| 1. |
- Midtvedt, Benjamin, et al.
(författare)
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Single-shot self-supervised object detection in microscopy
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Object detection is a fundamental task in digital microscopy, where machine learning has made great strides in overcoming the limitations of classical approaches. The training of state-of-the-art machine-learning methods almost universally relies on vast amounts of labeled experimental data or the ability to numerically simulate realistic datasets. However, experimental data are often challenging to label and cannot be easily reproduced numerically. Here, we propose a deep-learning method, named LodeSTAR (Localization and detection from Symmetries, Translations And Rotations), that learns to detect microscopic objects with sub-pixel accuracy from a single unlabeled experimental image by exploiting the inherent roto-translational symmetries of this task. We demonstrate that LodeSTAR outperforms traditional methods in terms of accuracy, also when analyzing challenging experimental data containing densely packed cells or noisy backgrounds. Furthermore, by exploiting additional symmetries we show that LodeSTAR can measure other properties, e.g., vertical position and polarizability in holographic microscopy.
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| 2. |
- Pavia, Henrik, 1964, et al.
(författare)
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Chemical defences against herbivores
- 2012
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Ingår i: Chemical ecology in aquatic systems. - New York, US : Oxford University Press. - 9780199583096 ; , s. 210-235
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Bokkapitel (refereegranskat)abstract
- In recent years it has become increasingly clear that chemical interactions play a fundamental role in aquatic habitats and have far-reaching evolutionary and ecological consequences. A plethora of studies have shown that aquatic organisms from most taxa and functional groups respond to minute concentrations of chemical substances released by other organisms. However, our knowledge of this 'chemical network' is still negligible. Chemical interactions can be divided into two larger sub-areas based on the function of the chemical substance. First, there are interactions where chemical substances are toxic to other organisms and are used as a defense against consumers (including both herbivores and predators) or a weapon against competitors (allelopathy). Second, chemical substances mey be used as a source for information of the environment; for example: how can I find the optimal habitat, the best food, the nicest partner, and avoid being eaten? Aquatic organisms are able to detect and respond to extremely low concentrations of chemical cues to answer all these questions. The book aims at connecting these intriguing chemical interactions with traditional knowledge of organism interactions. Chemical ecology in aquatic systems covers a wide range of studies, both plant and animal, from different geographic regions and habitats-pelagic as well as benthic. Most of the chemical interactions are similar in freshwater and marine habitats and this book therefor strives at integrating work on both systems. This accessible, research-level text is aimed at graduate students and professional researchers in the fields of limnology, marine ecology, evolutionary biology, behavioral ecology, and chemical ecology.
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| 3. |
- Selander, Erik, 1973, et al.
(författare)
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Copepods induce paralytic shellfish toxin production in marine dinoflagellates
- 2006
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Ingår i: Proceedings of the Royal Society B-Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 273:1594, s. 1673-1680
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Tidskriftsartikel (refereegranskat)abstract
- Among the thousands of unicellular phytoplankton species described in the sea, some frequently occurring and bloom-forming marine dinoflagellates are known to produce the potent neurotoxins causing paralytic shellfish poisoning. The natural function of these toxins is not clear, although they have been hypothesized to act as a chemical defence towards grazers. Here, we show that waterborne cues from the copepod Acartia tonsa induce paralytic shellfish toxin (PST) production in the harmful algal bloom-forming dinoflagellate Alexandrium minutum. Induced A. minutum contained up to 2.5 times more toxins than controls and was more resistant to further copepod grazing. Ingestion of non-toxic alternative prey was not affected by the presence of induced A. minutum. The ability of A. minutum to sense and respond to the presence of grazers by increased PST production and increased resistance to grazing may facilitate the formation of harmful algal blooms in the sea.
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| 4. |
- Toth, Gunilla B., 1973, et al.
