There is detectable variation in the lipidomic profile between stable and progressive patients with idiopathic pulmonary fibrosis (IPF)

Background Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial lung disease characterized by fibrosis and progressive loss of lung function. The pathophysiological pathways involved in IPF are not well understood. Abnormal lipid metabolism has been described in various other chronic lung diseases including asthma and chronic obstructive pulmonary disease (COPD). However, its potential role in IPF pathogenesis remains unclear. Methods In this study, we used ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) to characterize lipid changes in plasma derived from IPF patients with stable and progressive disease. We further applied a data-independent acquisition (DIA) technique called SONAR, to improve the specificity of lipid identification. Results Statistical modelling showed variable discrimination between the stable and progressive subjects, revealing differences in the detection of triglycerides (TG) and phosphatidylcholines (PC) between progressors and stable IPF groups, which was further confirmed by mass spectrometry imaging (MSI) in IPF tissue. Conclusion This is the first study to characterise lipid metabolism between stable and progressive IPF, with results suggesting disparities in the circulating lipidome with disease progression

THE STRUCTURE OF SUBTIDAL MACROALGAL ASSEMBLAGES AT THE TAMOIOS ECOLOGICAL STATION, A THREATENED CONSERVATION UNIT IN RIO DE JANEIRO, BRAZIL

The structure of subtidal rocky bottom communities at Tamoios Ecological Station (TES), situated in Ilha Grande Bay, Rio de Janeiro State, as well as in other Brazilian marine protected areas, is insufficiently characterized. The present study describes the macroalgal assemblages of shallow subtidal rocky bottoms on two islands of the TES-Imboassica (IM) and Búzios Pequena (BP)adopting species and genera as observational units. Two sites were surveyed on each island in summer 2011. Random 30x30 cm quadrats (n=3) were scraped to collect all macroalgae except crustose species. The subtidal assemblages, in which 58 macroalgal species occurred, were characterized by the high frequency and percent cover of Sargassum vulgare C. Agardh (56.8±8.4%). The sites differed significantly in total number of species and Shannon-Weiner diversity index (PERMANOVA, p5%) were Sargassum, Laurencia, Wrangelia, Canistrocarpus, Asparagopsis, Hypnea, Ceratodictyon, Gayliella, Spyridia and Chondria.Dissimilarities within and between the islands, as shown by nMDS of the cover data, suggest that different spatial scales should be considered in monitoring the rocky bottom communities of Ilha Grande Bay

Comparing the Invasibility of Experimental “Reefs” with Field Observations of Natural Reefs and Artificial Structures

Natural systems are increasingly being modified by the addition of artificial habitats which may facilitate invasion. Where invaders are able to disperse from artificial habitats, their impact may spread to surrounding natural communities and therefore it is important to investigate potential factors that reduce or enhance invasibility. We surveyed the distribution of non-indigenous and native invertebrates and algae between artificial habitats and natural reefs in a marine subtidal system. We also deployed sandstone plates as experimental ‘reefs’ and manipulated the orientation, starting assemblage and degree of shading. Invertebrates (non-indigenous and native) appeared to be responding to similar environmental factors (e.g. orientation) and occupied most space on artificial structures and to a lesser extent reef walls. Non-indigenous invertebrates are less successful than native invertebrates on horizontal reefs despite functional similarities. Manipulative experiments revealed that even when non-indigenous invertebrates invade vertical “reefs”, they are unlikely to gain a foothold and never exceed covers of native invertebrates (regardless of space availability). Community ecology suggests that invertebrates will dominate reef walls and algae horizontal reefs due to functional differences, however our surveys revealed that native algae dominate both vertical and horizontal reefs in shallow estuarine systems. Few non-indigenous algae were sampled in the study, however where invasive algal species are present in a system, they may present a threat to reef communities. Our findings suggest that non-indigenous species are less successful at occupying space on reef compared to artificial structures, and manipulations of biotic and abiotic conditions (primarily orientation and to a lesser extent biotic resistance) on experimental “reefs” explained a large portion of this variation, however they could not fully explain the magnitude of differences

Colonization and community development of fish assemblages associated with estuarine artificial reefs

