Now showing items 1-20 of 347

    • Baseline Behavioral Data and Behavioral Correlates of Disturbance for the Lake Oku Clawed Frog (Xenopus longipes)

      Dias, Jemma E.; Ellis, Charlotte; Smith, Tessa E; Hosie, Charlotte A; Tapley, Benjamin; Michaels, Christopher J.; University of Chester; Zoological Sciety of London Outer Circle
      Animal behavior and welfare science can form the basis of zoo animal management. However, even basic behavioral data are lacking for the majority of amphibian species, and species-specific research is required to inform management. Our goal was to develop the first ethogram for the critically endangered frog Xenopus longipes through observation of a captive population of 24 frogs. The ethogram was applied to produce a diurnal activity budget and to measure the behavioral impact of a routine health check where frogs were restrained. In the activity budget, frogs spent the vast majority of time swimming, resting in small amounts of time devoted to feeding, foraging, breathing, and (in males) amplexus. Using linear mixed models, we found no effect of time of day or sex on baseline behavior, other than for breathing, which had a greater duration in females. Linear mixed models indicated significant effects of the health check on duration of swimming, resting, foraging, feeding, and breathing behaviors for all frogs. This indicates a welfare trade-off associated with veterinary monitoring and highlights the importance of non-invasive monitoring where possible, as well as providing candidates for behavioral monitoring of acute stress. This investigation has provided the first behavioral data for this species which can be applied to future research regarding husbandry and management practices.
    • Long term analysis of social structure: evidence of age-based consistent associations in male Alpine ibex

      Brambilla, Alice; von Hardenberg, Achaz; Canedoli, Claudia; Brivio, Francesca; Sueur, Cédric; Stanley, Christina R.; University of Zurich; University of Chester; University of Milano Bicocca; University of Sassari; University de Strasbourg; Institut Universitaire de France (Wiley, 2022-06-28)
      Despite its recognized importance for understanding the evolution of animal sociality as well as for conservation, long term analysis of social networks of animal populations is still relatively uncommon. We investigated social network dynamics in males of a gregarious mountain ungulate (Alpine ibex, Capra ibex) over ten years focusing on groups, sub-groups and individuals, exploring the dynamics of sociality over different scales. Despite the social structure changing between seasons, the Alpine ibex population was highly cohesive: fission–fusion dynamics lead almost every male in the population to associate with each other male at least once. Nevertheless, we found that male Alpine ibex showed preferential associations that were maintained across seasons and years. Age seemed to be the most important factor driving preferential associations while other characteristics, such as social status, appeared less crucial. We also found that centrality measures were influenced by age and were also related to individual physical condition. The multi-scale and long-term frame of our study helped us show that ecological constrains, such as resource availability, may play a role in shaping associations in a gregarious species, but they cannot solely explain sociality and preferential association that are likely also to be driven by life-history linked physiological and social needs. Our results highlight the importance of long-term studies based on individually recognizable subjects to help us build on our understanding of the evolution of animal sociality.
    • An Examination of the Social and Physiological Experience of Captive Livingstone’s Fruit Bats (Pteropus livingstonii)

      Stanley, Christina; Smith, Tessa; Hosie, Lottie; Edwards, Morgan J. (University of Chester, 2022-02-01)
      This thesis presents a series of empirical studies designed to quantify the complex social and physiological experiences of individuals within the captive population of a critically endangered bat species, the Livingstone’s fruit bat (Pteropus livingstonii). The ultimate goal of this work was to apply leading-edge methodologies and technology to gain novel, evidence-based insights into the behaviour and welfare of this species in captivity. This work has not only informed the captive management of P. livingstonii, but has also developed techniques that can be applied to maximise the captive welfare of a range of other species. A brief summary, explaining how each chapter is embedded within the overall thesis and summarising its major findings, precedes each chapter. Chapter One, the introductory chapter, will start by evaluating our current understanding of the natural history and behavioural ecology of P. livingstonii, with a focus on captive behaviour. The following sections of this chapter will then provide necessary background information to the methodologies applied in subsequent data chapters, including social network analysis, space use assessment, hormone analysis and radio-frequency identification technology. The introductory chapter is intended to provide the reader with sufficient scientific context to interpret the results of each data chapter. Chapter Two outlines the implementation of social network analysis to characterise individual social experiences in the largest captive population of P. livingstonii, housed at Jersey Zoo. Variation in network complexity and significant individual variable-based assortment is identified in this chapter. Chapter Three presents principal component analysis as a novel compliment to traditional enclosure use assessment methodologies, quantifying the individual spatial preferences of P. livingstonii. This chapter also quantifies the relationship between high-value resource location within the enclosure at Jersey Zoo and population-level space use. Chapter Four outlines the validation and application of an enzyme immunoassay to non-invasively measure faecal cortisol in the P. livingstonii population. This chapter examines the relationship between cortisol titres, individual social roles and behavioural frequencies performed by individuals in the captive population. We find that males, older individuals and lactating females have higher concentrations of cortisol than non-lactating females and younger individuals and that social roles related to conspecific affiliation were linked to decreased cortisol titres. Lastly, Chapter Five demonstrates the application of unique radio-frequency identification technology to autonomously collect individual locational data. The resulting dataset was then utilised to interrogate the foraging network displayed by P. livingstonii and Pteropus rodricensis (a cohabitating heterospecific) populations housed at Jersey Zoo, elucidating the relationship between individual bat characteristics and social foraging patterns. Finally, the discussion chapter evaluates the significance of the main findings of each chapter of this thesis, highlighting the wider applicability of results and methodologies to the assessment of captive animal welfare. This section also critically discusses recent challenges to hypothesis testing in the field of animal social network analysis, to evaluate the validity of methods utilised throughout this thesis. Finally, future research directives leading on from this work which may provide further benefit to the management of captive populations are proposed.
    • Pre- and peri-operative clinical information, physiological observations and outcome measures following flexible ureterorenoscopy (FURS), for the treatment of kidney stones. A single-centre observational clinical pilot-study in 51 patients

