| 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. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 4. |
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| 5. |
- Yang, Han-Xin, et al.
(författare)
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Diversity-optimized cooperation on complex networks
- 2009
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - : American physical society. - 1063-651X .- 1095-3787. ; 79:5, s. 056107-
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Tidskriftsartikel (refereegranskat)abstract
- We propose a strategy for achieving maximum cooperation in evolutionary games on complex networks. Each individual is assigned a weight that is proportional to the power of its degree, where the exponent α is an adjustable parameter that controls the level of diversity among individuals in the network. During the evolution, every individual chooses one of its neighbors as a reference with a probability proportional to the weight of the neighbor, and updates its strategy depending on their payoff difference. It is found that there exists an optimal value of α, for which the level of cooperation reaches maximum. This phenomenon indicates that, although high-degree individuals play a prominent role in maintaining the cooperation, too strong influences from the hubs may counterintuitively inhibit the diffusion of cooperation. Other pertinent quantities such as the payoff, the cooperator density as a function of the degree, and the payoff distribution are also investigated computationally and theoretically. Our results suggest that in order to achieve strong cooperation on a complex network, individuals should learn more frequently from neighbors with higher degrees, but only to a certain extent.
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| 6. |
- Zhou, Dapeng, et al.
(författare)
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Immunologic mapping of glycomes: implications for cancer diagnosis and therapy.
- 2011
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Ingår i: Frontiers in bioscience (Scholar edition). - 1945-0524. ; 3, s. 1520-32
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Tidskriftsartikel (refereegranskat)abstract
- Cancer associated glycoconjugates are important biomarkers, as exemplified by globo-H, CA125, CA15.3 and CA27.29. However, the exact chemical structures of many such biomarkers remain unknown because of technological limitations. In this article, we propose the "immunologic mapping" of cancer glycomes based on specific immune recognition of glycan structures, which can be hypothesized theoretically, produced chemically, and examined biologically by immuno-assays. Immunologic mapping of glycans not only provides a unique perspective on cancer glycomes, but also may lead to the invention of powerful reagents for diagnosis and therapy.
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| 7. |
- Fu, Xi, et al.
(författare)
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Associations between species-level indoor microbiome, environmental characteristics, and asthma in junior high schools of Terengganu, Malaysia
- 2022
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Ingår i: Air quality, atmosphere and health. - : Springer Nature. - 1873-9318 .- 1873-9326. ; 15:6, s. 1043-1055
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Tidskriftsartikel (refereegranskat)abstract
- Indoor microbiome exposure is important for asthma development, but current studies characterize the microbiome at the genus or above levels due to technical limitations. We aim to profile bacterial and fungal composition and concentration at the species level and assess its potential health effects. Four hundred sixty-three students from 8 junior high schools in Terengganu, Malaysia, were surveyed for asthma symptoms. Full-length PacBio amplicon sequencing and qPCR were conducted to quantify the absolute microbial concentration in the vacuum dust of the selected classroom. In total, 1358 bacterial and 358 fungal species were characterized, and drastic compositional variation was observed among classrooms. Three-level linear regression analyses revealed that taxa richness in Cyanobacteria were negatively associated with asthma (FDR < 0.001). The absolute concentration of Nocardioides exalbidus was protectively associated with asthma, and four bacteria species were positively associated with asthma (FDR < 0.1). Interestingly, all five species were recently isolated and characterized in Asian countries and never reported to associate with asthma. Indoor NO2 and formaldehyde concentration were associated with the overall bacterial community variation and fungal richness, respectively (p < 0.05). No environmental characteristics were directly associated with asthma, but indoor relative humidity, CO2 concentration, and weight of vacuum dust were associated with the asthma-related species (p < 0.05), suggesting a potential indirect health effect on students. This is the first study to characterize indoor microbiome and asthma-associated microorganisms at the species level, representing a region-specific microbiome exposure pattern in a tropical Asian country.
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| 8. |
- Fu, Xi, et al.
(författare)
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Associations between the indoor microbiome, environmental characteristics and respiratory infections in junior high school students of Johor Bahru, Malaysia.
- 2021
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Ingår i: Environmental Science. - : Royal Society of Chemistry. - 2050-7887 .- 2050-7895. ; 23:8, s. 1171-1181
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Tidskriftsartikel (refereegranskat)abstract
- Pathogens are commonly present in the human respiratory tract, but symptoms are varied among individuals. The interactions between pathogens, commensal microorganisms and host immune systems are important in shaping the susceptibility, development and severity of respiratory diseases. Compared to the extensive studies on the human microbiota, few studies reported the association between indoor microbiome exposure and respiratory infections. In this study, 308 students from 21 classrooms were randomly selected to survey the occurrence of respiratory infections in junior high schools of Johor Bahru, Malaysia. Vacuum dust was collected from the floor, chairs and desks of these classrooms, and high-throughput amplicon sequencing (16S rRNA and ITS) and quantitative PCR were conducted to characterize the absolute concentration of the indoor microorganisms. Fifteen bacterial genera in the classes Actinobacteria, Alphaproteobacteria, and Cyanobacteria were protectively associated with respiratory infections (p < 0.01), and these bacteria were mainly derived from the outdoor environment. Previous studies also reported that outdoor environmental bacteria were protectively associated with chronic respiratory diseases, such as asthma, but the genera identified were different between acute and chronic respiratory diseases. Four fungal genera from Ascomycota, including Devriesia, Endocarpon, Sarcinomyces and an unclassified genus from Herpotrichillaceae, were protectively associated with respiratory infections (p < 0.01). House dust mite (HDM) allergens and outdoor NO2 concentration were associated with respiratory infections and infection-related microorganisms. A causal mediation analysis revealed that the health effects of HDM and NO2 were partially or fully mediated by the indoor microorganisms. This is the first study to explore the association between environmental characteristics, microbiome exposure and respiratory infections in a public indoor environment, expanding our understanding of the complex interactions among these factors.
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