| 1. |
- Edthofer, Alexander, et al.
(författare)
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Acoustofluidic Properties of Polystyrene Microparticles
- 2023
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Ingår i: Analytical Chemistry. - 0003-2700. ; 95:27, s. 10346-10352
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Tidskriftsartikel (refereegranskat)abstract
- Acoustophoresis has become a powerful tool to separate microparticles and cells, based on their material and biophysical properties, and is gaining popularity in clinical and biomedical research. One major application of acoustophoresis is to measure the compressibility of cells and small organisms, which is related to their contents. The cell compressibility can be extracted from the acoustic mobility, which is the main output of acoustic migration experiments, if the material properties and sizes of reference particles, the size of the cells, and the surrounding medium are known. Accurate methods to measure and calibrate the acoustic energy density in acoustophoresis systems are therefore critical. In this Perspective, polystyrene microparticles have become the most commonly used reference particles in acoustophoresis, due to their similar biophysical properties to cells. We utilized a two-step focusing method to measure the relative acoustic mobility of polystyrene beads of various sizes and colors and present a quantitative analysis of the variation in acousto-mechanical properties of polystyrene microparticles, showing a large spread in their material properties. A variation of more than 25% between different particle types was found. Thus, care is required when relying on polystyrene particles as a reference when characterizing acoustofluidics systems or acousto-mechanical properties of cells.
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| 2. |
- Havers, Megan, et al.
(författare)
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OPTIMISATION AND PERFORMANCE QUANTIFICATION ACOUSTIC TRAPPING USING SYNTHETIC NANOPARTICLES
- 2021
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Ingår i: MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. - 9781733419031 ; , s. 903-904
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Konferensbidrag (refereegranskat)abstract
- Acoustic trapping is becoming increasingly popular as a tool to isolate and enrich biological nanoparticles [1] (particularly extracellular vesicles [2]), yet an inherent problem with acoustic trapping of nanoparticles is calibration of the trapping efficiency. This abstract presents in-house synthesized nanoparticles with different sound scattering properties, either rigid high density gold nanoparticles (AuNPs) as model system for inorganic nanoparticles (NPs) or synthetic lipid bilayer nano vesicles to mimic the acoustic properties of biological vesicles. The rapid NP synthesis facilitates characterisation of the trapping performance of a single node acoustic trapping system, e.g. by designing application specific NPs size ladders. This is shown by the trapping of AuNPs of two different sizes and synthetic lipid bilayer vesicles and demonstrating a 6-11% NP recovery. The work demonstrates the potential of freshly synthesized nanoparticles as a tool for optimisation of acoustic trapping protocols as well as a fast and simple NP trapping performance verification by visual inspection.
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| 3. |
- Heilbronner, Goetz, et al.
(författare)
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Seeded strain-like transmission of beta-amyloid morphotypes in APP transgenic mice
- 2013
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Ingår i: EMBO Reports. - : NATURE PUBLISHING GROUP, MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND. - 1469-221X .- 1469-3178. ; 14:11, s. 1017-1022
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Tidskriftsartikel (refereegranskat)abstract
- The polymorphic beta-amyloid lesions present in individuals with Alzheimers disease are collectively known as cerebral beta-amyloidosis. Amyloid precursor protein (APP) transgenic mouse models similarly develop beta-amyloid depositions that differ in morphology, binding of amyloid conformation-sensitive dyes, and A beta 40/A beta 42 peptide ratio. To determine the nature of such beta-amyloid morphotypes, beta-amyloid-containing brain extracts from either aged APP23 brains or aged APPPS1 brains were intracerebrally injected into the hippocampus of young APP23 or APPPS1 transgenic mice. APPPS1 brain extract injected into young APP23 mice induced beta-amyloid deposition with the morphological, conformational, and A beta 40/A beta 42 ratio characteristics of beta-amyloid deposits in aged APPPS1 mice, whereas APP23 brain extract injected into young APP23 mice induced b-amyloid deposits with the characteristics of beta-amyloid deposits in aged APP23 mice. Injecting the two extracts into the APPPS1 host revealed a similar difference between the induced beta-amyloid deposits, although less prominent, and the induced deposits were similar to the beta-amyloid deposits found in aged APPPS1 hosts. These results indicate that the molecular composition and conformation of aggregated A beta in APP transgenic mice can be maintained by seeded conversion.
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| 4. |
- Kreckel, Holger, et al.
