Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding

With the growing importance of aquaculture worldwide, characterization of the microbiota of high-value aquaculture species and identification of their shifts induced by changes in fish physiology or nutrition is of special interest. Here we report the first 16S rRNA gene metabarcoding survey of the mid-intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and mid-intestinal samples and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles. Over 1000 operational taxonomic units were identified within the cohort, providing a first glimpse into the mid-intestinal microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the family Vibrionaceae. We anticipate that the workflow presented in this paper could be applied in other aquacultured fish species to capture variation or dysbiosis occurring as a result of changes in feed, health or environmental conditions

Pemberton hydroelectric power station: a teacher resource

This publication provides a resource for teachers of students in years seven to ten. Teachers are able to address a range of outcomes pertinent to the Western Australian curriculum within the context of the Pemberton Hydroelectric Power Station. The resource contains plans for four units of work, one in each of the following Learning Areas: Science, Mathematics, English, and Society and Environment

Levels of physical activity and sleep patterns among older people with dementia living in long-term care facilities: A 24-hour snapshot

Objectives To objectively measure over a 24-hour period the daytime and nighttime levels of physical activity and sleep patterns of older people with dementia living in long-term care facilities. Study design Nested within a larger research program, this cross-sectional study involved 415 residents, aged ≥60 years, with a documented diagnosis of dementia, from 28 long-term care facilities in south-east Queensland, Australia. Main outcome measures Residents wore SenseWear® activity armbands continuously for 24 hours, with data recorded for: step count; total energy expenditure; metabolic equivalent of task (MET); and the amount of time spent physically active, lying down, awake and asleep. Residents’ levels of cognitive impairment (assessed using the Rowland Universal Dementia Assessment Scale) and agitation (assessed using the Cohen-Mansfield Agitation Inventory-Short Form), and demographic data were also collected. Results From a total of 415 residents monitored with the SenseWear® activity armbands, 192 met the valid wear-time of 21 hours or more, and had activity and sleep data recorded. These residents were largely inactive during the daytime (engaged in an average of 1.8 hours of light physical activity), but achieved recommended amounts of sleep at night (average of 6.8 hours). There was considerable variation within the sample, and activity and sleep differed by sex (p<.001), age (p=.010), mobility (p<.001), and antipsychotic usage (p=.030). Conclusions These data can be used by long-term care clinicians to assist in planning interventions and care approaches which promote physical activity and good sleep practices, and are individualized to physical and cognitive capabilities. Australian New Zealand Clinical Trials Registry (ACTRN12614000508673).NHMR

The Peculiar Debris Disk of HD 111520 as Resolved by the Gemini Planet Imager

Using the Gemini Planet Imager (GPI), we have resolved the circumstellar debris disk around HD 111520 at a projected range of ~30-100 AU in both total and polarized $H$-band intensity. The disk is seen edge-on at a position angle of ~165$^{\circ}$ along the spine of emission. A slight inclination or asymmetric warping are covariant and alters the interpretation of the observed disk emission. We employ 3 point spread function (PSF) subtraction methods to reduce the stellar glare and instrumental artifacts to confirm that there is a roughly 2:1 brightness asymmetry between the NW and SE extension. This specific feature makes HD 111520 the most extreme examples of asymmetric debris disks observed in scattered light among similar highly inclined systems, such as HD 15115 and HD 106906. We further identify a tentative localized brightness enhancement and scale height enhancement associated with the disk at ~40 AU away from the star on the SE extension. We also find that the fractional polarization rises from 10 to 40% from 0.5" to 0.8" from the star. The combination of large brightness asymmetry and symmetric polarization fraction leads us to believe that an azimuthal dust density variation is causing the observed asymmetry.Comment: 9 pages, 8 Figures, 1 table, Accepted to Ap

Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies

Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions

PvDBPII elicits multiple antibody-mediated mechanisms that reduce growth in a Plasmodium vivax challenge trial

The receptor-binding domain, region II, of the Plasmodium vivax Duffy binding protein (PvDBPII) binds the Duffy antigen on the reticulocyte surface to mediate invasion. A heterologous vaccine challenge trial recently showed that a delayed dosing regimen with recombinant PvDBPII SalI variant formulated with adjuvant Matrix-MTM reduced the in vivo parasite multiplication rate (PMR) in immunized volunteers challenged with the Thai P. vivax isolate PvW1. Here, we describe extensive analysis of the polyfunctional antibody responses elicited by PvDBPII immunization and identify immune correlates for PMR reduction. A classification algorithm identified antibody features that significantly contribute to PMR reduction. These included antibody titre, receptor-binding inhibitory titre, dissociation constant of the PvDBPII-antibody interaction, complement C1q and Fc gamma receptor binding and specific IgG subclasses. These data suggest that multiple immune mechanisms elicited by PvDBPII immunization are likely to be associated with protection and the immune correlates identified could guide the development of an effective vaccine for P. vivax malaria. Importantly, all the polyfunctional antibody features that correlated with protection cross-reacted with both PvDBPII SalI and PvW1 variants, suggesting that immunization with PvDBPII should protect against diverse P. vivax isolates

