Timed Collinear Activation of Hox Genes during Gastrulation Controls the Avian Forelimb Position.

Limb position along the body is highly consistent within one species but very variable among vertebrates. Despite major advances in our understanding of limb patterning in three dimensions, how limbs reproducibly form along the antero-posterior axis remains largely unknown. Hox genes have long been suspected to control limb position; however, supporting evidences are mostly correlative and their role in this process is unclear. Here, we show that limb position is determined early in development through the action of Hox genes. Dynamic lineage analysis revealed that, during gastrulation, the forelimb, interlimb, and hindlimb fields are progressively generated and concomitantly patterned by the collinear activation of Hox genes in a two-step process. First, the sequential activation of Hoxb genes controls the relative position of their own collinear domains of expression in the forming lateral plate mesoderm, as demonstrated by functional perturbations during gastrulation. Then, within these collinear domains, we show that Hoxb4 anteriorly and Hox9 genes posteriorly, respectively, activate and repress the expression of the forelimb initiation gene Tbx5 and instruct the definitive position of the forelimb. Furthermore, by comparing the dynamics of Hoxb genes activation during zebra finch, chicken, and ostrich gastrulation, we provide evidences that changes in the timing of collinear Hox gene activation might underlie natural variation in forelimb position between different birds. Altogether, our results that characterize the cellular and molecular mechanisms underlying the regulation and natural variation of forelimb positioning in avians show a direct and early role for Hox genes in this process.

Moreau C, Caldarelli P, Rocancourt D, Roussel J, Denans N, Pourquie O, Gros J

Curr Biol. 2019 Jan 7;29(1):35-50.e4. doi: 10.1016/j.cub.2018.11.009.

Open Access

Molecular control of macroscopic forces drives formation of the vertebrate hindgut.

The embryonic gut tube is a cylindrical structure from which the respiratory and gastrointestinal tracts develop1. Although the early emergence of the endoderm as an epithelial sheet2,3 and later morphogenesis of the definitive digestive and respiratory organs4-6 have been investigated, the intervening process of gut tube formation remains relatively understudied7,8. Here we investigate the molecular control of macroscopic forces underlying early morphogenesis of the gut tube in the chick embryo. The gut tube has been described as forming from two endodermal invaginations-the anterior intestinal portal (AIP) towards the rostral end of the embryo and the caudal intestinal portal (CIP) at the caudal end-that migrate towards one another, internalizing the endoderm until they meet at the yolk stalk (umbilicus in mammals)1,6. Migration of the AIP to form foregut has been descriptively characterized8,9, but the hindgut is likely to form by a distinct mechanism that has not been fully explained10. We find that the hindgut is formed by collective cell movements through a stationary CIP, rather than by movement of the CIP itself. Further, combining in vivo imaging, biophysics and mathematical modelling with molecular and embryological approaches, we identify a contractile force gradient that drives cell movements in the hindgut-forming endoderm, enabling tissue-scale posterior extension of the forming hindgut tube. The force gradient, in turn, is established in response to a morphogenic gradient of fibroblast growth factor signalling. As a result, we propose that an important positive feedback arises, whereby contracting cells draw passive cells from low to high fibroblast growth factor levels, recruiting them to contract and pull more cells into the elongating hindgut. In addition to providing insight into the early gut development, these findings illustrate how large-scale tissue level forces can be traced to developmental signals during vertebrate morphogenesis.

Nerurkar NL, Lee C, Mahadevan L, Tabin CJ.

Nature. 2019 Jan;565(7740):480-484. doi: 10.1038/s41586-018-0865-9

Evolution of limb development in cephalopod mollusks

https://elifesciences.org/articles/43828

Oscar A Tarazona, Davys H Lopez, Leslie A Slota, Martin J Cohn 

Cephalopod mollusks evolved numerous anatomical novelties, including arms and tentacles, but little is known about the developmental mechanisms underlying cephalopod limb evolution. Here we show that all three axes of cuttlefish limbs are patterned by the same signaling networks that act in vertebrates and arthropods, although they evolved limbs independently. In cuttlefish limb buds, Hedgehog is expressed anteriorly. Posterior transplantation of Hedgehog-expressing cells induced mirror-image limb duplications. Bmp and Wnt signals, which establish dorsoventral polarity in vertebrate and arthropod limbs, are similarly polarized in cuttlefish. Inhibition of Bmp2/4 dorsally caused ectopic expression of Notum, which marks the ventral sucker field, and ectopic sucker development. Cuttlefish also show proximodistal regionalization of Hth, Exd, Dll, Dac, Sp8/9, and Wnt expression, which delineates arm and tentacle sucker fields. These results suggest that cephalopod limbs evolved by parallel activation of a genetic program for appendage development that was present in the bilaterian common ancestor.

