| 1. |
- Wieloch, Thomas, 1979-
(författare)
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Intramolecular isotope analysis reveals plant ecophysiological signals covering multiple timescales
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Our societies' wellbeing relies on stable and healthy environments. However, our current lifestyles, growth-oriented economic policies and the population explosion are leading to potentially catastrophic degradation of ecosystems and progressive disruption of food chains. Hopefully, more clarity about what the future holds in store will trigger stronger efforts to find, and adopt, problem-focused coping strategies and encourage environmentally friendly lifestyles.Forecasting environmental change/destruction is complicated (inter alia) by lack of complete understanding of plant-environment interactions, particularly those involved in slow processes such as plant acclimatisation and adaptation. This stems from deficiencies in tools to analyse such slow processes. The present work aims at developing tools that can provide retrospective ecophysiological information covering timescales from days to millennia.Natural archives, such as tree-rings, preserve plant metabolites over long timescales. Analyses of intramolecular isotope abundances in plant metabolites have the potential to provide retrospective information about metabolic processes and underlying environmental controls. Thus, my colleagues and I (hereafter we) analysed intramolecular isotope patterns in tree rings to develop analytical tools that can convey information about clearly-defined plant metabolic processes over multiple timescales. Such tools might help (inter alia) to constrain plants' capacities to sequester excess amounts of anthropogenic CO2; the so-called CO2 fertilisation effect. This, in turn, might shed light on plants' sink strength for the greenhouse gas CO2, and future plant performance and growth under climate change.In the first of three studies, reported in appended papers, we analysed intramolecular 13C/12C ratios in tree-ring glucose. In six angiosperm and six gymnosperm species we found pronounced intramolecular 13C/12C differences, exceeding 10‰. These differences are transmitted into major global C pools, such as soil organic matter. Taking intramolecular 13C/12C differences into account might improve isotopic characterisation of soil metabolic processes and soil CO2 effluxes. In addition, we analysed intramolecular 13C/12C ratios in a Pinus nigra tree-ring archive spanning the period 1961 to 1995. These data revealed new ecophysiological 13C/12C signals, which can facilitate climate reconstructions and assessments of plant-environment interactions at higher resolution; thus providing higher quality information. We proposed that 13C/12C signals at glucose C-1 to C-2 derive from carbon injection into the Calvin-Benson cycle via the oxidative pentose phosphate pathway. We concluded that intramolecular 13C/12C measurements provide valuable new information about long-term metabolic dynamics for application in biogeochemistry, plant physiology, plant breeding, and paleoclimatology.In the second study, we developed a comprehensive theory on the metabolic and ecophysiological origins of 13C/12C signals at tree-ring glucose C-5 and C-6. According to this theory and theoretical implications of the first study on signals at C-1 to C-3, analysis of such intramolecular signals can provide information about several metabolic processes. At C-3, a well-known signal reflecting CO2 uptake is preserved. The glucose-6-phosphate shunt around the Calvin-Benson cycle affects 13C/12C compositions at C-1 and C-2, while the 13C/12C signals at C-5 and C-6 reflect carbon fluxes into downstream metabolism. This theoretical framework enables further experimental studies to be conducted in a hypothesis-driven manner. In conclusion, the intramolecular approach provides information about carbon allocation in plant leaves. Thus, it gives access to long-term information on key ecophysiological processes, which could not be acquired by previous approaches.The abundance of the hydrogen isotope deuterium, δD, is important for linking the water cycle with plant ecophysiology. The main factors affecting δD in plant organic matter are commonly assumed to be the δD in source water and leaf-level evaporative enrichment. Current δD models incorporate biochemical D fractionations as constants. In the third study we showed that biochemical D fractionations respond strongly to low ambient CO2 levels and low light intensity. Thus, models of δD values in plant organic matter should incorporate biochemical fractionations as variables. In addition, we found pronounced leaf-level δD differences between α-cellulose and wax n-alkanes. We explained this by metabolite-specific contributions of distinct hydrogen sources during biosynthesis.Overall, this work advances our understanding of isotope distributions and isotope fractionations in plants. It reveals the immense potential of intramolecular isotope analyses for retrospective assessment of plant metabolism and associated environmental controls.
