Imaging Mass Spectrometry Reveals Alterations in N-Linked Glycosylation That Are Associated With Histopathological Changes in Nonalcoholic Steatohepatitis in Mouse and Human.

Nonalcoholic steatohepatitis (NASH) is the progressive form of nonalcoholic fatty liver disease (NAFLD) and is characterized by inflammation, hepatocyte injury, and fibrosis. Further, NASH is a risk factor for cirrhosis and hepatocellular carcinoma. Previous research demonstrated that serum N-glycan profiles can be altered in NASH patients. Here, we hypothesized that these N-glycan modifications may be associated with specific liver damage in NAFLD and NASH. To investigate the N-glycome profile in tissue, imaging mass spectrometry was used for a qualitative and quantitative in situ N-linked glycan analysis of mouse and human NAFLD/NASH tissue. A murine model was used to induce NAFLD and NASH through ad libitum feeding with either a high-fat diet or a Western diet, respectively. Mice fed a high-fat diet or Western diet developed inflammation, steatosis, and fibrosis, consistent with NAFLD/NASH phenotypes. Induction of NAFLD/NASH for 18 months using high caloric diets resulted in increased expression of mannose, complex/fucosylated, and hybrid N-glycan structures compared to control mouse livers. To validate the animal results, liver biopsy specimens from 51 human NAFLD/NASH patients representing the full range of NASH Clinical Research Network fibrosis stages were analyzed. Importantly, the same glycan alterations observed in mouse models were observed in human NASH biopsies and correlated with the degree of fibrosis. In addition, spatial glycan alterations were localized specifically to histopathological changes in tissue like fibrotic and fatty areas. We demonstrate that the use of standard staining's combined with imaging mass spectrometry provide a full profile of the origin of N-glycan modifications within the tissue. These results indicate that the spatial distribution of abundances of released N-glycans correlate with regions of tissue steatosis associated with NAFLD/NASH.

Minimum complexity integrated photonic architecture for delay-based reservoir computing.

Reservoir computing is an analog bio-inspired computation scheme for efficiently processing time-dependent signals, the photonic implementations of which promise a combination of massive parallel information processing, low power consumption, and high-speed operation. However, most of these implementations, especially for the case of time-delay reservoir computing, require extensive multi-dimensional parameter optimization to find the optimal combination of parameters for a given task. We propose a novel, largely passive integrated photonic TDRC scheme based on an asymmetric Mach-Zehnder interferometer in a self-feedback configuration, where the nonlinearity is provided by the photodetector, and with only one tunable parameter in the form of a phase shifting element that, as a result of our configuration, allows also to tune the feedback strength, consequently tuning the memory capacity in a lossless manner. Through numerical simulations, we show that the proposed scheme achieves good performance -when compared to other integrated photonic architectures- on the temporal bitwise XOR task and various time series prediction tasks, while greatly reducing hardware and operational complexity.

Experimental infection trials with European North Atlantic ranavirus (Iridoviridae) isolated from lumpfish (Cyclopterus lumpus, L.).

European North Atlantic ranavirus (ENARV, Iridoviridae), is a ranavirus species recently isolated from lumpfish (Cyclopterus lumpus, L.), which are used as cleaner fish in Atlantic salmon (Salmo salar) farming in Northern Europe. This study aimed to investigate (1) the virulence of ENARV isolates from Ireland, Iceland and the Faroe Islands to lumpfish; (2) horizontal transmission between lumpfish; and (3) virulence to Atlantic salmon parr. Lumpfish were challenged in a cohabitation model using intraperitoneally (IP) injected shedders, and naïve cohabitants. IP challenge with isolates from Iceland (1.9 × 107 TCID50  ml-1 ) and the Faroe Islands (5.9 × 107 TCID50  ml-1 ) reduced survival in lumpfish, associated with consistent pathological changes. IP challenge with the Irish strain (8.6 × 105 TCID50  ml-1 ) did not significantly reduce survival in lumpfish, but the lower challenge titre complicated interpretation. Horizontal transmission occurred in all strains tested, but no clinical impact was demonstrated in cohabitants. Salmon parr were challenged by IP injection with the Irish isolate, no virulence or virus replication were demonstrated. A ranavirus qPCR assay, previously validated for fish ranaviruses, was first used to detect ENARV in tissues of both in lumpfish and Atlantic salmon. This study provides the first data on the assessment of virulence of ENARV isolates to lumpfish and salmon, guidelines for the diagnosis of ENARV infection, and poses a basis for further investigations into virulence markers.