      Hughes, Stephen Fôn; orcid: 0000-0001-6558-9037; email:; Moyes, Alyson Jayne; Jones, Kevin; Bell, Christopher; Duckett, Abigail; Moussa, Ahmed; Shergill, Iqbal (BioMed Central, 2022-07-14)
      Abstract: Background: Kidney stone disease contributes to a significant proportion of routine urological practice and remains a common cause of worldwide morbidity. The main aim of this clinical-pilot study was to investigate the effect of flexible ureterorenoscopy (FURS) on pre- and peri-operative clinical information, physiological observations and outcome measures. Methods: Included were 51 patients (31 males, 20 females), who underwent elective FURS, for the treatment of kidney stones. Pre-operative and peri-operative clinical information, and post-operative physiological observations and outcome measures were collected using a standard case report form. Pre-operative clinical information included age, gender, BMI, previous history of stone formation and hypertension. Pre-operative stone information included the size (mm), Hounsfield units (HU), laterality and intra-renal anatomical location. Peri-operative surgical details included surgical time in minutes; Laser use; Duration and energy of laser; and post-operative stenting. The physiological outcomes measured included systolic and diastolic blood pressure (mmHg), Likert pain score, temperature, heart rate (bpm) and respiration rate (bpm). Following initial descriptive analysis, a series of Pearson’s correlation coefficient tests were performed to investigate the relationship between surgical factors other variable factors. Results: A series of significant, positive correlations were observed between; age and surgical time (p = 0.014, r = 0.373); stone size and Hounsfield unit (p = 0.029, r = 0.406); surgical time and duration of laser (p < 0.001, r = 0.702); surgical time and BMI (p = 0.035, r = 0.322); baseline heart rate and Hounsfield unit (p = 0.026, r = − 0.414); base line heart rate and BMI (p = 0.030, r = 0.307).; heart rate at 120-min post FURS and age (p = 0.038, r = − 0.308); baseline pain score and BMI (p = 0.010, r = 0.361); baseline respiration rate and BMI (p = 0.037, r = 0.296); respiration rate at 240-min post FURS and BMI (p = 0.038, r = 0.329); respiration rate at 120 min post FURS and age (p = 0.022, r = − 0.330). Four patients developed post-operative complications (3—UTIs with urinary retention, 1–urosepsis). Conclusions: We report that following FURS there is an association between various physiological, clinical and surgical parameters. Although these correlations are weak, they warrant further investigation as these may be linked with untoward complications, such as infection that can occur following FURS. This data, however, will need to be validated and reproduced in larger multi-centre studies.
    • Social roles influence cortisol levels in captive Livingstone's fruit bats (Pteropus livingstonii)

