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Results for “Developmental Biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 667 records · Page 37Linked to original sources

bioRxiv2018

Positional information specifies the site of organ regeneration and not tissue maintenance in planarians

Most animals undergo homeostatic tissue maintenance, yet those capable of robust regeneration in adulthood use mechanisms significantly overlapping with homeostasis. Here we show in planarians that modulations to body-wide patterning systems shift the target site for eye regeneration while still enabling homeostasis of eyes outside this region. The uncoupling of homeostasis and regeneration, which can occur during normal positional rescaling after axis truncation, is not due to altered injury signaling or stem cell activity, nor specific to eye tissue. Rather, pre-existing tissues, which are misaligned with patterning factor expression domains, compete with properly located organs for incorporation of migratory progenitors. These observations suggest that patterning factors determine sites of organ regeneration but do not solely determine the location of tissue homeostasis. These properties provide candidate explanations for how regeneration integrates pre-existing tissues and how regenerative abilities could be lost in evolution or development without eliminating long-term tissue maintenance and repair.\n\nOne Sentence SummaryHomeostatic tissue maintenance can occur independent of precise positional information in planarians.

developmental biology↗

bioRxiv2018

Auxin is not asymmetrically distributed in initiating Arabidopsis leaves

It has been proposed that asymmetric auxin levels within initiating leaves help establish leaf polarity, based in part on observations of the DII auxin sensor. Here we show that the mDII control sensor also exhibits an asymmetry and that according to the ratio-metric auxin sensor R2D2, no obvious asymmetry in auxin exists. Together with other recent findings, our results argue against the importance of auxin asymmetry in establishing leaf polarity.

developmental biology↗

bioRxiv2018

Effects of larval density on gene regulation in C. elegans during routine L1 synchronization

Bleaching gravid C. elegans followed by a short period of starvation of the L1 larvae is a routine method performed by worm researchers for generating synchronous populations for experiments. During the process of investigating dietary effects on gene regulation in L1 stage worms by single-worm RNA-Seq, we found that the density of resuspended L1 larvae affects expression of many mRNAs. Specifically, a number of genes related to metabolism and signalling are highly expressed in worms arrested at low density, but are repressed at higher arrest densities. We generated a GFP reporter strain based on one of the most density-dependent genes in our dataset - lips-15 - and confirmed that this reporter was expressed specifically in worms arrested at relatively low density. Finally, we show that conditioned media from high density L1 cultures was able to downregulate lips-15 even in L1 animals arrested at low density, and experiments using daf-22 mutant animals demonstrated that this effect is not mediated by the ascaroside family of signalling pheromones. Together, our data implicate a soluble signalling molecule in density sensing by L1 stage C. elegans, and provide guidance for design of experiments focused on early developmental gene regulation.

developmental biology↗

bioRxiv2018

Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

In situ hybridization based on the mechanism of hybridization chain reaction (HCR) has addressed multi-decade challenges to imaging mRNA expression in diverse organisms, offering a unique combination of multiplexing, quantitation, sensitivity, resolution, and versatility. Here, with third-generation in situ HCR, we augment these capabilities using probes and amplifiers that combine to provide automatic background suppression throughout the protocol, ensuring that even if reagents bind non-specifically within the sample they will not generate amplified background. Automatic background suppression dramatically enhances performance and robustness, combining the benefits of higher signal-to-background with the convenience of using unoptimized probe sets for new targets and organisms. In situ HCR v3.0 enables multiplexed quantitative mRNA imaging with subcellular resolution in the anatomical context of whole-mount vertebrate embryos, multiplexed quantitative mRNA flow cytometry for high-throughput single-cell expression profiling, and multiplexed quantitative single-molecule mRNA imaging in thick autofluorescent samples.\n\nSUMMARYIn situ hybridization chain reaction (HCR) v3.0 exploits automatic background suppression to enable multiplexed quantitative mRNA imaging and flow cytometry with dramatically enhanced ease-of-use and performance.

developmental biology↗

bioRxiv2018

Sequential regulation of maternal mRNAs through a conserved cis-acting element in their 3’UTRs

