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At least 253 records · Page 14Linked to original sources

bioRxiv2026

RHO GTPase of Plants contributes to robust establishment of cellular asymmetry during development from a single cell

A fundamental question in developmental biology is how highly complex, yet reproducible multicellular body plans form from a single cell. The multicellular haploid body of the land plant Marchantia polymorpha develops from a single isolated cell - the spore - that divides asymmetrically. This produces a small terminally differentiating basal cell, and a large proliferative apical cell that gives rise to the multicellular sporeling body. The genetic basis for the establishment of asymmetry, first within the spore, and later within the sporeling body has remained virtually unknown. Here, we show that the plant specific RHO-type GTPase - RHO OF PLANTS (ROP) - polarises to the spore basal pole to ensure spore division is highly and reproducibly asymmetric. We demonstrate this highly asymmetric division is necessary to specify the terminal differentiation of the basal cell. Furthermore, we show that ROP-mediated polarised outgrowth is required to establish asymmetry within the sporeling body derived from the apical cell. Our discovery highlights how ROP function confers developmental robustness and contributes to the establishment of asymmetry during plant development from a single isolated cell.

plant biology↗

bioRxiv2024

Novel Approach for Refractive Index Matching in Calcified Tissues

Tissue-clearing techniques have become indispensable in biomedical research, especially for three-dimensional (3D) imaging. These techniques enable the visualization of complex biological structures by rendering tissues transparent while preserving their structural integrity. Calcified tissues, such as bone and cartilage, pose a unique challenge in imaging studies due to their inherent opacity and rigidity. In this work, we introduce a novel modification to the BABB clearing protocol aimed at enhancing the clearing efficacy specifically for calcified tissues. Through this work, we provide an enhanced tissue-clearing method that addresses the specific challenges associated with calcified tissues. This advancement has the potential to facilitate more precise and comprehensive studies in fields such as developmental biology, orthopedics, and regenerative medicine.

cell biology↗

bioRxiv2023

A complete morphological characterization of all life stages of the phorid fly M. scalaris

Megaselia scalaris, commonly known as the scuttle fly, is a cosmopolitan species in the family Phoridae. It is an easily cultured fly species that is an emerging model organism in the fields of genetics and developmental biology. Its affinity for carrion and its predictable life cycle makes it useful in the field of forensic science for estimating the post-mortem interval (PMI) of human remains. Cases of human myasis caused by M. scalaris have also been reported in the medical literature. Despite its ubiquitous prevalence and its relevance across multiple fields, its morphology has not been adequately characterized. Here, we report the complete morphological characterization of all lifestages of M. scalaris, ranging from egg to adult. Scanning electron microscopy has enabled us to uncover morphological features and developmental processes that have previously not been reported in the literature. Our data lays the groundwork for future genetic studies: a morphological characterization of the wild type must be performed before mutants displaying different phenotypes can be identified. In this vein, we also report the observation of a acephalic, or headless, adult phenotype whose study could yield insights into the process of cephalogenesis.

zoology↗

bioRxiv2021

BMP signaling underlies the craniofacial heterochrony in phyllostomid bats, a hyperdiverse mammal group

The potential for variation and the capacity to evolve in response to ecological opportunity are important aspects of an adaptive radiation. Identifying the origin of phenotypic variation, in which natural selection might act upon, is a major goal of evolutionary developmental biology. The New World leaf-nosed bats (phyllostomids) are a textbook example of an adaptive radiation. Their cranial morphology is diverse along relative facial length, which is related to their diets. We previously used geometric morphometrics to reveal peramorphosis, a type of heterochrony, in the cranial evolution among phyllostomid bats. We then demonstrated that the mechanism of peramorphic diversity in phyllostomid rostrum length resulted from altered cellular proliferation. Here, we investigate the progenitors of the face, the cranial neural crest, and a key signaling pathway related to their proliferation and differentiation into mature tissues: the bone morphogenetic protein (BMP). With geometric morphometrics, immunofluorescence, and confocal imaging--in three phyllostomid species and one outgroup bat species--we show the molecular patterns that underlie the adaptive and innovative traits seen in phyllostomid bats. Then, with mouse genetics, we mimic the BMP molecular pattern observed in nectar feeding bats and recapitulate the elongated morphological variation in mice. Surprisingly, we also observe an expansion in the nose-tip of mice, akin to the expanding leaf-nose tissue in phyllostomid bats. These data, combined with the mouse genetics literature on BMP signaling, suggest the BMP developmental pathway plays a central role in shaping the craniofacial variation necessary for adaptation in bats. Further, we speculate that the BMP signaling pathway could underlie other bizarre facial phenotypes in mammals that are derived from frontonasal mesenchyme, such as the proboscis. Overall, this study combines a comparative framework to developmental data, with a genetic approach, to directly investigate the role of development on complex morphology.

