| 1. |
- Dupont, Chris L., et al.
(författare)
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Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:2, s. e89549-
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.
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| 2. |
- Westlund, Malin, et al.
(författare)
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Rätt att bo kvar : en handbok i organisering mot hyreshöjningar och gentrifiering
- 2016
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- Det här är en handbok som skrivits för att användas praktiskt i kampen om hyresrättens framtid. Boken har växt fram ur gemensamma erfarenheter av att ta strid mot renoveringar med höga hyreshöjningar som följd. Det har gett oss både kunskaper om lokal organisering och en övertygelse om vikten av att hyresgäster ska ha rätt till att påverka framtiden i de bostadsområden de bor i. De senaste åren har vi kunnat se hur hyreslägenheter renoveras med omfattande hyreshöjningar som följd. Konsekvenserna har blivit att många hyresgäster har tvingats flytta, ibland från bostadsområden de bott i under lång tid, då de inte längre har råd att betala hyran. Om inte hyresgäster går samman och kräver sina rättigheter kommer inget förändras och flera tusentals människor tvingas flytta. Den här handboken ska användas som ett praktiskt verktyg för lokal organisering. Vi som har gjort den här boken är engagerade i olika rörelser, några av oss är också forskare med inriktning mot bostad- spolitik och stadsutveckling. Boken har tillkommit genom en kollektiv process, där många varit inblandade för att bidra med sina erfarenheter och perspektiv. En lista med alla medverkande inklusive de rörelser som står bakom den här boken finns lägst bak.
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| 3. |
- Almström, Peter, 1972, et al.
(författare)
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How to improve productivity by 160%
- 2014
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Ingår i: The sixth Swedish Production Symposium.
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Konferensbidrag (refereegranskat)abstract
- There is a large capacity increase potential in Swedish industry through increasing productivity of existing resources without investing in more machines or personnel. This article presents a case study where the capacity could increase more than 160% percent. This was proven by a test in running production. This tremendous increase was made possible through standardization and time setting of all work tasks. A new scheduling system was made up of product activity sequences based on a vast library of over 800 standardized generic activities.
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| 4. |
- Asplund Samuelsson, Johannes, 1987-
(författare)
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Adaptations and constraints associated with autotrophy in microbial metabolism
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Carbon dioxide (CO2) emissions from human activities are driving climate change, but the pending crisis could be mitigated by a circular carbon economy where released CO2 is recycled into commodity chemicals. Autotrophic microbes can make a contribution by producing chemicals, such as biofuels, from CO2 and renewable energy. The primary natural CO2 fixation pathway is the Calvin cycle, in which the enzyme Rubisco carboxylates ribulose-1,5-bisphosphate. The present investigation used computational systems biology methods to map adaptations and constraints in autotrophic microbial metabolism based on the Calvin cycle. First, the metabolic network of the Calvin cycle-capable photoautotrophic cyanobacterium Synechocystis was contrasted with that of heterotrophic E. coli. Intracellular metabolite concentration ranges differed, leading to different capacity to provide thermodynamic driving forces to chemical production pathways. Second, the Calvin cycle in Synechocystis was modeled kinetically, showing that certain enzyme saturation and metabolite levels, for example high ribulose-1,5-bisphosphate concentration, were detrimental to stability. Control over reaction rates was distributed, but making certain enzymes faster, for example fructose-1,6-bisphosphatase, could increase overall carbon fixation rate. Third, Synechocystis was starved of CO2 and ribosome profiling was used to track the effect on translation. Stress response and CO2 uptake were upregulated, but constant Rubisco expression and ribosome pausing in 5' untranslated regions indicated readiness for reappearance of CO2. Finally, microbial genomes with and without the Calvin cycle were contrasted, revealing metabolic, energetic, and regulatory adaptations that describe the properties of a functional autotroph. These findings provide a background for future study and engineering of autotrophs for direct conversion of CO2 into commodity chemicals.
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| 5. |
- Asplund Samuelsson, Johannes, et al.
(författare)
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Diversity and expression of bacterial metacaspases in an aquatic ecosystem
- 2016
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 7, s. 1-18
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Tidskriftsartikel (refereegranskat)abstract
- Metacaspases are distant homologs of metazoan caspase proteases, implicated in stress response, and programmed cell death (PCD) in bacteria and phytoplankton. While the few previous studies on metacaspases have relied on cultured organisms and sequenced genomes, no studies have focused on metacaspases in a natural setting. We here present data from the first microbial community-wide metacaspase survey; performed by querying metagenomic and metatranscriptomic datasets from the brackish Baltic Sea, a water body characterized by pronounced environmental gradients and periods of massive cyanobacterial blooms. Metacaspase genes were restricted to ~4% of the bacteria, taxonomically affiliated mainly to Bacteroidetes, Alpha- and Betaproteobacteria and Cyanobacteria. The gene abundance was significantly higher in larger or particle-associated bacteria (<0.8 μm), and filamentous Cyanobacteria dominated metacaspase gene expression throughout the bloom season. Distinct seasonal expression patterns were detected for the three metacaspase genes in Nodularia spumigena, one of the main bloom-formers. Clustering of normalized gene expression in combination with analyses of genomic and assembly data suggest functional diversification of these genes, and possible roles of the metacaspase genes related to stress responses, i.e., sulfur metabolism in connection to oxidative stress, and nutrient stress induced cellular differentiation. Co-expression of genes encoding metacaspases and nodularin toxin synthesis enzymes was also observed in Nodularia spumigena. The study shows that metacaspases represent an adaptation of potentially high importance for several key organisms in the Baltic Sea, most prominently Cyanobacteria, and open up for further exploration of their physiological roles in microbes and assessment of their ecological impact in aquatic habitats.
