Responses of marine trophic levels to the combined effects of ocean acidification and warming.

Marine organisms are simultaneously exposed to anthropogenic stressors associated with ocean acidification and ocean warming, with expected interactive effects. Species from different trophic levels with dissimilar characteristics and evolutionary histories are likely to respond differently. Here, we perform a meta-analysis of controlled experiments including both ocean acidification and ocean warming factors to investigate single and interactive effects of these stressors on marine species. Contrary to expectations, we find that synergistic interactions are less common (16%) than additive (40%) and antagonistic (44%) interactions overall and their proportion decreases with increasing trophic level. Predators are the most tolerant trophic level to both individual and combined effects. For interactive effects, calcifying and non-calcifying species show similar patterns. We also identify climate region-specific patterns, with interactive effects ranging from synergistic in temperate regions to compensatory in subtropical regions, to positive in tropical regions. Our findings improve understanding of how ocean warming, and acidification affect marine trophic levels and highlight the need for deeper consideration of multiple stressors in conservation efforts.

Discovery of Five SOS2 Fragment Hits with Binding Modes Determined by SOS2 X-Ray Cocrystallography.

SOS1 and SOS2 are guanine nucleotide exchange factors that mediate RTK-stimulated RAS activation. Selective SOS1:KRAS PPI inhibitors are currently under clinical investigation, whereas there are no reports to date of SOS2:KRAS PPI inhibitors. SOS2 activity is implicated in MAPK rebound when divergent SOS1 mutant cell lines are treated with the SOS1 inhibitor BI-3406; therefore, SOS2:KRAS inhibitors are of therapeutic interest. In this report, we detail a fragment-based screening strategy to identify X-ray cocrystal structures of five diverse fragment hits bound to SOS2.

A Systematic Review of Assessment Methods for Seafarers' Mental Health and Well-Being During the COVID-19 Pandemic.

Seafarers spend more time at sea than on land, which makes them a hard-to-reach community. Since their mental health and well-being is usually addressed from a land-based perspective, dedicated and validated methods incorporating maritime specificities are lacking. During the COVID-19 pandemic, research into seafarers' mental health and well-being flourished. However, a systematic review of the literature to assess the type and appropriateness of assessment methods pertaining to the mental health and well-being of seafarers has yet to be undertaken. This study reviews 5 databases (ERIC, Scopus, PubMed, Google Scholar and EBSCO) to assess the methods used to examine seafarers' mental health and well-being during the pandemic. Peer-reviewed literature alongside grey literature that applied quantitative or qualitative instruments to measure seafarers' mental health and/or well-being, published in English between March 2020 and February 2023, was eligible for the review. Studies from all geographic regions and regardless of nationality, rank and ship type of the subjects were explored. Database searches produced 272 records. Five additional records were identified via other methods. We identified 27 studies suitable for review, including 24 published in peer-reviewed scientific journals and 3 reports and surveys produced by the industry or welfare organizations. Assessment methods used to measure seafarers' mental health and well-being vary significantly in the literature. The frequent use of ad hoc questionnaires limits the possibility to replicate and compare the studies due to various inconsistencies. Furthermore, several validation and reliability measures needed more solidity when applied to the seafaring population. Such inadequate measuring and a mix of assessment methods impacted the comparison of results and might inflate the risks of underreporting or overstating mental complaints.

Meta-analysis reveals variance in tolerance to climate change across marine trophic levels.

Marine ecosystems are currently facing a variety of anthropogenic perturbations, including climate change. Trophic differences in response to climate change may disrupt ecological interactions and thereby threaten marine ecosystem function. Yet, we still do not have a comprehensive understanding of how different trophic levels respond to climate change stressors in marine ecosystems. By including 1278 experiments, comprising 236 different marine species from 18 different phyla in a meta-analysis of studies measuring the direct effect of ocean acidification and ocean warming on marine organisms, we found that higher trophic level species display greater tolerance to ocean acidification but greater sensitivity to warming. In contrast, marine herbivores were the most vulnerable trophic level to both acidification and warming. Such imbalances in the community and a general reduction of biodiversity and biomass in lower trophic levels can significantly disrupt the system and could drive negative bottom-up effects. In conclusion, with ocean acidification and elevated temperatures, there is an alarming risk that trophic disparity may disrupt species interactions, and thereby drive community destabilization under ocean climate change.

