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

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  • September 23, 2015
  • 08:51 AM

“Eppur (non) si muove”: why cellular movements may not be essential to the formation of Turing patterns in biology.

by D. Bullara in the Node

D. Bullara* and Y. De Decker *   When Catarina Vicente (Community Manager of “The Node”) proposed us to write a post about our recent paper on pattern formation in zebrafish [Bullara2015] we were very glad for the opportunity she was giving us to tell the background story about our work in this blog. We[...]

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The post “Eppur (non) si muove”: why cellular movements may not be essential to the formation of Turing patterns in biology......... Read more »

De Decker Y, Tsekouras GA, Provata A, Erneux T, & Nicolis G. (2004) Propagating waves in one-dimensional discrete networks of coupled units. Physical review. E, Statistical, nonlinear, and soft matter physics, 69(3 Pt 2), 36203. PMID: 15089388  

Hamada, H., Watanabe, M., Lau, H., Nishida, T., Hasegawa, T., Parichy, D., & Kondo, S. (2013) Involvement of Delta/Notch signaling in zebrafish adult pigment stripe patterning. Development, 141(2), 318-324. DOI: 10.1242/dev.099804  

Nakamasu, A., Takahashi, G., Kanbe, A., & Kondo, S. (2009) Interactions between zebrafish pigment cells responsible for the generation of Turing patterns. Proceedings of the National Academy of Sciences, 106(21), 8429-8434. DOI: 10.1073/pnas.0808622106  

Turing, A. (1952) The Chemical Basis of Morphogenesis. Philosophical Transactions of the Royal Society B: Biological Sciences, 237(641), 37-72. DOI: 10.1098/rstb.1952.0012  

  • September 20, 2015
  • 06:47 PM

Novel mouse alleles allow for sequential mutagenesis using the dual recombinase technology

by dkirsch in the Node

Genetically engineered mouse models have been used extensively to study a wide variety of biological processes in vivo, and innovations in genetic engineering have made it possible to dissect more intricate biological questions. For example, the first mice that showed successful germline transmission of foreign DNA were created in the 1980s, and this allowed the[...]

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  • September 1, 2015
  • 10:25 AM

The blastocyst achieves on-time implantation by entosis

by Xiaofei Sun in the Node

The process of embryo implantation consists of multiple steps: blastocyst apposition, adhesion to uterine luminal epithelial (LE) cells, and removal of the epithelial cells encasing the blastocysts. How the blastocyst trophectoderm breaches the luminal epithelial barrier has been studied for decades, the mechanism of the abstraction of LE cells was not clearly understood. Since the[...]

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The post The blastocyst achieves on-time implantation by entosis appeared first on the Node.
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Finn CA, & McLaren A. (1967) A study of the early stages of implantation in mice. Journal of Reproduction and Fertility, 259-267. info:/10.1530/jrf.0.0130259

Krehbiel RH. (1937) Cytological Studies of the Decidual Reaction in the Rat during Early Pregnancy and in the Production of Deciduomata. Physiological Zoology, 212-234. info:/

Sun X, Zhang L, Xie H, Wan H, Magella B, Whitsett JA, & Dey SK. (2012) Kruppel-like factor 5 (KLF5) is critical for conferring uterine receptivity to implantation. Proceedings of the National Academy of Sciences of the United States of America, 109(4), 1145-1150. PMID: 22233806  

Wang H, & Dey SK. (2006) Roadmap to embryo implantation: clues from mouse models. Nature reviews. Genetics, 7(3), 185-199. PMID: 16485018  

  • August 13, 2015
  • 11:09 AM

Gap junctions: versatile mediators of long-range developmental signals

by Mike Levin in the Node

My lab works on developmental bioelectricity, studying how cells communicate via endogenous gradients of plasma membrane resting potential (Vmem) in order to coordinate their activity during pattern regulation (Levin, 2013; Levin, 2014b; Tseng and Levin, 2013). It is well-known that resting potential is an important regulatory parameter for individual cells’ proliferation, differentiation, and oncogenic potential[...]

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  • June 28, 2015
  • 10:11 AM

Cellular Senescence in Regeneration

by Max_Yun in the Node

Salamanders are remarkable organisms. Following the amputation or loss of complex structures such as parts of their eyes, hearts and brains, tails -including the spinal cord-, jaws and even full limbs, they are able to set up a regeneration programme which leads to the exact replacement of the missing structure, even as adults. As such, […]... Read more »

Eguchi, G., Eguchi, Y., Nakamura, K., Yadav, M., Millán, J., & Tsonis, P. (2011) Regenerative capacity in newts is not altered by repeated regeneration and ageing. Nature Communications, 384. DOI: 10.1038/ncomms1389  

van Deursen, J. (2014) The role of senescent cells in ageing. Nature, 509(7501), 439-446. DOI: 10.1038/nature13193  