Beyond the Womb and the Tomb: Identity, (Dis)embodiment and the Life Course

Grounded in the authors’ theoretical and ethnographic work on pregnancy and social life after death, this article explores the ways in which the body is involved in processes of identification. With a focus on the embodied nature of social identity, the article nonetheless problematizes a model of the life course that begins at the moments of birth and ends at death. Instead, it offers a more extended temporal perspective and examines other ways in which identity may be claimed, for example, via material objects and practices which evoke the body as imagined or remembered. By documenting pre-birth and post-mortem identity-making of this kind, it demonstrates how the unborn and the dead may come into social existence. In addition, a cultural privileging of both the body and visuality is shown to shore up the capacity of material objects and practices to shape social identities in a highly selective fashion. The article therefore proposes that models of the life course need to accommodate the meanings of pre-birth and post-mortem materialities and so incorporate a conceptualization of social identity as contested, relational and inevitably incomplete

Combining genetical genomics and bulked segregant analysis-based differential expression: an approach to gene localization

Positional gene isolation in unsequenced species generally requires either a reference genome sequence or an inference of gene content based on conservation of synteny with a genomic model. In the large unsequenced genomes of the Triticeae cereals the latter, i.e. conservation of synteny with the rice and Brachypodium genomes, provides a powerful proxy for establishing local gene content and order. However, efficient exploitation of conservation of synteny requires ‘homology bridges’ between the model genome and the target region that contains a gene of interest. As effective homology bridges are generally the sequences of genetically mapped genes, increasing the density of these genes around a target locus is an important step in the process. We used bulked segregant analysis (BSA) of transcript abundance data to identify genes located in a specific region of the barley genome. The approach is valuable because only a relatively small proportion of barley genes are currently placed on a genetic map. We analyzed eQTL datasets from the reference Steptoe × Morex doubled haploid population and showed a strong association between differential gene expression and cis-regulation, with 83% of differentially expressed genes co-locating with their eQTL. We then performed BSA by assembling allele-specific pools based on the genotypes of individuals at the partial resistance QTL Rphq11. BSA identified a total of 411 genes as differentially expressed, including HvPHGPx, a gene previously identified as a promising candidate for Rphq11. The genetic location of 276 of these genes could be determined from both eQTL datasets and conservation of synteny, and 254 (92%) of these were located on the target chromosome. We conclude that the identification of differential expression by BSA constitutes a novel method to identify genes located in specific regions of interest. The datasets obtained from such studies provide a robust set of candidate genes for the analysis and serve as valuable resources for targeted marker development and comparative mapping with other grass species

Spectrum of congenital anomalies among VACTERL cases: a EUROCAT population-based study

Background: The VACTERL (Vertebral anomalies, Anal atresia, Cardiac malformations, Tracheo-Esophageal fistula, Renal anomalies, Limb abnormalities) association is the non-random occurrence of at least three of these congenital anomalies: vertebral, anal, cardiac, tracheo-esophageal, renal, and limb anomalies. Diagnosing VACTERL patients is difficult, as many disorders have multiple features in common with VACTERL. The aims of this study were to clearly outline component features, describe the phenotypic spectrum among the largest group of VACTERL patients thus far reported, and to identify phenotypically similar subtypes. Methods: A case-only study was performed assessing data on 501 cases recorded with VACTERL in the JRC-EUROCAT (Joint Research Centre-European Surveillance of Congenital Anomalies) central database (birth years: 1980–2015). We differentiated between major and minor VACTERL features and anomalies outside the VACTERL spectrum to create a clear definition of VACTERL. Results: In total, 397 cases (79%) fulfilled our VACTERL diagnostic criteria. The most commonly observed major VACTERL features were anorectal malformations and esophageal atresia/tracheo-esophageal fistula (both occurring in 62% of VACTERL cases), followed by cardiac (57%), renal (51%), vertebral (33%), and limb anomalies (25%), in every possible combination. Three VACTERL subtypes were defined: STRICT-VACTERL, VACTERL-LIKE, and VACTERL-PLUS, based on severity and presence of additional congenital anomalies. Conclusion: The clearly defined VACTERL component features and the VACTERL subtypes introduced will improve both clinical practice and etiologic research.acceptedVersio