Here is June’s round-up of some of the interesting content that we spotted around the internet!

News & Research

– Daniel St Johnston predicts the renaissance of a new wave of developmental biology, in this piece published in PLOS Biology.

– The retirement debate– should older scientists stay at the bench or make way for the next generation? Nature considers the pros and cons.

– How the micropipette was invented– great historical account in this article from 2005 in EMBO Reports.

– A piece in Nature considers the history, potential and concerns of CRISPR.

– Two new websites with great outreach resources have been released: The ISSCR launched ‘A closer look at stem cells‘, while the Manchester Fly Facility released their website Droso4Schools, with great teaching resources to bring flies to the classroom. Also in the topic of outreach, a short piece in Science Careers discusses science education in prisons.

– How to apply for a postdoc or PhD position– Nobel Prize winners Paul Nurse and Martin Chalfie share their thoughts.

– The last couple months saw several honours bestowed on developmental biologists. Rudolph Jaenisch was awarded the 2015 March of Dimes prize and several researchers in the field were elected members of the National Academy of Science, the Royal Society and EMBO.

Weird & Wonderful:

– First author proposes to girlfriend in the acknowledgements of his latest paper in Current Biology. She said yes!

– The Sauka-Spengler lab released a ‘street view’ tour of their lab.

– And if you are a Tolkien fan, here is some Hobbit science!

Hobbit science! RT @Alexis_Verger ‘The hobbit — an unexpected deficiency’ https://t.co/hoUP8eosi1 pic.twitter.com/YEPxsrX767

— the Node (@the_Node) April 23, 2015

Beautiful & Interesting images:

– Explaining developmental Biology using sweets!

– If you like a pretty images check out the June release of The Journal of Experimental Biology desktop calendar.

– And the science of academic humour:

The science of academic humour, via @AcademicsSay pic.twitter.com/SC4G3YLi1M — the Node (@the_Node) May 20, 2015

Videos worth watching:

– Christiane Nüsslein-Volhard and Eric Wieschaus talk about their Nobel Prize winning work.

– National Geography released this fantastic video of bee development.

– The trailer for the PHD Movie 2 is now available!

– And how do you increase the funding for science? Manipulate the ‘funding gene’ of politicians!

Keep up with this and other content, including all Node posts and deadlines of coming meetings and jobs, by following the Node on Twitter

(1 votes)

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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 tissues are often highly curved and a single 2D image can be not sufficient to quantify their shape. To address this problem, 3D tools have been developed. Yet these require very large and high quality images, with deep penetration that is often not possible with live imaging. We have developed the image analysis software MorphoGraphX¹, that gets around these problems by working with curved 2D surface images. We like to call it image processing in “2.5D”.

MorphoGraphX was initially developed to answer specific questions in plant biology. A particularly challenging one was: Is there a difference in mechanical properties between the shoot apex stem cell niche and the surrounding cells²? To answer this question we used osmotic treatments to lower the cell internal pressure, with the idea to precisely track the shape change of the cells. Softer cells would be expected to deform more. However this approach presented a major technical problem. We needed to very precisely track small changes (~8-10% in area) in cell size on the surface of the shoot apex from 3D confocal image stacks. Due to the curvature of the apex, 2D sections would not work, and the image quality was not sufficient to do a full 3D segmentation, in particular because osmolytes contained in the medium scattered light.

Figure 1. The 3D confocal stack of an arabidopsis flower (a, in green) shows how curved many biological shapes can be. In this case, a flat projection of the 3D data (a, in grey) leads to too much distortion and cannot be used to study cell shape or quantify signal intensity. Instead, we first extract the global organ shape (b) from the 3D data and create a curved triangular mesh (c) that represents the surface. A narrow band of the 3D image data (d, purple) can then be projected onto the surface, creating a curved (2.5D) image of the cell outlines (here is grey scale). Scale bars: 20 μm. Adapted from (1).

To solve this problem, Richard Smith’s team had the idea of first extracting the global shape of the apex and then projecting the cell outlines onto this curved surface, creating a curved 2.5D image of the surface. This way, cells on the flanks of the organ would not be distorted by the projection. The process proved to be robust enough to extract relatively small changes in cell shape under difficult imaging conditions².

