Biology subjects

Leigh, C.

Publications and source records attributed to Leigh, C..

5 recordsLinked to original sources

bioRxiv2026

Morphological characteristics of the forelimb flexor digitorum muscles and their distinctive innervation pattern in koalas (Phascolarctos cinereus): implications for function and morphogenesis

Koalas (Phascolarctos cinereus) are marsupials highly specialized for arboreal life and are considered a representative example of convergent evolution with primates, which are also adapted to arboreal habitats. The forelimb digital flexors play a crucial role in arboreal locomotion by flexing the digits and enabling the claws or fingers to engage with tree trunks and branches. Although the morphology and function of the digital flexors have been extensively examined in primates, anatomical information on koala digital flexors has not been sufficiently updated in modern anatomical studies. In this study, we examined the digital flexor muscles and their innervation in four forelimbs from three koalas to clarify both shared and distinctive structural features among arboreal mammals. The flexor digitorum profundus (FDP) was markedly developed, formed a U-shaped muscle belly, and received dual innervation from the median and ulnar nerves. In contrast, the flexor digitorum superficialis (FDS) was small, arose from the superficial surface of the FDP, was partially enclosed by the FDP muscle belly, and gave rise to extremely slender tendons inserting into digits II-V. The branch supplying the FDS arose from the main trunk of the median nerve near the carpal region, ascended proximally in a recurrent course, and terminated within the FDS. This unusual course may be consistent with a morphogenetic process underlying FDS formation. These findings indicate that the koala digital flexors are characterized by a markedly developed FDP, a relatively reduced FDS, and a distinctive innervation pattern of the FDS. Thus, even among mammals adapted to arboreal life, koalas and primates appear to have achieved arboreal adaptation through different morphological specializations within the forearm digital flexor system.

zoology↗

bioRxiv2023

Novel crAssphage isolates exhibit conserved gene order and purifying selection of the host specificity protein

Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. tikkala strain Bc01, Kolpuevirus sp. frurule strain Bc03, and Rudgehvirus jaberico strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome. Impact statementBacteriophages play a crucial role in shaping microbial communities within the human gut. Among the most dominant bacteriophages in the human gut microbiome are Crassvirales phages, which infect Bacteroides. Despite being widely distributed, only a few Crassvirales genomes have been isolated, leading to a limited understanding of their biology, ecology, and evolution. This study isolated and characterized three novel Crassvirales genomes belonging to two different families, and three genera, but infecting one bacterial host, Bacteroides cellulosilyticus WH2. Notably, the observation confirmed the phages are not co-evolving with their bacterial hosts, rather have a shared ability to exploit similar features in their bacterial host. Additionally, the identification of a critical viral protein undergoing purifying selection and interacting with the bacterial receptors opens doors to targeted therapies against bacterial infections. Given Bacteroides role in polysaccharide degradation in the human gut, our findings advance our understanding of the phage-host interactions and could have important implications for the development of phage-based therapies. These discoveries may hold implications for improving gut health and metabolism to support overall well-being. Data summaryThe genomes used in this research are available on Sequence Read Archive (SRA) within the project, PRJNA737576. Bacteroides cellulosilyticus WH2, Kehishuvirus sp. tikkala strain Bc01, Kolpuevirus sp. frurule strain Bc03, and Rudgehvirus jaberico strain Bc11 are all available on GenBank with accessions NZ_CP072251.1 (B. cellulosilyticus WH2), QQ198717 (Bc01), QQ198718 (Bc03), and QQ198719 (Bc11), and we are working on making the strains available through ATCC. The 3D protein structures for the three Crassvirales genomes are available to download at doi.org/10.25451/flinders.21946034.

bioinformatics↗

bioRxiv2021

Gross anatomy of the gluteal and posterior thigh muscles in koalas based on their innervations