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| 2. |
- Sepehri, Sobhan, 1986, et al.
(författare)
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Characterization of Binding of Magnetic Nanoparticles to Rolling Circle Amplification Products by Turn-On Magnetic Assay
- 2019
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Ingår i: Biosensors-Basel. - : MDPI AG. ; 9:3
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Tidskriftsartikel (refereegranskat)abstract
- The specific binding of oligonucleotide-tagged 100 nm magnetic nanoparticles (MNPs) to rolling circle products (RCPs) is investigated using our newly developed differential homogenous magnetic assay (DHMA). The DHMA measures ac magnetic susceptibility from a test and a control samples simultaneously and eliminates magnetic background signal. Therefore, the DHMA can reveal details of binding kinetics of magnetic nanoparticles at very low concentrations of RCPs. From the analysis of the imaginary part of the DHMA signal, we find that smaller MNPs in the particle ensemble bind first to the RCPs. When the RCP concentration increases, we observe the formation of agglomerates, which leads to lower number of MNPs per RCP at higher concentrations of RCPs. The results thus indicate that a full frequency range of ac susceptibility observation is necessary to detect low concentrations of target RCPs and a long amplification time is not required as it does not significantly increase the number of MNPs per RCP. The findings are critical for understanding the underlying microscopic binding process for improving the assay performance. They furthermore suggest DHMA is a powerful technique for dynamically characterizing the binding interactions between MNPs and biomolecules in fluid volumes.
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| 3. |
- Jocher, Georg, et al.
(författare)
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Impact of Canopy Decoupling and Subcanopy Advection on the Annual Carbon Balance of a Boreal Scots Pine Forest as Derived From Eddy Covariance
- 2018
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Ingår i: Journal of Geophysical Research: Biogeosciences. - 2169-8953 .- 2169-8961. ; 123:2, s. 303-325
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Tidskriftsartikel (refereegranskat)abstract
- Apparent net uptake of carbon dioxide (CO 2 ) during wintertime by an ∼ 90 year old Scots pine stand in northern Sweden led us to conduct canopy decoupling and subcanopy advection investigations over an entire year. Eddy covariance (EC) measurements ran simultaneously above and within the forest canopy for that purpose. We used the correlation of above- and below-canopy standard deviation of vertical wind speed (σ w ) as decoupling indicator. We identified 0.33 m s -1 and 0.06 m s -1 as site-specific σ w thresholds for above- and below-canopy coupling during nighttime (global radiation < 20 W m -2 ) and 0.23 m s -1 and 0.06 m s -1 as daytime (global radiation > 20 W m -2 ) σ w thresholds. Decoupling occurred in 53% of the annual nighttime and 14% of the annual daytime. The annual net ecosystem exchange (NEE), gross ecosystem exchange (GEE), and ecosystem respiration (R eco ) derived via two-level filtered EC data were -357 g C m -2 , -1,138 g C m -2 , and 781 g C m -2 , respectively. In comparison, both single-level friction velocity (u * ) and quality filtering resulted in ~ 22% higher NEE, mainly caused by ~ 16% lower R eco . GEE remained similar among filtering regimes. Accounting for changes of CO 2 storage across the canopy in the single-level filtered data could only marginally decrease these discrepancies. Consequently, advection appears to be responsible for the major part of this divergence. We conclude that the two-level filter is necessary to adequately address decoupling and subcanopy advection at our site, and we recommend this filter for all forested EC sites.
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| 4. |
- McGinn, Steven, et al.
(författare)
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New Technologies for DNA analysis-A review of the READNA Project.
- 2016
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Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784.
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Forskningsöversikt (refereegranskat)abstract
- The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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| 5. |
- Rinne, J., et al.
(författare)
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Effect of the 2018 European drought on methane and carbon dioxide exchange of northern mire ecosystems
- 2020
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Ingår i: Philosophical Transactions of the Royal Society B-Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 375:1810
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Tidskriftsartikel (refereegranskat)abstract
- We analysed the effect of the 2018 European drought on greenhouse gas (GHG) exchange of five North European mire ecosystems. The low precipitation and high summer temperatures in Fennoscandia led to a lowered water table in the majority of these mires. This lowered both carbon dioxide (CO2) uptake and methane (CH4) emission during 2018, turning three out of the five mires from CO(2)sinks to sources. The calculated radiative forcing showed that the drought-induced changes in GHG fluxes first resulted in a cooling effect lasting 15-50 years, due to the lowered CH(4)emission, which was followed by warming due to the lower CO(2)uptake. This article is part of the theme issue 'Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.