Quickly it became apparent that the idea could be applied to other biological problems, both in plant and animal research. MorphoGraphX grew into a collaborative project, initially involving several groups in the Swiss SystemsX consortium, the “Plant Growth”, “Wing-X” and “SyBIT” projects. Today MorphoGraphX integrates code and algorithms from many different sources, and is used as a fully 3D image processing platform that can be extended in much the same way as ImageJ or Fiji. One key difference is that processes in MorphoGraphX (plugins) are written in C++, and much of the 3D image processing exploits the latest generation of graphics cards, which can have 1000s of computing cores. Combined, the platform gives the scientist the ability to integrate a variety of tools to create work-flows, test new ideas quickly, and visualize the results easily.

In our paper recently published in eLife¹, we show how the tools developed in MorphoGraphX can be applied to solve various problems in development (Figure 2). Among others applications, MorphoGraphX has been used to investigate mechanical properties in the shoot apex², quantify cell shape in Drosophila wing disk³, dissect how leaf shape emerges from gene expression and growth at the single cell level⁴, and automatically classify cells according to their tissue type in Arabidopsis embryo⁵. MorphoGraphX output can be also be used as a templates for numerical simulations in both 2D and 3D, to model hormone transport in roots⁶, cell division rules in developing embryos⁷ or mechanical stresses during germination⁸.

Figure 2. MorphoGraphX tools have proved to be valuable for image analysis in both plant and animal research. The surface of a Drosophila wing disk extracted after digitally removing the peripodial membrane from a 3D confocal stack (a), enabling researchers to analyze the cell shape and size (a) or transcription levels of genes (b), such as vestigial (left) and wingless (right). The software can also be used to track growth of individual cells, for example to analyse the effects of a growth-repressing gene in Arabidopsis leaves. Colorscale represents expansion over 24h in % (c). Cells of an Arabidopsis embryo are colored according to their tissue type. The classification was performed automatically, based cell shape and position extracted from 3D segmentation (d). Scale bars: 20 μm (a and b), 30 μm (c) and 20 μm (d). (a,b) adapted from (1), (c) from (4), (d) from (5).

We use MorphoGraphX in our own lab on a daily basis and collaborate with biologist from various labs around the world. With much of the code developed by people who actually use the software, the emphasize has been on the ease of use, speed, reliability, and the ability to combine algorithms from many sources. Our aim is to share our platform with anyone that finds it useful, and to integrate contributions from the community that are developed in the context of a a wide range of research goals.

For more informations, please visit: www.MorphoGraphX.org and the Smith lab website.

1. Barbier de Reuille, P., Routier-Kierzkowska, A., Kierzkowski, D., Bassel, G., Schüpbach, T., Tauriello, G., Bajpai, N., Strauss, S., Weber, A., Kiss, A., Burian, A., Hofhuis, H., Sapala, A., Lipowczan, M., Heimlicher, M., Robinson, S., Bayer, E., Basler, K., Koumoutsakos, P., Roeder, A., Aegerter-Wilmsen, T., Nakayama, N., Tsiantis, M., Hay, A., Kwiatkowska, D., Xenarios, I., Kuhlemeier, C., & Smith, R. (2015). MorphoGraphX: A platform for quantifying morphogenesis in 4D eLife, 4 DOI: 10.7554/eLife.05864

2. 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

3. 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

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

5. 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

6. 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

7. 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

8. 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

(4 votes)

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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 that active hematopoiesis is limited to embryonic and larval stages only and that the adult survives on the contribution of these earlier stages (Holz et al., 2003). However, adulthood is the most exploring phase of the fruit fly life, wherein chances of encountering different pathogens are comparatively high compared to larvae. We thus argued that the long lived hemocytes of earlier stages might not be sufficient to enable the fly to tide over diverse immune challenges.

We started off challenging the adult flies with bacteria. We noticed that post 24 hours infection the dorsal abdominal clusters were depleted of hemocytes and within another 48 hours they reverted back to wild type size. This made us wonder: how is the recovery achieved in these clusters? Is there any genesis of blood cells post infection within this cluster? Can these be the sites of new blood cell formation in the adult fruit fly? Our BrdU assay established that the otherwise quiescent plasmatocytes have entered into proliferation upon immune challenge indicating that they are not locked in senescence and can respond to insults.

For the past three years, we had been interested in exploring the contributions of embryo and larval stages to adulthood. Using the lineage tracing system we were trying to trace the lineages of hemocytes in the dorsal cluster of the adult Drosophila. In one such experiment, upon activation of the lineage tracing construct (Evans et al., 2009) with pan plasmatocyte driver hemolectin (hml) we were surprised to see several new plasmatocytes being born that lacked lineage tracing labeling but were actively expressing Hml indicating their genesis in adult.

