The influence of solvent representation on nuclear shielding calculations of protonation states of small biological molecules

In this study, we assess the influence of solvation on the accuracy and reliability of isotropic nuclear magnetic shielding calculations for amino acids in comparison to experimental data. We focus particularly on the performance of solvation methods for different protonation states, as biological molecules occur almost exclusively in aqueous solution and are subject to protonation with pH. We identify significant shortcomings of current implicit solvent models and present a hybrid solvation approach that improves agreement with experimental data by taking into account the presence of direct interactions between amino acid protonation state and water molecules

Ocean Acidification Amplifies the Olfactory Response to 2-Phenylethylamine: Altered Cue Reception as a Mechanistic Pathway?

With carbon dioxide (CO2) levels rising dramatically, climate change threatens marine environments. Due to increasing CO2 concentrations in the ocean, pH levels are expected to drop by 0.4 units by the end of the century. There is an urgent need to understand the impact of ocean acidification on chemical-ecological processes. To date, the extent and mechanisms by which the decreasing ocean pH influences chemical communication are unclear. Combining behaviour assays with computational chemistry, we explore the function of the predator related cue 2-phenylethylamine (PEA) for hermit crabs (Pagurus bernhardus) in current and end-of-the-century oceanic pH. Living in intertidal environments, hermit crabs face large pH fluctuations in their current habitat in addition to climate-change related ocean acidification. We demonstrate that the dietary predator cue PEA for mammals and sea lampreys is an attractant for hermit crabs, with the potency of the cue increasing with decreasing pH levels. In order to explain this increased potency, we assess changes to PEA’s conformational and charge-related properties as one potential mechanistic pathway. Using quantum chemical calculations validated by NMR spectroscopy, we characterise the different protonation states of PEA in water. We show how protonation of PEA could affect receptor-ligand binding, using a possible model receptor for PEA (human TAAR1). Investigating potential mechanisms of pH-dependent effects on olfactory perception of PEA and the respective behavioural response, our study advances the understanding of how ocean acidification interferes with the sense of smell and thereby might impact essential ecological interactions in marine ecosystems

A new insight into the influence of habitat on the biochemical properties of three commercial sea cucumber species

This work makes a comparative evaluation of the biochemical profile of three sea commercial cucumber species (Holothuria mammata, H. polii and H. tubulosa) caught from different locations of the Mediterranean Sea (SE Spain). All species had high levels of moisture (from 73.6% in H. mammata to 81.2% in H. tubulosa), crude ash (from 9.61% in H. mammata to 14.7% in H. tubulosa) and protein (3.01% in H. tubulosa to 11.1% in H. mammata). They also had a low fat content, from 0.21% in H. tubulosa to 0.55% in H. mammata. Holothuria polii had intermediate values between the other two species, for all considered variables. All species had adequate protein/lipid ratios (H. mammata, 20:1; H. polii, 23:1; H. tubulosa, 14:1) and low lipid levels, enriched in omega-3 polyunsaturated fatty acids, especially arachidonic acid. The fatty acid profile suggests that H. polii is feeding on sediments more influenced by terrestrial inputs than the remaining species. Holothuria mammata and H. tubulosa are feeding on marine food sources mainly, but also with some terrestrial influence. The most abundant amino acids detected were alanine, arginine, glutamic acid, and glycine. All species had similar contents of essential amino acids (EAA) and ratios of EAA/non-essential amino acids. Holothuria tubulosa had a high content of toxic metals including Cr, Pb and Ni. This work highlights differences in compositional characteristics between different species of the same genus (Holothuria) from different locations.info:eu-repo/semantics/publishedVersio

Modelling Antifouling compounds of Macroalgal Holobionts in Current and Future pH Conditions

