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| 2. |
- Jiang, Rays H. Y., et al.
(author)
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Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica
- 2013
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In: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 9:6, s. e1003272-
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Journal article (peer-reviewed)abstract
- Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica.
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| 3. |
- Mills, Gina, 1959, et al.
(author)
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Ozone pollution will compromise efforts to increase global wheat production
- 2018
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In: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 24:8, s. 3560-3574
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Journal article (peer-reviewed)abstract
- Introduction of high-performing crop cultivars and crop/soil water management practices that increase the stomatal uptake of carbon dioxide and photosynthesis will be instrumental in realizing the United Nations Sustainable Development Goal (SDG) of achieving food security. To date, however, global assessments of how to increase crop yield have failed to consider the negative effects of tropospheric ozone, a gaseous pollutant that enters the leaf stomatal pores of plants along with carbon dioxide, and is increasing in concentration globally, particularly in rapidly developing countries. Earlier studies have simply estimated that the largest effects are in the areas with the highest ozone concentrations. Using a modelling method that accounts for the effects of soil moisture deficit and meteorological factors on the stomatal uptake of ozone, we show for the first time that ozone impacts on wheat yield are particularly large in humid rain-fed and irrigated areas of major wheat-producing countries (e.g. United States, France, India, China and Russia). Averaged over 2010-2012, we estimate that ozone reduces wheat yields by a mean 9.9% in the northern hemisphere and 6.2% in the southern hemisphere, corresponding to some 85 Tg (million tonnes) of lost grain. Total production losses in developing countries receiving Official Development Assistance are 50% higher than those in developed countries, potentially reducing the possibility of achieving UN SDG2. Crucially, our analysis shows that ozone could reduce the potential yield benefits of increasing irrigation usage in response to climate change because added irrigation increases the uptake and subsequent negative effects of the pollutant. We show that mitigation of air pollution in a changing climate could play a vital role in achieving the above-mentioned UN SDG, while also contributing to other SDGs related to human health and well-being, ecosystems and climate change.
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| 4. |
- Brown, Brielin C., et al.
(author)
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Multiset correlation and factor analysis enables exploration of multi-omics data
- 2023
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In: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 3:8, s. 100359-
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Journal article (peer-reviewed)abstract
- Multi-omics datasets are becoming more common, necessitating better integration methods to realize their revolutionary potential. Here, we introduce multi-set correlation and factor analysis (MCFA), an unsupervised integration method tailored to the unique challenges of high-dimensional genomics data that enables fast inference of shared and private factors. We used MCFA to integrate methylation markers, protein expression, RNA expression, and metabolite levels in 614 diverse samples from the Trans-Omics for Precision Medicine/Multi-Ethnic Study of Atherosclerosis multi-omics pilot. Samples cluster strongly by ancestry in the shared space, even in the absence of genetic information, while private spaces frequently capture dataset-specific technical variation. Finally, we integrated genetic data by conducting a genome-wide association study (GWAS) of our inferred factors, observing that several factors are enriched for GWAS hits and trans-expression quantitative trait loci. Two of these factors appear to be related to metabolic disease. Our study provides a foundation and framework for further integrative analysis of ever larger multi-modal genomic datasets.
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| 5. |
- Jong, Wouter S. P., et al.
(author)
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Application of an E. coli signal sequence as a versatile inclusion body tag
- 2017
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In: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859. ; 16
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Journal article (peer-reviewed)abstract
- Background: Heterologous protein production in Escherichia coli often suffers from bottlenecks such as proteolytic degradation, complex purification procedures and toxicity towards the expression host. Production of proteins in an insoluble form in inclusion bodies (IBs) can alleviate these problems. Unfortunately, the propensity of heterologous proteins to form IBs is variable and difficult to predict. Hence, fusing the target protein to an aggregation prone polypeptide or IB-tag is a useful strategy to produce difficult-to-express proteins in an insoluble form. Results: When screening for signal sequences that mediate optimal targeting of heterologous proteins to the periplasmic space of E. coli, we observed that fusion to the 39 amino acid signal sequence of E. coli TorA (ssTorA) did not promote targeting but rather directed high-level expression of the human proteins hEGF, Pla2 and IL-3 in IBs. Further analysis revealed that ssTorA even mediated IB formation of the highly soluble endogenous E. coli proteins TrxA and MBP. The ssTorA also induced aggregation when fused to the C-terminus of target proteins and appeared functional as IB-tag in E. coli K-12 as well as B strains. An additive effect on IB-formation was observed upon fusion of multiple ssTorA sequences in tandem, provoking almost complete aggregation of TrxA and MBP. The ssTorA-moiety was successfully used to produce the intrinsically unstable hEGF and the toxic fusion partner SymE, demonstrating its applicability as an IB-tag for difficult-to-express and toxic proteins. Conclusions: We present proof-of-concept for the use of ssTorA as a small, versatile tag for robust E. coli-based expression of heterologous proteins in IBs.