(författare)
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Marine dinoflagellates show induced life-history shifts to escape parasite infection in response to water-borne signals
- 2004
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Ingår i: Proceedings of the Royal Society of London Series B-Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 271:1540, s. 733-738
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Tidskriftsartikel (refereegranskat)abstract
- Many dinoflagellate species form dormant resting cysts as a part of their life cycle, and in some freshwater species, hatching of these cysts can be delayed by the presence of water-borne signals from grazing zooplankton. Some marine dinoflagellates can form temporary cysts, which may function to resist unfavourable short-term environmental conditions. We investigated whether the marine dinoflagellate Alexandrium ostenfeldii is able to induce an increased resistance to the parasitic flagellate Parvilucifera infectans by forming temporary cysts. We performed several laboratory experiments where dinoflagellates were exposed either to direct contact with parasites or to filtered water from cultures of parasite-infected conspecifics (parasite-derived signals). Infection by P. infectans is lethal to motile A. ostenfeldii cells, but temporary cysts were more resistant to parasite infection. Furthermore, A. ostenfeldii induced a shift in life-history stage (from motile cells to temporary cysts) when exposed to parasite-derived water-borne signals. The response was relaxed within a couple of hours, indicating that A. ostenfeldii may use this behaviour as a short-term escape mechanism to avoid parasite infection. The results suggest that intraspecies chemical communication evoked by biotic interactions can be an important mechanism controlling life-history shifts in marine dinoflagellates, which may have implications for the development of toxic algal blooms.
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| 5. |
- Amato, Alberto, et al.
(författare)
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Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi
- 2018
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Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 12, s. 1594-1604
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Tidskriftsartikel (refereegranskat)abstract
- Diatoms and copepods are main actors in marine food webs. The prey-predator interactions between them affect bloom dynamics, shape marine ecosystems and impact the energy transfer to higher trophic levels. Recently it has been demonstrated that the presence of grazers may affect the diatom prey beyond the direct effect of grazing. Here, we investigated the response of the chain-forming centric diatom Skeletonema marinoi to grazer cues, including changes in morphology, gene expression and metabolic profile. S. marinoi cells were incubated with Calanus finmarchicus or with Centropages typicus and in both cases responded by reducing the chain length, whereas changes in gene expression indicated an activation of stress response, changes in the lipid and nitrogen metabolism, in cell cycle regulation and in frustule formation. Transcripts linked to G protein-coupled receptors and to nitric oxide synthesis were differentially expressed suggesting involvement of these signalling transduction pathways in the response. Downregulation of a lipoxygenase in the transcriptomic data and of its products in the metabolomic data also indicate an involvement of oxylipins. Our data contribute to a better understanding of the gene function in diatoms, providing information on the nature of genes implicated in the interaction with grazers, a crucial process in marine ecosystems.
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| 6. |
- Arias, A., et al.
(författare)
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Predator Chemical Cue Effects on the Diel Feeding Behaviour of Marine Protists
- 2021
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 82:2, s. 356-364
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Tidskriftsartikel (refereegranskat)abstract
- We have assessed the effect of copepod chemical cues on the diel feeding rhythms of heterotrophic and mixotrophic marine protists. All phagotrophic protists studied exhibited relatively high diurnal feeding rates. The magnitude of the diel feeding rhythm, expressed as the quotient of day and night ingestion rates, was inversely related to the time that phagotrophic protists were maintained in the laboratory in an environment without predators. In the case of the recently isolated ciliate Strombidium arenicola, the rhythm was lost after a few months. When challenged with chemical alarm signals (copepodamides) from the copepod Calanus finmarchicus at realistic concentrations (0.6-6 pM), S. arenicola partially re-established diurnal feeding. Conversely, the amplitude of the diel feeding rhythm for the ciliate Mesodinium rubrum was not affected by copepodamides, although the 24-h integrated food intake increased by approximately 23%. For the dinoflagellates Gyrodinium dominans and Karlodinium armiger, copepodamides significantly reduced the amplitude of their diel feeding rhythms; significant positive effects on total daily ingestion were only observed in G. dominans. Finally, the dinoflagellate Oxyrrhis marina, isolated >20 years ago, showed inconsistent responses to copepodamides, except for an average 6% increase in its total ingestion over 24 h. Our results demonstrate that the predation risk by copepods affects the diel feeding rhythm of marine protists and suggests a species-specific response to predation threats.
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| 7. |
- Bachimanchi, Harshith, et al.
(författare)
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Deep-learning-powered data analysis in plankton ecology
- 2024
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Ingår i: Limnology And Oceanography Letters. - 2378-2242.
