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Identification of mRNA-miRNA-lncRNA regulatory network associated with the immune response to Aeromonas salmonicides infection in the black rockfish (Sebastes schlegelii)
No full textIn aquaculture, Aeromonas salmonicides (A. salmonicida) is a main fish pathogen because of its nearly worldwide distribution, and broad host range. Recently, an increasing number of evidences have uncovered the roles of mRNA-miRNA-lncRNA network in fish diseases. In current study, RNA-seq was conducted in the black rockfish spleen following A. salmonicida infection at 0 h (Sp0 or control) and three different post-infection time-points (2 h: Sp2, 12 h: Sp12 and 24 h: Sp24, respectively) to comprehensively identify differentially expressed (DE) mRNAs, miRNAs and lncRNAs. Enrichment analysis and protein-protein interaction (PPI) analysis of DE mRNAs were performed. Then, expression and correlation analysis for mRNAs and their upstream miRNAs and lncRNAs were conducted. Finally, a total of 1364 mRNAs, 17 miRNAs and 1584 lncRNAs exhibited significantly differential expressions during bacterial infection in the black rockfish spleen. Functional enrichment analysis suggested that they were significantly enriched in several immune-related pathways, including Amino sugar and nucleotide sugar metabolism, Cell adhesion molecules (CAMs), Neuroactive ligand-receptor interaction, Nicotinate and nicotinamide metabolism, Pentose and glucuronate interconversions, Phagosome, Proteasome, etc. Subsequently, 1091 lncRNA-miRNA-mRNA pathways (323 in Sp2, 609 in Sp12 and 207 in Sp24) were constructed including 400 lncRNAs, 69 miRNAs, and 70 mRNAs. Meanwhile, NLRC3/novel-264/LNC_00116154 pathway demonstrated important immune modulating function in the black rockfish against A. salmonicida infection. Finally, the novel mRNA-miRNA-lncRNA sub-networks were established, among which all mRNAs and ncRNAs possessed significant predictive values for further studies for immune responses in the black rockfish
Author Correction: Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology
Full text linkCorrection to: Nature Genetics https://doi.org/10.1038/s41588-021-00973-1, published online 6 December 2021.
In the version of this article initially published, the affiliation for Nazli Başak appeared incorrectly. Nazli Başak is at Koç University, School of Medicine, KUTTAM-NDAL, Istanbul, Turkey, and not Bogazici University. The error has been corrected in the HTML and PDF versions of the article
Algorithmic estimation of adrenal volume based on body weight and CT landmarks in dogs
No full textComputed tomographic (CT) methods for quantifying adrenal size are helpful for identifying and directing management of adrenal disease in dogs. This retrospective, observational study aimed to use CT to determine anatomic landmarks associated with adrenal gland volume in dogs, and subsequently develop an algorithm to estimate adrenal volume for individual subjects. Abdominal CT images from 150 dogs without adrenal disease were assessed. The volume of the left and right adrenals, as well as dimensions from anatomic structures, were measured. Predictive models for adrenal volume were examined with cross validation. A further 29 dogs were used for external validation and model fit. Dogs in the test cohort weighed from 3.1 to 67.5 kg (mean 24.4 kg) with left (VLA) and right (VRA) adrenal volume ranging from 0.23 to 2.84 cm3 (mean 1.22 cm3) and 0.14 to 2.97 cm3 (mean 1.11 cm3), respectively. A predictive model for each adrenal based on weight (W) and L1 height (HL1) best explained the adrenal volume, with external validation confirming model fit. The final models, adjusted for bias, were: VLA = 0.154 + (0.02 × W) + (0.07 × HL1) (adjR2 = 0.62); and VRA = −0.116 + (0.02 × W) + (0.06 × HL1) (adjR2 = 0.64). In dogs undergoing CT, these algorithms can be used to estimate expected adrenal volume and allow comparison with the actual volume measured on CT, facilitating interpretation of CT findings, and clinical decision-making
The changing molecular epidemiology of Enterococcus faecium harbouring the van operon at a teaching hospital in Western Australia: A fifteen-year retrospective study
Full text linkIntroduction
Enterococcus faecium is an opportunistic pathogen that has become one of the leading causes of hospital acquired infection that are resistant to multiple critically important antimicrobials.