Giant periosteal aggressive epithelioid osteoblastoma: 21-year-old male presents case in the midshaft of his femur.

We report a rare case of giant periosteal osteoblastoma in the femur of a 21-year-old male. The patient presented with a painful, firm, non-tender mass in his left thigh. The pain was worse at night and was temporarily relieved with NSAIDS. He had no fevers, night sweats, or weight loss. The patient underwent preoperative radiological studies including plain radiographs, MRI, bone scan, and CT scan. An open biopsy was subsequently performed that was consistent with an aggressive, epithelioid osteoblastoma. Pathology demonstrated a neoplasm characterized by cohesive sheets of epithelioid osteoblasts, mixed with areas of conventional osteoblastoma displaying prominent osteoblastic rimming of woven bone trabeculae in a fibrovascular stroma. The patient subsequently underwent resection, cryosurgery, fixation, and bone grafting with cortical strut allografts. At final follow-up, 32 months postoperatively, there was no evidence of local recurrence. The patient had resumed all his normal activities. He could run without pain and had no restrictions with activities. The goal of this case report is to aid professionals in the diagnosis and treatment of highly uncommon aggressive osteoblastomas.

Local and systemic humoral immune response in farmed Atlantic salmon (Salmo salar L.) under a natural amoebic gill disease outbreak.

Amoebic gill disease (AGD), caused by the protozoan parasite Neoparamoeba perurans, is one of the most significant infectious diseases for Atlantic salmon (Salmo salar L.) mariculture. The present study investigated the humoral immune response (both local in gill mucus and systemic in serum) of farmed Atlantic salmon naturally infected with N. perurans in commercial sea pens, at two different stages of the disease and after freshwater treatment. Parameters analysed included activity of immune related enzymes (i.e. lysozyme, peroxidase, protease, anti-protease, esterase, alkaline phosphatase), IgM levels, and the terminal carbohydrate profile in the gill mucus. Overall, greater variations between groups were noted in the immune parameters determined in gill mucus than the equivalent in the serum. In gill mucus, IgM levels and peroxidase, lysozyme, esterase and protease activities were decreased in fish showing longer exposure time to the infection and higher disease severity, then showed a sequential increase after treatment. Results obtained highlight the capacity of gills to elicit a local response to the infection, indicate an impaired immune response at the later stages of the disease, and show partial reestablishment of the host immune status after freshwater treatment. In addition to providing data on the humoral response to AGD, this study increases knowledge on gill mucosal humoral immunity, since some of the parameters were analysed for the first time in gill mucus.

What Are the Functional Results and Complications With Long Stem Hemiarthroplasty in Patients With Metastases to the Proximal Femur?