Marine macroalgae are important ecosystem engineers in marine coastal habitats. Macroalgae can be negatively impacted through excessive colonization by harmful bacteria, fungi, microalgae, and macro-colonisers and thus employ a range of chemical compounds to minimize such colonization. Recent research suggests that environmental pH conditions potentially impact the functionality of such chemical compounds. Here we predict if and how naturally fluctuating pH conditions and future conditions caused by ocean acidification will affect macroalgal (antifouling) compounds and thereby potentially alter the chemical defence mediated by these compounds. We defined the relevant ecological pH range, analysed and scored the pH-sensitivity of compounds with antifouling functions based on their modelled chemical properties before assessing their distribution across the phylogenetic macroalgal groups, and the proportion of sensitive compounds for each investigated function. For some key compounds, we also predicted in detail how the associated ecological function may develop across the pH range. The majority of compounds were unaffected by pH, but compounds containing phenolic and amine groups were found to be particularly sensitive to pH. Future pH changes due to predicted average open ocean acidification pH were found to have little effect. Compounds from Rhodophyta were mainly pH-stable. However, key algal species amongst Phaeophyceae and Chlorophyta were found to rely on highly pH-sensitive compounds for their chemical defence against harmful bacteria, microalgae, fungi, and biofouling by macro-organisms. All quorum sensing disruptive compounds were found the be unaffected by pH, but the other ecological functions were all conveyed in part by pH-sensitive compounds. For some ecological keystone species, all of their compounds mediating defence functions were found to be pH-sensitive based on our calculations, which may not only affect the health and fitness of the host alga resulting in host breakdown but also alter the associated ecological interactions of the macroalgal holobiont with micro and macrocolonisers, eventually causing ecosystem restructuring and the functions (e.g. habitat provision) provided by macroalgal hosts. Our study investigates a question of fundamental importance because environments with fluctuating or changing pH are common and apply not only to coastal marine habitats and estuaries but also to freshwater environments or terrestrial systems that are subject to acid rain. Hence, whilst warranting experimental validation, this investigation with macroalgae as model organisms can serve as a basis for future investigations in other aquatic or even terrestrial systems

Becoming nose-blind—Climate change impacts on chemical communication

Chemical communication via infochemicals plays a pivotal role in ecological interactions, allowing organisms to sense their environment, locate predators, food, habitats, or mates. A growing number of studies suggest that climate change-associated stressors can modify these chemically mediated interactions, causing info-disruption that scales up to the ecosystem level. However, our understanding of the underlying mechanisms is scarce. Evidenced by a range of examples, we illustrate in this opinion piece that climate change affects different realms in similar patterns, from molecular to ecosystem-wide levels. We assess the importance of different stressors for terrestrial, freshwater, and marine ecosystems and propose a systematic approach to address highlighted knowledge gaps and cross-disciplinary research avenues

Acidification can directly affect olfaction in marine organisms

In the past decade, many studies have investigated the effects of low pH/high CO2 as a proxy for ocean acidification on olfactory-mediated behaviours of marine organisms. The effects of ocean acidification on the behaviour of fish vary from very large to none at all, and most of the maladaptive behaviours observed have been attributed to changes in acid–base regulation, leading to changes in ion distribution over neural membranes, and consequently affecting the functioning of gamma-aminobutyric acid-mediated (GABAergic) neurotransmission. Here, we highlight a possible additional mechanism by which ocean acidification might directly affect olfaction in marine fish and invertebrates. We propose that a decrease in pH can directly affect the protonation, and thereby, 3D conformation and charge distribution of odorants and/or their receptors in the olfactory organs of aquatic animals. This can sometimes enhance signalling, but most of the time the affinity of odorants for their receptors is reduced in high CO2/low pH; therefore, the activity of olfactory receptor neurons decreases as measured using electrophysiology. The reduced signal reception would translate into reduced activation of the olfactory bulb neurons, which are responsible for processing olfactory information in the brain. Over longer exposures of days to weeks, changes in gene expression in the olfactory receptors and olfactory bulb neurons cause these neurons to become less active, exacerbating the problem. A change in olfactory system functioning leads to inappropriate behavioural responses to odorants. We discuss gaps in the literature and suggest some changes to experimental design in order to improve our understanding of the underlying mechanisms and their effects on the associated behaviours to resolve some current controversy in the field regarding the extent of the effects of ocean acidification on marine fish

