| 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. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Haycock, Philip C., et al.
(författare)
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Association Between Telomere Length and Risk of Cancer and Non-Neoplastic Diseases A Mendelian Randomization Study
- 2017
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Ingår i: JAMA Oncology. - : American Medical Association. - 2374-2437 .- 2374-2445. ; 3:5, s. 636-651
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Tidskriftsartikel (refereegranskat)abstract
- IMPORTANCE: The causal direction and magnitude of the association between telomere length and incidence of cancer and non-neoplastic diseases is uncertain owing to the susceptibility of observational studies to confounding and reverse causation. OBJECTIVE: To conduct a Mendelian randomization study, using germline genetic variants as instrumental variables, to appraise the causal relevance of telomere length for risk of cancer and non-neoplastic diseases. DATA SOURCES: Genomewide association studies (GWAS) published up to January 15, 2015. STUDY SELECTION: GWAS of noncommunicable diseases that assayed germline genetic variation and did not select cohort or control participants on the basis of preexisting diseases. Of 163 GWAS of noncommunicable diseases identified, summary data from 103 were available. DATA EXTRACTION AND SYNTHESIS: Summary association statistics for single nucleotide polymorphisms (SNPs) that are strongly associated with telomere length in the general population. MAIN OUTCOMES AND MEASURES: Odds ratios (ORs) and 95% confidence intervals (CIs) for disease per standard deviation (SD) higher telomere length due to germline genetic variation. RESULTS: Summary data were available for 35 cancers and 48 non-neoplastic diseases, corresponding to 420 081 cases (median cases, 2526 per disease) and 1 093 105 controls (median, 6789 per disease). Increased telomere length due to germline genetic variation was generally associated with increased risk for site-specific cancers. The strongest associations (ORs [ 95% CIs] per 1-SD change in genetically increased telomere length) were observed for glioma, 5.27 (3.15-8.81); serous low-malignant-potential ovarian cancer, 4.35 (2.39-7.94); lung adenocarcinoma, 3.19 (2.40-4.22); neuroblastoma, 2.98 (1.92-4.62); bladder cancer, 2.19 (1.32-3.66); melanoma, 1.87 (1.55-2.26); testicular cancer, 1.76 (1.02-3.04); kidney cancer, 1.55 (1.08-2.23); and endometrial cancer, 1.31 (1.07-1.61). Associations were stronger for rarer cancers and at tissue sites with lower rates of stem cell division. There was generally little evidence of association between genetically increased telomere length and risk of psychiatric, autoimmune, inflammatory, diabetic, and other non-neoplastic diseases, except for coronary heart disease (OR, 0.78 [ 95% CI, 0.67-0.90]), abdominal aortic aneurysm (OR, 0.63 [ 95% CI, 0.49-0.81]), celiac disease (OR, 0.42 [ 95% CI, 0.28-0.61]) and interstitial lung disease (OR, 0.09 [ 95% CI, 0.05-0.15]). CONCLUSIONS AND RELEVANCE: It is likely that longer telomeres increase risk for several cancers but reduce risk for some non-neoplastic diseases, including cardiovascular diseases.
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| 5. |
- Chen, Jing-De, et al.
(författare)
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Hot-electron emission-driven energy recycling in transparent plasmonic electrode for organic solar cells
- 2022
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Ingår i: InfoMat. - : Wiley. - 2567-3165. ; 4:3
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Tidskriftsartikel (refereegranskat)abstract
- Plasmonic metal electrodes with subwavelength nanostructures are promising for enhancing light harvesting in photovoltaics. However, the nonradiative damping of surface plasmon polaritons (SPPs) during coupling with sunlight results in the conversion of the excited hot-electrons to heat, which limits the absorption of light and generation of photocurrent. Herein, an energy recycling strategy driven by hot-electron emission for recycling the SPP energy trapped in the plasmonic electrodes is proposed. A transparent silver-based plasmonic metal electrode (A-PME) with a periodic hexagonal nanopore array is constructed, which is combined with a luminescent organic emitter for radiative recombination of the injected hot-electrons. Owing to the suppressed SPP energy loss via broadband hot-electron emission, the A-PME achieves an optimized optical transmission with an average transmittance of over 80% from 380 to 1200 nm. Moreover, the indium-tin-oxide-free organic solar cells yield an enhanced light harvesting with a power conversion efficiency of 16.1%.