Decreasing toxicity of un-ionized ammonia on the gastropod Bellamya aeruginosa when moving from laboratory to field scale.

Along with a steady increasing use of artificial nitrogen fertilizer, concerns have been raised about the effects that high nitrogen loading may have on ecosystems. Due to the toxicity of unionized ammonia (NH3), tolerance criteria have been proposed for ambient water management in many countries; however, these are mainly based on acute or chronic tests carried out under lab conditions run with purified water. Aiming at understanding the responses of organisms to natural exposure to high ammonia concentrations, a Viviparidae gastropod, Bellamya aeruginosa, was tested at three experimental scales: standard 96-h lab test, one-month cage test in 6 experimental ponds with continuous nitrogen inputs, and intensive investigation of the B. aeruginosa from these ponds in spring and winter. The results were: 1) 96-h LC50 in the standard lab test was 0.56 mg NH3-N/L and 343.3 mg TAN/L (total ammonia expressed as N, standardized at pH 7 and 20 â„ƒ). 2) In the one-month cage test, the survival rate was 97% when NH3-N was 0.61 mg/L (i.e., a higher concentration than the lab 96-h LC50) and the body size of the gastropods actually increased with increasing NH3-N concentrations. 3) In the winter-spring investigation, little effect of ammonia on the standing crops of gastropods was found, and the body size of the gastropods tended to increase with increasing ammonia concentrations (NH3-N concentration range of 0.05 ~ 2.06 mg/L). Thus, B. aeruginosa showed higher tolerance to ammonia exposure (NH3-N concentration < 0.81 mg/L) in the field than under laboratory conditions. Our study points to the necessity of considering the relevant scale when determining criteria for ammonia toxicity in water management.

NMR in target driven drug discovery: why not?

No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophysical binding assays such as TR-FRET, SPR, thermophoresis and many others. Each method has its strengths and weaknesses, but none is as information rich and broadly applicable as NMR. Here we provide a number of examples of the utility of NMR for enabling and providing ongoing support for the early pre-clinical phase of small molecule drug discovery efforts. The examples have been selected for their usefulness in a commercial setting, with full understanding of the need for speed, cost-effectiveness and ease of implementation.

Transcriptomic resources for evolutionary studies in flat periwinkles and related species.

The flat periwinkles, Littorina fabalis and L. obtusata, comprise two sister gastropod species that have an enormous potential to elucidate the mechanisms involved in ecological speciation in the marine realm. However, the molecular resources currently available for these species are still scarce. In order to circumvent this limitation, we used RNA-seq data to characterize the transcriptome of four individuals from each species sampled in different locations across the Iberian Peninsula. Four de novo transcriptome assemblies were generated, as well as a pseudo-reference using the L. saxatilis reference transcriptome as backbone. After transcripts' annotation, variant calling resulted in the identification of 19,072 to 45,340 putatively species-diagnostic SNPs. The discriminatory power of a subset of these SNPs was validated by implementing an independent genotyping assay to characterize reference populations, resulting in an accurate classification of individuals into each species and in the identification of hybrids between the two. These data comprise valuable genomic resources for a wide range of evolutionary and conservation studies in flat periwinkles and related taxa.

Hybridization patterns between two marine snails, Littorina fabalis and L. obtusata.

Characterizing the patterns of hybridization between closely related species is crucial to understand the role of gene flow in speciation. In particular, systems comprising multiple contacts between sister species offer an outstanding opportunity to investigate how reproductive isolation varies with environmental conditions, demography and geographic contexts of divergence. The flat periwinkles, Littorina obtusata and L. fabalis (Gastropoda), are two intertidal sister species with marked ecological differences compatible with late stages of speciation. Although hybridization between the two was previously suggested, its extent across the Atlantic shores of Europe remained largely unknown. Here, we combined genetic (microsatellites and mtDNA) and morphological data (shell and male genital morphology) from multiple populations of flat periwinkles in north-western Iberia to assess the extent of current and past hybridization between L. obtusata and L. fabalis under two contrasting geographic settings of divergence (sympatry and allopatry). Hybridization signatures based on both mtDNA and microsatellites were stronger in sympatric sites, although evidence for recent extensive admixture was found in a single location. Misidentification of individuals into species based on shell morphology was higher in sympatric than in allopatric sites. However, despite hybridization, species distinctiveness based on this phenotypic trait together with male genital morphology remained relatively high. The observed variation in the extent of hybridization among locations provides a rare opportunity for future studies on the consequences of different levels of gene flow for reinforcement, thus informing about the mechanisms underlying the completion of speciation.

