| 1. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 2. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Forslund, Sofia K., et al.
(författare)
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Combinatorial, additive and dose-dependent drug–microbiome associations
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 600:7889, s. 500-505
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Tidskriftsartikel (refereegranskat)abstract
- During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery1–5. Here, through integrated multi-omics analyses of 2,173 European residents from the MetaCardis cohort, we show that the explanatory power of drugs for the variability in both host and gut microbiome features exceeds that of disease. We quantify inferred effects of single medications, their combinations as well as additive effects, and show that the latter shift the metabolome and microbiome towards a healthier state, exemplified in synergistic reduction in serum atherogenic lipoproteins by statins combined with aspirin, or enrichment of intestinal Roseburia by diuretic agents combined with beta-blockers. Several antibiotics exhibit a quantitative relationship between the number of courses prescribed and progression towards a microbiome state that is associated with the severity of cardiometabolic disease. We also report a relationship between cardiometabolic drug dosage, improvement in clinical markers and microbiome composition, supporting direct drug effects. Taken together, our computational framework and resulting resources enable the disentanglement of the effects of drugs and disease on host and microbiome features in multimedicated individuals. Furthermore, the robust signatures identified using our framework provide new hypotheses for drug–host–microbiome interactions in cardiometabolic disease.
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| 4. |
- Molinaro, Antonio, et al.
(författare)
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Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Microbiota-host-diet interactions contribute to the development of metabolic diseases. Imidazole propionate is a novel microbially produced metabolite from histidine, which impairs glucose metabolism. Here, we show that subjects with prediabetes and diabetes in the MetaCardis cohort from three European countries have elevated serum imidazole propionate levels. Furthermore, imidazole propionate levels were increased in subjects with low bacterial gene richness and Bacteroides 2 enterotype, which have previously been associated with obesity. The Bacteroides 2 enterotype was also associated with increased abundance of the genes involved in imidazole propionate biosynthesis from dietary histidine. Since patients and controls did not differ in their histidine dietary intake, the elevated levels of imidazole propionate in type 2 diabetes likely reflects altered microbial metabolism of histidine, rather than histidine intake per se. Thus the microbiota may contribute to type 2 diabetes by generating imidazole propionate that can modulate host inflammation and metabolism.
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| 5. |
- Varemo, Leif, et al.
(författare)
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Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes
- 2017
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Ingår i: Genome Medicine. - : BIOMED CENTRAL LTD. - 1756-994X .- 1756-994X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Background: Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to the disease alone. Therefore, here we set out to identify and characterize intrinsic properties of myocytes, associated independently with T2D or obesity. Methods: We generated and analyzed RNA-seq data from primary differentiated myotubes from 24 human subjects, using a factorial design (healthy/T2D and non-obese/obese), to determine the influence of each specific factor on genome-wide transcription. This setup enabled us to identify intrinsic properties, originating from muscle precursor cells and retained in the corresponding myocytes. Bioinformatic and statistical methods, including differential expression analysis, gene-set analysis, and metabolic network analysis, were used to characterize the different myocytes. Results: We found that the transcriptional program associated with obesity alone was strikingly similar to that induced specifically by T2D. We identified a candidate epigenetic mechanism, H3K27me3 histone methylation, mediating these transcriptional signatures. T2D and obesity were independently associated with dysregulated myogenesis, down-regulated muscle function, and up-regulation of inflammation and extracellular matrix components. Metabolic network analysis identified that in T2D but not obesity a specific metabolite subnetwork involved in sphingolipid metabolism was transcriptionally regulated. Conclusions: Our findings identify inherent characteristics in myocytes, as a memory of the in vivo phenotype, without the influence from a diabetic or obese extracellular environment, highlighting their importance in the development of T2D.
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| 6. |
- Anderson, Craig, 1976, et al.
