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Publication Diagnosis of sheep fasciolosis caused by Fasciola hepatica using cathepsin L enzyme-linked immunosorbent assays (ELISA)(Elsevier, 2021-07-13) López Corrales, Jesús; Cwiklinski, Krystyna; De Marco Verissimo, Carolina; Dorey, Amber; Lalor, Richard; Jewhurst, Heather; McEvoy, Amanda; Diskin, Michael; Duffy, Catherine; Cosby, S Louise; Keane, Orla M; Dalton, John Pius; European Research Council; Science Foundation IrelandFasciolosis, a global parasitic disease of agricultural livestock, is caused by the liver fluke Fasciola hepatica. Management and strategic control of fasciolosis on farms depends on early assessment of the extent of disease so that control measures can be implemented quickly. Traditionally, this has relied on the detection of eggs in the faeces of animals, a laborious method that lacks sensitivity, especially for sub-clinical infections, and identifies chronic infections only. Enzyme linked immunosorbent assays (ELISA) offer a quicker and more sensitive serological means of diagnosis that could detect early acute infection before significant liver damage occurs. The performance of three functionally-active recombinant forms of the major F. hepatica secreted cathepsins L, rFhCL1, rFhCL2, rFhCL3, and a cathepsin B, rFhCB3, were evaluated as antigens in an indirect ELISA to serologically diagnose liver fluke infection in experimentally and naturally infected sheep. rFhCL1 and rFhCL3 were the most effective of the four antigens detecting fasciolosis in sheep as early as three weeks after experimental infection, at least five weeks earlier than both coproantigen and faecal egg tests. In addition, the rFhCL1 and rFhCL3 ELISAs had a very low detection limit for liver fluke in lambs exposed to natural infection on pastures and thus could play a major role in the surveillance of farms and a 'test and treat' approach to disease management. Finally, antibodies to all three cathepsin L proteases remain high throughout chronic infection but decline rapidly after drug treatment with the flukicide, triclabendazole, implying that the test may be adapted to trace the effectiveness of drug treatment.Publication Co-selection of bacterial metal and antibiotic resistance in soil laboratory microcosms(MDPI, 2023-04-18) Heydari, Ali; Kim, Nick D.; Biggs, Patrick J.; Horswell, Jacqui; Gielen, Gerty J. H. P.; Siggins, Alma; Taylor, Matthew D.; Bromhead, Collette; Palmer, Barry R.Accumulation of heavy metals (HMs) in agricultural soil following the application of superphosphate fertilisers seems to induce resistance of soil bacteria to HMs and appears to co-select for resistance to antibiotics (Ab). This study aimed to investigate the selection of co-resistance of soil bacteria to HMs and Ab in uncontaminated soil incubated for 6 weeks at 25 °C in laboratory microcosms spiked with ranges of concentrations of cadmium (Cd), zinc (Zn) and mercury (Hg). Co-selection of HM and Ab resistance was assessed using plate culture on media with a range of HM and Ab concentrations, and pollution-induced community tolerance (PICT) assays. Bacterial diversity was profiled via terminal restriction fragment length polymorphism (TRFLP) assay and 16S rDNA sequencing of genomic DNA isolated from selected microcosms. Based on sequence data, the microbial communities exposed to HMs were found to differ significantly compared to control microcosms with no added HM across a range of taxonomic levels.Publication Phylogenetic, species richness and logistic influences on the biodiscovery process in Cnidaria(Frontiers Media, 2022-12-15) Johnson, Mark P.; Baker, Bill J.; Conneely, Ellie-Ann; McKeever, Kate; Young, Ryan M.; Laguionie-Marchais, Claire; Allcock, A. Louise; Science Foundation Ireland; Marine Institute; European Regional Development FundThe extent to which any particular taxon supplies novel natural products depends on biological and evolutionary differences, and on decisions made by (or constraints on) biodiscovery scientists. The influences of different sources of variability on the biodiscovery process were examined in a study of the Cnidaria, a group recognised as an important source of novel marine natural products. The number of species with at least one novel metabolite within a genus was related to the number of species in the genus. This pattern implies that different genera do not differ in the probability of containing a species with novel natural products. Outlying points of this relationship were consistent with the ease of obtaining material through culturing organisms. The most productive five species were the sources of over 100 