Sousa-Victor, P., Gutarra, S., García-Prat, L., Rodriguez-Ubreva, J., Ortet, L., Ruiz-Bonilla, V., Jardí, M., Ballestar, E., González, S., Serrano, A.... (2014) Geriatric muscle stem cells switch reversible quiescence into senescence. Nature, 506(7488), 316-321. DOI: 10.1038/nature13013  

Yun, M., Gates, P., & Brockes, J. (2013) Regulation of p53 is critical for vertebrate limb regeneration. Proceedings of the National Academy of Sciences, 110(43), 17392-17397. DOI: 10.1073/pnas.1310519110  

Muñoz-Espín D, Cañamero M, Maraver A, Gómez-López G, Contreras J, Murillo-Cuesta S, Rodríguez-Baeza A, Varela-Nieto I, Ruberte J, Collado M.... (2013) Programmed cell senescence during mammalian embryonic development. Cell, 155(5), 1104-1118. PMID: 24238962  

Storer, M., Mas, A., Robert-Moreno, A., Pecoraro, M., Ortells, M., Di Giacomo, V., Yosef, R., Pilpel, N., Krizhanovsky, V., Sharpe, J.... (2013) Senescence Is a Developmental Mechanism that Contributes to Embryonic Growth and Patterning. Cell, 155(5), 1119-1130. DOI: 10.1016/j.cell.2013.10.041  

Demaria, M., Ohtani, N., Youssef, S., Rodier, F., Toussaint, W., Mitchell, J., Laberge, R., Vijg, J., Van Steeg, H., Dollé, M.... (2014) An Essential Role for Senescent Cells in Optimal Wound Healing through Secretion of PDGF-AA. Developmental Cell, 31(6), 722-733. DOI: 10.1016/j.devcel.2014.11.012  

  • June 27, 2015
  • 06:38 AM

Friendly hello and a bit about stress & adult hippocampal neurogenesis

by cathlau in the Node

This is my first post for the Node, so I thought I would introduce myself a little bit… I just finished my MSc in Experimental Psychology (Behavioural Neuroscience) and now I am striving towards becoming a science communicator. Although, I would like to share the research that I am interested in and was involved in, […]... Read more »

Cohen, H., Zohar, J., Gidron, Y., Matar, M., Belkind, D., Loewenthal, U., Kozlovsky, N., & Kaplan, Z. (2006) Blunted HPA Axis Response to Stress Influences Susceptibility to Posttraumatic Stress Response in Rats. Biological Psychiatry, 59(12), 1208-1218. DOI: 10.1016/j.biopsych.2005.12.003  

Hanson, N., Owens, M., Boss-Williams, K., Weiss, J., & Nemeroff, C. (2011) Several stressors fail to reduce adult hippocampal neurogenesis. Psychoneuroendocrinology, 36(10), 1520-1529. DOI: 10.1016/j.psyneuen.2011.04.006  

Schoenfeld, T., & Gould, E. (2012) Stress, stress hormones, and adult neurogenesis. Experimental Neurology, 233(1), 12-21. DOI: 10.1016/j.expneurol.2011.01.008  

  • June 15, 2015
  • 08:59 AM

MorphoGraphX: A platform for quantifying morphogenesis in 4D

by Anne-Lise Routier-Kierzkowska in the Node

Quantifying shape, growth and gene expression at the cellular level are key to understanding morphogenesis, i.e. how organs are shaped. Many image processing tools have been developed towards this goal that operate on either 2D or 3D images. 2D tools are fast, easy to use, and typically involve datasets of modest size. However organs and […]... Read more »

Barbier de Reuille, P., Routier-Kierzkowska, A., Kierzkowski, D., Bassel, G., Schüpbach, T., Tauriello, G., Bajpai, N., Strauss, S., Weber, A., Kiss, A.... (2015) MorphoGraphX: A platform for quantifying morphogenesis in 4D. eLife. DOI: 10.7554/eLife.05864  

Kierzkowski, D., Nakayama, N., Routier-Kierzkowska, A., Weber, A., Bayer, E., Schorderet, M., Reinhardt, D., Kuhlemeier, C., & Smith, R. (2012) Elastic Domains Regulate Growth and Organogenesis in the Plant Shoot Apical Meristem. Science, 335(6072), 1096-1099. DOI: 10.1126/science.1213100  

Aegerter-Wilmsen, T., Heimlicher, M., Smith, A., de Reuille, P., Smith, R., Aegerter, C., & Basler, K. (2012) Integrating force-sensing and signaling pathways in a model for the regulation of wing imaginal disc size. Development, 139(17), 3221-3231. DOI: 10.1242/dev.082800  

