Periodontitis, Dental Procedures, and Young-Onset Cryptogenic Stroke

Periodontitis is associated with an increased risk of ischemic stroke, and the risk may be particularly high among young people with unexplained stroke etiology. Thus, we investigated in a case-control study whether periodontitis or recent invasive dental treatments are associated with young-onset cryptogenic ischemic stroke (CIS). We enrolled participants from a multicenter case-control SECRETO study including adults aged 18 to 49 y presenting with an imaging-positive first-ever CIS and stroke-free age- and sex-matched controls. Thorough clinical and radiographic oral examination was performed. Furthermore, we measured serum lipopolysaccharide (LPS) and lipotechoic acid (LTA) levels. Multivariate conditional regression models were adjusted for stroke risk factors, regular dentist visits, and patent foramen ovale (PFO) status. We enrolled 146 case-control pairs (median age 41.9 y; 58.2% males). Periodontitis was diagnosed in 27.5% of CIS patients and 20.1% of controls (P < 0.001). In the fully adjusted models, CIS was associated with high periodontal inflammation burden (odds ratio [OR], 95% confidence interval) with an OR of 10.48 (3.18-34.5) and severe periodontitis with an OR of 7.48 (1.24-44.9). Stroke severity increased with the severity of periodontitis, having an OR of 6.43 (1.87-23.0) in stage III to IV, grade C. Invasive dental treatments performed within 3 mo prestroke were associated with CIS, with an OR of 2.54 (1.01-6.39). Association between CIS and invasive dental treatments was especially strong among those with PFO showing an OR of 6.26 (1.72-40.2). LPS/LTA did not differ between CIS patients and controls but displayed an increasing trend with periodontitis severity. Periodontitis and recent invasive dental procedures were associated with CIS after controlling for multiple confounders. However, the role of bacteremia as a mediator of this risk was not confirmed.

EP300/CREBBP acetyltransferase inhibition limits steroid receptor and FOXA1 signaling in prostate cancer cells

The androgen receptor (AR) is a primary target for treating prostate cancer (PCa), forming the bedrock of its clinical management. Despite their efficacy, resistance often hampers AR-targeted therapies, necessitating new strategies against therapy-resistant PCa. These resistances involve various mechanisms, including AR splice variant overexpression and altered activities of transcription factors like the glucocorticoid receptor (GR) and FOXA1. These factors rely on common coregulators, such as EP300/CREBBP, suggesting a rationale for coregulator-targeted therapies. Our study explores EP300/CREBBP acetyltransferase inhibition's impact on steroid receptor and FOXA1 signaling in PCa cells using genome-wide techniques. Results reveal that EP300/CREBBP inhibition significantly disrupts the AR-regulated transcriptome and receptor chromatin binding by reducing the AR-gene expression. Similarly, GR's regulated transcriptome and receptor binding were hindered, not linked to reduced GR expression but to diminished FOXA1 chromatin binding, restricting GR signaling. Overall, our findings highlight how EP300/CREBBP inhibition distinctively curtails oncogenic transcription factors' signaling, suggesting the potential of coregulatory-targeted therapies in PCa.

Development and evolution of the Asteraceae capitulum

Asteraceae represent one of the largest and most diverse families of plants. The evolutionary success of this family has largely been contributed to their unique inflorescences, capitula that mimic solitary flowers but are typically aggregates of multiple florets. Here, we summarize the recent molecular and genetic level studies that have promoted our understanding of the development and evolution of capitula. We focus on new results on patterning of the enlarged meristem resulting in the iconic phyllotactic arrangement of florets in Fibonacci numbers of spirals. We also summarize the current understanding of the genetic networks regulating the characteristic reproductive traits in the family such as floral dimorphism and differentiation of highly specialized floral organs. So far, developmental studies in Asteraceae are still limited to a very narrow selection of model species. Along with the recent advancements in genomics and phylogenomics, Asteraceae and its relatives provide an outstanding model clade for extended evo-devo studies to exploit the morphological diversity and the underlying molecular networks and to translate this knowledge to the breeding of the key crops in the family.

Towards a taxonomy of geodiversity

Geodiversity is a topical concept in earth and environmental sciences. Geodiversity information is needed to conserve nature, use ecosystem services and achieve sustainable development goals. Despite the increasing demand for geodiversity data, there exists no comprehensive system for categorizing geodiversity. Here, we present a hierarchically structured taxonomy that is potentially applicable in mapping and quantifying geodiversity across different regions, environments and scales. In this taxonomy, the main components of geodiversity are geology, geomorphology, hydrology and pedology. We propose a six-level hierarchical system where the components of geodiversity are classified at progressively lower taxonomic levels based on their genesis, physical-chemical properties and morphology. This comprehensive taxonomy can be used to compile geodiversity information for scientific research and various applications of value to society and nature conservation. Ultimately, this hierarchical system is the first step towards developing a global geodiversity taxonomy. This article is part of the Theo Murphy meeting issue 'Geodiversity for science and society'.

Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing

Additive and dominance genetic variances underlying the expression of quantitative traits are important quantities for predicting short-term responses to selection, but they are notoriously challenging to estimate in most non-model wild populations. Specifically, large-sized or panmictic populations may be characterized by low variance in genetic relatedness among individuals which, in turn, can prevent accurate estimation of quantitative genetic parameters. We used estimates of genome-wide identity-by-descent (IBD) sharing from autosomal SNP loci to estimate quantitative genetic parameters for ecologically important traits in nine-spined sticklebacks (Pungitius pungitius) from a large, outbred population. Using empirical and simulated datasets, with varying sample sizes and pedigree complexity, we assessed the performance of different crossing schemes in estimating additive genetic variance and heritability for all traits. We found that low variance in relatedness characteristic of wild outbred populations with high migration rate can impair the estimation of quantitative genetic parameters and bias heritability estimates downwards. On the other hand, the use of a half-sib/full-sib design allowed precise estimation of genetic variance components and revealed significant additive variance and heritability for all measured traits, with negligible dominance contributions. Genome-partitioning and QTL mapping analyses revealed that most traits had a polygenic basis and were controlled by genes at multiple chromosomes. Furthermore, different QTL contributed to variation in the same traits in different populations suggesting heterogeneous underpinnings of parallel evolution at the phenotypic level. Our results provide important guidelines for future studies aimed at estimating adaptive potential in the wild, particularly for those conducted in outbred large-sized populations.

Effect of xenon on brain injury, neurological outcome, and survival in patients after aneurysmal subarachnoid hemorrhage-study protocol for a randomized clinical trial

BACKGROUND

Aneurysmal subarachnoid hemorrhage (aSAH) is a neurological emergency, affecting a younger population than individuals experiencing an ischemic stroke; aSAH is associated with a high risk of mortality and permanent disability. The noble gas xenon has been shown to possess neuroprotective properties as demonstrated in numerous preclinical animal studies. In addition, a recent study demonstrated that xenon could attenuate a white matter injury after out-of-hospital cardiac arrest.

METHODS

The study is a prospective, multicenter phase II clinical drug trial. The study design is a single-blind, prospective superiority randomized two-armed parallel follow-up study. The primary objective of the study is to explore the potential neuroprotective effects of inhaled xenon, when administered within 6 h after the onset of symptoms of aSAH. The primary endpoint is the extent of the global white matter injury assessed with magnetic resonance diffusion tensor imaging of the brain.

DISCUSSION

Despite improvements in medical technology and advancements in medical science, aSAH mortality and disability rates have remained nearly unchanged for the past 10 years. Therefore, new neuroprotective strategies to attenuate the early and delayed brain injuries after aSAH are needed to reduce morbidity and mortality.

TRIAL REGISTRATION

ClinicalTrials.gov NCT04696523. Registered on 6 January 2021. EudraCT, EudraCT Number: 2019-001542-17. Registered on 8 July 2020.

Preterm birth and asthma and COPD in adulthood: a nationwide register study from two Nordic countries

BACKGROUND

Preterm birth affects lungs in several ways but few studies have follow-up until adulthood. We investigated the association of the entire spectrum of gestational ages with specialist care episodes for obstructive airway disease (asthma and chronic obstructive pulmonary disease (COPD)) at age 18-50 years.