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Forskningsöversikt (refereegranskat)abstract
- The implementation of deep learning algorithms has brought new perspectives to plankton ecology. Emerging as an alternative approach to established methods, deep learning offers objective schemes to investigate plankton organisms in diverse environments. We provide an overview of deep-learning-based methods including detection and classification of phytoplankton and zooplankton images, foraging and swimming behavior analysis, and finally ecological modeling. Deep learning has the potential to speed up the analysis and reduce the human experimental bias, thus enabling data acquisition at relevant temporal and spatial scales with improved reproducibility. We also discuss shortcomings and show how deep learning architectures have evolved to mitigate imprecise readouts. Finally, we suggest opportunities where deep learning is particularly likely to catalyze plankton research. The examples are accompanied by detailed tutorials and code samples that allow readers to apply the methods described in this review to their own data.
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| 8. |
- Bachimanchi, Harshith, et al.
(författare)
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Microplankton life histories revealed by holographic microscopy and deep learning
- 2022
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Ingår i: eLife. - 2050-084X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- The marine microbial food web plays a central role in the global carbon cycle. However, our mechanistic understanding of the ocean is biased toward its larger constituents, while rates and biomass fluxes in the microbial food web are mainly inferred from indirect measurements and ensemble averages. Yet, resolution at the level of the individual microplankton is required to advance our understanding of the microbial food web. Here, we demonstrate that, by combining holographic microscopy with deep learning, we can follow microplanktons throughout their lifespan, continuously measuring their three-dimensional position and dry mass. The deep-learning algorithms circumvent the computationally intensive processing of holographic data and allow rapid measurements over extended time periods. This permits us to reliably estimate growth rates, both in terms of dry mass increase and cell divisions, as well as to measure trophic interactions between species such as predation events. The individual resolution provides information about selectivity, individual feeding rates, and handling times for individual microplanktons. The method is particularly useful to detail the rates and routes of organic matter transfer in micro-zooplankton, the most important and least known group of primary consumers in the oceans. Studying individual interactions in idealized small systems provides insights that help us understand microbial food webs and ultimately larger-scale processes. We exemplify this by detailed descriptions of micro-zooplankton feeding events, cell divisions, and long-term monitoring of single cells from division to division.
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| 9. |
- Bergkvist, Johanna, 1980, et al.
(författare)
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Grazer-induced chain length plasticity reduces grazing risk in a marine diatom
- 2012
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Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590. ; 57:1, s. 318-324
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Tidskriftsartikel (refereegranskat)abstract
- We show that Skeletonema marinoi suppresses chain formation in response to copepod cues. The presence of three different copepod species (Acartia tonsa, Centropages hamatus, or Temora longicornis) significantly reduced chain length. Furthermore, chain length was significantly reduced when S. marinoi was exposed to chemical cues from caged A. tonsa without physical contact with the responding cells. The reductions in chain length significantly reduced copepod grazing; grazing rates on chains (four cells or more) were several times higher compared to that of single cells. This suggests that chain length plasticity is a means for S. marinoi to reduce copepod grazing. In contrast, chain length was not suppressed in cultures exposed to the microzooplankton grazer Gyrodinium dominans. Size-selective predation may have played a key role in the evolution of chain formation and chain length plasticity in diatoms.
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| 10. |
- Bergkvist, Johanna, 1980, et al.
(författare)
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Induction of toxin production in dinoflagellates: the grazer makes a difference
- 2008
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Ingår i: Oecologia. - : Springer Science and Business Media LLC. - 0029-8549 .- 1432-1939. ; 156:1, s. 147-154
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Tidskriftsartikel (refereegranskat)abstract
- The dinoflagellate Alexandrium minutum has previously been shown to produce paralytic shellfish toxins (PST) in response to waterborne cues from the copepod Acartia tonsa. In order to investigate if grazer-induced toxin production is a general or grazer-specific response of A. minutum to calanoid copepods, we exposed two strains of A. minutum to waterborne cues from three other species of calanoid copepods, Acartia clausi, Centropages typicus and Pseudocalanus sp. Both A. minutum strains responded to waterborne cues from Centropages and Acartia with significantly increased cell-specific toxicity. Waterborne cues from Centropages caused the strongest response in the A. minutum cells, with 5 to > 20 times higher toxin concentrations compared to controls. In contrast, neither of the A. minutum strains responded with significantly increased toxicity to waterborne cues from Pseudocalanus. The absolute increase in PST content was proportional to the intrinsic toxicity of the different A. minutum strains that were used. The results show that grazer-induced PST production is a grazer-specific response in A. minutum, and its potential ecological importance will thus depend on the composition of the zooplankton community, as well as the intrinsic toxin-producing properties of the A. minutum population.
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