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Background A randomised clinical trial titled the Carer End of Life Planning Intervention (CELPI) in people dying with dementia evaluated the effect of carer education and support about palliative care on care recipient outcomes. We present a pre-planned qualitative analysis of data collected during the CELPI trial in which needs of carers randomised to the study intervention group were assessed using a novel instrument (Carer Needs Directed Assessment in Dementia (CANDID). This tool aimed to identify carers’ perceptions of their own and their care-recipients’ needs and is an important step in identifying support provision for dementia-specific, palliative cares services upon hospital discharge. Methods The CANDID tool was designed to identify the needs and experiences of primary carers and of their care recipients during the last twelve months of the care recipient’s life. The tool consisted of 33 open-ended questions evaluating: symptom management, emergency contacts, advance care planning, carer’s perception of the care recipient’s future needs, carer’s current needs, and a proposed current and future care plan. The researcher’s philosophical assumption of interpretative phenomenology informed the study and approach to data collection and analysis. Qualitative data collected during interviews using this tool were thematically analysed in five steps: compiling, disassembling, reassembling, interpreting and concluding. An interpretation of participants’ reality emerged from their common experiences and the subjective meanings assigned to actions attached to the phenomena studied. Results Thirty carer participants were included. Analysis identified three major themes: Carers’ perceived stressors, systemic barriers to care provision, and future planning. Issues identified included barriers to accessing supports, carer health and division between roles, financial burden, familial conflicts, adquate care in hospital and aged care facilities, concern about future needs, and end-of-life discussions. Conclusion The CANDID tool enabled an evaluation of carer needs and concerns. Identifying those needs may inform a referral to palliative care services where the level of management required may be benenficial for both the person living with dementia and their primary carer. Trial Registration Australian Clinical Trials Registration: (ACTRN12619001187134) .

Through a narrative inquiry involving a semi-structured interview and autobiographical reflection, the author explores the similarities and differences in literacy pedagogy between a literacy leader and a science teacher. Disciplinary literacy provides an opportunity for both teachers to better understand scientific literacy, and their different perspectives contribute to a rich conversation. Themes of similarities which emerge include embracing multiliteracies, investigation, a critical stance, and wonder Themes of differences include separating writing skills from form and confidence with numeracy and statistics. A collaborative approach to the implementation of disciplinary literacy and to further research is recommended.

Lest I belabour the point: smoker and smoking - not the same thing. If I see a sign on a restaurant door that says \"no bare feet,\" I don't think \"I have bare feet on under these socks and shoes - they're discriminating against me.\" It just means I keep my socks and shoes on. It's about hygiene. Equally absurd is the implied comparison to the bylaw made in Eric Johnson's column (Tribune, Jan.25) when he says, \"What's the next target...high fat chicken wings? French fries? Booze?\"

The ToxA effector is a major virulence gene of Pyrenophora tritici-repentis (Ptr), a necrotrophic fungus and the causal agent of tan spot disease of wheat. ToxA and co-located genes are believed to be the result of a recent horizontally transferred highly conserved 14kb region a major pathogenic event for Ptr. Since this event, monitoring isolates for pathogenic changes has become important to help understand the underlying mechanisms in play. Here we examined ToxA in 100 Ptr isolates from Australia, Europe, North and South America and the Middle East, and uncovered in isolates from Denmark, Germany and New Zealand a new variation, a novel 166 bp insertion element (PtrHp1) which can form a perfectly matched 59 bp inverted repeat hairpin structure located downstream of the ToxA coding sequence in the 3' UTR exon. A wider examination revealed PtrHp1 elements to be distributed throughout the genome. Analysis of genomes from Australia and North America had 50-112 perfect copies that often overlap other genes. The hairpin element appears to be unique to Ptr and the lack of ancient origins in other species suggests that PtrHp1 emerged after Ptr speciation. Furthermore, the ToxA UTR insertion site is identical for different isolates, which suggests a single insertion event occurred after the ToxA horizontal transfer. In vitro and in planta-detached leaf assays found that the PtrHp1 element insertion had no effect on ToxA expression. However, variation in the expression of ToxA was detected between the Ptr isolates from different demographic locations, which appears to be unrelated to the presence of the element. We envision that this discovery may contribute towards future understanding of the possible role of hairpin elements in Ptr.

