Biology subjects

Schmidt, A.

Publications and source records attributed to Schmidt, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

A systemic circadian nicotinic acid riboside (NaR) signal engages the unfolded protein response and adipogenesis via the prefoldin complex

Daily light-dark cycles impose predictable environmental fluctuations that require coordinated temporal regulation of cellular physiology. This coordination is mediated by the circadian clock, which operates as a network of tissue oscillators; however, the molecular signals that convey circadian information between organs remain incompletely defined. Here, we identify nicotinic acid riboside (NaR) as a circulating metabolite whose rhythmicity depends on the liver clock. In differentiating 3T3-L1 adipocytes, NaR engages unfolded protein response (UPR) gene programs and modulates adipogenic competence. Proteome-wide stability profiling implicates the prefoldin complex as a molecular target of NaR signaling, linking NaR exposure to altered proteostasis. Functionally, NaR-induced UPR signaling converges on the adipogenic transcription factor CEBPA, which is a central regulator of adipogenesis. Importantly, sustained NaR exposure suppresses adipocyte lipid deposition, whereas temporally restricted NaR stimulation enhances adipogenesis, indicating that NaR acts in a time-dependent manner. Together, these findings identify NaR as a liver clock-controlled circulating metabolite that couples systemic circadian metabolism to adipocyte proteostasis and differentiation, revealing a mechanism by which temporal metabolic signals shape tissue-specific physiological outcomes. HighlightsO_LIThe circadian clock is required for rhythmic regulation of circulating nicotinic acid riboside (NaR). C_LIO_LIThe liver clock is sufficient to generate NaR rhythmicity. C_LIO_LINaR engages the prefoldin complex to regulate unfolded protein response signaling and Cebpa expression. C_LIO_LITime-dependent NaR exposure differentially regulates CEBPA levels and adipocyte lipid deposition. C_LI

systems biology↗

bioRxiv2026

Heterogeneous dynamics of mobile genetic elements encode and spread antibiotic persistence in bacteria

Bacterial persisters are nonreplicating cells that transiently evade antibiotic killing within an otherwise susceptible, replicating population. While persister formation has traditionally been attributed to phenotypic heterogeneity, reversible functional variations among genetically identical cells, most studies lack direct genomic evidence to exclude the contribution of cryptic and reversible genetic variations. Here, we demonstrate that the dynamics of the Legionella pneumophila integrative and conjugative element (ICEs) pP36 encode and disseminate antibiotic persistence-like traits. During biofilm formation, pP36 undergoes heterogeneous chromosomal excision generating a subpopulation of nonreplicating persisters-like bacteria with a distinct molecular profile. pP36-mediated L. pneumophila growth rate heterogeneity significantly enhances bacterial survival under fluoroquinolone treatment. Our findings reveal that pP36 dynamics not only orchestrate physiological diversity but also serve as a vehicle for horizontal transfer of antibiotic persistence mechanisms among clinical Legionella isolates. While ICEs are recognized as key drivers of antibiotic resistance dissemination, this study establishes that ICEs-mediated phenotypic variations is a critical determinant of persister-like cell formation, reshaping our understanding of bacterial adaptability to antibiotic stress.

microbiology↗

bioRxiv2026

Recalibrating Nanoparticle Protein Corona Analysis for Accurate Biological Identity and Soluble Plasma Proteome Profiling

