Biology subjects

Henkel, C.

Publications and source records attributed to Henkel, C..

9 recordsLinked to original sources

bioRxiv2026

Evaluating in vitro spermatogenesis in Atlantic salmon using single-cell transcriptomics

Understanding how to maintain and direct spermatogenesis in vitro is central to advancing reproductive biotechnologies in aquaculture species where the ability to generate gametes outside the organism could facilitate selective breeding, genetic modification, and germline preservation. However, current culture systems remain poorly defined in farmed fish species. In Atlantic salmon (Salmo salar), progress has been further limited by the absence of a comprehensive reference atlas of testicular cell types, making it difficult to determine how cells maintained in culture relate to their native counterparts. To address this, we first established a single-cell RNA atlas of the Atlantic salmon testis from freshly isolated tissue, resolving somatic and germ cell populations across all major stages of spermatogenesis. Primary testicular cells were then cultured under distinct conditions designed to promote either proliferation or differentiation for 14 days and subsequently subjected to single-cell RNA sequencing. To assign cell identities in cultured samples, the transcriptional profiles of cultured cells were computationally mapped onto the atlas, allowing direct comparison of cultured and native cell states. This approach revealed pronounced, condition-specific shifts in cellular composition. Proliferation medium supplemented with epidermal growth factors (EGF) and insulin-like growth factor (IGF) enriched spermatogonial populations, indicating preferential support of undifferentiated and actively dividing germ cells. In contrast, basal medium favoured the preferential survival of Sertoli cells in the absence of defined growth cues. A differentiation medium containing hormones that stimulate male gonad development (gonadotropins and androgens) failed to robustly promote meiotic progression. Further, comparative analysis of Sertoli cells across different conditions (in vivo and in vitro) revealed a loss of canonical identity markers and induction of stress-associated transcriptional programs in vitro compared to in vivo, indicating a shift away from specialised somatic function. Together, these findings establish the first single-cell reference atlas of Atlantic salmon testis and provide a framework for evaluating and optimising testis culture systems in salmonids. While early germ cell populations could be maintained and enriched in vitro, progression through later stages of spermatogenesis remained limited, indicating that important biological requirements of the native testicular environment are not yet fully recapitulated under current culture conditions.

cell biology↗

bioRxiv2025

Photoperiod decoder 1 regulates seasonal changes in energy metabolism through the growth hormone signaling pathway

Seasonal changes in metabolism are crucial for animals to adapt to annual environmental fluctuations. However, the molecular mechanisms underlying these adaptations remain poorly understood. Here, we identified a novel gene, photoperiod decoder 1 (phod1), which exhibits a unique bimodal expression pattern under long-day conditions in Japanese medaka fish (Oryzias latipes). While phod1 is conserved across many vertebrates, except for eutherians, its function remained unknown. Single-cell RNA sequencing analysis revealed that phod1 is predominantly expressed in specific pituitary cells that co-express opsin and circadian clock genes. Transcriptomic analysis using phod1 knockout fish demonstrated that phod1 is essential for photoperiodic regulation of growth hormone. Furthermore, transcriptomic and metabolomic analyses of the liver, the primary target of growth hormone, revealed significant alterations in energy metabolism. Behavioral analysis also showed that phod1 knockout fish exhibited significantly reduced locomotor activity. These findings indicate that phod1 plays a crucial role in seasonal metabolic adaptation through modulation of the growth hormone signaling pathway.

physiology↗

bioRxiv2024

Ribonanza: deep learning of RNA structure through dual crowdsourcing

Prediction of RNA structure from sequence remains an unsolved problem, and progress has been slowed by a paucity of experimental data. Here, we present Ribonanza, a dataset of chemical mapping measurements on two million diverse RNA sequences collected through Eterna and other crowdsourced initiatives. Ribonanza measurements enabled solicitation, training, and prospective evaluation of diverse deep neural networks through a Kaggle challenge, followed by distillation into a single, self-contained model called RibonanzaNet. When fine tuned on auxiliary datasets, RibonanzaNet achieves state-of-the-art performance in modeling experimental sequence dropout, RNA hydrolytic degradation, and RNA secondary structure, with implications for modeling RNA tertiary structure.

