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Abstract Evidence on the effectiveness of climate change adaptation interventions in low- and middle-income countries has been rapidly growing in recent years, particularly in the agricultural and coastal sectors. Here we address the question of whether results are consistent across intervention types, and risk reduction versus development-related outcomes using a systematic review of 363 empirical observations published in the scientific literature. Generally, we found more evidence of risk reduction outcomes in the coastal sector than in the agricultural sector, and more evidence of development-related outcomes in the agricultural sector. Further, results indicate that nature-based solutions have the strongest positive effects for both the coastal and agricultural sectors. Social/behavioural interventions in the coastal sector show negative effects on development-related outcomes that will need to be further tested. Taken together, our results highlight the opportunity for development and climate adaptation practitioners to promote adaptation interventions with co-benefits beyond risk reduction, particularly in the case of nature-based solutions.

In geminiviruses belonging to the genus Begomovirus, coat protein (CP) expression depends on viral AL2 protein, which derepresses and activates the CP promoter through sequence elements that lie within the viral intergenic region (IR). However, AL2 does not exhibit sequence-specific DNA binding activity but is instead directed to responsive promoters through interactions with host factors, most likely transcriptional activators and/or repressors. In this study, we describe a repressive plant-specific transcription factor, Arabidopsis thaliana TCP24 (AtTCP24), that interacts with AL2 and recognizes a class II TCP binding site in the CP promoter (GTGGTCCC). This motif corresponds to the previously identified conserved late element (CLE). We also report that histone 3 lysine 27 trimethylation (H3K27me3), an epigenetic mark associated with facultative repression, is enriched over the viral IR. H3K27me3 is deposited by Polycomb Repressive Complex 2 (PRC2), a critical regulator of gene expression and development in plants and animals. Remarkably, mutation of the TCP24 binding site (the CLE) in tomato golden mosaic virus (TGMV) and cabbage leaf curl virus (CaLCuV) CP promoters greatly diminishes H3K27me3 levels on viral chromatin and causes a dramatic delay and attenuation of disease symptoms in infected Arabidopsis and Nicotiana benthamiana plants. Symptom remission is accompanied by decreased viral DNA levels in systemically infected tissue. Nevertheless, in transient replication assays CLE mutation delays but does not limit the accumulation of viral double-stranded DNA, although single-stranded DNA and CP mRNA levels are decreased. These findings suggest that TCP24 binding to the CLE leads to CP promoter repression and H3K27me3 deposition, while TCP24-AL2 interaction may recruit AL2 to derepress and activate the promoter. Thus, a repressive host transcription factor may be repurposed to target a viral factor essential for promoter activity. The presence of the CLE in many begomoviruses suggests a common scheme for late promoter regulation.

RNA viruses and viroids exist and evolve as quasispecies due to error-prone replication. Quasispecies consist of a few dominant master sequences alongside numerous variants that contribute to genetic diversity. Upon environmental changes, certain variants within quasispecies have the potential to become the dominant sequences, leading to the emergence of novel infectious strains. However, the emergence of new infectious variants remains unpredictable. Using mutant pools prepared by saturation mutagenesis of selected stem and loop regions, our study of potato spindle tuber viroid (PSTVd) demonstrates that mutants forming local three-dimensional (3D) structures similar to the wild type (WT) are more likely to accumulate in PSTVd quasispecies. The selection mechanisms underlying this biased accumulation are likely associated with cell-to-cell movement and long-distance trafficking. Moreover, certain trafficking-defective PSTVd mutants can be spread by functional sister genomes in the quasispecies. Our study reveals that the RNA 3D structure of stems and loops constrains the evolution of viroid quasispecies. Mutants with a structure similar to WT have a higher likelihood of being maintained within the quasispecies and can potentially give rise to novel infectious variants. These findings emphasize the potential of targeting RNA 3D structure as a more robust approach to defend against viroid infections.