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| 6. |
- Chi, Chaodan, et al.
(författare)
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Molecular beam epitaxy growth of GaSb1-xBix without rotation
- 2019
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Ingår i: Vacuum. - : Elsevier BV. - 0042-207X. ; 168
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Tidskriftsartikel (refereegranskat)abstract
- GaSb1-xBix thin film was grown on a 2 inch GaSb substrate by molecular beam epitaxy (MBE) without substrate rotation. Bi composition is found to vary from 2.76% to 3.98% across the wafer. The distribution of Bi content is mainly determined by spatial non-uniformity of Sb/Ga flux ratio, while Bi flux has slightly influence. Ostwald ripening process is confirmed to be reason for bigger Bi droplets via Bi surface diffusion. With the increase of Sb/Ga flux ratio, Ostwald ripening process is suppressed. At high Bi flux, excess Ga atoms accumulate on surface and form droplets.
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| 7. |
- Chi, Chaodan, et al.
(författare)
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Si-based InGaAs photodetectors on heterogeneous integrated substrate
- 2021
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Ingår i: Science China: Physics, Mechanics and Astronomy. - : Springer Science and Business Media LLC. - 1674-7348 .- 1869-1927. ; 64:6
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, InGaAs p-i-n photodetectors (PDs) on an InP/SiO2/Si (InPOI) substrate fabricated by ion-slicing technology are demonstrated and compared with the identical device on a commercial InP substrate. The quality of epitaxial layers on the InPOI substrate is similar to that on the InP substrate. The photo responsivities of both devices measured at 1.55 µm are comparable, which are about 0.808–0.828 A W−1. Although the dark current of PD on the InPOI substrate is twice as high as that of PD on the InP substrate at 300 K, the peak detectivities of both PDs are comparable. In general, the overall performance of the InPOI-based PD is comparable to the InP-based PD, demonstrating that the ion-slicing technology is a promising route to enable the high-quality Si-based InP platform for the full photonic integration on a Si substrate.
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| 8. |
- Fu, Xi, et al.
(författare)
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Classroom microbiome, functional pathways and sick-building syndrome (SBS) in urban and rural schools-Potential roles of indoor microbial amino acids and vitamin metabolites
- 2021
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Ingår i: Science of the Total Environment. - : Elsevier. - 0048-9697 .- 1879-1026. ; 795
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Tidskriftsartikel (refereegranskat)abstract
- Sick building symptoms (SBS) are defined as non-specific symptoms related to indoor exposures, including mucosal symptoms in eye, nose, throat, and skin, and general symptoms as headache and tiredness. Indoor microbial composition is associated with SBS symptoms, but the impact of microbial functional genes and potential metabolic products has not been characterized. We conducted a shotgun microbial metagenomic sequencing for vacuum dust collected in urban and rural schools in Shanxi province, China. SBS symptoms in students were surveyed, and microbial taxa and functional pathways related to the symptoms were identified using a multilevel linear regression model. SBS symptoms were common in students, and the prevalence of ocular and throat symptoms, headache, and tiredness was higher in urban than in rural areas (p < 0.05). A significant higher microbial alpha-diversity was found in rural areas than in urban areas (Chao1, p = 0.001; ACE, p = 0.002). Also, significant variation in microbial taxonomic and functional composition (beta-diversity) was observed between urban and rural areas (p < 0.005). Five potential risk Actinobacteria species were associated with SBS symptoms (p < 0.01); students in the classrooms with a higher abundance of an unclassified Geodermatophilaceae, Geodermatophilus, Fridmanniella luteola, Microlunatus phosphovorus and Mycetocola reported more nasal and throat symptoms and tiredness. Students with a higher abundance of an unclassified flavobacteriaceae reported fewer throat symptoms and tiredness. The abundance of microbial metabolic pathways related to the synthesis of B vitamins (biotin and folate), gamma-aminobutyric acid (GABA), short-chain fatty acids (SCFAs), and peptidoglycan and were protectively (negatively) associated with SBS symptoms (FDR < 0.05). The result is consistent with human microbiota studies, which reported that these microbial products are extensively involved in immunological processes and anti-inflammatory effects. This is the first study to report the functional potential of the indoor microbiome and the occurrence of SBS, providing new insights into the potential etiologic mechanisms in chronic inflammatory diseases.