evolutionary biology↗

bioRxiv2024

Disentangling cell-intrinsic and extrinsic factors underlying gene expression evolution

A key goal of developmental biology is to determine the extent to which cells and organs develop autonomously, as opposed to requiring interactions with other cells or environmental factors. Chimeras have played a foundational role in this by enabling qualitative classification of cell-intrinsically vs. extrinsically driven processes. Here, we extend this framework to precisely decompose evolutionary divergence in any quantitative trait into cell-intrinsic, extrinsic, and intrinsic-extrinsic interaction components. Applying this framework to thousands of gene expression levels in reciprocal rat-mouse chimeras, we found that the majority of their divergence is attributable to cell-intrinsic factors, though extrinsic factors also play an integral role. For example, a rat-like extracellular environment extrinsically up-regulates the expression of a key transcriptional regulator of the endoplasmic reticulum (ER) stress response in some but not all cell types, which in turn strongly predicts extrinsic up-regulation of its target genes and of the ER stress response pathway as a whole. This effect is also seen at the protein level, suggesting propagation through multiple regulatory levels. Applying our framework to a cellular trait, neuronal differentiation, revealed a complex interaction of intrinsic and extrinsic factors. Finally, we show that imprinted genes are dramatically mis-expressed in species-mismatched environments, suggesting that mismatch between rapidly evolving intrinsic and extrinsic mechanisms controlling gene imprinting may contribute to barriers to interspecies chimerism. Overall, our conceptual framework opens new avenues to investigate the mechanistic basis of developmental processes and evolutionary divergence across myriad quantitative traits in any multicellular organism.

evolutionary biology↗

bioRxiv2023

Evolution of the gene regulatory network of body axis by enhancer hijacking in amphioxus

A central goal of evolutionary developmental biology is to decipher the evolutionary pattern of gene regulatory networks (GRNs) that control morphogenesis during embryonic development, and the underlying molecular mechanism of the GRNs evolution. The Nodal signaling that governs the body axes of deuterostomes exhibits a conserved GRN orchestrated principally by Nodal, Gdf1/3 and Lefty. Despite that the GRN retains a conserved function in deuterostomes, the expression patterns of Gdf1/3 and Nodal are derived in cephalochordate amphioxus, implying a specific rewiring of the GRN in this lineage. Here we examined the regulatory mechanism and evolution of this GRN in amphioxus by functional genetic manipulations. We found that while the amphioxus Gdf1/3 orthologue shows nearly no expression during embryogenesis, its duplicate Gdf1/3-like linking to Lefty is zygotically expressed in a similar pattern as Lefty. Mutant and transgenic analyses revealed that Gdf1/3 is no longer crucial for amphioxus axial development. Instead, Gdf1/3-like assumes this responsibility, likely through hijacking Lefty enhancers. We also showed that amphioxus Nodal has become an indispensable maternal factor to compensate for the loss of maternal Gdf1/3 expression. We therefore demonstrated a case that the evolution of an ancestral GRN could be triggered by enhancer hijacking events. This pivotal event has allowed the emergence of a new GRN in the extant amphioxus, presumably evolving through a stepwise process. The co-expression of Gdf1/3-like and Lefty achieved by shared regulatory region may have provided developmental robustness during body axis formation in extant amphioxus, which provides a selection-based hypothesis for the phenomena called developmental system drift.

evolutionary biology↗

bioRxiv2022

The draft genome sequence of Japanese rhinoceros beetle Trypoxylus dichotomus

Beetles are the largest insect order and one of the most successful animal groups in terms of number of species. The Japanese rhinoceros beetle Trypoxylus dichotomus (Coleoptera, Scarabaeidae, Dynastini) is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10x Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. The detailed genomic and transcriptomic information of T. dichotomus is the most comprehensive among those reported for any species of Dynastinae. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.

genomics↗

bioRxiv2023

A fitness landscape instability governs the morphological diversity of tip-growing cells

