of work attractiveness and meaningfulness (Paper II). The safety climate was found to be relatively good, despite some risk acceptance (Paper III), although the results indicated shortcomings regarding occupational health and safety management (OHSM) (Papers III and IV). Moreover, motivation, management, occupational culture, and resources affect both participation and compliance in OHSM (Paper IV).Lifestyle-oriented work within the equine sector can be described as double-sided, i.e. both satisfying and demanding. The work is characterized by attraction, meaningfulness, prosocial behavior, and a strong occupational culture but also an acceptance of challenging working conditions, overwork and deficient conditions for OHSM. A systematic OHSM, where both health-promoting factors and risk factors are considered, is necessary to enhance employee health and well-being and to create attractive and sustainable employment.
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| 8. |
- Björk, Robert G., 1974, et al.
(författare)
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A Climate Change aspect on root dynamics and nitrogen partitioning in a tundra landscape
- 2005
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Ingår i: Sediment budgets and rates of sediment transfer across cold environments in Europe. 3rd Workshop of the ESF Network SEDIFLUX, Durham, UK, 15 – 19 December 2005..
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The Arctic Climate Impact Assessment (ACIA) recently reported that Arctic is rapidly changing due to Climate Change. Likewise, the mountains of Europe are going to experience large shifts in plant composition and 41-56% of the alpine species might be on the edge of extinction according to the 1st synthesis of the Global Observation Research Initiative in Alpine Environments (GLORIA). Although the tundra ecosystems are subjected to dramatical changes as a result of Climate Change, there is little knowledge of the effect on root dynamics and its implication on the nitrifying and denitrifying microbial community. Here, we compare nitrification enzyme activity (NEA) and denitrification enzyme activity (DEA) rates along an altitudinal gradient with the effects of climatic warming using Open Top Chambers (OTCs) in consideration with root dynamics and architecture. This study was conducted at Latnjajaure Field Station (LFS) located in the midalpine region in northern Sweden. LFS is the Swedish field site for the International Tundra Experiment (ITEX), established in 1993. This gives an opportunity to investigate long-term effects of climatic warming by OTCs and an altitudinal gradient (1000m to 1365m), both within a very small geographical range. The OTCs used at LFS increases the soil surface temperature by approximately 1.5ºC whereas air temperatures normally falls with 0.6ºC with every hundred meter of increased altitude. To analyse the NEA and DEA we used an anaerobic incubation technique, based on acetylene inhibition technique, resulting in N2O as the only end product, which then were analysed by gas chromatography. Soil cores were additionally sampled in the OTCs to study the effects of climatic warming on the root system. The specific root length, root length density and root biomass were determined for the different root fractions. The results from NEA and DEA contradict each other. The gradient study show decreased NEA and DEA rates with falling altitude, whereas the warming experiment show a slight non significant increase due to the temperature enhancement by OTCs. The preliminary results from the root sampling indicate that there is a plant community specific response in root architecture, which has an output on root biomass and particularly in the fraction of fine roots, although, climatic warming did not have any significant affect on the root biomass. The fact that altitudinal temperature decline did not reduce NEA and DEA rates might in part be explained of the variables measured here, although they are not conclusive.
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| 9. |
- Björk, Robert G., 1974, et al.
(författare)
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Long-term warming effects on root morphology, root mass distribution, and microbial activity in two dry tundra plant communities in northern Sweden
- 2007
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 176:4, s. 862-873
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Tidskriftsartikel (refereegranskat)abstract
- center dot Effects of warming on root morphology, root mass distribution and microbial activity were studied in organic and mineral soil layers in two alpine ecosystems over > 10 yr, using open-top chambers, in Swedish Lapland. center dot Root mass was estimated using soil cores. Washed roots were scanned and sorted into four diameter classes, for which variables including root mass (g dry matter (g DM) m(-2)), root length density (RLD; cm cm(-3) soil), specific root length (SRL; m g DM-1), specific root area (SRA; m(2) kg DM-1), and number of root tips m(-2) were determined. Nitrification (NEA) and denitrification enzyme activity (DEA) in the top 10 cm of soil were measured. center dot Soil warming shifted the rooting zone towards the upper soil organic layer in both plant communities. In the dry heath, warming increased SRL and SRA of the finest roots in both soil layers, whereas the dry meadow was unaffected. Neither NEA nor DEA exhibited differences attributable to warming. center dot Tundra plants may respond to climate change by altering their root morphology and mass while microbial activity may be unaffected. This suggests that carbon may be incorporated in tundra soils partly as a result of increases in the mass of the finer roots if temperatures rise.
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| 10. |
- Björk, Robert G., 1974, et al.
(författare)
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Nitrification and Denitrification Enzyme Activity: a successful tool in Arctic and Alpine soil ecology
- 2007
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Ingår i: The 14th ITEX workshop, Falls Creek, Victoria, Australia, 2–6 February 2007..