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| 6. |
- Seneviratne, Sonia I., et al.
(author)
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Impact of soil moisture-climate feedbacks on CMIP5 projections: First results from the GLACE-CMIP5 experiment
- 2013
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In: Geophysical Research Letters. - : American Geophysical Union (AGU). - 1944-8007 .- 0094-8276. ; 40:19, s. 5212-5217
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Journal article (peer-reviewed)abstract
- The Global Land-Atmosphere Climate Experiment-Coupled Model Intercomparison Project phase 5 (GLACE-CMIP5) is a multimodel experiment investigating the impact of soil moisture-climate feedbacks in CMIP5 projections. We present here first GLACE-CMIP5 results based on five Earth System Models, focusing on impacts of projected changes in regional soil moisture dryness (mostly increases) on late 21st century climate. Projected soil moisture changes substantially impact climate in several regions in both boreal and austral summer. Strong and consistent effects are found on temperature, especially for extremes (about 1-1.5K for mean temperature and 2-2.5K for extreme daytime temperature). In the Northern Hemisphere, effects on mean and heavy precipitation are also found in most models, but the results are less consistent than for temperature. A direct scaling between soil moisture-induced changes in evaporative cooling and resulting changes in temperature mean and extremes is found in the simulations. In the Mediterranean region, the projected soil moisture changes affect about 25% of the projected changes in extreme temperature.
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| 7. |
- Turner, David R., 1951, et al.
(author)
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Toward a Quality-Controlled and Accessible Pitzer Model for Seawater and Related Systems
- 2016
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In: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 3:139
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Journal article (peer-reviewed)abstract
- We elaborate the need for a quality-controlled chemical speciation model for seawater and related natural waters, work which forms the major focus of SCOR Working Group 145. Model development is based on Pitzer equations for the seawater electrolyte and trace components. These equations can be used to calculate activities of dissolved ions and molecules and, in combination with thermodynamic equilibrium constants, chemical speciation. The major tasks to be addressed are ensuring internal consistency of the Pitzer model parameters (expressing the interactions between pairs and triplets of species, which ultimately determines the calculated activities), assessing uncertainties, and identifying important data gaps that should be addressed by new measurements. It is recognised that natural organic matter plays an important role in many aquatic ecosystems, and options for including this material in a Pitzer-based model are discussed. The process of model development begins with the core components which include the seawater electrolyte and the weak acids controlling pH. This core model can then be expanded by incorporating additional chemical components, changing the standard seawater composition and/or broadening the range of temperature and pressure, without compromising its validity. Seven important areas of application are identified: open ocean acidification; micro-nutrient biogeochemistry and geochemical tracers; micro-nutrient behaviour in laboratory studies; water quality in coastal and estuarine waters; cycling of nutrients and trace metals in pore waters; chemical equilibria in hydrothermal systems; brines and salt lakes.
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| 8. |
- Berg, Alexis, et al.
