| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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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| 3. |
- Lewin, Marcus, et al.
(author)
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Hybrids between Rubus caesius and Rubus sect. Corylifolii (Rosaceae) and their relation to R. cyclomorphus, R. tiliaster, R. glauciformis, R. slesvicensis and R. firmus
- 2022
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In: Nordic Journal of Botany. - : Wiley. - 0107-055X .- 1756-1051. ; 2022:12
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Journal article (peer-reviewed)abstract
- Using flow cytometry and microsatellite DNA analysis (MSDA), we studied hybrids between Rubus caesius and various other Rubus species, with an emphasis on Sweden. We show that hybrids between Rubus caesius and Rubus sect. Corylifolii arise easily. They show a large variation in morphology, but can normally be recognised by a number of characters. They are typically hexaploids, but ~13% of the hybrids are pentaploids and ~8% tetraploids. With MSDA, they are harder to identify than hybrids with R. idaeus, partly because all Corylifolii species have themselves arisen from R. caesius hybrids and therefore share many alleles with R. caesius, partly because hybridisation with R. caesius seems to give rise to some variation in microsatellite regions. Hybrids with species of R. sect. Rubus are much rarer in Sweden and we have only identified one such case. We show that R. cyclomorphus and R. tiliaster are not proper apomictic species, at least not in Sweden, but rather a collection of genetically unrelated hybrids between R. caesius and R. raduloides or R. camptostachys. MSDA analysis of R. slesvicensis and R. firmus shows that these species are problematic. We identify two distinct taxa, one from Skåne in Sweden, which we describe as a new species, R. ruboculus and another from the neighbourhood of Viborg and Schleswig, although the latter is probably not identical with R. slesvicensis s.s. All the other samples form a diverse group of putative R. caesius hybrids at three different ploidy levels. Rubus glauciformis is uniform in Småland, Öland and Blekinge, but becomes harder to distinguish from various hybrids in Skåne. We conclude that once R. caesius and R. idaeus hybrids are properly identified, along with a small number of new apomictic species (often with a local distribution), the genus Rubus does not pose any serious taxonomical problems in Sweden.
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| 4. |
- Ryde, Ulf, et al.
(author)
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Hybrids between Rubus idaeus and Rubus sect. Corylifolii and their relation to R. pruinosus and R. rosanthus
- 2021
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In: Nordic Journal of Botany. - : Wiley. - 0107-055X .- 1756-1051. ; 39:8
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Journal article (peer-reviewed)abstract
- We have studied hybrids between Rubus idaeus and various members of R. sect. Corylifolii, primarily in Sweden. With the help of DNA-ploidy level determinations using flow cytometry and microsatellite DNA analysis of over 500 samples, we show that the material can be divided into four stable apomictic species (belonging to subsect. Subidaei) and a large number of primary hybrids. Stable species can be recognised by a distribution that is distinct from the Corylifolii parent, a uniform morphology and an almost invariant genetic pattern. We confirm that R. cordatiformis has arisen from the hybrid R. eluxatus × idaeus. Moreover, our study shows that R. lagerbergii has arisen from the hybrid R. dissimulans × idaeus. For R. onsalaënsis, we unexpectedly identify the Corylifolii ancestor as a previously unidentified species with a very restricted distribution in the northern part of the province of Halland, which is here described as R. antecedens. Furthermore, we show that R. pruinosus s. str. has arisen from the hybrid R. aureolus × idaeus and that it is known only from a rather restricted area in the provinces of Småland, Östergötland and Södermanland in eastern Sweden. On the other hand, the great majority of what has been called R. pruinosus is a diverse collection of primary hybrids between R. idaeus and various R. sect. Corylifolii species, which show a large variation both genetically and morphologically. The same applies to R. rosanthus, which represents R. norvegicus × idaeus hybrids: The microsatellite analysis shows that they have arisen independently and therefore should be considered as primary hybrids. We also identified primary hybrids between R. idaeus and R. gothicus (by far the most common hybrid in Sweden), R. aureolus, R. camptostachys, R. decurrentispinus, R. eluxatus, R. friesianus, R. hallandicus, R. lidforssii and R. norvegicus.
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