Maternal mRNAs are synthesized during oogenesis to initiate the development of future generations. Some maternal mRNAs are determinants of somatic or germline fate and must be translationally repressed until embryogenesis. However, the translational repressors themselves are also temporally regulated. We use polar granule component (pgc), a Drosophila maternal mRNA, as a model system to ask how maternal mRNAs are repressed while the regulatory landscape is continually shifting. pgc, a potent transcriptional silencer and germline determinant, is translationally regulated throughout oogenesis. We find that the 3UTR of pgc mRNA contains a conserved ten-nucleotide sequence that is bound by different conserved RNA binding proteins (RBPs) at different stages of oogenesis to continuously repress translation except for a brief expression in the stem cell daughter. Pumilio (Pum) binds to this sequence in undifferentiated and early differentiating oocytes and recruits other temporally restricted translational regulators to block pgc translation. After differentiation, Pum levels diminish and Bruno (Bru) levels increase, allowing Bru to bind the same 3UTR sequence and take over translational repression of pgc mRNA. We have identified a class of maternal mRNAs regulated during oogenesis by both Pum and Bru, including Zelda, activator of the zygotic genome, which contain this core 10-nt regulatory sequence. Our data suggests that this hand off mechanism is more generally utilized to inhibit translation of maternal mRNAs during oogenesis.

developmental biology↗

bioRxiv2018

Positional information encoded in the dynamic differences between neighbouring oscillators during vertebrate segmentation.

How cells track their position during the segmentation of the vertebrate body remains elusive. For decades, this process has been interpreted according to the clock-and-wavefront model, where molecular oscillators set the frequency of somite formation while the positional information is encoded in signaling gradients. Recent experiments using ex vivo explants challenge this interpretation, suggesting that positional information is encoded in the properties of the oscillators. Here, we propose that positional information is encoded in the differential levels of neighboring oscillators. The differences gradually increase because both the oscillator amplitude and the period increase with time. When this difference exceeds a certain threshold, the segmentation program starts. Using this framework, we quantitatively fit experimental data from in vivo and ex vivo mouse segmentation, and propose mechanisms of somite scaling. Our results suggest a novel mechanism of spatial pattern formation based on the local interactions between dynamic molecular oscillators.

developmental biology↗

bioRxiv2018

Label-free assessment of pre-implantation embryo quality by the Fluorescence Lifetime Imaging Microscopy (FLIM)-phasor approach

Development of quantitative, safe and rapid techniques for assessing embryo quality provides significant advances in Assisted Reproductive Technologies (ART). We apply the phasor-FLIM method to capture endogenous fluorescent biomarkers of pre-implantation embryos as a non-morphological caliber for embryo quality. Here, we identify the developmental, or \"D-trajectory\", that consists of fluorescence lifetime from different stages of mouse pre-implantation embryos. The D-trajectory correlates with intrinsic fluorescent species from a distinctive energy metabolism and oxidized lipids, as seen with Third Harmonic Generation (THG) that changes over time. In addition, we have defined an Embryo Viability Index (EVI) to distinguish pre-implantation embryo quality using the Distance Analysis, a machine learning algorithm to process the fluorescence lifetime distribution patterns. We show that the phasor-FLIM approach provides a much-needed non-invasive quantitative technology for identifying healthy embryos at the early compaction stage with 86% accuracy. This may increase embryo implantation success for in vitro fertilization clinics.\n\nHighlightsO_LIA label-free method of tracking metabolic trajectories during pre-implantation mouse embryo development.\nC_LIO_LIA non-invasive approach for assessing embryo quality and viability by a phasor-FLIM analysis.\nC_LI