The nanoparticle (NP) protein corona is considered the biological identity that determines NP fate, safety, targeting, and therapeutic effectiveness in biofluids. Nonetheless, standard corona isolation workflows assume the recovered protein signature originates primarily from plasma proteins adsorbed directly onto the NP surface, while largely overlooking co-isolation of endogenous nanoscale biological structures such as extracellular vesicles (EVs). This oversight can distort the apparent "biological identity" of the NP. Here, we show that EVs are a major hidden contributor to the perceived protein corona composition in human plasma. Using highly monodispersed polystyrene NPs (50-1000 nm) and superparamagnetic beads, we compared corona formation in standard human plasma and plasma depleted of an EV- enriched sedimentable fraction by ultracentrifugation at 100,000 x g for 2 h, with the recovered vesicles subsequently characterized by MACSPlex immunoaffinity analysis. Mass spectrometry revealed that EV depletion reduced the number of proteins identified on polystyrene NPs by 60-75% and on magnetic beads by 45-50%, demonstrating a substantial fraction of the conventionally assigned corona proteome arises from EV- associated carryover. EV depletion also restructured the apparent abundance hierarchy, increasing the relative prominence of soluble plasma proteins such as albumin and shifting dominant signals away from intracellular cytoskeletal component proteins that are characteristic of EV carryover towards genuine soluble plasma proteins and complement factors. These results highlight that standard corona workflows can inadvertently co-isolate a vast array of EV-associated material and thereby yield inaccurate assignments of protein origin. Distinguishing proteins adsorbed from the soluble phase from EV-surface and intravesicular material is essential for accurate interpretation of NP-biofluid interactions, biomarker discovery, and therapeutic targeting because molecular compartment determines both analytical meaning and drug accessibility. Significance StatementThe nanoparticle (NP) "protein corona" defines how engineered nanomaterials interact with living systems, influencing therapeutic safety, efficacy, and diagnostic utility. Conventionally, corona isolation workflows assume that recovered proteins were adsorbed directly from the fluid phase. This study reveals a major, previously overlooked source of analytical distortion: standard separation techniques routinely co-isolate endogenous extracellular vesicles (EVs), drastically distorting the perceived biological identity of NPs. Depletion of an EV-enriched sedimentable fraction by ultracentrifugation reduced identified corona proteins by up to 75% and restructures the apparent proteomic hierarchy. Distinguishing true soluble adsorbates from vesicular carryover is essential for accurately predicting NP behavior in vivo and prevents false positives in nano- diagnostics, establishing a critical new standard for high-fidelity biomarker discovery and nanomedicine.

bioengineering↗

bioRxiv2026

Cell cycle-dependent protein dynamics in budding yeast resolved by deconvolution of bulk proteomics

The cell division cycle is characterised by oscillatory dynamics in regulatory mechanisms and biosynthesis, coordinated with genome replication and segregation. To understand these dynamics, quantitative cell cycle-dependent protein concentration data is essential. Unfortunately, accurate resolution of cell cycle-dependent protein dynamics is challenging because single-cell proteomics is currently infeasible and bulk proteomics requires inherently imperfect cell synchronisation. Here, we developed a computational method to deconvolve cell cycle-dependent protein concentration dynamics and applied it to new budding yeast bulk proteome data. Key to this method was a yeast population model, parameterised with experimental cell cycle progression and volume growth data, for quantifying the desynchronisation in sampled populations. We performed deconvolution on 3373 proteins, using cross-validation to determine regularisation parameters, and identified 563 proteins with cell cycle-dependent dynamics. Many of these dynamics were consistent with known yeast biology and dynamic proteins were enriched for several metabolic process, extending previous observations and supporting the emerging picture of metabolic activity as varying substantially over cell cycle phases. We consider the generated cell cycle-resolved budding yeast proteome data a key resource.

systems biology↗

bioRxiv2026

Ribosome profiling reveals extensive translational alterations in steatohepatitis-associated hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one the most lethal cancer types. While infections with hepatitis B or hepatitis C viruses remain the primary risk factors for HCC development worldwide, metabolic disease-associated steatohepatitis has become the fastest growing etiology of HCC, particularly in the West. Our study characterizes, for the first time, the remodeling of the translation landscape in steatohepatitis-associated HCC using ribosome profiling and mass spectrometry techniques. In striking contrast with the transcriptional alterations, which do not show strong dependence on associated co-morbidity, translational alterations are broader in the steatohepatitis compared to the viral background. These alterations affect hundreds of genes, whose products are often involved in subcellular protein localization. By quantifying the relationship between the ribosome occupancy of upstream or downstream open reading frames (uORFs or dORFs) and coding regions (CDSs), we provide evidence of uORFs attenuating the translation efficiency of CDSs in HCC. We also identify numerous novel translated regions, including from RNAs currently annotated as non-coding, some yielding peptides that can be reproducibly identified in mass spectrometry datasets. Our study thus provides novel molecular data on HCC with a focus on the steatohepatitis etiology, reveals unexpectedly extensive translational control in this co-morbidity, and gives multiple hints and candidate targets for follow-up experiments.

