| 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. |
- Amorín, R. O., et al.
(författare)
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Ubiquitous broad-line emission and the relation between ionized gas outflows and Lyman continuum escape in Green Pea galaxies
- 2024
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 682
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Tidskriftsartikel (refereegranskat)abstract
- We report observational evidence of highly turbulent ionized gas kinematics in a sample of 20 Lyman continuum (LyC) emitters (LCEs) at low redshift (z ∼ 0.3). Detailed Gaussian modeling of optical emission line profiles in high-dispersion spectra consistently shows that both bright recombination and collisionally excited lines can be fitted as one or two narrow components with intrinsic velocity dispersion of σ ∼ 40 − 100 km s−1, in addition to a broader component with σ ∼ 100 − 300 km s−1, which contributes up to ∼40% of the total flux and is preferentially blueshifted from the systemic velocity. We interpret the narrow emission as highly ionized gas close to the young massive star clusters and the broader emission as a signpost of unresolved ionized outflows, resulting from massive stars and supernova feedback. We find a significant correlation between the width of the broad emission and the LyC escape fraction, with strong LCEs exhibiting more complex and broader line profiles than galaxies with weaker or undetected LyC emission. We provide new observational evidence supporting predictions from models and simulations; our findings suggest that gas turbulence and outflows resulting from strong radiative and mechanical feedback play a key role in clearing channels through which LyC photons escape from galaxies. We propose that the detection of blueshifted broad emission in the nebular lines of compact extreme emission-line galaxies can provide a new indirect diagnostic of Lyman photon escape, which could be useful to identify potential LyC leakers in the epoch of reionization with the JWST.
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| 3. |
- Gorasso, Vanessa, et al.
(författare)
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Burden of disease attributable to risk factors in European countries: a scoping literature review
- 2023
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Ingår i: Archives of Public Health. - 0778-7367 .- 2049-3258. ; 81:1
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Forskningsöversikt (refereegranskat)abstract
- Objectives: Within the framework of the burden of disease (BoD) approach, disease and injury burden estimates attributable to risk factors are a useful guide for policy formulation and priority setting in disease prevention. Considering the important differences in methods, and their impact on burden estimates, we conducted a scoping literature review to: (1) map the BoD assessments including risk factors performed across Europe; and (2) identify the methodological choices in comparative risk assessment (CRA) and risk assessment methods. Methods: We searched multiple literature databases, including grey literature websites and targeted public health agencies websites. Results: A total of 113 studies were included in the synthesis and further divided into independent BoD assessments (54 studies) and studies linked to the Global Burden of Disease (59 papers). Our results showed that the methods used to perform CRA varied substantially across independent European BoD studies. While there were some methodological choices that were more common than others, we did not observe patterns in terms of country, year or risk factor. Each methodological choice can affect the comparability of estimates between and within countries and/or risk factors, since they might significantly influence the quantification of the attributable burden. From our analysis we observed that the use of CRA was less common for some types of risk factors and outcomes. These included environmental and occupational risk factors, which are more likely to use bottom-up approaches for health outcomes where disease envelopes may not be available. Conclusions: Our review also highlighted misreporting, the lack of uncertainty analysis and the under-investigation of causal relationships in BoD studies. Development and use of guidelines for performing and reporting BoD studies will help understand differences, avoid misinterpretations thus improving comparability among estimates.
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| 4. |
- Guseva, S., et al.