(författare)
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Autoradiographic comparisons of radionuclide adsorption between subsurface anaerobic biofilms and granitic host rocks
- 2006
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Ingår i: Geomicrobiology Journal. - : Informa UK Limited. - 0149-0451 .- 1521-0529. ; 23:1, s. 15-29
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Tidskriftsartikel (refereegranskat)abstract
- In high level nuclear waste repositories, the host rock is considered to be an important barrier to radionuclide migration by adsorbing metals at fluid rock interfaces. In granitic rock environments the surfaces of hydraulically conductive fractures are covered with mixed community biofilms. Biofilms were grown in situ on glass and rock surfaces in high pressure flow cells using groundwater sourced from a borehole 450 meters below sea level in the Aspo hard rock laboratory, Sweden. Scanning electron microscopy (SEM), epifluorescence microscopy and energy dispersive X-Ray spectroscopy (EDS) revealed monolayer biofilms consisting of up to 2 x 10(4) bacteria/mm(2) surrounded by an extensive extracellular matrix and carbonate precipitates that covered
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| 7. |
- Anderson, Craig, 1976, et al.
(författare)
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Influence of in situ biofilm coverage on the radionuclide adsorption capacity of subsurface granite
- 2007
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Ingår i: Environmental Science & Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 41:3, s. 830-836
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Tidskriftsartikel (refereegranskat)abstract
- Any migration of radionuclides from nuclear waste repositories is expected to be mitigated by adsorption to the host rocks surrounding hydraulically conductive fractures. Fluid rock interfaces are considered to be important barriers for nuclear waste disposal schemes but their adsorptive capacity can be affected by the growth of microbial biofilms. This study indicates that biofilms growing on fracture surfaces decrease the rocks adsorption capacity for migrating radionuclides except for trivalent species. Potential suppression of adsorption by biofilms should, therefore, be accounted for in performance safety assessment models. In this study, the adsorptive capacity of in situ anaerobic biofilms grown 450 m underground on either glass or granite slides was compared to the capacity of the same surfaces without biofilms. Surfaces were exposed to the radiotracers Co-60(II), Pm-147(III), Am-241(III), Th-234(IV), and Np-237(V) for a period of 660 h in a pH neutral anaerobic synthetic groundwater. Adsorption was investigated at multiple time points over the 660 h using liquid scintillation and ICP-MS. Results indicate that these surfaces adsorb between 0 and 85% of the added tracers under the conditions of the specific experiments. After 660 h, the distribution coefficients, R (ratio between what is sorbed and what is left in the aqueous phase), approached 3 x 10(4) m for Co-60, 3 x 10(5) m for Pm-147 and 24 'Am, I x 106 m for 234Th, and 1 x 103 m for 237Np. The highest rate of adsorption was during the first 200 h of the adsorption experiments and started to approach equilibrium after 500 h. Adsorption to colloids and precipitates contributed to decreases of up to 20% in the available Co-60, Pm-147, Am-241, and Np-237 in the adsorption systems. In the 234Th system 95% of the aqueous 234Th was removed by adsorbing to colloids. Although the range of R values for each surface tested generally overlapped, the biofilms consistently demonstrated lower R values except for the trivalant Pm-147 and Am-241 adsorption systems.
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| 8. |
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| 9. |
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| 10. |
- Gourdon, Pontus Emanuel, 1978, et al.
(författare)
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Optimized in vitro and in vivo expression of proteorhodopsin: A seven-transmembrane proton pump
- 2008
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Ingår i: Protein Expression and Purification. - : Elsevier BV. - 1096-0279 .- 1046-5928. ; 58:1, s. 103-113
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Tidskriftsartikel (refereegranskat)abstract
- Proteorhodopsin is an integral membrane light-harvesting proton pump that is found in bacteria distributed throughout global surface waters. Here, we present a protocol for functional in vitro production of pR using a commercial cell-free synthesis system yielding 1.0 mg purified protein per milliliter of cell lysate. We also present an optimized protocol for in vivo over-expression of pR in Escherichia coli, and a two-step purification yielding 5 mg of essentially pure functional protein per liter of culture. Both approaches are straightforward, rapid, and easily scalable. Thus either may facilitate the exploitation of pR for commercial biotechnological applications. Finally, the implications of some observations of the in vitro synthesis behavior, as well as preliminary results towards a structural determination of pR are discussed.
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