Publikationen

Incomplete reporting of microscopy methods undermines transparency, reproducibility, and data reuse. Despite recent initiatives, comprehensive, broadly endorsed, and accessible reporting guidelines are still lacking. Here, we present a bare minimal microscopy reporting requirements checklist that integrates human- and machine-readable input to provide clear, actionable guidance for researchers, reviewers, and publishers and to advance community standards in microscopy.

Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning (ML) are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap encompasses key aspects of how ML is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of ML for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.

High-sugar diets cause human metabolic diseases, yet several bird lineages convergently adapted to feeding on sugar-rich nectar or fruits. We investigated the underlying molecular mechanisms in hummingbirds, parrots, honeyeaters, and sunbirds by generating nine new genomes and 90 tissue-specific transcriptomes. Comparative screens revealed an excess of repeated selection in both protein-coding and regulatory sequences in sugar-feeding birds, suggesting reuse of genetic elements. Sequence or expression changes in sugar-feeders affect genes involved in blood pressure regulation and lipid, amino acid, and carbohydrate metabolism, with experiments showing functional changes in honeyeater hexokinase 3. MLXIPL, a key regulator of sugar and lipid homeostasis, showed convergent sequence and regulatory changes across all sugar-feeding clades; experiments revealed enhanced sugar-induced transcriptional activity of hummingbird MLXIPL, highlighting its adaptive role in high-sugar diets.

The length regulation of microtubules and their organization into complex arrays inside cells occurs through the activity of polymerases, depolymerases as well as severing enzymes such as spastin and katanin. The latter hexamerize on the microtubule lattice, pull out single tubulin dimers in an ATP-dependent manner and eventually generate internal breaks in the microtubule. While spastin was shown to be regulated by posttranslational tubulin modifications, the impact of microtubule lattice defects on the severing characteristics of spastin has not been explored. To answer this question, we prepared GMPCPP-stabilized microtubules with varying defect densities - introduced either through specific polymerization conditions or by end-to-end annealing - for subsequent in vitro severing assays. We found that (i) the presence of defects accelerated the onset of the severing process and (ii) severing was twice as frequent in microtubule segments with defect sites as compared to random lattice segments. However, there was no evidence of preferential binding of spastin to defect sites. We therefore propose a severing mechanism in which defects do not actively promote microtubule severing but rather passively contribute to microtubule lattice instability, facilitating the process as fewer tubulin subunits are required to be removed for microtubule severing.

The origin of the extensive phenotypic divergence characterizing adaptive radiation could often be geographically localized and genetically simple. In a classic case of a trophically polymorphic cichlid fish (Herichthys minckleyi), we investigated alternative genomic processes that could have produced its extreme within-population variation in pharyngeal jaw tooth size. First, we generated a high-quality reference genome for its close relative (H. cyanoguttatus) to dissect the genetic architecture of this dental polymorphism. Then, using whole genome resequencing across the small Cuatro Ciénegas valley where H. minckleyi is endemic, we found substantial micro-geographic subdivision and effectively no genetic structure due to pharyngeal morphotype. We also employed quantitative trait loci mapping and genome wide association to pinpoint a single peak in an Iroquois-related (IRX) gene cluster associated with H. minckleyi's dental divergence. Interspecific introgression in this genomic region appears negligible, suggesting the genomic basis of the polymorphism likely arose within cichlids confined to Cuatro Ciénegas. Because H. minckleyi tooth size disparity is comparable to that found in all Central American cichlids, this offers a striking example of how genomic divergence at a single locus could produce a punctuated burst of eco-morphological divergence that generates phenotypic breadth comparable to a highly diverse cichlid adaptive radiation.

In this issue of Developmental Cell, Yu et al.1 reconstruct human embryonic gene co-expression networks (GCNs) that guide pancreatic endocrine lineage specification. Benchmarking stem cell-derived islet (SC-islet) differentiation protocols against fetal human pancreatic cells reveals early regulatory divergences, thereby enabling the design of a protocol with improved β-like cell production.