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| 6. |
- Ecke, Frauke, et al.
(författare)
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Landscape structure and the long-term decline of cyclic grey-sided voles in Fennoscandia
- 2010
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Ingår i: Landscape Ecology. - : Springer. - 0921-2973 .- 1572-9761. ; 25:4, s. 551-560
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Tidskriftsartikel (refereegranskat)abstract
- Changes in forest landscape structure have been suggested as a likely contributing factor behind the long-term decline in the numbers of cyclic grey-sided voles (Clethrionomys rufocanus) in northern Fennoscandian lowland regions in contrast to mountain regions due to the absence of forest management in the mountains. This study, for the first time, formally explored landscape structure in 29 lowland (LF) and 14 mountain forest (MF) landscapes (each 2.5 x 2.5 km) in northern Sweden, and related the results to the cumulated spring trapping index of the grey-sided vole in 2002-2006. The grey-sided vole showed striking contrasts in dynamics close in space and time. The MF landscapes were characterized by larger patches and less fragmentation of preferred forest types. The grey-sided vole was trapped in all of 14 analyzed MF landscapes but only in three out of 29 of the LF landscapes. MF and LF landscapes with grey-sided vole occurrence were characterized by similar focal forest patch size (mean 357 ha, minimum 82 ha and mean 360 ha, minimum 79 ha, respectively). In contrast, these MF compared to the LF landscapes were characterized by larger patches of preferred forest types and less fragmented preferred forest types and by a lower proportion of clear-cut areas. The present results suggest that landscape structure is important for the abundance of grey-sided voles in both regions. However, in the mountains the change from more or less seasonal dynamics to high-amplitude cycles between the mid 1990s and 2000s cannot be explained by changes in landscape structure.
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| 7. |
- Sepehri, Sobhan, 1986, et al.
(författare)
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Homogeneous Differential Magnetic Assay
- 2019
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Ingår i: Acs Sensors. - : American Chemical Society (ACS). - 2379-3694. ; 4:9, s. 2381-2388
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Tidskriftsartikel (refereegranskat)abstract
- Assays are widely used for detection of various targets, including pathogens, drugs, and toxins. Homogeneous assays are promising for the realization of point-of-care diagnostics as they do not require separation, immobilization, or washing steps. For low concentrations of target molecules, the speed and sensitivity of homogeneous assays have hitherto been limited by slow binding kinetics, time-consuming amplification steps, and the presence of a high background signal. Here, we present a homogeneous differential magnetic assay that utilizes a differential magnetic readout that eliminates previous limitations of homogeneous assays. The assay uses a gradiometer sensor configuration combined with precise microfluidic sample handling. This enables simultaneous differential measurement sample containing a synthesized Vibrio cholerae target and a negative control sample, which reduces the background signal and increases the readout speed. Very low concentrations of targets down to femtomolar levels are thus detectable without any additional amplification of the number of targets. Our homogeneous differential magnetic assay method opens new possibilities for rapid and highly sensitive diagnostics at the point of care.
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| 8. |
- Ciftci, S., et al.
