| 1. |
- 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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| 2. |
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| 3. |
- Di, Li, et al.
(författare)
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The Critical Role of Passive Permeability in Designing Successful Drugs
- 2020
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Ingår i: ChemMedChem. - : Wiley. - 1860-7179 .- 1860-7187. ; 15:20, s. 1862-1874
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Forskningsöversikt (refereegranskat)abstract
- Passive permeability is a key property in drug disposition and delivery. It is critical for gastrointestinal absorption, brain penetration, renal reabsorption, defining clearance mechanisms and drug-drug interactions. Passive diffusion rate is translatable across tissues and animal species, while the extent of absorption is dependent on drug properties, as well as in vivo physiology/pathophysiology. Design principles have been developed to guide medicinal chemistry to enhance absorption, which combine the balance of aqueous solubility, permeability and the sometimes unfavorable compound characteristic demanded by the target. Permeability assays have been implemented that enable rapid development of structure-permeability relationships for absorption improvement. Future advances in assay development to reduce nonspecific binding and improve mass balance will enable more accurately measurement of passive permeability. Design principles that integrate potency, selectivity, passive permeability and other ADMET properties facilitate rapid advancement of successful drug candidates to patients.
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| 4. |
- Douglas, Peter M. J., et al.
(författare)
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Clumped Isotopes Link Older Carbon Substrates With Slower Rates of Methanogenesis in Northern Lakes
- 2020
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Ingår i: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 47:6
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Tidskriftsartikel (refereegranskat)abstract
- The release of long-stored carbon from thawed permafrost could fuel increased methanogenesis in northern lakes, but it remains unclear whether old carbon substrates released from permafrost are metabolized as rapidly by methanogenic microbial communities as recently produced organic carbon. Here, we apply methane (CH4) clumped isotope (Delta(18)) and C-14 measurements to test whether rates of methanogenesis are related to carbon substrate age. Results from culture experiments indicate that Delta(18) values are negatively correlated with CH4 production rate. Measurements of ebullition samples from thermokarst lakes in Alaska and glacial lakes in Sweden indicate strong negative correlations between CH4 Delta(18) and the fraction modern carbon. These correlations imply that CH4 derived from older carbon substrates is produced relatively slowly. Relative rates of methanogenesis, as inferred from Delta(18) values, are not positively correlated with CH4 flux estimates, highlighting the likely importance of environmental variables other than CH4 production rates in controlling ebullition fluxes. Plain Language Summary There is concern that carbon from thawed permafrost will be emitted to the atmosphere as methane (CH4). It is currently uncertain whether old organic carbon from thawed permafrost can be converted to CH4 as rapidly as organic carbon recently fixed by primary producers. We address this question by combining radiocarbon and clumped isotope measurements of CH4 from lakes in permafrost landscapes. Radiocarbon (C-14) measurements indicate the age of CH4 carbon sources. We present data from culture experiments that support the hypothesis that clumped isotope values are dependent on microbial CH4 production rate. In lake bubble samples, we observe a strong correlation between these two measurements, which implies that CH4 formed from older carbon is produced relatively slowly. We also find that higher rates of CH4 production, as inferred from clumped isotopes, are not linked to higher rates of CH4 emissions, implying that variables other than CH4 production rate strongly influence emission rates.
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| 5. |
- Erzurumluoglu, A. Mesut, et al.
(författare)
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Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci
- 2020
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Ingår i: Molecular Psychiatry. - : Nature Publishing Group. - 1359-4184 .- 1476-5578. ; 25:10, s. 2392-2409
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Tidskriftsartikel (refereegranskat)abstract
- Smoking is a major heritable and modifiable risk factor for many diseases, including cancer, common respiratory disorders and cardiovascular diseases. Fourteen genetic loci have previously been associated with smoking behaviour-related traits. We tested up to 235,116 single nucleotide variants (SNVs) on the exome-array for association with smoking initiation, cigarettes per day, pack-years, and smoking cessation in a fixed effects meta-analysis of up to 61 studies (up to 346,813 participants). In a subset of 112,811 participants, a further one million SNVs were also genotyped and tested for association with the four smoking behaviour traits. SNV-trait associations with P < 5 × 10-8 in either analysis were taken forward for replication in up to 275,596 independent participants from UK Biobank. Lastly, a meta-analysis of the discovery and replication studies was performed. Sixteen SNVs were associated with at least one of the smoking behaviour traits (P < 5 × 10-8) in the discovery samples. Ten novel SNVs, including rs12616219 near TMEM182, were followed-up and five of them (rs462779 in REV3L, rs12780116 in CNNM2, rs1190736 in GPR101, rs11539157 in PJA1, and rs12616219 near TMEM182) replicated at a Bonferroni significance threshold (P < 4.5 × 10-3) with consistent direction of effect. A further 35 SNVs were associated with smoking behaviour traits in the discovery plus replication meta-analysis (up to 622,409 participants) including a rare SNV, rs150493199, in CCDC141 and two low-frequency SNVs in CEP350 and HDGFRP2. Functional follow-up implied that decreased expression of REV3L may lower the probability of smoking initiation. The novel loci will facilitate understanding the genetic aetiology of smoking behaviour and may lead to the identification of potential drug targets for smoking prevention and/or cessation.
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| 7. |
- Luhr, JJ, et al.
