Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation

We characterize allelic and gene expression variation between populations of the Glanville fritillary butterfly (Melitaea cinxia) from two fragmented and two continuous landscapes in northern Europe. The populations exhibit significant differences in their life history traits, e.g. butterflies from fragmented landscapes have higher flight metabolic rate and dispersal rate in the field, and higher larval growth rate, than butterflies from continuous landscapes. In fragmented landscapes, local populations are small and have a high risk of local extinction, and hence the long-term persistence at the landscape level is based on frequent re-colonization of vacant habitat patches, which is predicted to select for increased dispersal rate. Using RNA-seq data and a common garden experiment, we found that a large number of genes (1,841) were differentially expressed between the landscape types. Hexamerin genes, the expression of which has previously been shown to have high heritability and which correlate strongly with larval development time in the Glanville fritillary, had higher expression in fragmented than continuous landscapes. Genes that were more highly expressed in butterflies from newly-established than old local populations within a fragmented landscape were also more highly expressed, at the landscape level, in fragmented than continuous landscapes. This result suggests that recurrent extinctions and re-colonizations in fragmented landscapes select a for specific expression profile. Genes that were significantly up-regulated following an experimental flight treatment had higher basal expression in fragmented landscapes, indicating that these butterflies are genetically primed for frequent flight. Active flight causes oxidative stress, but butterflies from fragmented landscapes were more tolerant of hypoxia. We conclude that differences in gene expression between the landscape types reflect genomic adaptations to landscape fragmentation.     

Rationally Engineered Synthetic Coculture for Improved Biomass and Product Formation

In microbial ecosystems, bacteria are dependent on dynamic interspecific interactions related to carbon and energy flow. Substrates and end-metabolites are rapidly converted to other compounds, which protects the community from high concentrations of inhibitory molecules. In biotechnological applications, pure cultures are preferred because of the more straight-forward metabolic engineering and bioprocess control. However, the accumulation of unwanted side products can limit the cell growth and process efficiency. In this study, a rationally engineered coculture with a carbon channeling system was constructed using two well-characterized model strains Escherichia coli K12 and Acinetobacter baylyi ADP1. The directed carbon flow resulted in efficient acetate removal, and the coculture showed symbiotic nature in terms of substrate utilization and growth. Recombinant protein production was used as a proof-of-principle example to demonstrate the coculture utility and the effects on product formation. As a result, the biomass and recombinant protein titers of E. coli were enhanced in both minimal and rich medium simple batch cocultures. Finally, harnessing both the strains to the production resulted in enhanced recombinant protein titers. The study demonstrates the potential of rationally engineered cocultures for synthetic biology applications.     

Methodological Aspects of Applying Life Cycle Assessment to Industrial Symbioses

In view of recent studies of the historical development and current status of industrial symbiosis (IS), life cycle assessment (LCA) is proposed as a general framework for quantifying the environmental performance of by‐product exchange. Recent guidelines for LCA (International Reference Life Cycle Data System [ILCD] guidelines) are applied to answer the main research questions in the IS literature reviewed. A typology of five main research questions is proposed: (1) analysis, (2) improvement, and (3) expansion of existing systems; (4) design of new eco‐industrial parks, and (5) restructuring of circular economies. The LCA guidelines were found useful in framing the question and choosing an appropriate reference case for comparison. The selection of a correct reference case reduces the risk of overestimating the benefits of by‐product exchange. In the analysis of existing systems, environmentally extended input‐output analysis (EEIOA) can be used to streamline the analysis and provide an industry average baseline for comparison. However, when large‐scale changes are applied to the system, more sophisticated tools are necessary for assessment of the consequences, from market analysis to general equilibrium modeling and future scenario work. Such a rigorous application of systems analysis was not found in the current IS literature, but would benefit the field substantially, especially when the environmental impact of large‐scale economic changes is analyzed.     

Characterization of low-density granulocytes in COVID-19

Severe COVID-19 is characterized by extensive pulmonary complications, to which host immune responses are believed to play a role. As the major arm of innate immunity, neutrophils are one of the first cells recruited to the site of infection where their excessive activation can contribute to lung pathology. Low-density granulocytes (LDGs) are circulating neutrophils, whose numbers increase in some autoimmune diseases and cancer, but are poorly characterized in acute viral infections. Using flow cytometry, we detected a significant increase of LDGs in the blood of acute COVID-19 patients, compared to healthy controls. Based on their surface marker expression, COVID-19-related LDGs exhibit four different populations, which display distinctive stages of granulocytic development and most likely reflect emergency myelopoiesis. Moreover, COVID-19 LDGs show a link with an elevated recruitment and activation of neutrophils. Functional assays demonstrated the immunosuppressive capacities of these cells, which might contribute to impaired lymphocyte responses during acute disease. Taken together, our data confirms a significant granulocyte activation during COVID-19 and suggests that granulocytes of lower density play a role in disease progression.     