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Nitrogen is consideration to be a limiting factor for plants and microbes in arctic and alpine ecosystems and the rates of mineralization, nitrification, and denitrifi¬cation are known to be generally low. However, Climate Change is expected to alter the nitrogen availability and dynamics and, as a consequence, affect plant community composition and production. The general consensus today is that increased temperature will lead to greater microbial activity and more plant-available nitrogen. Nevertheless, nitrification and denitrification are restricted by a number of environmental factors such as low tem¬perature and low pH. The C/N ratio and the water content of the soils also play an important role in determining the rates of nitrification and denitrification. Since 2002 microbial studies has been undertaken at Latnjajure, and comprise several microbial techniques, e.g. Nitrification Enzyme Activity (NEA), Denitrification Enzyme Activity (DEA), Phospholipid fatty acid analysis (PFLA), and Temperature Gradient Gel Electrophoresis (TGGE). These studies focuses on the interaction between plants and microbes along natural environmental gradients, both within plant communities and within the landscape, but also entails the OTCs used in the ITEX studies at Latnjajaure. Here we present the techniques NEA and DEA and give some brief results from how these have been successfully applied at Latnjajaure. In ecosystems with low nitrification activity, small amounts of NO3-/NO2- will be formed and it is thus difficult to measure low fluxes. However, NO3-/NO2- can be converted to N2O and then analysed by gas chromatography, whereby the detection limit is increased at least 1000 times compared to the spectroscopical technique. These techniques are referred to Nitrification (NEA) and Denitrification Enzyme Activity (DEA) and give a potential measure on the nitrification and denitrification rates, which goes back to the actual populations of nitrifiers and denitrifiers in the soil. For instance, NEA has been proved to better correlate with extractable NH4+ concentration than net nitrification does, and still after twelve weeks show a strong correlation with the initial extractable NH4+ concentration. Therefore, these variables, in particular NEA, have the advantage of being a much more stable variable than, for instance, extractable N concentrations and net nitrification, and NEA and DEA are therefore suitable when working in fringe environments with restricted logistics like the Latnjajaure catchment. NEA is measured using a two-step incubation technique; first by incubate the soil with a nutrient solution for 24 hours in darkness, at room temperature on a rotary shaker. Sub-samples are then withdrawn after a specified time schedule. The second step allows NO3- to be reduced to N2O by adding a modified denitrifying bacterium, Pseudomonas chlororaphis ATCC 43928, together with a carbon source. This strain of bacteria lacks the enzyme to reduce N2O to N2. The samples are then again incubated in darkness, at room temperature for 24 hours, and analysed by gas chromatography. This method was first used by Lensi et al. (1985, 1986), to study nitrification potentials in forest soils. Furthermore, the method has been developed for soils with low pH and small amounts of NO3- and the analysis makes the quantification without interference of organic matter, which makes it suitable for arctic and alpine ecosystems. To analyse DEA an anaerobic incubation technique is used, based on acetylene inhibition of the N2O-reductase resulting in N2O as the only end product. The soil sample is evacuated and flushed with N2. Thereafter acetylene is inserted to a final acetylene concentration of 10%, and the samples are shaken continuously and gas samples are withdrawn after a specified time schedule, which is then analysed by gas chromatography. This provides an estimate of the maximum concentration of functional denitrifying enzymes in the soil. Denitrifiers, in contrast to nitrifiers, are heterotrophs and can switch from using NO3- as an alternative electron acceptor to O2 under aerobic conditions. This makes other factors in the soil important determinants of DEA, e.g. availability of oxygen and C. Hence, the presence of denitrifiers is rarely a limitation for denitrification and they usually make up a reasonably large fraction of the soil bacteria. At Latnjajaure NEA shows a larger differentiation across plant communities than DEA. However, the spatial variability in the landscape, at the meso-scale, was in the same range in both variables and increased with altitude from 1000 to 1365 m a.s.l, particularly in heath plant communities. This result suggests that the decrease in mean annual temperature with altitude (0.6ºC with every one hundred meters) did not reduce nitrification and denitrification rates, as one might have expected. None of the other variable studied could explain the altitudinal increase in all cases, and the factors controlling the nitrification and denitrification rates seem to vary with the vegetation type. Furthermore, neither NEA nor DEA exhibited any changes between the ambient and warmed plots in the warming experiments. However, the warming experiment in the dry heath exhibited a change in root morphology via increased specific root length (SRL; m gDM-1) and specific root area (SRA; m2 kgDM -1). As both heterotrophic microbes and plants out-compete nitrifiers for NH4+, a change in root morphology, as seen in the warming experiment, may also explain the increased activity of nitrifying and denitrifying microbes with altitude.
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