METHODS

We used nationwide registry data on 706 717 people born 1987-1998 in Finland (4.8% preterm) and 1 669 528 born 1967-1999 in Norway (5.0% preterm). Care episodes of asthma and COPD were obtained from specialised healthcare registers, available in Finland for 2005-2016 and in Norway for 2008-2017. We used logistic regression to estimate odds ratios (ORs) for having a care episode with either disease outcome.

RESULTS

Odds of any obstructive airway disease in adulthood for those born at <28 or 28-31 completed weeks were 2-3-fold of those born full term (39-41 completed weeks), persisting after adjustments. For individuals born at 32-33, 34-36 or 37-38 weeks, the odds were 1.1- to 1.5-fold. Associations were similar in the Finnish and the Norwegian data and among people aged 18-29 and 30-50 years. For COPD at age 30-50 years, the OR was 7.44 (95% CI 3.49-15.85) for those born at <28 weeks, 3.18 (95% CI 2.23-4.54) for those born at 28-31 weeks and 2.32 (95% CI 1.72-3.12) for those born at 32-33 weeks. Bronchopulmonary dysplasia in infancy increased the odds further for those born at <28 and 28-31 weeks.

CONCLUSION

Preterm birth is a risk factor for asthma and COPD in adulthood. The high odds of COPD call for diagnostic vigilance when adults born very preterm present with respiratory symptoms.

Plasma membrane aquaporins of the PIP1 and PIP2 subfamilies facilitate hydrogen peroxide diffusion into plant roots

BACKGROUND

The permeability of plasma membrane aquaporins (PIPs) to small solutes other than water greatly diversifies their potential functions in plant development and metabolic processes. One such process is stress signalling in which hydrogen peroxide (H₂O₂) plays a major role. Based on transport assays carried out in yeast, there are differences in the degree to which PIPs of Arabidopsis thaliana, are permeable to H₂O₂ and thus they may differentially facilitate transmembrane diffusion. Here, we test whether specific PIPs aid in the transmembrane diffusion of H₂O₂ to such an extent that knocking-out PIPs affects plant phenotype. We examined changes in growth and morphology, including biomass accumulation, root system architecture and relative water content, as well as gas exchange, across two H₂O₂ treatments in knockout mutants of A. thaliana.

RESULTS

We could infer that PIP-type aquaporins are permeable to H₂O₂ in planta and that this permeability is physiologically relevant in a plant's response to oxidative stress. In particular, the lack of functional PIP2;3 confers resistance to exogenously applied H₂O₂ indicating that it facilitates H₂O₂ entry into root cells. Additionally, PIP1;1 and PIP2;6 were found to facilitate H₂O₂ diffusion, while PIP2;2 is required for proper root growth under controlled conditions.

MAIN FINDINGS

We conclude that PIPs are physiologically relevant conduits for H₂O₂ diffusion in the A. thaliana roots and participate in the regulation of stress responses.

Skin microbiota of oxazolone-induced contact hypersensitivity mouse model

Contact allergy is a common skin allergy, which can be studied utilising contact hypersensitivity (CHS) animal model. However, it is not clear, whether CHS is a suitable model to investigate skin microbiota interactions. We characterised the effect of contact dermatitis on the skin microbiota and studied the biological effects of oxazolone (OXA) -induced inflammation on skin thickness, immune cell numbers and changes of the microbiota in CHS mouse model (n = 72) for 28 days. Through 16S rRNA gene sequencing we defined the composition of bacterial communities and associations of bacteria with inflammation. We observed that the vehicle solution of acetone and olive oil induced bacterial community changes on day 1, and OXA-induced changes were observed mainly on day 7. Many of the notably enriched bacteria present in the OXA-challenged positive group represented the genus Faecalibaculum which were most likely derived from the cage environment. Additionally, skin inflammation correlated negatively with Streptococcus, which is considered a native skin bacterium, and positively with Muribacter muris, which is typical in oral environment. Skin inflammation favoured colonisation of cage-derived faecal bacteria, and additionally mouse grooming transferred oral bacteria on the skin. Due to the observed changes, we conclude that CHS model could be used for certain skin microbiome-related research set-ups. However, since vehicle exposure can alter the skin microbiome as such, future studies should include considerations such as careful control sampling and statistical tests to account for potential confounding factors.

Human myelin proteolipid protein structure and lipid bilayer stacking

The myelin sheath is an essential, multilayered membrane structure that insulates axons, enabling the rapid transmission of nerve impulses. The tetraspan myelin proteolipid protein (PLP) is the most abundant protein of compact myelin in the central nervous system (CNS). The integral membrane protein PLP adheres myelin membranes together and enhances the compaction of myelin, having a fundamental role in myelin stability and axonal support. PLP is linked to severe CNS neuropathies, including inherited Pelizaeus-Merzbacher disease and spastic paraplegia type 2, as well as multiple sclerosis. Nevertheless, the structure, lipid interaction properties, and membrane organization mechanisms of PLP have remained unidentified. We expressed, purified, and structurally characterized human PLP and its shorter isoform DM20. Synchrotron radiation circular dichroism spectroscopy and small-angle X-ray and neutron scattering revealed a dimeric, α-helical conformation for both PLP and DM20 in detergent complexes, and pinpoint structural variations between the isoforms and their influence on protein function. In phosphatidylcholine membranes, reconstituted PLP and DM20 spontaneously induced formation of multilamellar myelin-like membrane assemblies. Cholesterol and sphingomyelin enhanced the membrane organization but were not crucial for membrane stacking. Electron cryomicroscopy, atomic force microscopy, and X-ray diffraction experiments for membrane-embedded PLP/DM20 illustrated effective membrane stacking and ordered organization of membrane assemblies with a repeat distance in line with CNS myelin. Our results shed light on the 3D structure of myelin PLP and DM20, their structure-function differences, as well as fundamental protein-lipid interplay in CNS compact myelin.

Foliar stable isotope ratios of carbon and nitrogen in boreal forest plants exposed to long-term pollution from the nickel-copper smelter at Monchegorsk, Russia

Long-term exposure to primary air pollutants, such as sulphur dioxide (SO2) and nitrogen oxides (NOx), alters the structure and functions of forest ecosystems. Many biochemical and biogeochemical processes discriminate against the heavier isotopes in a mixture; thus, the values of δ13C and δ15N (i.e. the ratio of stable isotopes 13C to 12C and that of 15 N to 14 N, respectively) may give insights into changes in ecosystem processes and identify the immediate drivers of these changes. We studied sources of variation in the δ13C and δ15N values in the foliage of eight boreal forest C3 plants at 10 sites located at the distance of 1-40 km from the Monchegorsk nickel-copper smelter in Russia. From 1939‒2019, this smelter emitted over 14,000,000 metric tons (t) of SO2, 250,000 t of metals, primarily nickel and copper, and 140,000 t of NOx. The δ13C value in evergreen plants and the δ15N value in all plants increased near the smelter independently of the plant mycorrhizal type. We attribute the pollution-related increase in the foliar δ13C values of evergreen species mainly to direct effects of SO2 on stomatal conductance, in combination with pollution-related water stress, which jointly override the potential opposite effect of increasing ambient CO2 concentration on δ13C values. Stomatal uptake of NOx and root uptake of 15N-enriched organic N compounds and NH4+ may explain the increased foliar δ15N values and elevated foliar N concentrations, especially in the evergreen trees (Pinus sylvestris), close to Monchegorsk, where the soil inorganic N supply is reduced due to the impact of long-term SO2 and heavy metal emissions on plant biomass. We conclude that, despite the uncertainties in interpreting δ13C and δ15N responses to pollution, the Monchegorsk smelter has imposed and still imposes a great impact on C and N cycling in the surrounding N-limited subarctic forest ecosystems.

Contrasting temperature responses in seasonal timing of cercariae shedding by Rhipidocotyle trematodes

Global warming is likely to lengthen the seasonal duration of larval release by parasites. We exposed freshwater mussel hosts, Anodonta anatina, from 2 high-latitude populations to high, intermediate and low temperatures throughout the annual cercarial shedding period of the sympatric trematodes Rhipidocotyle fennica and R. campanula, sharing the same transmission pathway. At the individual host level, under warmer conditions, the timing of the cercarial release in both parasite species shifted towards seasonally earlier period while its duration did not change. At the host population level, evidence for the lengthening of larvae shedding period with warming was found for R. fennica. R. campanula started the cercarial release seasonally clearly earlier, and at a lower temperature, than R. fennica. Furthermore, the proportion of mussels shedding cercariae increased, while day-degrees required to start the cercariae shedding decreased in high-temperature treatment in R. fennica. In R. campanula these effects were not found, suggesting that warming can benefit more R. fennica. These results do not completely support the view that climate warming would invariably increase the seasonal duration of larval shedding by parasites, but emphasizes species-specific differences in temperature-dependence and in seasonality of cercarial release.