We were excited to see a similar event also happening with crystal cells. This cell type is abundant in immature stages, but was reported to be absent in adult (Binggeli et al., 2014). Our analysis could detect them in a 5-day-old fly by Lozenge expression indicating the existence of a precursor from which they are derived. We decided to follow the crystal cell development in the dorsal abdominal cluster. Since activation of Notch (N) pathway precedes Lz expression in crystal cells (Duvic et al., 2002), a reporter of Notch pathway, Su(H) lacZ was employed for this purpose. Su(H) lacZ-positive cells are first seen in the cluster 2 post eclosion, whereas the expression of lz-GFP is observed only on 3 day post emergence. Interestingly, some of these lz- GFP-positive cells still have low levels of Su(H)lacZ expression. These results, therefore, clearly demonstrate the de novo origin of lz-GFP-positive crystal cells from Su(H)lacZ-positive cells within the cluster. These dorsal abdominal clusters are thus the active site for new blood cell formation and specification in adult fruit fly. This hemocyte aggregation is embedded in an intense network of extracellular matrix that facilitates the formation of the hub. On disturbing the plasmatocyte migration in earlier stages we found that larval hemocytes of do home into these hubs.

Deep seated, secluded from the rest of the abdominal cavity, this hematopoietic hub, enriched with Laminin A and collagen IV like protein, seems to be a simple version of the bone marrow. In vertebrates, the hematopoietic stem cells (HSCs) originate from hemangioblast and undergo maturation and expansion by an intricate developmental process that requires the involvement of the yolk sac, the aorta-gonad-mesonephros (AGM) region, the placenta and the fetal liver before finally colonizing into bone marrow (Mikkola and Orkin, 2006). Interesting, the progenitors that we detected in the fruit-fly hub arrive at the hub from the reserve population of hemocytes of the larval hematopoietic organ. This organ harbors blood cell progenitors originating from hemangioblasts that develop from a region analogous to the AGM of vertebrates (Mandal et al., 2004). Our investigation reveals that upon undergoing expansion within the lymph gland, some of these precursors actually home into the adult hematopoietic hub.

We believe that this simple version of bone marrow found through our investigation will help establish Drosophila adult hematopoiesis as a simpler yet genetically testable model to address questions related to blood stem cells as well as development , immunity, wound healing and aging (Ghosh et al., 2015).

Main paper:

Ghosh, S., Singh, A., Mandal, S., & Mandal, L. (2015). Active Hematopoietic Hubs in Drosophila Adults Generate Hemocytes and Contribute to Immune Response Developmental Cell, 33 (4), 478-488 DOI: 10.1016/j.devcel.2015.03.014

References

Binggeli, O., Neyen, C., Poidevin, M., & Lemaitre, B. (2014). Prophenoloxidase Activation Is Required for Survival to Microbial Infections in Drosophila PLoS Pathogens, 10 (5) DOI: 10.1371/journal.ppat.1004067

Bossinger, B., Strasser, T., Janning, W., Klapper, R., & Holz, A. (2003). The two origins of hemocytes in Drosophila Development, 130 (20), 4955-4962 DOI: 10.1242/dev.00702

Duvic, B., Hoffmann, J., Meister, M., & Royet, J. (2002). Notch Signaling Controls Lineage Specification during Drosophila Larval Hematopoiesis Current Biology, 12 (22), 1923-1927 DOI: 10.1016/S0960-9822(02)01297-6

Evans, C., Olson, J., Ngo, K., Kim, E., Lee, N., Kuoy, E., Patananan, A., Sitz, D., Tran, P., Do, M., Yackle, K., Cespedes, A., Hartenstein, V., Call, G., & Banerjee, U. (2009). G-TRACE: rapid Gal4-based cell lineage analysis in Drosophila Nature Methods, 6 (8), 603-605 DOI: 10.1038/nmeth.1356

Evans, C.J., Sinenko, S.A., Mandal, L., Martinez-Agosto, J.A., Hartenstein, V., & Banerjee, U. (2007). Genetic Dissection of Hematopoiesis Using Drosophila as a Model System Advances in Developmental Biology, 18, 259-299 DOI: 10.1016/S1574-3349(07)18011-X