(författare)
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The sweet detection of rolling circle amplification : Glucose-based electrochemical genosensor for the detection of viral nucleic acid
- 2020
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Ingår i: Biosensors & bioelectronics. - : Elsevier Ltd. - 0956-5663 .- 1873-4235. ; 151
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Tidskriftsartikel (refereegranskat)abstract
- Herein, an isothermal padlock probe-based assay for the simple and portable detection of pathogens coupled with a glucose oxidase (GOx)-based electrochemical readout is reported. Infectious diseases remain a constant threat on a global scale, as in recurring pandemics. Rapid and portable diagnostics hold the promise to tackle the spreading of diseases and decentralising healthcare to point-of-care needs. Ebola, a hypervariable RNA virus causing fatalities of up to 90% for recent outbreaks in Africa, demands immediate attention for bedside diagnostics. The design of the demonstrated assay consists of a rolling circle amplification (RCA) technique, responsible for the generation of nucleic acid amplicons as RCA products (RCPs). The RCPs are generated on magnetic beads (MB) and subsequently, connected via streptavidin-biotin bonds to GOx. The enzymatic catalysis of glucose by the bound GOx allows for an indirect electrochemical measurement of the DNA target. The RCPs generated on the surface of the MB were confirmed by scanning electron microscopy, and among other experimental conditions such as the type of buffer, temperature, concentration of GOx, sampling and measurement time were evaluated for the optimum electrochemical detection. Accordingly, 125 μg mL−1 of GOx with 5 mM glucose using phosphate buffer saline (PBS), monitored for 1 min were selected as the ideal conditions. Finally, we assessed the analytical performance of the biosensing strategy by using clinical samples of Ebola virus from patients. Overall, this work provides a proof-of-concept bioassay for simple and portable molecular diagnostics of emerging pathogens using electrochemical detection, especially in resource-limited settings.
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| 9. |
- Franz, D, et al.
(författare)
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Towards long-term standardised carbon and greenhouse gas observations for monitoring Europe´s terrestrial ecosystems: a review
- 2018
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Ingår i: International Agrophysics. - : Walter de Gruyter GmbH. - 0236-8722 .- 2300-8725. ; 32, s. 439-455
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Tidskriftsartikel (refereegranskat)abstract
- Research infrastructures play a key role in launching a new generation of integrated long-term, geographically distributed observation programmes designed to monitor climate change, better understand its impacts on global ecosystems, and evaluate possible mitigation and adaptation strategies. The pan-European Integrated Carbon Observation System combines carbon and greenhouse gas (GHG; CO2, CH4, N2O, H2O) observations within the atmosphere, terrestrial ecosystems and oceans. High-precision measurements are obtained using standardised methodologies, are centrally processed and openly available in a traceable and verifiable fashion in combination with detailed metadata. The Integrated Carbon Observation System ecosystem station network aims to sample climate and land-cover variability across Europe. In addition to GHG flux measurements, a large set of complementary data (including management practices, vegetation and soil characteristics) is collected to support the interpretation, spatial upscaling and modelling of observed ecosystem carbon and GHG dynamics. The applied sampling design was developed and formulated in protocols by the scientific community, representing a trade-off between an ideal dataset and practical feasibility. The use of open-access, high-quality and multi-level data products by different user communities is crucial for the Integrated Carbon Observation System in order to achieve its scientific potential and societal value.
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| 10. |
- Moor, Helen, et al.
(författare)
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Towards a trait-based ecology of wetland vegetation
- 2017
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Ingår i: Journal of Ecology. - : Wiley. - 0022-0477 .- 1365-2745. ; 105:6, s. 1623-1635
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Forskningsöversikt (refereegranskat)abstract
- 1. Functional traits mechanistically capture plant responses to environmental gradients as well as plant effects on ecosystem functioning. Yet most trait-based theory stems from terrestrial systems and extension to other habitats can provide new insights. 2. Wetlands differ from terrestrial systems in conditions (e.g. soil water saturation, anoxia, pH extremes), plant adaptations (e.g. aerenchyma, clonality, ubiquity of bryophytes) and important processes (e.g. denitrification, peat accumulation, methane emission). Wetland plant adaptations and trait (co-)variation can be situated along major plant trait trade-off axes (e.g. the resource economics spectrum), but soil saturation represents a complex stress gradient beyond a simple extension of commonly studied water availability gradients. 3. Traits that affect ecosystem functioning overlap with patterns in terrestrial systems. But wetland-specific traits that mediate plant effects on soil redox conditions, microbial communities and on water flow, as well as trait spectra of mosses, vary among wetland types. 4. Synthesis. With increasing availability of quantitative plant traits a trait-based ecology of wetlands is emerging, with the potential to advance process-based understanding and prediction. We provide an interactive cause-and-effect framework that may guide research efforts to disentangle the multiple interacting processes involved in scaling from environmental conditions to ecosystem functioning via plant communities.
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