developmental biology↗

bioRxiv2018

Developmental genetics in a complex adaptive structure, the weevil rostrum

The rostrum of weevils (Curculionidae) is a novel, complex, adaptive structure that has enabled this huge beetle radiation to feed on and oviposit in a wide spectrum of plant hosts, correlated with diverse life histories and tremendous disparity in rostrum forms. In order to understand the development and evolution of this structure, transcriptomes were produced in de novo assemblies from the developing pre-pupal head tissues of two distantly related curculionids, the rice weevil (Sitophilus oryzae) and the mountain pine beetle (Dendroctonus ponderosae), which have highly divergent rostra. While there are challenges in assessing differences among transcriptomes and in relative gene expression from divergent taxa, tests for differential expression patterns of transcripts yielded lists of candidate genes to examine in future work. RNA interference was performed with S. oryzae for functional insight into the Hox gene Sex combs reduced. Scr has a conserved function in labial and prothoracic identities, but it also demonstrates a novel role in reduction of ventral head structures, namely the gula, submentum, and associated sulci, in weevils. Ultimately, this study makes strides towards elucidating how the weevil rostrum initially formed and the profound phenotypic diversity it has acquired throughout the curculionoid lineages. It furthermore initiates a better understanding of the genetic framework that permitted the diversification of such an immense lineage as the weevils.\n\nSummary statementThis study begins exploring the development of a novel, complex structure in one of the largest families of organisms, the weevils.

developmental biology↗

bioRxiv2018

A novel cell segmentation method for developing embryos using machine learning

Cell segmentation is crucial in the study of morphogenesis in developing embryos, but it is limited in its accuracy. In this study we provide a novel method for cell segmentation using machine-learning, termed Cell Segmenter using Machine Learning (CSML). CSML performed better than state-of-the-art methods, such as RACE and watershed, in the segmentation of ectodermal cells in the Xenopus embryo. CSML required only one whole embryo image for training a Fully Convolutional Network classifier, and it took 20 seconds per each image to return a segmented image. To validate its accuracy, we compared it to other methods in assessing several indicators of cell shape. We also examined the generality by measuring its performance in segmenting independent images. Our data demonstrates the superiority of CSML, and we expect this application to significantly improve efficiency in cell shape studies.

developmental biology↗

bioRxiv2018

Cell-lineage specificity of primary cilia during epididymis post-natal development

Primary cilia are sensory organelles that orchestrate major signaling pathways during organ development and homeostasis. By using a double Arl13b/mCherry-Cetn2/GFP transgenic mouse model, we characterized the spatio-temporal localization of primary cilia in the epididymis, from birth to adulthood. We report here a constitutive localisation of primary cilia in peritubular myoid cells and a dynamic profiling in differentiated epithelial cells throughout post-natal development. While primary cilia are present at the apical pole of the undifferentiated epithelial cells from birth to puberty, they are absent from the apical pole of the epithelium in adults, where they appear exclusively associated with cytokeratin 5-positive basal cells. Exogenous labeling of primary cilia marker Arl13b and IFT88 confirmed the cell lineage specific localization of primary cilia in basal cells and myoid cells in human epididymides. From whole epididymis tissues and serum-free cultures of DC2 murine epididymal principal cell lines we determined that primary cilia from the epididymis are associated with the polycystic kidney disease-related proteins polycystin 1 (PC1) and polycystin 2 (PC2), and Gli3 Hedgehog signaling transcription factor. Thus, our findings unveil the existence of primary cilia sensory organelles, which have the potential to mediate mechano/ chemo-signaling events in the epididymis.

developmental biology↗

bioRxiv2018

Small non-coding RNA expression in developing mouse nephron progenitor cells

MicroRNAs (miRNAs) are small non-coding RNAs that are essential for the regulation of gene expression and play critical roles in human health and disease. Here we present comprehensive miRNA profiling data for mouse nephron progenitors, which give rise to most of the cell-types of the nephron, the functional units of the kidney. We describe a miRNA expression profile for nephron progenitors, with 162 miRNAs differentially expressed in nephron progenitors when compared to whole kidney. We also annotated 52, and experimentally validated 4 novel miRNAs, which are expressed in developing kidney. Our data is available as a public resource, so that it can be integrated into future studies and analyzed in the context of other functional and epigenomic data in kidney development. Specifically, it will be useful in the effort to shed light on molecular mechanisms underlying processes essential for normal kidney development, such as nephron progenitor specification, self-renewal and differentiation.

developmental biology↗

bioRxiv2018

Single cell transcriptome profiling of mouse and hESC-derived pancreatic progenitors

