An unusual new fossil shark (Pisces: Chondrichthyes) from the Late Devonian of South Africa

A new stem-group chondrichthyan fish, PlesioselacJllIs macracanthlls gen. et sp. nov., is described from the Late Devonian Witpoort Formation, representing an estuarine lagoon site, near Grahamstown, South Africa. Based on a single, fairly complete specimen, it is distinctive in its a single dorsal fin braced by a large, stout spine with numerous ribs and posterior denticles, apparently no second dorsal or anal fin, an amphistylic jaw suspension, and a distinctive triangular palatoquadrate. It is suggested that the species may represent a high-latitude, Late Devonian relict taxon

Land cover and vegetation data from an ecological survey of `key habitat' landscapes in England, 1992-1993

Since 1978, a series of national surveys (Countryside Survey, CS) have been carried out by the Centre for Ecology and Hydrology (CEH) (formerly the Institute of Terrestrial Ecology, ITE) to gather data on the natural environment in Great Britain (GB). As the sampling framework for these surveys is not optimised to yield data on rarer or more localised habitats, a survey was commissioned by the then Department of the Environment (DOE, now the Department for Environment, Food and Rural Affairs, DEFRA) in the 1990s to carry out additional survey work in English landscapes which contained semi-natural habitats that were perceived to be under threat, or which represented areas of concern to the ministry. The landscapes were lowland heath, chalk and limestone (calcareous) grasslands, coasts and uplands. The information recorded allowed an assessment of the extent and quality of a range of habitats defined during the project, which can now be translated into standard UK broad and priority habitat classes. The survey, known as the "Key Habitat Survey", followed a design which was a series of gridded, stratified, randomly selected 1 km squares taken as representative of each of the four landscape types in England, determined from statistical land classification and geological data ("spatial masks"). The definitions of the landscapes are given in the descriptions of the spatial masks, along with definitions of the surveyed habitats. A total of 213 of the 1 km2 square sample sites were surveyed in the summers of 1992 and 1993, with information being collected on vegetation species, land cover, landscape features and land use, applying standardised repeatable methods. The database contributes additional information and value to the long-term monitoring data gathered by the Countryside Survey and provides a valuable baseline against which future ecological changes may be compared, offering the potential for a repeat survey. The data were analysed and described in a series of contract reports and are summarised in the present paper, showing for example that valuable habitats were restricted in all landscapes, with the majority located within protected areas of countryside according to different UK designations. The dataset provides major potential for analyses, beyond those already published, for example in relation to climate change, agri-environment policies and land management. Precise locations of the plots are restricted, largely for reasons of landowner confidentiality. However, the representative nature of the dataset makes it highly valuable for evaluating the status of ecological elements within the associated landscapes surveyed. Both land cover data and vegetation plot data were collected during the surveys in 1992 and 1993 and are available via the following DOI: https://doi.org/10.5285/7aefe6aa-0760-4b6d-9473-fad8b960abd4. The spatial masks are also available from https://doi.org/10.5285/dc583be3-3649-4df6-b67e-b0f40b4ec895

Methods for exploring the faecal microbiome of premature infants: a review

The premature infant gut microbiome plays an important part in infant health and development, and recognition of the implications of microbial dysbiosis in premature infants has prompted significant research into these issues. The approaches to designing investigations into microbial populations are many and varied, each with its own benefits and limitations. The technique used can influence results, contributing to heterogeneity across studies. This review aimed to describe the most common techniques used in researching the preterm infant microbiome, detailing their various limitations. The objective was to provide those entering the field with a broad understanding of available methodologies, so that the likely effects of their use can be factored into literature interpretation and future study design. We found that although many techniques are used for characterising the premature infant microbiome, 16S rRNA short amplicon sequencing is the most common. 16S rRNA short amplicon sequencing has several benefits, including high accuracy, discoverability and high throughput capacity. However, this technique has limitations. Each stage of the protocol offers opportunities for the injection of bias. Bias can contribute to variability between studies using 16S rRNA high throughout sequencing. Thus, we recommend that the interpretation of previous results and future study design be given careful consideration

Rigid motion revisited: rigid quasilocal frames

We introduce the notion of a rigid quasilocal frame (RQF) as a geometrically natural way to define a "system" in general relativity. An RQF is defined as a two-parameter family of timelike worldlines comprising the worldtube boundary of the history of a finite spatial volume, with the rigidity conditions that the congruence of worldlines is expansion-free (constant size) and shear-free (constant shape). This definition of a system is anticipated to yield simple, exact geometrical insights into the problem of motion in general relativity. It begins by answering the questions what is in motion (a rigid two-dimensional system boundary), and what motions of this rigid boundary are possible. Nearly a century ago Herglotz and Noether showed that a three-parameter family of timelike worldlines in Minkowski space satisfying Born's 1909 rigidity conditions has only three degrees of freedom instead of the six we are familiar with from Newtonian mechanics. We argue that in fact we can implement Born's notion of rigid motion in both flat spacetime (this paper) and arbitrary curved spacetimes containing sources (subsequent papers) - with precisely the expected three translational and three rotational degrees of freedom - provided the system is defined quasilocally as the two-dimensional set of points comprising the boundary of a finite spatial volume, rather than the three-dimensional set of points within the volume.Comment: 10 pages (two column), 24 pages (preprint), 1 figur

