Intraspecific variation in the cochleae of harbour porpoises (Phocoena phocoena) and its implications for comparative studies across odontocetes

In morphological traits, variation within species is generally considered to be lower than variation among species, although this assumption is rarely tested. This is particularly important in fields like palaeontology, where it is common to use a single individual as representative of a species due to the rarity of fossils. Here, we investigated intraspecific variation in the cochleae of harbour porpoises (Phocoena phocoena). Interspecific variation of cochlear morphology is well characterised among odontocetes (toothed whales) because of the importance of the structure in echolocation, but generally these studies use only a single cochlea to represent each species. In this study we compare variation within the cochleae of 18 specimens of P. phocoena with variations in cochlear morphology across 51 other odontocete species. Using both 3D landmark and linear measurement data, we performed Generalised Procrustes and principal component analyses to quantify shape variation. We then quantified intraspecific variation in our sample of P. phocoena by estimating disparity and the coefficient of variation for our 3D and linear data respectively. Finally, to determine whether intraspecific variation may confound the results of studies of interspecific variation, we used multivariate and univariate analyses of variance to test whether variation within the specimens of P. phocoena was significantly lower than that across odontocetes. We found low levels of intraspecific variation in the cochleae of P. phocoena, and that cochlear shape within P. phocoena was significantly less variable than across odontocetes. Although future studies should attempt to use multiple cochleae for every species, our results suggest that using just one cochlea for each species should not strongly influence the conclusions of comparative studies if our results are consistent across Cetacea

“Catch 22”: biosecurity awareness, interpretation and practice amongst poultry catchers

Campylobacter contamination of chicken on sale in the UK remains at high levels and has a substantial public health impact. This has prompted the application of many interventions in the supply chain, including enhanced biosecurity measures on-farm. Catching and thinning are acknowledged as threats to the maintenance of good biosecurity, yet the people employed to undertake this critical work (i.e. ‘catchers’) are a rarely studied group. This study uses a mixed methods approach to investigate catchers’ (n = 53) understanding of the biosecurity threats posed by the catching and thinning, and the barriers to good biosecurity practice. It interrogated the role of training in both the awareness and practice of good biosecurity. Awareness of lapses in biosecurity was assessed using a Watch-&-Click hazard awareness survey (n = 53). Qualitative interviews (n = 49 catchers, 5 farm managers) explored the understanding, experience and practice of catching and biosecurity. All of the catchers who took part in the Watch-&-Click study identified at least one of the biosecurity threats with 40% detecting all of the hazards. Those who had undergone training were significantly more likely to identify specific biosecurity threats and have a higher awareness score overall (48% compared to 9%, p = 0.03). Crucially, the individual and group interviews revealed the tensions between the high levels of biosecurity awareness evident from the survey and the reality of the routine practice of catching and thinning. Time pressures and a lack of equipment rather than a lack of knowledge appear a more fundamental cause of catcher-related biosecurity lapses. Our results reveal that catchers find themselves in a ‘catch-22′ situation in which mutually conflicting circumstances prevent simultaneous completion of their job and compliance with biosecurity standards

Northern Ghana hydrogeological assessment project

Groundwater is the most viable source of potable water in northern Ghana, West Africa, especially for the 80% rural inhabitants. Millions of dollars have been expended there on groundwater-based water supply infrastructures, and these expenditures are likely to continue in coming decades. The Hydrogeological Assessment Project (HAP) of the Northern Regions of Ghana was initiated to provide scientific background for groundwater-based supply projects as well as resource management. This paper summarizes the technical approaches and results to date, which include a compilation of available data, targeted field data collection, and the development of a regional hydrogeological synthesis

Polarisation of equine pregnancy outcome associated with a maternal MHC class I allele: preliminary evidence

Identification of risk factors which are associated with severe clinical signs can assist in the management of disease outbreaks and indicate future research areas. Pregnancy loss during late gestation in the mare compromises welfare, reduces fecundity and has financial implications for horse owners. This retrospective study focussed on the identification of risk factors associated with pregnancy loss among 46 Thoroughbred mares on a single British stud farm, with some but not all losses involving equid herpesvirus-1 (EHV-1) infection. In a sub-group of 30 mares, association between pregnancy loss and the presence of five common Thoroughbred horse haplotypes of the equine Major Histocompatibility Complex (MHC) was assessed. This involved development of sequence specific, reverse transcriptase polymerase chain reactions and in several mares, measurement of cytotoxic T lymphocyte activity. Of the 46 mares, 10 suffered late gestation pregnancy loss or neonatal foal death, five of which were EHV-1 positive. Maternal factors including age, parity, number of EHV-1 specific vaccinations and the number of days between final vaccination and foaling or abortion were not significantly associated with pregnancy loss. In contrast, a statistically significant association between the presence of the MHC class I B2 allele and pregnancy loss was identified, regardless of the fetus / foal’s EHV-1 status (p=0.002). In conclusion, this study demonstrated a significantly positive association between pregnancy loss in Thoroughbred mares and a specific MHC class I allele in the mother. This association requires independent validation and further investigation of the mechanism by which the mare’s genetic background contributes to pregnancy outcome

The bowfin genome illuminates the developmental evolution of ray-finned fishes.