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| 6. |
- Asplund-Samuelsson, Johannes, et al.
(författare)
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Prokaryotic Caspase Homologs : Phylogenetic Patterns and Functional Characteristics Reveal Considerable Diversity
- 2012
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:11, s. e49888-
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Tidskriftsartikel (refereegranskat)abstract
- Caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. The existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. Despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. Aiming at providing a more detailed picture of prokaryotic caspase homologs, we applied a computational approach based on Hidden Markov Model search profiles to identify and functionally characterize putative metacaspases in bacterial and archaeal genomes. Out of the total of 1463 analyzed genomes, merely 267 (18%) were identified to contain putative metacaspases, but their taxonomic distribution included most prokaryotic phyla and a few archaea (Euryarchaeota). Metacaspases were particularly abundant in Alphaproteobacteria, Deltaproteobacteria and Cyanobacteria, which harbor many morphologically and developmentally complex organisms, and a distinct correlation was found between abundance and phenotypic complexity in Cyanobacteria. Notably, Bacillus subtilis and Escherichia coli, known to undergo genetically regulated autolysis, lacked metacaspases. Pfam domain architecture analysis combined with operon identification revealed rich and varied configurations among the metacaspase sequences. These imply roles in programmed cell death, but also e.g. in signaling, various enzymatic activities and protein modification. Together our data show a wide and scattered distribution of caspase homologs in prokaryotes with structurally and functionally diverse subgroups, and with a potentially intriguing evolutionary role. These features will help delineate future characterizations of death pathways in prokaryotes.
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| 7. |
- Asplund-Samuelsson, Johannes, et al.
(författare)
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Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential
- 2018
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Ingår i: Metabolic engineering. - : Academic Press Inc.. - 1096-7176 .- 1096-7184. ; 45, s. 223-236
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Tidskriftsartikel (refereegranskat)abstract
- Introducing biosynthetic pathways into an organism is both reliant on and challenged by endogenous biochemistry. Here we compared the expansion potential of the metabolic network in the photoautotroph Synechocystis with that of the heterotroph E. coli using the novel workflow POPPY (Prospecting Optimal Pathways with PYthon). First, E. coli and Synechocystis metabolomic and fluxomic data were combined with metabolic models to identify thermodynamic constraints on metabolite concentrations (NET analysis). Then, thousands of automatically constructed pathways were placed within each network and subjected to a network-embedded variant of the max-min driving force analysis (NEM). We found that the networks had different capabilities for imparting thermodynamic driving forces toward certain compounds. Key metabolites were constrained differently in Synechocystis due to opposing flux directions in glycolysis and carbon fixation, the forked tri-carboxylic acid cycle, and photorespiration. Furthermore, the lysine biosynthesis pathway in Synechocystis was identified as thermodynamically constrained, impacting both endogenous and heterologous reactions through low 2-oxoglutarate levels. Our study also identified important yet poorly covered areas in existing metabolomics data and provides a reference for future thermodynamics-based engineering in Synechocystis and beyond. The POPPY methodology represents a step in making optimal pathway-host matches, which is likely to become important as the practical range of host organisms is diversified.
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| 8. |
- Asplund-Samuelsson, Johannes, et al.