      Edwards, Morgan J.; Stanley, Christina R.; Hosie, Charlotte A.; Richdon, Sarah; Price, Eluned; Wormell, Dominic; Smith, Tessa E.; University of Chester; Bristol Zoological Society; Durrell Wildlife Conservation Trust (Elsevier, 2022-06-27)
      A critical component of conserving and housing species ex situ is an explicit scientific understanding of the physiological underpinnings of their welfare. Cortisol has been repeatedly linked to stress, and therefore used as an indicator of welfare for many species. In order to measure cortisol in the Livingstone's fruit bat (Pteropus livingstonii; a critically endangered keystone species) without disturbing the captive population, we have developed and validated a non-invasive, novel hormone extraction procedure and faecal glucocorticoid assay. A total of 92 faecal samples, 73 from the P. livingstonii breeding colony at Jersey Zoo, Channel Islands and 19 samples from P. livingstonii housed at Bristol Zoological Gardens, UK, have been collected and analyzed. Mixed-effect modelling of the influence of physiological state variables on cortisol concentration revealed that lactating females had higher cortisol levels than non-lactating females, indicating that our assay is measuring biologically relevant hormone concentrations. Males and older bats also had higher cortisol than non-lactating females and younger individuals. Further analysis applied social network methodology to compare the cortisol levels of bats with different social roles. We found that individuals that linked social groups possessed higher than average cortisol levels and conversely, individuals with high-quality, positive relationships had lower cortisol levels. These results demonstrate, for the first time in a bat species, social mediation of stress hormones. Lastly, the frequency of vocalisation was found to positively correlate with cortisol concentration in males, suggesting that this behaviour may be used by animal management as a visual indicator of a bat's hormonal status. Hence, this research has provided unique insights and empirical scientific knowledge regarding the relationship between the physiology and social behaviour of P. livingstonii, therefore allowing for recommendations to be made to optimise bat welfare at the individual level.
    • Phylogenetic placement and life history trait imputation for Grenada Dove Leptotila wellsi

      Peters, Catherine; Geary, Matthew; Nelson, Howard; Rusk, Bonnie; von Hardenberg, Achaz; Muir, Anna P.; University of Chester; University of Cambridge; Grenada Dove Conservation Programme
      Phylogenetic analyses can be used to resolve taxonomic uncertainties and reconstruct a species’ evolutionary history. This can be combined with ecological data to predict missing life history traits which are important for creation of conservation management strategies. We investigated the evolutionary and life history of the Critically Endangered Grenada Dove Leptotila wellsi by estimating its phylogenetic placement and using this new phylogeny to test the accuracy of phylogenetic comparative methods for estimating both documented and unknown life history traits. We extracted DNA from two Grenada Dove samples and obtained sequences from three mitochondrial markers: Cytochrome oxidase I (COI), NADH dehydrogenase 2 (ND2) and Cytochrome b (Cyt b); and one nuclear marker: β-Fibrinogen intron 7 (β-FIB). We present the first genetic data obtained for the Grenada Dove. Our data identifies the Grey-Chested Dove Leptotila cassinii as the species which shares both a most recent common ancestor, with an estimated divergence of approximately 2.53 million years ago, and the smallest genetic distance (p=0.0303) with the Grenada dove. Life history trait values for the Grenada Dove predicted from our analyses using phylogenetic imputation are: clutch size=2 (±0.09) eggs, clutches per year=1.4 (±0.81), incubation time=14.2 (±0.75) days, hatching weight=3.8 (±1.05) grams and single imputation: fledging age (genus median) =15.5 days, longevity (genus median) =8.6 years. This study contributes novel information regarding evolutionary history and life history characteristics to inform long-term conservation actions for a Critically Endangered species.
    • New haplotypes found in stranded long-finned pilot whales (Globicephala melas) in the eastern North Atlantic and adjacent waters

      Ball, Rachel J.; Kitchiner, Ashleigh; Davison, Nicholas J.; Berrow, Simon; McKeown, Niall J.; IJsseldijk, Lonneke L.; Geary, Matthew; McDowall, Ian; Muir, Anna P.; University of Chester; University of Glasgow; Scottish Marine Animal Stranding Scheme; Irish Whale and Dolphin Group; Galway-Mayo Institute of Technology; Aberystwyth University; Utrecht University (Wiley, 2021-12-17)
      Long-finned pilot whale (Globicephala melas) mitochondrial (mtDNA) genetic diversity is considered low, especially in the North Atlantic, where only six haplotypes have been recorded using a 345bp portion of the control region. Previous studies have been based on a small number of samples and have not included samples from Ireland or the Netherlands. We utilized mtDNA control region sequencing of individuals stranded around Ireland, Scotland, and the Netherlands between 1995-2019 (n=180) to assess regional diversity. Following alignment of 631bp, nine haplotypes were identified, of which five were newly described (haplotype diversity (h)=0.511). Pairwise tests revealed significant differentiation between the Irish and Scottish samples. Potential confounding factors are discussed but, given the dangers of failing to recognize population structure this needs to be investigated further using nuclear markers and individual-based approaches before population isolation is assumed. The analyzed samples included six mass stranding events. One of the mass strandings reported two haplotypes, confirming mixing of matrilines within a North Atlantic stranding for the first time. This study shows that stranding sample databases are a useful tool for assessment of genetic diversity and provides new insights into genetic diversity of long-finned pilot whale haplotypes in the eastern North Atlantic and adjacent waters.
    • Anthropogenic influences on habitat use by African Houbaras Chlamydotis undulata on Lanzarote, Canary Islands

