| 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. |
- Ballantyne, Kaye N., et al.
(författare)
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Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats
- 2014
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Ingår i: Human Mutation. - : John Wiley & Sons. - 1059-7794 .- 1098-1004. ; 35:8, s. 1021-1032
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Tidskriftsartikel (refereegranskat)abstract
- Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, greater than99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RMY-STRs in identifying and separating unrelated and related males and provides a reference database.
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| 3. |
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| 4. |
- Manderstedt, Lena, 1966-, et al.
(författare)
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Meeting eye to eye: the power relations in triadic mentoring of the degree project in teacher education
- 2023
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Ingår i: Mentoring & Tutoring. - : Taylor & Francis Group. - 1361-1267 .- 1469-9745. ; 31:4, s. 512-531
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Tidskriftsartikel (refereegranskat)abstract
- This study highlights and discusses power aspects within discourses discerned in articulations on triadic mentoring in degree projects in teacher education in Sweden. Each mentoring triad consisted of a pre-service teacher, a professional teacher acting as co-mentor, and a university mentor. As teacher education is to be based on a scientific foundation and proven experience, a symmetrical and complementary approach was to be implemented. Data from interviews, logbooks, and observations of mentoring were analysed discursively using CDA. Two main discourses were distinguished: The hegemony of science, and A gateway to the profession and science: The potential third space. The study shows that the academic paradigm tends to overshadow the symmetrical and complementary approach, but that the third space, the metaphorical meeting outside of the participants’ comfort zone, potentially balances up the mentoring triads through the pre-service teachers’ ownership of the process.
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| 5. |
- Manderstedt, Lena, 1966-, et al.
(författare)
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Win-win through triadic supervision and collaboration : Structures for L1 degree projects
- 2022
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Konferensbidrag (refereegranskat)abstract
- According to the Higher Education Act (SFS 1992:1434), the education, as well as the degree project, must be based on scientific foundation and proven experience. In order to achieve that balance, sustainable models of collaboration between universities and schools must be developed (ULF-avtal, n.d.).In 2021, a pilot project encompassing four student teachers’ degree projects was carried out within a practice-based theoretical framework (Rönnerman, 2018; Rönnerman & Olin, 2021). Each student teacher in the pilot project was supervised in a triad, with a university lecturer and a L1 schoolteacher.The aim of this study is to present the pilot project, and one example of the degree projects, and discuss how the L1 subjects in schools and teacher education are impacted. The research questions are:(a) How are the L1 school subjects and the teacher education impacted by the triadic supervision and collaboration?(b) Which are the benefits of triadic supervision?The gathered material consists of two interviews, and two logbook posts per participant, and one observation of the supervised sessions of each triad (Bruneel & Vanassche, 2021; Viklund et al., 2022). The data was analysed thematically (Cresswell, 2014).The result shows the benefits of the pilot project on different levels. Firstly, from a school-perspective where the student teacher works closely with teachers at a school. This provides a relevant subject for the degree project and helps other L1 teachers to develop their teaching (Nilsson, 2021). Secondly, the pilot project contributes with an organizational-perspective (Thorsten, 2021), where the results are presented to stakeholders. Thirdly, the university and the L1 teachers gain theoretical, practical and useful knowledge through the degree projects’ L1 perspective. The collaboration regarding co-supervision of degree projects will become a permanent part of the teacher education at the university in question, encompassing other collaborating partners, and student teachers.
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| 6. |
- Palo, Thomas, et al.
(författare)
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Distribution Of Winter Browsing By Moose: Evidence Of Long-Term Stability In Northern Sweden
- 2015
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Ingår i: Alces. - 0835-5851. ; 51, s. 35-43
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Tidskriftsartikel (refereegranskat)abstract
- Predicting spatial distribution of large herbivore foraging is important for successfulmanagement, but accurate predictions remain elusive against a background of multiple causes modifiedby environmental stochasticity. Moose (Alces alces) might prefer to browse areas with high plant density,but if snow depth co-varies with plant density, this could restrict access to these sites and force useof sites with lower plant density and snow depth. Moose browsing was measured in 72 plots distributedwithin the subarctic birch (Betula spp.) forest landscape at Abisko in northern Sweden in 1996. In 2010,the same plots were revisited and the measurements repeated. A generalized linear model predictedmoose browsing on birch in 2010 from the browsing pattern on birch measured in 1996. The modelsuggested that neither total density of willow and birch stems nor snow depth were influential of foragingdistribution of birch at multiple spatial scales. The spatial scale at which clustering of browsing on birchoccurred, coincided with the scale of clustering of birch and willow (Salix spp.) stems at distances of1000–2500 m; at lesser distance browsing was distributed randomly. We concluded that moose demonstratestability in spatial browsing patterns after 14 years which corresponds to 3–4 generations of moose,and that plant density represents a cue for moose only at certain scales. Predictability of feeding sites isvaluable for long-term moose and forest management, and conservation planning.
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| 7. |
- Sommarin, Mikael N.E., et al.