BACKGROUND: Traditional treatments for pathological fractures of the proximal femur resulting from metastatic bone disease include fixation with intramedullary nailing supplemented with polymethylmethacrylate, osteosynthesis with a plate-screw construct and polymethylmethacrylate, or endoprosthetic reconstruction. Despite the frequent practice of these treatments, treatment outcomes have not been rigorously compared. In addition, very few studies examine specific approaches to endoprosthetic reconstruction such as long stem hemiarthroplasty. QUESTIONS/PURPOSES: This study examines survival, functional outcomes, and complications associated with long stem hemiarthroplasty in a small group of patients treated for impending and actual pathologic fractures of the proximal femur resulting from metastatic bone disease. METHODS: Between 2012 and 2015, 21 patients were treated with long stem cemented hemiarthroplasty in 22 limbs. During that time, indications for this approach included lesions from metastases, myeloma, or lymphoma involving the proximal femur that resulted in an impending or actual pathological fracture. An impending fracture was classified as a painful lesion with at least 50% cortical erosion. During the study period, six patients with proximal femoral metastases not deemed to meet these indications were treated with other surgical approaches such as intramedullary nailing supplemented with polymethylmethacrylate and osteosynthesis with a plate-screw construct and polymethylmethacrylate. Mortality was tracked through medical records and phone calls to the patients and their families. Followup for the entire group of patients (n = 22) ranged from 1 to 27 months with a mean duration of 11 months. For patients with at least 1 year of followup (n = 11), the mean duration was 18 months (range, 12-27 months) and for patients with less than 1 year of followup (n = 11), the mean duration was 3 months (range, 1-11 months). Functional outcomes were evaluated according to the Musculoskeletal Tumor Society (MSTS) scoring system for lower extremities, the Eastern Cooperative Oncology Group (ECOG) Scale of Performance Status, and the Karnofsky Performance Scale (KPS) Index. Scores and complications were determined by direct patient examination, retrospective chart review, review of a longitudinally maintained institutional database, and followup phone calls. RESULTS: Ten patients died of disease within the followup period. Before surgery, the median total MSTS score for the entire group of patients (n = 22) was 4.5 (range, 0-23), the median ECOG score was 3.5 (range, 1-4), and the median KPS score was 40 (range, 30-70). Postoperatively, the median total MSTS score (measured at most recent followup) for the entire group of patients was 21 (range, 5-30), the median ECOG score was 2 (range, 0-3, 68% ≤ 2), and the median KPS score was 60 (range, 40-100). For the 11 patients with at least 1 year of followup, the median total MSTS score (measured at most recent followup) was 27 (range, 21-30), the median ECOG score was 1 (range, 0-2, 100% ≤ 2), and the median KPS score was 80 (range, 60-100). For the remaining 11 patients with less than 1 year of followup, the median total MSTS score (measured at most recent followup) was 11 (range, 5-25), the median ECOG score was 3 (range, 1-3, 36% ≤ 2), and the median KPS score was 40 (range, 40-80). Complications included one periprosthetic fracture resulting from a fall, three cases of radiation-induced edema, and two cases of sciatica that developed unrelated to the procedure. CONCLUSIONS: Long stem cemented hemiarthroplasty results in fair levels of function in a complex population of patients whose prognosis is sometimes measured only in months and who otherwise might be disabled by their metastatic lesions. Comparative trials applying consistent indications and inclusion criteria should be performed between this approach and fixation with intramedullary nailing supplemented with polymethylmethacrylate as well as osteosynthesis with a plate-screw construct and polymethylmethacrylate. LEVEL OF EVIDENCE: Level IV, therapeutic study.

Molecular composition of organic aerosols at urban background and road tunnel sites using ultra-high resolution mass spectrometry.

Organic aerosol composition in the urban atmosphere is highly complex and strongly influenced by vehicular emissions which vary according to the make-up of the vehicle fleet. Normalized test measurements do not necessarily reflect real-world emission profiles and road tunnels are therefore ideal locations to characterise realistic traffic particle emissions with minimal interference from other particle sources and from atmospheric aging processes affecting their composition. In the current study, the composition of fine particles (diameter ≤2.5 µm) at an urban background site (Elms Road Observatory Site) and a road tunnel (Queensway) in Birmingham, UK, were analysed with direct infusion, nano-electrospray ionisation ultrahigh resolution mass spectrometry (UHRMS). The overall particle composition at these two sites is compared with an industrial harbour site in Cork, Ireland, with special emphasis on oxidised mono-aromatics, polycyclic aromatic hydrocarbons (PAHs) and nitro-aromatics. Different classification criteria, such as double bond equivalents, aromaticity index and aromaticity equivalent are used and compared to assess the fraction of aromatic components in the approximately one thousand oxidized organic compounds at the different sampling locations.

Assessment of Impulsive and Continuous Low-Frequency Noise in Irish Waters.

