| 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. |
- Deng, Tao, et al.
(författare)
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Modeling and Optimization of Mobility-Aware Dynamic Caching With Time-Varying Content Popularity
- 2020
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Ingår i: IEEE Transactions on Vehicular Technology. - 0018-9545 .- 1939-9359. ; 69:1, s. 1157-1162
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Tidskriftsartikel (refereegranskat)abstract
- A mobility-aware dynamic caching optimization problem (MDCP) is modelled for optimal caching when the contents' popularity may vary over time. The NP-hardness of MDCP is proved. For the problem's solution, first, by providing a reformulation, the optimum of MDCP can be computed in up to medium-scale system scenarios. In addition, a time-efficient algorithm is developed for large-scale scenarios. The results of performance evaluation are provided.
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| 3. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 4. |
- Fu, Xi, et al.
(författare)
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Associations between respiratory infections and bacterial microbiome in student dormitories in Northern China.
- 2020
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Ingår i: Indoor Air. - : Hindawi Limited. - 0905-6947 .- 1600-0668. ; 30:5, s. 816-826
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies reveal that the microbial diversity and composition in the respiratory tract are related to the susceptibility, development, and progression of respiratory infections. Indoor microorganisms can transmit into the respiratory tract through breathing, but their role in infections is unclear. Here, we present the first association study between the indoor microbiome and respiratory infections. In total, 357 students living in 86 dormitory rooms in Shanxi University were randomly selected to survey symptoms of infections. Settled air dust was collected to characterize bacterial compositions by 16S rRNA sequencing. The overall microbial richness was not associated with respiratory infections, but microorganisms from specific phylogenetic classes showed various associations. Taxa richness and abundance of Actinobacteria were protectively associated with infections (P < .05). The abundance of several genera in Gammaproteobacteria, including Haemophilus, Klebsiella, Buttiauxella, and Raoultella, was positively associated with infections (P < .005). The role of these microorganisms was consistent with previous human microbiota studies. Building age was associated with the overall microbial composition variation in dormitories and negatively associated with three potential risk genera in Proteobacteria (P < .05). The weight of vacuum dust was positively associated with a protective genus, Micrococcus in Actinobacteria (P < .05).
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| 5. |
- Fu, Xi, et al.
(författare)
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Continental-Scale Microbiome Study Reveals Different Environmental Characteristics Determining Microbial Richness, Composition, and Quantity in Hotel Rooms
- 2020
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Ingår i: mSystems. - : AMER SOC MICROBIOLOGY. - 2379-5077. ; 5:3
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Tidskriftsartikel (refereegranskat)abstract
- Culture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome composition and the associated environmental characteristics have not been characterized in hotel environments. We presented here the first continental-scale microbiome study of hotel rooms (n = 68) spanning Asia and Europe. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified in the same sequencing depth, but most fungal taxa showed a restricted distribution compared to bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for -80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbiome and 16 indoor and outdoor environmental characteristics. Fungal composition and absolute quantity showed concordant associations with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea, and visible mold, while fungal richness was negatively associated with heavy traffic (95% confidence interval [CI] = -127.05 to -0.25) and wall-to-wall carpet (95% CI = -47.60 to -3.82). Bacterial compositional variation was associated with latitude, quality of the interior, and floor type, while bacterial richness was negatively associated with recent redecoration (95% CI -179.00 to -44.55) and mechanical ventilation (95% CI = -136.71 to -5.12). IMPORTANCE This is the first microbiome study to characterize the microbiome data and associated environmental characteristics in hotel environments. In this study, we found concordant variation between fungal compositional variation and absolute quantity and discordant variation between community variation/quantity and richness. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.
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| 6. |
- Fu, Xi, et al.
(författare)
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Indoor microbiome, environmental characteristics and asthma among junior high school students in Johor Bahru, Malaysia
- 2020
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Ingår i: Environment International. - : Elsevier BV. - 0160-4120 .- 1873-6750. ; 138
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Tidskriftsartikel (refereegranskat)abstract
- Indoor microbial diversity and composition are suggested to affect the prevalence and severity of asthma by previous home microbiome studies, but no microbiome-health association study has been conducted in a school environment, especially in tropical countries. In this study, we collected floor dust and environmental characteristics from 21 classrooms, and health data related to asthma symptoms from 309 students, in junior high schools in Johor Bahru, Malaysia. The bacterial and fungal composition was characterized by sequencing 16s rRNA gene and internal transcribed spacer (ITS) region, and the absolute microbial concentration was quantified by qPCR. In total, 326 bacterial and 255 fungal genera were characterized. Five bacterial (Sphingobium, Rhodomicrobium, Shimwellia, Solirubrobacter, Pleurocapsa) and two fungal (Torulaspora and Leptosphaeriaceae) taxa were protective for asthma severity. Two bacterial taxa, Izhakiella and Robinsoniella, were positively associated with asthma severity. Several protective bacterial taxa including Rhodomicrobium, Shimwellia and Sphingobium have been reported as protective microbes in previous studies, whereas other taxa were first time reported. Environmental characteristics, such as age of building, size of textile curtain per room volume, occurrence of cockroaches, concentration of house dust mite allergens transferred from homes by the occupants, were involved in shaping the overall microbial community but not asthma-associated taxa; whereas visible dampness and mold, which did not change the overall microbial community for floor dust, was negatively associated with the concentration of protective bacteria Rhodomicrobium (beta =-2.86, p = 0.021) of asthma. The result indicates complex interactions between microbes, environmental characteristics and asthma symptoms. Overall, this is the first indoor microbiome study to characterize the asthma-associated microbes and their environmental determinant in the tropical area, promoting the understanding of microbial exposure and respiratory health in this region.