Complementary use of the Ecosystem Service Concept and Multi-criteria Decision Analysis in Water Management

The ecosystem service (ES) concept has increasingly been applied in environmental planning, while there are several decades of experience in applying multi-criteria decision analysis (MCDA) in complex planning situations. The aim of this article is to assess how the ES concept has been used in water management projects together with MCDA and to examine the experiences gained and make recommendations to overcome any identified challenges. Our conclusions are based on a systematic analysis of 23 articles that were selected among 206 articles focused on water-related studies using, for example, the terms multi-criteria and ecosystem services in the title, abstract or keywords. Here, we explore (i) at what level of detail ESs are included in the decision hierarchy, (ii) the pros and cons of the complementary use of the two approaches, and (iii) how the potential challenges related to the use of MCDA, such as the large number of criteria, double-counting, or assigning criteria weights, are addressed in the selected cases. The results reveal large differences between the case studies. It is shown that only a few case studies used ES categories to classify criteria in the decision hierarchy, that these cases included different numbers of ES criteria and non-ES criteria, and that most case studies elicited stakeholder preferences in MCDA. Although the paper focuses on water management projects, the conclusions regarding the advantages and pitfalls of the complementary use of the methods, as well as our recommendations, are also applicable to other environmental management contexts.

Production of galactosylated complex-type N-glycans in glycoengineered Saccharomyces cerevisiae

Abstract

N-glycosylation is an important posttranslational modification affecting the properties and quality of therapeutic proteins. Glycoengineering in yeast aims to produce proteins carrying human-compatible glycosylation, enabling the production of therapeutic proteins in yeasts. In this work, we demonstrate further development and characterization of a glycoengineering strategy in a Saccharomyces cerevisiae Δalg3 Δalg11 strain where a truncated Man₃GlcNAc₂ glycan precursor is formed due to a disrupted lipid-linked oligosaccharide synthesis pathway. We produced galactosylated complex-type and hybrid-like N-glycans by expressing a human galactosyltransferase fusion protein both with and without a UDP-glucose 4-epimerase domain from Schizosaccharomyces pombe. Our results showed that the presence of the UDP-glucose 4-epimerase domain was beneficial for the production of digalactosylated complex-type glycans also when extracellular galactose was supplied, suggesting that the positive impact of the UDP-glucose 4-epimerase domain on the galactosylation process can be linked to other processes than its catalytic activity. Moreover, optimization of the expression of human GlcNAc transferases I and II and supplementation of glucosamine in the growth medium increased the formation of galactosylated complex-type glycans. Additionally, we provide further characterization of the interfering mannosylation taking place in the glycoengineered yeast strain.

Key points

• Glycoengineered Saccharomyces cerevisiae can form galactosylated N-glycans.

• Genetic constructs impact the activities of the expressed glycosyltransferases.

• Growth medium supplementation increases formation of target N-glycan structure.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11727-8.

Seasonal variations in bird selection pressure on prey colouration

The direction and strength of selection for prey colouration by predators vary in space and time and depend on the composition of the predator community. We tested the hypothesis that bird selection pressure on prey colouration changes through the season due to changes in the proportion of naïve juvenile individuals in the bird community, because naïve and educated birds differ in their responses to prey colours. Bird predation on caterpillar-shaped plasticine models in two boreal forest sites increased sevenfold from early summer to mid-summer, and the time of this increase coincides with the fledging of juvenile birds. In early summer, cryptic (black and green) models were attacked at fivefold higher rates compared with conspicuous (red and yellow) models. By contrast, starting from fledging time, cryptic and conspicuous models were attacked at similar rates, hinting at a lower selectivity by naïve juvenile birds compared with educated adult birds. Cryptic models exposed in a group together with conspicuous models were attacked by birds at a threefold lower rate than cryptic models exposed singly, thus supporting the aposematic commensalism hypothesis. However, this effect was not observed in mid- and late summer, presumably due to the lack of avoidance of conspicuous prey by the juvenile birds. We conclude that selection pressure on prey colouration weakens considerably when naïve birds dominate in the community, because the survival advantages of aposematic colouration are temporarily lost for both the conspicuous and their neighbouring cryptic prey.

Identifying the paths of climate effects on population dynamics: dynamic and multilevel structural equation model around the annual cycle

How environmental factors influence population dynamics in long-distance migrants is complicated by the spatiotemporal diversity of the environment the individuals experience during the annual cycle. The effects of weather on several different aspects of life history have been well studied, but a better understanding is needed on how weather affects population dynamics through the different associated traits. We utilise 77 years of data from pied flycatcher (Ficedula hypoleuca), to identify the most relevant climate signals associated with population growth rate. The strongest signals on population growth were observed from climate during periods when the birds were not present in the focal location. The population decline was associated with increasing precipitation in the African non-breeding quarters in the autumn (near the arrival of migrants) and with increasing winter temperature along the migration route (before migration). The number of fledglings was associated positively with increasing winter temperature in non-breeding area and negatively with increasing winter temperature in Europe. These possible carry-over effects did not arise via timing of breeding or clutch size but the exact mechanism remains to be revealed in future studies. High population density and low fledgling production were the intrinsic factors reducing the breeding population. We conclude that weather during all seasons has the potential to affect the reproductive success or population growth rate of this species. Our results show how weather can influence the population dynamics of a migratory species through multiple pathways, even at times of the annual cycle when the birds are in a different location than the climate signal.

Protocol: Adeno-Associated Virus-Mediated Gene Transfer in Ex Vivo Cultured Embryonic Mammary Gland

Branching morphogenesis of the murine mammary gland starts during late embryogenesis. It is regulated by the signals emanating both from the epithelium and the mesenchyme, yet the molecular mechanisms regulating this process remain poorly understood. We have previously developed a unique whole organ culture technique for embryonic mammary glands, which provides a powerful tool to monitor and manipulate branching morphogenesis ex vivo. Nowadays, RNA sequencing and other transcriptional profiling techniques provide robust methods to identify components of gene regulatory networks driving branching morphogenesis. However, validation of the candidate genes still mainly depends on the use of the transgenic mouse models, especially in mammary gland studies. By comparing different serotypes of recombinant adeno-associated virus (rAAVs), we found out that rAAVs provide sufficient efficiency for gene transfer with different tissue preferences depending on the serotypes of the virus. AAV-2 and AAV-8 preferentially target epithelial and mesenchymal compartments, respectively, while AAV-9 infects both tissues. Here, we describe a protocol for AAV-mediated gene transfer in ex vivo cultured murine embryonic mammary gland facilitating gene function studies on mammary gland branching morphogenesis.

Parasitoids indicate major climate-induced shifts in arctic communities

Climatic impacts are especially pronounced in the Arctic, which as a region is warming twice as fast as the rest of the globe. Here, we investigate how mean climatic conditions and rates of climatic change impact parasitoid insect communities in 16 localities across the Arctic. We focus on parasitoids in a widespread habitat, Dryas heathlands, and describe parasitoid community composition in terms of larval host use (i.e., parasitoid use of herbivorous Lepidoptera vs. pollinating Diptera) and functional groups differing in their closeness of host associations (koinobionts vs. idiobionts). Of the latter, we expect idiobionts-as being less fine-tuned to host development-to be generally less tolerant to cold temperatures, since they are confined to attacking hosts pupating and overwintering in relatively exposed locations. To further test our findings, we assess whether similar climatic variables are associated with host abundances in a 22 year time series from Northeast Greenland. We find sites which have experienced a temperature rise in summer while retaining cold winters to be dominated by parasitoids of Lepidoptera, with the reverse being true for the parasitoids of Diptera. The rate of summer temperature rise is further associated with higher levels of herbivory, suggesting higher availability of lepidopteran hosts and changes in ecosystem functioning. We also detect a matching signal over time, as higher summer temperatures, coupled with cold early winter soils, are related to high herbivory by lepidopteran larvae, and to declines in the abundance of dipteran pollinators. Collectively, our results suggest that in parts of the warming Arctic, Dryas is being simultaneously exposed to increased herbivory and reduced pollination. Our findings point to potential drastic and rapid consequences of climate change on multitrophic-level community structure and on ecosystem functioning and highlight the value of collaborative, systematic sampling effort.