      Geary, Matthew; Cooper, Joseph R.; Collar, Nigel J.; University of Chester; BirdLife International (Elsevier, 2022-06-27)
      African Houbara Chlamydotis undulata is threatened in North Africa by unsustainable hunting and massive overuse of captive-bred birds to replace wild losses. A small population on the Canary Islands is protected from these threats, but the archipelago is economically dependent on tourism which has led to extensive land-use change, particularly close to the coasts. We investigated the drivers of houbara distribution and abundance in and around the large semi-desert El Jable region of northern Lanzarote in order to identify potential measures to conserve this important population. All houbaras seen during point counts in the centre of 30 tetrads (2 km ×2 km) were recorded, along with their location. We used negative binomial regression to evaluate the effects of land use and human activity on the abundance of birds at tetrad scale. At finer scale we used logistic regression to assess the effect of land use on the distribution of displaying males. We recorded 196 houbara sightings on our surveys, although only 10 males were observed displaying. Houbara abundance had a quadratic relationship with the proportion of huerta (agricultural gardens) in a tetrad. The distribution of male displays was positively related to the proportion of long-abandoned farmland within a 100 m radius of their display site. African Houbaras favour the vicinity of small-scale agriculture and abandoned farmland, but avoid areas with higher levels of human land-use. Reduction of extensive land-use change and disturbance in El Jable are key conservation measures.
    • Targeting burrows improves detection in giant pangolin Smutsia gigantea camera trap surveys

      Matthews, Naomi; Nixon, Stuart; von Hardenberg, Achaz; Geary, Matthew; University of Chester; North of England Zoological Society; Chester Zoo
      The Endangered giant pangolin (Smutsia gigantea) is rare and elusive across its central African range. Due to its solitary and nocturnal nature, the species is difficult to study and subsequently its ecology is poorly known. Pangolins are considered the World’s most-trafficked mammals. Therefore, accurately confirming presence and monitoring trends in distribution and abundance is essential to inform and prioritise conservation efforts. Camera traps are a popular tool for surveying rare and cryptic species. However non-targeted camera trap surveys yield low camera trapping rates for pangolins. Here we use camera trap data from surveys conducted within three protected areas in Uganda to test whether targeted placement of cameras improves giant pangolin detection probability in occupancy models. The results indicate that giant pangolin detection probability is highest when camera traps are targeted on burrows. The median number of days from camera deployment to first giant pangolin event was 12, with 97.5% of events captured within 32 days from deployment. The median interval between giant pangolin events at a camera trap site was 33 days. We demonstrate that camera trap surveys can be designed to improve detection of giant pangolins and outline a set of recommendations to maximise the effectiveness of efforts to survey and monitor the species.
    • Zooarchaeology through the lens of collagen fingerprinting at Denisova Cave

      Brown, Samantha; Wang, Naihui; Oertle, Annette; Kozlikin, Maxim B.; Shunkov, Michael V.; Derevianko, Anatoly P.; Comeskey, Daniel; Jope-Street, Blair; Harvey, Virginia L.; Chowdhury, Manasij Pal; et al. (Nature Research, 2021-07-29)
      Denisova Cave, a Pleistocene site in the Altai Mountains of Russian Siberia, has yielded significant fossil and lithic evidence for the Pleistocene in Northern Asia. Abundant animal and human bones have been discovered at the site, however, these tend to be highly fragmented, necessitating new approaches to identifying important hominin and faunal fossils. Here we report the results for 8253 bone fragments using ZooMS. Through the integration of this new ZooMS-based data with the previously published macroscopically-identified fauna we aim to create a holistic picture of the zooarchaeological record of the site. We identify trends associated with climate variability throughout the Middle and Upper Pleistocene as well as patterns explaining the process of bone fragmentation. Where morphological analysis of bones from the site have identified a high proportion of carnivore bones (30.2%), we find that these account for only 7.6% of the ZooMS assemblage, with large mammals between 3 and 5 more abundant overall. Our analysis suggests a cyclical pattern in fragmentation of bones which sees initial fragmentation by hominins using percussive tools and secondary carnivore action, such as gnawing and digestion, likely furthering the initial human-induced fragmentation.
    • Medieval fish remains on the Newport ship identified by ZooMS collagen peptide mass fingerprinting