Aim
The objective of the study was to describe the molecular characteristics and relationship between major strains of E. faecium harbouring the van operon and to determine if the strains had increasing virulence and antimicrobial resistance determinants over time.
Methods
E. faecium harbouring the van operon detected using PCR from surveillance rectal swabs of patients that were admitted to high-risk units at a Perth teaching hospital from 2001 to 2015 were retrospectively analysed using a whole genome sequencing and bioinformatics approach.
Results
ST18, ST78, ST80, ST173, ST203 and ST555 were identified as the major STs accounting for 93.7% of E. faecium isolates. Except for ST173, major STs identified at Royal Perth Hospital (RPH) have been reported across Australia and internationally. Isolates from each ST formed independently branched phylogenetic clusters with each harbouring unique virulence and antimicrobial resistance profiles. Depending on the ST, different genes conferring resistance to similar antimicrobial classes were identified. Except for ST80 which harboured the vanA type operon, all major strains harboured the vanB operon conferring only vancomycin resistance.
Conclusion
Major strains of E. faecium isolated over 15-years showed unique virulome and resistome profiles with no indication of increasing virulence or antimicrobial resistance determinants. Strains were distantly related and the acquisition of different genes encoding similar antimicrobial resistances suggest the independent evolution of each strain
2021 Asia‐Pacific League of Associations for Rheumatology clinical practice guideline for treatment of gout
No full textBackground
Gout is the most prevalent inflammatory arthritis in the Asia-Pacific region and worldwide. This clinical practice guideline (CPG) aims to provide recommendations based on systematically obtained evidence and values and preferences tailored to the unique needs of patients with gout and hyperuricemia in Asia, Australasia, and the Middle East. The target users of these guidelines are general practitioners and specialists, including rheumatologists, in these regions.
Methods
Relevant clinical questions were formulated by the Steering Committee. Systematic reviews of evidence were done, and certainty of evidence was assessed using Grading of Recommendations Assessment, Development and Evaluation methodology. A multi-sectoral consensus panel formulated the final recommendations.
Results
The Asia-Pacific League of Associations for Rheumatology Task Force developed this CPG for treatment of gout with 3 overarching principles and 22 recommendation statements that covered the treatment of asymptomatic hyperuricemia (2 statements), treatment of acute gout (4 statements), prophylaxis against gout flare when initiating urate-lowering therapy (3 statements), urate-lowering therapy (3 statements), treatment of chronic tophaceous gout (2 statements), treatment of complicated gout and non-responders (2 statements), treatment of gout with moderate to severe renal impairment (1 statement), and non-pharmacologic interventions (5 statements).
Conclusion
Recommendations for clinically relevant scenarios in the management of gout were formulated to guide physicians in administering individualized care
Ceria-supported niobium oxide catalyst for low-temperature oxidation of 1,3-butadiene
No full textLow-temperature oxidation represents an economically efficient way to convert spinoff hydrocarbons such as butadiene into nontoxic species. This study investigates the catalytic oxidation of 1,3-butadiene over ceria-supported niobium oxide, exploring the synthesis routes and catalytic performances. Experimental characterization techniques, including X-ray spectroscopy and diffractometry, microscopy, and other micro-characterisations, elucidate the structure of the catalysts as corroborated by the density functional theory (DFT) method. DFT calculations constructed the underlying oxidative reaction mechanisms that ensue through accessible activation energies in steps that feature subsequent Csingle bondC bond fissions, H transfer reactions, CO desorption, and formation of CO2 molecules. The results show that, the niobium oxide assumes mainly the form of Nb2O5 on ceria supports, and plays a significant role in switching the physicochemical nature of ceria and the resulting catalysts. Despite a relatively lower surface area, the NbOx/CeO2 catalysts exhibit superior performances in the conversion of butadiene compared to pure ceria. The catalyst prepared with 10 wt.% of Nb has the best catalytic performance with 82% conversion of butadiene, highest reaction rate, and selectivity towards CO2 of 95% at the temperature range of 300 – 400 °C and a gas hourly space velocity (GHSV) of 34,600 h−1. Obtained results entail practical environmental implications in the catalytic destruction of stable hydrocarbon species
Next generation restoration metrics: Using soil eDNA bacterial community data to measure trajectories towards rehabilitation targets
