Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.21.213843v1?rss=1

Authors: Kugler, E. C., Rampun, A., Chico, T., Armitage, P.

Abstract:

Light sheet fluorescent microscopy allows imaging of zebrafish vascular development in great detail. However, interpretation of data often relies on visual assessment and approaches to validate image analysis steps are broadly lacking. Here, we compare different enhancement and segmentation approaches to extract the zebrafish cerebral vasculature, provide comprehensive validation, study segmentation robustness, examine sensitivity, apply the validated method to quantify embryonic cerebrovascular volume, and examine applicability to different transgenic reporter lines. The best performing segmentation method was used to train different deep learning networks for segmentation. We found that U-Net based architectures outperform SegNet. While there was a slight overestimation of vascular volume using the U-Net methodologies, variances were low, suggesting that sensitivity to biological changes would still be obtained.

HighlightsO_LIGeneral filtering is less applicable than Sato enhancement to enhance zebrafish cerebral vessels.

C_LIO_LIBiological data sets help to overcome the lack of segmentation gold-standards and phantom models.

C_LIO_LISato enhancement followed by Otsu thresholding is highly accurate, robust, and sensitive.

C_LIO_LIDirect generalization of the segmentation approach to transgenics, other than the one optimized for, should be treated with caution.

C_LIO_LIDeep learning based segmentation is applicable to the zebrafish cerebral vasculature, with U-Net based architectures outperforming SegNet architectures.

C_LI

Graphical Abstract

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.21.214692v1?rss=1

Authors: Chakravarti, A., Thirimanne, H. N., Calvi, B. R.

Abstract:

p53 gene family members in humans and other organisms encode a large number of protein isoforms whose functions are largely undefined. Using Drosophila as a model, we find that a p53B isoform is expressed predominantly in the germline where it colocalizes with p53A into subnuclear bodies. It is only p53A, however, that mediates the apoptotic response to ionizing radiation in the germline and soma. In contrast, p53A and p53B both respond to meiotic DNA breaks and are required during oogenesis to prevent persistent germline DNA breaks, an activity that is more crucial when meiotic recombination is defective. We find that in oocytes with persistent DNA breaks p53A is required to activate a meiotic pachytene checkpoint. Our findings indicate that Drosophila p53 isoforms have DNA lesion and cell type-specific functions, with parallels to the functions of mammalian p53 family members in the genotoxic stress response and oocyte quality control.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.22.215962v1?rss=1

Authors: Yee, M., Cohen, E. D., Haak, J., Dylag, A. M., O'Reilly, M. A.

Abstract:

The severity of COVID-19 lung disease is higher in the elderly and people with pre-existing co-morbidities. People who were born preterm may be at greater risk for COVID-19 because their early exposure to oxygen at birth increases their risk of being hospitalized when infected with RSV and other respiratory viruses. Our prior studies in mice showed how high levels of oxygen (hyperoxia) between postnatal days 0-4 increases the severity of influenza A virus infections by reducing the number of alveolar epithelial type 2 (AT2) cells. Because AT2 cells express the SARS-CoV-2 receptors angiotensin converting enzyme (ACE2) and transmembrane protease/serine subfamily member 2 (TMPRSS2), we expected their expression would decline as AT2 cells were depleted by hyperoxia. Instead, we made the surprising discovery that expression of Ace2 and Tmprss2 mRNA increases as mice age and is accelerated by exposing mice to neonatal hyperoxia. ACE2 is primarily expressed at birth by airway Club cells and becomes detectable in AT2 cells by one year of life. Neonatal hyperoxia increases ACE2 expression in Club cells and makes it detectable in 2-month-old AT2 cells. This early and increased expression of SARS-CoV-2 receptors was not seen in adult mice who had been administered the mitochondrial superoxide scavenger mitoTEMPO during hyperoxia. Our finding that early life insults such as hyperoxia enhances the age-dependent expression of SARS-CoV-2 receptors in the respiratory epithelium helps explain why COVID-19 lung disease is greater in the elderly and people with pre-existing co-morbidities.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.20.211342v1?rss=1

Authors: Esteves de Lima, J., Blavet, C., Bonnin, M.-A., Hirsinger, E., Comai, G., Yvernogeau, L., Bellenger, l., Mella, S., Nassari, S., Robin, C., Schweitzer, R., Fournier-Thibault, C., Tajbakhsh, S., Relaix, F., DUPREZ, D.