      Buckley, Michael; Harvey, Virginia L.; Pettifer, David; Russ, Hannah; Wouters, Wim; Van Neer, Wim; University of Manchester; University of Birmingham; University of Wales Trinity Saint David; Royal Belgian Institute of Natural Sciences (Springer, 2022-02-11)
      Fish represent a key economic, social and ecological group of species that humans have exploited for tens of thousands of years. However, as many fish stocks are going into decline and with little known about the anthropogenic impacts on the health of the marine ecosystem pre-Industrial Revolution, understanding historical and archaeological exploitation of fish species is key to accurately modelling these changes. Here, we explore the potential of collagen peptide mass fingerprinting (also known as Zooarchaeology by Mass Spectrometry, or ZooMS) for identifying fish remains from the Medieval (fifteenth century) Newport ship wreck (Wales, UK), and in doing so we establish a set of biomarkers we consider useful in discriminating between European fish taxa through the inclusion of over 50 reference taxa. The archaeological results identified nine distinct taxonomic groups, dominated by ling (> 40%), and a substantial amount of cod (> 20%) and hake (~ 20%). The vast majority of samples (> 70%) were identified to species level, and the inability to identify the remaining taxonomic groups with confidence using ZooMS was due to the fact that the reference collection, despite being relatively large in comparison to those presented in mammalian studies, reflects only a small proportion of fish biodiversity from this region. Although the results clearly demonstrate the potential for ZooMS as a means of fish bone identification, the sheer number of different fish species that potentially make up ichthyoarchaeological assemblages leads to obvious requirements for the analysis on much greater numbers of modern reference specimens, or the acquisition of collagen sequences.
    • Extrinsic and intrinsic factors affecting the activity budget of alpine marmots ( Marmota marmota )

      Ferrari, Caterina; orcid: 0000-0002-6316-9706; email:; email:; Pasquaretta, Cristian; orcid: 0000-0001-8308-9968; Caprio, Enrico; orcid: 0000-0002-5997-5959; Ranghetti, Luigi; Bogliani, Giuseppe; orcid: 0000-0001-9066-6540; Rolando, Antonio; orcid: 0000-0002-3432-1780; Bertolino, Sandro; orcid: 0000-0002-1063-8281; Bassano, Bruno; von Hardenberg, Achaz; orcid: 0000-0002-9899-1687 (Springer Berlin Heidelberg, 2022-03-15)
      Abstract: Extrinsic and intrinsic factors may influence the activity budget of wild animals, resulting in a variation in the time spent in different activities among populations or individuals of the same species. In this study, we examined how extrinsic and intrinsic factors affect the behaviour of the alpine marmot (Marmota marmota), a hibernating social rodent inhabiting high-elevation prairies in the European Alps. We collected behavioural observations during scan sampling sessions on marked individuals at two study sites with different environmental characteristics. We used Bayesian hierarchical multinomial regression models to analyse the influence of both intrinsic (sex and age-dominance status) and extrinsic (environmental and climatic variables) factors on the above-ground activity budget. Marmots spent most of their time above ground foraging, and were more likely to forage when it was cloudy. Extrinsic factors such as the site, period of the season (June, July–August, and August–September), and time of the day were all related to the probability of engaging in vigilance behaviour, which reaches its peak in early morning and late afternoon and during July, the second period included in the study. Social behaviours, such as affiliative and agonistic behaviours, were associated mostly with sex and age-dominance status, and yearlings were the more affiliative individuals compared to other status. Overall, our results suggest that in alpine marmots, intrinsic factors mostly regulate agonistic and affiliative behaviours, while extrinsic factors, with the unexpected exception of temperature, affect the probabilities of engaging in all types of behavioural categories.
    • Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences

      Harvey, Virginia L.; Keating, Joseph N.; Buckley, Michael; University of Manchester; University of Bristol (The Royal Society, 2021-08-11)
      Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher order relationships. Such analyses are rightfully regarded as the ‘gold standard’ for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. By contrast, some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ∼293 million years (Ma), the base of Teleostei at ∼211 Ma and the radiation of percomorphs beginning at ∼141 Ma (∼350 Ma, ∼250–283 Ma and ∼120–133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing.
    • Proteome Variation with Collagen Yield in Ancient Bone