novel metabolites each. The distribution of novel metabolites across species showed no signs of exhausting novelty for the most productive source species. Novel metabolite drug likeness (ADMET-score) varied among genera. However, this pattern of variation was of the same degree as observed for molecular weights of metabolites, suggesting that differences among genera are generated by the decisions of analysts with different interests and do not reflect underlying biology. Biogeographic patterns of soft coral species with novel natural products were matched to regional species richness. Overall, the evidence for phylogenetic or spatial influences on the chance of finding novel metabolites was weak. The patterns are consistent with a constant chance of finding novel natural products across different species, with some constraints linked to ease of sampling or culturing and some reinforcement of biodiscovery in species that have previously been the source of novel metabolites.Publication PhycoCanopy: An R Shiny tool for exploring primary production in macroalgal canopies(Wiley, 2022-03-16) Johnson, Mark P.; Irish Research eLibrary1. Macroalgal canopies are considered important for coastal food webs and may have a role in carbon sequestration. Until recently, measures of canopy photosynthesis have been relatively rare, and simulations have sometimes omitted key aspects (e.g. self-shading, photosynthesis in air). PhycoCanopy offers a way of exploring how different algal parameters and environmental settings can affect net canopy photosynthesis. 2. The model uses the approach of dividing the canopy into vertical layers, calculating the available light for photosynthesis in each layer with respect to attenuation by the water column and the canopy. A total of 23 parameters can be varied to investigate the consequences of changes in key processes such as the tidal cycle, position of algae relative to the low tide mark and photosynthesis in air. 3. Predicted net photosynthesis can vary within a day as the timing of tides interacts with the light level at different times. The model offers a means of exploring the sensitivity of different parameters and building a fuller understanding of canopy photosynthesis. 4. PhycoCanopy allows users to visualize net canopy photosynthesis and to make predictions in situations where parameters are well characterized. The results give an integrated insight into net photosynthesis, particularly as intertidal observations cannot be maintained continuously over the tidal cycle. The model also demonstrates important covariates, such as the area of algal thallus m¿2 (thallus area index, TAI), that should be measured to interpret observed variation in canopy photosynthesis.Publication Improved diagnosis of SARS-CoV-2 by using nucleoprotein and spike protein fragment 2 in quantitative dual ELISA tests(Cambridge University Press, 2021-06-08) De Marco Verissimo, Carolina; O'Brien, Carol; López Corrales, Jesús; Dorey, Amber; Cwiklinski, Krystyna; Lalor, Richard; Doyle, Jack M.; Field, Stephen; Masterson, Claire; Ribes Martinez, Eduardo; Hughes, Gerry; Bergin, Colm; Walshe, Kieran; McNicholas, Bairbre; Laffey, John G.; Dalton, John P.; Kerr, Colm; Doyle, Sean; Science Foundation IrelandThe novel coronavirus, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), is the causative agent of the 2020 worldwide coronavirus pandemic. Antibody testing is useful for diagnosing historic infections of a disease in a population. These tests are also a helpful epidemiological tool for predicting how the virus spreads in a community, relating antibody levels to immunity and for assessing herd immunity. In the present study, SARS-CoV-2 viral proteins were recombinantly produced and used to analyse serum from individuals previously exposed, or not, to SARS-CoV-2. The nucleocapsid (Npro) and spike subunit 2 (S2Frag) proteins were identified as highly immunogenic, although responses to the former were generally greater. These two proteins were used to develop two quantitative enzyme-linked immunosorbent assays (ELISAs) that when used in combination resulted in a highly reliable diagnostic test. Npro and S2Frag-ELISAs could detect at least 10% more true positive coronavirus disease-2019 (COVID-19) cases than the commercially available ARCHITECT test (Abbott). Moreover, our quantitative ELISAs also show that specific antibodies to SARS-CoV-2 proteins tend to wane rapidly even in patients who had developed severe disease. As antibody tests complement COVID-19 diagnosis and determine population-level surveillance during this pandemic, the alternative diagnostic we present in this study