Mikkola, H., & Orkin, S.H. (2006). The journey of developing hematopoietic stem cells Development, 133 (19), 3733-3744 DOI: 10.1242/dev.02568

Mandal, L., Banerjee, U., & Hartenstein, V. (2004). Evidence for a fruit fly hemangioblast and similarities between lymph-gland hematopoiesis in fruit fly and mammal aorta-gonadal-mesonephros mesoderm Nature Genetics, 36 (9), 1019-1023 DOI: 10.1038/ng1404

(6 votes)

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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 the structural level and the cortical column at the functional level. While the formation of cortical laminae has long been thought to be the direct result of neuronal migration during embryonic and early postnatal development, whether assembly of the cortical column is influenced by similar developmental processes, such as neuronal production and migration, has remained largely unexplored. In a recent study published in Neuron from our lab, He et al. showed that the previously described inside-out radial migration is crucial for the formation of electrical and subsequent chemical synapses between lineage-related excitatory neurons². Therefore, in addition to generating the correct number and composition of cells to form a structurally intact cortex, normal development appears to also play an important role in the precise functional assembly of cortical microcircuits.

A developmental origin for the cortical column

First described by Vernon Mountcastle in 1957, and later rediscovered by Hubel and Wiesel in their seminal work in the 1960s and 1970s, the cortical column—a group of neurons that are radially aligned throughout the cortical thickness and encode similar features—is thought to be the basic functional unit of the mammalian cortex. Yet, despite the long history of success (primarily in cats and monkeys) in identifying cortical columns functionally through electrophysiological recordings, identification of its anatomical basis and construction has proven difficult. In the last few years, a series of studies in mice have pointed to a possible developmental origin of cortical columns.

          Neocortical excitatory neurons are generated from radial glial progenitors (RGPs) in the ventricular zone during embryonic development, and migrate out radially along radial glial fibers to populate the cortex. Yu and He et al. used EGFP-expressing retroviruses to label individual RGPs in mouse embryos (E12-E13) and examined the functional connectivity of their progeny postnatally through electrophysiological recordings. Using this strategy, they discovered that lineage-related sister excitatory neurons derived from the same RGPs are preferentially connected via electrical synapses at early postnatal stages (P1-P4), which facilitates subsequent chemical synapse formation (P10-P21)^3,4. In a different study, Li et al. used in vivo two-photon calcium imaging to demonstrate that sister excitatory neurons in the mouse visual cortex exhibit similar orientation tuning response properties—a feature highly reminiscent of the cortical columns observed in cats and monkeys, suggesting that lineage relationship instructs precise microcircuit assembly, which may contribute to the emergence of functional columnar organization in the neocortex⁵ (Figure 1). However, when and how electrical synapses are initially formed among sister excitatory neurons remained an open question. These questions were the main focus of the study now published by He et al. in Neuron².

The emergence of lineage-specific electrical synapses

Gap junction-mediated adhesion has been previously shown to facilitate the migration of newborn excitatory neurons along the radial glial fiber. However, whether these gap junctions are conductive (i.e., a functional electrical synapse) is unknown. Using retroviral labeling and electrophysiological recordings, He et al. found that functional electrical synapses do exist between RGPs and newborn progeny in the subventricular zone (SVZ). Importantly, a lineage-dependent bias is already established at this stage: while a RGP is electrically coupled with its own daughters in 100% of cases examined (43 out of 43), the rate of electrical coupling between similarly situated, non lineage-related RGP and SVZ cells is only 16% (8 out of 48)².

          He et al. next examined the emergence of electrical synapses between neurons in the cortical plate—the precursor of neocortex. Again, they observed a significant lineage-dependent bias: while 21% of sister pairs are electrically coupled (9 out of 42), virtually none of the non-sister pairs were coupled (1 out of 66). Furthermore, they found that electrical synapses among sister neurons are formed progressively over embryonic development, increasing from 11% at E16 to 21% at E18, and reaching a peak of 40% at P1-2^2,4.