(författare)
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Variable Physical Drivers of Near-Surface Turbulence in a Regulated River
- 2021
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Ingår i: Water resources research. - : American Geophysical Union (AGU). - 0043-1397 .- 1944-7973. ; 57:11
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Tidskriftsartikel (refereegranskat)abstract
- Inland waters, such as lakes, reservoirs and rivers, are important sources of climate forcing trace gases. A key parameter that regulates the gas exchange between water and the atmosphere is the gas transfer velocity, which itself is controlled by near-surface turbulence in the water. While in lakes and reservoirs, near-surface turbulence is mainly driven by atmospheric forcing, in shallow rivers and streams it is generated by bottom friction of gravity-forced flow. Large rivers represent a transition between these two cases. Near-surface turbulence has rarely been measured in rivers and the drivers of turbulence have not been quantified. We analyzed continuous measurements of flow velocity and quantified turbulence as the rate of dissipation of turbulent kinetic energy over the ice-free season in a large regulated river in Northern Finland. Measured dissipation rates agreed with predictions from bulk parameters, including mean flow velocity, wind speed, surface heat flux, and with a one-dimensional numerical turbulence model. Values ranged from to . Atmospheric forcing or gravity was the dominant driver of near-surface turbulence for similar fraction of the time. Large variability in near-surface dissipation rate occurred at diel time scales, when the flow velocity was strongly affected by downstream dam operation. By combining scaling relations for boundary-layer turbulence at the river bed and at the air-water interface, we derived a simple model for estimating the relative contributions of wind speed and bottom friction of river flow as a function of depth.Plain Language SummaryInland water bodies such as lakes, reservoirs and rivers are an important source of climate forcing trace gases to the atmosphere. Gas exchange between water and the atmosphere is regulated by the gas transfer velocity and the concentration difference between the water surface and the atmosphere. The gas transfer velocity depends on near-surface turbulence, but robust formulations have not been developed for river systems. Their surface area is sufficiently large for meteorological forcing to cause turbulence, as in lakes and reservoirs, but turbulence generated from bed and internal friction of gravity-driven flows is also expected to contribute. Here we quantify near-surface turbulence using data from continuous air and water side measurements conducted over the ice-free season in a large subarctic regulated river in Finland. We find that turbulence, quantified as the dissipation rate of turbulent kinetic energy, is well described using equations for predicting turbulence from meteorological data for sufficiently high wind speeds whereas the contribution from bottom shear dominated at higher flow velocities. A one-dimensional river model successfully captured these processes. We provide a fundamental model for estimating the relative contributions of atmospheric forcing and bottom friction as a function of depth.
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| 5. |
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| 6. |
- Bäbler, Matthäus, 1977-, et al.
(författare)
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Breakup of small aggregates in bounded and unbounded turbulent flows
- 2020
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Ingår i: ETC 2013 - 14th European Turbulence Conference. - : Zakon Group LLC.
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Konferensbidrag (refereegranskat)abstract
- Breakup of small tracer-like aggregates is studied by means of numerical simulations in four different flows, namely homogeneous isotropic turbulence, smooth stochastic flow, turbulent channel flow, and developing boundary layer flow. Aggregate breakup occurs when the local hydrodynamic stress σ ∼ ε1/2, where ε is the local energy dissipation, overcomes a given threshold value σcr [or equivalently εcr ∼ σcr2 ] characteristic for a given type of aggregates. Following the aggregate trajectory upon release and detecting the first occurrence of local energy dissipation exceeding the predefined threshold allows for estimating the breakup rate as a function of εcr. Results show that the breakup rate decreases with increasing threshold. For small values of the threshold, this decrease assumes consistent scaling among the different flows which is explained by universal small scale flow properties.
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| 7. |
- Bäbler, Matthäus, et al.
(författare)
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Numerical simulations of aggregate breakup in bounded and unbounded turbulent flows
- 2015
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Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 766
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Tidskriftsartikel (refereegranskat)abstract
- Breakup of small aggregates in fully developed turbulence is studied by means of direct numerical simulations in a series of typical bounded and unbounded flow configurations, such as a turbulent channel flow, a developing boundary layer and homogeneous isotropic turbulence. The simplest criterion for breakup is adopted, whereby aggregate breakup occurs when the local hydrodynamic stress sigma similar to epsilon(1/2), with epsilon being the energy dissipation at the position of the aggregate, overcomes a given threshold sigma(cr), which is characteristic for a given type of aggregate. Results show that the breakup rate decreases with increasing threshold. For small thresholds, it develops a scaling behaviour among the different flows. For high thresholds, the breakup rates show strong differences between the different flow configurations, highlighting the importance of non-universal mean-flow properties. To further assess the effects of flow inhomogeneity and turbulent fluctuations, the results are compared with those obtained in a smooth stochastic flow. Furthermore, we discuss the limitations and applicability of a set of independent proxies.
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| 8. |
- Guseva, S., et al.