Despite the long history of the development of artificial structures in NSW estuaries there are no studies that provide any comprehensive scientific evaluation of post-deployment goals. We assessed the effectiveness of estuarine artificial reefs as a fisheries enhancement initiative; described the diversity and abundance of species associated with them, and detailed the patterns of colonization and community development associated with an artificial reef deployment in Lake Macquarie, a large coastal barrier lagoon on the southeast coast of Australia. Six artificial reefs (one artificial reef group), constructed from artificial reef units (Reef Balls®), were deployed in December 2005 and sampled six times per season over two years using baited remote underwater video (BRUV). Colonization of the artificial reef group was relatively rapid with the majority of species identified over the two-year study period observed within the first year post-deployment. Overall, 27 species from 17 families were identified. Key colonising species included Pelates sexlineatus (Terapontidae), Acanthopagrus australis (Sparidae), Pagrus auratus (Sparidae) and Rhabdosargus sarba (Sparidae). Species richness showed evidence of potential seasonal fluctuations, being higher in warm water months (Summer/Autumn), and lower in the colder water months (Winter/Spring), while species diversity increased significantly with reef age. Fish assemblage composition remained relatively stable after the first year of sampling, with few discernible patterns in assemblage structure evident after the first year. Distinct separation in reef age groupings was evident during the second year of sampling; a pattern primarily driven by a decrease in abundance of P. sexlineatus, a result of the isolated nature of the artificial reefs and the interrelated effects of density dependence and predation.A despeito da longa história do desenvolvimento de estruturas artificiais nos estuários de NSW, não existem estudos que apresentem uma avaliação global sobre os efeitos obtidos com o estabelecimento dessas estruturas. No presente trabalho abordamos a efetividade dos recifes artificiais estuarinos como iniciativa para aumento da pesca; descrevemos a diversidade e abundância das espécies a eles associadas; descrevemos os padrões de colonização e o desenvolvimento das comunidades associadas a um recife artificial colocado no Lago Macquaire, extensa lagoa de barreira situada na costa sudeste da Australia. Seis recifes artificiais (formando um único grupo), construídos a partir de unidades artificiais (Reef Balls®), foram lançados em Dezembro de 2005 e amostrados seis vezes a cada estação do ano, durante dois anos, utilizando video subaquático remoto (BRUV). A colonizaç��o dentro do grupo de recifes ocorreu de maneira relativamente rápida, sendo que a maioria das espécies identificadas nos dois anos de estudo foi observada durante o primeiro ano de amostragem. Um total de 27 espécies pertencentes a 17 famílias foram identificadas. As espécies chave do processo de colonização foram Pelates sexlineatus (Teraponidae), Acanthopagrus australis (Sparidae), Pagrus auratus (Sparidae) and Rhabdosargus sarba (Sparidea). A riqueza de espécies mostrou evidência de sazonalidade, enquanto a diversidade aumentou significativamente com o aumento da idade do recife. A composição da assembléia de peixes permaneceu relativamente estável após o primeiro ano de amostragem, com poucos padrões identificáveis relativos à estrutura. Durante o segundo ano tornou-se evidente a formação de grupos por idade, padrão primariamente ocasionado pelo decréscimo na abundância de P. sexlineatus; por sua vez este decréscimo mostrou ser resultado da natureza isolada do recife artificial e dos efeitos interdependentes de abundância e predação

Genetic characterisation of molecular targets in carcinoma of unknown primary

Abstract Background Carcinoma of unknown primary (CUP) is a metastatic epithelial malignancy in the absence of an identifiable primary tumour. Prognosis for patients with CUP is poor because treatment options are generally limited to broad spectrum chemotherapy. A shift towards personalised cancer management based on mutation profiling offers the possibility of new treatment paradigms. This study has explored whether actionable, oncogenic driver mutations are present in CUP that have potential to better inform treatment decisions. Methods Carcinoma of unknown primary cases (n = 21) were selected and DNA was isolated from formalin-fixed paraffin embedded sections prior to amplification and sequencing. Two distinct yet complementary targeted gene panels were used to assess variants in up to 76 known cancer-related genes for the identification of biologically relevant and actionable mutations. Results Variants were detected in 17/21 cases (81%) of which 11 (52%) were potentially actionable with drugs currently approved for use in known primary cancer types or undergoing clinical trials. The most common variants detected were in TP53 (47%), KRAS (12%), MET (12%) and MYC (12%). Differences at the molecular level were seen between common CUP histological subtypes. CUP adenocarcinomas and poorly differentiated carcinomas harboured the highest frequency of variants in genes involved in signal transduction pathways (e.g. MET, EGFR, HRAS, KRAS, and BRAF). In contrast, squamous cell carcinoma exhibited a higher frequency of variants in cell cycle control and DNA repair genes (e.g. TP53, CDKN2A and MLH1). Conclusion Taken together, mutations in biologically relevant genes were detected in the vast majority of CUP tumours, of which half provided a potentially novel treatment option not generally considered in CUP

MOESM1 of Genetic characterisation of molecular targets in carcinoma of unknown primary

Additional file 1: Table S1. Combined gene list of the Oncomine Focus Assay (OFA) and Cancer Hotspot v2 (CHPv2) panel (ThermoFisher Scientific)

Untargeted metabolomics of human plasma reveal lipid markers unique to chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis

Chronic obstructive pulmonary disease (COPD) is characterised by airway inflammation and progressive airflow limitation, whereas idiopathic pulmonary fibrosis (IPF) is characterised by a restrictive pattern due to fibrosis and impaired gas exchange. We undertook metabolomic analysis of blood samples in IPF, COPD and healthy controls (HC) to determine differences in circulating molecules and identify novel pathogenic pathways. An untargeted metabolomics using an ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometer (UHPLC-QTOF-MS) was performed to profile plasma of patients with COPD (n = 21), and IPF (n = 24) in comparison to plasma from healthy controls (HC; n = 20). The most significant features were identified using multiple database matching. One-way ANOVA and variable importance in projection (VIP) scores were also used to highlight metabolites that influence the specific disease groups. Non-polar metabolites such as fatty acids (FA) and membrane lipids were well resolved and a total of 4805 features were identified. The most prominent metabolite composition differences in lipid mediators identified at ∼2–3 fold higher in both diseases compared to HC were palmitoleic acid, oleic acid and linoleic acid; and dihydrotestosterone was lower in both diseases. We demonstrated that COPD and IPF were characterised by systemic changes in lipid constituents such as essential FA sampled from circulating plasma

Circulating RNA differences between patients with stable and progressive idiopathic pulmonary fibrosis

Britt Clynick, Helen E. Jo, Tamera J. Corte, Ian N. Glaspole, Christopher Grainge, Peter M.A. Hopkins ... et al