There are not many descriptions of the muscle morphology of marsupials, despite the fact that they should show diversity according to the adaptation and dispersal to a variety of environments. Most of the previous studies regarding the gross anatomy of marsupials were conducted in the 1800 - 1900s, and many issues still remain that need to be reexamined. For instance, the muscle identification had been performed based only on their attachments and thus, muscle descriptions are often inconsistent among the studies. These classic studies often do not include figures or photographs, so the discrepancies in the descriptions of the muscles could only be verified by performing the muscle identification again with a more reliable method. This problem can be solved by performing muscle identification by innervation. This method, which focuses on the ontogenic origin of the muscle as opposed to the attachment site, is prone to individual and interspecies variation and is a common technique in recent anatomical research. This technique is more reliable than previous methods and is suitable for comparison with other taxa (i.e., eutherians). In this study, we first conducted muscle identification based on innervation in the gluteal and posterior thighs of koalas in order to reorganize the anatomical knowledge of marsupials. This is because the gluteus and posterior thighs of koalas are the areas where previous studies have been particularly inconsistent. We dissected five individual koalas and clarified discrepancies in previous studies, as well as investigated the unique muscle morphology and their function in koalas. Specifically, the koalas gluteal muscle group is suitable for abduction, while the posterior thigh muscles are particularly suitable for flexion. In the future, we will update the anatomical findings of marsupials in the same way to clarify the adaptive dissipation process of marsupials, as well as to contribute to the understanding of the evolutionary morphology of mammals.

zoology↗

bioRxiv2019

Using virtual reality and thermal imagery to improve statistical modelling of vulnerable and protected species

Biodiversity loss and sparse observational data mean that critical conservation decisions may be based on little to no information. Emerging technologies, such as airborne thermal imaging and virtual reality, may facilitate species monitoring and improve predictions of species distribution. Here we combined these two technologies to predict the distribution of koalas, specialized arboreal foliovores facing population declines in many parts of eastern Australia. For a study area in southeast Australia, we complemented ground-survey records with presence and absence observations from thermal-imagery obtained using Remotely-Piloted Aircraft Systems. These field observations were further complemented with information elicited from koala experts, who were immersed in 360-degree images of the study area. The experts were asked to state the probability of observing a koala at sites they viewed and to assign each probability a confidence rating. We fit logistic regression models to the ground survey data and the ground plus thermal-imagery survey data and a beta regression model to the expert elicitation data. We then combined parameter estimates from the expert-elicitation model with those from each of the survey models to predict koala presence and absence in the study area. The model that combined the ground, thermal-imagery and expert-elicitation data substantially reduced the uncertainty around parameter estimates and increased the accuracy of classifications (koala presence vs absence), relative to the model based on ground-survey data alone. Our findings suggest that data elicited from experts using virtual reality technology can be combined with data from other emerging technologies, such as airborne thermal-imagery, using traditional statistical models, to increase the information available for species distribution modelling and the conservation of vulnerable and protected species.

ecology↗

bioRxiv2019

Predicting sediment and nutrient concentrations from high-frequency water-quality data

Water-quality monitoring in rivers often focuses on the concentrations of sediments and nutrients, constituents that can smother biota and cause eutrophication. However, the physical and economic constraints of manual sampling prohibit data collection at the frequency required to adequately capture the variation in concentrations through time. Here, we developed models to predict total suspended solids (TSS) and oxidized nitrogen (NOx) concentrations based on high-frequency time series of turbidity, conductivity and river level data from in situ sensors in rivers flowing into the Great Barrier Reef lagoon. We fit generalized-linear mixed-effects models with continuous first-order autoregressive correlation structures to water-quality data collected by manual sampling at two freshwater sites and one estuarine site and used the fitted models to predict TSS and NOx from the in situ sensor data. These models described the temporal autocorrelation in the data and handled observations collected at irregular frequencies, characteristics typical of water-quality monitoring data. Turbidity proved a useful and generalizable surrogate of TSS, with high predictive ability in the estuarine and fresh water sites. Turbidity, conductivity and river level served as combined surrogates of NOx. However, the relationship between NOx and the covariates was more complex than that between TSS and turbidity, and consequently the ability to predict NOx was lower and less generalizable across sites than for TSS. Furthermore, prediction intervals tended to increase during events, for both TSS and NOx models, highlighting the need to include measures of uncertainty routinely in water-quality reporting. Our study also highlights that surrogate-based models used to predict sediments and nutrients need to better incorporate temporal components if variance estimates are to be unbiased and model inference meaningful. The transferability of models across sites, and potentially regions, will become increasingly important as organizations move to automated sensing for water-quality monitoring throughout catchments.

ecology↗