Human embryonic stem cells (hESCs) are a potential unlimited source of insulin-producing {beta}-cells for diabetes treatment. A greater understanding of how {beta}-cells form during embryonic development will improve current hESC differentiation protocols. As {beta}-cells are formed from NEUROG3-expressing endocrine progenitors, this study focused on characterizing the single-cell transcriptomes of mouse and hESC-derived endocrine progenitors. To do this, 7,223 E15.5 and 6,852 E18.5 single cells were isolated from Neurog3-Cre; Rosa26mT/mG embryos, allowing for enrichment of endocrine progenitors (yellow; tdTomato + EGFP) and endocrine cells (green; EGFP). From a NEUROG3-2A-eGFP CyT49 hESC reporter line (N5-5), 4,497 hESC-derived endocrine progenitor cells were sequenced. Differential expression analysis reveals enrichment of markers that are consistent with progenitor, endocrine, or novel cell-state populations. This study characterizes the single-cell transcriptomes of mouse and hESC-derived endocrine progenitors and serves as a resource (https://lynnlab.shinyapps.io/embryonic_pancreas/) for improving the formation of functional {beta}-like cells from hESCs.

developmental biology↗

bioRxiv2018

Deep proteomic analysis of chicken erythropoiesis

In contrast to mammalian erythroid cells that lost their nucleus at the end of the differentiation process, circulating chicken erythrocytes, like erythrocytes of most other non-mammalian vertebrates, are nucleated although their nucleus is believed to be transcriptionally silent. This major difference suggests that the erythroid differentiation process is likely to present both similarities and differences in mammals compared to other vertebrates. Since proteins are the major cellular effectors, analysis of the proteome is more prone to reflect true differences than analysis of the pattern of mRNA expression. We have previously reported the evolution of the proteome of human erythroid cells throughout their differentiation process. Here we report the analysis of the proteome of chicken erythroblasts during their terminal differentiation. We used the T2EC cellular model that allows to obtain homogenous populations of immature erythroblasts. Induction of their terminal differentiation led to their maturation and the possibility to obtain cells at different differentiation stages. Mass spectrometry analysis of these cell populations allowed the absolute quantification of 6167 proteins throughout the terminal differentiation process. Beside many proteins with similar expression patterns between chicken and human erythroblasts, like SLC4A1 (Band3), GATA1 or CD44, this analysis also revealed that other important proteins like Kit or other GATA transcription factors exhibit fully different patterns of expression.

developmental biology↗

bioRxiv2018

The lysine demethylase dKDM2 is non-essential for viability, but regulates circadian rhythms in Drosophila

Post-translational modification of histones, such as histone methylation controlled by specific methyltransferases and demethylases, play critical roles in modulating chromatin dynamics and transcription in eukaryotes. Misregulation of histone methylation can lead to aberrant gene expression, thereby contributing to abnormal development and diseases such as cancer. As such, the mammalian lysine-specific demethylase 2 (KDM2) homologs, KDM2A and KDM2B, are either oncogenic or tumor suppressive, depending on specific pathological contexts. However, the role of KDM2 proteins during development in the whole organisms remains poorly understood. Unlike vertebrates, Drosophila has only one KDM2 homolog (dKDM2), but its functions in vivo remain elusive due to the complexities of the existing mutant alleles. To address this problem, we have generated two dKdm2 null alleles using the CRISPR/Cas9 technique. These dKdm2 homozygous mutants are fully viable and fertile, with no developmental defects observed under laboratory conditions. However, the dKdm2 null mutant adults display defects in circadian rhythms. Most of the dKdm2 mutants become arrhythmic under constant darkness, while the circadian period of the rhythmic mutant flies is approximately one hour shorter than the control. Interestingly, opposite defects are observed when dKDM2 is overexpressed in circadian pacemaker neurons. Taken together, these results demonstrate that dKdm2 is not essential for viability; instead, dKDM2 protein plays important roles in regulating circadian rhythms in Drosophila. Further analyses of the molecular mechanisms of how dKDM2 and its orthologs in vertebrates regulate circadian rhythms will advance our understanding of the epigenetic regulations of circadian clocks.

developmental biology↗

bioRxiv2018

Two Active X-chromosomes Modulate the Growth, Pluripotency Exit and DNA Methylation Landscape of Mouse Naive Pluripotent Stem Cells through Different Pathways