could play a role in controlling the spread of the virus.Publication Born with bristles: New insights on the Kölliker’s organs of Octopus skin(Frontiers Media, 2021-05-10) Villanueva, Roger; Coll-Lladó, Montserrat; Bonnaud-Ponticelli, Laure; Carrasco, Sergio A.; Escolar, Oscar; Fernández-Álvarez, Fernando Ángel; Gleadall, Ian G.; Nabhitabhata, Jaruwat; Ortiz, Nicolás; Rosas, Carlos; Sánchez, Pilar; Voight, Janet R.; Swoger, Jim; Irish Research Council; Japan Science and Technology Agency; Okinawa Institute of Science and Technology; Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica; Spanish Ministry of ScienceThe entire skin surface of octopus embryos, hatchlings and juveniles bears scattered tufts of tiny chitinous setae within small pockets, from which they can be everted and retracted. Known as Kölliker’s organs (KO), they disappear before the subadult stage. The function of these structures during the early life of the octopus is unknown, despite having been first described nearly two centuries ago. To investigate these organs further, general trends in size of KO distribution and density were analyzed in hatchlings and juveniles of 17 octopod species from all oceans, representing holobenthic, holopelagic and meropelagic modes of life. The size of the KO is fairly constant across species, unrelated to mode of life or hatchling size. The density of KO is similar on ventral and dorsal body surfaces, but hatchlings of smaller size tend to have a higher density of KO on the aboral surface of the arms. Analysis of a series of post-hatching Octopus vulgaris shows KO size to be constant throughout ontogeny; it is therefore a consistent structure during the octopus early life from planktonic hatchling to benthic juvenile. New KO are generated on the skin of the arm tips during the planktonic period and initial benthic lives of juveniles. Their density, on both the mantle and arms, gradually decreases as the octopus grows. In older benthic juveniles, the KO degrades, losing its setae and the base of its follicle becomes exposed as a nearly circular stump of muscle. It is estimated that fully everted KO increase the body surface area by around two-thirds compared to when the KO are retracted. This modular mechanism of body surface extension and roughness probably influences flow-related forces such as drag and propulsion of the moving surface of the young octopus while it is of small size with a relatively large surface area. In addition, the distribution of these organs on the aboral surface of the arms of the octopus and their birefringent properties suggest a role in camouflage. Further research is needed to test these hypotheses of KO function in live animals.Publication A standardised flexibility assessment methodology for demand response(Emerald, 2019-05-30) O’Connell, Sarah; Reynders, Glenn; Seri, Federico; Sterling, Raymond; Keane, Marcus M.; Horizon 2020Purpose The purpose of this paper is to present a standardised four-step flexibility assessment methodology for evaluating the available electrical load reduction or increase a building can provide in response to a signal from an aggregator or grid operator. Design/methodology/approach The four steps in the methodology consist of Step 1: systems, loads, storage and generation identification; Step 2: flexibility characterisation; Step 3: scenario modelling; and Step 4: key performance indicator (KPI) label. Findings A detailed case study for one building, validated through on-site experiments, verified the feasibility and accuracy of the approach. Research limitations/implications The results were benchmarked against available demonstration studies but could benefit from the future development of standardised benchmarks. Practical implications The ease of implementation enables building operators to quickly and cost effectively evaluate the flexibility of their building. By clearly defining the flexibility range, the KPI label enables contract negotiation between stakeholders for demand side services. It may also be applicable as a smart readiness indicator. Social implications The novel KPI label has the capability to operationalise the concept of building flexibility to a wider spectrum of society, enabling smart grid demand response roll-out to residential and small commercial customers. Originality/value This paper fulfils an identified need for an early-stage flexibility assessment which explicitly includes source selection that can be implemented in an offline manner without the need for extensive real-time data acquisition, ICT platforms or additional meter and sensor installations.Publication First record of the