While the prioritisation of scarce resources for climate adaptation is becoming a priority for low and middle income countries, the climate service literature addressing adaptation prioritisation decisions is scarce. This paper contributes to filling this gap by presenting a co-creation process carried out in the Maldives among representatives of government, civil society and researchers. Together, we identified the need to improve a ranking method currently used by the Maldivian government to prioritise islands for investments in erosion prevention. As a solution we developed a layered index. The first layer of this index captures the objective dimension of the problem through an erosion hazard subindex, using the three variables wave energy, reef health and reef flat minimum width. The second layer captures the normative dimension through a multi-criteria analysis using the erosion hazard subindex as one criterion next to other stakeholder selected criteria such as critical infrastructure, economic activity, per capita income and the potential to house additional people that resettle from riskier places as sea-level rise progresses. Results of this new ranking method show that socioeconomic criteria were considered more important by the stakeholders than the biophysical criterion of erosion hazard. Among the top-ranked islands are many regional centres but also less populous islands that have a large potential to house additional people. Lessons learnt from the co-creation process highlight the importance of assembling interdisciplinarity teams, fostering mutual learning among project participants, and designing research projects that do not prescribe upfront the exact problems to be addressed and methods to be applied.

Land reclamation in the Maldives is widespread. Current land reclamation practices, however, lack a systematic approach to anticipate sea-level rise and do not account for local flood risk differences to inform location and design choices. To address these limitations, this paper applies two decision-support tools: a hazard threshold analysis, and a cost-benefit analysis. Both tools produce site-specific estimates of land elevations or flood defence heights but do so for different goals. The hazard threshold analysis identifies hazard-based solutions that meet an acceptable flood probability for an intended lifespan without follow-up actions by reliability optimisation. The cost-benefit analysis identifies risk-based solutions using dynamic programming. We apply both tools to two land reclamation sites, a newly reclaimed airport island and a land extension of an inhabited island, in the Maldives. We find that total hazard-based heights for long-term planning horizons are highly uncertain, with local height differences of up to 1.9 m across sea-level rise scenarios by 2100. Risk-based Island elevations, in contrast, differ much less across scenarios, offering a practical advantage for decision-making. However, land reclamation choices on location, land elevation and investment in flood protection are not only driven by hazard-related aspects, such as reef characteristics, swell exposure, and sea-level rise, but also by estimates of exposed assets, reclamation, and flood protection costs. Taken together, the two decision-support tools are helpful for improving adaptation decisions and are also applicable in other small island regions.

The bacterium Vibrio cholerae has caused seven recorded cholera pandemics. The factors responsible for the decline of 6th pandemic classical biotype strains are not well understood. Here, Kostiuk et al. propose that classical strains underwent sequential mutations in type-six secretion system genes that disadvantaged them when confronted with 7th pandemic El Tor biotype strains.

Tobacco mosaic virus movement protein (TMV MP) is essential for virus spread between cells. To accomplish its task, TMV MP binds viral RNA, interacts with components of the cytoskeleton, and increases the size exclusion limit (SEL) of plasmodesmata. Plasmodesmata are gated intercellular channels that allow passage of small molecules and macromolecules, including RNA and protein, between plant cells. Moreover, plasmodesmata are diverse and those connecting different cell types appear to have unique mechanisms to regulate macromolecular trafficking, which likely contributes to the establishment of distinct cell boundaries. Consequently, TMV MP might be competent to mediate RNA transport through some but not all plasmodesmal gates. Due to a lack of viral mutants defective for movement between specific cell types, the ability of TMV MP in this regard is incompletely understood. In contrast, a number of trafficking impaired Potato spindle tuber viroid (PSTVd) mutants have been identified. PSTVd is a systemically infectious non-coding RNA that nevertheless can perform all functions required for replication as well as cell-to-cell and systemic spread. Previous studies have shown that PSTVd employs different structure and sequence elements to move between diverse cell types in host plants, and mutants defective for transport between specific cell types have been identified. Therefore, PSTVd may serve as a tool to analyze the functions of MPs of viral and cellular origin. To probe the RNA transport activity of TMV MP, transgenic plants expressing the protein were inoculated with PSTVd mutants. Remarkably, TMV MP complemented a PSTVd mutant defective for mesophyll entry but could not support two mutants impaired for phloem entry, suggesting it fails to productively interface with plasmodesmata at the phloem boundary and that additional viral and host factors may be required. Consistent with this idea, TMV co-infection, but not the combination of MP and coat protein (CP) expression, was able to complement one of the phloem entry mutants. These observations suggest that phloem loading is a critical impediment to establishing systemic infection that could involve the entire ensemble of TMV proteins. They also demonstrate a novel strategy for analysis of MPs.