(författare)
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Bulk Transfer Coefficients Estimated From Eddy-Covariance Measurements Over Lakes and Reservoirs
- 2023
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Ingår i: Journal of Geophysical Research - Atmospheres. - : American Geophysical Union (AGU). - 2169-897X .- 2169-8996. ; 128:2
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Tidskriftsartikel (refereegranskat)abstract
- The drag coefficient, Stanton number and Dalton number are of particular importance for estimating the surface turbulent fluxes of momentum, heat and water vapor using bulk parameterization. Although these bulk transfer coefficients have been extensively studied over the past several decades in marine and large-lake environments, there are no studies analyzing their variability for smaller lakes. Here, we evaluated these coefficients through directly measured surface fluxes using the eddy-covariance technique over more than 30 lakes and reservoirs of different sizes and depths. Our analysis showed that the transfer coefficients (adjusted to neutral atmospheric stability) were generally within the range reported in previous studies for large lakes and oceans. All transfer coefficients exhibit a substantial increase at low wind speeds (<3 m s(-1)), which was found to be associated with the presence of gusts and capillary waves (except Dalton number). Stanton number was found to be on average a factor of 1.3 higher than Dalton number, likely affecting the Bowen ratio method. At high wind speeds, the transfer coefficients remained relatively constant at values of 1.6.10(-3), 1.4.10(-3), 1.0.10(-3), respectively. We found that the variability of the transfer coefficients among the lakes could be associated with lake surface area. In flux parameterizations at lake surfaces, it is recommended to consider variations in the drag coefficient and Stanton number due to wind gustiness and capillary wave roughness while Dalton number could be considered as constant at all wind speeds. Plain Language Summary In our study, we investigate the bulk transfer coefficients, which are of particular importance for estimation the turbulent fluxes of momentum, heat and water vapor in the atmospheric surface layer, above lakes and reservoirs. The incorrect representation of the surface fluxes above inland waters can potentially lead to errors in weather and climate prediction models. For the first time we made this synthesis using a compiled data set consisting of existing eddy-covariance flux measurements over 23 lakes and 8 reservoirs. Our results revealed substantial increase of the transfer coefficients at low wind speeds, which is often not taken into account in models. The observed increase in the drag coefficient (momentum transfer coefficient) and Stanton number (heat transfer coefficient) could be associated with the presence of wind gusts and capillary waves. In flux parameterizations at lake surface, it is recommended to consider them for accurate flux representation. Although the bulk transfer coefficients were relatively constant at high wind speeds, we found that the Stanton number systematically exceeds the Dalton number (water vapor transfer coefficient), despite the fact they are typically considered to be equal. This difference may affect the Bowen ratio method and result in biased estimates of lake evaporation.
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| 9. |
- Kiryushkin, Alexey S., et al.
(författare)
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Hairy CRISPR : Genome Editing in Plants Using Hairy Root Transformation
- 2022
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Ingår i: PLANTS. - : MDPI AG. - 2223-7747. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- CRISPR/Cas-mediated genome editing is a powerful tool of plant functional genomics. Hairy root transformation is a rapid and convenient approach for obtaining transgenic roots. When combined, these techniques represent a fast and effective means of studying gene function. In this review, we outline the current state of the art reached by the combination of these approaches over seven years. Additionally, we discuss the origins of different Agrobacterium rhizogenes strains that are widely used for hairy root transformation; the components of CRISPR/Cas vectors, such as the promoters that drive Cas or gRNA expression, the types of Cas nuclease, and selectable and screenable markers; and the application of CRISPR/Cas genome editing in hairy roots. The modification of the already known vector pKSE401 with the addition of the rice translational enhancer OsMac3 and the gene encoding the fluorescent protein DsRed1 is also described.
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| 10. |
- Kiryushkin, Alexey S., et al.
(författare)
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Lateral Root Initiation in Cucumber (Cucumis sativus) : What Does the Expression Pattern of Rapid Alkalinization Factor 34 (RALF34) Tell Us?
- 2023
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Ingår i: International Journal of Molecular Sciences. - 1661-6596 .- 1422-0067. ; 24:9
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Tidskriftsartikel (refereegranskat)abstract
- In Arabidopsis, the small signaling peptide (peptide hormone) RALF34 is involved in the gene regulatory network of lateral root initiation. In this study, we aimed to understand the nature of the signals induced by RALF34 in the non-model plant cucumber (Cucumis sativus), where lateral root primordia are induced in the apical meristem of the parental root. The RALF family members of cucumber were identified using phylogenetic analysis. The sequence of events involved in the initiation and development of lateral root primordia in cucumber was examined in detail. To elucidate the role of the small signaling peptide CsRALF34 and its receptor CsTHESEUS1 in the initial stages of lateral root formation in the parental root meristem in cucumber, we studied the expression patterns of both genes, as well as the localization and transport of the CsRALF34 peptide. CsRALF34 is expressed in all plant organs. CsRALF34 seems to differ from AtRALF34 in that its expression is not regulated by auxin. The expression of AtRALF34, as well as CsRALF34, is regulated in part by ethylene. CsTHESEUS1 is expressed constitutively in cucumber root tissues. Our data suggest that CsRALF34 acts in a non-cell-autonomous manner and is not involved in lateral root initiation in cucumber.
