| 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. |
- Liu, Lianhua, et al.
(författare)
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Heavy metal accumulation, geochemical fractions, and loadings in two agricultural watersheds with distinct climate conditions
- 2020
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Ingår i: Journal of Hazardous Materials. - : Elsevier. - 0304-3894 .- 1873-3336. ; 389
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Tidskriftsartikel (refereegranskat)abstract
- The main aim of this study was to explore the effects of climate conditions on the transport and transformation of heavy metals. Sedimentary geochemical analysis and watershed modeling were used to investigate the distinctions between heavy metal pollution under different climate conditions. The results showed that the average concentrations of Cu, Cd, and Pb in sediments of the subtropical watershed (36.64, 0.60, and 133.69 mg/kg, respectively) were higher than those of the temperate watershed (26.58, 0.19, and 23.17 mg/kg, respectively) because of surface runoff-induced heavy metal loadings under higher precipitation. Also, the labile fractions, which mainly originated from anthropogenic sources, showed higher percentages in the subtropical watershed (67.84-91.33%), thereby indicating that the transport of heavy metals was promoted by surface runoff. Moreover, higher percentages of acid-soluble fractions of Cu and Pb (23.55-33.60%) in the subtropical watershed suggested that higher temperatures accelerated the transformation of heavy metal fractions, thus contributing to the transportation of heavy metals. Overall, climate conditions were the dominant factors for the differences between the subtropical and temperate watersheds. The results of this study suggest that the effects of climate conditions on the transport, enrichment, and bioavailability of heavy metals are of great significance. Such effects should therefore be the focus of future studies.
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| 3. |
- Mueller, Christian P., et al.
(författare)
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The Cortical Neuroimmune Regulator TANK Affects Emotional Processing and Enhances Alcohol Drinking : A Translational Study
- 2019
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Ingår i: Cerebral Cortex. - : OXFORD UNIV PRESS INC. - 1047-3211 .- 1460-2199. ; 29:4, s. 1736-1751
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Tidskriftsartikel (refereegranskat)abstract
- Alcohol abuse is a major public health problem worldwide. Understanding the molecular mechanisms that control regular drinking may help to reduce hazards of alcohol consumption. While immunological mechanisms have been related to alcohol drinking, most studies reported changes in immune function that are secondary to alcohol use. In this report, we analyse how the gene "TRAF family member-associated NF-kappa B activator" (TANK) affects alcohol drinking behavior. Based on our recent discovery in a large GWAS dataset that suggested an association of TANK, SNP rs197273, with alcohol drinking, we report that SNP rs197273 in TANK is associated both with gene expression (P = 1.16 x 10(-19)) and regional methylation (P = 5.90 x 10(-25)). A tank knock out mouse model suggests a role of TANK in alcohol drinking, anxiety-related behavior, as well as alcohol exposure induced activation of insular cortex NF-kappa B. Functional and structural neuroimaging studies among up to 1896 adolescents reveal that TANK is involved in the control of brain activity in areas of aversive interoceptive processing, including the insular cortex, but not in areas related to reinforcement, reward processing or impulsiveness. Our findings suggest that the cortical neuroimmune regulator TANK is associated with enhanced aversive emotional processing that better protects from the establishment of alcohol drinking behavior.
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| 4. |
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| 5. |
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| 6. |
- Zeng, Yinping, et al.
(författare)
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Thermodynamic description and solidified microstructure of the Co-Ge system
- 2019
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Ingår i: Journal of Alloys and Compounds. - : ELSEVIER SCIENCE SA. - 0925-8388 .- 1873-4669. ; 793, s. 480-491
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Tidskriftsartikel (refereegranskat)abstract
- The Co-Ge binary system was reassessed by CALPHAD method in view of new phase diagram data and drawbacks of the previous modeling. A three-sublattice model (Co,Va)(1)(Co)(1)(Ge)(1 )was used to describe the B8(2)-type beta Co5Ge3-phase based on its crystal structure. In order to describe the transformation between ordered L1(2)-type phase (Co3Ge) and the disordered fcc_Al phase (alpha Co), one single Gibbs energy function was used for both ordered and disordered phases. In almost all the previous thermodynamic calculations, the ordered phase with a negligible homogeneity range, such as Co3Ge, is treated as a stoichiometric compound. Such a treatment is not physically sound. For (alpha Co) and (alpha Co), the magnetic contribution to Gibbs energy is taken into account. Both substitutional solution model and associated model were applied to describe the liquid phase, and thus two sets of self-consistent thermodynamic parameters for this system were obtained. It was found that the associated model can account for the experimental data more satisfactorily than the substitutional solution model, especially for the partial enthalpy of mixing data for the liquid phase. Five representative as-cast Co-Ge alloys were prepared to compare the solidified microstructure with that predicted according to thermodynamic calculations. According to the calculated Scheil solidification curves of two key alloys, the solidified microstructure for the alloys was analyzed. Also, the calculated amounts of the solidified phases in five as-cast alloys are compared with the experimental data resulting from automatic image analysis of the BSE images, showing a good agreement between the calculation and experiment, in particular for the case in which the associated model is used to describe the properties of the liquid phase. It is demonstrated that the combined use of the thermodynamic calculation and decisive experiment is an efficient strategy to obtain the desired microstructure.