The use of systems thinking (ST) to handle complexity and wicked policy problems is gaining traction in government and the Civil Service, but policy-makers and civil servants can encounter several challenges in practice. How best to support them in understanding and applying ST in policy-making is not well understood. This study aims to explore civil servant and expert perspectives on the drivers and values of ST and the challenges, successes and solutions for its adoption in policy-making. We conducted semi-structured interviews with 31 civil servants across 17 UK government departments, agencies and public bodies, and 5 experts skilled in supporting ST use in policy-making. Via thematic analysis, we identified the values, challenges and successes interviewees experienced when implementing ST and their definitions of the term systems thinking. Civil servants were drawn into an ST approach by their academic training and exposure to it in their previous role(s), workshops, networking events and apprenticeships and through appreciating its values. Civil servants provided various interpretations of ST concepts and values with a strong emphasis on ‘complexity’ and ‘interrelationship’. Our analysis identified eight challenge themes for the implementation of ST in policy-making, including (i) ST language and interpretation, (ii) the policy landscape, (iii) government structure and operation, (iv) methodology and technical aspects, (v) capacity and expertise, (vi) conceptualisation, expectations and buy-in, (vii) stakeholders, engagement and collaboration and (viii) evaluation and evidence. Despite the high interest in ST among civil servants across different policy areas within the UK government and the Civil Service, implementation is challenging. Recommendations for implementation include ST language in policy, systems leadership, policy-specific capacity development and evaluation processes for collecting evidence of impacts.

RNA viruses and viroids exist and evolve as quasispecies due to error-prone replication. Quasispecies consist of a few dominant master sequences alongside numerous variants that contribute to genetic diversity. Upon environmental changes, certain variants within quasispecies have the potential to become the dominant sequences, leading to the emergence of novel infectious strains. However, the emergence of new infectious variants remains unpredictable. Using mutant pools prepared by saturation mutagenesis of selected stem and loop regions, our study of potato spindle tuber viroid (PSTVd) demonstrates that mutants forming local three-dimensional (3D) structures similar to the wild type (WT) are more likely to accumulate in PSTVd quasispecies. The selection mechanisms underlying this biased accumulation are likely associated with cell-to-cell movement and long-distance trafficking. Moreover, certain trafficking-defective PSTVd mutants can be spread by functional sister genomes in the quasispecies. Our study reveals that the RNA 3D structure of stems and loops constrains the evolution of viroid quasispecies. Mutants with a structure similar to WT have a higher likelihood of being maintained within the quasispecies and can potentially give rise to novel infectious variants. These findings emphasize the potential of targeting RNA 3D structure as a more robust approach to defend against viroid infections. Author summary: Our study investigates the world of RNA viruses and viroids, which are constantly evolving due to error-prone replication. These pathogens exist as quasispecies, featuring dominant master sequences and numerous variants. Understanding how new infectious strains emerge from this genetic diversity remains challenging. Focusing on potato spindle tuber viroid (PSTVd), targeted mutagenesis of specific stem and loop regions was performed to generate mutant pools. Plants were infected with mutant pools, and progeny were analyzed following cell-to-cell movement and long-distance trafficking. Our results reveal that mutants with 3D structures similar to the wild type viroid are more likely to accumulate within quasispecies. This accumulation is associated with the ability to move between cells and travel long distances within the plant host. Even mutants with impaired mobility can be spread by functional counterparts within the quasispecies. This study highlights the role of RNA 3D structures in shaping viroid quasispecies evolution. Mutants resembling the wild type viroid have a greater chance of persisting within quasispecies and may give rise to new infectious variants. These findings offer insight into viroid quasispecies dynamics and identify RNA 3D structure as a promising avenue for resistance strategies. [ABSTRACT FROM AUTHOR]

