Mastodawn

📰 "Near-critical gene expression in embryonic boundary precision"
https://arxiv.org/abs/2505.11212
#DrosophilaMelanogaster
#Physics.Bio-Ph #Drosophila #Q-Bio.Mn #Embryo

Near-critical gene expression in embryonic boundary precision

Embryonic development relies on the formation of sharp, precise gene expression boundaries. In the fruit fly Drosophila melanogaster, boundary formation has been proposed to occur at a dynamical critical point. Yet, in the paradigmatic case of the hunchback (hb) gene, evidence suggests that boundary formation occurs in a bistable regime, not at the dynamical critical point. We develop a minimal model for hb expression and identify a single parameter that tunes the system from its monostable regime to its bistable regime, crossing the critical point in between. We find that boundary precision is maximized when the system is weakly bistable--near, but not at, the critical point--optimally negotiating the tradeoff between two key effects of bistability: sharpening the boundary and amplifying its noise. Incorporating the diffusion of Hb proteins into our model, we show that boundary precision is maximized simultaneously at an optimal degree of bistability and an optimal diffusion strength. Our work elucidates design principles of precise boundary formation and has general implications for pattern formation in multicellular systems.

arXiv.org

WordofTheHour May 14

#embryo : the germ of the plant, which is inclosed in the seed and which is developed by germination

- French: embryon

- German: der Embryo

- Italian: embrione

- Portuguese: embrião

- Spanish: embrión

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Thank you so much for being a member of our community!

Tainome May 13

An ominous embryo floating inside a levitating rock of amber, my display stand for today's #pixel_dailies. Playing with dithering and hard shadows, 7 colors, 160×144 pixels. #pixelart #ドット絵 #illustration #embryo #amber #ominous #DisplayStand #mastoart @pixel_dailies

flypapers May 8

📰 "Regulation of Transcriptional Bursting and Spatial Patterning in Early Drosophila Embryo Development"
https://www.biorxiv.org/content/10.1101/2025.05.02.651973v1?rss=1
#DrosophilaMelanogaster
#Evenskipped #Drosophila #Embryo

Regulation of Transcriptional Bursting and Spatial Patterning in Early Drosophila Embryo Development

Nascent RNA synthesis often occurs in periods of high transcriptional activity, interspersed with basal or no activity periods. This phenomenon, known as transcriptional bursting, drives high intercellular variability in gene expression levels. How do key patterning genes in early Drosophila melanogaster embryos overcome this variability to establish precise spatial patterns for tissue development? To address this question, we study single cell transcriptional activity from MS2-based live imaging data of four transgenic constructs ( rho , Kr , sna shadow, sna proximal enhancers) and the endogenous eve gene. We developed an algorithm to infer promoter states in hundreds of cells within the embryo using transcriptional activity data. Results show that while mean transcription levels exhibit spatial gradients, the burst duration and inter-burst timing remain surprisingly invariant across the embryo and different constructs. The time between consecutive bursts was consistent with a memoryless exponential distribution, whereas the burst duration exhibited tighter control with lesser stochastic variations. Our analysis identified two regulatory mechanisms for gene expression gradients: (1) similar burst-timing statistics across genes, with the activity time (the time from the first to the last burst) being modulated to regulate distinct expression levels; (2) for the same gene with different enhancers ( sna shadow and sna proximal), we observed changes in the mean burst duration and variability of the inter-burst timing. This study provides a comprehensive approach to analyzing transcriptional bursting kinetics, revealing activity time as a major regulator of spatiotemporal expression patterning in early embryonic development. ### Competing Interest Statement The authors have declared no competing interest. National Institutes of Health, R35GM133425, R35GM148351

bioRxiv

flypapers Apr 29

📰 "Recently evolved, stage-specific genes are enriched at life stage transitions in flies"
https://www.biorxiv.org/content/10.1101/2025.04.28.650992v1?rss=1
#DrosophilaMelanogaster
#Drosophila #Genomics #Adult
#Embryo #Larva

Recently evolved, stage-specific genes are enriched at life stage transitions in flies