As part of the European Union Marine Strategy Framework Directive (MSFD), member states are required to address noise pollution in the marine environment under Descriptor 11. This study aimed to provide a practical desk-based application of Descriptor 11 assessment, focusing on the main contributors of ocean noise pollution in Irish waters, seismic surveying and shipping. To highlight specific geographical areas subject to elevated levels of noise pollution, the proportion of days over a calendar year that seismic air guns were operational was calculated and the vessel density per 50-km(2) grids was determined across Ireland's exclusive economic zone (EEZ). Additionally, cetacean sighting data were used to determine the degree of spatial overlap between areas of elevated noise pollution and areas of cetacean abundance.

The Use of Deep Water Berths and the Effect of Noise on Bottlenose Dolphins in the Shannon Estuary cSAC.

The Shannon Estuary on the west coast of Ireland is one of Europe's premier deepwater berths catering for ships up to 200,000 deadweight tonnage. It is also Ireland's only designated candidate special area of conservation for bottlenose dolphins under the EU Habitats Directive. Long-term static acoustic monitoring was carried out at a number of intensive shipping sites. In 2012, noise monitoring took place over a 6-month period (at 1 site) as part of Ireland's requirements under the Marine Strategy Framework Directive (MSFD). This is the first assessment of the potential effect of vessel traffic on the behavior of this discrete dolphin population.

Single-particle speciation of alkylamines in ambient aerosol at five European sites.

Alkylamines are associated with both natural and anthropogenic sources and have been detected in ambient aerosol in a variety of environments. However, little is known about the ubiquity or relative abundance of these species in Europe. In this work, ambient single-particle mass spectra collected at five sampling sites across Europe have been analysed for their alkylamine content. The aerosol time-of-flight mass spectrometer (ATOFMS) data used were collected in Ireland (Cork), France (Paris, Dunkirk and Corsica) and Switzerland (Zurich) between 2008 and 2013. Each dataset was queried for mass spectral marker ions associated with the following ambient alkylamines: dimethylamine (DMA), trimethylamine (TMA), diethylamine (DEA), triethylamine (TEA), dipropylamine (DPA) and tripropylamine (TPA). The fraction of ambient particles that contained detectable alkylamines ranged from 1 to 17 % depending on location, with the highest fractions observed in Paris and Zurich in the winter months. The lowest fractions were observed at coastal sites, where the influence of animal husbandry-related alkylamine emissions is also expected to be lowest. TMA was the most ubiquitous particle phase alkylamine detected and was observed at all locations. Alkylamines were found to be internally mixed with both sulphate and nitrate for each dataset, suggesting that aminium salt formation may be important at all sites investigated. Interestingly, in Corsica, all alkylamine particles detected were also found to be internally mixed with methanesulphonic acid (MSA), indicating that aminium methanesulphonate salts may represent a component of marine ambient aerosol in the summer months. Internal mixing of alkylamines with sea salt was not observed, however. Alkylamine-containing particle composition was found to be reasonably homogeneous at each location, with the exception of the Corsica and Dunkirk sites, where two and four distinct mixing states were observed, respectively.

Distribution models of baleen whale species in the Irish Exclusive Economic Zone to inform management and conservation.

Irish waters are under increasing pressure from anthropogenic sources including the development of offshore renewable energy, vessel traffic and fishing activity. Spatial planning requires robust datasets on species distribution and the identification of important habitats to inform the planning process. Despite limited survey effort, long-term citizen science data on whale presence are available and provide an opportunity to fill information gaps. Using presence-only data as well as a variety of environmental variables, we constructed seasonal ensemble species distribution models based on five different algorithms for minke whales, fin whales, humpback whales, sei whales, and blue whales. The models predicted that the coastal waters off the south and west of Ireland are particularly suitable for minke, fin and humpback whales. Offshore waters in the Porcupine Seabight area were identified as a relevant habitat for fin whales, sei whales and blue whales. We combined model outputs with data on maritime traffic, fishing activity and offshore wind farms to measure the exposure of all the species to these pressures, identifying areas of concern. This study serves as a baseline for the species presence in Irish waters over the last two decades to help develop appropriate marine spatial plans in the future.

Export pathways of biosolid derived microplastics in soil systems - Findings from a temperate maritime climate.