Seawater carbonate chemistry and olfactory sensitivity of Gilthead Seabream

The effects of ocean acidification on fish are only partially understood. Studies on olfaction are mostly limited to behavioral alterations of coral reef fish; studies on temperate species and/or with economic importance are scarce. The current study evaluated the effects of short- and medium-term exposure to ocean acidification on the olfactory system of gilthead seabream (Sparus aurata), and attempted to explain observed differences in sensitivity by changes in the protonation state of amino acid odorants. Short-term exposure to elevated PCO2 decreased olfactory sensitivity to some odorants, such as L-serine, L-leucine, L-arginine, L-glutamate, and conspecific intestinal fluid, but not to others, such as L-glutamine and conspecific bile fluid. Seabream were unable to compensate for high PCO2 levels in the medium term; after 4 weeks exposure to high PCO2, the olfactory sensitivity remained lower in elevated PCO2 water. The decrease in olfactory sensitivity in high PCO2 water could be partly attributed to changes in the protonation state of the odorants and/or their receptor(s); we illustrate how protonation due to reduced pH causes changes in the charge distribution of odorant molecules, an essential component for ligand-receptor interaction. However, there are other mechanisms involved. At a histological level, the olfactory epithelium contained higher densities of mucus cells in fish kept in high CO2 water, and a shift in pH of the mucus they produced to more neutral. These differences suggest a physiological response of the olfactory epithelium to lower pH and/or high CO2 levels, but an inability to fully counteract the effects of acidification on olfactory sensitivity. Therefore, the current study provides evidence for a direct, medium term, global effect of ocean acidification on olfactory sensitivity in fish, and possibly other marine organisms, and suggests a partial explanatory mechanism

Becoming nose-blind-Climate change impacts on chemical communication.

Chemical communication via infochemicals plays a pivotal role in ecological interactions, allowing organisms to sense their environment, locate predators, food, habitats, or mates. A growing number of studies suggest that climate change-associated stressors can modify these chemically mediated interactions, causing info-disruption that scales up to the ecosystem level. However, our understanding of the underlying mechanisms is scarce. Evidenced by a range of examples, we illustrate in this opinion piece that climate change affects different realms in similar patterns, from molecular to ecosystem-wide levels. We assess the importance of different stressors for terrestrial, freshwater, and marine ecosystems and propose a systematic approach to address highlighted knowledge gaps and cross-disciplinary research avenues

Sensitivity of tetrodotoxin and saxitoxin to changing ocean conditions

This dataset, consisting of 3 separate files, provides the basis for our manuscript entitled "Saxitoxin and tetrodotoxin bioavailability increases in future oceans". Each file contains the data for one figure. For detailed calculation methods please refer to the method and supplementary information sections of the associated manuscript. Fig1_STX_and_TTX_pH-availability contains abundance data of saxitoxin (STX) and tetrodotoxin (TTX) protonation states across the pH range from 6 to 10 at 3 different temperatures. It is calculated based on published pKa data using the Henderson-Hasselbalch equation. Temperature is taken into account employing a pKa-influencing factor of -0.2/+10C. Fig2_Dinos_HAEDAT_STX_concatenated contains all the information required for plotting the pH and temperature dependent global toxicity map. It combines georeferenced records for localities with STX-related HABs (extracted from the Harmful Algal Information System metadatabase - HAEDAT) and the distribution of two dinoflagellate genera, which are known to produce STX, Gymnodinium and Alexandrium (extracted from the NOAA COPEPOD database). For each location we also extracted current and future pH and sea surface temperature from the Global marine environment dataset (GMED)/ IPCC (WCRP CMIP3) multi-model database. We calculated the abundance of the toxic STX form based on the pH and temperature for each of the respective locations in current and future conditions. Fig3_STXinClamTissue contains the compiled total STX content in clam tissue data from the PSP Program website of the Quagan Tayagungin Tribe for the time frame between June 2012 and July 2018 for each month at Spit Beach, Sand Point (Alaska). Based on this data we further calculated the current and future toxic proportion of this total STX content for the location's specific current and future temperature and pH data