      Harvey, Virginia L.; Procopio, Noemi; Hopkins, Rachel J. A.; Buckley, Michael; Northumbria University; University of Manchester; University of New Mexico (American Chemical Society, 2021-02-02)
      Isotope analyses are some of the most common analytical methods applied to ancient bone, aiding the interpretation of past diets and chronology. For this, the evaluation of “collagen yield” (as defined in radiocarbon dating and stable isotope research) is a routine step that allows for the selection of specimens that are deemed adequate for subsequent analyses, with samples containing less than ∼1% “collagen yield” normally being used for isotopic analysis but discounted for radiocarbon dating. The aims of this study were to use proteomic methods of MALDI–TOF (matrix assisted laser desorption ionization time-of-flight mass spectrometry) and LC−ESI−MS/MS (liquid chromatography electrospray ionization tandem mass spectrometry) to investigate the endogeneity of the dominant proteinaceous biomolecules within samples that are typically considered to contain poorly preserved protein. Taking 29 archaeological samples, we evaluated the proteome variability between different acid-soluble fractions removed prior to protein gelatinization and considered waste as part of the radiocarbon dating process. We then correlated these proteomes against the commonly used “collagen yield” proxy for preservation. We found that these waste fractions contained a significant amount of both collagenous and noncollagenous proteins (NCPs) but that the abundance of these was not correlated with the acquired “collagen yield”. Rather than a depleted protein load as would be expected from a low “collagen yield”, the variety of the extracted NCPs was comparable with that commonly obtained from ancient samples and included informative proteins useful for species identification, phylogenetic studies, and potentially even for isotopic analyses, given further method developments. Additionally, we did not observe any correlation between “collagen yield” and peptide mass fingerprint success or between the different fractions taken from the same sample but at different radiocarbon pretreatment stages. Overall, these findings highlight the value in retaining and analyzing sample fractions that are otherwise discarded as waste during the radiocarbon dating process but more importantly, that low “collagen yield” specimens that are often misinterpreted by archaeologists as being devoid of protein can still yield useful molecular sequence-based information.
    • Experimental taphonomy of fish bone from warm and cold water species: Testing the effects of amino acid composition on collagen breakdown in modern fish bone using thermal maturation experiments

      Harvey, Virginia L.; Wogelius, Roy A.; Manning, Phillip L.; Buckley, Michael; University of Manchester (Elsevier, 2021-01-12)
      Decay experiments have the potential to provide useful analogues in the interpretation of archaeological remains. Previous studies have focused on how physical properties or processing methods can influence fish bone distributions within archaeological sites. However, the means by which intrinsic chemical properties of fish bone, such as baseline collagen type I [‘collagen (I)’] chemistry, may affect both biomolecule and whole bone degradation has not been the focus of any prior study. The variation of facies and resulting impact on taphonomy is not a new concept, but an understanding of the discrete relationship between temperature and the breakdown of collagen (I) in bone material has not been well explored. Here, modern fish bone powder is subjected to differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and water-immersed heat experiments. This is to test whether taxa with less thermally stable collagen (I) configurations, such as cold-water species with reduced proline and hydroxyproline concentrations (Pro+Hyp), will generate collagen breakdown products (TOC and TN) more rapidly than those with more thermally stable arrangements, such as warm-water fish with typically increased Pro+Hyp. Our results show that bone collagen (I) in the cold-water fish species in this study (cod and herring with lower Pro+Hyp concentrations) display significantly increased decomposition rates than collagen (I) from the warm-water fishes in this study (amberjack and tilapia with higher Pro+Hyp concentrations), given the same experimental conditions (heating in water at 75 °C for up to eight days). Initial reaction rate estimates, based on TOC and TN product concentrations, suggest that cod bone (15.6% Pro+Hyp) reacts ~9 times faster than tilapia bone (20.3% Pro+Hyp). We suggest that the primary influencer of collagen (I) stability in bone is the concentration of Pro+Hyp residues and not a function of physical bone structure. Our results suggest that a reduction in collagen (I) stability is likely to lead to a decrease in whole bone stability following deposition, due to the intimate association between organic and inorganic phases of bone. Therefore, species composition based upon bone remains may vary in archaeological and palaeontological sites, as a function of the thermal stability of collagen (I).
    • Translating from egg- to antigen-based indicators for Schistosoma mansoni elimination targets: A Bayesian latent class analysis study