Understanding how genomic information is selectively utilized across different life stages is essential for deciphering the developmental and evolutionary strategies of metazoans. In holometabolous insects, the dynamic expression of genes enables distinct functional adaptations at embryonic, larval, pupal and adult stages, likely contributing to their evolutionary success. While Drosophila melanogaster has been extensively studied, less is known about the evolutionary dynamics that could govern stage-specific gene expression. To address this question, we compared the distribution of stage-specific genes, i.e., genes expressed in temporally restricted developmental stages, across development of D.melanogaster and Aedes aegypti . Using tau-scoring, a computational method to determine gene expression specificity, we found that, on average, a large proportion of genes (20 to 30% of all protein-coding genes) in both species exhibit restricted expression to specific developmental stages. Phylostratigraphy analysis, a method to date the age of genes, further revealed that stage-specific genes fall into two major categories: highly conserved and recently evolved. Notably, many of the recently evolved and stage-specific genes identified in A.aegypti and D.melanogaster are restricted to Diptera order (20 to 35% of all stage-specific genes), highlighting ongoing evolutionary processes that continue to shape life-stage transitions. Overall, our findings underscore the complex interplay between gene evolutionary age, expression specificity, and morphological transformations in development. These results suggest that the attraction of genes to critical life stage transitions is an ongoing process that may not be constant across evolutionary time or uniform between different lineages, offering new insights into the adaptability and diversification of dipteran genomes. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft, https://ror.org/018mejw64, LE 2787/4-1 and STA 850/60-1 as part of SPP 2349 (GEVOL)

bioRxiv

flypapers Apr 29

📰 "Global maps of transcription factor properties reveal threshold-based formation of DNA-bound and mobile clusters"
https://www.biorxiv.org/content/10.1101/2025.04.24.650477v1?rss=1
#Drosophila #Behaviour #Embryo

Global maps of transcription factor properties reveal threshold-based formation of DNA-bound and mobile clusters

The relationship between bulk transcription factor concentration and DNA binding has been a central question in gene regulation for decades. Recent studies propose that DNA-bound transcription factor hubs, or clusters, aid in fast and precise transcriptional interpretation. Using live imaging techniques, we quantify the concentration, binding, and mobility of the morphogen Dorsal (Dl), both in bulk and in clusters, in Drosophila blastoderm embryo. Our experiments encompass multiple length and time scales, allowing us to obtain a nucleus-wide view of the mechanism connecting hub formation to bulk Dl concentration. Our results show that previously unobserved, slowly-moving clusters of Dl are present, in addition to the expected populations of freely mobile and DNA-bound Dl. Furthermore, both mobile clusters and DNA-bound Dl appear only once a threshold concentration in the nucleus is surpassed, a behavior consistent with liquid-liquid phase separation. Thus, our work elucidates how bulk transcription factor concentration dictates the formation and spatiotemporal changes of different populations needed for gene regulation. ### Competing Interest Statement The authors have declared no competing interest. NIH, , R01GM151409, R01GM139913, R01GM152815 NSF, , MCB-2105619, GRFP Koret-UC Berkeley-Tel Aviv University Initiative in Computational Biology and Bioinformatics, , Winkler Scholar Faculty Award, , Chan Zuckerberg Initiative Grant, , CZIF2024-010479

bioRxiv

Nielso Apr 25

Ein gewisses Ritual: Diese Musik hören, bevor ich eine bestimmte andere Musik(aufnahme) weiter abmische.

In Stimmung kommen, die Ohren eintunen auf eine bestimmte Lautstärke und Lautheit, einen gewissen Sound und eine gewisse Musikrichtung.

https://embryoband.bandcamp.com/track/alphorn-prayer

#nielsotunes #music #musik #embryo #krautrock

Alphorn Prayer, by embryo

from the album Auf Auf

embryo

flypapers Apr 24

📰 "Maturation of GABAergic signalling times the opening of a critical period in Drosophila melanogaster"
https://www.biorxiv.org/content/10.1101/2025.04.24.650400v1?rss=1
#DrosophilaMelanogaster
#Drosophila #Sensory
#Embryo #Larva