systems biology↗

bioRxiv2026

Ca2+ and DRP1 drive endocytic lysosome reformation at tripartite contact sites

Lysosomes are essential in maintaining cellular health. Endocytic lysosome reformation (ELR) regenerates functional lysosomes following degradation of endocytic cargo, yet the mechanisms driving this process remain largely unknown. Here, we define the molecular machinery underlying ELR. We find that unlike autophagic lysosome reformation (ALR), ELR proceeds independently of mTOR and dynamin 2, but requires the mitochondrial fission GTPase DRP1. DRP1 mediates scission of endolysosomal tubules at contact sites with the endoplasmic reticulum (ER) and mitochondria. Disruption of DRP1 function or ER-endolysosome contact results in elongated tubules, indicating defective lysosome reformation. Moreover, mitochondrial activity is essential for tubule initiation, and Ca2+ transfer from endolysosomes to mitochondria is crucial for ELR onset. Our findings reveal a dual role for mitochondria in ELR: first in ELR initiation and second in DRP1-dependent tubule fission at ER-mitochondria-endolysosome tripartite contact sites, uncovering the previously unappreciated role of mitochondria in endolysosome remodeling and fission.

cell biology↗

bioRxiv2025

Citizen science and detailed searches reveal widespread occurrence of hybrid-like Syrian x Great-spotted woodpeckers

The Syrian Woodpecker (hereafter SW) expansion into Europe since the end of the 19th century has enabled its hybridisation with the Great spotted Woodpecker (hereafter GW). This phenomenon, however, has generally been considered sporadic. Here, we examined the occurrence of mixed pairs and hybrids based on our own field observations and citizen science data. Interspecific pairs and individuals of SW and GW were found to be generally scarce but occurred in all parts of the area investigated, not only at the edges of the SWs range. The proportion of hybrid occurrence in woodpecker populations was found to be similar across the whole SWs range in Europe and in both urban and rural populations. However, on a local level, hybrids seemed to be more abundant in certain regions, for example, E Austria, Moravia, SE Poland, W Russia, S Ukraine, Bulgaria, E Greece and W Turkey. Generally, females were 1.4 times more frequent among hybrids. Three major phenotypical hybrid forms were identified: GW-like, SW-like, and intermediate, with first two forms being more frequent in the central and south of Europe respectively. Whereas proportion of the intermediate form was relatively constant across the whole range of hybrid occurrence. The results indicate that hybrids of the two species have become significant part of woodpecker populations and thus should be considered in research and nature conservation projects.

zoology↗

bioRxiv2025

The vault associates with membranes in situ

The eukaryotic vault particle is a giant ribonucleoprotein complex that assembles into an iconic barrel-like cage. Its cellular function has remained elusive despite extensive characterization. Using cryo-electron tomography of Dictyostelium discoideum cells, we define the distribution, structural states and interaction landscape of vault particles in situ. Surprisingly, we detect a subpopulation of vault particles associated with the endoplasmic reticulum (ER) and nuclear envelope membranes. This association occurs at a defined barrel height of the vault particle and at patches of reduced membrane bilayer thickness and altered curvature. We further find that a substantial fraction of vaults encloses 80S ribosomes in highly ordered orientations. These structural findings are further corroborated by proximity labeling experiments which identify ER-resident proteins and numerous ribosomal components as vault particle interactors. The membrane-bound and ribosome-encapsulating vault populations that we uncover will direct future studies towards revealing vault function.

cell biology↗

bioRxiv2025

Genetic characterization of the apterous Life Span Enhancer in Drosophila melanogaster

The selector gene apterous (ap) of Drosophila melanogaster is best known for its prominent role in wing formation. apnull flies are viable but have no wings. However, apnull flies are associated with another phenotype whose analysis was largely neglected in the past 40 years: adults die precociously 2-3 days after eclosion. We have recently published a comprehensive analysis on the physiology of this striking phenotype. We showed that Ap protein is essential early in metamorphosis during hindgut remodeling where it is required for rectal papillae formation in the rectal ampulla. Wild-type flies have four rectal papillae that are involved in selective reabsorption of essential ions and metabolites from the primary urine produced by the Malpighian tubules. In apnull flies, rectal papillae formation is aborted prematurely. The corresponding papillar cells remain stuck in the rectal lumen. This leads to complete intestinal blockage and a cascade of pathologies resulting in premature death. In this study, we genetically identify and functionally dissect a novel tissue specific cis- regulatory element that directs Ap expression in the hindgut. This Life Span Enhancer (apLSE) maps to a [~]400 bp DNA fragment that is activated via only two small regulatory modules. Genetic analysis of apLSE alleles proves that they are essential for papilla formation and thus for adult survival. Our studies solve the 110-year-old enigma about the ap syndrome. They establish the apLSE as a key player linking hindgut morphogenesis and survival. We propose that several aspects of the ap syndrome are a consequence of drastic changes in endocrine homeostasis.