Cellular morphology affects many aspects of cellular and organismal physiology. This makes it challenging to understand the evolutionary basis for specific morphologies since the various facets of cellular physiology may exert competing selective pressures on this trait. The influence of these pressures, moreover, will depend on the mechanisms of cellular morphogenesis. To address this problem, we combined experimental cell biology with mechanics-based theory to analyze the morphological diversity of tip-growing cells from across the tree of life. We discovered that an instability in the convergent mechanism of "inflationary" growth shared by these cells leads directly to a bifurcation in their fitness landscape, which imposes a strong global constraint on their morphologies. Additionally, we found that co-selection for cell size and elongation rate explains variation among observable morphologies. This analysis rationalizes the morphology - and provides quantitative insight into the ecology - of an enormous diversity of important fungal, plant, protistan, and bacterial systems. Additionally, our study elucidates a fundamental principle of evolutionary-developmental biology that would be difficult to rigorously demonstrate in more complex systems.

cell biology↗

bioRxiv2025

Analysis of duplication and possible sub-functionalization of wing gene network components in pea aphids

A fundamental focus of evolutionary-developmental biology is uncovering the genetic mechanisms responsible for the gain and loss of characters. One approach to this question is to investigate changes in the coordinated expression of a group of genes important for the development of a character of interest (a gene regulatory network). Here we consider the possibility that modifications to the wing gene regulatory network (wGRN), as defined by work primarily done in Drosophila melanogaster, were involved in the evolution of wing dimorphisms of the pea aphid (Acyrthosiphon pisum). We hypothesize that this may have occurred via changes in expression levels or duplication followed by sub-functionalization of wGRN components. To test this, we annotated members of the wGRN in the pea aphid genome and assessed their expression levels in first and third nymphal instars of winged and wingless morphs of males and asexual females. We find that only two of the 32 assessed genes exhibit morph-biased expression. We also find that three wing genes (apterous (ap), warts (wts), and decapentaplegic (dpp)) have undergone gene duplication. In each case, the resulting paralogs show signs of functional divergence, exhibiting either sex-, morph-, or stage-specific expression. Two gene duplicates, wts2 and dpp3, are of particular interest with respect to wing dimorphism, as they exhibit a wingless male-specific isoform and wingless male-biased expression, respectively. These results supplement our understanding of trends in developmental gene network evolution, such as side-stepping pleiotropic constraint via duplication and sub-functionalization, underlying the emergence of novel phenotypes.

evolutionary biology↗

bioRxiv2016

How domain growth is implemented determines the long term behaviour of a cell population through its effect on spatial correlations.

Domain growth plays an important role in many biological systems, and so the inclusion of domain growth in models of these biological systems is important to understanding how these biological systems function. In this work we present methods to include the effects of domain growth on the evolution of spatial correlations in a continuum approximation of a lattice-based model of cell motility and proliferation. We show that, depending on the way in which domain growth is implemented, different steady-state densities are predicted for an agent population. Furthermore, we demonstrate that the way in which domain growth is implemented can result in the evolution of the agent density depending on the size of the domain. Continuum approximations that ignore spatial correlations cannot capture these behaviours, while those that account for spatial correlations do. These results will be of interest to researchers in developmental biology, as they suggest that the nature of domain growth can determine the characteristics of cell populations.

Systems Biology↗

bioRxiv2024

Non-invasive laser speckle imaging of extra-embryonic blood vessels in intact few-days-old avian eggs

Imaging blood vessels in early-stage avian embryos has a wide range of practical applications for developmental biology studies, drug and vaccine testing, and early sex determination. Optical imaging such as brightfield transmission imaging offers a compelling solution due to its safe non-ionizing radiation, and operational benefits. However, it comes with challenges such as eggshell opacity and light scattering. To address these, we have revisited an approach based on laser speckle contrast imaging (LSCI) and demonstrated a high quality, comprehensive and non-invasive visualization of blood vessels in few-days-old chicken eggs, with blood vessel as small as 100 {micro}m in diameter (with LSCI profile full-width-at-half-maximum of 275 {micro}m). We present its non-invasive use for monitoring blood flow, measuring the embryos heartbeat, and determining the embryos developmental stages using machine learning with 85% accuracy from stage HH15 to HH22. This method can potentially be used for non-invasive longitudinal studies of cardiovascular development and angiogenesis, as well as egg screening for the poultry industry.

