Biology subjects

van Schalkwyk, L.

Publications and source records attributed to van Schalkwyk, L..

4 recordsLinked to original sources

bioRxiv2026

Long read sequencing of retinal RNA improves killifish transcriptome annotation

Purpose The African Turquoise Killifish has recently emerged as a powerful model for aging and age-related disease research studies. However, molecular based investigations have been limited by preliminary genome and transcriptome builds with incomplete reference genome sequence, fragmented chromosome assembly, and missing gene annotations. These issues make primary (alignment and quantification) and secondary (Gene Ontology, Gene Set Enrichment Analysis, cross-species comparisons) analyses difficult to reliably implement and interpret. This study seeks to generate a complete retinal reference transcriptome to facilitate future killifish transcriptomic, epigenetic, and proteomic studies of the visual system. Methods We generated an enhanced retina transcriptome using long-read PacBio RNAseq data that was processed using a robust computational pipeline to merge reads, classify genes, and annotate with nearest orthologous gene names from other species. This new annotation was compared to available references and validated using bulk and single cell RNAseq datasets. Results Comparison of the widely used Nfu_20140520 and the newly released NfurGRZ-RIMD1 genome builds identified NfurGRZ-RIMD1 to be more contiguous and complete. However, we identified limitations with both transcriptomes, including the lack of annotation of certain retina specific genes and many uninformative gene names. Using long-read PacBio sequencing of RNA collected from young and old Killifish retinas, we annotated a deep retinal transcriptome onto the NfurGRZ-RIMD1 reference genome. This analysis identified thousands of previously unannotated transcripts from retinas of young and old killifish. By matching each translated protein sequence to its nearest ortholog, we increased the number and proportion of genes with meaningful gene names. Mapping of bulk and single-cell RNAseq data showed substantial increase in mapping rate and identified hundreds of genes and transcripts with age-dependent expression dynamics. Conclusions Assembly of an enhanced retinal transcriptome for the killifish improved both primary and secondary analyses of bulk and single cell RNAseq data. Improvements will benefit future studies investigating the mechanisms of aging in the killifish and to best utilize this powerful model to understand human disease.

genomics↗

bioRxiv2025

Fine-scale animal proximity detection and localization via multi-sensor biologgers

O_LIAccurately quantifying spatial interactions is central to understanding social behavior, information flow, predator-prey dynamics, and disease transmission. Proximity loggers that record received signal strength indicator (RSSI) offer a promising approach for estimating pairwise distances, particularly in environments where GPS is unavailable or imprecise. However, RSSI is often dismissed as too noisy for fine-scale inference, with performance that depends on environmental conditions, tag orientation, and between-device variability. Incorporating additional tag-measured data may improve RSSI performance and enable its use as a continuous measure of distance in variable environments. C_LIO_LIHere, we assess the utility of continuous RSSI as a fine-scale distance estimator and localization tool using a novel multi-sensor WiFi biologger (WildFi). We conducted four experiments: (1) testing how tag orientation affects RSSI-distance relationships; (2) evaluating whether environmental covariates measured by onboard sensors improve proximity estimates; (3) assessing the accuracy of trilateration-based tag localization using fixed gateway arrays; and (4) comparing RSSI- and GPS-inferred proximity in free-ranging Egyptian fruit bats (Rousettus aegyptiacus). C_LIO_LIWhile RSSI alone could predict distance with reasonable accuracy, incorporating additional tag-sensed information (e.g., temperature, humidity, barometric pressure) and accounting for tag-level heterogeneity significantly improved predictive accuracy. Based on RSSI predictions, we could estimate tag location with a median error of 2.6 meters, accurate enough to indirectly estimate proximity networks without tag-to-tag communication. In deployments on free-flying bats, we found that RSSI and GPS were only weakly concordant, with GPS unreliable for detecting fine-scale interactions (<50 m). In contrast, RSSI could capture both fine-scale and some long-range interactions up to [~]250m. C_LIO_LIThese findings highlight RSSIs potential as a robust metric for proximity logging, particularly when combined with multi-sensor data and pre-deployment validations. Integrating multi-sensor data streams further enhances RSSI interpretability. Future biologger designs should prioritize synergy among data streams for integrated insights into proximity and animal behavior. C_LI Data and code for peer review statementData and code to reproduce the results of the paper are provided in a zip folder for peer review. We also provided our compiled code.

ecology↗

bioRxiv2023

Importance of wildlife in the circulation and maintenance of SAT1 and SAT2 foot-and-mouth disease viruses in Africa

Author summaryFoot and mouth disease (FMD) viruses are endemic in sub-Saharan Africa. Due to the complexity of the disease epidemiology and the lack of available data, there is a need to use phylogenetic approaches to understand the role of potential hosts involved in the circulation and maintenance of the viruses. The uneven host sampling of the available sequences requires us to take advantage of the recent advances in phylogenetic reconstruction. Therefore, using two structural coalescent model approximations we estimated the circulation of FMD virus serotypes SAT1 and SAT2 between cattle, buffalo and impala populations. Our results suggest that in Africa, the impala population seems to act as an intermediate host between the cattle and buffalo populations and play a more important role in the circulation of the viruses than was previously suspected. Until now, the role of the impala population in the circulation of FMDV has been suggested, but never explicitly shown.

molecular biology↗

bioRxiv2021

Viral dynamics and immune responses to foot-and-mouth disease virus in African buffalo (Syncerus caffer).

Foot-and-mouth disease (FMD) is one of the most important livestock diseases restricting international trade. While it is clear that African buffalo (Syncerus caffer) act as the main wildlife reservoir, viral and immune response dynamics during FMD virus acute infection have not been described before in this species. We used experimental needle inoculation and contact infections with three Southern African Territories serotypes to assess clinical, virological and immunological dynamics for thirty days post infection. Clinical FMD in the needle inoculated buffaloes was mild and characterised by pyrexia. Despite the absence of generalised vesicles, all contact animals were readily infected with their respective serotypes within the first 2-9 days after being mixed with needle challenged buffaloes. Irrespective of the route of infection or serotype there were positive associations between the viral loads in blood and the induction of host innate pro-inflammatory cytokines and acute phase proteins. Viral loads in blood and tonsils were tightly correlated during the acute phase of the infection, however, viraemia significantly declined after a peak at 4 days post infection (dpi), which correlated with the presence of detectable neutralising antibodies. In contrast, infectious virus was isolated in the tonsils until the last sampling point (30 dpi) in most animals. The pattern of virus detection in serum and tonsil swabs was similar for all three serotypes in the direct challenged and contact challenged animals. We have demonstrated for the first time, that African buffalo are indeed systemically affected by FMD virus and clinical FMD in buffalo is characterized by a transient pyrexia. Despite the lack of FMD lesions, infection of African buffalo was characterised by high viral loads in blood and oropharynx, rapid and strong host innate and adaptive immune responses and high transmissibility.

zoology↗