| 1. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
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.
|
|
| 2. |
- Kohler, Annegret, et al.
(författare)
-
Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
- 2015
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:4, s. 176-410
-
Tidskriftsartikel (refereegranskat)abstract
- To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.
|
|
| 3. |
- Plomion, Christophe, et al.
(författare)
-
Oak genome reveals facets of long lifespan
- 2018
-
Ingår i: NATURE PLANTS. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 4:7, s. 440-452
-
Tidskriftsartikel (refereegranskat)abstract
- Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
|
|
| 4. |
|
|
| 5. |
- Vidal, Brenda, 1987-, et al.
(författare)
-
Assessing the sustainability of on-site sanitation systems using multi-criteria analysis
- 2019
-
Ingår i: Environmental Science. - Cambridge : Royal Society of Chemistry. - 2053-1400 .- 2053-1419. ; 5:9, s. 1599-1615
-
Tidskriftsartikel (refereegranskat)abstract
- Small on-site sanitation systems are widely present in suburban and rural areas in many countries. As these systems often underperform and have an impact on receiving waters, understanding their overall sustainability is of interest for policy and decision-makers. However, the definition and estimation of indicators defining sustainability are challenging, as it is finding the methodological approach to combine qualitative and quantitative indicators into one comprehensive assessment. In this study, twelve indicators defined by environmental, economic, social, technical and health-related criteria were used to compare nine alternatives of on-site sanitation for single households. A non-compensatory method for multi-criteria decision analysis, ELECTRE III, was used for the assessment together with weights assigned to each indicator by a reference group. Several scenarios were developed to reflect different goals and a sensitivity analysis was conducted. Overall, the graywater-blackwater separation system resulted as the most sustainable option and, in terms of polishing steps for phosphorus removal, chemical treatment was preferred over the phosphorus filter, both options being implemented together with sand filters. Assessing the robustness of the systems was a crucial step in the analysis given the high importance assigned to the aforementioned indicator by the stakeholders, thus the assessment method must be justified. The proposed multi-criteria approach contributes to aid the assessment of complex information needed in the selection of sustainable sanitation systems and in the provision of informed preferences. © 2019 The Royal Society of Chemistry.
|
|