Interrogating the Essential Bacterial Cell Division Protein FtsQ with Fragments Using Target Immobilized NMR Screening (TINS).

The divisome is a large protein complex that regulates bacterial cell division and therefore represents an attractive target for novel antibacterial drugs. In this study, we report on the ligandability of FtsQ, which is considered a key component of the divisome. For this, the soluble periplasmic domain of Escherichia coli FtsQ was immobilized and used to screen a library of 1501 low molecular weight (< 300 Da), synthetic compounds for those that interact with the protein. A primary screen was performed using target immobilized NMR screening (TINS) and yielded 72 hits. Subsequently, these hits were validated in an orthogonal assay. At first, we aimed to do this using surface plasmon resonance (SPR), but the lack of positive control hampered optimization of the experiment. Alternatively, a two-dimensional heteronuclear single quantum coherence (HSQC) NMR spectrum of FtsQ was obtained and used to validate these hits by chemical shift perturbation (CSP) experiments. This resulted in the identification of three fragments with weak affinity for the periplasmic domain of FtsQ, arguing that the ligandability of FtsQ is low. While this indicates that developing high affinity ligands for FtsQ is far from straightforward, the identified hit fragments can help to further interrogate FtsQ interactions.

Are assortative mating and genital divergence driven by reinforcement?

The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favor reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence.

Bi-directional plasticity: Rotifer prey adjust spine length to different predator regimes.

Numerous prey organisms, including many rotifers, exhibit inducible defensive plasticity, such as spines, in response to predators. Here, we test the hypothesis that prey modify their defence response to different predator sizes with a bi-directional adjustment in spine length. First, we show experimentally, that large-sized predators induce a reduction in prey spine length. Second, we conducted a complementary field monitoring study showing that the spine length of the prey rotifer Keratella cochlearis changed in opposite directions, in response to the shift in dominance between small-sized and large-sized predators. Third, in order to test the generality of our novel findings, we conducted a meta-analysis covering a wide array of rotifer prey taxa, strengthening the conclusions from our experimental and field studies. Hence, by combining evidence from experiments and studies in the field with a meta-analysis, we, for the first time, demonstrate that rotifer prey distinguish between predators and adjust their protective spine length accordingly, i.e. rapidly adjust spine length to escape either below or above the dominant predator's gape size window. In a broader perspective, our conclusions advance our knowledge on observed spatial and temporal variations in protective morphologies among prey organisms.

Climate warming and heat waves affect reproductive strategies and interactions between submerged macrophytes.

Extreme climatic events, such as heat waves, are predicted to increase in frequency and intensity during the next hundred years, which may accelerate shifts in hydrological regimes and submerged macrophyte composition in freshwater ecosystems. Since macrophytes are profound components of aquatic systems, predicting their response to extreme climatic events is crucial for implementation of climate change adaptation strategies. We therefore performed an experiment in 24 outdoor enclosures (400 L) separating the impact of a 4 °C increase in mean temperature with the same increase, that is the same total amount of energy input, but resembling a climate scenario with extreme variability, oscillating between 0 °C and 8 °C above present conditions. We show that at the moderate nutrient conditions provided in our study, neither an increase in mean temperature nor heat waves lead to a shift from a plant-dominated to an algal-dominated system. Instead, we show that species-specific responses to climate change among submerged macrophytes may critically influence species composition and thereby ecosystem functioning. Our results also imply that more fluctuating temperatures affect the number of flowers produced per plant leading to less sexual reproduction. Our findings therefore suggest that predicted alterations in climate regimes may influence both plant interactions and reproductive strategies, which have the potential to inflict changes in biodiversity, community structure and ecosystem functioning.

Evidence of weaker phenotypic plasticity by prey to novel cues from non-native predators.

