Explore the vast range of titles available.

This essay addresses the long-term effectiveness of urban climate change adaptation approaches, based, inter alia, on work in the C40 city network. We argue that in most cities, the dominant framing of climate risk management almost exclusively focuses on short-term incrementalities and preventive solutions directly tackling hazards, vulnerability, and exposure. This approach has serious flaws, leading to missed opportunities for longer-term sustainable urban development. Until very recently, climate science usually provided only a marginal input to long-term urban planning and design. We argue that any analysis of urban climate risk management and the associated climate services should be broadened beyond solely climate focusing on impacts. In this context, the development of positive urban visions is a key gap for both research and practice. A change is required from negatively addressing risks to positively pursuing a positive vision of attractive, resilient, and sustainable cities. The emphasis on short-term incremental solutions should shift towards long-term transformation. This embodies a paradigm shift from “function follows system” to “system follows function”. For many cities, this also means a change in procedural practice from siloed top-down to integrated, participatory urban transformation. Our main argument in this paper is that simple, longer-term sustainable urban transformation would not only reduce climate risks but also enhance overall environmental quality, economic opportunities, and social wellbeing.

Arbuscular mycorrhizal fungi (AMF) are root-inhabiting fungi that form mutualistic symbioses with their host plants. AMF are made up of coenocytic networks of hyphae through which nuclei and organelles can freely migrate. In this study, we investigated the possibility of a genetic bottleneck and segregation of allelic variation at sporulation for a low-copy Polymerase1-like gene, PLS. Specifically, our objectives were (1) to estimate what allelic diversity is passed on to a single spore (2) to determine whether this diversity is less than the total amount of variation found in all spores (3) to investigate whether there is any differential segregation of allelic variation. We inoculated three tomato plants with a single spore of Glomus etunicatum each and after six months sampled between two and three daughter spores per tomato plant. Pyrosequencing PLS amplicons in eight spores revealed high levels of allelic diversity; between 43 and 152 alleles per spore. We corroborated the spore pyrosequencing results with Sanger- and pyrosequenced allele distributions from the original parent isolate. Both sequencing methods retrieved the most abundant alleles from the offspring spore allele distributions. Our results indicate that individual spores contain only a subset of the total allelic variation from the pooled spores and parent isolate. Patterns of allele diversity between spores suggest the possibility for segregation of PLS alleles among spores. We conclude that a genetic bottleneck could potentially occur during sporulation in AMF, with resulting differences in genetic variation among sister spores. We suggest that the effects of this bottleneck may be countered by anastomosis (hyphal fusion) between related hyphae.

Background Microbiome samples often represent mixtures of communities, where each community is composed of overlapping assemblages of species. Such mixtures are complex, the number of species is huge and abundance information for many species is often sparse. Classical methods have a limited value for identifying complex features within such data. Results Here, we describe a novel hierarchical model for Bayesian inference of microbial communities (BioMiCo). The model takes abundance data derived from environmental DNA, and models the composition of each sample by a two-level hierarchy of mixture distributions constrained by Dirichlet priors. BioMiCo is supervised, using known features for samples and appropriate prior constraints to overcome the challenges posed by many variables, sparse data, and large numbers of rare species. The model is trained on a portion of the data, where it learns how assemblages of species are mixed to form communities and how assemblages are related to the known features of each sample. Training yields a model that can predict the features of new samples. We used BioMiCo to build models for three serially sampled datasets and tested their predictive accuracy across different time points. The first model was trained to predict both body site (hand, mouth, and gut) and individual human host. It was able to reliably distinguish these features across different time points. The second was trained on vaginal microbiomes to predict both the Nugent score and individual human host. We found that women having normal and elevated Nugent scores had distinct microbiome structures that persisted over time, with additional structure within women having elevated scores. The third was trained for the purpose of assessing seasonal transitions in a coastal bacterial community. Application of this model to a high-resolution time series permitted us to track the rate and time of community succession and accurately predict known ecosystem-level events. Conclusion BioMiCo provides a framework for learning the structure of microbial communities and for making predictions based on microbial assemblages. By training on carefully chosen features (abiotic or biotic), BioMiCo can be used to understand and predict transitions between complex communities composed of hundreds of microbial species.