Identification of target genes for a MYB-type anthocyanin regulator in Gerbera hybrida

Genetic modification of the flavonoid pathway has been used to produce novel colours and colour patterns in ornamental plants as well as to modify the nutritional and pharmaceutical properties of food crops. It has been suggested that co-ordinate control of multiple steps of the pathway with the help of regulatory genes would lead to a more predictable control of metabolic flux. Regulation of anthocyanin biosynthesis has been studied in a common ornamental plant, Gerbera hybrida (Asteraceae). An R2R3-type MYB factor, GMYB10, shares high sequence similarity and is phylogenetically grouped together with previously characterized regulators of anthocyanin pigmentation. Ectopic expression of GMYB10 leads to strongly enhanced accumulation of anthocyanin pigments as well as to an altered pigmentation pattern in transgenic gerbera plants. Anthocyanin analysis indicates that GMYB10 specifically induces cyanidin biosynthesis in undifferentiated callus and in vegetative tissues. Furthermore, in floral tissues enhanced pelargonidin production is detected. Microarray analysis using the gerbera 9K cDNA array revealed a highly predicted set of putative target genes for GMYB10 including new gene family members of both early and late biosynthetic genes of the flavonoid pathway. However, completely new candidate targets, such as a serine carboxypeptidase-like gene as well, as two new MYB domain factors, GMYB11 and GMYB12, whose exact function in phenylpropanoid biosynthesis is not clear yet, were also identified.     

Dissolved iron:phosphate ratio as an indicator of phosphate release to oxic water of the inner and outer coastal Baltic Sea

Pore water concentrations and benthic fluxes of dissolved Fe, P and N were measured at two coastal basins in the Gulf of Finland, northern Baltic Sea, during a seasonal cycle. The bioturbated inner coastal basin, where exchange of near-bottom water is efficient, had a better ability to retain P in sediments than the outer basin, where near-bottom water O₂ concentration decreases during summer. Under the presence of O₂ high pore water dissolved Fe:P ratio (>3.6 w:w) in surface layer of the sediment, measured especially in winter, indicated negligible or low P-release and high N:P ratio in the efflux. On the contrary, low Fe:P ratio (<3.6), measured in summer and autumn, indicated high efflux of P and low N:P flux ratio. The low dissolved Fe:P ratio suggested that there was not enough diffusing Fe to form Fe³⁺ oxide-rich layer in the oxic surface zone of the sediments or near-bottom water to bind the P diffusing from the sediment. However, in sediments bioturbated by the abundant bivalve Macoma baltica, small efflux of P were measured almost throughout the study period. Thus, the Fe:P ratio cannot alone explain the P-release in bioturbated sediments. The low N:P ratio in the efflux measured in summer and autumn partly explains the measured low N:P ratio in the near-bottom water and thus N limitation of primary production in the Gulf. Additionally, it is evident that the release of P in the Gulf itself is of great importance for the trophic state of the Gulf of Finland.     

Midsummer spatial variation in methane efflux from stands of littoral vegetation in a boreal meso-eutrophic lake

1. Spatial variation of methane (CH₄) efflux from the littoral zone of a meso‐eutrophic boreal lake was studied with a closed‐chamber technique for three summer days in 22 vegetation stands, consisting of three emergent and three floating‐leaved species. 2. Between‐species differences in CH₄ emission were significant. The highest emissions were measured from the emergent Phragmites australis stands (0.5–1.7 mmol m^?2 h^?1), followed by Schoenoplectus lacustris > Equisetum fluviatile > Nuphar lutea > Sparganium gramineum > Potamogeton natans. Within‐species differences between stands were not significant. 3. In P. australis stands, the stand‐specific mean CH₄ emission was significantly correlated with solar radiation, probably indicating the role of effective pressurised ventilation on CH₄ fluxes. The proportion of net primary production emitted as CH₄ was significantly higher in P. australis stands (7.4%) than in stands of S. lacustris and E. fluviatile (both 0.5%). 4. In N. lutea stands, CH₄ efflux was negatively correlated with the mean fetch and positively with the percentage cover of leaves on the water surface. There were no differences in CH₄ efflux between intact N. lutea leaves and those grazed by coleopteran Galerucella nymphaeae. In S. graminaeum and P. natans stands, CH₄ effluxes were not related to any of the measured environmental variables. 5. For all vegetation stands, the biomass above water level explained about 60% of the observed spatial variation in CH₄ emission, indicating the important role of plants as gas conduits and producers of substrates for methanogens in the anoxic sediment.