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the Node is a community blog for and by developmental biologists.

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  • May 18, 2015
  • 04:24 AM

Camelid antibodies go fishing

by Paolo Panza in the Node

Figure 1. “Cytoplasm”, illustration by David S. Goodsell, the Scripps Research Institute.   When contemplating the illustrations by David S. Goodsell (Figure 1), the first thing that stands out is how cells are packed full with those wonderful little machines we call proteins. They move, interact and change shape to produce cellular functions, so our ability […]... Read more »

Panza, P., Maier, J., Schmees, C., Rothbauer, U., & Sollner, C. (2015) Live imaging of endogenous protein dynamics in zebrafish using chromobodies. Development, 142(10), 1879-1884. DOI: 10.1242/dev.118943  

  • May 14, 2015
  • 12:55 AM

Cell motion associated with stemness

by Daisuke Nanba in the Node

Stem cells play crucial roles in development as well as tissue homeostasis, repair, and regeneration, and their dysregulation is involved in diseases and aging of the tissues. The stem cell is defined as a cell that has the ability to self-renew and also to produce differentiated progeny for a long-term. Yet, stem cells require other […]... Read more »

Nanba, D., Toki, F., Matsushita, N., Matsushita, S., Higashiyama, S., & Barrandon, Y. (2013) Actin filament dynamics impacts keratinocyte stem cell maintenance. EMBO Molecular Medicine, 5(4), 640-653. DOI: 10.1002/emmm.201201839  

Nanba, D., Toki, F., Tate, S., Imai, M., Matsushita, N., Shiraishi, K., Sayama, K., Toki, H., Higashiyama, S., & Barrandon, Y. (2015) Cell motion predicts human epidermal stemness. The Journal of Cell Biology, 209(2), 305-315. DOI: 10.1083/jcb.201409024  

  • May 7, 2015
  • 10:15 PM

Adventures in Studying Brain Sex Differences

by BNugent in the Node

by Peg McCarthy and Bridget Nugent The biological phenomenon of hormonally induced sexual differentiation of the brain has been an empirical topic of study for over 50 years1 but much remains to be discovered in terms of both mechanism and functional impact. In the McCarthy lab we exploit the many advantages of the laboratory rat […]... Read more »

Lenz, K., Nugent, B., Haliyur, R., & McCarthy, M. (2013) Microglia Are Essential to Masculinization of Brain and Behavior. Journal of Neuroscience, 33(7), 2761-2772. DOI: 10.1523/JNEUROSCI.1268-12.2013  

Nugent, B., Wright, C., Shetty, A., Hodes, G., Lenz, K., Mahurkar, A., Russo, S., Devine, S., & McCarthy, M. (2015) Brain feminization requires active repression of masculinization via DNA methylation. Nature Neuroscience, 18(5), 690-697. DOI: 10.1038/nn.3988  

  • May 1, 2015
  • 04:16 AM

Neuroblastoma may arise from problems with embryonic nerve development

by lukeawylie in the Node

Neuroblastoma is a tumour derived from the peripheral nervous system and is the most common cancer diagnosed within the first year of life. Although is a fairly rare disease, it does account for 15% of all pediatric cancer deaths. However, neuroblastoma is quite unique in that some, particularly very young, patients spontaneously regress requiring only […]... Read more »

  • April 29, 2015
  • 08:20 AM

Towards a mechanistic understanding of branching innovations in plant evolution.

by Jill Harrison in the Node

Jill Harrison and Yoan Coudert.   The conquest of land by plants was one of the most significant events in our planet’s history, and was underpinned by a series of innovations in plant architecture. Amongst these, the innovation of branching stands out in allowing plants to colonize new volumes of space in the subaerial environment. […]... Read more »

Laenen, B., Shaw, B., Schneider, H., Goffinet, B., Paradis, E., Désamoré, A., Heinrichs, J., Villarreal, J., Gradstein, S., McDaniel, S.... (2014) Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts. Nature Communications, 5134. DOI: 10.1038/ncomms6134  

Bennett, T., Liu, M., Aoyama, T., Bierfreund, N., Braun, M., Coudert, Y., Dennis, R., O’Connor, D., Wang, X., White, C.... (2014) Plasma Membrane-Targeted PIN Proteins Drive Shoot Development in a Moss. Current Biology, 24(23), 2776-2785. DOI: 10.1016/j.cub.2014.09.054  

