Click-click, who’s there? Acoustically derived estimates of sperm whale size distribution off western Ireland

Understanding the structure of populations is a critical element to the establishment of management and conservation measures. Sperm whales Physeter macrocephalus are characterised by a demographic spatial segregation, associated with a conspicuous sexual dimorphism reflected in their vocalisations. These characteristics make acoustic techniques very relevant to the study of sperm whale population structure, especially in remote, challenging environments. The reliability of using inter-pulse intervals of sperm whale clicks to infer body size has long been verified and extensively used. We provide the first size structure estimates of the sperm whale population in an area where assumptions on population structure mainly relied on sparse observations at sea, whaling records and stranding data. Over 10,000 hours of acoustic data collected using both static acoustic recorders and towed hydrophone arrays in Irish offshore waters were processed using a machine learning-based tool aimed at automatically extracting inter-pulse intervals from sperm whale recordings. Our analyses suggested that, unlike previously thought, large males would not account for the majority of the animals recorded in the area. We showed that adult females/juvenile males (length 9-12 m) were predominant, accounting for 49% (n = 788) of the number of individuals recorded (n = 1,595), while the proportions of immature individuals (length<9 m) and adult males (length >12 m) were well balanced, accounting for 25% (n = 394) and 26% (n = 413) of the recorded whales, respectively. Our data also suggested some size segregation may be occurring within the area, with smaller individuals to the south. The implications of such findings are crucial to the management of the population and provide an important baseline to monitor changes in population structure, particularly relevant under changing habitat conditions

Temporal and spatial trends in stranding records of cetaceans on the Irish coast, 2002–2014

Using Irish strandings data collected between 2002 and 2014, seasonal and annual trends in the number of strandings for all strandings identified to species level (N ¼ 1480), and for the five most frequently reported species: common dolphin (25.7% of records), harbour porpoise (22.2%), long-finned pilot whale (8.8%), striped dolphin (6.9%) and bottlenose dolphin (6.9%) were investigated. With the exception of bottlenose dolphins, there was a significant linear increase in the number of strandings across years for all species and for all strandings collectively, that were identified to species-level. Only common dolphins demonstrated a significant increase in the proportion of records relative to all other strandings, which may be indicative of a real rise in the number of strandings of this species. Common dolphins and harbour porpoises showed a similar significant difference in monthly strandings, with more strandings occurring during the earlier months of the year.\ud Significant differences in the gender of stranded animals were found in common, striped, bottlenose and Atlantic white-sided dolphins and sperm and pygmy sperm whales. Live and mass stranding events were primarily comprised of pelagic species. Most strandings occurred on the south and west coasts, with two hotspots for live and mass strandings identified. The patterns and trends identified are discussed in relation to the caveats in interpreting strandings data. Specifically to Ireland, the findings highlight the urgent need to build on the current volunteer reporting network and augment this comprehensive dataset with post-mortem examinations to better understand the cause of the trends identified. The importance of strandings data in informing conservation and management guidelines of these species’ is discussed

On the origin of the selectivity of plasmidic H-NS towards horizontally acquired DNA: Linking H-NS oligomerization and cooperative DNA binding

The nucleoid-associated protein H-NS is a global modulator of the expression of genes associated with adaptation to environmental changes. A variant of H-NS expressed in the R27 plasmid was previously shown to selectively modulate the expression of horizontally acquired genes, with minimal effects on core genes that are repressed by the chromosomal form of H-NS. Both H-NS proteins are formed by an oligomerization domain and a DNA-binding domain, which are connected by a linker that is highly flexible in the absence of DNA. We studied DNA binding by means of oligomer-forming chimeric proteins in which domains of the chromosomal and plasmidic variants are exchanged, as well as in monomeric truncated forms containing the DNA-binding domain and variable portions of the linker. Point mutations in the linker were also examined in full-length and truncated H-NS constructs. These experiments show that the linker region contributes to DNA binding affinity and that it is a main component of the distinct DNA binding properties of chromosomal and plasmidic H-NS. We propose that interactions between the linker and DNA limit the flexibility of the connection between H- NS oligomerization and DNA binding and provide an allosteric indirect readout mechanism to detect long- range distortions of DNA, thus enabling discrimination between core and horizontally acquired DNA

Breeding habitat of poorly studied humpback whales (Megaptera novaeangliae) in Boa Vista, Cape Verde

The waters surrounding Cape Verde comprise one of two known breeding grounds for humpback whales in the North Atlantic. The population remains very small and has apparently failed to recover since the cessation of whaling there. During the breeding seasons of 2011 and 2012, sighting surveys were carried out for humpback whales off Boa Vista, the easternmost island of the Cape Verde Island archipelago. The distribution and relative abundance of humpback whales and mother-calf pairs was investigated by plotting effort-corrected sightings using a 2km2 grid-square. The study area, a 206km2 region from the coastline up to 8km offshore, covered the western half of Boa Vista where whales have previously been regularly recorded. Following 1,954km of search effort, 117 sightings of humpback whales were made. An encounter rate of 0.11 whales per km was recorded for both years. It is hoped that these data may assist in implementing conservation measures to protect humpback whales and the habitat of Baia Sal Rei, which appears to be the single most important bay for winter breeding, calving and nursing humpback whales in the eastern North Atlantic