Abstract:

Positional information driving limb muscle patterning is contained in lateral plate mesoderm-derived tissues, such as tendon or muscle connective tissue but not in myogenic cells themselves. The long-standing consensus is that myogenic cells originate from the somitic mesoderm, while connective tissue fibroblasts originate from the lateral plate mesoderm. We challenged this model using cell and genetic lineage tracing experiments in birds and mice, respectively, and identified a subpopulation of myogenic cells at the muscle tips close to tendons originating from the lateral plate mesoderm and derived from connective tissue gene lineages. Analysis of single-cell RNA-sequencing data obtained from limb cells at successive developmental stages revealed a subpopulation of cells displaying a dual muscle and connective tissue signature, in addition to independent muscle and connective tissue populations. Active BMP signalling was detected in this junctional cell sub-population and at the tendon/muscle interface in developing limbs. BMP gain- and loss-of-function experiments performed in vivo and in vitro showed that this signalling pathway regulated a fibroblast-to-myoblast conversion. We propose that localised BMP signalling converts a subset of lateral plate mesoderm-derived fibroblasts to a myogenic fate and establishes a boundary of fibroblast-derived myonuclei at the muscle/tendon interface to control the muscle pattern during limb development.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.21.213512v1?rss=1

Authors: Tyser, R. C. V., Mahammadov, E., Nakanoh, S., Vallier, L., Scialdone, A., Srinivas, S.

Abstract:

Gastrulation is the fundamental process during the embryogenesis of all multicellular animals through which the basic body plan is first laid down. It is pivotal in generating cellular diversity coordinated with spatial patterning. Gastrulation in humans occurs in the third week following fertilization. Our understanding of this process in humans is extremely limited, and based almost entirely on experimental models. Here, we characterize in a spatially resolved manner the single cell transcriptional profile of an entire gastrulating human embryo approximately 16 to 19 days after fertilization. We used these data to provide the first unequivocal demonstration that human embryonic stem cells represent the early post implantation epiblast. We identified both primordial germ cells and red blood cells, which had never been characterized so early during human development. Comparison with mouse gastrula transcriptomes revealed many commonalities between the human and mouse but also several key differences, particularly in FGF signaling, that we validated experimentally. This unique dataset offers a unique glimpse into a central but generally inaccessible stage of our development, provides new context for interpreting experiments in other model systems and represents a valuable resource for guiding directed differentiation of human cells in vitro.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.20.213199v1?rss=1

Authors: Yaseen-Badarneh, W., Kraft-Sheleg, O., Zaffryar-Eilot, S., Melamed, S., Sun, C., Millay, D., Hasson, P.

Abstract:

Vertebrate muscles and tendons are derived from distinct embryonic origins yet they must interact in order to facilitate muscle contraction and body movements. How robust muscle tendon junctions (MTJs) form to be able to withstand contraction forces is still not understood. Using techniques at a single cell resolution we reexamined the classical view of distinct identities for the tissues composing the musculoskeletal system. We identified fibroblasts that have switched on a myogenic program and demonstrate these dual identity cells fuse into the developing muscle fibers along the MTJs facilitating the introduction of fibroblast-specific transcripts into the elongating myofibers. We suggest this mechanism resulting in a hybrid muscle fiber, primarily along the fiber tips, enables a smooth transition from muscle fiber characteristics towards tendon features essential for forming robust MTJs. We propose that dual characteristics of junctional cells could be a common mechanism for generating stable interactions between tissues throughout the musculoskeletal system.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.21.213561v1?rss=1

Authors: Kubota, Y., Ohnishi, Y., Hamasaki, T., Yasui, G., Ota, N., Kitagawa, H., Esaki, A., Fahmi, M., Ito, M.