Dysregulations within the epidermal proteolytic network can cause hyperproliferative and inflammatory disorders. While the metalloprotease meprin α is localized in the stratum basale in healthy skin, increased levels are found in the upper epidermal layers in wound healing and psoriatic lesions. To investigate a link between meprin α expression and keratinocyte proliferation, we developed a mouse model for inducible expression of pathological meprin α levels (K5Mα). K5Mα mice developed a skin phenotype characterized by hyperkeratosis, acanthosis, parakeratosis and barrier defect. Keratinocyte hyperproliferation and local inflammation were induced upon induction of meprin α expression. By N-terminomics we identified dermokine, a regulator of keratinocyte proliferation and epidermal immune response, as a putative substrate of meprin α. We validated the proteolysis and identified the cleavage site, which is highly conserved in mammals, suggesting that dermokine degradation by meprin α represents a central mechanism in wound healing and hyperproliferative skin diseases.

Organ injury triggers nonneuronal electric currents essential for regeneration. However, the mechanisms by which electrical signals are generated, sensed, and transmitted upon damage to promote organ growth remain unclear. Here, we uncover that organ repair relies on dynamic electrochemical coupling between membrane potential depolarization and intracellular signaling, essential to activate cell proliferation. By subsecond live imaging of locally injured zebrafish larval fins, we identify events across time and space: a millisecond, long-range, membrane depolarization gradient, followed by second-persistent intracellular calcium responses. In the subsequent hour, voltage sensing phosphatase senses the injury-driven membrane potential change and autonomously translates the electric signal intracellularly, promoting tissue-wide cell proliferation. Connecting these dynamics with an electrodiffusive model showed that ionic fluxes and electric potential become coupled in the fin's interstitial space, enabling organ-wide signal spreading. Our work reveals the coupling between fast electrical signals and slower intracellular signaling, ensuring complete organ recovery.

Organoids derived from pluripotent stem cells have emerged as powerful models to study human development. To investigate signaling pathways regulating human pancreas differentiation and morphogenesis, we developed a high-content, image-based screen and quantitative multivariate analysis pipelines robust to heterogeneity to extract single-cell and organoid features using pancreatic progenitor organoids. Here, we identified 54 compounds affecting cell identity and/or morphological landscape. Focusing on one family of compounds, we found that glycogen synthase kinase 3α/β (GSK3A/B) inhibition via wingless/int-1 (WNT) signaling has a reversible effect on cell identity, repressing pancreatic progenitor markers and inducing a poised state in progenitors transitioning to acinar cells. We show that additional fibroblast growth factor (FGF) repression enables further differentiation of acinar cells, recapitulating pancreatic acinar morphogenesis and function. The ability to produce acinar cells is valuable for future studies on pancreatic exocrine function and cancer initiation in humans, as acinar cells are thought to be an important cell of origin for pancreatic adenocarcinoma.

Multipolar migration is a conserved neuronal migration mode in the developing brain, enabling emerging neurons to navigate in crowded environments and reach precise laminar positions. Yet, how these cells interpret external cues to guide their migration is not fully understood. We investigate this question using retinal horizontal cells as a model. Combining transcriptomics, targeted CRISPR screening, and live imaging, we reveal the spatiotemporal guidance system underlying horizontal cell lamination: repulsive Slit1b/2-Robo2 signaling in the amacrine cell layer initiates apical horizontal cell migration, while attractive neurturin-Gfrα1/2 signaling from photoreceptors fine-tunes final positioning beneath the photoreceptor layer. Disruption of these pathways causes basal retention of horizontal cells, highlighting the importance of spatially coordinated signaling for proper lamination and functional retinal circuitry. Our results uncover how positional signals and tissue architecture cooperate to achieve neuronal migration precision, a principle likely relevant across the developing central nervous system.