The environmental fate of microplastics (MPs) added to agricultural soils remains poorly understood, particularly regarding their mobility in soils. Here we investigate the potential for MP export from soil to surface waters and groundwater in two agricultural settings with a 20-year history of biosolid treatment. A third site where biosolids had never been applied served as a reference (Field R). The potential for MP export along overland and interflow pathways to surface waters was determined from MP abundances in shallow surface cores (10 cm) along ten down-slope transects (five each for Field A and B), and through MP abundances in effluent from a sub-surface land drain. The risk of vertical MP migration was assessed from 2 m cores, and from MP abundances in groundwater sampled from the core boreholes. XRF Itrax core scanning was conducted on two of the deep cores to capture high-resolution optical and 2-D radiographic imaging. Results suggest limited MP mobility at depths >35 cm, with MPs largely recovered in surface soils characterised by lower compaction. Furthermore, abundances of MPs across the surface cores were comparable, with no evidence of MP accumulations observed. Average MP abundance in the top 10 cm of soil across Field A and B was 365 ± 302 MP kg-1, with 0.3 MP l-1 and 1.6 MP l-1 recovered from the groundwater and field drainpipe water samples, respectively. MP abundances were significantly higher in fields treated with biosolids than in Field R (90 ± 32 MP kg-1 soil). Findings suggest ploughing is the most significant driver of MP mobility in upper soil layers, however the potential for overland or interflow movement cannot be excluded, particularly for fields that may be artificially drained.

Reconfigurable Multifunctional van der Waals Ferroelectric Devices and Logic Circuits.

Emerging reconfigurable devices are fast gaining popularity in the search for next-generation computing hardware, while ferroelectric engineering of the doping state in semiconductor materials has the potential to offer alternatives to traditional von-Neumann architecture. In this work, we combine these concepts and demonstrate the suitability of reconfigurable ferroelectric field-effect transistors (Re-FeFETs) for designing nonvolatile reconfigurable logic-in-memory circuits with multifunctional capabilities. Modulation of the energy landscape within a homojunction of a 2D tungsten diselenide (WSe2) layer is achieved by independently controlling two split-gate electrodes made of a ferroelectric 2D copper indium thiophosphate (CuInP2S6) layer. Controlling the state encoded in the program gate enables switching between p, n, and ambipolar FeFET operating modes. The transistors exhibit on-off ratios exceeding 106 and hysteresis windows of up to 10 V width. The homojunction can change from Ohmic-like to diode behavior with a large rectification ratio of 104. When programmed in the diode mode, the large built-in p-n junction electric field enables efficient separation of photogenerated carriers, making the device attractive for energy-harvesting applications. The implementation of the Re-FeFET for reconfigurable logic functions shows how a circuit can be reconfigured to emulate either polymorphic ferroelectric NAND/AND logic-in-memory or electronic XNOR logic with a long retention time exceeding 104 s. We also illustrate how a circuit design made of just two Re-FeFETs exhibits high logic expressivity with reconfigurability at runtime to implement several key nonvolatile 2-input logic functions. Moreover, the Re-FeFET circuit demonstrates high compactness, with an up to 80% reduction in transistor count compared to standard CMOS design. The 2D van de Waals Re-FeFET devices therefore exhibit promising potential for both More-than-Moore and beyond-Moore future of electronics, in particular for an energy-efficient implementation of in-memory computing and machine learning hardware, due to their multifunctionality and design compactness.

Accounting for the effects of lipids in stable isotope (δ13C and δ15N values) analysis of skin and blubber of balaenopterid whales.

