Biology subjects

Barlow, A.

Publications and source records attributed to Barlow, A..

11 recordsLinked to original sources

bioRxiv2026

Burn Wound Excision Drives Acute Hypermetabolism in Mice with Scald Burns

Hypermetabolism (elevated resting energy expenditure) is a hallmark of the pathophysiological response to burns. The contribution of wound excision to acute burn-induced hypermetabolism remains unclear. Importantly, while burn wound excision is a standard component of clinical burn care, it is not typically included in rodent models of burn injury. Here, we tested the hypothesis that burn wound excision drives the acute hypermetabolic response to burn trauma. C57BL/6J mice (n=12-18 per group; ~6-weeks old; 50% male) were acclimated to thermoneutral housing (30C) for 6-weeks. All mice underwent baseline body composition scans and metabolic phenotyping to determine total (TEE) and resting energy expenditure (REE). Mice were then randomized to either sham (control), scald burn (burn), wound excision (excision), or scald burn followed by immediate wound excision (burn+excision) groups. Burns and wound excisions involved ~15% of the body surface area. Mice then recovered for 14 days while individually housed in metabolic phenotyping cages. At day 14 post-injury, mice underwent a second body composition scan prior to euthanasia. There were no fatalities in the control or burn groups, whereas 23% (n=7) and 34% (n=11) of mice in the excision and burn+excision groups died or were euthanized during the 14-day recovery period. Male and female mice exhibited broadly similar responses to injury in terms of REE and TEE. Compared to control, REE was greater in burn (47%), excision (102%), and burn+excision groups (136%) during the first week post-injury (P<0.001 for all). Compared to control mice, wound excision (alone or following burns) resulted in a greater acute loss in body mass than burn injury alone. However, this cachectic response was more sustained in male mice compared to females. Similarly, wound excision (alone or following burns) resulted in greater bone mineral content and density loss compared to sham and burn alone in both sexes. Wound excision is a key contributor to the hypermetabolic and cachectic response to burn trauma in mice. We posit that rodent studies aiming to recapitulate burn-induced hypermetabolism and cachexia should include burn wound excision to better model the clinical sequelae to burns.

physiology↗

bioRxiv2026

Quantification of Mouse Total Body Surface Area: Implications for Preclinical Burn Research

Clinically, burn severity is reported as the size (and depth) of burn wounds relative to total body surface area (TBSA). This nomenclature is also often used in rodent models of burns. Accordingly, accurate determination and reporting of rodent TBSA is required to ensure the rigor and reproducibility of preclinical burn research. Rodent TBSA is typically estimated indirectly as a function of body mass. Further, empirical quantification of rodent TBSA through pelt dissection does not consider differences in rodent and human anatomy, making comparison of relative burn size in rodents and humans a challenge. Here, we compared commonly used approaches to directly determine or indirectly estimate rodent TBSA to demonstrate the impact different approaches can have on the calculation of relative burn size. A total of n=48 C57BL/6J background mice (55% male) ranging from 4 to 45 weeks of age and 17 to 40 grams were used. Mice were weighed prior to euthanasia. After euthanasia, mouse length was measured from the nose to anus. Mice were then placed into clear polypropylene sheet protectors (21.6 x 27.9 cm) to trace the areas of both the dorsal and ventral surfaces as well as all four limbs (dorsal-ventral (DV) tracing). Next, the pelt was carefully excised from the body through cutting a lateral line from the mouth to the genitalia, then again proximally to distally on all four limbs. The pelt was gently placed on a sheet protector and traced when both relaxed and stretched. The ears and tail were removed and traced separately. Photographs were taken of all tracings next to a ruler for scale and analyzed in ImageJ. Stretched pelt measurements of TBSA were 34% (79.4{+/-}7.6 vs. 57.5{+/-}7.5 cm2, P<0.001) and 30% (70.6{+/-}10.9 vs. 52.7{+/-}8.1 cm2, P<0.001) greater than relaxed pelt TBSA measurements in male and female mice respectively. TBSA estimated by DV tracing was 9% greater in males (62.5{+/-}10.9 vs. 57.5{+/-}7.5 cm2) and 15% in females (60.6{+/-}12.3 vs. 52.7{+/-}8.1 cm2) compared to TBSA measurements made on relaxed pelts. Accordingly, empirically derived Meeh constants (k) from DV tracing were greater than those derived from relaxed pelt measurements for both males (7.14{+/-}0.59 vs. 6.58{+/-}0.72) and females (7.72{+/-}0.58 vs. 6.78{+/-}0.80). In contrast k values derived from stretched pelt measures of TBSA were significantly greater than those determined in relaxed pelts for males (8.91{+/-}0.87 vs. 6.58{+/-}0.72, P<0.001) and females (8.85{+/-}1.25 vs. 6.78{+/-}0.80, P>0.001). The combined ears and tail represent approximately 7% and 8% of the TBSA measured by the relaxed pelt approach, respectively. Exclusion of the tail and ears from the calculated TBSA results in derived k values that are [~]16-17% lower. The approach used to determine TBSA in mice significantly influences measured areas and thus derived k values. We suggest that stretching the pelt prior to tracing inflates TBSA values, where measurements made from relaxed pelts or by DV tracing likely provide more accurate estimates of actual TBSA. Further, exclusion of the tail and ears (the latter of which is not typically considered in estimates of TBSA in humans) may be a useful approach relating relative burn sizes of mice to those of humans.