(författare)
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Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes
- 2021
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Ingår i: PloS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 17:2
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge of the genetic basis for autotrophic metabolism is valuable since it relates to both the emergence of life and to the metabolic engineering challenge of incorporating CO2 as a potential substrate for biorefining. The most common CO2 fixation pathway is the Calvin cycle, which utilizes Rubisco and phosphoribulokinase enzymes. We searched thousands of microbial genomes and found that 6.0% contained the Calvin cycle. We then contrasted the genomes of Calvin cycle-positive, non-cyanobacterial microbes and their closest relatives by enrichment analysis, ancestral character estimation, and random forest machine learning, to explore genetic adaptations associated with acquisition of the Calvin cycle. The Calvin cycle overlaps with the pentose phosphate pathway and glycolysis, and we could confirm positive associations with fructose-1,6-bisphosphatase, aldolase, and transketolase, constituting a conserved operon, as well as ribulose-phosphate 3-epimerase, ribose-5-phosphate isomerase, and phosphoglycerate kinase. Additionally, carbohydrate storage enzymes, carboxysome proteins (that raise CO2 concentration around Rubisco), and Rubisco activases CbbQ and CbbX accompanied the Calvin cycle. Photorespiration did not appear to be adapted specifically for the Calvin cycle in the non-cyanobacterial microbes under study. Our results suggest that chemoautotrophy in Calvin cycle-positive organisms was commonly enabled by hydrogenase, and less commonly ammonia monooxygenase (nitrification). The enrichment of specific DNA-binding domains indicated Calvin-cycle associated genetic regulation. Metabolic regulatory adaptations were illustrated by negative correlation to AraC and the enzyme arabinose-5-phosphate isomerase, which suggests a downregulation of the metabolite arabinose-5-phosphate, which may interfere with the Calvin cycle through enzyme inhibition and substrate competition. Certain domains of unknown function that were found to be important in the analysis may indicate yet unknown regulatory mechanisms in Calvin cycle-utilizing microbes. Our gene ranking provides targets for experiments seeking to improve CO2 fixation, or engineer novel CO2-fixing organisms.
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| 9. |
- Benlloch, Reyes, et al.
(författare)
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Crystal structure and functional characterization of Photosystem II-associated carbonic anhydrase CAH3 in Chlamydomonas reinhardtii
- 2015
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Ingår i: Plant Physiology. - : American Society of Plant Biologists. - 0032-0889 .- 1532-2548. ; 167:3, s. 950-962
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Tidskriftsartikel (refereegranskat)abstract
- In oxygenic photosynthesis, light energy is stored in the form of chemical energy by converting CO2 and water into carbohydrates.The light-driven oxidation of water that provides the electrons and protons for the subsequent CO2 fixation takes place inphotosystem II (PSII). Recent studies show that in higher plants, HCO3– increases PSII activity by acting as a mobile acceptor ofthe protons produced by PSII. In the green alga Chlamydomonas reinhardtii, a luminal carbonic anhydrase, CrCAH3, was suggested toimprove proton removal from PSII, possibly by rapid reformation of HCO3– from CO2. In this study, we investigated the interplaybetween PSII and CrCAH3 by membrane inlet mass spectrometry and x-ray crystallography. Membrane inlet mass spectrometrymeasurements showed that CrCAH3 was most active at the slightly acidic pH values prevalent in the thylakoid lumen underillumination. Two crystal structures of CrCAH3 in complex with either acetazolamide or phosphate ions were determined at 2.6- and2.7-Å resolution, respectively. CrCAH3 is a dimer at pH 4.1 that is stabilized by swapping of the N-terminal arms, a feature notpreviously observed in a-type carbonic anhydrases. The structure contains a disulfide bond, and redox titration of CrCAH3 functionwith dithiothreitol suggested a possible redox regulation of the enzyme. The stimulating effect of CrCAH3 and CO2/HCO3– on PSIIactivity was demonstrated by comparing the flash-induced oxygen evolution pattern of wild-type and CrCAH3-less PSIIpreparations. We showed that CrCAH3 has unique structural features that allow this enzyme to maximize PSII activity at lowpH and CO2 concentration.
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| 10. |
- Berg, Carlo, et al.
(författare)
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Dissection of Microbial Community Functions during a Cyanobacterial Bloom in the Baltic Sea via Metatranscriptomics
- 2018
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Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745.
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Tidskriftsartikel (refereegranskat)abstract
- Marine and brackish surface waters are highly dynamic habitats that undergo repeated seasonal variations in microbial community composition and function throughout time. While succession of the various microbial groups has been well investigated, little is known about the underlying gene-expression of the microbial community. We investigated microbial interactions via metatranscriptomics over a spring to fall seasonal cycle in the brackish Baltic Sea surface waters, a temperate brackish water ecosystem periodically promoting massive cyanobacterial blooms, which have implications for primary production, nutrient cycling, and expansion of hypoxic zones. Network analysis of the gene expression of all microbes from 0.22 to 200 mu m in size and of the major taxonomic groups dissected the seasonal cycle into four components that comprised genes peaking during different periods of the bloom. Photoautotrophic nitrogen-fixing Cyanobacteria displayed the highest connectivity among the microbes, in contrast to chemoautotrophic ammonia-oxidizing Thaumarchaeota, while heterotrophs dominated connectivity among pre- and post-bloom peaking genes. The network was also composed of distinct functional connectivities, with an early season balance between carbon metabolism and ATP synthesis shifting to a dominance of ATP synthesis during the bloom, while carbon degradation, specifically through the glyoxylate shunt, characterized the post-bloom period, driven by Alphaproteobacteria as well as by Gammaproteobacteria of the SAR86 and SAR92 clusters. Our study stresses the exceptionally strong biotic driving force executed by cyanobacterial blooms on associated microbial communities in the Baltic Sea and highlights the impact cyanobacterial blooms have on functional microbial community composition.
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