A central question in evolutionary biology is how coevolutionary history between predator and prey influences their interactions. Contemporary global change and range expansion of exotic organisms impose a great challenge for prey species, which are increasingly exposed to invading non-native predators, with which they share no evolutionary history. Here, we complete a comprehensive survey of empirical studies of coevolved and naive predator-prey interactions to assess whether a shared evolutionary history with predators influences the magnitude of predator-induced defenses mounted by prey. Using marine bivalves and gastropods as model prey, we found that coevolved prey and predator-naive prey showed large discrepancies in magnitude of predator-induced phenotypic plasticity. Although naive prey, predominantly among bivalve species, did exhibit some level of plasticity - prey exposed to native predators showed significantly larger amounts of phenotypic plasticity. We discuss these results and the implications they may have for native communities and ecosystems.

Structure-Based Identification of Inhibitory Fragments Targeting the p300/CBP-Associated Factor Bromodomain.

The P300/CBP-associated factor plays a central role in retroviral infection and cancer development, and the C-terminal bromodomain provides an opportunity for selective targeting. Here, we report several new classes of acetyl-lysine mimetic ligands ranging from mM to low micromolar affinity that were identified using fragment screening approaches. The binding modes of the most attractive fragments were determined using high resolution crystal structures providing chemical starting points and structural models for the development of potent and selective PCAF inhibitors.

Increasing chemical space coverage by combining empirical and computational fragment screens.

Most libraries for fragment-based drug discovery are restricted to 1,000-10,000 compounds, but over 500,000 fragments are commercially available and potentially accessible by virtual screening. Whether this larger set would increase chemotype coverage, and whether a computational screen can pragmatically prioritize them, is debated. To investigate this question, a 1281-fragment library was screened by nuclear magnetic resonance (NMR) against AmpC ß-lactamase, and hits were confirmed by surface plasmon resonance (SPR). Nine hits with novel chemotypes were confirmed biochemically with KI values from 0.2 to low mM. We also computationally docked 290,000 purchasable fragments with chemotypes unrepresented in the empirical library, finding 10 that had KI values from 0.03 to low mM. Though less novel than those discovered by NMR, the docking-derived fragments filled chemotype holes from the empirical library. Crystal structures of nine of the fragments in complex with AmpC ß-lactamase revealed new binding sites and explained the relatively high affinity of the docking-derived fragments. The existence of chemotype holes is likely a general feature of fragment libraries, as calculation suggests that to represent the fragment substructures of even known biogenic molecules would demand a library of minimally over 32,000 fragments. Combining computational and empirical fragment screens enables the discovery of unexpected chemotypes, here by the NMR screen, while capturing chemotypes missing from the empirical library and tailored to the target, with little extra cost in resources.

Express yourself: bold individuals induce enhanced morphological defences.

Organisms display an impressive array of defence strategies in nature. Inducible defences (changes in morphology and/or behaviour within a prey's lifetime) allow prey to decrease vulnerability to predators and avoid unnecessary costs of expression. Many studies report considerable interindividual variation in the degree to which inducible defences are expressed, yet what underlies this variation is poorly understood. Here, we show that individuals differing in a key personality trait also differ in the magnitude of morphological defence expression. Crucian carp showing risky behaviours (bold individuals) expressed a significantly greater morphological defence response when exposed to a natural enemy when compared with shy individuals. Furthermore, we show that fish of different personality types differ in their behavioural plasticity, with shy fish exhibiting greater absolute plasticity than bold fish. Our data suggest that individuals with bold personalities may be able to compensate for their risk-prone behavioural type by expressing enhanced morphological defences.

Parallel evolution of local adaptation and reproductive isolation in the face of gene flow.

Parallel evolution of similar phenotypes provides strong evidence for the operation of natural selection. Where these phenotypes contribute to reproductive isolation, they further support a role for divergent, habitat-associated selection in speciation. However, the observation of pairs of divergent ecotypes currently occupying contrasting habitats in distinct geographical regions is not sufficient to infer parallel origins. Here we show striking parallel phenotypic divergence between populations of the rocky-shore gastropod, Littorina saxatilis, occupying contrasting habitats exposed to either wave action or crab predation. This divergence is associated with barriers to gene exchange but, nevertheless, genetic variation is more strongly structured by geography than by ecotype. Using approximate Bayesian analysis of sequence data and amplified fragment length polymorphism markers, we show that the ecotypes are likely to have arisen in the face of continuous gene flow and that the demographic separation of ecotypes has occurred in parallel at both regional and local scales. Parameter estimates suggest a long delay between colonization of a locality and ecotype formation, perhaps because the postglacial spread of crab populations was slower than the spread of snails. Adaptive differentiation may not be fully genetically independent despite being demographically parallel. These results provide new insight into a major model of ecologically driven speciation.