physiology↗

bioRxiv2024

Postglacial recolonization of the Southern Ocean by elephant seals occurred from multiple glacial refugia

The Southern Ocean is warming more rapidly than other parts of our planet. How this regions endemic biodiversity will respond to such changes can be illuminated by studying past events, through genetic analyses of time-series data sets including historic and fossil remains. Archaeological and subfossil remains show that the southern elephant seal (Mirounga leonina) was common along the coasts of Australia and New Zealand in the recent past. This species is now mostly confined to sub-Antarctic islands and the southern tip of South America. We analysed ancient seal samples from Australia (Tasmania), New Zealand, and the Antarctic mainland to examine how southern elephant seals have responded to a changing climate and anthropogenic pressures during the Holocene. Our analyses show that these seals formed part of a broader Australasian lineage, comprising seals from all sampled locations from the south Pacific sector of the Southern Ocean. Our study demonstrates that southern elephant seal populations have dynamically altered both range and population sizes under climatic and human pressures, over surprisingly short evolutionary timeframes for such a large, long-lived mammal. Significance StatementGenetic data, alongside historic, archaeological, and subfossil remains show that Australasian populations of the southern elephant seal have been shaped by range expansions and contractions following the Last Glacial Maximum, with subsequent contractions during the late Holocene. These expansion and contraction events are likely to have been a direct result of climate change-induced habitat expansion and contraction, along with Indigenous and European sealing. Prehistoric climate change and more recent human pressures have substantially altered the geographic distribution and population size of southern elephant seals over short evolutionary timescales.

ecology↗

bioRxiv2024

Ancient biomolecules suggest learned foraging strategy in extinct cave bears

Studying the behavioural ecology of long-extinct species is challenging due to the difficulty in measuring the behavioural phenotype and correlating this with genetic and environmental factors. However, a multidisciplinary approach integrating isotope analysis of diet and ancient DNA analysis of genetic relationships offers a potential framework to test the proximate causes of dietary preferences. Our study focuses on Late Pleistocene cave bears from the Romanian Carpathians. Stable isotope analysis of bone collagen reveals substantial lifetime variation in food plant preferences among individuals. We find that bears with similar diets do not cluster according to their population structure, sex, time period, climatic conditions, or location. This disconnect suggests that diet preference in cave bears is not genetically inherited, and instead that individuals adapted their diets based on foraging experience. This integrative approach opens new avenues for understanding Pleistocene animal behaviour, leveraging ancient biomolecules synergistically to reveal insights otherwise inaccessible.

evolutionary biology↗

bioRxiv2023

High standing diversity masks extreme genetic erosion in a declining snake.

Average heterozygosity is frequently used as a proxy for genetic health, and to compare genetic diversity between species and populations. However, this measurement could be misleading if the distribution of heterozygosity across the genome is highly skewed. We investigated this pitfall in methodology using whole-genome sequencing of the adder (Vipera berus), a species experiencing dramatic declines in the UK. We find that mean heterozygosity in adders is notably high, exceeding that of other vertebrates typically regarded as genetically diverse. Their genome-wide distribution of heterozygosity, however, approximates a negative exponential distribution, with most genome regions showing extremely low heterozygosity. Modelling approaches show that this pattern is likely to have resulted from a recent, severe bottleneck and fragmentation most likely caused by anthropogenic activity in a previously large, interconnected adder population. Our results highlight that high standing diversity may mask severe genetic erosion when declines are recent and rapid. In such situations, whole-genome sequencing may provide the best option for genetic risk assessment and targeted conservation actions.

genomics↗

bioRxiv2022

First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages

The sun bear Helarctos malayanus is one of the most endangered ursids, and to date classification of sun bear populations has been based almost exclusively on geographic distribution and morphology. The very few molecular studies focusing on this species were limited in geographic scope. Using archival and non-invasively collected sample material, we have added a substantial number of complete or near-complete mitochondrial genome sequences from sun bears of several range countries of the species distribution. We here report 32 new mitogenome sequences representing sun bears from Cambodia, Thailand, Peninsular Malaysia, Sumatra and Borneo. Reconstruction of phylogenetic relationships revealed two matrilines that diverged [~]290 thousand years ago: one restricted to portions of mainland Indochina (China, Cambodia, Thailand; "Mainland clade"), and one comprising bears from Borneo, Sumatra, Peninsular Malaysia but also Thailand ("Sunda clade"). Generally recent coalescence times in the mitochondrial phylogeny suggest that recent or historical demographic processes have resulted in a loss of mtDNA variation. Additionally, analysis of our data in conjunction with shorter mtDNA sequences revealed that the Bornean sun bear, classified as a distinct subspecies (H. m. euryspilus), does not harbour a distinctive matriline. Further molecular studies of H. malayanus are needed, which should ideally include data from nuclear loci.