(author)
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Interannual Coupling between Summertime Surface Temperature and Precipitation over Land: Processes and Implications for Climate Change
- 2015
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In: Journal of Climate. - 1520-0442. ; 28:3, s. 1308-1328
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Journal article (peer-reviewed)abstract
- Widespread negative correlations between summertime-mean temperatures and precipitation over land regions are a well-known feature of terrestrial climate. This behavior has generally been interpreted in the context of soil moisture atmosphere coupling, with soil moisture deficits associated with reduced rainfall leading to enhanced surface sensible heating and higher surface temperature. The present study revisits the genesis of these negative temperature precipitation correlations using simulations from the Global Land Atmosphere Coupling Experiment phase 5 of the Coupled Model Intercomparison Project (GLACE-CMIP5) multimodel experiment. The analyses are based on simulations with five climate models, which were integrated with prescribed (noninteractive) and with interactive soil moisture over the period 1950-2100. While the results presented here generally confirm the interpretation that negative correlations between seasonal temperature and precipitation arise through the direct control of soil moisture on surface heat flux partitioning, the presence of widespread negative correlations when soil moisture atmosphere interactions are artificially removed in at least two out of five models suggests that atmospheric processes, in addition to land surface processes, contribute to the observed negative temperature precipitation correlation. On longer time scales, the negative correlation between precipitation and temperature is shown to have implications for the projection of climate change impacts on near-surface climate: in all models, in the regions of strongest temperature precipitation anticorrelation on interannual time scales, long-term regional warming is modulated to a large extent by the regional response of precipitation to climate change, with precipitation increases (decreases) being associated with minimum (maximum) warming. This correspondence appears to arise largely as the result of soil moisture atmosphere interactions.
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| 9. |
- Wirdelius, Håkan, 1963, et al.
(author)
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Validation of models for Laser Ultrasonic spectra as a function of the grain size in steel
- 2018
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In: 12th European Conference on Non-Destructive Testing (ECNDT 2018). - 9789163962172
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Conference paper (peer-reviewed)abstract
- To reduce costs of production and increase economic sustainability it is necessary to introduce quality assessment in an early stage in the manufacturing process. In an ongoing European project (Product Uniformity Control – PUC), the intention is to use ultrasonic information to assess microstructure parameters that are related to macroscale qualities such as mechanical properties. Laser induced ultrasonic technique (LUS) requires no media and can generate and detect ultrasonic information at some distance from the component. This technique is therefore addressed within this project as a solution to measure ultrasonic properties in an industrial environment. Mathematical modelling of the ultrasonic wave propagation problem has been used in order to get a deeper understanding of the physics and to identify ultrasonic properties that can be used as an indirect measurement of grain size. The use of both analytical and numerical models enabled extensive parametric studies together with investigation of ultrasonic interactions with well-defined individual microstructures. The LUS technique has previously been applied to e.g. monitor grain growth during thermomechanical processing of metals. These applications identified and used a correlation with the frequency content of the attenuation. This have been investigated as a possible indirect measurement of grain size, also in this project. The models have been used to verify the correlations and to evaluate different procedures that could be applied as an industrial solution. The suggested procedure is based on deconvolving two successive echoes and has been experimentally validated by two different LUS systems. The reference samples used in the validation were produced by changing the annealing temperature and time to obtain a variation in grain sizes. These grain sizes were then identified by EBSD and the samples were examined in terms of grain size influence on spectral attenuation
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| 10. |
- Potapov, Anton M., et al.
(author)
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Globally invariant metabolism but density-diversity mismatch in springtails
- 2023
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Journal article (peer-reviewed)abstract
- Soil life supports the functioning and biodiversity of terrestrial ecosystems. Springtails (Collembola) are among the most abundant soil arthropods regulating soil fertility and flow of energy through above- and belowground food webs. However, the global distribution of springtail diversity and density, and how these relate to energy fluxes remains unknown. Here, using a global dataset representing 2470 sites, we estimate the total soil springtail biomass at 27.5 megatons carbon, which is threefold higher than wild terrestrial vertebrates, and record peak densities up to 2 million individuals per square meter in the tundra. Despite a 20-fold biomass difference between the tundra and the tropics, springtail energy use (community metabolism) remains similar across the latitudinal gradient, owing to the changes in temperature with latitude. Neither springtail density nor community metabolism is predicted by local species richness, which is high in the tropics, but comparably high in some temperate forests and even tundra. Changes in springtail activity may emerge from latitudinal gradients in temperature, predation and resource limitation in soil communities. Contrasting relationships of biomass, diversity and activity of springtail communities with temperature suggest that climate warming will alter fundamental soil biodiversity metrics in different directions, potentially restructuring terrestrial food webs and affecting soil functioning.
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