Biology subjects

Wibisana, J. N.

Publications and source records attributed to Wibisana, J. N..

5 recordsLinked to original sources

bioRxiv2026

Feeding experiments with Senegal bichir Polypterus senegalus provide evidence for diet-related tooth damage and dental microwear

Dental microwear is a useful tool for reconstructing jaw movements and diet in toothed vertebrates, but its application to fishes (Actinopterygii and Chondrichthyes) remains limited. This is partly due to the lack of experiments directly linking diet and microwear in these groups; only one highly-derived teleost (Actinopterygii, or ray-finned fishes) species of recent origins, the three-spined stickleback Gasterosteus aculeatus, has been subject to controlled feeding experiments. As sticklebacks are suction or ram feeders that live on macroplankton and insect larvae and do not use their dentitions for prey processing, the absence of experimental data from other fish species limits our ability to interpret dental microwear and infer diet and feeding style in a wider range of fossil and living species with various ecologies. Here we present the results of a second feeding experiment involving fishes using the basally-branching, biting, often-piscivorous ray-finned fish Senegal bichir Polypterus senegalus to evaluate whether controlled diet differences can generate detectable tooth damage and dental microwear patterns. Individuals were fed four different food items - loaches, shrimp, pellets, and mealworms - for one, two, and three months. We then examined tooth tip damage and linear microwear (scratches). Shrimp and mealworm feeding produced short scratches, whereas pellet and loach feeding produced long scratches. Most teeth exhibited apical tip damage despite the presence of a solid enameloid acrodin cap (a characteristic of ray-finned fishes), with damage being larger in loach-fed individuals and smaller in those fed with mealworms. Our results suggest a possible relationship between diet, tooth damage, and dental microwear in non-durophagous fishes which never-the-less use teeth for prey capture and processing, offering a framework for inferring diet in extinct forms with similar ecomorphology to Polypterus.

paleontology↗

bioRxiv2024

Less, but more: new insights from appendicularians on chordate Fgf evolution and the divergence of tunicate lifestyles.

The impact of gene loss on the divergence of taxa and the generation of evolutionary innovations is a fundamental aspect of Evolutionary Biology that remains unclear. Here, using the evolution of the Fibroblast Growth Factors (FGFs) in appendicularians as a case study, we investigate how gene losses have influenced the evolution of chordates, especially the divergence among tunicates. Our work reveals an unprecedented case of massive losses of all Fgf gene subfamilies, except for the Fgf9/16/20 and Fgf11/12/13/14, which in turn suffered two bursts of gene duplications. Phylogenetic inferences and genomic analyses of gene synteny conservation, gene architecture, alternative splicing and protein 3D-structure have allowed us to reconstruct the history of appendicularian Fgf genes in the context of chordate evolution, providing compelling evidence supporting the paracrine secreting functions and the intracellular functions of the Fgf9/16/20 and Fgf11/12/13/14 subfamilies, respectively. Exhaustive analysis of developmental Fgf expression in Oikopleura dioica as a model for appendicularians reveals a paradigmatic case of what could be referred as "less, but more", providing a conceptual evolutionary framework characterized by four associated evolutionary patterns: conservation of ancestral Fgf expression domains; function shuffling between paralogs upon gene loss; innovation of new expression domains after the bursts of Fgf duplications; and the extinction of Fgf functions linked to gene losses. The findings of this work allow us to formulate novel hypotheses about the potential impact of losses and duplications of Fgf genes on the transition from an ancestral ascidian-like biphasic lifestyle to a fully free-living style of appendicularians. These hypotheses include the massive co-option of Fgf genes for the patterning of the oikoblast responsible of the house architecture, and for the development of the tail fin; the recruitment of Fgf11/12/13/14 genes into the evolution of a new mouth, and their role modulating neuronal excitability; the evolutionary innovation of an "anterior tail" FGF signaling mesodermal source upon the loss of retinoic acid signaling; and the potential link between the loss of Fgf7/10/22 and Fgf8/17/18 and the loss of drastic metamorphosis, mesenchymal cells and lack of tail absorption in appendicularians, in contrast to ascidians.

evolutionary biology↗

bioRxiv2024

The complete mitogenome of an unidentified Oikopleura species

1.Appendicularians are planktonic tunicates abundant all over the world. Currently, only two complete annotated mitochondrial genome assemblies are available for appendicularians, both for cryptic species of Oikopleura dioica. This underrepresentation of available appendicularian mitochondrial genomes limits environmental DNA sequencing (eDNA) studies that rely on mitochondrial markers as a taxonomic barcode. We report the complete mitochondrial genome assembly and annotation of an unknown appendicularian species isolated from the Amami Oshima island, Kagoshima prefecture, Japan, that has significant sequence difference with other currently available assemblies and will serve as a useful resource for ecological studies and further mitochondrial studies of appendicularians.

genomics↗

bioRxiv2023

Modification of clinical dental impression methods to obtain dental traits from living and whole non-mammalian vertebrates

Dental impressions, developed for accurate capture of oral characteristics in human clinical settings, are seldom used in research on non-livestock, non-primate, and especially non-mammalian, vertebrates due to a lack of appropriate tools. Studies of dentitions in most vertebrate species usually require euthanasia and specimen dissection, microCT and other scans with size and resolution tradeoffs, and/or ad-hoc individual impressions or removal of single teeth. These approaches prevent in-vivo studies that factor in growth and other chronological changes and separates teeth from the context of the whole mouth. Here, we describe a non-destructive method for obtaining high resolution dentition-related traits that can be used on both living animals and museum specimens for almost all vertebrates, involving a customizable and printable dental impression tray. This method has repeatedly and accurately capture whole-mouth morphology and detailed features at high resolution in the living non-teleost actinopterygian fish, Polypterus senegalus, in a laboratory setting. It can be used for comparative morphology and to observe temporal changes such as the presence of microwear, tooth replacement rates, and occlusal and morphological changes through ontogeny. Summary statementThis study presents a cheap and customizable method using a printable tray to measure oral morphological traits in vertebrates humanely and accurately.

evolutionary biology↗

bioRxiv2021

Imaging and single cell sequencing analyses of super-enhancer activation mediated by NF-κB in B cells

The transcription factor NF-{kappa}B, which plays an important role in cell fate determination, is involved in the activation of super-enhancers (SEs). However, the biological functions of the NF-{kappa}B SEs in gene control are not fully elucidated. We investigated the characteristics of NF-{kappa}B-mediated SE activity using fluorescence live-cell imaging of RelA, single-cell transcriptome, and chromatin accessibility analyses in anti-IgM-stimulated B cells. Cell stimulation induced nuclear foci formation of RelA and gene expression in a switch-like manner. The gained SEs induced a higher fold-change expression and enhanced cell-to-cell variability in transcriptional response. These properties were correlated with the number of gained cis-regulatory interactions, while switch-like gene induction was associated with the number of NF-{kappa}B binding sites in SE. Our study suggests that NF-{kappa}B SEs have unique roles for quantitative control of gene expression through direct binding to accessible DNA and enhanced DNA contacts.

molecular biology↗