      Clark, Jessia; Moses, Arinaitwe; Nankasi, Andrina; Faust, Christina L.; Adriko, Moses; Ajambo, Diana; Besigye, Fred; Atuhaire, Arron; Wamboko, Aidah; Rowel, Candia; et al.
      Schistosomiasis is a parasitic disease affecting over 240-million people. World Health Organization (WHO) targets for Schistosoma mansoni elimination are based on Kato-Katz egg counts, without translation to the widely used, urine-based, point-of-care circulating cathodic antigen diagnostic (POC-CCA). We aimed to standardize POC-CCA score interpretation and translate them to Kato-Katz-based standards, broadening diagnostic utility in progress towards elimination. A Bayesian latent-class model was fit to data from 210 school-aged-children over four timepoints pre- to six-months-post-treatment. We used 1) Kato-Katz and established POC-CCA scoring (Negative, Trace, +, ++ and +++), and 2) Kato-Katz and G-Scores (a new, alternative POC-CCA scoring (G1 to G10)). We established the functional relationship between Kato-Katz counts and POC-CCA scores, and the score-associated probability of true infection. This was combined with measures of sensitivity, specificity, and the area under the curve to determine the optimal POC-CCA scoring system and positivity threshold. A simulation parametrized with model estimates established antigen-based elimination targets. True infection was associated with POC-CCA scores of ≥ + or ≥G3. POC-CCA scores cannot predict Kato-Katz counts because low infection intensities saturate the POC-CCA cassettes. Post-treatment POC-CCA sensitivity/specificity fluctuations indicate a changing relationship between egg excretion and antigen levels (living worms). Elimination targets can be identified by the POC-CCA score distribution in a population. A population with ≤2% ++/+++, or ≤0.5% G7 and above, indicates achieving current WHO Kato-Katz-based elimination targets. Population-level POC-CCA scores can be used to access WHO elimination targets prior to treatment. Caution should be exercised on an individual level and following treatment, as POC-CCAs lack resolution to discern between WHO Kato-Katz-based moderate- and high-intensity-infection categories, with limited use in certain settings and evaluations.
    • ABO Blood Groups Do Not Predict Schistosoma mansoni Infection Profiles in Highly Endemic Villages of Uganda

      Francoeur, Rachel; Atuhaire, Alon; Arinaitwe, Moses; Adriko, Moses; Ajambo, Diana; Nankasi, Andrina; Babayan, Simon A.; Lamberton, Poppy H. L.; University of Glasgow; University of Chester; Ministry of Health, Uganda
      Schistosoma mansoni is a parasite which causes significant public-health issues, with over 240 mil-lion people infected globally. In Uganda alone, approximately 11.6 million people are affected. Despite over a decade of mass drug administration in this country, hyper-endemic hotspots persist, and individuals who are repeatedly heavily and rapidly reinfected are observed. Human blood-type antigens are known to play a role in the risk of infection for a variety of diseases, due to cross-reactivity between host antibodies and pathogenic antigens. There have been conflicting results on the effect of blood type on schistosomiasis infection and pathology. Moreover, the ef-fect of blood type as a potential intrinsic host factor on S. mansoni prevalence, intensity, clearance, and reinfection dynamics and on co-infection risk remains unknown. Therefore, the epidemio-logical link between host blood type and S. mansoni infection dynamics was assessed in three hyper-endemic communities in Uganda. Longitudinal data incorporating repeated pretreatment S. mansoni infection intensities and clearance rates were used to analyse associations between blood groups in school-aged children. Soil-transmitted helminth coinfection status and biometric parameters were incorporated in a generalised linear mixed regression model including age, gender, and body mass index (BMI), which have previously been established as significant factors influencing the prevalence and intensity of schistosomiasis. The analysis revealed no associations between blood type and S. mansoni prevalence, infection intensity, clearance, reinfection, or coinfection. Variations in infection profiles were significantly different between the villages, and egg burden significantly decreased with age. While blood type has proven to be a predictor of several diseases, the data collected in this study indicate that it does not play a significant role in S. mansoni infection burdens in these high-endemicity communities.
    • Reconciling egg- and antigen-based estimates of Schistosoma mansoni clearance and reinfection: a modelling study