Coudert, Y., Palubicki, W., Ljung, K., Novak, O., Leyser, O., & Harrison, C. (2015) Three ancient hormonal cues co-ordinate shoot branching in a moss. eLife. DOI: 10.7554/eLife.06808  

Domagalska, M., & Leyser, O. (2011) Signal integration in the control of shoot branching. Nature Reviews Molecular Cell Biology, 12(4), 211-221. DOI: 10.1038/nrm3088  

  • April 1, 2015
  • 02:08 PM

The small beginnings of gastruloids

by Christele Gonneau in the Node

Mouse embryonic stem cells (mESCs) are by definition cells that can self-renew (make identical copies of themselves) and specialize into any cell type of the body. Since their discovery, scientists have used them to produce various specialized cell types in culture but also to produce transgenic mouse lines. When injected into a mouse early embryo, […]... Read more »

van den Brink, S., Baillie-Johnson, P., Balayo, T., Hadjantonakis, A., Nowotschin, S., Turner, D., & Martinez Arias, A. (2014) Symmetry breaking, germ layer specification and axial organisation in aggregates of mouse embryonic stem cells. Development, 141(22), 4231-4242. DOI: 10.1242/dev.113001  

  • February 11, 2015
  • 10:37 AM

How to eradicate an organ

by Manuel Stemmer in the Node

 Phreatichthys andruzzii, lateral view (left), frontal view (right) Adaptations of some fish species to their environment can be most peculiar, especially within cave dwelling kinds. The so called troglomorphisms slowly turn these fish into almost grotesque looking creatures with no eyes, lost pigments and no scales on the one hand, but with enhanced alternative sensory […]... Read more »

  • February 5, 2015
  • 11:15 AM

Specifying stem cells, specifically

by WIMMBlogEditor in the Node

Bone marrow transplants save lives. It’s as simple as that. The reason bone marrow transplants are so effective is because this squishy tissue is home to haematopoietic stem cells (HSCs), which spend their lives happily producing every single blood cell that will ever circulate around your body. As a result, if anything goes wrong with […]... Read more »

Swiers, G., Rode, C., Azzoni, E., & de Bruijn, M. (2013) A short history of hemogenic endothelium. Blood Cells, Molecules, and Diseases, 51(4), 206-212. DOI: 10.1016/j.bcmd.2013.09.005  

Clements, W., Kim, A., Ong, K., Moore, J., Lawson, N., & Traver, D. (2011) A somitic Wnt16/Notch pathway specifies haematopoietic stem cells. Nature, 474(7350), 220-224. DOI: 10.1038/nature10107  

Leung A, Ciau-Uitz A, Pinheiro P, Monteiro R, Zuo J, Vyas P, Patient R, & Porcher C. (2013) Uncoupling VEGFA functions in arteriogenesis and hematopoietic stem cell specification. Developmental cell, 24(2), 144-58. PMID: 23318133  

Wilkinson, R., Pouget, C., Gering, M., Russell, A., Davies, S., Kimelman, D., & Patient, R. (2009) Hedgehog and Bmp Polarize Hematopoietic Stem Cell Emergence in the Zebrafish Dorsal Aorta. Developmental Cell, 16(6), 909-916. DOI: 10.1016/j.devcel.2009.04.014  

Pimanda, J., Donaldson, I., de Bruijn, M., Kinston, S., Knezevic, K., Huckle, L., Piltz, S., Landry, J., Green, A., Tannahill, D.... (2007) The SCL transcriptional network and BMP signaling pathway interact to regulate RUNX1 activity. Proceedings of the National Academy of Sciences, 104(3), 840-845. DOI: 10.1073/pnas.0607196104  

  • January 22, 2015
  • 04:46 PM

Stem cells…now showing in 3D

by Christele Gonneau in the Node

    Growing organs in vitro is one of the ultimate dreams of any stem cell biologist. As such, it seems obvious that some of these organs will need to be grown in 3D. This is why stem cell 3D culture systems are very fashionable among scientists. They are increasingly successful and a fair amount […]... Read more »

Meinhardt, A., Eberle, D., Tazaki, A., Ranga, A., Niesche, M., Wilsch-Bräuninger, M., Stec, A., Schackert, G., Lutolf, M., & Tanaka, E. (2014) 3D Reconstitution of the Patterned Neural Tube from Embryonic Stem Cells. Stem Cell Reports, 3(6), 987-999. DOI: 10.1016/j.stemcr.2014.09.020  