Alzheimer´s Disease-associated Aβ42 Peptide: Expression and Purification for NMR Structural Studies

Background: The aggregation of the amyloid-beta peptide (Aβ) in the brain is strongly associated with Alzheimer´s disease (AD). However, the heterogeneous and transient nature of this process has prevented identification of the exact molecular form of Aβ responsible for the neurotoxicity observed in this disease. Therefore, characterizing Aβ aggregation is of utmost importance in the field of AD. Nuclear magnetic resonance spectroscopy (NMR) is a technique that holds great potential to achieve this goal. However, it requires the use of specific labels introduced through recombinant expression of Aβ. Objective: In this paper, we report on a straightforward expression and purification protocol to obtain [U-15N] and [U-2H,13C,15N] Aβ42. Method: Aβ42 is expressed fused to Small Ubiquitin-like Modifier (SUMO) protein, which prevents Aβ42 aggregation. Results: The solubilizing capacity of SUMO has allowed us to design a purification protocol involving immobilized metal affinity chromatography (IMAC), a desalting step, and two size exclusion chromatography (SEC) purifications. Conclusion: This approach, which does not require the use of costly and time-consuming reversed phase high performance liquid chromatography (RP-HPLC), offers a much straightforward strategy to those previously described to obtain [U-15N] Aβ42 and it is the first protocol through which to achieve [U-2H,13C,15N] Aβ42. The peptides obtained are of high purity and have the required isotope enrichment to support NMR-based structural studies

Response of cetaceans to fluctuations of pelagic fish stocks and environmental conditions within the Celtic Sea ecosystem

Inshore waters off the south coast of Ireland are an important foraging area for a range of cetacean species. Some of the main prey species of these cetaceans are herring and sprat, two economically valuable fish species in the region. The Celtic Sea herring stock suffered a marked decline in 2013. The present study aimed to investigate potential changes in the ecosystem associated to the herring decline and to determine the potential impacts on predators. Here we analyzed sightings information of common dolphins, fin, minke, humpback and unidentified whale species, acoustic data of herring and sprat, and a range of environmental variables mainly derived from satellites. Firstly, we characterized spatio-temporal patterns in the relative abundance of predator and prey species, and environmental variables, and compared periods before and since the herring decline. Since the 2013 herring decline, (i) the herring stock has mainly concentrated in south-eastern coastal waters and southern offshore Irish waters, (ii) sprat density has increased, (iii) chlorophyll concentration has decreased, (iv) sea surface temperature has risen, and (v) the euphotic layer has extended deeper. Secondly, we modelled the effects of prey density and environmental conditions on the relative abundance and distribution of cetaceans, as well as the effects of environmental conditions on prey density, between 2005-2018 by applying Hurdle Generalized Additive Models. The models for herring and sprat support the idea that these species have different environmental relationships, for example herring tended to be found in shallower waters than was the case for sprat. The presence and relative abundance of common dolphins were significantly affected by both environmental conditions and herring density, whereas whale species presence and relative abundance were found to be correlated with sea surface temperature and prey density. The model results suggest differences in prey choice among whale species. Understanding the dynamic relationships between predators, prey and the environment is important to inform an ecosystem-based approach to fisheries management

Exploring environmental and biological drivers of cetacean occurrence in the cross-border region of the Malin Shelf using data from a European fishery survey

Irish and Scottish waters are important habitats for cetaceans in Europe. Yet, little data is available for the region of the Malin Shelf, north of Ireland. Despite a rich species diversity, relative cetacean abundance appears low compared to hotspots documented west of Scotland and Ireland. Whether this perceived low prevalence accurately portrays an ecological discontinuity or arises from a lack of published results and low survey effort in that transborder area remains unclear. Here, we used sighting records from a multi-disciplinary fisheries survey, the Western European Shelf Pelagic Acoustic Survey (WESPAS), to explore cetacean habitat preferences over the Malin and Hebridean shelves. Northern minke whale and common dolphin occurrence was modelled within a Bayesian Additive Regression Trees (BART) framework, against selected environmental and biological variables. No correlation was observed between cetacean presence and in-situ prey biomass. Minke whales distribution was better explained by oceanography, notably proxies for frontal activity, and primary productivity. Common dolphins similarly showed preferences for shelf waters within 5-25km of fronts, but also affinities for fine substrates. Favourable habitats identified by the models were consistent with literature around the Hebrides and shed light on potentially important areas along the Islay front and north of Donegal, so far unreported due to data deficiency. Results will contribute towards informing future monitoring, strategic management and conservation efforts in this cross-border region