Top-down factors contribute to differences in insect herbivory between saplings and mature trees in boreal and tropical forests

Ontogenetic changes in herbivory are generally not consistent with ontogenetic changes in defensive traits of woody plants. This inconsistency suggests that other factors may affect ontogenetic trajectories in herbivory. We tested the hypothesis that top-down factors contribute to differences in foliar losses to insects between juvenile and mature trees in tropical and boreal forests. We used artificial caterpillars made of modelling clay to compare predation rates between saplings and mature trees of two common forest species, Siparuna guianensis in Brazil (tropical site) and Betula pubescens in Finland (boreal site). Leaf area losses to chewing insects in saplings were 2.5-fold higher than in mature trees in both species. Physical plant defences (measured as specific leaf area, SLA) did not differ between saplings and mature trees in the boreal forest, whereas in the tropical forest, SLA was greater in saplings than in mature trees. Attack rates on the model prey by birds were higher in the boreal forest, whereas attack rates by arthropod predators were higher in the tropical forest. Overall, predation rates on model prey were consistently higher on mature trees than on saplings at both sites, but in the boreal site, this pattern was primarily driven by birds, whereas in the tropical site, it was primarily driven by arthropod predators. We conclude that the effect of predation on herbivorous insects may considerably contribute to ontogenetic differences in herbivory, but the relative roles of different predatory groups and of top-down and bottom-up factors may vary between environments.

Buried in water, burdened by nature-Resilience carried the Iron Age people through Fimbulvinter

Levänluhta is a unique archaeological site with the remains of nearly a hundred Iron Age individuals found from a water burial in Ostrobothnia, Finland. The strongest climatic downturn of the Common Era, resembling the great Fimbulvinter in Norse mythology, hit these people during the 6th century AD. This study establishes chronological, dietary, and livelihood synthesis on this population based on stable carbon and nitrogen isotopic and radiocarbon analyses on human remains, supported by multidisciplinary evidence. Extraordinarily broad stable isotopic distribution is observed, indicating three subgroups with distinct dietary habits spanning four centuries. This emphasizes the versatile livelihoods practiced at this boundary of marine, freshwater, and terrestrial ecosystems. While the impact of the prolonged cold darkness of the 6th century was devastating for European communities relying on cultivation, the broad range of livelihoods provided resilience for the Levänluhta people to overcome the abrupt climatic decline.

Identification and characterisation of common glow-worm RNA viruses

The common glow-worms (Lampyris noctiluca) are best known for emission of green light by their larvae and sexually active adult females. However, both their DNA and RNA viruses remain unknown. Glow-worms are virologically interesting, as they are non-social and do not feed as adults, and hence their viral transmission may be limited. We identified viral sequences from 11 different virus taxa by the RNA-sequencing of two Finnish populations of adult glow-worms. The viruses represent nine different virus families and have negative, positive, or double-stranded RNA genomes. We also found a complete retroviral genome. Similar viral sequences were found from the sequencing data of common eastern firefly of North America, a species belonging to the same family (Lampyridae) as that of the common glow-worm. On average, an individual glow-worm had seven different RNA virus types and most of them appeared to establish a stable infection since they were found from glow-worms during two consecutive years. Here we present the characterization of load, prevalence, and interactions for each virus. Most of the glow-worm RNA viruses seem to be transmitted vertically, which may reflect the biology of glow-worms as non-social capital breeders, i.e., they invest stored resources in reproduction.

Lakes as nitrous oxide sources in the boreal landscape

Estimates of regional and global freshwater N2 O emissions have remained inaccurate due to scarce data and complexity of the multiple processes driving N2 O fluxes the focus predominantly being on summer time measurements from emission hot spots, agricultural streams. Here, we present four-season data of N2 O concentrations in the water columns of randomly selected boreal lakes covering a large variation in latitude, lake type, area, depth, water chemistry, and land use cover. Nitrate was the key driver for N2 O dynamics, explaining as much as 78% of the variation of the seasonal mean N2 O concentrations across all lakes. Nitrate concentrations varied among seasons being highest in winter and lowest in summer. Of the surface water samples, 71% were oversaturated with N2 O relative to the atmosphere. Largest oversaturation was measured in winter and lowest in summer stressing the importance to include full year N2 O measurements in annual emission estimates. Including winter data resulted in fourfold annual N2 O emission estimates compared to summer only measurements. Nutrient-rich calcareous and large humic lakes had the highest annual N2 O emissions. Our emission estimates for Finnish and boreal lakes are 0.6 and 29 Gg N2 O-N/year, respectively. The global warming potential of N2 O from lakes cannot be neglected in the boreal landscape, being 35% of that of diffusive CH4 emission in Finnish lakes.

Population fluctuations and spatial synchrony in an arboreal rodent

Climatic conditions, trophic links between species and dispersal may induce spatial synchrony in population fluctuations. Spatial synchrony increases the extinction risk of populations and, thus, it is important to understand how synchrony-inducing mechanisms affect populations already threatened by habitat loss and climate change. For many species, it is unclear how population fluctuations vary over time and space, and what factors potentially drive this variation. In this study, we focus on factors determining population fluctuations and spatial synchrony in the Siberian flying squirrel, Pteromys volans, using long-term monitoring data from 16 Finnish populations located 2–400 km apart. We found an indication of synchronous population dynamics on a large scale in flying squirrels. However, the synchrony was not found to be clearly related to distance between study sites because the populations seemed to be strongly affected by small-scale local factors. The regularity of population fluctuations varied over time. The fluctuations were linked to changes in winter precipitation, which has previously been linked to the reproductive success of flying squirrels. Food abundance (tree mast) and predator abundance were not related to population fluctuations in this study. We conclude that spatial synchrony was not unequivocally related to distance in flying squirrels, as has been observed in earlier studies for more abundant rodent species. Our study also emphasises the role of climate in population fluctuations and the synchrony of the species.

Random forest-based imputation outperforms other methods for imputing LC-MS metabolomics data: a comparative study

BACKGROUND

LC-MS technology makes it possible to measure the relative abundance of numerous molecular features of a sample in single analysis. However, especially non-targeted metabolite profiling approaches generate vast arrays of data that are prone to aberrations such as missing values. No matter the reason for the missing values in the data, coherent and complete data matrix is always a pre-requisite for accurate and reliable statistical analysis. Therefore, there is a need for proper imputation strategies that account for the missingness and reduce the bias in the statistical analysis.

RESULTS

Here we present our results after evaluating nine imputation methods in four different percentages of missing values of different origin. The performance of each imputation method was analyzed by Normalized Root Mean Squared Error (NRMSE). We demonstrated that random forest (RF) had the lowest NRMSE in the estimation of missing values for Missing at Random (MAR) and Missing Completely at Random (MCAR). In case of absent values due to Missing Not at Random (MNAR), the left truncated data was best imputed with minimum value imputation. We also tested the different imputation methods for datasets containing missing data of various origin, and RF was the most accurate method in all cases. The results were obtained by repeating the evaluation process 100 times with the use of metabolomics datasets where the missing values were introduced to represent absent data of different origin.

CONCLUSION

Type and rate of missingness affects the performance and suitability of imputation methods. RF-based imputation method performs best in most of the tested scenarios, including combinations of different types and rates of missingness. Therefore, we recommend using random forest-based imputation for imputing missing metabolomics data, and especially in situations where the types of missingness are not known in advance.