 

BMP9 stimulates joint regeneration at digit amputation wounds in mice

• Ling Yu, 
• Lindsay A. Dawson, 
• Mingquan Yan, 
• Katherine Zimmel, 
• Yu-Lieh Lin, 
• Connor P. Dolan, 
• Manjong Han & 
• Ken Muneoka 

Nature Communicationsvolume 10, Article number: 424 (2019) 

Abstract

A major goal of regenerative medicine is to stimulate tissue regeneration after traumatic injury. We previously discovered that treating digit amputation wounds with BMP2 in neonatal mice stimulates endochondral ossification to regenerate the stump bone. Here we show that treating the amputation wound with BMP9 stimulates regeneration of a synovial joint that forms an articulation with the stump bone. Regenerated structures include a skeletal element lined with articular cartilage and a synovial cavity, and we demonstrate that this response requires the Prg4 gene. Combining BMP2 and BMP9 treatments in sequence stimulates the regeneration of bone and joint. These studies provide evidence that treatment of growth factors can be used to engineer a regeneration response from a non-regenerating amputation wound.

Hox Timing Determines Limb Placement

sci-hub.tw/10.1016/j.cub.2018.11.068

Young, J. J., Grayson, P., & Tabin, C. J. (2019). Developmental Biology: Hox Timing Determines Limb Placement. Current Biology, 29(2), R52–R54. 

Hox genes are known to determine vertebral identity along with being required for normal limb patterning. A new study now finds that differential expression timing of Hox genes in the lateral plate mesoderm determines limb placement as well. 

Memes got me!

Long silent time. Not caused from any shortage of coffee or interest about science but  the last few years my life have been quite weird. The revival of this blog should be short, just to discuss a few points about memetics. 

During a 24h vacation from my actual preoccupations I came across a paper from Maarten Boudry (get a copy here) : 

Replicate after reading: on the extraction and evocation of cultural information
Maarten Boudry, Biology & Philosophy (2018) 33:27 https://doi.org/10.1007/s10539-018-9637-z

My interest was triggered by a tweet: — Maarten Boudry (@mboudry) July 11, 2018

Old joke presented here and there are a few variants about its conclusion.  I have use it to illustrate how the same stimulus may elicit different responses depending on the system under investigation and its receptors, say doxycycline used for expression of a transgene under a TetOn promoter and the role of the antibiotic on angiogenesis inhibition; that may be tricky if your transgene is also supposed to inhibit angiogenesis, right?

Anyway, I got a copy of Boudry’s paper and I started reading. The way I used the joke is contradicting the assertion on page 26:

For the system to work, every participant already needs all the jokes stored in memory, along with the corresponding numbers. This, of course, is the point of the punch line: if you start laughing, you must have heard the joke before.

Well…
Another Real World example to support my objection.is the evolution of the metabolic pathways producing THC; they didn’t evolve for recreational or medical use, right? Same stimulus, different receptor, different effect.

But that’s something to discuss about and it’s fun to start discussing about jokes. I’ll put that aside, maybe for later.

But than Boudry starts discussing about Sperber and on page 27 he cites from  Sperber D (2000) An objection to the memetic approach to culture. In: Aunger R (ed) Darwinizing culture: the status of memetics as a science. Oxford University Press, Oxford, pp 163–173

In general terms, Sperber proposes three “minimal conditions for true replication”. For B to be a copy of A, 

1. B must be caused by A (together with background conditions)
2. B must be similar in relevant respects to A
3. The process that generates B must obtain the information that makes B similar to A from A. 

Now, when you talk about true replication to a biologist you have his attention. Instantly. Of the various types of biological replication my favorite is the rolling circle some bacteriophages use. And it is used also for in vitro isothermal amplification. Certainly not the most common one, so I’ll stick with the more used one here.

Let’s examine the three points Sperber proposes for B to be a copy of A and if it’s possible to qualify DNA replication as true.

Point 1 is OK I think if we take in the background conditions the DNA polymerase, the dNTPs and a bunch of other stuff. I singled out the enzyme and the dNTPs because I want to discuss them below.

Point 2 is problematic. In fact, from a double stranded DNA molecule A we can obtain two double stranded DNA molecules indistinguishable from A (no mutations for the moment and the necessary machinerie to polish the ends of the molecules.) During the replication process, the DNA polymerase synthesise two DNA strands that are the reverse complement of the strand serving as matrix! 
Because the two strands of the initial DNA molecule are antiparallel and each one the reverse complement of the other, because of that and only because of that, the two final molecules are similar. And the DNA replication being semi-conservative each of the two resulting molecules is composed by half of the initial one!

 

So, according to point 2 of Sperber’s DNA replication is not a true replication. I think that Meselson–Stahl or Crick-Watson would be quite sad to learn that.

Is it necessary to go to point 3? Probably not, we already know that we are in a GIGO situation here. But just for the fun of it and maybe for future use in a more appropriate set of rules let’s examine how the DNA polymerase knows what must be the next base to incorporate in the neosynthetised strand: it doesn’t.