elusive oceanic squid Thysanoteuthis rhombus Troschel, 1857 (Cephalopoda: Thysanoteuthidae) in the Catalan coast(Consejo Superior de Investigaciones Científicas, 2021) Fernández-Álvarez, Fernando Ángel; Colmenero, Ana I.; Barría, Claudio; Irish Research CouncilThe diamondback squid Thysanoteuthis rhombus Troschel, 1857 is a large and elusive oceanic squid spe- cies. Here, we provide the first record of the species for the Catalan coast and integrate this finding in the current knowledge of the species in close areas.Publication El globito de Cthulhu: una nueva joya del Mediterráneo(Quercus, 2021-03) Fernández-Álvarez, Fernando Ángel; Sanchez, Pilar; Villanueva, Roger[No abstract available]Publication Biochemical and cellular characterisation of the Plasmodium falciparum M1 alanyl aminopeptidase (Pf M1AAP) and M17 leucyl aminopeptidase (Pf M17LAP)(Nature Research, 2021-02-03) Mathew, Rency; Wunderlich, Juliane; Thivierge, Karine; Cwiklinski, Krystyna; Dumont, Claire; Tilley, Leann; Rohrbach, Petra; Dalton, John P.; Science Foundation Ireland; Natural Sciences and Engineering Research Council of Canada; Canada Foundation for Innovation; Fonds Québécois de la Recherche sur la Nature et les TechnologiesThe Plasmodium falciparum M1 alanyl aminopeptidase and M17 leucyl aminopeptidase, PfM1AAP and PfM17LAP, are potential targets for novel anti-malarial drug development. Inhibitors of these aminopeptidases have been shown to kill malaria parasites in culture and reduce parasite growth in murine models. The two enzymes may function in the terminal stages of haemoglobin digestion, providing free amino acids for protein synthesis by the rapidly growing intra-erythrocytic parasites. Here we have performed a comparative cellular and biochemical characterisation of the two enzymes. Cell fractionation and immunolocalisation studies reveal that both enzymes are associated with the soluble cytosolic fraction of the parasite, with no evidence that they are present within other compartments, such as the digestive vacuole (DV). Enzyme kinetic studies show that the optimal pH of both enzymes is in the neutral range (pH 7.0–8.0), although PfM1AAP also possesses some activity (< 20%) at the lower pH range of 5.0–5.5. The data supports the proposal that PfM1AAP and PfM17LAP function in the cytoplasm of the parasite, likely in the degradation of haemoglobin-derived peptides generated in the DV and transported to the cytosol.Publication Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver(BMC, 2021-01-11) Cwiklinski, Krystyna; Robinson, Mark W.; Donnelly, Sheila; Dalton, John P.; European Research Council; Science Foundation Ireland; Biotechnology and Biological Sciences Research CouncilBackground The major pathogenesis associated with Fasciola hepatica infection results from the extensive tissue damage caused by the tunnelling and feeding activity of immature flukes during their migration, growth and development in the liver. This is compounded by the pathology caused by host innate and adaptive immune responses that struggle to simultaneously counter infection and repair tissue damage. Results Complementary transcriptomic and proteomic approaches defined the F. hepatica factors associated with their migration in the liver, and the resulting immune-pathogenesis. Immature liver-stage flukes express ~ 8000 transcripts that are enriched for transcription and translation processes reflective of intensive protein production and signal transduction pathways. Key pathways that regulate neoblast/pluripotent cells, including the PI3K-Akt signalling pathway, are particularly dominant and emphasise the importance of neoblast-like cells for the parasite’s rapid development. The liver-stage parasites display different secretome profiles, reflecting their distinct niche within the host, and supports the view that cathepsin peptidases, cathepsin peptidase inhibitors, saposins and leucine aminopeptidases play a central role in the parasite’s destructive migration, and digestion of host tissue and blood. Immature flukes are also primed for countering immune attack by secreting immunomodulating fatty acid binding proteins (FABP) and helminth defence molecules (FhHDM). Combined with published host microarray data, our results suggest that considerable immune cell infiltration and subsequent fibrosis of the liver tissue exacerbates oxidative stress within parenchyma that compels the expression of a range of antioxidant molecules within both host and parasite. Conclusions The migration of immature F. hepatica parasites within the liver is associated with an increase in protein production, expression of signalling pathways