Sea-level rise (SLR) confronts coastal societies and stakeholders with increasing hazards and coastal risks with large uncertainties associated to these changes. Adaptation to SLR requires societal and policy decision-making to consider these changing risks, which are in turn defined by socio-economic development objectives and the local societal context. Here, we review some of the key challenges facing governments, stakeholders and scientists in adapting to SLR, and key aspects of successful adaptation, by exploring different approaches to SLR and coastal adaptation planning in three western European countries, the Netherlands, Germany and the United Kingdom. Several common challenges of SLR adaptation emerge across the different settings, including the inherent uncertainty regarding future conditions, the significant social and socio-economic consequences, the consideration and distribution of (residual) risk over communities, and the long legacy of present-day decisions that affect future risk and management options supporting future generations. These challenges are addressed differently in the three countries, e.g. in the governance level at which adaptation is initiated, although common elements also emerge. One common emerging element is adaptive pathways planning, which entails dynamic decision-making that breaks uncertain decisions into manageable elements or steps over time, while keeping options for the future. Another common element is the development of effective local science-policy interfaces, as engagement of local decision-makers and citizens is essential to manage conflicting interests. Lastly, we find that social and communication sciences have great potential to support effective science-policy interfaces, e.g. though identifying societal tipping points. Yet, in decisions on SLR adaptation, insights from these fields are rarely used to date. We conclude that supporting science-policy interactions for adaptation decision-making at relevant (inter)national to local scales through tailored multi-disciplinary scientific assessments is an important way forward for SLR adaptation in Europe.

Climate services are ideally co-developed by scientists and stakeholders working together to identify decisions and user needs. Yet, while climate services have been developed at regional to local scales, relatively little attention has been paid to the global scale. Global climate services involve decisions that rely on climate information from many locations in different world regions, and are increasingly salient. Increasing interconnections in the global financial system and supply chains expose private companies and financial institutions to climate risk in multiple locations in different world regions. Further, multilateral decisions on greenhouse gas emission reduction targets, disaster risk finance or international migration should make use of global scale climate risk assessments. In order to advance global climate service development, we present a typology of decisions relying on global (i.e., non-local) climate risk information. We illustrate each decision type through examples of current practice from the coastal domain drawn from the literature and stakeholder interviews. We identify 8 types of decisions making use of global climate information. At a top-level, we distinguish between “multilateral climate policy decisions,” and “portfolio decisions involving multiple locations.” Multilateral climate policy decisions regard either “mitigation targets” or “multilateral adaptation” decisions. Portfolio decisions regard either “choice of location” or “choice of financial asset” decisions. Choice of location decisions can be further distinguished as to whether they involve “direct climate risks,” “supply chain risks” or “financial network risks.” Our survey of examples shows that global climate service development is more advanced for portfolio decisions taken by companies with experience in climate risk assessment, i.e., (re-)insurers, whereas many multilateral climate policy decisions are at an earlier stage of decision-making. Our typology thus provides an entry-point for global climate service development by pointing to promising research directions for supporting global (non-local) decisions that account for climate risks.