The first Bothriolepsis-associated Devonian fish fauna from Africa

An advanced diplacanthid (Climatiiformes) is described from a Famennian estuarine environment of South Africa. It is characterized by having exceptionally long thin fin spines and a deep body form. Unusual details of the fins and fin spine insertions are preserved. This is the first record of a diplacanthid from the Southern Hemisphere

The bacterial gut microbiome of probiotic-treated very-preterm infants: changes from admission to discharge

Background: Preterm birth is associated with the development of acute and chronic disease, potentially, through the disruption of normal gut microbiome development. Probiotics may correct for microbial imbalances and mitigate disease risk. Here, we used amplicon sequencing to characterise the gut microbiome of probiotic-treated premature infants. We aimed to identify and understand variation in bacterial gut flora from admission to discharge and in association with clinical variables. Methods: Infants born <32 weeks gestation and <1500 g, and who received probiotic treatment, were recruited in North Queensland Australia. Meconium and faecal samples were collected at admission and discharge. All samples underwent 16S rRNA short amplicon sequencing, and subsequently, a combination of univariate and multivariate analyses. Results: 71 admission and 63 discharge samples were collected. Univariate analyses showed significant changes in the gut flora from admission to discharge. Mixed-effects modelling showed significantly lower alpha diversity in infants diagnosed with either sepsis or retinopathy of prematurity (ROP) and those fed formula. In addition, chorioamnionitis, preeclampsia, sepsis, necrotising enterocolitis and ROP were also all associated with the differential abundance of several taxa. Conclusions: The lower microbial diversity seen in infants with diagnosed disorders or formula-fed, as well as differing abundances of several taxa across multiple variables, highlights the role of the microbiome in the development of health and disease. This study supports the need for promoting healthy microbiome development in preterm neonates

To Probiotic or Not to Probiotic: A Metagenomic Comparison of the Discharge Gut Microbiome of Infants Supplemented With Probiotics in NICU and Those Who Are Not

Background: Preterm birth is associated with the development of both acute and chronic disease, and the disruption of normal gut microbiome development. Recent studies have sought to both characterize and understand the links between disease and the microbiome. Probiotic treatment may correct for these microbial imbalances and, in turn, mitigate disease. However, the criteria for probiotic supplementation in NICU's in North Queensland, Australia limits its usage to the most premature (<32 weeks gestation) and small for gestational age infants (<1,500 g). Here we use a combination of amplicon and shotgun metagenomic sequencing to compare the gut microbiome of infants who fulfill the criteria for probiotic-treatment and those who do not. The aims of this study were to determine if probiotic-supplemented preterm infants have significantly different taxonomic and functional profiles when compared to non-supplemented preterm infants at discharge. Methods: Preterm infants were recruited in North Queensland, Australia, with fecal samples collected just prior to discharge (36 ± 0.5 weeks gestation), to capture potential changes that could be probiotic induced. All samples underwent 16S rRNA gene amplicon sequencing, with a subset also used for shotgun metagenomics. Mixed effects models were used to assess the effect of probiotics on alpha diversity, beta diversity and taxonomic abundance, whilst accounting for other known covariates. Results: Mixed effects modeling demonstrated that probiotic treatment had a significant effect on overall community composition (beta diversity), characterized by greater alpha diversity and differing abundances of several taxa, including Bifidobacterium and Lactobacillus, in supplemented infants. Conclusion: Late preterm-infants who go without probiotic-supplementation may be missing out on stabilizing-effects provided through increased alpha diversity and the presence of commensal microbes, via the use of probiotic-treatment. These findings suggest that late-preterm infants may benefit from probiotic supplementation. More research is needed to both understand the consequences of the differences observed and the long-term effects of this probiotic-treatment

Exploring the long-term colonisation and persistence of probiotic-prophylaxis species on the gut microbiome of preterm infants: a pilot study

Preterm infants suffer from a higher incidence of acute diseases such as necrotising enterocolitis and sepsis. This risk can be mitigated through probiotic prophylaxis during admission. This reduction in risk is likely the result of acute modulation of the gut microbiome induced by probiotic species, which has been observed to occur up until discharge. We aimed to determine if this modulation, and the associated probiotic species, persisted beyond discharge. We conducted both a cross-sectional analysis (n= 18), at similar to 18 months of age, and a longitudinal analysis (n= 6), from admission to 18 months of the gut microbiome of preterm infants using both shotgun metagenomics and 16S rRNA profiling respectively. The 16S amplicon sequencing revealed that the microbial composition of the probiotic-supplemented infants changed dramatically over time, stabilising at discharge. However, species from the probiotic Infloran (R), as well as positive modulatory effects previously associated with supplementation, do not appear to persist beyond discharge and once prophylaxis has stopped. Conclusions: Although differences exist between supplemented and non-supplemented groups, the implications of these differences remain unclear. Additionally, despite a lack of long-term colonisation, the presence of probiotics during early neonatal life may still have modulatory effects on the microbiome assembly and immune system training