and neoblast proliferation that drive their rapid growth and development. The secretion of a defined set of molecules, particularly cathepsin L peptidases, peptidase-inhibitors, saponins, immune-regulators and antioxidants allow the parasite to negotiate the liver micro-environment, immune attack and increasing levels of oxidative stress. This data contributes to the growing F. hepatica -omics information that can be exploited to understand parasite development more fully and for the design of novel control strategies to prevent host liver tissue destruction and pathology.Publication Morphological and molecular assessments of bobtail squids (Cephalopoda: Sepiolidae) reveal a hidden history of biodiversity(Frontiers Media, 2021-01-20) Fernández-Álvarez, Fernando Ángel; Sánchez, Pilar; Villanueva, Roger; Irish Research Council; Spanish Ministry of Economy and CompetitivenessMolecular species delimitation assists taxonomic decisions for challenging species, like cryptic species complexes. Bobtail squids (Family Sepiolidae Leach, 1817) are a very diverse group of benthic and nektonic small to medium size cephalopods with many taxonomic questions to solve. In this study we provided new sequence data for 12 out 17 Mediterranean bobtail squid species including all the genera present i n the area. Other relevant species from other parts of the world were used as comparison. The combined use of several molecular species delimitation methods consistently showed a picture of hidden biodiversity within this family which hinders the use of molecular data isolated from morphological characters. On the one hand, those methods provided contrasting results for the number of recognized species of some morphologically well-defined species. We suggest this can be an effect of recent speciation phenomena followed by an intense morphological drift. On the other hand, cryptic biodiversity was detected among members of several monophyletic clades assigned to the same nominal species, pointing to recent speciation phenomena without a parallel morphological evolution. Although Mediterranean bobtail diversity has been extensively studied for more than a century, a new species of Stoloteuthis Verrill (1881) was discovered and described here, both using molecular and morphological methods. This new research stresses the necessity of combined morphological and molecular studies to correctly assess cephalopod diversity. urn:lsid:zoobank.org:act:57AFBB38-18EA-4F80-B1D4-73519C12694F.Publication An atypical and functionally diverse family of Kunitz-type cysteine/serine proteinase inhibitors secreted by the helminth parasite Fasciola hepatica.(Nature Research, 2020-11-26) Smith, David; Cwiklinski, Krystyna; Jewhurst, Heather; Tikhonova, Irina G.; Dalton, John P.; Department for Employment and Learning, Northern Ireland; European Research Council; Science Foundation Ireland; Horizon 2020Fasciola hepatica is a global parasite of humans and their livestock. Regulation of parasite-secreted cathepsin L-like cysteine proteases associated with virulence is important to fine-tune parasite-host interaction. We uncovered a family of seven Kunitz-type (FhKT) inhibitors dispersed into five phylogenetic groups. The most highly expressed FhKT genes (group FhKT1) are secreted by the newly excysted juveniles (NEJs), the stage responsible for host infection. The FhKT1 inhibitors do not inhibit serine proteases but are potent inhibitors of parasite cathepsins L and host lysosomal cathepsin L, S and K cysteine proteases (inhibition constants¿Publication Potentially handicapped but otherwise functional: Malformations in prey capture tools show no impacts on octopus life(Wiley, 2020-10-17) Fernández-Álvarez, Fernando Ángel; Farré, Marc; Antoni Sánchez‐Márquez, Antoni; Villanueva, Roger; Escolar, Oscar; Navarro, Joan; Irish Research Council; Spanish Ministry of Economy and Competitiveness; European Regional Development Fund; Spanish Ministry of Science, Innovation and UniversitiesLarval mortality is a keystone ecological factor for many benthic octopus since it mostly occurs before their settlement in the sea bottom as benthic juveniles. The literature had revealed that records of adult animals with morphological abnormalities (teratologies) are fewer in species with complex life cycle than in those with direct development. This is a direct consequence of the morphological, physiological, and development challenges that the transition from the larval to the adult morphology represents. During a routine fishing sample, we found an immature female horned octopus with additional buccal structures in two suckers of its ventral arms, likely