Inside-out radial migration is required for electrical coupling among sister neurons

Migration of neocortical excitatory neurons occurs in an “inside-out” fashion, where later born neurons migrate past earlier born neurons to progressively occupy more superficial layers. Since sister neurons migrate along a similar path, He et al. reasoned that the inevitable encounter between them may promote their electrical coupling. To test this, they examined the Reeler mice, in which lack of the protein REELIN disrupts the “inside-out” migration and results in an “inverted” cortex^6,7. In Reeler mice, sister neurons are unlikely to encounter each other during migration (Figure 2). Using the same retroviral labeling and electrophysiological recording approach, He et al. found that in Reeler mice, although electrical coupling between RGPs and their SVZ progeny remains intact, the preferential electrical coupling between sister neurons in the cortical plate is largely abolished, and subsequent chemical synapse formation is impaired. Clonal knock down of Disabled-1 (Dab1), an essential downstream effector of the REELIN signaling pathway, in wild type mice produced a similar effect, further supporting the notion that the inside-out radial migration of clonally related excitatory neurons is essential for the formation of electrical synapses among them. Furthermore, the authors found that when clones become more dispersed due to an increase in Ephrin-A and receptor signaling⁹, the electrical coupling among sister neurons is also reduced, suggesting that migration along a similar path is important for electrical coupling between sister neurons².

The path forward

In their landmark 1974 paper¹⁰, Hubel and Wiesel postulated, “the cells behave as though they shared certain connections among themselves, but not with cells of neighboring columns, and in this sense a single group of cells is looked upon as a more or less autonomous functional unit…It may be that there is a great developmental advantage in designing such machinery once only, and repeating it over and over monotonously, like a crystal.” New evidence is beginning to shed light on the developmental origin of this fundamental functional unit in the cortex. It appears that clones of excitatory neurons produced from the same RGPs may provide a blueprint for assembling the future functional column. In this process, the preferential electrical coupling between sister neurons represents the very first step of microcircuit assembly. He et al. demonstrated that inside-out migration and spatial localization of neurons serves as a determinant of lineage-dependent electrical synapse formation². However, like many other important discoveries, this study creates more questions than it has answered. For example, how is the specificity achieved between a RGP and its own daughter neuron, as well as between sister neurons? How does a neuron distinguish its sisters from the numerous non-related cells it encounters along the migratory path? There are likely lineage-specific molecules that facilitate this recognition process. Further, electrical synapses are transient during development, and largely disappear before chemical synapses emerge. How is the transition controlled? The answers to these questions will light a path ahead to a deeper understanding of the most fundamental unit of the mammalian neocortex.

References:

1. Pivetta, C., Esposito, M., Sigrist, M., & Arber, S. (2014). Motor-Circuit Communication Matrix from Spinal Cord to Brainstem Neurons Revealed by Developmental Origin Cell, 156 (3), 537-548 DOI: 10.1016/j.cell.2013.12.014

2. He, S., Li, Z., Ge, S., Yu, Y., & Shi, S. (2015). Inside-Out Radial Migration Facilitates Lineage-Dependent Neocortical Microcircuit Assembly Neuron, 86 (5), 1159-1166 DOI: 10.1016/j.neuron.2015.05.002

3. Yu, Y.C., Bultje, R.S., Wang, X., & Shi, S.H. (2009). Specific synapses develop preferentially among sister excitatory neurons in the neocortex. Nature, 458 (7237), 501-4 PMID: 19204731

4. Yu, Y., He, S., Chen, S., Fu, Y., Brown, K., Yao, X., Ma, J., Gao, K., Sosinsky, G., Huang, K., & Shi, S. (2012). Preferential electrical coupling regulates neocortical lineage-dependent microcircuit assembly Nature, 486, 113-117 DOI: 10.1038/nature10958

5. Li, Y., Lu, H., Cheng, P., Ge, S., Xu, H., Shi, S., & Dan, Y. (2012). Clonally related visual cortical neurons show similar stimulus feature selectivity Nature, 486, 118-121 DOI: 10.1038/nature11110

6. D’Arcangelo, G., Miao, G.G., Chen, S.C., Soares, H.D., Morgan, J.I., & Curran, T. (1995). A protein related to extracellular matrix proteins deleted in the mouse mutant reeler. Nature, 374 (6524), 719-723 PMID: 7715726

7. Ogawa, M., Miyata, T., Nakajimat, K., Yagyu, K., Seike, M., Ikenaka, K., Yamamoto, H., & Mikoshibat, K. (1995). The reeler gene-associated antigen on cajal-retzius neurons is a crucial molecule for laminar organization of cortical neurons Neuron, 14 (5), 899-912 DOI: 10.1016/0896-6273(95)90329-1