bioengineering↗

bioRxiv2017

Manuscript 101: A Data-Driven Writing Exercise For Beginning Scientists

Learning to write a scientific manuscript is one of the most important and rewarding scientific training experiences, yet most young scientists only embark on this experience relatively late in graduate school, after gathering sufficient data in the lab. Yet, familiarity with the process of writing a scientific manuscript and receiving peer reviews, often leads to a more focused and driven experimental approach. To jump-start this training, we developed a protocol for teaching manuscript writing and reviewing in the classroom, appropriate for new graduate or upper-level undergraduate students of developmental biology. First, students are provided one of four cartoon data sets, which are focused on genetic models of animal development. Students are instructed to use their creativity to convert evidence into argument, and then to integrate their interpretations into a manuscript, including an illustrated, mechanistic model figure. After student manuscripts are submitted, manuscripts are redacted and distributed to classmates for peer review. Here, we present our cartoon datasets, homework instructions, and grading rubrics as a new resource for the scientific community. We also describe methods for developing new datasets so that instructors can adapt this activity to other disciplines. Our data-driven manuscript writing exercise, as well as the formative and summative assessments resulting from the peer review, enables students to learn fundamental concepts in developmental genetics. In addition, students practice essential skills of scientific communication, including arguing from evidence, developing and testing models, the unique conventions of scientific writing, and the joys of scientific story telling.

scientific communication and education↗

bioRxiv2022

Matrix-seq: An adjustable-resolution spatial transcriptomics via microfluidic matrix-based barcoding.

Spatial transcriptomics technology complements the spatial information lost in single-cell RNA sequencing, which enables visualization and quantitative analysis of transcriptomics of cells in tissue sections. Although this technology is a promising tool to study complex biological processes, its popularization is limited by cumbersome barcoding steps. We presented a microfluidics-based barcoding strategy called Matrix-seq, which gets rid of both precision instruments and the in situ indexing. The deterministic barcoding matrix is fabricated by the crossflow of Barcode-X and Barcode-Y. The overlapping areas (spot) formed deterministic barcoding primers (Barcode-X-Y) via the ligation reaction. Matrices with different spot size (ranging from 10 to 50 m), which was decided by the width of microchannels, were fabricated and then applied to a mouse main olfactory bulb section and a mouse brain section. While maintaining high performance and resolution, this technology greatly reduces the technical threshold and cost of spatial barcoding. As a result, Matrix-seq can be rapidly applied in various fields including developmental biology, neuroscience and clinical pathology. TeaserMatrix-seq provides an orthogonal microchannel-based barcoding strategy for adjustable-resolution spatial transcriptomics.

bioengineering↗

bioRxiv2025

A highly efficient knock-in strategy using fast-annealed 3'-extended dsDNA templates for emerging model insects

CRISPR-Cas genome editing toolkits have expanded the scope of genetic studies in various emerging model organisms. However, their applications are limited mainly to knockout experiments due to technical difficulties in establishing knock-in strains, which enable in vivo molecular tagging-based experiments. Here, we investigated knock-in strategies in the harlequin ladybug Harmonia axyridis, a model insect for evolutionary developmental biology, which shows more than 200 color pattern variations within a species. We tested several knock-in strategies using synthetic DNA templates. We found that ssDNA templates generated founder knock-in strains efficiently (2.5-11%), whereas the 5 regions of ssDNA templates were frequently deleted when the insert length exceeded [~]40 bases. To overcome this limitation, we designed several 3 extended DNA templates. Fast-annealed 3-extended double-stranded DNA templates, which were designed for tagging endogenous proteins with epitope tags, showed high founder generation efficiency (9.9-20.9%) and accuracy (30.8-85.7%). This strategy is also applicable to the two-spotted cricket Gryllus bimaculatus, suggesting that the fast-annealed 3-extended dsDNA template is a versatile DNA template for generating knock-in strains in emerging model insects for developmental genetic studies. Summary statementFast-annealed 3-extended dsDNA templates facilitate efficient CRISPR-Cas9-mediated knock-in in emerging model insects.

bioengineering↗

bioRxiv2025

Evolutionary Analysis of Gene-expression Localization in the Model Crustacean, Daphnia pulex