Abstract:

Histone deacetylases (HDACs) are divided into four classes. Class-I HDAC, HDAC-1 forms three types of complexes, namely the Nucleosome Remodeling Deacetylase complex, the Sin3 complex, and the CoREST complex, with specific corepressor component Mi2/CHD-3, Sin3, and RCOR1 in human, respectively. The functions of these HDAC-1 complexes are regulated by their corepressors, however, their exact mechanistic roles in several biological processes remain unexplored, such as in embryonic development. Here, we report that each of the corepressors, LET-418, SIN-3, and SPR-1, the homologous of Mi2, Sin3, and RCOR1, respectively, were expressed throughout Caenorhabditis elegans embryonic development and served essential roles in the process. Moreover, genetic analysis suggested that three pathways (i.e., LET-418- SIN-3-SPR-1, SIN-3-SPR-1, and LET-418) participated in embryonic development. Our terminal-phenotype observations of single mutants of each corepressor implied that LET-418, SIN-3, and SPR-1 played similar roles in promoting advancement to the middle and late embryonic stages. Genome-wide comparative-transcriptome analysis indicated that 47.5% and 42.3% of genes were commonly increased and decreased in sin-3 and spr-1 mutants, respectively. These results suggest that among the three pathways studied, the SIN-3-SPR-1 pathway mainly serves to regulate embryonic development. Comparative-Gene Ontology analysis indicated that these three pathways played overlapping and distinct roles in regulating C. elegans embryonic development.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.19.211383v1?rss=1

Authors: Kimura, T., Saito, H., Kawsaki, M., Takeichi, M.

Abstract:

Microtubules (MTs) regulate numerous cellular processes, but their roles in brain morphogenesis are not well known. Here we show that CAMSAP3, a non-centrosomal microtubule regulator, is important for shaping the lateral ventricles. In differentiating ependymal cells, CAMSAP3 became concentrated at the apical domains, serving to generate MT networks at these sites. Camsap3-mutated mice showed abnormally narrow lateral ventricles, in which excessive stenosis or fusion was induced, leading to a decrease of neural stem cells at the ventricular and subventricular zones. This defect was ascribed at least in part to a failure of neocortical ependymal cells to broaden their apical domain, a process necessary for expanding the ventricular cavities. mTORC1 was required for ependymal cell growth but its activity was downregulated in mutant cells. Lysosomes, which mediate mTORC1 activation, tended to be reduced at the apical regions of the mutant cells, along with disorganized apical MT networks at the corresponding sites. These findings suggest that CAMSAP3 supports mTORC1 signaling required for ependymal cell growth via MT network regulation, and, in turn, shaping of the lateral ventricles.

Summary statementCAMSAP3, which mediates non-centrosomal microtubule assembly, is required for mTORC1-dependent maturation of ependymal cells at the neocortex of developing mouse brains. Loss of CAMSAP3 causes deformation of the lateral ventricles.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.20.212282v1?rss=1

Authors: Moreno-Ayala, R., Olivares-Chauvet, P., Schäfer, R., Junker, J. P.

Abstract:

Embryonic development seemingly proceeds with almost perfect precision. However, it is largely unknown how much microscopic variability is hidden beneath this macroscopic accuracy. Here, we quantified embryo-to-embryo variability in vertebrate development, by studying cell number variation in the zebrafish endoderm. We noticed that the size of a subpopulation of the endoderm, the dorsal forerunner cells (which later form the left-right organizer), is highly variable between individual embryos. We found that the frequency of left-right laterality defects is increased drastically in embryos with a low number of dorsal forerunner cells, and we observed that these fluctuations are largely nonhereditary. Hence, a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be caused by variable deposition of maternal factors involved in specification of the dorsal forerunner cells. In summary, we here dissect cause and consequence of embryo-to-embryo variability in a vertebrate model.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.19.210658v1?rss=1

Authors: Cole, A. G., Kaul, S., Jahnel, S. M., Steger, J., Zimmermann, B., Reischl, R., Richards, G. S., Rentzsch, F., Steinmetz, P., Technau, U.

Abstract:

The evolutionary mechanisms underlying the emergence of new cell types are still unclear. Here, we address the origin and diversification of muscle cells in the diploblastic sea anemone Nematostella vectensis. We discern two fast and two slow-contracting muscle cell populations in Nematostella differing by extensive sets of paralogous genes. The regulatory gene set of the slow cnidarian muscles and the bilaterian cardiac muscle are remarkably similar. By contrast, the two fast muscles differ substantially from each other, while driving the same set of paralogous structural protein genes. Our data suggest that extensive gene duplications and co-option of individual effector modules may have played an important role in cell type diversification during metazoan evolution.

One Sentence SummaryThe study of the simple sea anemone suggests a molecular mechanism for cell type evolution and morphological complexity.

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