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

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  • November 17, 2014
  • 05:43 PM
  • 56 views

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
  • 53 views

A TALE OF LIMBS AND GENITALS

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
  • 139 views

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
  • 129 views

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
  • 158 views

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
  • 126 views

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
  • 129 views

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
  • 154 views

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
  • 179 views

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
  • 189 views

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 »

  • August 4, 2014
  • 07:31 AM
  • 244 views

‘‘Transit amplification in the cerebellum evolved via a heterochronic shift in NeuroD1 expression’’

by Thomas Butts in the Node

They are a mouthful, paper titles, sometimes. This is exactly the sort of title that would have made me ignore it in the days when I worked on the evolution of Hox genes. But I now find myself frequently justifying to people who work on evolution why the nervous system deserves attention, and of justifying […]... Read more »

  • July 3, 2014
  • 07:55 AM
  • 256 views

Goalward-bound: why biological research is like football

by Christele Gonneau in the Node

The 2014 FIFA World Cup has mesmerised football fans all around the world over the past weeks, but besides just the fancy footwork on display, we’ve also seen some amazing athleticism. Many of the matches have taken place under scorching, highly humid conditions! Though this might not be foremost in our minds as marvel at […]... Read more »

  • June 24, 2014
  • 08:49 AM
  • 229 views

On segmentation

by Thomas Butts in the Node

‘Increasing knowledge leads to triumphant loss of clarity’ ‘The study of segmentation: that way leads only to madness’ Alfred Romer (1894 – 1973), Director of the Museum of Comparative Zoology and Professor of Biology, Harvard University   Some problems in biology excite such interest as to become symptomatic of a field. This is true, I […]... Read more »

Aguinaldo, A., Turbeville, J., Linford, L., Rivera, M., Garey, J., Raff, R., & Lake, J. (1997) Evidence for a clade of nematodes, arthropods and other moulting animals. Nature, 387(6632), 489-493. DOI: 10.1038/387489a0  

Stollewerk, A., Schoppmeier, M., & Damen, W. (2003) Involvement of Notch and Delta genes in spider segmentation. Nature, 423(6942), 863-865. DOI: 10.1038/nature01682  

Dray, N., Tessmar-Raible, K., Le Gouar, M., Vibert, L., Christodoulou, F., Schipany, K., Guillou, A., Zantke, J., Snyman, H., Behague, J.... (2010) Hedgehog Signaling Regulates Segment Formation in the Annelid Platynereis. Science, 329(5989), 339-342. DOI: 10.1126/science.1188913  

Dias, A., de Almeida, I., Belmonte, J., Glazier, J., & Stern, C. (2014) Somites Without a Clock. Science, 343(6172), 791-795. DOI: 10.1126/science.1247575  

  • June 17, 2014
  • 12:02 PM
  • 240 views

Electrifying news for embryologists

by Elsa Mazari and Aitana Perea-Gomez in the Node

Electroporation: an efficient technique for embryologists During embryonic development, the specification of different cell types giving rise to the future organs involves a precise spatiotemporal regulation of cell proliferation, migration, and differentiation. Studying these processes requires tools to manipulate gene expression locally in the developing embryo.To this aim, embryologists have widely used the technique of […]... Read more »

Fox, M., Esveld, D., Valero, A., Luttge, R., Mastwijk, H., Bartels, P., Berg, A., & Boom, R. (2006) Electroporation of cells in microfluidic devices: a review. Analytical and Bioanalytical Chemistry, 385(3), 474-485. DOI: 10.1007/s00216-006-0327-3  

Kim, J., Cho, K., Shin, M., Lee, W., Jung, N., Chung, C., & Chang, J. (2008) A novel electroporation method using a capillary and wire-type electrode. Biosensors and Bioelectronics, 23(9), 1353-1360. DOI: 10.1016/j.bios.2007.12.009  

Mazari, E., Zhao, X., Migeotte, I., Collignon, J., Gosse, C., & Perea-Gomez, A. (2014) A microdevice to locally electroporate embryos with high efficiency and reduced cell damage. Development, 141(11), 2349-2359. DOI: 10.1242/dev.106633  

Momose, T., Tonegawa, ., Takeuchi, J., Ogawa, H., Umesono, K., & Yasuda, K. (1999) Efficient targeting of gene expression in chick embryos by microelectroporation. Development, Growth and Differentiation, 41(3), 335-344. DOI: 10.1046/j.1440-169X.1999.413437.x  

Nakamura, H., & Funahashi, J. (2013) Electroporation: Past, present and future. Development, Growth , 55(1), 15-19. DOI: 10.1111/dgd.12012  