The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era

Cervical epithelial damage promotes Ureaplasma parvum ascending infection, intrauterine inflammation and preterm birth induction in mice

Around 40% of preterm births are attributed to ascending intrauterine infection, and Ureaplasma parvum (UP) is commonly isolated in these cases. Here we present a mouse model of ascending UP infection that resembles human disease, using vaginal inoculation combined with mild cervical injury induced by a common spermicide (Nonoxynol-9, as a surrogate for any mechanism of cervical epithelial damage). We measure bacterial load in a non-invasive manner using a luciferase-expressing UP strain, and post-mortem by qPCR and bacterial titration. Cervical exposure to Nonoxynol-9, 24 h pre-inoculation, facilitates intrauterine UP infection, upregulates pro-inflammatory cytokines, and increases preterm birth rates from 13 to 28%. Our results highlight the crucial role of the cervical epithelium as a barrier against ascending infection. In addition, we expect the mouse model will facilitate further research on the potential links between UP infection and preterm birth

Lagomorpha as a model morphological system

Due to their global distribution, invasive history, and unique characteristics, European rabbits are recognizable almost anywhere on our planet. Although they are members of a much larger group of living and extinct mammals [Mammalia, Lagomorpha (rabbits, hares, and pikas)], the group is often characterized by several well-known genera (e.g., Oryctolagus, Sylvilagus, Lepus, and Ochotona). This representation does not capture the extraordinary diversity of behavior and form found throughout the order. Model organisms are commonly used as exemplars for biological research, but there are a limited number of model clades or lineages that have been used to study evolutionary morphology in a more explicitly comparative way. We present this review paper to show that lagomorphs are a strong system in which to study macro- and micro-scale patterns of morphological change within a clade that offers underappreciated levels of diversity. To this end, we offer a summary of the status of relevant aspects of lagomorph biology.Brian Kraatz, Rafik Belabbas, Łucja Fostowicz-Frelik, De-Yan Ge, Alexander N. Kuznetsov, Madlen M. Lang ... et al

Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity

Persistent infection with oncogenic Human Papillomavirus (HPV) is necessary for cervical carcinogenesis. Although evidence suggests that the vaginal microbiome plays a functional role in the persistence or regression of HPV infections, this has yet to be described in women with cervical intra-epithelial neoplasia (CIN). We hypothesised that increasing microbiome diversity is associated with increasing CIN severity. llumina MiSeq sequencing of 16S rRNA gene amplicons was used to characterise the vaginal microbiota of women with low-grade squamous intra-epithelial lesions (LSIL; n = 52), high-grade (HSIL; n = 92), invasive cervical cancer (ICC; n = 5) and healthy controls (n = 20). Hierarchical clustering analysis revealed an increased prevalence of microbiomes characterised by high-diversity and low levels of Lactobacillus spp. (community state type-CST IV) with increasing disease severity, irrespective of HPV status (Normal = 2/20,10%; LSIL = 11/52,21%; HSIL = 25/92,27%; ICC = 2/5,40%). Increasing disease severity was associated with decreasing relative abundance of Lactobacillus spp. The vaginal microbiome in HSIL was characterised by higher levels of Sneathia sanguinegens (P < 0.01), Anaerococcus tetradius (P < 0.05) and Peptostreptococcus anaerobius (P < 0.05) and lower levels of Lactobacillus jensenii (P < 0.01) compared to LSIL. Our results suggest advancing CIN disease severity is associated with increasing vaginal microbiota diversity and may be involved in regulating viral persistence and disease progression

Identifying metabolite markers for preterm birth in cervicovaginal fluid by magnetic resonance spectroscopy

Introduction Preterm birth (PTB) may be preceded by changes in the vaginal microflora and metabolite profiles. Objectives We sought to characterise the metabolite profile of cervicovaginal fluid (CVF) of pregnant women by 1H NMR spectroscopy, and assess their predictive value for PTB. Methods A pair of high-vaginal swabs was obtained from pregnant women with no evidence of clinical infection and grouped as follows: asymptomatic low risk (ALR) women with no previous history of PTB, assessed at 20–22 gestational weeks, g.w., n = 83; asymptomatic high risk (AHR) women with a previous history of PTB, assessed at both 20–22 g.w., n = 71, and 26–28 g.w., n = 58; and women presenting with symptoms of preterm labor (PTL) (SYM), assessed at 24–36 g.w., n = 65. Vaginal secretions were dissolved in phosphate buffered saline and scanned with a 9.4 T NMR spectrometer. Results Six metabolites (lactate, alanine, acetate, glutamine/glutamate, succinate and glucose) were analysed. In all study cohorts vaginal pH correlated with lactate integral (r = -0.62, p\0.0001). Lactate integrals were higher in the term ALR compared to the AHR (20–22 g.w.) women (p = 0.003). Acetate integrals were higher in the preterm versus term women for the AHR (20–22 g.w.) (p = 0.048) and SYM (p = 0.003) groups; and was predictive of PTB\37 g.w. (AUC 0.78; 95 % CI 0.61–0.95), and delivery within 2 weeks of the index assessment (AUC 0.84; 95 % CI 0.64–1) in the SYM women, whilst other metabolites were not. Conclusion High CVF acetate integral of women with symptoms of PTL appears predictive of preterm delivery, as well as delivery within 2 weeks of presentation