(författare)
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Maturation of Monocyte-Derived DCs Leads to Increased Cellular Stiffness, Higher Membrane Fluidity, and Changed Lipid Composition
- 2020
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Ingår i: Frontiers in immunology. - : Frontiers Media SA. - 1664-3224. ; 11, s. 590121-
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Tidskriftsartikel (refereegranskat)abstract
- Dendritic cells (DCs) are professional antigen-presenting cells of the immune system. Upon sensing pathogenic material in their environment, DCs start to mature, which includes cellular processes, such as antigen uptake, processing and presentation, as well as upregulation of costimulatory molecules and cytokine secretion. During maturation, DCs detach from peripheral tissues, migrate to the nearest lymph node, and find their way into the correct position in the net of the lymph node microenvironment to meet and interact with the respective T cells. We hypothesize that the maturation of DCs is well prepared and optimized leading to processes that alter various cellular characteristics from mechanics and metabolism to membrane properties. Here, we investigated the mechanical properties of monocyte-derived dendritic cells (moDCs) using real-time deformability cytometry to measure cytoskeletal changes and found that mature moDCs were stiffer compared to immature moDCs. These cellular changes likely play an important role in the processes of cell migration and T cell activation. As lipids constitute the building blocks of the plasma membrane, which, during maturation, need to adapt to the environment for migration and DC-T cell interaction, we performed an unbiased high-throughput lipidomics screening to identify the lipidome of moDCs. These analyses revealed that the overall lipid composition was significantly changed during moDC maturation, even implying an increase of storage lipids and differences of the relative abundance of membrane lipids upon maturation. Further, metadata analyses demonstrated that lipid changes were associated with the serum low-density lipoprotein (LDL) and cholesterol levels in the blood of the donors. Finally, using lipid packing imaging we found that the membrane of mature moDCs revealed a higher fluidity compared to immature moDCs. This comprehensive and quantitative characterization of maturation associated changes in moDCs sets the stage for improving their use in clinical application.
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| 8. |
- Monteil, Guillaume, et al.
(författare)
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The regional European atmospheric transport inversion comparison, EUROCOM : First results on European-wide terrestrial carbon fluxes for the period 2006-2015
- 2020
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 20:20, s. 12063-12091
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Tidskriftsartikel (refereegranskat)abstract
- Atmospheric inversions have been used for the past two decades to derive large-scale constraints on the sources and sinks of CO2 into the atmosphere. The development of dense in situ surface observation networks, such as ICOS in Europe, enables in theory inversions at a resolution close to the country scale in Europe. This has led to the development of many regional inversion systems capable of assimilating these high-resolution data, in Europe and elsewhere. The EUROCOM (European atmospheric transport inversion comparison) project is a collaboration between seven European research institutes, which aims at producing a collective assessment of the net carbon flux between the terrestrial ecosystems and the atmosphere in Europe for the period 2006 2015. It aims in particular at investigating the capacity of the inversions to deliver consistent flux estimates from the country scale up to the continental scale. The project participants were provided with a common database of in situ-observed CO2 concentrations (including the observation sites that are now part of the ICOS network) and were tasked with providing their best estimate of the net terrestrial carbon flux for that period, and for a large domain covering the entire European Union. The inversion systems differ by the transport model, the inversion approach, and the choice of observation and prior constraints, enabling us to widely explore the space of uncertainties. This paper describes the intercomparison protocol and the participating systems, and it presents the first results from a reference set of inversions, at the continental scale and in four large regions. At the continental scale, the regional inversions support the assumption that European ecosystems are a relatively small sink (-0:21 ± 0:2 Pg C yr-1). We find that the convergence of the regional inversions at this scale is not better than that obtained in state-of-the-art global inversions. However, more robust results are obtained for subregions within Europe, and in these areas with dense observational coverage, the objective of delivering robust countryscale flux estimates appears achievable in the near future.
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| 9. |
- Persson Skare, Tor, et al.
(författare)
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Marginal zone lymphoma expression of histidine-rich glycoprotein correlates with improved survival
- 2020
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Ingår i: eJHaem. - : Wiley. - 2688-6146. ; 1:1, s. 199-207
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Tidskriftsartikel (refereegranskat)abstract
- The abundant hepatocyte-expressed plasma protein histidine-rich glycoprotein (HRG) enhances antitumor immunity by polarizing inflammatory and immune cells in several mouse models, however, the clinical relevance of HRG in human cancer is poorly explored. The expression and role of HRG in human B-cell lymphomas was investigated in order to find new tools for prognosis and treatment. Findings Immunohistochemical (IHC) analysis and RNA hybridization of tissue microarrays showed that (i) HRG was expressed by tumor cells in marginal zone lymphoma (MZL), in 36% of 59 cases. Expression was also detected in follicular lymphoma (22%), mantle cell lymphoma (19%), and indiffuse large B-cell lymphoma (DLBCL;5%) while primary CNS lymphoma (PCNSL) lacked expression of HRG. (ii) MZL patients positive for HRG showed a superior overall survival outcome (HR = 0.086, 95% CI = 0.014-0.518, P-value = .007), indicating a protective role for HRG independent of stage, age and sex. (iii) HRG-expressing MZL displayed significantly increased transcript and protein levels of the host defense peptide alpha defensin 1. In addition, global transcript analyses showed significant changes in gene ontology terms relating to immunity and inflammation, however, infiltration of immune and inflammatory cells detected by IHC was unaffected by HRG expression. Conclusion HRG expression by MZL tumor cells correlates with an altered transcription profile and improved overall survival.
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