Wang, M., Orwar, O., Olofsson, J., & Weber, S. (2010) Single-cell electroporation. Analytical and Bioanalytical Chemistry, 397(8), 3235-3248. DOI: 10.1007/s00216-010-3744-2  

  • June 17, 2014
  • 04:40 AM
  • 247 views

Nuclear sponges in embryonic stem cells

by kjchalut in the Node

Once upon a time, physicists got curious about the cytoskeleton. They characterised the cytoskeleton – using tools of soft matter, statistical and polymer physics – as a mesoscale material whose physical properties govern its dynamics. They showed that the cytoskeleton is an interconnected scaffold that, depending on the time scale, can behave like a shape-morphing […]... Read more »

Deng, L., Trepat, X., Butler, J., Millet, E., Morgan, K., Weitz, D., & Fredberg, J. (2006) Fast and slow dynamics of the cytoskeleton. Nature Materials, 5(8), 636-640. DOI: 10.1038/nmat1685  

Gardel, M., Schneider, I., Aratyn-Schaus,, Y., & Waterman, C. (2010) Mechanical Integration of Actin and Adhesion Dynamics in Cell Migration. Annual Review of Cell and Developmental Biology, 26(1), 315-333. DOI: 10.1146/annurev.cellbio.011209.122036  

Swift, J., Ivanovska, I., Buxboim, A., Harada, T., Dingal, P., Pinter, J., Pajerowski, J., Spinler, K., Shin, J., Tewari, M.... (2013) Nuclear Lamin-A Scales with Tissue Stiffness and Enhances Matrix-Directed Differentiation. Science, 341(6149), 1240104-1240104. DOI: 10.1126/science.1240104  

Kind, J., Pagie, L., Ortabozkoyun, H., Boyle, S., de Vries, S., Janssen, H., Amendola, M., Nolen, L., Bickmore, W., & van Steensel, B. (2013) Single-Cell Dynamics of Genome-Nuclear Lamina Interactions. Cell, 153(1), 178-192. DOI: 10.1016/j.cell.2013.02.028  

Pagliara, S., Franze, K., McClain, C., Wylde, G., Fisher, C., Franklin, R., Kabla, A., Keyser, U., & Chalut, K. (2014) Auxetic nuclei in embryonic stem cells exiting pluripotency. Nature Materials, 13(6), 638-644. DOI: 10.1038/nmat3943  

Pajerowski, J., Dahl, K., Zhong, F., Sammak, P., & Discher, D. (2007) Physical plasticity of the nucleus in stem cell differentiation. Proceedings of the National Academy of Sciences, 104(40), 15619-15624. DOI: 10.1073/pnas.0702576104  

Nagano, T., Lubling, Y., Stevens, T., Schoenfelder, S., Yaffe, E., Dean, W., Laue, E., Tanay, A., & Fraser, P. (2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature, 502(7469), 59-64. DOI: 10.1038/nature12593  

Ying, Q., Wray, J., Nichols, J., Batlle-Morera, L., Doble, B., Woodgett, J., Cohen, P., & Smith, A. (2008) The ground state of embryonic stem cell self-renewal. Nature, 453(7194), 519-523. DOI: 10.1038/nature06968  

Evans, K.E., & Alderson, A. (2000) Auxetic Materials: Functional Materials and Structures from Lateral Thinking!. Advanced materials, 12(9), 617-628. info:/

Chalut, K., Höpfler, M., Lautenschläger, F., Boyde, L., Chan, C., Ekpenyong, A., Martinez-Arias, A., & Guck, J. (2012) Chromatin Decondensation and Nuclear Softening Accompany Nanog Downregulation in Embryonic Stem Cells. Biophysical Journal, 103(10), 2060-2070. DOI: 10.1016/j.bpj.2012.10.015  

  • June 6, 2014
  • 12:24 PM
  • 273 views

Gastrulation: Local actions, global movements and self-organisation

by Octavian Voiculescu in the Node

Cells move in (still) mysterious ways to achieve morphogenesis. Prominently, cells of an early vertebrate embryo (blastula, a mass of undifferentiated cells) move extensively during gastrulation to generate the three basic layers of the organism: ectoderm at the surface, endoderm presaging the digestive tube, and the mesoderm in between. At the end of the process, […]... Read more »

  • May 29, 2014
  • 03:33 PM
  • 335 views

GATA6 and the power of single cells

by Nestor Saiz in the Node

Any mammal who celebrated Mother’s Day earlier this month realizes how important mothers are for us and the tight bond between them and their children. Forget clean shirts and packed lunch every day; for us developmental biologists, there is no better reflection of this bond than the extraembryonic membranes that support the growth of the […]... Read more »