genomics↗

bioRxiv2021

3D genomic capture of regulatory immuno-genetic profiles in COVID-19 patients for prognosis of severe COVID disease outcome

Human infection with the SARS-CoV-2 virus leads to coronavirus disease (COVID-19). A striking characteristic of COVID-19 infection in humans is the highly variable host response and the diverse clinical outcomes, ranging from clinically asymptomatic to severe immune reactions leading to hospitalization and death. Here we used a 3D genomic approach to analyse blood samples at the time of COVID diagnosis, from a global cohort of 80 COVID-19 patients, with different degrees of clinical disease outcomes. Using 3D whole genome EpiSwitch(R) arrays to generate over 1 million data points per patient, we identified a distinct and measurable set of differences in genomic organization at immune-related loci that demonstrated prognostic power at baseline to stratify patients with mild forms of illness and those with severe forms that required hospitalization and intensive care unit (ICU) support. Further analysis revealed both well established and new COVID-related dysregulated pathways and loci, including innate and adaptive immunity; ACE2; olfactory, G{beta}{psi}, Ca2+ and nitric oxide (NO) signalling; prostaglandin E2 (PGE2), the acute inflammatory cytokine CCL3, and the T-cell derived chemotactic cytokine CCL5. We identified potential therapeutic agents for mitigation of severe disease outcome, with several already being tested independently, including mTOR inhibitors (rapamycin and tacrolimus) and general immunosuppressants (dexamethasone and hydrocortisone). Machine learning algorithms based on established EpiSwitch(R) methodology further identified a subset of 3D genomic changes that could be used as prognostic molecular biomarker leads for the development of a COVID-19 disease severity test.

biochemistry↗

bioRxiv2018

Consensify: a method for generating pseudohaploid genome sequences from palaeogenomic datasets with reduced error rates

A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, typically by selecting a single high quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic analysis, we find that Consensify is less affected by branch length artefacts than methods based on standard pseudohaploidisation, and it performs similarly for population clustering analysis based on genetic distances. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other available methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consenify will be a useful tool for future studies of palaeogenomes.

genomics↗

bioRxiv2018

Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations

BackgroundResolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts?\n\nResultsIn this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages ([~]710 Ka), with the European ancient samples as sister to all Asian lineages ([~]483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor ([~]122 Ka), and we find one Javan sample nested within these.\n\nConclusionsThe phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.

evolutionary biology↗

bioRxiv2018

Microbial adaptation to venom is common in snakes and spiders

Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane disrupting activity against multi-drug resistant bacteria. However, bite wound infections are common in developing nations. Investigating the oral and venom microbiome of five snake and two spider species, we evidence viable microorganisms potentially unique to venom for black-necked spitting cobras (Naja nigricollis). Among these are two venom-resistant novel sequence types of Enterococcus faecalis; the genome sequence data of these isolates feature an additional 45 genes, nearly half of which improve membrane integrity. Our findings challenge the dogma of venom sterility and indicate an increased primary infection risk in the clinical management of venomous animal bite wounds. One Sentence SummaryIndependent bacterial colonization of cobra venom drives acquisition of genes antagonistic to venom antimicrobial peptides.

microbiology↗

bioRxiv2017

Population and conservation genomics of the world's rarest hyena species, the brown hyena (Parahyena brunnea)

With an estimated population size of less than 10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) has been listed as near threatened by the IUCN. Despite this rank, studies involving DNA analyses of the brown hyena are limited. Little consideration has been focussed towards population structure within the brown hyena, which could provide valuable insights about its evolutionary history and aid in conservation efforts of the species. Here we report both mitochondrial and nuclear genomes of wild-caught brown hyena individuals from across southern Africa. Mitochondrial DNA shows little to no phylogeographic structure, whereas low-coverage nuclear genomes reveal several potential sub-populations. Moreover, we find that brown hyenas harbour the lowest genetic diversity for a species on both the mitochondrial and nuclear level when compared to a number of mammalian species for which such information is currently available. Our data also reveal that at least on the nuclear DNA level, this low diversity could be the result of a continuous and ongoing decline in effective population size that started about one million years ago and dramatically accelerated towards the end of the Pleistocene. Moreover, our findings also show that the correlation between genetic diversity and the perceived risk of extinction is not particularly strong, since many species with higher genetic diversity than the brown hyena are considered to be at greater risk of extinction. Taken together, our results have important implications for the conservation status and conservation approaches of the brown hyena.

evolutionary biology↗