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| 11. |
- Kiryushkin, Alexey S., et al.
(författare)
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Lateral Root Initiation in the Parental Root Meristem of Cucurbits : Old Players in a New Position
- 2019
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- While in most higher plants, including the model system Arabidopsis thaliana, the formation of lateral root primordia is induced in the elongation zone of the parental root, in seven plant families, including Cucurbitaceae, an alternative root branching mechanism is established such that lateral roots are initiated directly in the apical meristem of the parental root. In Arabidopsis, the transcription factor GATA23 and MEMBRANE-ASSOCIATED KINASE REGULATOR4 (MAKR4) are involved in the gene regulatory network of lateral root initiation. Among all marker genes examined, these are the earliest known marker genes up-regulated by auxin during lateral root initiation. In this study, putative functional orthologs of Arabidopsis GATA23 and MAKR4 were identified in cucumber (Cucumis sativus) and squash (Cucurbita pepo). Both cucurbits contained 26 genes encoding GATA family transcription factors and only one MAKR4 gene. Phylogenetic and transcriptional analysis of up-regulation by auxin led to the identification of GATA23 putative functional orthologs in Cucurbitaceae - CpGATA24 and CsGATA24. In squash, CpMAKR4 was up-regulated by naphthylacetic acid (NM) and, similar to MAKR4 in Arabidopsis, indole-3-butyric acid (IBA). A detailed analysis of the expression pattern of CpGATA24 and CpMAKR4 in squash roots from founder cell specification until emergence of lateral root primordia was carried out using promoter-fluorescent reporter gene fusions and confocal microscopy. Their expression was induced in the protoxylem, and then expanded to founder cells in the pericycle. Thus, while the overall expression pattern of these genes was significantly different from that in Arabidopsis, in founder cells their expression was induced in the same order as in Arabidopsis. Altogether, these findings suggest that in Cucurbitaceae the putative functional orthologs of GATA23 and MAKR4 might play a role in founder cell specification and primordium positioning during lateral root initiation. The role of the protoxylem in auxin transport as a trigger of founder cells specification and lateral root initiation is discussed.
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| 12. |
- Shumilina, Julia, et al.
(författare)
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Integrative Proteomics and Metabolomics Analysis Reveals the Role of Small Signaling Peptide Rapid Alkalinization Factor 34 (RALF34) in Cucumber Roots
- 2023
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Ingår i: International Journal of Molecular Sciences. - 1661-6596 .- 1422-0067. ; 24:8
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Tidskriftsartikel (refereegranskat)abstract
- The main role of RALF small signaling peptides was reported to be the alkalization control of the apoplast for improvement of nutrient absorption; however, the exact function of individual RALF peptides such as RALF34 remains unknown. The Arabidopsis RALF34 (AtRALF34) peptide was proposed to be part of the gene regulatory network of lateral root initiation. Cucumber is an excellent model for studying a special form of lateral root initiation taking place in the meristem of the parental root. We attempted to elucidate the role of the regulatory pathway in which RALF34 is a participant using cucumber transgenic hairy roots overexpressing CsRALF34 for comprehensive, integrated metabolomics and proteomics studies, focusing on the analysis of stress response markers. CsRALF34 overexpression resulted in the inhibition of root growth and regulation of cell proliferation, specifically in blocking the G2/M transition in cucumber roots. Based on these results, we propose that CsRALF34 is not part of the gene regulatory networks involved in the early steps of lateral root initiation. Instead, we suggest that CsRALF34 modulates ROS homeostasis and triggers the controlled production of hydroxyl radicals in root cells, possibly associated with intracellular signal transduction. Altogether, our results support the role of RALF peptides as ROS regulators.
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