Polycyclic Aromatic Hydrocarbons Phenanthrene and Retene Modify the Action Potential via Multiple Ion Currents in Rainbow Trout Oncorhynchus mykiss Cardiac Myocytes

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous contaminants in aqueous environments. They affect cardiovascular development and function in fishes. The 3-ring PAH phenanthrene has recently been shown to impair cardiac excitation-contraction coupling by inhibiting Ca²⁺ and K⁺ currents in marine warm-water scombrid fishes. To see if similar events take place in a boreal freshwater fish, we studied whether the PAHs phenanthrene and retene (an alkylated phenanthrene) modify the action potential (AP) via effects on Na⁺ (I_Na ), Ca²⁺ (I_CaL ), or K⁺ (I_Kr , I_K1 ) currents in the ventricular myocytes of the rainbow trout (Oncorhynchus mykiss) heart. Electrophysiological characteristics of myocytes were measured using whole-cell patch clamp. Micromolar concentrations of phenanthrene and retene modified the shape of the ventricular AP, and retene profoundly shortened the AP at low micromolar concentrations. Both PAHs increased I_Na and reduced I_CaL and I_Kr , but retene was more potent. Neither of the PAHs had an effect on I_K1 . Our results show that phenanthrene and retene affect cardiac function in rainbow trout by a mechanism that involves multiple cardiac ion channels, and the final outcome of these changes (shortening of AP) is opposite to that observed in scombrid fishes (prolongation of AP). The results also show that retene and aryl hydrocarbon receptor (AhR) agonist have an additional mechanism of toxicity besides the previously known AhR-mediated, transcription-dependent one. Environ Toxicol Chem 2019;38:2145-2153. © 2019 SETAC.

Cohort profile: Finnish Health and Early Life Microbiota (HELMi) longitudinal birth cohort

PURPOSE

HELMi (Health and Early Life Microbiota) is a longitudinal, prospective general population birth cohort, set up to identify environmental, lifestyle and genetic factors that modify the intestinal microbiota development in the first years of life and their relation to child health and well-being.

PARTICIPANTS

The HELMi cohort consists of 1055 healthy term infants born in 2016-2018 mainly at the capital region of Finland and their parents. The intestinal microbiota development of the infants is characterised based on nine, strategically selected, faecal samples and connected to extensive online questionnaire-collected metadata at weekly to monthly intervals focusing on the diet, other exposures and family's lifestyle as well as the health and growth of the child. Motor and cognitive developmental screening takes place at 18 months. Infant's DNA sample, mother's breast milk sample and both parent's spot faecal samples have been collected.

FINDINGS TO DATE

The mean age of the mothers was 32.8 (SD 4.1) and fathers/coparents 34.8 (5.3) years at the time of enrolment. Seventeen percentage (n=180) of the infants were born by caesarean section. Just under half (49%) were firstborns; 50.7% were males. At 3 months of age, 86% of the babies were exclusively breastfed and 2% exclusively formula-fed.

FUTURE PLANS

The current follow-up from pregnancy to first 24 months will be completed in March 2020, totalling to over 10 000 biological samples and over 50 000 questionnaire entries. The results are expected to identify environmental and host factors that affect early gut microbiota development and health, and hence give indications of how to prevent or reverse microbiota perturbations in infancy. This prospective cohort will be followed up further to identify how the early microbiota relates to later health outcomes, especially weight gain, infections and allergic and other chronic diseases.

TRIAL REGISTRATION NUMBER

NCT03996304; Pre-results.

Organic animal farms increase farmland bird abundance in the Boreal region

Agriculture is a primary driver of biodiversity loss worldwide, and several expensive schemes have been designed to make modern farming landscapes more hospitable for wildlife. One such market-based mechanisms is the agri-environment-climate schemes (AES) in the European Union (EU). AES compensate farmers for reducing land-use intensity and maintaining or introducing biodiversity-rich habitats. Despite their high costs, impacts of AES vary by measure, region and taxonomic group considered, and have rarely been studied over large areas covering an entire country. Here we assess the country-wide impact of several AES measures on bird abundance using citizen science data on birds and detailed information on AES take up from across Finland. We report a positive impact of organic animal farming on abundance of all farmland associated birds. This effect was particularly strong for insectivorous species, species that are associated to farmyards and long-distance species. None of the other AES measures considered for study did show any relationship with bird abundance. Overall, these findings highlight the potential positive impact that some compensatory measures, such as organic animal farming, may have on wildlife. Traditional animal husbandry is based on grazing of animals and restriction on external inputs, similarly to what is stipulated under organic production contract. As such, traditional animal husbandry may represent an effective landscape management tool for restoring or maintaining threatened species and ecosystems in rural areas of the EU. Ultimately, the apparent lack of a measurable effect of the other AES considered here supports the current move towards evidence-based regional targeting of compensatory measures, so as to concentrate scarce resources to where they can yield the highest ecological benefits.

Aquaculture as a source of empirical evidence for coevolution between CRISPR-Cas and phage

So far, studies on the bacterial immune system CRISPR-Cas and its ecological and evolutionary effects have been largely limited to laboratory conditions. While providing crucial information on the constituents of CRISPR-Cas, such studies may overlook fundamental components that affect bacterial immunity in natural habitats. Translating laboratory-derived predictions to nature is not a trivial task, owing partly to the instability of natural communities and difficulties in repeated sampling. To this end, we review how aquaculture, the farming of fishes and other aquatic species, may provide suitable semi-natural laboratories for examining the role of CRISPR-Cas in phage/bacterium coevolution. Existing data from disease surveillance conducted in aquaculture, coupled with growing interest towards phage therapy, may have already resulted in large collections of bacterium and phage isolates. These data, combined with premeditated efforts, can provide empirical evidence on phage-bacterium dynamics such as the bacteriophage adherence to mucus hypothesis, phage life cycles and their relationship with CRISPR-Cas and other immune defences. Typing of CRISPR spacer content in pathogenic bacteria can also provide practical information on diversity and origin of isolates during outbreaks. In addition to providing information of CRISPR functionality and phage-bacterium dynamics, aquaculture systems can significantly impact perspectives on design of phage-based disease treatment at the current era of increasing antibiotic resistance. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.

Elimination of the flavodiiron electron sink facilitates long-term H2 photoproduction in green algae

BACKGROUND

The development of renewable and sustainable biofuels to cover the future energy demand is one of the most challenging issues of our time. Biohydrogen, produced by photosynthetic microorganisms, has the potential to become a green biofuel and energy carrier for the future sustainable world, since it provides energy without CO₂ emission. The recent development of two alternative protocols to induce hydrogen photoproduction in green algae enables the function of the O₂-sensitive [FeFe]-hydrogenases, located at the acceptor side of photosystem I, to produce H₂ for several days. These protocols prevent carbon fixation and redirect electrons toward H₂ production. In the present work, we employed these protocols to a knockout Chlamydomonas reinhardtii mutant lacking flavodiiron proteins (FDPs), thus removing another possible electron competitor with H₂ production.

RESULTS

The deletion of the FDP electron sink resulted in the enhancement of H₂ photoproduction relative to wild-type C. reinhardtii. Additionally, the lack of FDPs leads to a more effective obstruction of carbon fixation even under elongated light pulses.

CONCLUSIONS

We demonstrated that the rather simple adjustment of cultivation conditions together with genetic manipulation of alternative electron pathways of photosynthesis results in efficient re-routing of electrons toward H₂ photoproduction. Furthermore, the introduction of a short recovery phase by regular switching from H₂ photoproduction to biomass accumulation phase allows to maintain cell fitness and use photosynthetic cells as long-term H₂-producing biocatalysts.

Tricholoma matsutake may take more nitrogen in the organic form than other ectomycorrhizal fungi for its sporocarp development: the isotopic evidence

Tricholoma matsutake is an ectomycorrhizal (ECM) fungus capable of in vitro saprotrophic growth, but the sources of C and N used to generate sporocarps in vivo are not well understood. We examined natural abundance isotope data to investigate this phenomenon. For this purpose, C, N and their stable isotopes (13C, 15N) content of fungal sporocarps and their potential nutrient sources (i.e., foliage, litter, fine roots, wood, and soil) were investigated from two well-studied sites in Finland and Japan. Our results show that δ13C values of T. matsutake and other fungal groups are consistent with those of most studies, but a very high δ15N value (16.8‰ ± 2.3) is observed in T. matsutake. Such isotopic pattern of fungal δ15N suggests that matsutake has a greater proteolytic potential to digest chemically complex 15N-enriched organic matter and hydrophobic hyphae. This assumption is further supported by a significant and positive correlation between δ13Ccap-stipe and δ15Ncap-stipe exclusively in T. matsutake, which suggests common C and N sources (protein) possible for isotopically enriched cap. The 13C increase of caps relative to stipe presumably reflects greater contents of 13C-enriched protein than 13C-depleted chitin. We conclude that T. matsutake is a typical ECM fungus which obtains for its sporocarp development for both C and N from a common protein source (vs. photosynthetic carbon) present in soil organic matter.

Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb

Arbuscular mycorrhizal (AM) fungi form diverse communities and are known to influence above-ground community dynamics and biodiversity. However, the multiscale patterns and drivers of AM fungal composition and diversity are still poorly understood. We sequenced DNA markers from roots and root-associated soil from Plantago lanceolata plants collected across multiple spatial scales to allow comparison of AM fungal communities among neighbouring plants, plant subpopulations, nearby plant populations, and regions. We also measured soil nutrients, temperature, humidity, and community composition of neighbouring plants and nonAM root-associated fungi. AM fungal communities were already highly dissimilar among neighbouring plants (c. 30 cm apart), albeit with a high variation in the degree of similarity at this small spatial scale. AM fungal communities were increasingly, and more consistently, dissimilar at larger spatial scales. Spatial structure and environmental drivers explained a similar percentage of the variation, from 7% to 25%. A large fraction of the variation remained unexplained, which may be a result of unmeasured environmental variables, species interactions and stochastic processes. We conclude that AM fungal communities are highly variable among nearby plants. AM fungi may therefore play a major role in maintaining small-scale variation in community dynamics and biodiversity.

Skin and gut microbiomes of a wild mammal respond to different environmental cues

BACKGROUND

Animal skin and gut microbiomes are important components of host fitness. However, the processes that shape the microbiomes of wildlife are poorly understood, particularly with regard to exposure to environmental contaminants. We used 16S rRNA amplicon sequencing to quantify how exposure to radionuclides impacts the skin and gut microbiota of a small mammal, the bank vole Myodes glareolus, inhabiting areas within and outside the Chernobyl Exclusion Zone (CEZ), Ukraine.

RESULTS

Skin microbiomes of male bank voles were more diverse than females. However, the most pronounced differences in skin microbiomes occurred at a larger spatial scale, with higher alpha diversity in the skin microbiomes of bank voles from areas within the CEZ, whether contaminated by radionuclides or not, than in the skin microbiomes of animals from uncontaminated locations outside the CEZ, near Kyiv. Similarly, irrespective of the level of radionuclide contamination, skin microbiome communities (beta diversity) showed greater similarities within the CEZ, than to the areas near Kyiv. Hence, bank vole skin microbiome communities are structured more by geography than the level of soil radionuclides. This pattern presents a contrast with bank vole gut microbiota, where microbiomes could be strikingly similar among distant (~ 80 km of separation), uncontaminated locations, and where differences in microbiome community structure were associated with the level of radioactivity. We also found that the level of (dis)similarity between the skin and gut microbiome communities from the same individuals was contingent on the potential for exposure to radionuclides.

CONCLUSIONS

Bank vole skin and gut microbiomes have distinct responses to similar environmental cues and thus are structured at different spatial scales. Our study shows how exposure to environmental pollution can affect the relationship between a mammalian host's skin and gut microbial communities, potentially homogenising the microbiomes in habitats affected by pollution.

From microbial eukaryotes to metazoan vertebrates: Wide spectrum paleo-diversity in sedimentary ancient DNA over the last ~14,500 years

Most studies that utilize ancient DNA have focused on specific groups of organisms or even single species. Instead, the whole biodiversity of eukaryotes can be described using universal phylogenetic marker genes found within well-preserved sediment cores that cover the post-glacial period. Sedimentary ancient DNA samples from Lake Lielais Svētiņu, eastern Latvia, at a core depth of 1,050 cm in ~150 year intervals were used to determine phylotaxonomy in domain Eukaryota. Phylotaxonomic affiliation of >1,200 eukaryotic phylotypes revealed high richness in all major eukaryotic groups-Alveolata, Stramenopiles, Cercozoa, Chlorophyta, Charophyta, Nucletmycea, and Holozoa. The share of organisms that originate from terrestrial ecosystems was about one third, of which the most abundant molecular operational taxonomic units were Fungi and tracheal/vascular plants, which demonstrates the usefulness of using lake sediments to reconstruct the terrestrial paleoecosystems that surround them. Phylotypes that originate from the lake ecosystem belonged to various planktonic organisms; phyto-, proto,- and macrozooplankton, and vascular aquatic plants. We observed greater richness of several planktonic organisms that can be associated with higher trophic status during the warm climate period between 4,000 and 8,000 years ago and an increase in eukaryotic richness possibly associated with moderate human impact over the last 2,000 years.

Lung function in adults born preterm

Very preterm birth, before the gestational age (GA) of 32 weeks, increases the risk of obstructed airflow in adulthood. We examined whether all preterm births (GA<37 weeks) are associated with poorer adult lung function and whether any associations are explained by maternal, early life/neonatal, or current life factors. Participants of the ESTER Preterm Birth Study, born between 1985 and 1989 (during the pre-surfactant era), at the age of 23 years participated in a clinical study in which they performed spirometry and provided detailed medical history. Of the participants, 139 were born early preterm (GA<34 weeks), 239 late preterm (GA: 34-<37 weeks), and 341 full-term (GA≥37 weeks). Preterm birth was associated with poorer lung function. Mean differences between individuals born early preterm versus full-term were -0.23 standard deviation (SD) (95% confidence interval (CI): -0.40, -0.05)) for forced vital capacity z-score (zFVC), -0.44 SD (95% CI -0.64, -0.25) for forced expiratory volume z-score (zFEV1), and -0.29 SD (95% CI -0.47, -0.10) for zFEV1/FVC. For late preterm, mean differences with full-term controls were -0.02 SD (95% CI -0.17, 0.13), -0.12 SD (95% CI -0.29, 0.04) and -0.13 SD (95% CI -0.29, 0.02) for zFVC, zFEV1, and zFEV1/FVC, respectively. Examination of finer GA subgroups suggested an inverse non-linear association between lung function and GA, with the greatest impact on zFEV1 for those born extremely preterm. The subgroup means were GA<28 weeks: -0.98 SD; 28-<32 weeks: -0.29 SD; 32-<34 weeks: -0.44 SD; 34-<36 weeks: -0.10 SD; 36-<37weeks: -0.11 SD; term-born controls (≥37weeks): 0.02 SD. Corresponding means for zFEV1/FVC were -1.79, -0.44, -0.47, -0.48, -0.29, and -0.02. Adjustment for maternal pregnancy conditions and socioeconomic and lifestyle factors had no major impact on the relationship. Preterm birth is associated with airflow limitation in adult life. The association appears to be attributable predominantly to those born most immature, with only a modest decrease among those born preterm at later gestational ages.

Borrelia afzelii alters reproductive success in a rodent host

The impact of a pathogen on the fitness and behaviour of its natural host depends upon the host-parasite relationship in a given set of environmental conditions. Here, we experimentally investigated the effects of Borrelia afzelii, one of the aetiological agents of Lyme disease in humans, on the fitness of its natural rodent host, the bank vole (Myodes glareolus), in semi-natural conditions with two contrasting host population densities. Our results show that B. afzelii can modify the reproductive success and spacing behaviour of its rodent host, whereas host survival was not affected. Infection impaired the breeding probability of large bank voles. Reproduction was hastened in infected females without alteration of the offspring size at birth. At low density, infected males produced fewer offspring, fertilized fewer females and had lower mobility than uninfected individuals. Meanwhile, the infection did not affect the proportion of offspring produced or the proportion of mating partner in female bank voles. Our study is the first to show that B. afzelii infection alters the reproductive success of the natural host. The effects observed could reflect the sickness behaviour due to the infection or they could be a consequence of a manipulation of the host behaviour by the bacteria.