biophysics↗

bioRxiv2023

Photoperiod regulates gonadotrope cell division in medaka via melatonin, Tsh and folliculostellate cells

In vertebrates, pituitary gonadotropins (follicle-stimulating and luteinizing hormones: FSH and LH) regulate gonadal development and maturation, therefore playing an essential role in reproduction. The seasonal regulation of gonadotropins has been widely studied in mammals and birds, and in these taxa thyroid-stimulating hormone (TSH) was found to play a critical role. By contrast, the seasonal regulation of gonadotropins remains unclear in teleost fish. In addition, the seasonal regulation of gonadotrope (gonadotropin-producing cell) proliferation has not been elucidated in any vertebrate group. Using the teleost fish medaka as a model, we show for the first time that long photoperiod enables reproduction by stimulating gonadotropin mRNA synthesis and gonadotrope cell proliferation. In female medaka, this proliferation is achieved by gonadotrope mitosis. We then demonstrate that in female medaka, photoperiod stimulates gonadotropin mRNA production and mitosis via an indirect intra-pituitary pathway, involving pituitary Tsh cells. We show that non-endocrine folliculostellate cells in the pituitary mediate the Tsh signal regulating gonadotrope activity and proliferation, as they are the only pituitary cells to express Tsh receptors and send projections to gonadotropes. Finally, we show that melatonin suppresses pituitary tshba expression in fish exposed to long photoperiod, suggesting that short photoperiod inhibits gonadotropin synthesis via melatonin in both fish and mammals. This study therefore demonstrates that in fish, photoperiod regulates gonadotrope cell activity and mitosis via a melatonin-Tsh pathway. It also reveals the existence of a novel intra-pituitary pathway for seasonal regulation of gonadotropes, involving folliculostellate cells, which we propose might also exist in other vertebrates. SIGNIFICANCEIn seasonally breeding mammals and birds, the production of the hormones that regulate reproduction (gonadotropins) by gonadotropes is controlled by the pituitary thyroid-stimulating hormone (TSH) through an indirect pathway via the brain. However, in fish, how seasonal environmental signals influence gonadotropins remains unclear. Here, we show that in a long day seasonally breeding fish, medaka, photoperiod not only regulates the activity (hormone production) of the gonadotropes but also their proliferation. We also reveal a novel intra-pituitary pathway that regulates gonadotrope cell activity and number. This pathway involves melatonin, Tsh, and folliculostellate cells. Interestingly, as all these components are also found in the mammalian pituitary, this study suggests the existence of an alternative regulatory mechanism of seasonal gonadotropin production across vertebrates.

neuroscience↗

bioRxiv2022

The effect of short-term activation of AHL15 on long-term plant developmental change and transcriptome profile

We have previously documented that overexpression of the Arabidopsis nuclear protein AHL15 leads to reprogramming of somatic cells to embryonic cells (Karami et al., 2021) and to suppression of plant ageing (Karami et al., 2020). Here we show that transient (4 hours) activation of overexpressed AHL15-GR in Arabidopsis seedlings has long-term effects on plant development. RNA sequencing analysis detected an extensive reprogramming of the transcriptome 4 hours after AHL15-GR activation, with respectively 540 and 1107 genes showing more than 2-fold up- and down-regulation. AHL15 seemed to act in a transcription leveldependent manner, activating predominantly low expressed genes and repressing mostly highly expressed genes. Rapid decondensation of heterochromatin was observed after AHL15 activation in leaf primordia and axillary meristems, indicating that the global reprogramming of the transcriptome by transient activation of this AT-Hook domain protein might be caused by extensive modulation of the chromatin configuration. We also found that co-activated or co-repressed genes were often physically linked in small chromosomal clusters, which is in line with regulation at the chromatin level.