  • January 5, 2015
  • 08:20 AM

The rabbit blastocyst modelling (for) vertebrate gastrulation

by Christoph Viebahn in the Node

Form and function of animal gastrulation have been longstanding classics accompanying the rise of experimental embryology, and – as if to square the circle in the literal sense – the blastopore of Haeckel’s original ‘gastrea’ stage[1] was soon (and still is) considered analogous to the straight primitive streak of birds and mammals[2-4]. Both forms are […]... Read more »

Bertocchini, F., Alev, C., Nakaya, Y., & Sheng, G. (2013) A little winning streak: The reptilian-eye view of gastrulation in birds. Development, Growth , 55(1), 52-59. DOI: 10.1111/dgd.12014  

Osteil, P., Tapponnier, Y., Markossian, S., Godet, M., Schmaltz-Panneau, B., Jouneau, L., Cabau, C., Joly, T., Blachere, T., Gocza, E.... (2013) Induced pluripotent stem cells derived from rabbits exhibit some characteristics of naive pluripotency. Biology Open, 2(6), 613-628. DOI: 10.1242/bio.20134242  

  • November 17, 2014
  • 05:43 PM

Applications of homologous recombination-mediated genome engineering

by Jimann Shin in the Node

We recently demonstrated an improved method for homologous recombination (HR)-mediated genome editing using TALEN (Transcription activator-like effector nuclease) in zebrafish (Shin et al., 2014). In the study, we identified that a total of 3kb of homology in the targeting construct, 1kb of one arm and 2kb of the other arm, is sufficient to induce HR-mediated knock-in. […]... Read more »

  • November 17, 2014
  • 04:23 PM


by patricktschopp in the Node

The morphological evolution of limbs and external genitalia were both essential adaptions to a life on land. While the former deals with the novel locomotory challenges facing an animal invading a terrestrial environment, the latter is concerned with something even more essential: reproduction! Living on land means that gametes can no longer be fertilized externally […]... Read more »

Kondo T, Zákány J, Innis JW, & Duboule D. (1997) Of fingers, toes and penises. Nature, 390(6655), 29. PMID: 9363887  

Yamada, G., Suzuki, K., Haraguchi, R., Miyagawa, S., Satoh, Y., Kamimura, M., Nakagata, N., Kataoka, H., Kuroiwa, A., & Chen, Y. (2006) Molecular genetic cascades for external genitalia formation: An emerging organogenesis program. Developmental Dynamics, 235(7), 1738-1752. DOI: 10.1002/dvdy.20807  

Tschopp, P., Sherratt, E., Sanger, T., Groner, A., Aspiras, A., Hu, J., Pourquié, O., Gros, J., & Tabin, C. (2014) A relative shift in cloacal location repositions external genitalia in amniote evolution. Nature. DOI: 10.1038/nature13819  

Wagner, G. (2007) The developmental genetics of homology. Nature Reviews Genetics, 8(6), 473-479. DOI: 10.1038/nrg2099  

Shubin, N., Tabin, C., & Carroll, S. (2009) Deep homology and the origins of evolutionary novelty. Nature, 457(7231), 818-823. DOI: 10.1038/nature07891  

  • November 13, 2014
  • 11:58 AM

Neurogenesis in “non-neurogenic” regions

by Federico Luzzati in the Node

In the early ‘90s, the discovery of neural stem cells in the adult brain aroused hope to exploit these cells to treat neurodegenerative diseases or even induce brain regeneration. Yet, the real potential of these cells is still unclear. In the last 15 years we have learned that during development neural stem cells are an […]... Read more »

Luzzati, F., Peretto, P., Aimar, P., Ponti, G., Fasolo, A., & Bonfanti, L. (2003) Glia-independent chains of neuroblasts through the subcortical parenchyma of the adult rabbit brain. Proceedings of the National Academy of Sciences, 100(22), 13036-13041. DOI: 10.1073/pnas.1735482100  

Luzzati F, De Marchis S, Fasolo A, & Peretto P. (2006) Neurogenesis in the caudate nucleus of the adult rabbit. The Journal of Neuroscience, 26(2), 609-621. PMID: 16407559  