The complementary  base, able to establish the adequate number of hydrogen bonds with the one of the template (A::T or C:::G) will be correctly positioned to allow the catalysis of its incorporation. The DNA polymerase only sees that it is able to catalyse the formation of a new phosphodiester bond. That’s quite convenient when you need to incorporate to the neosynthesised strand some nucleotide analog, using say dig-dUTP an analog of TTP. And such altered DNA strands may be used as matrices to produce more canonical reverse complements later on.

So, what would true replication be? 

We surely have information transfer from one object to other objects, in the case of DNA replication discussed above in the two resulting double stranded molecules. In other systems we may have transfer of the information in several other molecules. That’s what I like in the rolling circle replication system where a single matrix molecule is used to produce hundreds of daughter (reverse complement) strands each of them circularised and encapsulated in a virion in the replication of say filamentous phages.

Some times the information is stored in a similar medium (say DNA or RNA or PNA). Or it can be stored in a completely different medium: for genetic information in silico instead in carbon based molecules. I salute here Craig Venter and his team who brought us the proof of concept. So, the nature of the support doesn’t matter. Sperber’s point 3 is pertinent here, but still not point 2.

I can’t imagine anything else to define a true replication. Maybe you do and the comments are open.
But I suggest that Sperber’s definition should be respectfully discarded and not used in memetics as it can’t be used in biology.

 

 

Vertebrate limb bud formation is initiated by localized epithelial-to-mesenchymal transition

Vertebrate limbs first emerge as small buds at specific locations along the trunk. Although a fair amount is known about the molecular regulation of limb initiation and outgrowth, the cellular events underlying these processes have remained less clear. We show that the mesenchymal limb progenitors arise through localized epithelial-to-mesenchymal transition (EMT) of the coelomic epithelium specifically within the presumptive limb fields. This EMT is regulated at least in part by Tbx5 and Fgf10, two genes known to control limb initiation. This work shows that limb buds initiate earlier than previously thought, as a result of localized EMT rather than differential proliferation rates.

Gros J, Tabin CJ.

Science 14 March 2014:  Vol. 343 no. 6176 pp. 1253-1256, doi:10.1126/science.1248228

Arnold Munnich

Dans Le Point du 17 octobre 2013, p 74-75, une mise au point d’Arnold Munnich (responsable du département de génétique de l’hôpital Necker-Enfants malades à Paris), titrée « La médecine n’est pas le tiercé ». Les propos sont recueillis par Jérôme Vincent qui signe également l’encadré de la p 75 sur « ce qui est autorisé, ce qui est interdit ». Excellent pour une prise de bec !

NB le dossier du Point est à lire, les autres intervenants semblent avoir les pieds sur Terre, aux kiosques !

D’abord, cartes sur table, je travaille pour Portable Genomics Inc., une société américaine, démarrée par des francais éxilés aux USA (à cause de l’ineptie qu’est la loi bioéthique française), et dont le business est lié cet espace de la génétique et de la génomique personnelle.

Avant une dissection en règle de cette mise au point deux choses que je souhaite clairs :

– Effectivement, la médecine, ce n’est pas le tiercé. Je suis entièrement d’accord.
– La génétique personnelle n’est pas le tiercé non plus; elle demande des médecins capables d’exploiter les connaissances actuelles et justement, pour éviter le tiercé,  je ne laisserai jamais un médecin comme Munnich s’occuper de moi ou des gens auxquels je tiens.

Rats! & NDE: SQUEAK

NDE have been used as proof of the existence of souls in a large set of stupid arguments.
Following this trend, it seems that prophet Sir Terry Pratchett revealed that rats have souls, managed by the DEATH of Rats of course, in his novels.
Now scientific evidence come to support either:

• the existence of rats’ souls, or
• the non-supernatural, quite materialistic, explanation of NDE.

Jimo Borjigin, UnCheol Lee, Tiecheng Liu, Dinesh Pal, Sean Huff, Daniel Klarr, Jennifer Sloboda, Jason Hernandez, Michael M. Wang, and George A. Mashour
Surge of neurophysiological coherence and connectivity in the dying brain

PNAS 2013 ; published ahead of print August 12, 2013, doi:10.1073/pnas.1308285110

The brain is assumed to be hypoactive during cardiac arrest. However, the neurophysiological state of the brain immediately following cardiac arrest has not been systematically investigated. In this study, we performed continuous electroencephalography in rats undergoing experimental cardiac arrest and analyzed changes in power density, coherence, directed connectivity, and cross-frequency coupling. We identified a transient surge of synchronous gamma oscillations that occurred within the first 30 s after cardiac arrest and preceded isoelectric electroencephalogram. Gamma oscillations during cardiac arrest were global and highly coherent; moreover, this frequency band exhibited a striking increase in anterior–posterior-directed connectivity and tight phase-coupling to both theta and alpha waves. High-frequency neurophysiological activity in the near-death state exceeded levels found during the conscious waking state. These data demonstrate that the mammalian brain can, albeit paradoxically, generate neural correlates of heightened conscious processing at near-death.

Illustration by ~Smaggers

Just for Hits – Richard Dawkins