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| 7. |
- Zhang, Ruyang, et al.
(författare)
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Independent Validation of Early-Stage Non-Small Cell Lung Cancer Prognostic Scores Incorporating Epigenetic and Transcriptional Biomarkers With Gene-Gene Interactions and Main Effects
- 2020
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Ingår i: Chest. - : Elsevier BV. - 0012-3692. ; 158:2, s. 808-819
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Tidskriftsartikel (refereegranskat)abstract
- Background: DNA methylation and gene expression are promising biomarkers of various cancers, including non-small cell lung cancer (NSCLC). Besides the main effects of biomarkers, the progression of complex diseases is also influenced by gene-gene (G×G) interactions. Research Question: Would screening the functional capacity of biomarkers on the basis of main effects or interactions, using multiomics data, improve the accuracy of cancer prognosis? Study Design and Methods: Biomarker screening and model validation were used to construct and validate a prognostic prediction model. NSCLC prognosis-associated biomarkers were identified on the basis of either their main effects or interactions with two types of omics data. A prognostic score incorporating epigenetic and transcriptional biomarkers, as well as clinical information, was independently validated. Results: Twenty-six pairs of biomarkers with G×G interactions and two biomarkers with main effects were significantly associated with NSCLC survival. Compared with a model using clinical information only, the accuracy of the epigenetic and transcriptional biomarker-based prognostic model, measured by area under the receiver operating characteristic curve (AUC), increased by 35.38% (95% CI, 27.09%-42.17%; P = 5.10 × 10–17) and 34.85% (95% CI, 26.33%-41.87%; P = 2.52 × 10–18) for 3- and 5-year survival, respectively, which exhibited a superior predictive ability for NSCLC survival (AUC3 year, 0.88 [95% CI, 0.83-0.93]; and AUC5 year, 0.89 [95% CI, 0.83-0.93]) in an independent Cancer Genome Atlas population. G×G interactions contributed a 65.2% and 91.3% increase in prediction accuracy for 3- and 5-year survival, respectively. Interpretation: The integration of epigenetic and transcriptional biomarkers with main effects and G×G interactions significantly improves the accuracy of prognostic prediction of early-stage NSCLC survival.
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| 8. |
- Zhang, Ruyang, et al.
(författare)
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SIPA1L3 methylation modifies the benefit of smoking cessation on lung adenocarcinoma survival : an epigenomic–smoking interaction analysis
- 2019
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Ingår i: Molecular Oncology. - : Wiley. - 1574-7891 .- 1878-0261. ; 13:5, s. 1235-1248
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Tidskriftsartikel (refereegranskat)abstract
- Smoking cessation prolongs survival and decreases mortality of patients with non-small-cell lung cancer (NSCLC). In addition, epigenetic alterations of some genes are associated with survival. However, potential interactions between smoking cessation and epigenetics have not been assessed. Here, we conducted an epigenome-wide interaction analysis between DNA methylation and smoking cessation on NSCLC survival. We used a two-stage study design to identify DNA methylation–smoking cessation interactions that affect overall survival for early-stage NSCLC. The discovery phase contained NSCLC patients from Harvard, Spain, Norway, and Sweden. A histology-stratified Cox proportional hazards model adjusted for age, sex, clinical stage, and study center was used to test DNA methylation–smoking cessation interaction terms. Interactions with false discovery rate-q ≤ 0.05 were further confirmed in a validation phase using The Cancer Genome Atlas database. Histology-specific interactions were identified by stratification analysis in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) patients. We identified one CpG probe (cg02268510 SIPA 1L3 ) that significantly and exclusively modified the effect of smoking cessation on survival in LUAD patients [hazard ratio (HR) interaction = 1.12; 95% confidence interval (CI): 1.07–1.16; P = 4.30 × 10 –7 ]. Further, the effect of smoking cessation on early-stage LUAD survival varied across patients with different methylation levels of cg02268510 SIPA 1L3 . Smoking cessation only benefited LUAD patients with low methylation (HR = 0.53; 95% CI: 0.34–0.82; P = 4.61 × 10 –3 ) rather than medium or high methylation (HR = 1.21; 95% CI: 0.86–1.70; P = 0.266) of cg02268510 SIPA 1L3 . Moreover, there was an antagonistic interaction between elevated methylation of cg02268510 SIPA 1L3 and smoking cessation (HR interaction = 2.1835; 95% CI: 1.27–3.74; P = 4.46 × 10 −3 ). In summary, smoking cessation benefited survival of LUAD patients with low methylation at cg02268510 SIPA 1L3 . The results have implications for not only smoking cessation after diagnosis, but also possible methylation-specific drug targeting.
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