No full textIn post-mining rehabilitation, successful mine closure planning requires specific, measurable, achievable, relevant and time-bound (SMART) completion criteria, such as returning ecological communities to match a target level of similarity to reference sites. Soil microbiota are fundamentally linked to the restoration of degraded ecosystems, helping to underpin ecological functions and plant communities. High-throughput sequencing of soil eDNA to characterise these communities offers promise to help monitor and predict ecological progress towards reference states. Here we demonstrate a novel methodology for monitoring and evaluating ecological restoration using three long-term (>25 year) case study post-mining rehabilitation soil eDNA-based bacterial community datasets. Specifically, we developed rehabilitation trajectory assessments based on similarity to reference data from restoration chronosequence datasets. Recognising that numerous alternative options for microbiota data processing have potential to influence these assessments, we comprehensively examined the influence of standard versus compositional data analyses, different ecological distance measures, sequence grouping approaches, eliminating rare taxa, and the potential for excessive spatial autocorrelation to impact on results. Our approach reduces the complexity of information that often overwhelms ecologically-relevant patterns in microbiota studies, and enables prediction of recovery time, with explicit inclusion of uncertainty in assessments. We offer a step change in the development of quantitative microbiota-based SMART metrics for measuring rehabilitation success. Our approach may also have wider applications where restorative processes facilitate the shift of microbiota towards reference states
Evidence that digital game players neglect age classification systems when deciding which games to play
Full text linkThis article considers players’ experiences seeking out new games to play, and their use of the Australian National Classification Scheme in doing so. The global video game industry is booming, with hundreds of games being released each month across numerous platforms. As a result, players have an unprecedented number of games available when choosing what games to purchase. However, a number of confounding issues around the emergent content of games and the subjective nature of game reviewing makes it difficult to relate what kinds of experiences a given game will facilitate. In this study, we surveyed game players in order to find their game platform and acquisition preferences; strategies and experiences when choosing games; and attitudes towards classification systems. Our findings suggest that players find it difficult to choose what games to purchase, and that existing classification systems are mostly only beneficial when choosing games for minors
The Thinking Frames Approach: Improving high school students’ written explanations of phenomena in science
Full text linkSecondary school students find it difficult to write elaborated causal explanations of scientific phenomena. They frequently present their own opinions and write descriptions of their observations rather than linking observations with logical chains of causal reasoning, underpinned by a theoretical framework, to provide explanations of scientific phenomena. Science teachers also express difficulties in supporting students to develop scientific writing skills. In order to improve students’ written scientific explanations, a teaching strategy known as the Thinking Frames Approach (TFA) was introduced into two Grade 9 classrooms over two years. This multidimensional conceptual change strategy makes use of the affordances of student-generated multiple representations, teacher-student questioning, and small group discussions to support students in constructing understanding and written explanations. Students are also taught to reflect on and evaluate their written explanations. Students’ written responses explaining observations of scientific phenomena were collected over a nine-month period and evaluated using the analysis system for student explanations developed by de Andrade et al. (Res Sci Educ 49:787-807, 2019). A significant improvement in students’ written explanations linking observations with logical chains of reasoning and scientific theories was observed over this period. The TFA provides a strategy that teachers may implement to support students in developing skills in writing explanations by providing an appropriate level of scaffolding in the writing process. An added benefit of this approach was students’ increased confidence in producing written explanations
Worldwide diversity of endophytic fungi and insects associated with dormant tree twigs
Full text linkInternational trade in plants and climate change are two of the main factors causing damaging tree pests (i.e. fungi and insects) to spread into new areas. To mitigate these risks, a large-scale assessment of tree-associated fungi and insects is needed. We present records of endophytic fungi and insects in twigs of 17 angiosperm and gymnosperm genera, from 51 locations in 32 countries worldwide. Endophytic fungi were characterized by high-throughput sequencing of 352 samples from 145 tree species in 28 countries. Insects were reared from 227 samples of 109 tree species in 18 countries and sorted into taxonomic orders and feeding guilds. Herbivorous insects were grouped into morphospecies and were identified using molecular and morphological approaches. This dataset reveals the diversity of tree-associated taxa, as it contains 12,721 fungal Amplicon Sequence Variants and 208 herbivorous insect morphospecies, sampled across broad geographic and climatic gradients and for many tree species. This dataset will facilitate applied and fundamental studies on the distribution of fungal endophytes and insects in trees