Gamete-mediated mate choice: towards a more inclusive view of sexual selection

'Sperm competition'-where ejaculates from two or more males compete for fertilization-and 'cryptic female choice'-where females bias this contest to suit their reproductive interests-are now part of the everyday lexicon of sexual selection. Yet the physiological processes that underlie these post-ejaculatory episodes of sexual selection remain largely enigmatic. In this review, we focus on a range of post-ejaculatory cellular- and molecular-level processes, known to be fundamental for fertilization across most (if not all) sexually reproducing species, and point to their putative role in facilitating sexual selection at the level of the cells and gametes, called 'gamete-mediated mate choice' (GMMC). In this way, we collate accumulated evidence for GMMC across different mating systems, and emphasize the evolutionary significance of such non-random interactions among gametes. Our overall aim in this review is to build a more inclusive view of sexual selection by showing that mate choice often acts in more nuanced ways than has traditionally been assumed. We also aim to bridge the conceptual divide between proximal mechanisms of reproduction, and adaptive explanations for patterns of non-random sperm-egg interactions that are emerging across an increasingly diverse array of taxa.

Genetic drift precluded adaptation of an insect seed predator to a novel host plant in a long-term selection experiment

Host specialization is considered a primary driver of the enormous diversity of herbivorous insects. Trade-offs in host use are hypothesized to promote this specialization, but they have mostly been studied in generalist herbivores. We conducted a multi-generation selection experiment to examine the adaptation of the specialist seed-feeding bug, Lygaeus equestris, to three novel host plants (Helianthus annuus, Verbascum thapsus and Centaurea phrygia) and to test whether trade-offs promote specialization. During the selection experiment, body size of L. equestris increased more on the novel host plant H. annuus compared to the primary host plant, Vincetoxicum hirundinaria, but this effect was not observed in other fitness related traits. In addition to selection, genetic drift caused variation among the experimental herbivore populations in their ability to exploit the host plants. Microsatellite data indicated that the level of within-population genetic variation decreased and population differentiation increased more in the selection line feeding on H. annuus compared to V. hirundinaria. We found a negative correlation between genetic differentiation and heterozygosity at the end of the experiment, suggesting that differentiation was significantly affected by genetic drift. We did not find fitness trade-offs between L. equestris feeding on the four hosts. Thus, trade-offs do not seem to promote specialization in L. equestris. Our results suggest that this insect herbivore is not likely to adapt to a novel host species in a time-scale of 20 generations despite sufficient genetic variation and that genetic drift disrupted the response to selection.

Binding of EphrinA5 to RET receptor tyrosine kinase: An in vitro study

Eph/Ephrin signaling pathways are crucial in regulating a large variety of physiological processes during development, such as cell morphology, proliferation, migration and axonal guidance. EphrinA (efn-A) ligands, in particular, can be activated by EphA receptors at cell-cell interfaces and have been proposed to cause reverse signaling via RET receptor tyrosine kinase. Such association has been reported to mediate spinal motor axon navigation, but conservation of the interactive signaling pathway and the molecular mechanism of the interaction are unclear. Here, we found Danio rerio efn-A5b bound to Mus musculus EphA4 with high affinity, revealing structurally and functionally conserved EphA/efn-A signaling. Interestingly, we observed no interaction between efn-A5b and RET from zebrafish, unlike earlier cell-based assays. Their lack of association indicates how complex efn-A signaling is and suggests that there may be other molecules involved in efn-A5-induced RET signaling.

The influence of oxygen and methane on nitrogen fixation in subarctic Sphagnum mosses

Biological nitrogen fixation is an important source of bioavailable nitrogen in Sphagnum dominated peatlands. Sphagnum mosses harbor a diverse microbiome including nitrogen-fixing and methane (CH4) oxidizing bacteria. The inhibitory effect of oxygen on microbial nitrogen fixation is documented for many bacteria. However, the role of nitrogen-fixing methanotrophs in nitrogen supply to Sphagnum peat mosses is not well explored. Here, we investigated the role of both oxygen and methane on nitrogen fixation in subarctic Sphagnum peat mosses. Five species of Sphagnum mosses were sampled from two mesotrophic and three oligotrophic sites within the Lakkasuo peatland in Orivesi, central Finland. Mosses were incubated under either ambient or low oxygen conditions in the presence or absence of methane. Stable isotope activity assays revealed considerable nitrogen-fixing and methane-assimilating rates at all sites (1.4 ± 0.2 µmol 15N-N2 g-1 DW day-1 and 12.0 ± 1.1 µmol 13C-CH4 g-1 DW day-1, respectively). Addition of methane did not stimulate incorporation of 15N-nitrogen into biomass, whereas oxygen depletion increased the activity of the nitrogen-fixing community. Analysis of the 16S rRNA genes at the bacterial community level showed a very diverse microbiome that was dominated by Alphaproteobacteria in all sites. Bona fide methane-oxidizing taxa were not very abundant (relative abundance less than 0.1%). Based on our results we conclude that methanotrophs did not contribute significantly to nitrogen fixation in the investigated peatlands.

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin

Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD) simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM) to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins.

Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1

Bacteria of the genus Pectobacterium are economically important plant pathogens that cause soft rot disease on a wide variety of plant species. Here, we report the genome sequence of Pectobacterium carotovorum strain SCC1, a Finnish soft rot model strain isolated from a diseased potato tuber in the early 1980's. The genome of strain SCC1 consists of one circular chromosome of 4,974,798 bp and one circular plasmid of 5524 bp. In total 4451 genes were predicted, of which 4349 are protein coding and 102 are RNA genes.

Will the Oxygen-Phosphorus Paradigm Persist? - Expert Views of the Future of Management and Restoration of Eutrophic Lakes

In the age of climate change, the demand and lack of pure water challenges many communities. Substantial amount of effort is put in every year to manage and restore degraded lakes while the long-term effects of those efforts are only poorly known or monitored. Oxygenation, or aeration, is used extensively for the restoration of eutrophic lakes, although many studies question whether this process improves the status of the lakes in the long-term. The desired effect of oxygenation is based on paradigmatic theories that, in the light of recent literature, might not be adequate when long-term improvements are sought. This article canvasses expert views on the feasibility of the 'oxygen-phosphorus paradigm' as well as the future of the management and restoration of eutrophic lakes, based on an international, two-rounded, expert panel survey (Delphi study), employing 200 freshwater experts from 33 nationalities, contacted at three conferences on the topic. The conclusion is that the oxygen-phosphorus paradigm seems to be rather persistent. The experts considered oxygenation to be a valid short-term lake restoration method, but not without harmful side-effects. In addition, experts' low level of trust in the adequacy of the scientific knowledge on the effects of restorations and in the use of the scientific knowledge as a basis of choice of restoration methods, could be signs of a paradigm shift towards an outlook emphasizing more effective catchment management over short-term restorations. The expert panel also anticipated that reducing external nutrient loads from both point and diffuse sources will succeed in the future.

De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

BACKGROUND

Propionibacterium freudenreichii is an industrially important bacterium granted the Generally Recognized as Safe (the GRAS) status, due to its long safe use in food bioprocesses. Despite the recognized role in the food industry and in the production of vitamin B12, as well as its documented health-promoting potential, P. freudenreichii remained poorly characterised at the genomic level. At present, only three complete genome sequences are available for the species.

RESULTS

We used the PacBio RS II sequencing platform to generate complete genomes of 20 P. freudenreichii strains and compared them in detail. Comparative analyses revealed both sequence conservation and genome organisational diversity among the strains. Assembly from long reads resulted in the discovery of additional circular elements: two putative conjugative plasmids and three active, lysogenic bacteriophages. It also permitted characterisation of the CRISPR-Cas systems. The use of the PacBio sequencing platform allowed identification of DNA modifications, which in turn allowed characterisation of the restriction-modification systems together with their recognition motifs. The observed genomic differences suggested strain variation in surface piliation and specific mucus binding, which were validated by experimental studies. The phenotypic characterisation displayed large diversity between the strains in ability to utilise a range of carbohydrates, to grow at unfavourable conditions and to form a biofilm.

CONCLUSION

The complete genome sequencing allowed detailed characterisation of the industrially important species, P. freudenreichii by facilitating the discovery of previously unknown features. The results presented here lay a solid foundation for future genetic and functional genomic investigations of this actinobacterial species.

Indoor microbiota in severely moisture damaged homes and the impact of interventions

BACKGROUND

The limited understanding of microbial characteristics in moisture-damaged buildings impedes efforts to clarify which adverse health effects in the occupants are associated with the damage and to develop effective building intervention strategies. The objectives of this current study were (i) to characterize fungal and bacterial microbiota in house dust of severely moisture-damaged residences, (ii) to identify microbial taxa associated with moisture damage renovations, and (iii) to test whether the associations between the identified taxa and moisture damage are replicable in another cohort of homes. We applied bacterial 16S rRNA gene and fungal ITS amplicon sequencing complemented with quantitative PCR and chemical-analytical approaches to samples of house dust, and also performed traditional cultivation of bacteria and fungi from building material samples.