Overexploitation and subsequent collapse of major worldwide fisheries has made it clear that marine stocks are not inexhaustible. Unfortunately, the perception remains that marine fishes are resilient to large population reductions, as even a commercially 'collapsed' stock will still consist of millions of individuals. Coupled with this notion is the idea that fisheries can, therefore, have little effect on the genetic diversity of stocks. We used DNA from archived otoliths collected between 1924 and 1972 together with 2002 juvenile's tissue to estimate effective population size (Ne) in plaice (Pleuronectes platessa). Ne was estimated at 20 000 in the North Sea and 2000 in Iceland. These values are five orders of magnitude smaller than the estimated census size for the two locations. Populations examined between 1924 and 1960 were in Hardy-Weinberg equilibrium, whereas populations examined after approximately 1970 were not. Extensive testing was performed to rule out genotyping artefacts and Wahlund effects. The significant heterozygote deficiencies found from 1970 onward were attributed to inbreeding. The emergence of inbreeding between 1950 and 1970 coincides with the increase in fishing mortality after World War II. Although the biological mechanisms remain speculative, our demonstration of inbreeding signals the need for understanding the social and mating behaviour in commercially important fishes.

Madole & Harden argue that the Mendelian reshuffling of genes and genomes is analogous to randomised controlled trials. We are not convinced by their arguments. First, their recipe for meeting the demands on randomised experiments is inherently inconsistent. Second, disequilibrium across chromosomes conflicts with their assumption of statistical independence. Third, the genome-wide association study (GWAS) method has many pitfalls, including low repeatability.

Since its release in 2014, the Knowledge Portal for Spatial Adaptation has evolved into the central web portal for climate adaptation in the Netherlands, supporting regional and local adaptation efforts. This paper reflects on how co-production shaped the development of the portal and evaluates its use and the usability of the most frequently accessed tool, the ‘Climate Adaptation Atlas’. Analysis of evaluation reports and web-statistics revealed a substantial, diverse and regularly returning group of visitors to the portal. For example, municipalities use the atlas to understand how their municipality can be impacted by climate change to support spatial planning. Using the usability criteria of fit, interplay and interaction, the analysis showed that the atlas fits the needs of creating awareness and integrating climate information with other spatial information. However, the interplay of new climate information with other currently used information varies amongst municipalities. Interactions between scientists and users were found at different stages involving different actors. Based on the development and use of the portal, seven lessons have been derived emphasising the importance of a continuous co-production process with users; a modular setup to acknowledge the diversity in approaches; encouraging users by providing showcases of adaptation initiatives and enabling exchange of information amongst users; the need for political support; the ability and will to act even in case of uncertainty; flexibility in project design to incorporate changes in user needs and the beneficial role of boundary organisations in improving mutual understanding. Through this paper, contributions to the understanding of how adaptation web portals can be developed and improved are made.