Costs of inducible defence along a resource gradient.

In addition to having constitutive defence traits, many organisms also respond to predation by phenotypic plasticity. In order for plasticity to be adaptive, induced defences should incur a benefit to the organism in, for example, decreased risk of predation. However, the production of defence traits may include costs in fitness components such as growth, time to reproduction, or fecundity. To test the hypothesis that the expression of phenotypic plasticity incurs costs, we performed a common garden experiment with a freshwater snail, Radix balthica, a species known to change morphology in the presence of molluscivorous fish. We measured a number of predator-induced morphological and behavioural defence traits in snails that we reared in the presence or absence of chemical cues from fish. Further, we quantified the costs of plasticity in fitness characters related to fecundity and growth. Since plastic responses may be inhibited under limited resource conditions, we reared snails in different densities and thereby levels of competition. Snails exposed to predator cues grew rounder and thicker shells, traits confirmed to be adaptive in environments with fish. Defence traits were consistently expressed independent of density, suggesting strong selection from predatory molluscivorous fish. However, the expression of defence traits resulted in reduced growth rate and fecundity, particularly with limited resources. Our results suggest full defence in predator related traits regardless of resource availability, and costs of defence consequently paid in traits related to fitness.

Predator-induced morphological plasticity across local populations of a freshwater snail.

The expression of anti-predator adaptations may vary on a spatial scale, favouring traits that are advantageous in a given predation regime. Besides, evolution of different developmental strategies depends to a large extent on the grain of the environment and may result in locally canalized adaptations or, alternatively, the evolution of phenotypic plasticity as different predation regimes may vary across habitats. We investigated the potential for predator-driven variability in shell morphology in a freshwater snail, Radix balthica, and whether found differences were a specialized ecotype adaptation or a result of phenotypic plasticity. Shell shape was quantified in snails from geographically separated pond populations with and without molluscivorous fish. Subsequently, in a common garden experiment we investigated reaction norms of snails from populations' with/without fish when exposed to chemical cues from tench (Tinca tinca), a molluscivorous fish. We found that snails from fish-free ponds had a narrow shell with a well developed spire, whereas snails that coexisted with fish had more rotund shells with a low spire, a shell morphology known to increase survival rate from shell-crushing predators. The common garden experiment mirrored the results from the field survey and showed that snails had similar reaction norms in response to chemical predator cues, i.e. the expression of shell shape was independent of population origin. Finally, we found significant differences for the trait means among populations, within each pond category (fish/fish free), suggesting a genetic component in the determination of shell morphology that has evolved independently across ponds.

The adaptive value of phenotypic plasticity in two ecotypes of a marine gastropod.

BACKGROUND: Few surveys have concentrated on studying the adaptive value of phenotypic plasticity within genetically-distinct conspecific ecotypes. Here, we conduct a test to assess the adaptive value that partial phenotypic plasticity may have for survival in the marine gastropod Littorina saxatilis. This species has evolved canalized ecotypes but, nevertheless, the ecotypes show some phenotypic plasticity for the traits under divergent selection between wave-exposed and high-predation habitats. RESULTS: We exposed juveniles of each ecotype to several environmental treatments under laboratory conditions in order to produce shape variation associated with plasticity. The two ecotypes from different treatments were then transplanted to the wave-exposed habitat and the survival rate was monitored. Ecotype explained the largest distinction in survival rate while treatment caused variation in survival rate within the ecotype released into its parental habitat which was correlated with plastic changes in shell shape. Snails that had experienced a treatment mimicking the environment of the transplantation location survived with the highest rate, while individuals from the contrary experimental treatment had lower survivorship. CONCLUSIONS: We conclude that the partial plastic response shown in Littorina saxatilis has a significant impact on fitness, although this remains small compared to the overall adaptive difference between ecotypes.