Biology subjects

Stemmer, M.

Publications and source records attributed to Stemmer, M..

7 recordsLinked to original sources

bioRxiv2025

Cognitive ethology of nest building in a shell-dwelling cichlid

Across animal taxa, nest-building behavior is performed using a generalizable and flexible mental representation of an action sequence - a schema. In order to accomplish its goal (a stable nest), the brain appears to compare intermediate steps in the process to stored mental images, or templates. Deviations from these templates drive progress, preferences, and corrections in the execution of this behavior. The stereotypy vs. plasticity of both schema and mental templates have rarely been defined in an experimentally accessible system. Here we investigated nest building by the cichlid Lamprologus ocellatus, a fish species that manipulates abandoned snail shells to build shelters for breeding and protection. We find that nest building is composed of a sequence of behaviors that are tied together by a series of stimulus-response loops, allowing for restarts and shortcuts as the behavioral program unfolds. The attraction to a shell object is innate, as is the final appearance of the nest. The behavior in an inexperienced animal is initially uncoordinated, but is fine-tuned by repeated building opportunities. Shells need to conform to rigid geometric criteria in order to be acceptable as a potential home. Nest building is accompanied by focused neural activity in brain regions homologous to the mammalian hippocampus and neocortex. In conclusion, we have uncovered the constraints and flexibility of cognitive template matching underlying an instinctive, goal-directed behavior.

animal behavior and cognition↗

bioRxiv2024

Positional information drives distinct traits in transcriptomically identified neuronal types

Neuronal phenotypic traits such as morphology, connectivity, and function are dictated, to a large extent, by a specific combination of differentially expressed genes. Clusters of neurons in transcriptomic space correspond to distinct cell types and in some cases (e. g., C. elegans neurons1 and retinal ganglion cells2-4) have been shown to share morphology and function. The zebrafish optic tectum is composed of a spatial array of neurons that transforms visual inputs into motor outputs. While the visuotopic map is continuous, subregions of the tectum are functionally specialized5,6. To uncover the cell-type architecture of the tectum, we transcriptionally profiled its neurons, revealing more than 60 cell types that are organized in distinct anatomical layers. We then measured the visual responses of thousands of tectal neurons by two-photon calcium imaging and matched them with their transcriptional profile. Furthermore, we characterized the morphologies of transcriptionally identified neurons using specific transgenic lines. Surprisingly, we found that neurons that are transcriptionally similar can diverge functionally and morphologically. Incorporating the spatial coordinates of neurons within the tectal volume revealed functionally and morphologically defined anatomical subclusters within individual transcriptomic clusters. Our findings demonstrate that extrinsic, position-dependent factors expand the phenotypic repertoire of genetically similar neurons.

neuroscience↗

bioRxiv2023

Brood care in shell-dwelling cichlids is timed by independent maternal and larval clocks

Successful brood care requires a finely tuned interplay between caregiving parent and offspring. Cichlids are a diverse group of teleost fish known for their extensive parental care of altricial young. Female Lamprologus ocellatus lay their eggs in the protective confines of an abandoned snail shell, where they raise them to free-swimming larvae. Here we investigated whether the transition to larval independence is driven by the behavior of the mother, the offspring, or an interaction between the two. Using 3D printed shells with a window, we were able to observe the behavior of both mother and offspring inside the nest using automated object detection and tracking. We found that, once hatched, the larvae remain in the deep chambers of the shell, and at 9 dpf, actively emerge from the shell during the day. An inversion of larval phototactic behavior from dark- to light-seeking leads up to this emergence. Removal of the mother causes premature emergence of the larvae by a few days. The natural schedule (emergence at 9 dpf) is restored if the larvae are supplied with fresh water in the mothers absence. In cross-fostering experiments, we found that swapping out the mothers own clutch for older larvae forces a delay in emergence, as the foster mother prevents the larvae from leaving at 9 dpf. We conclude that larval and maternal behavior are each controlled by independent internal clocks, which, although normally synchronized, can be experimentally manipulated and brought into conflict. This study has thus revealed an innate sequence of behavioral adaptations that orchestrate brood care in shell-dwelling cichlids.

