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.

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.

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.

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.

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.

A solid-state NMR study of changes in lipid phase induced by membrane-fusogenic LV-peptides.

Membrane fusion requires restructuring of lipid bilayers mediated by fusogenic membrane proteins. Peptides that correspond to natural transmembrane sequences or that have been designed to mimic them, such as low-complexity "Leu-Val" (LV) peptide sequences, can drive membrane fusion, presumably by disturbing the lipid bilayer structure. Here, we assess how peptides of different fusogenicity affect membrane structure using solid state NMR techniques. We find that the more fusogenic variants induce an unaligned lipid phase component and a large degree of phase separation as observed in (31)P 2D spectra. The data support the idea that fusogenic peptides accumulate PE in a non-bilayer phase which may be critical for the induction of fusion.

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.

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.

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.

13C and 15N NMR evidence for peripheral intercalation of uniformly labeled fusogenic peptides incorporated in a biomimetic membrane.

Membrane fusion requires drastic and transient changes of bilayer curvature and here we have studied the interaction of three de novo designed synthetic hydrophobic peptides with a biomimetic three-lipid mixture by solid state NMR. An experimental approach is presented for screening of peptide-lipid interactions and their aggregation, and their embedding in a biomimetic membrane system using established proton-decoupled 13C,15N and proton spin diffusion heteronuclear 1H-13C correlation NMR methods at high magnetic field. Experiments are presented for a set of de-novo designed fusion peptides in interaction with their lipid environment. The data provide additional support for the transmembrane model for the least fusogenic peptide, L16, while the peripheral intercalation model is preferred for the fusogenic peptides LV16 and LV16G8P9. This contributes to converging evidence that peripheral intercalation is both necessary and sufficient to trigger the fusion process for a lipid mixture close to a critical point for phase separation across the bilayer.

Testing the grain-size model for the evolution of phenotypic plasticity.

Phenotypic plasticity is the ability of a genotype to modify its phenotypic characteristics in response to different environments. Theory predicts that adaptive plasticity should primarily evolve in organisms that experience heterogeneous environments. An organism's dispersal rate is a key component in these models, because the degree of dispersal partly determines the extent of environmental heterogeneity. Here, I provide the first large-scale test of the theoretical prediction that phenotypic plasticity evolves in association with dispersal rate using meta-analysis of data from 258 experiments from the literature on plasticity in marine invertebrates. In line with predictions, phenotypic plasticity is generally greater in species with higher dispersal rates, suggesting that dispersal and environmental heterogeneity are important selective agents for evolution of plasticity in marine habitats.

Depletion of high energy phosphates implicates post-exercise mortality in carp and trout; an in vivo 31P-NMR study.

As in vivo 31P-Nuclear Magnetic Resonance spectroscopy is currently the state of the art method to measure continuously intracellular pH (pH(i)) and energy status of muscle tissue, we used this method to study the recovery from exhaustive exercise. The biochemical changes during recovery are not well understood and it was suggested that post-exercise mortality could be caused by low pH(i); other studies however indicate that energy depletion might be more important. To analyse the mechanism of post-exercise recovery pH(i), ATP, P(i), and PCr must be measured at the same time, which is possible using in vivo 31P-NMR. Common carp and rainbow trout of about 100 g were exercised to exhaustion in a swim tunnel. After swimming 10 h at 1.5 body lengths (BL)/s (aerobic control), 50% of the fish were forced to swim at 6 BL/s until exhaustion. Recovery of energy rich phosphates was found to be faster in carp (1.2-1.9 h) than in trout (1.5-2.3 h). The same applied for the recovery from acidosis, which took 1.75 h in carp and 5.75 h in trout. In parallel experiments the energy phosphates and lactate levels were measured in liver, red muscle, and white muscle. Exhaustion caused a significant drop in the energy status of red and white muscle tissue of trout and carp (corroborates NMR data), while no change at all was observed in liver tissue. The lactate levels were increased in the muscle but not in liver and blood. While all experimental animals looked healthy after exhaustion, 40-50% of the carp as well as trout died during the recovery phase. The energy status of those individuals measured by 31P-NMR was much lower than that of the survivors, while in contrast there was no difference in pH(i). Thus, it appears that not acidosis but depletion of high energy phosphates disabled muscle function and therefore may have been the cause of death of the non-survivors.

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.

Evolution of adaptation through allometric shifts in a marine snail.

Variation in ontogenetic development among individuals may be a major contributor to morphological variation within species. Evolution of different growth trajectories might, for example, evolve as a response to varying ecological contexts of individuals living in different environments, or by life-stage or gender differences. The intertidal periwinkle Littorina saxatilis is strongly polymorphic in shell shape. We compared ontogenetic trajectories between life stages, local populations, and sexes to understand how different morphological end points are reached during ontogeny and what might cause these differences. Applying landmark-based geometric morphometrics, we captured shell shape variation for four Swedish populations of this species. We also derived a method to visualize ontogenetic trajectories described by the relationship of size to the multivariate shape space. We found that growth trajectories differed between individuals living in different habitats, as well as between sexes and maturity stages. Males living on rocky cliffs grew isometrically throughout life, whereas females from the same habitat switched from isometric growth as juveniles to allometric growth as adults. In contrast, males and females living on boulders grew allometrically as juveniles but changed to isometric growth at sexual maturity. Thus, in this species, ontogenetic growth seems influenced by habitat-associated selection as well as by gender and age-specific selection. These differing selection regimes result in ontogenetic shifts in allometry in three of the four groups examined.

TINS, target immobilized NMR screening: an efficient and sensitive method for ligand discovery.

We propose a ligand screening method, called TINS (target immobilized NMR screening), which reduces the amount of target required for the fragment-based approach to drug discovery. Binding is detected by comparing 1D NMR spectra of compound mixtures in the presence of a target immobilized on a solid support to a control sample. The method has been validated by the detection of a variety of ligands for protein and nucleic acid targets (K(D) from 60 to 5000 muM). The ligand binding capacity of a protein was undiminished after 2000 different compounds had been applied, indicating the potential to apply the assay for screening typical fragment libraries. TINS can be used in competition mode, allowing rapid characterization of the ligand binding site. TINS may allow screening of targets that are difficult to produce or that are insoluble, such as membrane proteins.