(författare)
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High-resolution storage-ring measurements of the dissociative recombination of H-3(+) using a supersonic expansion ion source
- 2010
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Ingår i: Physical Review A. Atomic, Molecular, and Optical Physics. - 1050-2947 .- 1094-1622. ; 82:4, s. 042715-
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Tidskriftsartikel (refereegranskat)abstract
- We have performed measurements of the dissociative electron recombination (DR) of H-3(+) at the ion storage ring TSR utilizing a supersonic expansion ion source. The ion source has been characterized by continuous wave cavity ring-down spectroscopy. We present high-resolution DR rate coefficients for different nuclear spin modifications of H-3(+) combined with precise fragment imaging studies of the internal excitation of the H-3(+) ions inside the storage ring. The measurements resolve changes in the energy dependence between the ortho-H-3(+) and para-H-3(+) rate coefficients at low center-of-mass collision energies. Analysis of the imaging data indicates that the stored H-3(+) ions may have higher rotational temperatures than previously assumed, most likely due to collisional heating during the extraction of the ions from the ion source. Simulations of the ion extraction shed light on possible origins of the heating process and how to avoid it in future experiments.
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| 5. |
- Novotny, Andreas, et al.
(författare)
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Diet-overlap between planktivorous fish in the pelagic Baltic Sea
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Marine communities undergo rapid changes because of human-induced ecosystem pressures. The Baltic Sea pelagic food web has experienced several regime-shifts during the past century, resulting in a system where competition between planktivorous mesopredators is assumed to be high. While the two clupeids sprat and herring reveal signs of competition, the stickleback population has increased drastically during the past decades. Here, we investigate diet overlap between the three dominating planktivorous fish in the Baltic Sea, utilizing DNA metabarcoding, targeted qPCR, and microscopy. Our results show a niche differentiation between clupeids and stickleback and that rotifers play an important function in niche partitioning of stickleback, as a resource that is not being used, neither by the clupeids nor by other zooplankton. This study suggests that rotifers and other understudied soft-bodied prey may have an important function in the pelagic food web and that the growing population of pelagic stickleback is supported by the unutilized feeding niche offered by the rotifers.
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| 6. |
- Novotny, Andreas, 1991-, et al.
(författare)
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DNA metabarcoding highlights cyanobacteria as the main source of primary production in a pelagic food web model
- 2023
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Ingår i: Science Advances. - 2375-2548. ; 9:17
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Tidskriftsartikel (refereegranskat)abstract
- Models that estimate rates of energy flow in complex food webs often fail to account for species-specific prey selectivity of diverse consumer guilds. While DNA metabarcoding is increasingly used for dietary studies, methodological biases have limited its application for food web modeling. Here, we used data from dietary metabarcoding studies of zooplankton to calculate prey selectivity indices and assess energy fluxes in a pelagic resource-consumer network. We show that food web dynamics are influenced by prey selectivity and temporal match-mismatch in growth cycles and that cyanobacteria are the main source of primary production in the investigated coastal pelagic food web. The latter challenges the common assumption that cyanobacteria are not supporting food web productivity, a result that is increasingly relevant as global warming promotes cyanobacteria dominance. While this study provides a method for how DNA metabarcoding can be used to quantify energy fluxes in a marine food web, the approach presented here can easily be extended to other ecosystems.
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| 7. |
- Novotny, Andreas, et al.
(författare)
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DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species
- 2021
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 288:1953
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Tidskriftsartikel (refereegranskat)abstract
- Alternative pathways of energy transfer guarantee the functionality and productivity in marine food webs that experience strong seasonality. Nevertheless, the complexity of zooplankton interactions is rarely considered in trophic studies because of the lack of detailed information about feeding interactions in nature. In this study, we used DNA metabarcoding to highlight the diversity of trophic niches in a wide range of micro- and mesozooplankton, including ciliates, rotifers, cladocerans, copepods and their prey, by sequencing 16- and 18S rRNA genes. Our study demonstrates that the zooplankton trophic niche partitioning goes beyond both phylogeny and size and reinforces the importance of diversity in resource use for stabilizing food web efficiency by allowing for several different pathways of energy transfer. We further highlight that small, rarely studied zooplankton (rotifers and ciliates) fill an important role in the Baltic Sea pelagic primary production pathways and the potential of ciliates, rotifers and crustaceans in the utilization of filamentous and picocyanobacteria within the pelagic food web. The approach used in this study is a suitable entry point to ecosystem-wide food web modelling considering species-specific resource use of key consumers.