RATIONALE: Stable isotope values (δ(13)C and δ(15)N) of darted skin and blubber biopsies can shed light on habitat use and diet of cetaceans, which are otherwise difficult to study. Non-dietary factors affect isotopic variability, chiefly the depletion of (13)C due to the presence of (12)C-rich lipids. The efficacy of post hoc lipid-correction models (normalization) must be tested. METHODS: For tissues with high natural lipid content (e.g., whale skin and blubber), chemical lipid extraction or normalization is necessary. C:N ratios, δ(13)C values and δ(15)N values were determined for duplicate control and lipid-extracted skin and blubber of fin (Balaenoptera physalus), humpback (Megaptera novaeangliae) and minke whales (B. acutorostrata) by continuous-flow elemental analysis isotope ratio mass spectrometry (CF-EA-IRMS). Six different normalization models were tested to correct δ(13)C values for the presence of lipids. RESULTS: Following lipid extraction, significant increases in δ(13)C values were observed for both tissues in the three species. Significant increases were also found for δ(15)N values in minke whale skin and fin whale blubber. In fin whale skin, the δ(15)N values decreased, with no change observed in humpback whale skin. Non-linear models generally out-performed linear models and the suitability of models varied by species and tissue, indicating the need for high model specificity, even among these closely related taxa. CONCLUSIONS: Given the poor predictive power of the models to estimate lipid-free δ(13)C values, and the unpredictable changes in δ(15)N values due to lipid-extraction, we recommend against arithmetical normalization in accounting for lipid effects on δ(13)C values for balaenopterid skin or blubber samples. Rather, we recommend that duplicate analysis of lipid-extracted (δ(13)C values) and non-treated tissues (δ(15)N values) be used.

Host Response of Atlantic Salmon (Salmo salar) Re-Inoculated with Paramoeba perurans.

In aquaculture, recurrence rates of amoebic gill disease (AGD) caused by the ectoparasite Paramoeba perurans are high and no prophylactic strategies exist for disease prevention. In this study, Atlantic salmon (Salmo salar) were initially inoculated with P. perurans and following the development of amoebic gill disease were treated with freshwater immersion on day 21 and day 35 post inoculation. Fish were re-inoculated following a negative qPCR analysis for the presence of P. perurans. The gill host immune response was investigated at 7, 14, and 18 days post re-inoculation. Differential proteome expression of immune related proteins was assessed by comparison of each time point against naïve controls. In the gill, some proteins of the innate immune system were expressed in response to gill re-colonization by P. perurans, while no features of adaptive immunity were found to be differentially expressed. Many of the proteins identified are novel in the context of AGD and their expression profiles suggest that their roles in the response to disease development and progression in single or multiple infections warrant further investigation.

Investigation of the Initial Host Response of Naïve Atlantic Salmon (Salmo salar) Inoculated with Paramoeba perurans.

Amoebic Gill Disease (AGD), caused by the ectoparasite Paramoeba perurans is characterised by hyperplasia of the gill epithelium and lamellar fusion. In this study, the initial host response of naïve Atlantic salmon (Salmo salar) inoculated with P. perurans was investigated. Using gel-free proteomic techniques and mass spectrometry gill and serum samples were analysed at 7 timepoints (2, 3, 4, 7, 9, 11 and 14 days) post-inoculation with P. perurans. Differential expression of immune related proteins was assessed by comparison of protein expression from each time point against naïve controls. Few host immune molecules associated with innate immunity showed increased expression in response to gill colonisation by amoebae. Furthermore, many proteins with roles in immune signalling, phagocytosis and T-cell proliferation were found to be inhibited upon disease progression. Initially, various immune factors demonstrated the anticipated increase in expression in response to infection in the serum while some immune inhibition became apparent at the later stages of disease progression. Taken together, the pro-immune trend observed in serum, the lack of a robust early immune response in the gill and the diversity of those proteins in the gill whose altered expression negatively impact the immune response, support the concept of a pathogen-derived suppression of the host response.

Differential Exoproteome and Biochemical Characterisation of Neoparamoeba perurans.

Infection with the protozoan ectoparasite Neoparamoeba perurans, the causative agent of AGD, remains a global threat to salmonid farming. This study aimed to analyse the exoproteome of both an attenuated and virulent N. perurans isolate using proteomics and cytotoxicity testing. A disproportionate presence of proteins from the co-cultured microbiota of N. perurans was revealed on searching an amalgamated database of bacterial, N. perurans and Amoebozoa proteins. LC-MS/MS identified 33 differentially expressed proteins, the majority of which were upregulated in the attenuated exoproteome. Proteins of putative interest found in both exoproteomes were maltoporin, ferrichrome-iron receptor, and putative ferric enterobactin receptor. Protease activity remained significantly elevated in the attenuated exoproteome compared with the virulent exoproteome. Similarly, the attenuated exoproteome had a significantly higher cytotoxic effect on rainbow trout gill cell line (RTgill W1) cells compared with the virulent exoproteome. The presence of a phosphatase and serine protease in the virulent exoproteome may facilitate AGD infection but do not appear to be key players in causing cytotoxicity. Altogether, this study reveals prolonged culture of N. perurans affects the exoproteome composition in favour of nutritional acquisition, and that the current culturing protocol for virulent N. perurans does not facilitate the secretion of virulence factors.