developmental biology↗

bioRxiv2025

Ketamine and Psilocybin Differentially Impact Sensory Learning During the Mismatch Negativity

Ketamine and psilocybin show potential as therapies for various mental illnesses, including major depressive disorder. However, further investigation into their neural mechanisms is required to understand their effects on the brain. By combining computational modelling with electroencephalography (EEG), we examine the effects of ketamine and psilocybin on hierarchical sensory pwPE learning in the context of the auditory mismatch negativity, an event-related potential consistently shown to be reduced under psychotomimetic interventions. We employed a Bayesian framework and re-analyzed a previously acquired EEG dataset (Schmidt et al., 2012) by modelling single-trial EEG data using the Hierarchical Gaussian Filter. Using a placebo-controlled within-subject crossover design, healthy subjects were administered either S-ketamine or psilocybin during an auditory roving paradigm of pure sinusoidal tones. Our findings elucidate distinct neural impacts of ketamine and psilocybin on sensory learning: ketamine led to a larger reduction in the effect of sensory precision compared to placebo from 207 to 316 ms peaking at 277 ms in the frontal central channels, while psilocybin showed no significant effect. Both drugs reduced the expression of belief precision between 160 to 184 ms, peaking at 172 ms. For higher-level volatility pwPEs, ketamine reduced the expression at 312 ms while psilocybin had a null effect. For perception of elementary imagery, ketamine had a greater effect than psilocybin on sensory and volatility precision, while psilocybin had a greater effect on volatility pwPEs. Our findings suggest hallucinogens have distinct effects on sensory learning that could inform tailored therapies for major depression.

neuroscience↗

bioRxiv2025

Coenzyme A depletion causes antibiotic tolerance in Pseudomonas aeruginosa

The widespread use of antibiotics promotes both resistance and tolerance. While resistance enables bacterial growth in the presence of drugs, tolerance allows survival during treatment, generating persisters that seed relapse and promote resistance. Despite its clinical relevance, the molecular basis of tolerance remains poorly understood. Using proteomic and metabolomic profiling combined with machine learning, we identified thiol oxidation as a robust predictor of tolerance in the human pathogen Pseudomonas aeruginosa. Single-cell analyses established a direct link between thiol oxidation and drug survival, indicating that redox imbalance drives persistence. Whereas depletion of coenzyme A (CoA), a central thiol-containing metabolite, scaled with tolerance, restoring CoA using engineered catalysts from Staphylococcus aureus abolished tolerance, establishing a causal relation between CoA availability and drug susceptibility. Thiol-based predictors also accurately capture tolerance of clinical P. aeruginosa isolates. These findings establish CoA-centered redox control as a key determinant of tolerance, opening opportunities for diagnostics and therapeutic interventions to prevent infection relapses.

microbiology↗

bioRxiv2025

The influence of power-training and aging on endomysium content and fiber cross-sectional area in the human soleus muscle

The Master Athletic Laboratory Study of Intramuscular Connective Tissue (MALICoT, DRKS00015764) set out to analyze the endomysium content of the human soleus muscle in response to athletic exercise and aging. Forty-three healthy male study participants were grouped into young (20-35 years) non-physically active controls (n=12), young power-trained athletes (n=10), older (60-75 years) non-physically active controls (n=11), and older power-trained athletes (n=10). A single biopsy was taken from the left soleus muscle of each participant, and cryo-sections were used for i) routine histological staining and myopathological evaluation, ii) deep learning-based image analysis of the H&E- and MHC-stained sections, iii) laminin-{gamma}-1/collagen IV double- and collagen I and III single-immunofluorescence staining, and iv) quantitative proteomic analysis. Examiner-based myopathological evaluation revealed normal skeletal muscle in 26 participants, while 11, 4, 1 and 1 biopsies showed unspecific myopathological changes, chronic neurogenic atrophy, type II fiber atrophy, and unspecific myositic changes, respectively. Analysis of the H&E- and MHC-stained sections as well as the laminin-{gamma}-1/collagen I-, collagen III- and collagen IV-immunostained sections revealed an approximately 1.3-fold increase in the mean fiber area in response to power-training in young participants and aging in unathletic participants. No significant change was detected in endomysium thickness or area. Furthermore, proteomic analysis did not reveal any group-specific change except for plasma membrane calcium-transporting ATPase 2 being less abundant in the soleus muscles of aged power-trained athletes. Overall, the data show that neither athletic exercise nor age significantly affected the content or composition of the endomysium in human soleus muscle tissue. New & NoteworthyMALICoT (DRKS00015764) set out to analyze the endomysium of soleus muscle in response to athletic exercise and aging. Myopathological evaluation of biopsies from 43 asymptomatic male study participants revealed normal skeletal muscle in only 26 of them. Neither exercise nor age significantly affected the endomysium content or proteomic profiles of human soleus muscle tissue. However, power-training in young participants and aging in unathletic participants were associated with significant increases in soleus muscle fiber cross-sectional area.