RESULTS

Active microbial growth on building materials had significant though small influence on the house dust bacterial and fungal communities. Moisture damage interventions-including actual renovation of damaged homes and cases where families moved to another home-had only a subtle effect on bacterial community structure, seen as shifts in abundance weighted bacterial profiles after intervention. While bacterial and fungal species richness were reduced in homes that were renovated, they were not reduced for families that moved houses. Using different discriminant analysis tools, we were able identify taxa that were significantly reduced in relative abundance during renovation of moisture damage. For bacteria, the majority of candidates belonged to different families within the Actinomycetales order. Results for fungi were overall less consistent. A replication study in approximately 400 homes highlighted some of the identified taxa, confirming associations with observations of moisture damage and mold.

CONCLUSIONS

The present study is one of the first studies to analyze changes in microbiota due to moisture damage interventions using high-throughput sequencing. Our results suggest that effects of moisture damage and moisture damage interventions may appear as changes in the abundance of individual, less common, and especially bacterial taxa, rather than in overall community structure.

Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes

Fomitopsis pinicola is a species of Polyporales frequently encountered in Nordic temperate and boreal forests. In nature, the fungus causes destructive brown rot in wood, colonizing tree trunks often occupied by other Basidiomycota species. We mimicked these species-species interactions by introducing F. pinicola to five white rot species, all common saprotrophs of Norway spruce. Hyphal interactions and mycelial growth in various combinations were recorded, while activities of lignocellulose-acting CAZymes and oxidoreductases were followed in co-cultures on two different carbon-source media. Of the species, Phlebia radiata and Trichaptum abietinum were the strongest producers of lignin-modifying oxidoreductases (laccase, manganese peroxidase) when evaluated alone, as well as in co-cultures, on the two different growth media (low-nitrogen liquid medium containing ground coniferous wood, and malt extract broth). F. pinicola was an outstanding producer of oxalic acid (up to 61 mM), whereas presence of P. radiata prevented acidification of the growth environment in the liquid malt-extract cultures. When enzyme profiles of the species combinations were clustered, time-dependent changes were observed on wood-supplemented medium during the eight weeks of growth. End-point acidity and production of mycelium, oxalic acid and oxidoreductase activities, in turn clustered the fungal combinations into three distinct functional groups, determined by the presence of F. pinicola and P. radiata, by principal component analysis. Our findings indicate that combinations of wood-decay fungi have dramatic dynamic effects on the production of lignocellulose-active enzymes, which may lead to divergent degradative processes of dead wood and forest litter.

Variability in the production of tannins and other polyphenols in cell cultures of 12 Nordic plant species

The polyphenol profiles of 18 cell cultures from 12 plant species were screened. The detected polyphenol fingerprints were diverse and differed from polyphenol profiles typically found in corresponding plant species. Cell cultures originating from 12 different plant species growing or grown in the Nordic countries were screened for their ability to synthesize polyphenols to assess their suitability for future studies and applications. The focus was on plant families Rosaceae and Ericaceae. On average, the Rosaceae cultures were the most efficient to produce hydrolysable tannins and the Ericaceae cultures were the most efficient to produce proanthocyanidins. This is in line with the general trend of polyphenols found in Rosaceae and Ericaceae leaves and fruits, even though several individual cell cultures differed from natural plants in their polyphenolic composition. Overall, several of the studied cell cultures exhibited capability in producing a large variety of polyphenols, including tannins with a high molecular weight, thus also showing promise for further studies concerning, for example, the accumulation of specific polyphenols or biosynthesis of polyphenols in the cell cultures.

Reliability of temperature signal in various climate indicators from northern Europe

We collected relevant observational and measured annual-resolution time series dealing with climate in northern Europe, focusing in Finland. We analysed these series for the reliability of their temperature signal at annual and seasonal resolutions. Importantly, we analysed all of the indicators within the same statistical framework, which allows for their meaningful comparison. In this framework, we employed a cross-validation procedure designed to reduce the adverse effects of estimation bias that may inflate the reliability of various temperature indicators, especially when several indicators are used in a multiple regression model. In our data sets, timing of phenological observations and ice break-up were connected with spring, tree ring characteristics (width, density, carbon isotopic composition) with summer and ice formation with autumn temperatures. Baltic Sea ice extent and the duration of ice cover in different watercourses were good indicators of winter temperatures. Using combinations of various temperature indicator series resulted in reliable temperature signals for each of the four seasons, as well as a reliable annual temperature signal. The results hence demonstrated that we can obtain reliable temperature information over different seasons, using a careful selection of indicators, combining the results with regression analysis, and by determining the reliability of the obtained indicator.

Inheritance of brewing-relevant phenotypes in constructed Saccharomyces cerevisiae × Saccharomyces eubayanus hybrids

BACKGROUND

Interspecific hybridization has proven to be a potentially valuable technique for generating de novo lager yeast strains that possess diverse and improved traits compared to their parent strains. To further enhance the value of hybridization for strain development, it would be desirable to combine phenotypic traits from more than two parent strains, as well as remove unwanted traits from hybrids. One such trait, that has limited the industrial use of de novo lager yeast hybrids, is their inherent tendency to produce phenolic off-flavours; an undesirable trait inherited from the Saccharomyces eubayanus parent. Trait removal and the addition of traits from a third strain could be achieved through sporulation and meiotic recombination or further mating. However, interspecies hybrids tend to be sterile, which impedes this opportunity.

RESULTS

Here we generated a set of five hybrids from three different parent strains, two of which contained DNA from all three parent strains. These hybrids were constructed with fertile allotetraploid intermediates, which were capable of efficient sporulation. We used these eight brewing strains to examine two brewing-relevant phenotypes: stress tolerance and phenolic off-flavour formation. Lipidomics and multivariate analysis revealed links between several lipid species and the ability to ferment in low temperatures and high ethanol concentrations. Unsaturated fatty acids, such as oleic acid, and ergosterol were shown to positively influence growth at high ethanol concentrations. The ability to produce phenolic off-flavours was also successfully removed from one of the hybrids, Hybrid T2, through meiotic segregation. The potential application of these strains in industrial fermentations was demonstrated in wort fermentations, which revealed that the meiotic segregant Hybrid T2 not only didn't produce any phenolic off-flavours, but also reached the highest ethanol concentration and consumed the most maltotriose.

CONCLUSIONS

Our study demonstrates the possibility of constructing complex yeast hybrids that possess traits that are relevant to industrial lager beer fermentation and that are derived from several parent strains. Yeast lipid composition was also shown to have a central role in determining ethanol and cold tolerance in brewing strains.

Two Birch Species Demonstrate Opposite Latitudinal Patterns in Infestation by Gall-Making Mites in Northern Europe

Latitudinal patterns in herbivory, i.e. variations in plant losses to animals with latitude, are generally explained by temperature gradients. However, earlier studies suggest that geographical variation in abundance and diversity of gall-makers may be driven by precipitation rather than by temperature. To test the above hypothesis, we examined communities of eriophyoid mites (Acari: Eriophyoidea) on leaves of Betula pendula and B. pubescens in boreal forests in Northern Europe. We sampled ten sites for each of five latitudinal gradients from 2008-2011, counted galls of six morphological types and identified mites extracted from these galls. DNA analysis revealed cryptic species within two of six morphologically defined mite species, and these cryptic species induced different types of galls. When data from all types of galls and from two birch species were pooled, the percentage of galled leaves did not change with latitude. However, we discovered pronounced variation in latitudinal changes between birch species. Infestation by eriophyoid mites increased towards the north in B. pendula and decreased in B. pubescens, while diversity of galls decreased towards the north in B. pendula and did not change in B. pubescens. The percentage of galled leaves did not differ among geographical gradients and study years, but was 20% lower in late summer relative to early summer, indicating premature abscission of infested leaves. Our data suggest that precipitation has little effect on abundance and diversity of eriophyoid mites, and that climate warming may impose opposite effects on infestation of two birch species by galling mites, favouring B. pendula near the northern tree limit.