Investigation of the transcriptomic response in Atlantic salmon (Salmo salar) gill exposed to Paramoeba perurans during early onset of disease.

Amoebic Gill Disease (AGD), caused by the protozoan extracellular parasite Paramoeba perurans (P. perurans) is a disease affecting Atlantic salmon (Salmo salar). This study investigated the gill transcriptomic profile of pre-clinical AGD using RNA-sequencing (RNA-seq) technology. RNA-seq libraries generated at 0, 4, 7, 14 and 16 days post infection (dpi) identified 19,251 differentially expressed genes (DEGs) of which 56.2% were up-regulated. DEGs mapped to 224 Gene Ontology (GO) terms including 140 biological processes (BP), 45 cellular components (CC), and 39 molecular functions (MF). A total of 27 reference pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and 15 Reactome gene sets were identified. The RNA-seq data was validated using real-time, quantitative PCR (qPCR). A host immune response though the activation of complement and the acute phase genes was evident at 7 dpi, with a concurrent immune suppression involving cytokine signalling, notably in interleukins, interferon regulatory factors and tumour necrosis factor-alpha (tnf-α) genes. Down-regulated gene expression with involvement in receptor signalling pathways (NOD-like, Toll-like and RIG-1) were also identified. The results of this study support the theory that P. perurans can evade immune surveillance during the initial stages of gill colonisation through interference of signal transduction pathways.

Comparative proteomic profiling of newly acquired, virulent and attenuated Neoparamoeba perurans proteins associated with amoebic gill disease.

The causative agent of amoebic gill disease, Neoparamoeba perurans is reported to lose virulence during prolonged in vitro maintenance. In this study, the impact of prolonged culture on N. perurans virulence and its proteome was investigated. Two isolates, attenuated and virulent, had their virulence assessed in an experimental trial using Atlantic salmon smolts and their bacterial community composition was evaluated by 16S rRNA Illumina MiSeq sequencing. Soluble proteins were isolated from three isolates: a newly acquired, virulent and attenuated N. perurans culture. Proteins were analysed using two-dimensional electrophoresis coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS). The challenge trial using naïve smolts confirmed a loss in virulence in the attenuated N. perurans culture. A greater diversity of bacterial communities was found in the microbiome of the virulent isolate in contrast to a reduction in microbial community richness in the attenuated microbiome. A collated proteome database of N. perurans, Amoebozoa and four bacterial genera resulted in 24 proteins differentially expressed between the three cultures. The present LC-MS/MS results indicate protein synthesis, oxidative stress and immunomodulation are upregulated in a newly acquired N. perurans culture and future studies may exploit these protein identifications for therapeutic purposes in infected farmed fish.

Polycyclic aromatic hydrocarbons (PAHs) in seabird eggs in Ireland.

Seabird eggs are considered a favourable matrix for monitoring marine pollutants and are widely used as higher trophic level indicators. Concentrations of Polycyclic aromatic hydrocarbons (Σ15PAH) were determined in the eggs of four piscivorous seabirds in Ireland from multiple colonies for the first time, Common Guillemot Uria aalge, Northern Gannet Morus bassanus, Common Tern Sterna hirundo and Arctic Tern S. paradisaea. PAH concentrations were generally lower than levels detected in eggs from other seabird studies and considerably lower than concentrations associated with no adverse effect in the eggs of domestic avian species. This study indicates potential site and species differences in PAH concentrations. Baseline data of PAHs in a range of seabird species from this study may provide an important reference point should a major pollution event occur in European waters, such as an oil spill.