physiology↗

bioRxiv2025

Epistasis between drug resistance-conferring mutations in Mycobacterium tuberculosis

Studies in model organisms show that mutations conferring resistance to different antibiotics can interact epistatically, but the biological and epidemiological consequences of such interactions are unknown. Here we show that in Mycobacterium tuberculosis (Mtb), positive sign epistasis between RpoB and GyrA mutations causing resistance to rifampicin and fluoroquinolone, respectively, can lead to double-resistant strains with high in vitro fitness. Two of these RpoB-GyrA mutation combinations account for 53% in a global collection of highly drug-resistant Mtb clinical isolates, compared to <0.7% for RpoB-GyrA combinations with low in vitro fitness. Moreover, the two high-fitness RpoB-GyrA combinations are associated with a more benign and idiosyncratic proteome perturbation compared to low-fitness combinations. Our findings highlight the relevance of epistasis for the emergence and spread of antimicrobial resistance.

microbiology↗

bioRxiv2025

Thalamic Nuclei Volumes Across Psychiatric and Neurological Disorders: A Multi-Site Magnetic Resonance Imaging Study

The human thalamus is an integrative hub for multiple cortical and subcortical circuits involved in sensory processing and higher cognitive functions. Thalamic volume differences have been reported across multiple psychiatric and neurological disorders, but previous studies have typically relied on small samples, focused on one or a limited number of disorders, or investigated the thalamus as a whole without considering its functional subdivisions. In this multi-site study, we compared thalamic nuclei volumes across mild cognitive impairment (MCI), dementia (DEM), major depressive disorder, schizophrenia spectrum disorder (SCZ), clinical high risk for schizophrenia, bipolar spectrum disorder, autism spectrum disorder, attention-deficit/hyperactivity disorder, Parkinsons disease, multiple sclerosis (MS), and healthy controls (N > 8 000). Using structural MRI, we segmented 25 bilateral thalamic nuclei, corresponding to six anatomical groups. Linear models revealed that anterior, medial and lateral regions of the thalamus were significantly smaller in several conditions, with largest effects observed for MCI, DEM, SCZ and MS. In contrast, the ventral and intralaminar groups were relatively normal. This pattern of effects largely corresponds to the canonical functional subdivision of the thalamus into higher-order and sensory regions. At the level of individual nuclei, the clinical conditions were associated with distinct patterns of alterations, while left and right lateral geniculate nuclei were implicated in six of the disorders, suggesting a possible relation with circadian and sleep disturbances. Together, the results highlight a role for the higher-order thalamus in common brain disorders and a differential involvement at the nuclei level, refining our understanding of thalamic pathology across common brain disorders.

neuroscience↗

bioRxiv2025

Multi-millennial genetic resilience of Baltic diatom populations disturbed in the past centuries