Magnusson, J., Goritz, C., Tatarishvili, J., Dias, D., Smith, E., Lindvall, O., Kokaia, Z., & Frisen, J. (2014) A latent neurogenic program in astrocytes regulated by Notch signaling in the mouse. Science, 346(6206), 237-241. DOI: 10.1126/science.346.6206.237  

  • November 4, 2014
  • 04:41 AM

Can you beat a chicken sexer? Revisiting embryo manipulation of the avian chick.

by hirokin in the Node

Chicken, quail, zebra finch, emu, duck, crow……a simple glimpse and we immediately realize how the Aves have, as a model system left their traces in various fields of biological research. And within the Aves class, the domestic fowl Gallus gallus is no doubt revered highly among the developmental biologists for their certainly distinguished career. Discovery […]... Read more »

  • October 31, 2014
  • 11:44 AM

Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9

by Shashank Gandhi in the Node

Researchers have always been interested in tissue-specific loss of function to probe the role of specific genes in embryonic development, cell physiology and disease conditions. Migration of lateral plate primordial germ cells in zebrafish, border cell migration during oogenesis in drosophila, interaction of T-cells with their target, and numerous other cases have continued to give […]... Read more »

Stolfi, A., Gandhi, S., Salek, F., & Christiaen, L. (2014) Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9. Development, 141(21), 4115-4120. DOI: 10.1242/dev.114488  

  • October 26, 2014
  • 07:26 AM

Biology and maths partner to understand life decisions

by Christele Gonneau in the Node

Starting with the one fertilized egg that we all once were, embryonic development is made of cell divisions and most importantly of cell decisions. These first life decisions are the first steps of the development of various cell types, which will further divide, decide, specialize, organize, form specialized organs and ultimately an entire very complex […]... Read more »

Bessonnard, S., De Mot, L., Gonze, D., Barriol, M., Dennis, C., Goldbeter, A., Dupont, G., & Chazaud, C. (2014) Gata6, Nanog and Erk signaling control cell fate in the inner cell mass through a tristable regulatory network. Development, 141(19), 3637-3648. DOI: 10.1242/dev.109678  

  • October 18, 2014
  • 01:42 AM

Full-term developmet of quail chick by ICSI

by Mizushima S in the Node

The eggs of domestic birds have been used in the study of developmental biology, leading to the extensive accumulation of knowledge on embryonic development. However, the early events involved in bird development, particularly the mechanism underlying fertilization, have not been elucidated in as much detail as those of other species of animals. The ooplasm in […]... Read more »

Mizushima, S., Hiyama, G., Shiba, K., Inaba, K., Dohra, H., Ono, T., Shimada, K., & Sasanami, T. (2014) The birth of quail chicks after intracytoplasmic sperm injection. Development, 141(19), 3799-3806. DOI: 10.1242/dev.111765  

  • October 3, 2014
  • 06:46 PM

Tough decisions for the developing brain

by Misato Iwashita in the Node

To form complex organs, somatic stem cells proliferate and then differentiate during development. In this process, intrinsic factors, i.e. the sequential expression of transcriptional genes, and extrinsic factors, i.e. extracellular microenvironment, are intimately involved. Recent in vitro studies have revealed that the physical properties of the extracellular niche, possibly tissue stiffness, may play an important […]... Read more »

  • October 2, 2014
  • 06:37 AM

What do sperm have to do with brain tumors?

by pknoepfler in the Node

  This post was originally published in the Knoepfler Lab Stem Cell Blog.      Sometimes in science there are unexpected threads tying seemingly very different things together. Unraveling the knots in these threads can lead to new insights into important developmental processes and mechanisms of disease. My lab studies epigenomic and transcription factors including […]... Read more »

Yuen, B., Bush, K., Barrilleaux, B., Cotterman, R., & Knoepfler, P. (2014) Histone H3.3 regulates dynamic chromatin states during spermatogenesis. Development, 141(18), 3483-3494. DOI: 10.1242/dev.106450  

  • September 24, 2014
  • 12:48 PM

Towards a synthetic embryo

by Aryeh Warmflash in the Node

Waddington, whose writings on the epigenetic landscape continue to influence developmental biology to this day, called the developing embryo “the most intriguing object that nature has to offer”(Waddington, 1966). The mechanisms of pattern formation and morphogenesis have fascinated biologists for centuries. One question that is difficult to answer is what are the minimal requirements for […]... Read more »

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