During early mammalian development, the two X-chromosomes in female cells are active. Dosage compensation between XX female and XY male cells is then achieved by X-chromosome inactivation in female cells. Reprogramming female mouse somatic cells into induced pluripotent stem cells (iPSCs) leads to X-chromosome reactivation. The extent to which increased X-chromosome dosage (X-dosage) in female iPSCs leads to differences in the molecular and cellular properties of XX and XY iPSCs is still unclear. We show that chromatin accessibility in mouse iPSCs is modulated by X-dosage. Specific sets of transcriptional regulator motifs are enriched in chromatin with increased accessibility in XX or XY iPSCs. We show that the transcriptome, growth and pluripotency exit are also modulated by X-dosage in iPSCs. To understand the mechanisms by which increased X-dosage modulates the molecular and cellular properties of mouse pluripotent stem cells, we used heterozygous deletions of the X-linked gene Dusp9 in XX embryonic stem cells. We show that X-dosage regulates the transcriptome, open chromatin landscape, growth and pluripotency exit largely independently of global DNA methylation. Our results uncover new insights into X-dosage in pluripotent stem cells, providing principles of how gene dosage modulates the epigenetic and genetic mechanisms regulating cell identity.

developmental biology↗

bioRxiv2018

Partial reprogramming induces a steady decline in epigenetic age before loss of somatic identity

Induced pluripotent stem cells (IPSCs), with their unlimited regenerative capacity, carry the promise for tissue replacement to counter age-related decline. However, attempts to realise in vivo iPSC have invariably resulted in the formation of teratomas. Partial reprogramming in prematurely aged mice has shown promising results in alleviating age-related symptoms without teratoma formation. Does partial reprogramming lead to rejuvenation (i.e. \"younger\" cells), rather than dedifferentiation, which bears the risk of cancer? Here we analyse the dynamics of cellular age during human iPSC reprogramming and find that partial reprogramming leads to a reduction in the epigenetic age of cells. We also find that the loss of somatic gene expression and epigenetic age follow different kinetics, suggesting that they can be uncoupled and there could be a safe window where rejuvenation can be achieved with a minimised risk of cancer.

developmental biology↗

bioRxiv2018

Rainbow-seq: combining cell lineage tracking with single-cell RNA sequencing in preimplantation embryos

Single-cell RNA-seq experiments cannot record cell division history and therefore cannot directly connect intercellular differences at a later developmental stage to their progenitor cells. We developed Rainbow-seq to combine cell division lineage tracing with single-cell RNA-seq. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA-seq experiment to simultaneously read single-cell transcriptomes and decode the lineage marker genes. We traced the lineages deriving from each blastomere in two-cell mouse embryos and observed inequivalent contributions to the embryonic and abembryonic poles in 72% of the blastocysts evaluated. Rainbow-seq on four- and eight-cell embryos with lineage tracing triggered at two-cell stage exhibited remarkable transcriptome-wide differences between the two cell lineages at both stages, including genes involved in negative regulation of transcription and signaling. These data provide critical insights on cell fate choices in cleavage embryos. Rainbow-seq bridged a critical gap between cellular division history and single-cell RNA-seq assays.

developmental biology↗

bioRxiv2018

A non-cell autonomous actin redistribution enables isotropic retinal growth

Tissue shape is often established early in development and needs to be scaled isotropically during growth. However, the cellular contributors and ways in which cells interact inside tissues to enable coordinated isotropic tissue scaling are not yet understood. Here, we follow cell and tissue shape changes in the zebrafish retinal neuroepithelium, which forms a cup with a smooth surface early in development and maintains this architecture as it grows. By combining 3D analysis and theory, we show that a global increase in cell height is necessary to maintain this tissue shape during growth. Timely cell height increase is governed by non-cell autonomous actin redistribution. Blocking actin redistribution and cell height increase perturbs isotropic scaling and leads to disturbed, folded tissue shape. Taken together, our data show how global changes in cell shape enable isotropic growth of the developing retinal neuroepithelium, a concept that could also apply to other systems.

developmental biology↗