rendering these suckers as inefficient. Based on the literature about the natural history of octopus, we provide evidence that these abnormalities were present at the moment of hatch. We evaluated the impact of the teratologies by comparing the shape of the buccal beaks and the trophic niche of the individual with five normal conspecifics. Although the beaks showed a different shape than normal individuals, the trophic niche was similar. Surprisingly, the teratological condition of the individual likely had no severe impacts on its life, even though it likely represents a handicap for its survival during its planktonic life. We also comment on other previous records from the literature of teratological adult octopus to highlight the amazing adaptive capacity of octopus to deal with challenging morphologies.Publication Schistosoma mansoni immunomodulatory molecule Sm16/SPO-1/SmSLP is a member of the trematode-specific helminth defence molecules (HDMs)(Public Library of Science, 2020-07-09) Shiels, Jenna; Cwiklinski, Krystyna; Alvarado, Raquel; Thivierge, Karine; Cotton, Sophie; Gonzales Santana, Bibiana; To, Joyce; Donnelly, Sheila; Taggart, Clifford C.; Weldon, Sinead; Dalton, John P.; Department for the Economy; Canadian Institute of Health Research; Science Foundation Ireland; Medical Research Council, UKBackground Sm16, also known as SPO-1 and SmSLP, is a low molecular weight protein (~16kDa) secreted by the digenean trematode parasite Schistosoma mansoni, one of the main causative agents of human schistosomiasis. The molecule is secreted from the acetabular gland of the cercariae during skin invasion and is believed to perform an immune-suppressive function to protect the invading parasite from innate immune cell attack. Methodology/Principal findings We show that Sm16 homologues of the Schistosomatoidea family are phylogenetically related to the helminth defence molecule (HDM) family of immunomodulatory peptides first described in Fasciola hepatica. Interrogation of 69 helminths genomes demonstrates that HDMs are exclusive to trematode species. Structural analyses of Sm16 shows that it consists predominantly of an amphipathic alpha-helix, much like other HDMs. In S. mansoni, Sm16 is highly expressed in the cercariae and eggs but not in adult worms, suggesting that the molecule is of importance not only during skin invasion but also in the pro-inflammatory response to eggs in the liver tissues. Recombinant Sm16 and a synthetic form, Sm16 (34–117), bind to macrophages and are internalised into the endosomal/lysosomal system. Sm16 (34–117) elicited a weak pro-inflammatory response in macrophages in vitro but also suppressed the production of bacterial lipopolysaccharide (LPS)-induced inflammatory cytokines. Evaluation of the transcriptome of human macrophages treated with a synthetic Sm16 (34–117) demonstrates that the peptide exerts significant immunomodulatory effects alone, as well as in the presence of LPS. Pathways most significantly influenced by Sm16 (34–117) were those involving transcription factors peroxisome proliferator-activated receptor (PPAR) and liver X receptors/retinoid X receptor (LXR/RXR) which are intricately involved in regulating the cellular metabolism of macrophages (fatty acid, cholesterol and glucose homeostasis) and are central to inflammatory responses. Conclusions/Significance These results offer new insights into the structure and function of a well-known immunomodulatory molecule, Sm16, and places it within a wider family of trematode-specific small molecule HDM immune-modulators with immuno-biotherapeutic possibilities.Publication Fasciola hepatica serine protease inhibitor family (serpins): Purposely crafted for regulating host proteases(Public Library of Science, 2020-08-06) De Marco Verissimo, Carolina; Jewhurst, Heather L.; Tikhonova, Irina G.; Urbanus, Rolf T.; Maule, Aaron G.; Dalton, John P.; Cwiklinski, Krystyna; Science Foundation Ireland; Department of Education and Learning, Northern IrelandSerine protease inhibitors (serpins) regulate proteolytic events within diverse biological processes, including digestion, coagulation, inflammation and immune responses. The presence of serpins in Fasciola hepatica excretory-secretory products indicates that the parasite exploits these to regulate proteases encountered during its development within vertebrate hosts. Interrogation of the F. hepatica genome identified a multi-gene serpin family of seven members that has expanded by gene duplication and divergence to create an array of inhibitors with distinct specificities. We investigated the molecular properties and functions of two representatives, FhSrp1 