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| 9. |
- Fu, Xi, et al.
(författare)
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Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China : association with asthma, rhinitis and rhinoconjunctivitis in high school students
- 2021
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Ingår i: Microbiome. - : Springer Nature. - 2049-2618. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundStudies in developed countries have reported that the prevalence of asthma and rhinitis is higher in urban areas than in rural areas, and this phenomenon is associated with urbanization and changing indoor microbiome exposure. Developing countries such as China have experienced rapid urbanization in past years, but no study has investigated microbiome exposure and urban-rural health effects in these countries.MethodsNine high schools from urban and rural areas were randomly selected in Shanxi Province, China, and classroom vacuum dust was collected for shotgun metagenomic sequencing. A self-administered questionnaire was collected from 1332 students for personal information and health data. Three-level logistic regression was performed between microbial richness/abundance/functional pathways and the occurrence of asthma and rhinitis symptoms.ResultsConsistent with developed countries, the prevalence of wheeze and rhinitis was higher in urban areas than in rural areas (p < 0.05). Metagenomic profiling revealed 8302 bacterial, 395 archaeal, 744 fungal, 524 protist and 1103 viral species in classroom dust. Actinobacteria (mean relative abundance 49.7%), Gammaproteobacteria (18.4%) and Alphaproteobacteria (10.0%) were the most abundant bacterial classes. The overall microbiome composition was significantly different between urban and rural schools (p = 0.001, Adonis). Species from Betaproteobactera, Gammaproteobacteria and Bacilli were enriched in urban schools, and species from Actinobacteria and Cyanobacteria were enriched in rural schools. Potential pathogens were present in higher abundance in urban schools than in rural schools (p < 0.05). Pseudoalteromonas, Neospora caninum and Microbacterium foliorum were positively associated with the occurrence of wheeze, rhinitis and rhinoconjunctivitis, and Brachybacterium was protectively (negatively) associated with rhinitis (p < 0.01). The abundance of human endocrine and metabolic disease pathways was positively associated with rhinitis (p = 0.008), and butyrate and propionate metabolic genes and pathways were significantly enriched in rural schools (p < 0.005), in line with previous findings that these short-chain fatty acids protect against inflammatory diseases in the human gut.ConclusionsWe conducted the first indoor microbiome survey in urban/rural environments with shotgun metagenomics, and the results revealed high-resolution microbial taxonomic and functional profiling and potential health effects.
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| 10. |
- Fu, Xi, et al.
(författare)
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Microbial Virulence Factors, Antimicrobial Resistance Genes, Metabolites, and Synthetic Chemicals in Cabins of Commercial Aircraft
- 2023
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Ingår i: Metabolites. - : MDPI. - 2218-1989 .- 2218-1989. ; 13:3
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Tidskriftsartikel (refereegranskat)abstract
- Passengers are at a higher risk of respiratory infections and chronic diseases due to microbial exposure in airline cabins. However, the presence of virulence factors (VFs), antimicrobial resistance genes (ARGs), metabolites, and chemicals are yet to be studied. To address this gap, we collected dust samples from the cabins of two airlines, one with textile seats (TSC) and one with leather seats (LSC), and analyzed the exposure using shotgun metagenomics and LC/MS. Results showed that the abundances of 17 VFs and 11 risk chemicals were significantly higher in TSC than LSC (p < 0.01). The predominant VFs in TSC were related to adherence, biofilm formation, and immune modulation, mainly derived from facultative pathogens such as Haemophilus parainfluenzae and Streptococcus pneumoniae. The predominant risk chemicals in TSC included pesticides/herbicides (carbofuran, bromacil, and propazine) and detergents (triethanolamine, diethanolamine, and diethyl phthalate). The abundances of these VFs and detergents followed the trend of TSC > LSC > school classrooms (p < 0.01), potentially explaining the higher incidence of infectious and chronic inflammatory diseases in aircraft. The level of ARGs in aircraft was similar to that in school environments. This is the first multi-omic survey in commercial aircraft, highlighting that surface material choice is a potential intervention strategy for improving passenger health.
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