Le Bin, G., Munoz-Descalzo, S., Kurowski, A., Leitch, H., Lou, X., Mansfield, W., Etienne-Dumeau, C., Grabole, N., Mulas, C., Niwa, H.... (2014) Oct4 is required for lineage priming in the developing inner cell mass of the mouse blastocyst. Development, 141(5), 1001-1010. DOI: 10.1242/dev.096875  

Ohnishi, Y., Huber, W., Tsumura, A., Kang, M., Xenopoulos, P., Kurimoto, K., Oleś, A., Araúzo-Bravo, M., Saitou, M., Hadjantonakis, A.... (2013) Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages. Nature Cell Biology, 16(1), 27-37. DOI: 10.1038/ncb2881  

  • May 27, 2014
  • 04:07 PM
  • 216 views

It’s decision time!

by Christele Gonneau in the Node

Decisions, decisions…aren’t those one of our main worries? It is certainly the everyday worry of a stem cell! Understanding stem cell decisions is a central question in the field: how do stem cells manage to keep the right balance between self-renewal (make identical copies of themselves) and differentiation (produce specialized cells)? How do stem cells […]... Read more »

Liao, H., Chen, W., Chen, Y., Kao, T., Tseng, Y., Lee, C., Chiu, Y., Lee, P., Lin, Q., Ching, Y.... (2014) DNMT3L promotes quiescence in postnatal spermatogonial progenitor cells. Development. DOI: 10.1242/dev.105130  

  • May 18, 2014
  • 12:29 PM
  • 334 views

Use it or Lose it: Insights on neuronal connections in the vertebrate retina

by Reed College Dev Neuro in the Node

This is the final post from our developmental neurobiology seminar this semester. Two students wrote about our discussion of the importance of neuronal activity during synaptogenesis and their professor combined and edited the pieces. As usual, we focused  on development in the vertebrate retina. Hope you’ve enjoyed our contributions, we’ve enjoyed sharing our new-found understanding. […]... Read more »

  • May 9, 2014
  • 01:17 PM
  • 332 views

Grasping tendon development with the zebrafish

by Jenna Galloway in the Node

by Jessica Chen and Jenna Galloway   Animals can contort their bodies into a diversity of movements: running, jumping, climbing, and swimming to name a few. All of these movements are possible because tendons transmit the force produced by the muscles to the bones. Most of us do not pay much attention to our tendons […]... Read more »

Bassett, D., Bryson-Richardson, R. J., Daggett, D. F., Gautier, P., Keenan, D. G., & Currie, P. D. (2003) Dystrophin is required for the formation of stable muscle attachments in the zebrafish embryo. Development, 130(23), 5851-5860. DOI: 10.1242/dev.00799  

Charvet, B., Guiraud, A., Malbouyres, M., Zwolanek, D., Guillon, E., Bretaud, S., Monnot, C., Schulze, J., Bader, H., Allard, B.... (2013) Knockdown of col22a1 gene in zebrafish induces a muscular dystrophy by disruption of the myotendinous junction. Development, 140(22), 4602-4613. DOI: 10.1242/dev.096024  

Charvet, B., Malbouyres, M., Pagnon-Minot, A., Ruggiero, F., & Guellec, D. (2011) Development of the zebrafish myoseptum with emphasis on the myotendinous junction. Cell and Tissue Research, 346(3), 439-449. DOI: 10.1007/s00441-011-1266-7  

Kaufman, C., White, R., & Zon, L. (2009) Chemical genetic screening in the zebrafish embryo. Nature Protocols, 4(10), 1422-1432. DOI: 10.1038/nprot.2009.144  

Schweitzer R, Chyung JH, Murtaugh LC, Brent AE, Rosen V, Olson EN, Lassar A, & Tabin CJ. (2001) Analysis of the tendon cell fate using Scleraxis, a specific marker for tendons and ligaments. Development, 128(19), 3855-66. PMID: 11585810  

Summers, A., & Koob, T. (2002) The evolution of tendon — morphology and material properties. Comparative Biochemistry and Physiology Part A: Molecular , 133(4), 1159-1170. DOI: 10.1016/S1095-6433(02)00241-6  

Yan YL, Miller CT, Nissen RM, Singer A, Liu D, Kirn A, Draper B, Willoughby J, Morcos PA, Amsterdam A.... (2002) A zebrafish sox9 gene required for cartilage morphogenesis. Development, 129(21), 5065-5079. PMID: 12397114  

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