and FhSrp2, highly expressed in the invasive newly excysted juvenile (NEJ). Consistent with marked differences in the reactive centre loop (RCL) that executes inhibitor-protease complexing, the two recombinant F. hepatica serpins displayed distinct inhibitory profiles against an array of mammalian serine proteases. In particular, rFhSrp1 efficiently inhibited kallikrein (Ki = 40 nM) whilst rFhSrp2 was a highly potent inhibitor of chymotrypsin (Ki = 0.07 nM). FhSrp1 and FhSrp2 are both expressed on the NEJ surface, predominantly around the oral and ventral suckers, suggesting that these inhibitors protect the parasites from the harmful proteolytic effects of host proteases, such as chymotrypsin, during invasion. Furthermore, the unusual inhibition of kallikrein suggests that rFhSrp1 modulates host responses such as inflammation and vascular permeability by interfering with the kallikrein-kinin system. A vaccine combination of rFhSrp1 and rFhSrp2 formulated in the adjuvant Montanide ISA 206VG elicited modest but non-significant protection against a challenge infection in a rat model, but did induce some protection against liver pathogenesis when compared to a control group and a group vaccinated with two well-studied vaccine candidates, F. hepatica cathepsin L2 and L3. This work highlights the importance of F. hepatica serpins to regulate host responses that enables parasite survival during infection and, coupled with the vaccine data, encourages future vaccine trials in ruminants.Publication The invasive land flatworm Obama nungara (Platyhelminthes: Geoplanidae) reaches a natural environment in the oceanic island of São Miguel (Açores)(Magnolia Press, 2020) Lago-Barcia, Domingo; González-López, José Rafael; Fernández-Álvarez, Fernando Ángel; Irish Research CouncilWe report a new finding of the invasive land flatworm Obama nungara Carbayo et al., 2016 in a natural reserve of the oceanic island of São Miguel (Açores, Portugal) at 947 meters of altitude. This is the first record for this oceanic archipelago and the highest ever reported, representing the sixth island invaded by the species. O. nungara is a top predator of soil fauna, representing a new threat to the fauna of this isolated archipelago.Publication The role of the natural aquatic environment in the dissemination of extended spectrum beta-lactamase and carbapenemase encoding genes: A scoping review(Elsevier, 2020-05-07) Hooban, Brigid; Joyce, Aoife; Fitzhenry, Kelly; Chique, Carlos; Morris, Dearbháile; Environmental Protection Agency, Ireland; Health Service ExecutiveThe natural aquatic environment is a significant contributor to the development and circulation of clinically significant antibiotic resistance genes (ARGs). The potential for the aquatic environment to act as a reservoir for ARG accumulation in areas receiving anthropogenic contamination has been thoroughly researched. However, the emergence of novel ARGs in the absence of external influences, as well as the capacity of environmental bacteria to disseminate ARGs via mobile genetic elements remain relatively unchallenged. In order to address these knowledge gaps, this scoping literature review was established focusing on the detection of two important and readily mobile ARGs, namely, extended spectrum beta-lactamase (ESBL) and carbapenemase genes. This review included 41 studies from 19 different countries. A range of different water bodies including rivers (n = 26), seawaters (n = 6) and lakes (n = 3), amongst others, were analysed in the included studies. ESBL genes were reported in 29/41 (70.7%) studies, while carbapenemase genes were reported in 13/41 (31.7%), including joint reporting in 9 studies. The occurrence of mobile genetic elements was evaluated, which included the detection of integrons (n = 22), plasmids (n = 18), insertion sequences (n = 4) and transposons (n = 3). The ability of environmental bacteria to successfully transfer resistance genes via conjugation was also examined in 11 of the included studies. The findings of this scoping review expose the presence of clinically significant ARGs in the natural aquatic environment and highlights the potential ability of environmental isolates to disseminate these genes among different bacterial species. As such, the results presented demonstrate how anthropogenic point discharges may not act as the sole contributor to the development and spread of clinically significant antibiotic resistances. A number of critical knowledge gaps in current research were also identified. Key highlights include the limited number of studies focusing on antibiotic resistance in uncontaminated aquatic