We studied the population genetics of two antimicrobial peptide (AMP) loci, called Mytilin B and Mytilus galloprovincialis defensin 2 (MGD2), in the secondary contact mosaic hybrid zone between Mytilus edulis and M. galloprovincialis. The isolation period between the two species was estimated to be ~1 million years (range, 0.5 million to 2 million years) long. During this period, coevolution between microbes and the immune system has likely occurred. The secondary contact, which would date back to ~25,000 (0-200,000) years, recently allowed these coadaptations to be rearranged through hybridization. Distinctive polymorphisms were uncovered in coding sequences of the two AMP loci such as insertion/deletion of codons or bisubstituted codons. Very low levels of differentiation were observed between populations of the two species at both loci, while other nuclear loci often showed marked structure among the same samples. The absence of population differentiation proved to be the consequence of secondary introgression of highly divergent alleles. While only a few recombinants were observed at the Mytilin B locus, the MGD2 locus showed a high intragenic recombination rate, which increased in the exon coding for the mature peptide. In addition, standard neutrality tests revealed significant deviations from the mutation-drift equilibrium at both loci. These results suggest that either balancing or directional selection is likely to play a role in the evolution of the two AMPs and introgression would be adaptive. However, evidence accumulated at the Mytilin B locus allows neither for identification of the direction of selection nor for any conclusions on whether selection acted directly on the antimicrobial peptide itself. At the MGD2 locus, a spatial variation of polymorphism patterns along the sequence suggests that selection was direct, although the precise nature of the selection (directional vs. balancing) remains unclear. This study concurs with previous reports of an effect of slight selection on AMP genes evolution in other invertebrates, although selection does not necessarily act on the mature peptides.

Arbuscular mycorrhizal fungi (AMF) are root-inhabiting fungi that form mutualistic symbioses with their host plants. AMF are made up of coenocytic networks of hyphae through which nuclei and organelles can freely migrate. In this study, we investigated the possibility of a genetic bottleneck and segregation of allelic variation at sporulation for a low-copy Polymerase1-like gene, PLS. Specifically, our objectives were (1) to estimate what allelic diversity is passed on to a single spore (2) to determine whether this diversity is less than the total amount of variation found in all spores (3) to investigate whether there is any differential segregation of allelic variation. We inoculated three tomato plants with a single spore of Glomus etunicatum each and after six months sampled between two and three daughter spores per tomato plant. Pyrosequencing PLS amplicons in eight spores revealed high levels of allelic diversity; between 43 and 152 alleles per spore. We corroborated the spore pyrosequencing results with Sanger- and pyrosequenced allele distributions from the original parent isolate. Both sequencing methods retrieved the most abundant alleles from the offspring spore allele distributions. Our results indicate that individual spores contain only a subset of the total allelic variation from the pooled spores and parent isolate. Patterns of allele diversity between spores suggest the possibility for segregation of PLS alleles among spores. We conclude that a genetic bottleneck could potentially occur during sporulation in AMF, with resulting differences in genetic variation among sister spores. We suggest that the effects of this bottleneck may be countered by anastomosis (hyphal fusion) between related hyphae.

The disruption in blood supply due to myocardial infarction is a critical determinant for infarct size and subsequent deterioration in function. The identification of factors that enhance cardiac repair by the restoration of the vascular network is, therefore, of great significance. Here, we show that the transcription factor Zinc finger E-box-binding homeobox 2 (ZEB2) is increased in stressed cardiomyocytes and induces a cardioprotective cross-talk between cardiomyocytes and endothelial cells to enhance angiogenesis after ischemia. Single-cell sequencing indicates ZEB2 to be enriched in injured cardiomyocytes. Cardiomyocyte-specific deletion of ZEB2 results in impaired cardiac contractility and infarct healing post-myocardial infarction (post-MI), while cardiomyocyte-specific ZEB2 overexpression improves cardiomyocyte survival and cardiac function. We identified Thymosin β4 (TMSB4) and Prothymosin α (PTMA) as main paracrine factors released from cardiomyocytes to stimulate angiogenesis by enhancing endothelial cell migration, and whose regulation is validated in our in vivo models. Therapeutic delivery of ZEB2 to cardiomyocytes in the infarcted heart induces the expression of TMSB4 and PTMA, which enhances angiogenesis and prevents cardiac dysfunction. These findings reveal ZEB2 as a beneficial factor during ischemic injury, which may hold promise for the identification of new therapies. ZEB2 transcription factor is increased in a subset of cardiomyocytes during stress to induce cardioprotective effects after injury. Here the authors show that therapeutic delivery of ZEB2 prevents cardiac dysfunction after ischemic damage and promotes the activation of pro-angiogenic signals.