developmental biology↗

bioRxiv2021

Ectopic expression of lipid homeostasis genes in rare cells of the teleost pituitary gland

Directing both organismal homeostasis and physiological adaptation, the pituitary is a key endocrine gland in all vertebrates. It communicates the needs of the organism to different organs by secreting hormones into the bloodstream. Here, we have used the model fish medaka to investigate the developmental dynamics in the pituitary using a comprehensive RNA-seq time series. By linking developmental expression trends to single-cell RNA-seq profiles, we show how the transcriptional activities of cell types change during sexual maturation. One of the most prominent changes is the decline of the non-endocrine folliculo-stellate cell populations, and especially of rare cells expressing genes encoding secreted lipid transport proteins. As these genes are typically associated with the liver, this reveals the existence of unexpected connections between endocrine communication, lipid homeostasis, and sexual maturation.

physiology↗

bioRxiv2021

3D atlas of the pituitary gland of the model fish medaka

In vertebrates, the anterior pituitary plays a crucial role in regulating several essential physiological processes via the secretion of at least seven peptide hormones by different endocrine cell types. Comparative and comprehensive knowledge of the spatial distribution of those endocrine cell types is required to better understand their role during the animal life. Using medaka as the model and several combinations of multi-color fluorescence in situ hybridization, we present the first 3D atlas revealing the gland-wide distribution of seven endocrine cell populations: lactotropes, thyrotropes, Lh and Fsh gonadotropes, somatotropes, and pomca-expressing cells (corticotropes and melanotropes) in the anterior pituitary of a teleost fish. By combining in situ hybridization and immunofluorescence techniques, we deciphered the location of corticotropes and melanotropes within the pomca-expressing cell population. The 3D localization approach reveals sexual dimorphism of tshba- and pomca-expressing cells in the adult medaka pituitary. Finally, we show the existence of bi-hormonal cells co-expressing lhb-fshb, fshb-tshba and lhb-sl using single-cell transcriptomics analysis and in situ hybridization. This study offers a solid basis for future comparative studies of the teleost pituitary and its developmental plasticity. Highlights- We offer the first 3D atlas of a teleost pituitary, which presents a valuable resource to the endocrinology and model fish community. - The atlas reveals the 3D spatial distribution of the seven endocrine cell types and blood vessels in the juvenile/adult male and female pituitary. - Gene expression for tshba and pomca, as well as the population size of cells expressing these genes, displays obvious sexual dimorphism in the adult medaka pituitary. - Multi-color in situ hybridization and single cell RNA-seq reveal the existence of bi-hormonal cells, co-expressing lhb-fshb, fshb-tshba, lhb-sl, and a few multi-hormonal cells. - An online version of the atlas is available at https://www.nmbu.no/go/mpg-atlas.

neuroscience↗

bioRxiv2020

Characterization of hormone-producing cell types in the teleost pituitary gland using single-cell RNA-seq

The pituitary is the vertebrate endocrine gland responsible for the production and secretion of several essential peptide hormones. These, in turn, control many aspects of an animals physiology and development, including growth, reproduction, homeostasis, metabolism and stress responses. In teleost fish, each hormone is presumably produced by a specific cell type. However, key details on the regulation of, and communication between these cell types remain to be resolved. We have therefore used single-cell sequencing to generate gene expression profiles for 2592 and 3804 individual cells from the pituitaries of female and male adult medaka (Oryzias latipes), respectively. Based on expression profile clustering, we define 15 and 16 distinct cell types in the female and male pituitary, respectively, of which ten are involved in the production of a single peptide hormone. Collectively, our data provide a high-quality reference for studies on pituitary biology and the regulation of hormone production, both in fish and in vertebrates in general.

physiology↗

bioRxiv2020

Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing

Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points. With only three ONT flow cells we were able to identify thousands of organisms, including bacteriophages, from which a large part at species level. It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in >1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. These results show that our approach is suitable for scalable genomic investigations such as monitoring oceanic biodiversity and provides a new platform for education in biodiversity

bioinformatics↗