Little is known about the genetic diversity and stability of natural populations over millennial time scales, although the current biodiversity crisis calls for heightened understanding. Marine phytoplankton, the primary producers forming the basis of food webs in the oceans, play a pivotal role in maintaining marine ecosystems health and serve as indicators of environmental change. This study examines the genetic diversity and shifts in allelic composition in the diatom species Skeletonema marinoi over [~] 8000 years in the Baltic Sea by analyzing chloroplast and mitochondrial genomes. Ancient environmental DNA (aeDNA) from sediment cores demonstrates stability and resilience of genetic composition and diversity of this species across millennia in the context of major climate events. Accelerated change in allelic composition is observed from historical periods onwards, coinciding with times of intensifying human activity, like the Roman Empire, the Viking Age, and the Hanseatic Age, suggesting that anthropogenic stressors have profoundly impacted this species for the last two millennia. The data indicate a very high natural stability and resilience of the genomic composition of the species and underscore the importance of uncovering genomic disruptions caused by human impact on organisms, even those not directly exploited, to better predict and manage future biodiversity.

genomics↗

bioRxiv2025

The yeast phosphofructokinase β-subunit has ATP-dependent RNA unwinding activity and modulates cell cycle progression

Phosphofructokinase (PFK) is a rate-limiting glycolytic enzyme that also possesses an unexplored RNA binding activity. Here, we show that the - and {beta}-subunits of yeast PFK, encoded by PFK1 and PFK2, respectively, bind hundreds of mRNAs in cells, including ones coding for proteins involved in regulation of mitotic cell cycle. Pkf2p directly binds in a Mg-ATP-dependent manner to short GA-, UC-, AU- and U-rich motifs overrepresented in its mRNA targets. Strikingly, Pfk2p displays directional 5 - 3 double-stranded RNA unwinding activity not seen with Pfk1p. Furthermore, Pfk2p dynamically associates with ribosomes and promotes translation of cell cycle genes. Consequently, pfk2{Delta}, but not pfk1{Delta}, mutant cells show severely delayed G1/S phase transition which is independent of the enzymes glycolytic activity. Our results uncovered a hidden function for the Pfk2 subunit as a translational activator of mitotic cell cycle gene transcripts possibly through energy-dependent RNA unwinding activity.

molecular biology↗

bioRxiv2024

Two distinct durable human class-switched memory B cell populations are induced by vaccination and infection

Memory lymphocytes are durable cells that persist in the absence of antigen, but few human B cell subsets have been characterized in terms of durability. The relative durability of eight non-overlapping human B cell sub-populations covering 100% of all human class-switched B cells was interrogated. Only two long-lived B cell populations persisted in the relative absence of antigen. In addition to canonical germinal center-derived switched-memory B cells with an IgD-CD27+ CXCR5+ phenotype, a second, non-canonical, but distinct memory population of IgD-CD27- CXCR5+ DN1 B cells was also durable, exhibited a unique TP63-linked transcriptional and anti-apoptotic signature, had low levels of somatic hypermutation, but was more clonally expanded than canonical switched-memory B cells. DN1 B cells likely evolved to preserve immunological breadth and may represent the human counterparts of rodent extrafollicular memory B cells that, unlike canonical memory B cells, can enter germinal centers and facilitate B cell and antibody evolution. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/624972v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@169c77forg.highwire.dtl.DTLVardef@1a872f5org.highwire.dtl.DTLVardef@1360cforg.highwire.dtl.DTLVardef@38d7ed_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Single-cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches

Hematopoietic stem cells (HSCs) and more committed progenitors (collectively referred to as HSPCs) emerge from vessels during development, via Endothelial-to-Hematopoietic Transition (EHT). Recently, using the zebrafish embryo, we showed that two EHT cell types emerge from the aorta, raising the question of their subsequent fate. To address this issue, we established a complex pipeline based on single-cell photoconversion and transgenic lines to characterize the transcriptomic profiles of single EHT cell type progenies. We obtained, at unprecedented resolution in the early larva, a cartography of HSPCs and highly diversified differentiated populations, notably NK-like cell types, innate lymphoid cells and early eosinophils. We show that the two EHT cell types previously characterized indeed lead to differentially fated cells, with significant differences in thymus colonization and T-lymphoid lineage commitment. Using HSPC signatures retrieved from our datasets - namely gata2b and cd34/podocalyxin -, and to address niches, we performed in situ gene expression analyses via RNAscope. Unexpectedly, we unveil a niche contacting the supra-intestinal artery. Finally, integration with previous datasets reveal that our populations contain potential developmental HSCs bearing signatures highly similar with adult HSCs. Summary StatementSingle cell photoconversion of emerging hematopoietic precursor cells and transcriptomics unravel the diversity of hematopoietic stem and progenitor cell populations and homing in developmental niches in toto, during zebrafish development.

developmental biology↗