(författare)
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Single-cell multiomics of human fetal hematopoiesis define a developmental-specific population and a fetal signature
- 2023
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Ingår i: Blood Advances. - 2473-9529. ; 7:18, s. 5325-5340
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge of human fetal blood development and how it differs from adult blood is highly relevant to our understanding of congenital blood and immune disorders and childhood leukemia, of which the latter can originate in utero. Blood formation occurs in waves that overlap in time and space, adding to heterogeneity, which necessitates single-cell approaches. Here, a combined single-cell immunophenotypic and transcriptional map of first trimester primitive blood development is presented. Using CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing), the molecular profile of established immunophenotype-gated progenitors was analyzed in the fetal liver (FL). Classical markers for hematopoietic stem cells (HSCs), such as CD90 and CD49F, were largely preserved, whereas CD135 (FLT3) and CD123 (IL3R) had a ubiquitous expression pattern capturing heterogenous populations. Direct molecular comparison with an adult bone marrow data set revealed that the HSC state was less frequent in FL, whereas cells with a lymphomyeloid signature were more abundant. An erythromyeloid–primed multipotent progenitor cluster was identified, potentially representing a transient, fetal-specific population. Furthermore, differentially expressed genes between fetal and adult counterparts were specifically analyzed, and a fetal core signature was identified. The core gene set could separate subgroups of acute lymphoblastic leukemia by age, suggesting that a fetal program may be partially retained in specific subgroups of pediatric leukemia. Our detailed single-cell map presented herein emphasizes molecular and immunophenotypic differences between fetal and adult blood cells, which are of significance for future studies of pediatric leukemia and blood development in general.
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| 8. |
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| 9. |
- Öhmark, Sara, 1980-, et al.
(författare)
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Spatially segregated foraging patterns of moose (Alces alces) and mountain hare (Lepus timidus) in a subarctic landscape: different tables in the same restaurant?
- 2015
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Ingår i: Canadian Journal of Zoology. - : Canadian Science Publishing. - 0008-4301 .- 1480-3283. ; 93:5, s. 391-396
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Tidskriftsartikel (refereegranskat)abstract
- Differences in body sizes of mountain hares (Lepus timidus L., 1758) and moose (Alces alces (L., 1758)) affect their abilityto perceive and respond to environmental heterogeneity and plant density. Therefore, we expect these species to show nicheseparation at different scales in the same environment. Results showed that the numbers of mountain birches (Betula pubescenssubsp. czerepanovii L.) browsed by moose per unit area was inversely related to hare browsing. Moose browsed larger birchescompared with hares, and while hares targeted areas with high birch densities regardless of tree sizes, moose preferentiallybrowsed areas with high densities of large birches. Moose browsing was clustered at spatial intervals of 1000–1500 m, while harebrowsing was clustered at intervals of less than 500 m. Willows (genus Salix L.) in the study area were heavily browsed by moose,while few observations of hare browsing on willow were made. Regarding both hare and moose, numbers of birch stems withnew browsing per sample plot were positively correlated with the numbers of birch stems with old browsing, indicating thathare and moose preferred the same foraging sites from year to year. These findings have implications for management of thespecies because they show the importance of scale and landscape perspectives in planning and actions.
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| 10. |
- Öhmark, Sara, 1980-
(författare)
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Winter browsing by moose and hares in subarctic birch forest : Scale dependency and responses to food addition
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Despite their difference in body size and morphology, the moose (Alces alces) andthe mountain hare (Lepus timidus) sustain themselves during winter on similar plantspecies and plant parts in in subarctic environments, namely apical twigs ofmountain birch (Betula pubescens ssp. czerepanovii). Herbivores must select areas anditems of food that provide sufficient intake rates and food nutritional quality whilebalancing this against their intake of dietary fiber and potentially detrimental plantsecondary metabolites. This selection takes place simultaneously at multiple spatialscales, from individual plants and plant parts to patches of food and parts of the wider landscape. While the herbivores must consider their need for food to sustaindaily activities, for body growth and reproduction it is also necessary to avoid predators and harsh environmental conditions. For managers, an understanding of key factors for animal foraging distributions is pivotal to reach intended goals ofmanagement and conservation plans. Knowledge in this area is also important formodels to make accurate predictions of foraging responses of herbivores to resource distributions. The mountain birch forest displays a naturally heterogeneous distribution of trees and shrubs which presents herbivores with a challenge to findgood feeding areas. In an investigation of the spatial distribution of moose browsing on birch and willows (Salix spp.) in two winter seasons separated in time by 14 years,it was found that moose browsing patterns in 1996 were correlated to those observed in 2010. It was also found that moose browsing was spatially clustered within the same distances (1000-2500 m) as densities of willow and birch, but at other spatial scales, browsing was mostly randomly distributed. It was concluded that foragedensity is a cue for moose but only at certain spatial scales. Similarly, a comparison of foraging distribution by hare and moose showed that high birch density was a key factor for both species. In spite of this, hares and moose used different parts ofthe same environment because they respond to food resource distribution at different spatial scales. Hares fed from smaller plants, and focused their foraging activity on smaller spatial scales than moose. These results emphasize the importance of taking into account the distribution of food resources at spatial scales relevant for each species in plans for conservation and management. In an experimental study it was found that intensified browsing on natural forage by mountain hares can be induced locally through placement of food. The induced browsing varied with the amount and quality of the added food, but also with thedensity of natural food plants and natural foraging distribution by hares. Finally, ina last experiment habitat preference of mountain hares across edges between open and forested areas was studied. The results were not consistent; hares utilized baitto a greater extent within forested areas than bait placed on a nearby lake ice, butbait on mires and heaths was either preferred over bait in nearby forest, or utilizedto a similar extent. A possible explanation is that hares have knowledge of their environment such that both forested areas and subarctic mires and heaths are partof its natural home range, whilst the extreme environment on the lake ice is not. During recent decades arctic areas have had an increase in vegetation density andwill be affected by future climate warming and therefore, factors that determineforaging ecology of key herbivores need to be identified. This thesis sheds some light on these factors in relation to spatial scale and forage distribution for two high profile herbivores in the subarctic.
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