8. Rakic, P. (1988). Specification of cerebral cortical areas Science, 241 (4862), 170-176 DOI: 10.1126/science.3291116

9. Torii, M., Hashimoto-Torii, K., Levitt, P., & Rakic, P. (2009). Integration of neuronal clones in the radial cortical columns by EphA and ephrin-A signalling. Nature, 461 (7263), 524-528 PMID: 19759535

10. Hubel, D., & Wiesel, T. (1974). Uniformity of monkey striate cortex: A parallel relationship between field size, scatter, and magnification factor The Journal of Comparative Neurology, 158 (3), 295-305 DOI: 10.1002/cne.901580305

(1 votes)

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Dear all who love embryology,

 

Lots of opportunities to interact with speakers, YEN organisers, and members of the Developmental Biology community in London. Tea and Coffee will be available for this seminar.

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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, avoiding intercourse in the days before ovulation, achieving female orgasm, increasing sodium and potassium intake, decreasing calcium and magnesium intake, avoiding exercise, avoiding the missionary position, and increasing caffeine intake by the father.

As a scientist, it’s easy to dismiss such claims as folklore. Yet, science is sometimes no less tangled up with claims that amount to folklore, but which are widely accepted as scientific fact. This entanglement is well-illustrated in another manifestation of fascination with sex: the study of the human sex ratio.

Investigations of the sex ratio (often calculated as the proportion of males) date back at least to Graunt (1662) who described an excess of male births (Campbell 2001). By the late 1800s it was clear that more males than females die during later pregnancy (Nichols 1907). By the 1920s, the claim that the sex ratio at conception or “primary” sex ratio (PSR) is more male-biased than the birth sex ratio was widespread (e.g., Parkes 1926). Just how startling this is can be understood by considering what people knew back then. Other than the excess of male births, what data were available that could allow inference of the pre-birth sex ratio? Only samples of spontaneous abortions (Tschuprow 1915); the resulting sex ratio estimates were often, but not always, male-biased. Sexing was based on morphology, which is likely to generate a male-bias, especially for young fetuses. What data were not available? There were no sex ratio data derived from samples of embryos and/or extant pregnancies; such samples are now available from assisted reproductive technology (ART) and from chorionic-villus sampling and amniocentesis (techniques to sample fetal cells). There were no biochemical or molecular methods to detect the sex of a fetus or to assess whether it was karyotypically normal. In addition, there were no statistical methods to properly account for the complexities of data sets involving proportions.

Despite the concerns raised by some as to the problematic nature of inferring the PSR from spontaneous abortion data (e.g., MacDowell and Lord 1925), the male-bias of the PSR became a scientific fact. One reason is that scientists abhor a vacuum. This is not inherently problematic. After all, scientists could do nothing if “complete” knowledge was a prerequisite for any analysis. What is problematic is that claims for the male-biased PSR were usually shorn of connection with underlying data. Consider, for example, Shettles’ (1961, p. 122) opening statement that “In every population, more males than females are born, and still more are conceived.” This “digestible” fact about the PSR is memorable because of its unqualified simplicity, which makes it highly transmissible, especially given its main constituency: medical doctors (readers of Obstetrics and Gynecology). (Shettles provided citations later in his paper that he regarded as supporting his claim. He does not discuss the data; none of the citations contain data that are necessarily consistent with a male-biased PSR and not all even contain a claim about the PSR.) “Drinking from a firehose” comes to mind as an apt descriptor of medical training, so much so that the acquisition of this kind of digestible fact is an essential cognitive “device” for the completion of training. In this context, this device supercharged the spread of the claim of a male-biased PSR shorn of connection with data.

The post-WWII standardization of medical training in part driven by the wide adoption of a few textbooks accelerated the spread of the digestible fact about the PSR. For example, Stern’s (1960) widely-used and high-quality textbook on human genetics presented the claim that the PSR is male-biased and even went so far as to describe some of the data; however, possible sampling biases associated with the data went unmentioned.

The spread was also facilitated because many types of scientists regarded the male-biased PSR as basic knowledge. Groups with an interest in the topic included cell biologists, developmental biologists, demographers, epidemiologists, evolutionary biologists, gynecologists, and statisticians. This “balkanization” provided a perfect opportunity for a fact to be accepted more on its perceived acceptance by others than on the data themselves. One can readily imagine that, say, demographers pressed about the empirical basis for the male-biased PSR would state something along the lines of, say, “the gynecologists figured that out”. In part, the knowledge dynamic is similar to the game of “telephone” in which partial information at best is (re)transmitted. Here, the scientific argument underlying the message got lost in the transmission. Ironically, this occurred even though multiple professions had a stake in the problem, which at first blush one imagines might have fostered independent investigations. Instead, the presence of multiple professions likely had the opposite effect.