Whole-genome sequencing provides lists of genes of putative relevance to organismal biology. However, in all metazoans, a large fraction of inferred genes has no known functions, in some cases with no orthologs in related species, and even orthology at the DNA-sequence level often not providing indisputable evidence of gene function. A first step towards resolving the functional features of gene encyclopedias in multicellular species is to evaluate the tissues in which individual genes are expressed. Here, we report on assays of expression for the full sets of protein-coding and long-noncoding RNA (lncRNA) genes across eight tissues of the microcrustacean Daphnia pulex. We also take advantage of a large database on levels of polymorphism and divergence for each gene to infer various features of selection operating on genes expressed in different tissues, including novel genes restricted to particular Daphnia lineages. In addition to generating a resource for future work on the molecular, cellular, and developmental biology of the model species D. pulex, this study highlights a number of novel findings. These include the identification of sets of genes experiencing unusual forms of positive selection, the discovery of unusual patterns of evolution in the pool of testes-specific genes, rapid turnover and sequence evolution of lncRNA genes, and the pervasive operation of selection on genes thought to be D. pulex-specific.

evolutionary biology↗

bioRxiv2020

Transcribed germline-limited coding sequences in Oxytricha trifallax

The germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein coding sequences whose gene expression is terminated by DNA elimination.

genomics↗

bioRxiv2025

Nucleosome positioning and sensitivity suggest novel functional organization of the purple sea urchin (Strongylocentrotus purpuratus) genome

The eukaryotic nucleosome is the fundamental subunit of chromatin and plays functional roles in DNA templated processes, including replication and transcription. In eukaryotic promoters, nucleosome organization is highly structured, with nucleosomes occupying canonical positions flanking the transcription start site (TSS), thereby regulating access of the transcriptional machinery to the underlying DNA. We determine whether this canonical distribution is present in the purple sea urchin, Strongylocentrotus purpuratus, a species of ecological importance and a model organism for developmental biology and climate science. We used titrations of micrococcal nuclease to produce high throughput maps of nucleosome distribution and sensitivity to digestion from female urchin gonad tissue. Unlike yeast, flies, zebrafish, maize, mice or humans, urchins have extended nucleosome repeat lengths and lack a nucleosome depleted region over TSSs. Urchin promoters are dominated by strongly positioned and highly occupied +1 and +2 nucleosomes which are most prominent in highly expressed genes. Additionally, urchin promoters exhibit distinct patterns of susceptibility to nuclease digestion, with heightened sensitivity upstream of the TSS and limited resistance to nuclease digestion. Discretely positioned sensitive nucleosomes were enriched in promoters of highly expressed genes, suggesting a relationship between nucleosome sensitivity and transcriptional regulation. Collectively, we present a comprehensive overview of the unique interplay between nucleosome positioning and chromatin sensitivity in sea urchins. Our study not only provides a better understanding of dynamics of gene expression in a key developmental organism, but also reveals potential heterogeneity in a key structural property of chromatin previously thought to be homogeneous in model eukaryotes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/653534v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@c724dforg.highwire.dtl.DTLVardef@45c163org.highwire.dtl.DTLVardef@19b6043org.highwire.dtl.DTLVardef@1ccf475_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2026

New chromosome-level haplotyped genome assemblies and annotation for the Japanese Quail (Coturnix Japonica)

The Japanese quail (Coturnix japonica) is a widely used model organism in developmental biology, genetics, and agriculture. Here, we present new, haplotyped, high-quality genome assemblies of the Japanese quail, generated using a combination of state-of-the-art sequencing technologies, including PacBio HiFi long reads, Oxford Nanopore sequencing, and Hi-C scaffolding. This assembly has a total length of 1.19 Gb, 80% of which is included in chromosomes, and is highly complete (BUSCO score aves_odb10: 97.3). Assembly metrics show a marked improvement in contiguity, with a significantly higher scaffold N50 and a lower number of contigs compared to the reference genome assembly. Remarkably, the assembly extends previously truncated chromosome ends, with 31 telomeres detected. In addition, we merged the existing Ensembl and Refseq annotations and obtained a combined set of 26,102 genes, of which 25,038 genes were successfully mapped on the improved assembly haplotype 1 (Cjap1.hap1). Together, these new genome assemblies and their enriched annotation provide a robust genomic framework for future research. They enhance our ability to investigate developmental processes, genetic and epigenetic inheritance, and host-pathogen interactions. Furthermore, they offer valuable insights for conservation genetics and sustainable breeding programs. This resource represents a critical step forward in leveraging the full potential of the Japanese quail as a model species in both basic and applied research.

genomics↗