      Clark, Jessica; Arinaitwe, Moses; Nankasi, Andrina; Faust, Christina L.; Moses, Adriko; Ajambo, Diana; Besigye, Fred; Atuhaire, Aaron; Carruthers, Lauren V.; Francoeur, Rachel; et al.
      Background Despite decades of interventions, 240 million people have schistosomiasis. Infections cannot be directly observed, and egg-based Kato-Katz thick smears lack sensitivity, affected treatment efficacy and reinfection rate estimates. The point-of-care circulating cathodic antigen (referred to from here as POC-CCA+) test is advocated as an improvement on the Kato-Katz method, but improved estimates are limited by ambiguities in the interpretation of trace results. Method We collected repeated Kato-Katz egg counts from 210 school-aged children and scored POC-CCA tests according to the manufacturer’s guidelines (referred to from here as POC-CCA+) and the externally developed G score. We used hidden Markov models parameterized with Kato-Katz; Kato-Katz and POC-CCA+; and Kato-Katz and G-Scores, inferring latent clearance and reinfection probabilities at four timepoints over six-months through a more formal statistical reconciliation of these diagnostics than previously conducted. Our approach required minimal but robust assumptions regarding trace interpretations. Results Antigen-based models estimated higher infection prevalence across all timepoints compared with the Kato-Katz model, corresponding to lower clearance and higher reinfection estimates. Specifically, pre-treatment prevalence estimates were 85% (Kato-Katz; 95% CI: 79%–92%), 99% (POC-CCA+; 97%–100%) and 98% (G-Score; 95%–100%). Post-treatment, 93% (Kato-Katz; 88%–96%), 72% (POC-CCA+; 64%–79%) and 65% (G-Score; 57%–73%) of those infected were estimated to clear infection. Of those who cleared infection, 35% (Kato-Katz; 27%–42%), 51% (POC-CCA+; 41%–62%) and 44% (G-Score; 33%–55%) were estimated to have been reinfected by 9-weeks. Conclusions Treatment impact was shorter-lived than Kato-Katz–based estimates alone suggested, with lower clearance and rapid reinfection. At 3 weeks after treatment, longer-term clearance dynamics are captured. At 9 weeks after treatment, reinfection was captured, but failed clearance could not be distinguished from rapid reinfection. Therefore, frequent sampling is required to understand these important epidemiological dynamics.
    • Regucalcin ameliorates doxorubicin-induced cytotoxicity in Cos-7 kidney cells and translocates from the nucleus to the mitochondria.

      Mohammed, Noor A; Hakeem, Israa J; Hodges, Nikolas; Michelangeli, Francesco; orcid: 0000-0002-4878-046X (2022-01-01)
      Doxorubicin (DOX) is a potent anticancer drug, which can have unwanted side-effects such as cardiac and kidney toxicity. A detailed investigation was undertaken of the acute cytotoxic mechanisms of DOX on kidney cells, using Cos-7 cells as kidney cell model. Cos-7 cells were exposed to DOX for a period of 24 h over a range of concentrations, and the LC50 was determined to be 7 µM. Further investigations showed that cell death was mainly via apoptosis involving Ca2+ and caspase 9, in addition to autophagy. Regucalcin (RGN), a cytoprotective protein found mainly in liver and kidney tissues, was overexpressed in Cos-7 cells and shown to protect against DOX-induced cell death. Subcellular localization studies in Cos-7 cells showed RGN to be strongly correlated with the nucleus. However, upon treatment with DOX for 4 h, which induced membrane blebbing in some cells, the localization appeared to be correlated more with the mitochondria in these cells. It is yet to be determined whether this translocation is part of the cytoprotective mechanism or a consequence of chemically induced cell stress.
    • Preliminary investigation of the effects of a concert on the behavior of zoo animals

      Harley, Jessica J.; Rowden, Lewis J.; Clifforde, Lisa M.; Power, Aisling; Stanley, Christina; University of Chester; Knowsley Safari Park, ZSL; Tayto Park (Wiley, 2022-02-09)
      To increase visitor footfall and engagement, zoos may host public events which may extend outside of typical opening hours. With plans to hold a 2-day concert at Tayto Park, Ireland, this study aimed to identify the behavioral response to the music event of a selected group of species in the zoo. Twenty-two species were observed across three Phases of the event (pre-, during and post-event). Specific behaviors of interest were categorized as active, resting, asleep, abnormal, and out of sight, with repeated observations being made at each enclosure during each Phase. Alongside these behavioral data, Sound Pressure Levels (SPLs) were concurrently recorded at the observation locations in terms of both dB(A) and dB(C). The median dB(C) levels during the event were found to be significantly higher (mdn = 64.5dB) when compared with both pre- (mdn = 60.7dB) and post-event Phases (mdn = 59.4dB), whilst dB(A) levels were only significantly higher during the event (51.7dB) when compared with the pre-event Phase (mdn = 49.8dB). We found some species-specific behavioral changes (mainly associated with active and resting behaviors) correlated with increased SPLs and/or event itself. However, the behavioral responses varied between species and there were numerous species which did not respond with any change in behavior to the increased SPLs or the event itself. This variation in response across species reinforces the need for monitoring of behavioral changes as well as consideration of their natural behavioral ecology when implementing appropriate mitigation strategies. Further research should be encouraged to provide evidence-based assessment of how music events may affect animal welfare and behavior and to test the efficacy of mitigation strategies that are implemented to safeguard animal welfare.