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| 7. |
- Gelabert, Pere, et al.
(författare)
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Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet
- 2020
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 30:1, s. 108-114
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Tidskriftsartikel (refereegranskat)abstract
- As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati Zoo in 1918 [1]. The cause of its extinction remains contentious: besides excessive mortality associated to habitat destruction and active hunting, their survival could have been negatively affected by its range having become increasingly patchy [2] or by the exposure to poultry pathogens [3, 4]. In addition, the Carolina parakeet showed a pre-dilection for cockleburs, an herbaceousplant that contains a powerful toxin, carboxyatractyloside, or CAT [5], which did not seem to affect them but made the birds notoriously toxic to most predators [3]. To explore the demographic history of this bird, we generated the complete genomic sequence of a preserved specimen held in a private collection in Espinelves (Girona, Spain), as well as of a close extant relative, Aratinga solstitialis. We identified two non-synonymous genetic changes in two highly conserved proteins known to interact with CAT that could underlie a specific dietary adaptation to this toxin. Our genomic analyses did not reveal evidence of a dramatic past demographic decline in the Carolina parakeet; also, its genome did not exhibit the long runs of homozygosity that are signals of recent inbreeding and are typically found in endangered species. As such, our results suggest its extinction was an abrupt process and thus likely solely attributable to human causes.
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| 8. |
- Sun, Yu, et al.
(författare)
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Shotgun metagenomics of dust microbiome from flight deck and cabin in civil aviation aircraft
- 2020
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Ingår i: Indoor Air. - : Wiley. - 0905-6947 .- 1600-0668. ; 30:6, s. 1199-1212
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Tidskriftsartikel (refereegranskat)abstract
- Microbial exposure is related to the health of passengers on commercial aircraft, but no studies characterized the microbial composition at the species level and identified their ecological determinants. We collected vacuum dust from floor and seat surfaces in flight decks and cabins of 18 aircraft, and amplification-free shotgun metagenomics was conducted to characterize the microbial composition. In total, 7437 microbial taxa were identified. The relative abundance for bacteria, eukaryote, viruses, and archaea was 96.9%, 1.8%, 0.3%, and 0.03%, respectively. The top bacterial species mainly derived from outdoor air and human skin included Sphingomonas, Corynebacterium, Micrococcus luteus, Variovorax paradoxus, Paracoccus dentrificans, and Propionibacterium acnes. The abundance of NIAID-defined pathogens was low, accounted for only 0.23% of total microbes. The microbial species and functional composition were structured by the indoor surface type (R-2 = 0.38, Adonis), followed by the manufacturer of the aircraft (R-2 = 0.12) and flight duration (R-2 = 0.07). Indoor surfaces affected species derived from different habitats; the abundance of dry skin and desiccated species was higher on textile surfaces, whereas the abundance of moist and oily skin species was higher on leather surfaces. The growth rates for most microbes were stopped and almost stopped.
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| 9. |
- Wang, F., et al.
(författare)
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A comprehensive review on high-temperature fuel cells with carbon capture
- 2020
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Ingår i: Applied Energy. - : Elsevier Ltd. - 0306-2619 .- 1872-9118. ; 275
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Forskningsöversikt (refereegranskat)abstract
- High-temperature fuel cells and their hybrid systems represent one of the most promising technologies with high conversion efficiency. The configuration of such kind of system could facilitate an easy capture of CO2. Several novel CO2 capture strategies have been developed based on high-temperature fuel cells, such as solid oxide fuel cell (SOFC), molten carbonate fuel cell (MCFC) and direct carbon fuel cell (DCFC). However, related review which focus on their system integration and performance evaluation is still rare. The aim of this study is to improve interest in high-temperature fuel cell with CO2 capture by providing an overview of the status of such kind of cutting-edge technologies. To approach this goal, the major strategies and technologies for fuel cells and their hybrid system with CO2 capture have been reviewed. Simultaneously, the characteristics of fuel cell technologies are summarized and the technical and economic performance of the fuel cell with CO2 capture are explored and discussed as well. The existing challenges that required to be overcome in fuel cell with CO2 capture technology are highlighted with aspects on fuel cell module scale-up, cost, safety, reliability and capture energy, etc. Finally, opportunities for the future development of high-temperature fuel cell with CO2 capture technologies are discussed. The conclusion remarks of this investigation indicate that fuel cell integrating CO2 capture process is a promising route to sustainable future, and could even be more effective if fuel cell technology can be commercialized.
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