environments as well as the lack of standardisation among methodologies of reviewed investigations.Publication Schistosoma mansoni immunomodulatory molecule Sm16/SPO-1/SmSLP is a member of the trematode-specific helminth defence molecules (HDMs)(Public Library of Science, 2020-07-09) Shiels, Jenna; Cwiklinski, Krystyna; Alvarado, Raquel; Thivierge, Karine; Cotton, Sophie; Gonzales Santana, Bibiana; To, Joyce; Donnelly, Sheila; Taggart, Clifford C.; Weldon, Sinead; Dalton, John P.; Science Foundation IrelandSm16, also known as SPO-1 and SmSLP, is a low molecular weight protein (~16kDa) secreted by the digenean trematode parasite Schistosoma mansoni, one of the main causative agents of human schistosomiasis. The molecule is secreted from the acetabular gland of the cercariae during skin invasion and is believed to perform an immune-suppressive function to protect the invading parasite from innate immune cell attack. We show that Sm16 homologues of the Schistosomatoidea family are phylogenetically related to the helminth defence molecule (HDM) family of immunomodulatory peptides first described in Fasciola hepatica. Interrogation of 69 helminths genomes demonstrates that HDMs are exclusive to trematode species. Structural analyses of Sm16 shows that it consists predominantly of an amphipathic alpha-helix, much like other HDMs. In S. mansoni, Sm16 is highly expressed in the cercariae and eggs but not in adult worms, suggesting that the molecule is of importance not only during skin invasion but also in the pro-inflammatory response to eggs in the liver tissues. Recombinant Sm16 and a synthetic form, Sm16 (34-117), bind to macrophages and are internalised into the endosomal/lysosomal system. Sm16 (34-117) elicited a weak pro-inflammatory response in macrophages in vitro but also suppressed the production of bacterial lipopolysaccharide (LPS)-induced inflammatory cytokines. Evaluation of the transcriptome of human macrophages treated with a synthetic Sm16 (34-117) demonstrates that the peptide exerts significant immunomodulatory effects alone, as well as in the presence of LPS. Pathways most significantly influenced by Sm16 (34-117) were those involving transcription factors peroxisome proliferator-activated receptor (PPAR) and liver X receptors/retinoid X receptor (LXR/RXR) which are intricately involved in regulating the cellular metabolism of macrophages (fatty acid, cholesterol and glucose homeostasis) and are central to inflammatory responses. These results offer new insights into the structure and function of a well-known immunomodulatory molecule, Sm16, and places it within a wider family of trematode-specific small molecule HDM immune-modulators with immuno-biotherapeutic possibilities.Publication Global biodiversity of the genus Ommastrephes (Ommastrephidae: Cephalopoda): an allopatric cryptic species complex(Oxford University Press (OUP), 2020-03-20) Fernández-Álvarez, Fernando Ángel; Braid, Heather E.; Nigmatullin, Chingis M.; Bolstad, Kathrin S. R.; Haimovici, Manuel; Sánchez, Pilar; Sajikumar, Kurichithara K.; Ragesh, Nadakkal; Villanueva, RogerCryptic speciation among morphologically homogeneous species is a phenomenon increasingly reported in cosmopolitan marine invertebrates. This situation usually leads to the discovery of new species, each of which occupies a smaller fraction of the original distributional range. The resolution of the taxonomic status of species complexes is essential because species are used as the unit of action for conservation and natural resource management politics. Before the present study, Ommastrephes bartramii was considered a monotypic cosmopolitan species with a discontinuous distribution. Here, individuals from nearly its entire distributional range were evaluated with mitochondrial DNA (cytochrome c oxidase subunit I and 16S rRNA). Four distinct species were consistently identified using four molecular species delimitation methods. These results, in combination with morphological and metabolic information from the literature, were used to resurrect three formerly synonymized names (Ommastrephes brevimanus, Ommastrephes caroli and Ommastrephes cylindraceus) and to propose revised distributional ranges for each species. In addition, diagnostic characters from the molecular sequences were incorporated in the species description. At present, only one of the four newly recognized species (Ommastrephes bartramii) is commercially exploited by fisheries in the North Pacific, but it now appears that the distributional range of this species is far smaller than previously believed, which is an essential consideration for effective fisheries management