Sex ratio data derived from spontaneous abortions could provide a meaningful estimate of the PSR. Why did this not happen? The degraded knowledge dynamic described above limited any serious engagement with the complexities of how to use such data to estimate the PSR. For example, many fetuses die without the mother knowing she is pregnant and so are not included in samples of spontaneous abortions. Backwards extrapolation of the early sex ratio from later sex ratio data is possible but must be done very carefully. In addition, spontaneous abortions were usually regarded as unbiased samples from a population of fetuses having a male-biased PSR. The alternative possibility that the estimates arose from biased samples of a population having an unbiased PSR received little attention, and so possible corrections for a sampling bias went undeveloped.

My colleagues and I recently estimated the trajectory of the sex ratio from conception to birth by analyzing three-to-six-day-old embryos derived from ART procedures, fetuses from induced abortions, fetuses that have undergone chorionic-villus sampling or amniocentesis, and US census records of fetal deaths and live births (Orzack et al. 2015).

The trajectory of the cohort sex ratio from conception to birth. “PGD All” and “PGD Normal” denote the total and normal sex ratio estimates based on ART embryos, CVS denotes the estimated sex ratio trend based on chorionic-villus sampling data, ABORTION denotes the estimated trend based on induced abortions, AMNIO denotes the estimated trend based on amniocentesis data, and FDN denotes the trend of cohort sex ratio based on US fetal deaths and live births. A dashed line denotes a sex ratio of 0.5.

Our assemblage of data is the most comprehensive ever assembled to estimate the PSR and the sex ratio trajectory and is the first to include all of these types of data. We found that the sex ratio at conception is unbiased, the proportion of males increases during the first trimester, and total female mortality during pregnancy exceeds total male mortality (contrary to long-held opinion); these are fundamental insights into early human development (Austad 2015).

Our analyses avoided the perils of backward extrapolation (because we have data from embryos that are just a few days old) and the potential bias of estimates based on spontaneous abortions (because we did not use such data). On the other hand, our estimate of the PSR is potentially biased because most, but not all, ART embryos are conceived outside of mothers. Our estimate of the trajectory of the sex ratio after conception might also be biased because it is based in part on sex ratio data from mothers undergoing diagnostic procedures. As described in our paper, we believe that these potential biases do not influence our estimate of the PSR and of the trajectory. Nonetheless, we encourage scrutiny of potential biases influencing our analyses. Whatever the outcome of such scrutiny, our analyses set a new standard for analyses of the pre-birth human sex ratio, one that we hope will end the degraded knowledge dynamic that has long held sway in the study of the pre-birth human sex ratio.

References:

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

Campbell, R. (2001). John Graunt, John Arbuthnott, and the Human Sex Ratio Human Biology, 73 (4), 605-610 DOI: 10.1353/hub.2001.0048

Graunt, J. 1662. Natural and Political Observations Made Upon the Bills of Mortality. London: Martyn.

MacDowell, E. C., and E. M. Lord. 1925. Data on the Primary Sex Ratio in the Mouse. Anatomical Record 31: 143–148.

Nichols, J. B. 1907. The Numerical Proportions of the Sexes at Birth. Memoirs of the American. Anthropological Association 1 (4): 247–300.

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

Shettles, L. B. 1961. Conception and Birth Sex Ratios. Obstetrics and Gynecology 18 (1): 122–130.

Stern, C. 1960. Principles of Human Genetics. 2nd ed. San Francisco: W. H. Freeman.

Tschuprow, A A. 1915. Zur Frage Des Sinkenden Knabenüberschusses Unter Den Ehelich Geborenen. Bulletin de L’institut International de Statistique 20 (2): 378–492.

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On behalf of the organizing committee I would like to draw your attention to the 8th International PhD School Plant Development (IPSPD VIII) (www.plant-development.org).

The meeting will take place October 07-09 at Zellingen-Retzbach close to Würzburg, Germany.

Conference website:  www.plant-development.org

Registration costs are 195 Euro per person (includes accommodation, meals, conference dinner, conference fee).