evolutionary biology↗

bioRxiv2023

Diverse prey capture strategies in teleost larvae

Animal behavior is adapted to the sensory environment in which it evolved, while also being constrained by physical limits, evolutionary history, and developmental trajectories. The hunting behavior of larval zebrafish (Danio rerio), a cyprinid native to streams in Eastern India, has been well characterized. However, it is unknown if the complement and sequence of movements employed during prey capture by zebrafish is universal across freshwater teleosts. Here, we explore the syntax of prey capture behavior in larval fish belonging to the clade Percomorpha, whose last common ancestor with cyprinids lived [~]240 million years ago. We compared the behavior of four cichlid species from Lake Tanganyika endemic to deep benthic parts of the lake (Lepidiolamprologus attenuatus, Lamprologus ocellatus, and Neolamprologus multifasciatus) or inhabiting rivers (Astatotilapia burtoni) with that of medaka (Oryzias latipes), a fish found in rice paddies in East Asia. Using high speed videography and neural networks, we tracked eye movements and extracted swim kinematics during hunting from larvae of these five species. Notably, we found that the repertoire of hunting movements of cichlids is broader than that of zebrafish, but shares basic features, such as eye convergence, positioning of prey centrally in the binocular visual field, and discrete prey capture bouts, including two kinds of capture strikes. In contrast, medaka swim continuously, track the prey monocularly without eye convergence, and position prey laterally before capturing them with a side swing. This configuration of kinematic motifs suggests that medaka may judge distance to prey predominantly by motion parallax, while cichlids and zebrafish may mainly use binocular visual cues. Together, our study documents the diversification of locomotor and oculomotor adaptations among hunting teleost larvae.

animal behavior and cognition↗

bioRxiv2021

Choice of alignment pipeline strongly influences clustering quality of scRNA-seq datasets

BackgroundSingle-cell RNA sequencing (scRNA-seq) has quickly become one of the most dominant techniques in modern transcriptome assessment. In particular, 10X Genomics Chromium system, with its high throughput approach, turn key and thorough user guide made this cutting-edge technique accessible to many laboratories using diverse animal models. However, standard pre-processing, including the alignment and cell filtering pipelines might not be ideal for every organism or tissue. Here we applied an alternative strategy, based on the pseudoaligner kallisto, on twenty-two publicly available single cell sequencing datasets from a wide range of tissues of eight organisms and compared the results with the standard 10X Genomics Cell Ranger pipeline. ResultsIn most of the tested samples, kallisto produced higher sequencing read alignment rates and total gene detection rates in comparison to Cell Ranger. Although datasets processed with Cell Ranger had higher cell counts, outside of human and mouse datasets, these additional cells were routinely of low quality, containing low gene detection rates. Thorough downstream analysis of one kallisto processed dataset, obtained from the zebrafish pineal gland, revealed clearer clustering, allowing the identification of an additional photoreceptor cell type that previously went undetected. The finding of the new cluster suggests that the photoreceptive pineal gland is essentially a bi-chromatic tissue containing both green and red cone-like photoreceptors and implies that the alignment and pre-processing pipeline can affect the discovery of biologically-relevant cell types. ConclusionWhile Cell Ranger favors higher cell numbers, using kallisto results in datasets with higher median gene detection per cell. We could demonstrate that cell type identification was not hampered by the lower cell count, but in fact improved as a result of the high gene detection rate and the more stringent filtering. Depending on the acquired dataset, it can be beneficial to favor high quality cells and accept a lower cell count, leading to an improved classification of cell types.

genomics↗

bioRxiv2020

Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior

Retinal ganglion cells (RGCs) form an array of feature detectors, which convey visual information to central brain regions. Characterizing RGC diversity is required to understand the logic of the underlying functional segregation. Using single-cell transcriptomics, we systematically classified RGCs in adult and larval zebrafish, thereby identifying marker genes for at least 33 stable and transient cell types. We used this dataset to engineer transgenic driver lines, enabling experimental access to specific RGC types. Strikingly, expression of one or few transcription factors often predicts dendrite morphologies and axonal projections to specific tectal layers and extratectal targets. In vivo calcium imaging revealed that molecularly defined RGCs exhibit highly specific functional tuning. Finally, chemogenetic ablation of eomesa+ RGCs, which comprise melanopsin-expressing types with projections to a small subset of central targets, selectively impaired phototaxis. Together, our study establishes a framework for systematically studying the functional architecture of the visual system.

neuroscience↗

bioRxiv2018

Patterning of a telencephalon-like region in the adult brain of amphioxus

The evolutionary origin of the vertebrate telencephalon remains unsolved. A major challenge has been the identification of homologous brain parts in invertebrate chordates. Here we report evidence for a telencephalic region in the brain of amphioxus, the most basally branching invertebrate chordate. This region is characterised, like its vertebrate counterpart, by the combined expression of the telencephalic markers FoxG1, Emx and Lhx2/9. It is located at the anterior neural border and dorsal-ventrally patterned, as in vertebrates, by the antagonistic expression of Pax4/6 and Nkx2.1, and a ventral Hh signal. This part of the brain develops only after metamorphosis via sustained proliferation of neuronal progenitors at the ventricular zone. This is concomitant with a massive expansion of late differentiating neuronal types as revealed by neuropeptide and neurotransmitter profiling. Overall, our results suggest that the adult amphioxus brain shows remarkable similarities to the vertebrate embryonic brain, thus providing a key missing link in understanding the invertebrate-to-vertebrate transition in chordate brain evolution.

evolutionary biology↗