Vlad, D., Kierzkowski, D., Rast, M., Vuolo, F., Dello Ioio, R., Galinha, C., Gan, X., Hajheidari, M., Hay, A., Smith, R.... (2014) Leaf Shape Evolution Through Duplication, Regulatory Diversification, and Loss of a Homeobox Gene. Science, 343(6172), 780-783. DOI: 10.1126/science.1248384  

Montenegro-Johnson, T., Stamm, P., Strauss, S., Topham, A., Tsagris, M., Wood, A., Smith, R., & Bassel, G. (2015) Digital Single-Cell Analysis of Plant Organ Development Using 3DCellAtlas. The Plant Cell, 27(4), 1018-1033. DOI: 10.1105/tpc.15.00175  

Santuari, L., Scacchi, E., Rodriguez-Villalon, A., Salinas, P., Dohmann, E., Brunoud, G., Vernoux, T., Smith, R., & Hardtke, C. (2011) Positional Information by Differential Endocytosis Splits Auxin Response to Drive Arabidopsis Root Meristem Growth. Current Biology, 21(22), 1918-1923. DOI: 10.1016/j.cub.2011.10.002  

Yoshida, S., Barbier de Reuille, P., Lane, B., Bassel, G., Prusinkiewicz, P., Smith, R., & Weijers, D. (2014) Genetic Control of Plant Development by Overriding a Geometric Division Rule. Developmental Cell, 29(1), 75-87. DOI: 10.1016/j.devcel.2014.02.002  

Bassel, G., Stamm, P., Mosca, G., Barbier de Reuille, P., Gibbs, D., Winter, R., Janka, A., Holdsworth, M., & Smith, R. (2014) Mechanical constraints imposed by 3D cellular geometry and arrangement modulate growth patterns in the Arabidopsis embryo. Proceedings of the National Academy of Sciences, 111(23), 8685-8690. DOI: 10.1073/pnas.1404616111  

  • June 11, 2015
  • 08:58 AM

Active hematopoietic sites in Drosophila Adult

by LolitikaMandal in the Node

Studies in the last decade have established Drosophila as the best invertebrate model to study hematopoiesis. Blood cell development in the fruitfly has been shown to have similarities to that of vertebrates both at the level of its origins and important signaling molecules necessary for their formation and differentiation (Evans et al., 2003). It was believed […]... Read more »

  • June 10, 2015
  • 08:14 AM

Cortical Microcircuit Assembly: The Migratory Path Matters

by Kate Gao in the Node

By Peng Kate Gao Developmental neuroscience has traditionally focused on understanding the structural assembly of the nervous system. However, recently it has increasingly been recognized that development also plays a key role in orchestrating the functional assembly of neural circuits1. The neocortex, the center of higher functions in the mammalian brain, can be characterized by its stereotypic lamination at […]... Read more »

  • June 9, 2015
  • 11:42 AM

The human sex ratio at conception and the conception of scientific “facts”

by steven orzack in the Node

Few things interest many people more than sex. For some, this means interest in practices and partners. For others, it means producing a son. There is an ocean of claims about how to do this. A quick Google search reveals claims that a woman can up the odds of a son by taking cough syrup, […]... Read more »

Austad, S. (2015) The human prenatal sex ratio: A major surprise: Fig. 1. Proceedings of the National Academy of Sciences, 112(16), 4839-4840. DOI: 10.1073/pnas.1505165112  

Orzack, S., Stubblefield, J., Akmaev, V., Colls, P., Munné, S., Scholl, T., Steinsaltz, D., & Zuckerman, J. (2015) The human sex ratio from conception to birth. Proceedings of the National Academy of Sciences, 112(16). DOI: 10.1073/pnas.1416546112  

Parkes, A. (1926) The Mammalian Sex-Ratio. Biological Reviews, 2(1), 1-51. DOI: 10.1111/j.1469-185X.1926.tb00600.x  

  • May 28, 2015
  • 04:44 AM

How The Bird Got Its Beak

by Abzhanov in the Node

Nature’s most interesting secrets can sometimes be found in our own backyards. One such secret is related to all birds, those pigeons, thrushes and sparrows that we see everyday. This familiarity means that we do not think too much of birds passing them by on our way to work or school. However, if the birds […]... Read more »

Bhullar, B., Marugán-Lobón, J., Racimo, F., Bever, G., Rowe, T., Norell, M., & Abzhanov, A. (2012) Birds have paedomorphic dinosaur skulls. Nature, 487(7406), 223-226. DOI: 10.1038/nature11146  

Alberch,P., Gould,S.J., Oster,G.F., & Wake,D.B. (1979) Size and shape in ontogeny and phylogeny. Paleobiology , 296-317. info:/

Hodges, S., & Arnold, M. (1995) Spurring Plant Diversification: Are Floral Nectar Spurs a Key Innovation?. Proceedings of the Royal Society B: Biological Sciences, 262(1365), 343-348. DOI: 10.1098/rspb.1995.0215  

  • 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  

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