Registration deadline: August 14, 2015

Organizing committee: Kay Schneitz, Markus Schmid, Rita Gross-Hardt

General information:

With the growing complexity of biological research projects in the last decades it has become increasingly important for scientists to communicate and collaborate across geographical and subject boundaries. Thus, young scientists not only need to be trained early in their career to present data at international meetings and discuss it with peers and leaders in the field but also to organize chair sessions as well as to network and identify potential collaboration partners. The PhD School on Plant Development was set up in 2008 with the aim of training young scientists in these skills and give them a platform for communication and collaboration.

Plant developmental biology is an exciting and fast moving field, which has seen many breakthroughs over the last decade. However, apart from this PhD School we are not aware of a signature meeting that is aimed at international graduate students and young postdocs.

The International PhD School consists of ten successive sessions that are each introduced by an internationally renowned keynote speaker. These sessions cover a broad range of topics, such as stem cells and meristem function, vegetative and reproductive development, hormone signaling, embryogenesis, gametophyte and germ line formation, seed development, cell biology as well as aspects such as epigenetics, evolution, systems biology and mathematical modeling. It is expected that two to three PhD students/young scientists represent their research data in each of the sessions that shall be chaired by other PhD students/young scientists. It will be at their responsibility to initiate fruitful discussions and guide constructive conversations. Two poster sessions will provide extra time and informal opportunities for discussions.

The IPSPD will take place at the congress center “Benediktushöhe” in Zellingen-Retzbach, a small town near Würzburg (http://www.benediktushoehe.de). This place is distinguished by its central location, which can be easily reached by train from throughout Germany, including from central international airports such as Frankfurt Airport or Nürnberg. Furthermore, past experience has shown that Benediktushöhe provides a professional seminar venue with nice rooms, excellent catering and a friendly and professional atmosphere. At the same time, the center charges moderate fees, which allows for registration costs that are easily affordable for students and young postdocs alike.

Invited speakers include:

Maria Albani (MPI Köln)

Martin Bayer (MPI Tübingen)

Miguel Blazquez (University of Valencia)

Thomas Dresselhaus (University of Regensburg)

Veronica Grieneisen (JIC, Norwich)

Ueli Grossniklaus (University of Zürich)

Marcus Heisler (EMBL Heidelberg)

Alexis Maizel (University of Heidelberg)

Moritz Nowak (VIB, Ghent)

Karin Schumacher (University of Heidelberg)

Dolf Weijers (University of Wageningen)

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Hi there,

the School of Life Sciences Weihenstephan at TU Munich invites applications for an assistant professorship in Plant Genetics. More information can be found at the link below. If you have any questions don’t hesitate to email me at kay.schneitz@tum.de.

Kay

http://portal.mytum.de/jobs/professuren/NewsArticle_20150601_151423

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Epigenomics of Common Diseases

6-9 November 2015
Wellcome Trust Genome Campus, Hinxton, UK
Conference hashtag: #ECD15

Bursary deadline: 8 September | Abstract deadline: 22 September | Registration deadline: 6 October

The 5th Wellcome Trust Epigenomics of Common Diseases conference will bring together leading scientists from the fields of epigenomics, genetics and bioinformatics to discuss the latest developments in this fast-moving area.

Epigenetic variation plays an important role in disease processes and provides a promising focus for disease prediction, prevention and treatment. Technological advancements in the past few years have fuelled a dramatic increase in the scale, breadth and availability of epigenomic reference data. In addition, novel developments such as single cell analysis and gene editing present exciting new opportunities. Associations between epigenetic variation, a variety of risk factors and the development of many diseases continue to emerge but causality has, in many instances, not yet been established.

This meeting will focus on epigenomic studies across of a wide range of common and other diseases, including approaches from a variety of different disciplines. It will explore technological and methodological developments and provide a forum to present and discuss recent advances in epigenomics of relevance to human disease. We welcome abstracts from all areas relevant to epigenetic and epigenomic research. Several oral presentations will be chosen from the abstracts submitted.

Topics will include:
Epigenomics of disease
Chromatin organisation
Model systems: animal and cellular models
Population epigenetics
Clinical epigenetics
Single cell epigenetics
Epigenetic engineering
Informatics and technology

Scientific programme committee:
Stephan Beck, University College London, UK
Susan Clark, The Garvan Institute of Medical Research, Australia
Andy Feinberg, Johns Hopkins University School of Medicine, USA
Edith Heard, Institut Curie, France
Caroline Relton, University of Bristol, UK

For further information, visit: https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=515

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