| 1. |
- Bartholomew, David, et al.
(författare)
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Bornean tropical forests recovering from logging at risk of regeneration failure
- 2024
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Ingår i: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 30:3
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Tidskriftsartikel (refereegranskat)abstract
- Active restoration through silvicultural treatments (enrichment planting, cutting climbers and liberation thinning) is considered an important intervention in logged forests. However, its ability to enhance regeneration is key for long-term recovery of logged forests, which remains poorly understood, particularly for the production and survival of seedlings in subsequent generations. To understand the long-term impacts of logging and restoration we tracked the diversity, survival and traits of seedlings that germinated immediately after a mast fruiting in North Borneo in unlogged and logged forests 30–35 years after logging. We monitored 5119 seedlings from germination for ~1.5 years across a mixed landscape of unlogged forests (ULs), naturally regenerating logged forests (NR) and actively restored logged forests via rehabilitative silvicultural treatments (AR), 15–27 years after restoration. We measured 14 leaf, root and biomass allocation traits on 399 seedlings from 15 species. Soon after fruiting, UL and AR forests had higher seedling densities than NR forest, but survival was the lowest in AR forests in the first 6 months. Community composition differed among forest types; AR and NR forests had lower species richness and lower evenness than UL forests by 5–6 months post-mast but did not differ between them. Differences in community composition altered community-weighted mean trait values across forest types, with higher root biomass allocation in NR relative to UL forest. Traits influenced mortality ~3 months post-mast, with more acquisitive traits and relative aboveground investment favoured in AR forests relative to UL forests. Our findings of reduced seedling survival and diversity suggest long time lags in post-logging recruitment, particularly for some taxa. Active restoration of logged forests recovers initial seedling production, but elevated mortality in AR forests lowers the efficacy of active restoration to enhance recruitment or diversity of seedling communities. This suggests current active restoration practices may fail to overcome barriers to regeneration in logged forests, which may drive long-term changes in future forest plant communities.
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| 2. |
- 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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| 3. |
- Cao, Junyue, et al.
(författare)
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Principles of Systems Biology, No. 21
- 2017
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Ingår i: CELL SYSTEMS. - : CELL PRESS. - 2405-4712. ; 5:3, s. 158-160
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- This month: relating single cells to populations (Cao/Packer, Wu/Altschuler, O'Brien, Friedman), an excess of ribosomes (Barkai), human pathology atlas (Uhlen), signatures of feedback (Rahi), and major genome redesign (Baumgart).
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| 4. |
- Cao, Junyue, et al.
(författare)
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Principles of Systems Biology, No. 21 : Editorial
- 2017
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Ingår i: CELL SYSTEMS. - : Elsevier BV. - 2405-4712. ; 5:3, s. 158-160
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- This month: relating single cells to populations (Cao/Packer, Wu/Altschuler, O'Brien, Friedman), an excess of ribosomes (Barkai), human pathology atlas (Uhlen), signatures of feedback (Rahi), and major genome redesign (Baumgart).
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| 5. |
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| 6. |
- Kim, Anna A., et al.
(författare)
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Independently paced Ca2+ oscillations in progenitor and differentiated cells in an ex vivo epithelial organ
- 2022
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Ingår i: Journal of Cell Science. - : The Company of Biologists. - 0021-9533 .- 1477-9137. ; 135:14
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Tidskriftsartikel (refereegranskat)abstract
- Cytosolic Ca2+ is a highly dynamic, tightly regulated and broadly conserved cellular signal. Ca2+ dynamics have been studied widely in cellular monocultures, yet organs in vivo comprise heterogeneous populations of stem and differentiated cells. Here, we examine Ca2+ dynamics in the adult Drosophila intestine, a self-renewing epithelial organ in which stem cells continuously produce daughters that differentiate into either enteroendocrine cells or enterocytes. Live imaging of whole organs ex vivo reveals that stem-cell daughters adopt strikingly distinct patterns of Ca2+ oscillations after differentiation: enteroendocrine cells exhibit single-cell Ca2+ oscillations, whereas enterocytes exhibit rhythmic, long-range Ca2+ waves. These multicellular waves do not propagate through immature progenitors (stem cells and enteroblasts), of which the oscillation frequency is approximately half that of enteroendocrine cells. Organ-scale inhibition of gap junctions eliminates Ca2+ oscillations in all cell types – even, intriguingly, in progenitor and enteroendocrine cells that are surrounded only by enterocytes. Our findings establish that cells adopt fate-specific modes of Ca2+ dynamics as they terminally differentiate and reveal that the oscillatory dynamics of different cell types in a single, coherent epithelium are paced independently.
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| 7. |
- Kim, Anna A, et al.
(författare)
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Microfluidics for mechanobiology of model organisms
- 2018
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Ingår i: Microfluidics in Cell Biology Part A. - : Elsevier. - 9780128142806 ; , s. 217-259
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Bokkapitel (refereegranskat)abstract
- Mechanical stimuli play a critical role in organ development, tissue homeostasis, and disease. Understanding how mechanical signals are processed in multicellular model systems is critical for connecting cellular processes to tissue- and organism-level responses. However, progress in the field that studies these phenomena, mechanobiology, has been limited by lack of appropriate experimental techniques for applying repeatable mechanical stimuli to intact organs and model organisms. Microfluidic platforms, a subgroup of microsystems that use liquid flow for manipulation of objects, are a promising tool for studying mechanobiology of small model organisms due to their size scale and ease of customization. In this work, we describe design considerations involved in developing a microfluidic device for studying mechanobiology. Then, focusing on worms, fruit flies, and zebrafish, we review current microfluidic platforms for mechanobiology of multicellular model organisms and their tissues and highlight research opportunities in this developing field.
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| 8. |
- Kim, Anna A, et al.
(författare)
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Regional Calcium Dynamics in Drosophila Adult Midgut
- 2019
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Ingår i: Mol. Biol. Cell.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Although calcium dynamics are widely studied in cell culture, little has been reported on the topic for adult organs. We find striking regional and cell-type specific differences in calcium dynamics in the three major cell types of the adult Drosophila intestine. The adult fruit fly intestine is a compelling platform for studying intercellular dynamics and interactions. This stem cell-based epithelium is a reductionist model system of the mammalian small bowel with conserved features. The multi-cellular epithelium consists of three major cell types: progenitor cells that give rise to new cells (including stem cells), enteroendocrine cells that are hormone signaling cells, and enterocytes that are large absorptive cells.We find regional and cell-type specific variations in calcium signaling dynamics within this functionally compartmentalized organ, using confocal imaging of ex vivo cultured fly intestines. Progenitor and enteroendocrine cells indicate oscillatory intracellular calcium dynamics of slower and faster frequencies respectively, and enterocytes demonstrate the presence of traveling calcium waves. Our findings may establish a novel model for studying spatio-temporal organization of cellular to organ-level calcium dynamics in a renewable adult organ.
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