Background Necrotrophic effector proteins secreted by fungal pathogens are important virulence factors that mediate the development of disease in wheat. Pyrenophora tritici-repentis (Ptr), the causal agent of wheat tan spot, has a race structure dependent on the combination of effectors. In Ptr, ToxA and ToxB are known proteinaceous effectors responsible for necrosis and chlorosis respectively. While Ptr ToxA is encoded by the single gene ToxA , ToxB has multiple loci in the Ptr genome, which is postulated to be directly related to the level of ToxB production and leaf chlorosis. Although previous analysis has indicated that the majority of the ToxB loci lie on a single chromosome, the exact number and chromosomal locations for all the ToxB loci have not been fully identified. Results In this study, we have sequenced the genome of a race 5 ToxB-producing isolate (DW5), using PacBio long read technology, and found that ToxB duplications are nested in the complex subtelomeric chromosomal regions. A total of ten identical ToxB gene copies were identified and based on flanking sequence identity, nine loci appeared associated with chromosome 11 and a single copy with chromosome 5. Chromosome 11 multiple ToxB gene loci were separated by large sequence regions between 31 and 66 kb within larger segmental duplications in an alternating pattern related to loci strand, and flanked by transposable elements. Conclusion This work provides for the first time the full accompaniment of ToxB loci and surrounding regions, and identifies the organization and distribution of ten ToxB loci to subtelomeric regions. To our knowledge, this is the first report of an interwoven strand-related duplication pattern event. This study further highlights the importance of resolving the highly complex distal chromosomal regions, that remain difficult to assemble, and can harbour important effectors and virulence factors.

Background Pyrenophora tritici-repentis (Ptr) is a necrotrophic fungal pathogen that causes the major wheat disease, tan spot. We set out to provide essential genomics-based resources in order to better understand the pathogenicity mechanisms of this important pathogen. Results Here, we present eight new Ptr isolate genomes, assembled and annotated; representing races 1, 2 and 5, and a new race. We report a high quality Ptr reference genome, sequenced by PacBio technology with Illumina paired-end data support and optical mapping. An estimated 98% of the genome coverage was mapped to 10 chromosomal groups, using a two-enzyme hybrid approach. The final reference genome was 40.9 Mb and contained a total of 13,797 annotated genes, supported by transcriptomic and proteogenomics data sets. Conclusions Whole genome comparative analysis revealed major chromosomal segmental rearrangements and fusions, highlighting intraspecific genome plasticity in this species. Furthermore, the Ptr race classification was not supported at the whole genome level, as phylogenetic analysis did not cluster the ToxA producing isolates. This expansion of available Ptr genomics resources will directly facilitate research aimed at controlling tan spot disease.

Metabolite identification is the greatest challenge when analysing metabolomics data, as only a small proportion of metabolite reference standards exist. Clustering MS/MS spectra is a common method to identify similar compounds, however interrogation of underlying signature fragmentation patterns within clusters can be problematic. Previously published high-resolution LC-MS/MS data from the bioluminescent beetle ( Photinus pyralis ) provided an opportunity to mine new specialized metabolites in the lucibufagin class, compounds important for defense against predation. We aimed to 1) provide a workflow for hierarchically clustering MS/MS spectra for metabolomics data enabling users to cluster, visualise and easily interrogate the identification of underlying cluster ion profiles, and 2) use the workflow to identify key fragmentation patterns for lucibufagins in the hemolymph of P. pyralis . Features were aligned to their respective MS/MS spectra, then product ions were dynamically binned and resulting spectra were hierarchically clustered and grouped based on a cutoff distance threshold. Using the simplified visualization and the interrogation of cluster ion tables the number of lucibufagins was expanded from 17 to a total of 29.

Objectives The assembly of fungal genomes using short-reads is challenged by long repetitive and low GC regions. However, long-read sequencing technologies, such as PacBio and Oxford Nanopore, are able to overcome many problematic regions, thereby providing an opportunity to improve fragmented genome assemblies derived from short reads only. Here, a necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) isolate 134 (Ptr134), which causes tan spot disease on wheat, was sequenced on a MinION using Oxford Nanopore Technologies (ONT), to improve on a previous Illumina short-read genome assembly and provide a more complete genome resource for pan-genomic analyses of Ptr. Results The genome of Ptr134 sequenced on a MinION using ONT was assembled into 28 contiguous sequences with a total length of 40.79 Mb and GC content of 50.81%. The long-read assembly provided 6.79 Mb of new sequence and 2846 extra annotated protein coding genes as compared to the previous short-read assembly. This improved genome sequence represents near complete chromosomes, an important resource for large scale and pan genomic comparative analyses.