Accurate calculation of mutation rates for viruses and viroids is necessary for evolutionary studies and to evaluate adaptation potential. However, estimation of in vivo mutation rates is complicated by selection, which leads to loss or proliferation of certain mutations. To minimize this concern, lethal mutations, including nonsense and non-synonymous mutations, have been used to determine mutation rates for several viruses and viroids, including Potato spindle tuber viroid (PSTVd). However, this approach has limitations, including focus on a relatively small number of genome sites and the possibility that mutations may not actually be lethal or may be maintained by wild type individuals. To avoid selection bias altogether, we sequenced minus-strand PSTVd dimers from concatemeric replication intermediates. The underlying rationale is that mutations found in only one of the monomers were likely generated de novo during RNA polymerase II (Pol II) transcription of the circular plus-strand RNA genome. This approach yielded an apparent Pol II error rate of ~1/1837 nucleotides per transcription cycle, and an estimated mutation rate of ~1/919 nucleotides for a single replication cycle. Remarkably, de novo mutations were nearly absent from the most conserved, replication-critical regions of the PSTVd genome, suggesting that sequence conservation is a consequence of both essential function and template optimization for greater Pol II fidelity. Such biased fidelity may constitute a novel strategy to ensure population success while allowing abundant sampling of sequence space in other genome regions. Comparison with variants in progeny populations derived from a cloned, wild type PSTVd master sequence revealed that most de novo mutations were lost through selection.

Geminiviruses are a significant group of emergent plant DNA viruses causing devastating diseases in food crops worldwide, including the Southern United States, Central America and the Caribbean. Crop failure due to geminivirus-related disease can be as high as 100%. Improved global transportation has enhanced the spread of geminiviruses and their vectors, supporting the emergence of new, more virulent recombinant strains. With limited coding capacity, geminiviruses encode multifunctional proteins, including the AC2/C2 gene that plays a central role in the viral replication-cycle through suppression of host defenses and transcriptional regulation of the late viral genes. The AC2/C2 proteins encoded by mono- and bipartite geminiviruses and the curtovirus C2 can be considered virulence factors, and are known to interact with both basal and inducible systems. This review highlights the role of AC2/C2 in affecting the jasmonic acid and salicylic acid (JA and SA) pathways, the ubiquitin/proteasome system (UPS), and RNA silencing pathways. In addition to suppressing host defenses, AC2/C2 play a critical role in regulating expression of the coat protein during the viral life cycle. It is important that the timing of CP expression is regulated to ensure that ssDNA is converted to dsDNA early during an infection and is sequestered late in the infection. How AC2 interacts with host transcription factors to regulate CP expression is discussed along with how computational approaches can help identify critical host networks targeted by geminivirus AC2 proteins. Thus, the role of AC2/C2 in the viral life-cycle is to prevent the host from mounting an efficient defense response to geminivirus infection and to ensure maximal amplification and encapsidation of the viral genome.

Potato spindle tuber viroid (PSTVd) is a circular non-coding RNA of 359 nucleotides that replicates and spreads systemically in host plants, thus all functions required to establish an infection are mediated by sequence and structural elements in the genome. The PSTVd secondary structure contains 26 Watson-Crick base-paired stems and 27 loops. Most of the loops are believed to form three-dimensional (3D) structural motifs through non-Watson-Crick base pairing, base stacking, and other local interactions. Homology-based prediction using the JAR3D online program revealed that loop 27 (nucleotides 177-182) most likely forms a 3D structure similar to the loop of a conserved hairpin located in the 3' untranslated region of histone mRNAs in animal cells. This stem-loop, which is involved in 3'-end maturation, is not found in polyadenylated plant histone mRNAs. Mutagenesis showed that PSTVd genomes containing base substitutions in loop 27 predicted by JAR3D to disrupt the 3D structure were unable to replicate in Nicotiana benthamiana leaves following mechanical rub inoculation, with one exception: a U178G/U179G double mutant was replication-competent and able to spread within the upper epidermis of inoculated leaves, but was confined to this cell layer. Remarkably, direct delivery of the U178G/U179G mutant into the vascular system by needle puncture inoculation allowed it to spread systemically and enter mesophyll cells and epidermal cells of upper leaves. These findings highlight the importance of RNA 3D structure for PSTVd replication and intercellular trafficking and indicate that loop 27 is required for epidermal exit, but not epidermal entry or transit between other cell types. Thus, requirements for RNA trafficking between epidermal and underlying palisade mesophyll cells are unique and directional. Our findings further suggest that 3D structure and RNA-protein interactions constrain RNA sequence evolution, and validate JAR3D as a tool to predict RNA 3D structure.