Biology subjects

Teo, Y. V.

Publications and source records attributed to Teo, Y. V..

6 recordsLinked to original sources

bioRxiv2025

Evaluating drone-mounted thermal infrared sensors for macropod monitoring in Tasmania

Thermal drones offer significant advantages for monitoring wildlife in low-light conditions; however, detection performance is influenced by technical settings and environmental factors. This study evaluates the use of nocturnal drone surveys to detect macropods in Tasmania, with the aim of determining optimal flight parameters for balancing detection accuracy and survey efficiency. Field surveys were conducted in Narawntapu National Park using varying flight altitudes and image overlap settings, and detection rates were compared across thermal datasets. Manual annotations and basic thresholding method were used to quantify detection success. Results showed that detection rates were highest when surveys were conducted under cooler ambient temperatures and at moderate altitudes (e.g. 60 metres AGL) with 50% image overlap. These findings provide practical guidance for designing nocturnal drone surveys and offers baseline recommendations for using drone-mounted thermal sensors to monitor large-bodied, crepuscular mammals, with broader implications for scalable wildlife monitoring programs.

ecology↗

bioRxiv2025

Automated detection of macropods in Tasmania using drone surveys and convolutional neural networks (CNNs)

Manual annotation of drone imagery is labour-intensive and prone to observer bias, particularly when applied to large datasets across varied environments. To address this, a deep-learning pipeline was developed and evaluated for identifying macropods in visual (RGB) drone imagery, using a convolutional neural network (CNN) adapted from the DeepForest framework. The model was trained on annotated images of Forester kangaroos (Macropus giganteus tasmaniensis) and Bennetts wallabies (Notamacropus rufogriseus) collected across two Tasmanian study sites. Performance was assessed using independent test sets from each site, representing open and forest-edge habitats, as well as a combined multi-site test set. Detection accuracy was quantified using precision, recall, and F1 scores, with further analyses evaluating the effect of solar altitude angle on model performance. The model achieved high recall across sites, indicating strong potential for minimising missed detections under diverse conditions. These results demonstrate the feasibility of applying transfer learning to drone-based wildlife surveys and highlight the promise of deep learning models for reducing manual effort in macropod monitoring, with applications for broader conservation and management workflows.

ecology↗

bioRxiv2021

Single Cell Transcriptomics Reveals Global Markers of Transcriptional Diversity Across Different Forms of CellularSenescence

Cellular Senescence is a state of irreversible cell cycle arrest, and the accumulation of senescent cells contributes to age- related organismal decline. The detrimental effects of cellular senescence are due to the senescence associated secretory phenotype (SASP), an array of signaling molecules and growth factors secreted by senescent cells that contribute to the sterile inflammation associated with aging tissues. Recent studies, both in vivo and in vitro, have highlighted the heterogeneous nature of the senescence phenotype. In particular, single cell transcriptomics has revealed that Oncogene Induced Senescence (OIS) is characterized by the presence of subpopulations of cells expressing different SASP profiles. We have generated a comprehensive dataset via single-cell transcriptional profiling of genetically homogenous clonal cell lines from different forms of senescence, including OIS, Replicative Senescence (RS), and DNA Damage Induced Senescence (DDIS). We identified subpopulations of cells that are common to all three major forms of senescence and show that the expression profiles of these subpopulations are driven by markers formerly identified in individual forms of senescence. These common signatures are characterized by chromatin modifiers, inflammation, extracellular matrix remodeling, and Ribosomal protein expression. The expression patterns of these subpopulations recapitulate primary and secondary senescence, a phenomenon where a preexisting (primary) senescent cell induces senescence in a neighboring (secondary) cell through cell-to-cell contact. Since it is still unclear what type of senescence occurs in-vivo with age, it is important to know that the formation of primary and secondary populations is common to multiple types of senescence since this mechanism could help explain how senescent cells accumulate in aged organisms. Finally, we show that these subpopulations show differential susceptibility to the senolytic agent Navitoclax, suggesting that senolytic agents targeting the apoptotic pathways may be clearing only a subset of senescent cells based on their inflammatory profiles in-vivo.

genomics↗

bioRxiv2021

Single-cell transcriptomics of peripheral blood in the aging mouse

Compositional and transcriptional changes in the hematopoietic system have been used as biomarkers of immunosenescence and aging. Here, we use single-cell RNA-sequencing to study the aging peripheral blood in mice, and characterize the changes in cell-type composition and transcriptional profiles associated with age. We identified 17 clusters from a total of 14,588 single cells. We detected a general upregulation of antigen processing and presentation and chemokine signaling pathways and a downregulation of genes involved in ribosome pathways with age. We also observed increased percentage of cells expressing markers of senescence, Cdkn1a and Cdkn2a, in old peripheral blood. In addition, we detected a cluster of activated T cells that are exclusively found in old blood, with lower expression of Cd28 and higher expression of Bcl2 and Cdkn2a, suggesting that the cells are senescent and resistant to apoptosis.

molecular biology↗

bioRxiv2019

Notch signalling mediates secondary senescence

Oncogene induced senescence (OIS) is a tumour suppressive response to oncogene activation that can be transmitted to neighbouring cells through secreted factors of the senescence associated secretory phenotype (SASP). Using single-cell transcriptomics we observed two distinct endpoints, a primary marked by Ras and a secondary by Notch. We find that secondary senescence in vitro and in vivo requires Notch, rather than SASP alone as previously thought. Currently, primary and secondary senescent cells are not thought of as functionally distinct endpoints. A blunted SASP response and the induction of fibrillar collagens in secondary senescence compared to OIS point towards a functional diversification. One Sentence SummaryNotch signalling is an essential driver of secondary senescence with primary and secondary senescence being distinct molecular endpoints.

genomics↗

bioRxiv2016

A comparative study of metagenomics analysis pipelines at the species level

Many metagenomics classification tools have been developed with the rapid growth of the metagenomics field. However, the classification of closely related species remains a challenge for this field. Here, we compared MetaPhlAn2, kallisto and Kraken for their performances in two metagenomics settings, human metagenomics and environmental metagenomics. Our comparative study showed that kallisto demonstrated higher sensitivity than MetaPhlAn2 and Kraken and better quantification accuracy than Kraken at the species level. We also showed that classification tools that run on full reference genomes misidentified many species that were not truly present. In order to reduce false positives, we introduced marker genes from MetaPhlAn2 into our pipeline, which uses kallisto for the classification step, as an additional filtering step for species detection.

genomics↗