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| 8. |
- Novotny, Andreas, 1991-
(författare)
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Functional diversity of zooplankton in marine food webs : Integrating DNA metabarcoding and network modeling
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The oceans are important regulators of the Earth’s climate system by sequestering carbon from the atmosphere taken up by primary producers. Zooplankton, including protozoans and metazoans of different phyla and size classes, occupies several trophic niches and regulates energy flow between primary producers and fish. The structural configuration of the food web determines the rates at which primary production is either enriched to sustain organisms at higher trophic levels or exported to the ocean floor. However, limited knowledge about plankton interactions causes uncertainty of how the oceans will respond to climate changes. This thesis presents a framework for studying and modeling pelagic food webs using novel implementations of DNA metabarcoding. Study I shows that DNA metabarcoding of zooplankton sampled in their natural environment reveals a broader and more complex diet than zooplankton in classic grazing observations. We also show that differential feeding strategies facilitate species coexistence and that the zooplankton diet is largely dependent on prey availability. The approach was extended in Study II, where we include the smaller fraction of zooplankton that is often overseen in food web studies to broaden the perspective of functional diversity in pelagic food webs. We show that different populations have unique functions in channeling the primary production of different sources and especially highlight the role of filter-feeders in making detrital nutrients available for other organisms in the food web. In Study III, we shifted focus to trophic links between zooplankton and fish by comparing niche overlap between the three main planktivorous fish in the Baltic Sea - stickleback, sprat, and herring. The results from the three first studies were finally used to calculate selectivity indices between each predator and prey. This information was implemented in Study IV in a network model quantifying fluxes of energy through the food web. The model revealed cyanobacteria as the primary contributor to secondary production in the Baltic Sea food web and that the spring bloom of diatoms and dinoflagellates remains largely unutilized by the zooplankton. This is the first time DNA metabarcoding is used to compare niche differences of several zooplankton species in a pelagic guild and to quantify fluxes in a food web model. The thesis refines our knowledge of pelagic community and food web structure, and the framework presented here is a suitable entry point for food web modeling in other ecosystems.
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| 9. |
- Novotny, Andreas, et al.
(författare)
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Integrating DNA metabarcoding and biomonitoring data reveals trophic pathways of primary production in a flux-balance marine food web
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Estimating energy fluxes, or weight of trophic interactions, in food webs allows linking food web structure to properties of ecosystem functioning. Due to limitations in traditional methods, resolved food-web models are often binary or based on body size. Species-specific feeding traits and weights of interactions are typically not included, particularly at the base of the pelagic food web. Consequently, models are prone to underestimate the trophic diversity of species interactions.Here, we focus on trophic pathways of primary production in the Baltic Sea using a bioenergetic model that includes several trophic levels from primary producers to fish. For the first time, dietary DNA metabarcoding data of zooplankton are combined with accumulated biomass data from long-term pelagic monitoring and metabolic theory in a network model to describe energy pathways, including the diversity of planktonic organisms.We show that picocyanobacteria and filamentous cyanobacteria are the main contributors to secondary production in the Baltic Sea and that the latter experience high predation pressure from zooplankton. In contrast, the combination of high biomasses and low predation pressure on dinoflagellates and diatoms suggests that a significant fraction of the spring bloom is not utilized in the pelagic food web, explaining the high export of biological material to the sea seafloor.This study can be used to address ecosystem management objectives in the Baltic Sea under changing environmental conditions. Furthermore, the novel framework presented in this study, integrating DNA metabarcoding and biomonitoring data to assess energy fluxes, can be extended to dynamic food web modeling in other ecosystems.
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| 10. |
- Novotny, Andreas, 1991-, et al.
(författare)
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Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy
- 2022
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Marine communities undergo rapid changes related to human-induced ecosystem pressures. The Baltic Sea pelagic food web has experienced several regime shifts during the past century, resulting in a system where competition between the dominant planktivorous mesopredatory clupeid fish species herring (Clupea harengus) and sprat (Sprattus sprattus) and the rapidly increasing stickleback (Gasterosteus aculeatus) population is assumed to be high. Here, we investigate diet overlap between these three planktivorous fishes in the Baltic Sea, utilizing DNA metabarcoding on the 18S rRNA gene and the COI gene, targeted qPCR, and microscopy. Our results show niche differentiation between clupeids and stickleback, and highlight that rotifers play an important role in this pattern, as a resource that is not being used by the clupeids nor by other zooplankton in spring. We further show that all the diet assessment methods used in this study are consistent, but also that DNA metabarcoding describes the plankton-fish link at the highest taxonomic resolution. This study suggests that rotifers and other understudied soft-bodied prey may have an important function in the pelagic food web and that the growing population of pelagic stickleback may be supported by the open feeding niche offered by the rotifers.
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