Maturation of GABAergic signalling times the opening of a critical period in Drosophila melanogaster

The occurrence of critical periods during the development of neural networks is widely documented. Activity manipulation when these periods are open can lead to permanent, and often debilitating, effects to the mature neural network. Detailed understanding of the specific contribution of critical periods to network development, however, remains elusive. This is partly because identified critical periods in mammals are present in complex sensory networks (e.g., visual and auditory) that make focused experimental manipulation challenging. It is significant, therefore, that critical periods have been identified in simpler model systems. A critical period occurs during the development of the embryonic locomotor network in the fruit fly, Drosophila melanogaster. Perturbation of neuronal activity during this period is sufficient to permanently destabilise the mature larval locomotor network: leaving it prone to induced seizures. Given a clear role of γ-aminobutyric acid (GABA) in the timing of the mammalian critical period of ocular dominance, we sought to establish whether this neurotransmitter also regulates the opening of the Drosophila locomotor critical period. Utilising GABA agonists, antagonists, and genetics, we manipulated the embryonic GABAergic system and, at the end of larval life, measured an induced seizure phenotype in mature third-instar larvae. We found that potentiating GABAergic signalling, via embryonic exposure to diazepam or overexpression of the GABAA receptor rdl, induced precocious opening of the critical period. By contrast, exposure to the GABA antagonist gabazine, or knockdown of the GABA-synthetic enzyme Gad1, delayed opening. Thus, we show that critical period timing within the Drosophila CNS is dictated by GABAergic signalling, indicating a phylogenetically conserved role. ### Competing Interest Statement The authors have declared no competing interest.

bioRxiv

settima Apr 16

#Bales2025FilmChallenge of April 16: A film set in India in remembrance of Gandhi's #હડતાળ [#hartal], a peaceful protest against the #JallianwalaBaghMassacre, in the form of a nationwide fast and prayer, on April 16, 1919.

Vagabunden Karawane [Vagabond’s Band] (Werner Penzel, 1980)

In 1979, #krautrock group #Embryo toured Iran, Afghanistan and India by bus, while performing with local musicians and documenting their trip.

https://write.underworld.fr/settima/section-class-boxinfo-markdown-1-m33l

#cinemastodon #film

Vagabunden Karawane [Vagabond’s Band] (Werner Penzel, 1980)

Vagabunden Karawane [Vagabond’s Band] (Werner Penzel, 1980) Apr 16 હડતાળ A member of Embryo plays a harmonium with a bemused साधु [...

settima

flypapers Apr 4

📰 "HyDrop v2: Scalable atlas construction for training sequence-to-function models"
https://www.biorxiv.org/content/10.1101/2025.04.02.646792v1?rss=1
#Drosophila #Genomics #Embryo

HyDrop v2: Scalable atlas construction for training sequence-to-function models

Deciphering cis-regulatory logic underlying cell type identity is a fundamental question in biology. Single-cell chromatin accessibility (scATAC-seq) data has enabled training of sequence-to-function deep learning models allowing decoding of enhancer logic and design of synthetic enhancers. Training such models requires large amounts of high-quality training data across species, organs, development, aging, and disease. To facilitate the cost-effective generation of large scATAC-seq atlases for model training, we developed a new version of the open-source microfluidic system HyDrop with increased sensitivity and scale: HyDrop v2. We generated HyDrop v2 atlases for the mouse cortex and Drosophila embryo development and compared them to atlases generated on commercial platforms. HyDrop v2 data integrates seamlessly with commercially available chromatin accessibility methods (10x Genomics). Differentially accessible regions and motif enrichment across cell types are equivalent between HyDrop-v2 and 10x atlases. Sequence-to-function models trained on either atlas are comparable as well in terms of enhancer predictions, sequence explainability, and transcription factor footprinting. By offering accessible data generation, enhancer models trained on HyDrop-v2 and mixed atlases can contribute to unraveling cell-type specific regulatory elements in health and disease. ### Competing Interest Statement The authors have declared no competing interest.

bioRxiv