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Osbourn and Haseloff: Discussion

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Osbourn and Haseloff: Discussion
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2015
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English

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Subject Area
systems Altbier plant plant
mode physical chemist Quantitative mechanism metabolic plant quantum gene case genetic information formulation cell Simulation control modifications chemical formulae type progress surface properties dynamics Genetic marker genome source man mutation systems model function RNA
titrations physical chemist sense biosynthesis mechanism metabolic plant operation Bifurcation theory gene striking cluster genetic information formulation specific cell division cell transcription overexpression modifications grain period processes organizations DNA steps genome additional complexes pressure slides end branches systems Wasserstoff clusterization metabolic pathway chemical structures regulation separation hopes modules
Phosphorsäureester Prolin growth metabolic gene interface penicillin cluster enzymes rapid Terpene transcription factors localization organizations Maische Gases steps genome eukaryotes firm death clusterization sequence selective DNA recombinant biosynthesis bear species mechanism activities plant dried Diet food specific cell overexpression homolog parents Butcher level Färben natural products Rye bread glass dynamics translocation Hydroxamsäuren synthase metabolic pathway initial function substrates
I guess initially with some other we
were using experimental parameters that we could derive either from published work for our own work and then the immersion behavior was came out of that physical model but as we're moving into plant systems we're more explicitly
using say for example make an example is within my County a very simple asexual propagules which under development under the microscope you can get very good quantitative data for cell geometries and properties that you can map onto that process and try to describe geometries in ways that you can classify interactions it is important to us so using graph that type approaches to formalize the description of solar directions we'll see what exempt being different in different at marys I guess yeah it's quite it's an early stage in the work but I think that's really important and to think of all creative ways of trying to integrate genetical properties physical progress and dynamics and by the way I have a comment to me hilaria h es there's a group in France actually and in Germany trying to use category theory and we know its birthplace here are trying to model are those graphs how the mid formula how do you call that especially in plants one must look what we have to have a certain cozy of the networks and you code in this is a question because the attack mode it has the quality information if you mean well I think that depends a little bit on the data they're using and the abstraction some of its 2d abstractions of three-dimensional data by surface projections and your we're making at this point simplifications as fast as we can to try and identify keys or things that are recognizable and to get correlates essentially that we can then explore further so because a lot of its dynamic and it's not obvious purchased inspection is so in Europe we went offshore simulations will be the mecca me what my identities or plan we'd like to me she when use the genetic information or 15 seconds yes the question is about whether epigenetic information has been included in in some of the models and I think well in a way because we're using genetic markers in some cases which are governed not just by genetic but also epigenetic constraints so some of those epigenetic information is implicit in what we're measuring but not explicit at this point but having said that what are the nice things about my County here is that it has a very streamlined genome I get into details but these very primitive plants have very little genetic redundancy so often unlike in higher plants where you have large gene families associated with say office cell or other specializations in my County oh they're very streamlined and straightforward and some of the RNA
metabolism and other machinery associated with epigenetic control is accessible for mutation and we have things like Chris Burke s9 techniques for knocking jeans out or modifying genes directly so there's a whole range of experiments which are suggesting themselves to start modifying directly the mechanisms for epigenetic modification in ways that might be helped you know so there's an integration of a system where you can measure things directly but also manipulate some of the information speeding into the system particularly sharing information any questions from the audience yes when you're sure that there is a video of the growing plants can you imagine do you think that vary the principle of like a leaf action friendly or when it grew as you say least at least action principle like variational formulation asia not just like you better define it from poor biology question okay like a ray when you light already want to do to minimize both time and energy you know in physical science everything can be derived from more purchase or least action principle I I have no idea yes which I doubt it out of your head yeah this question why well they easily have to have this question because it's like a five man would put every quantum dynamics all together into it actually no but I was only in physics only along
and because no helmets anywhere else yeah it's completely because you can do the same ooh because you can do the same by reaching boy know what as you know that is no reason for east by grindage well you could say if you like i may just because this is a personal interest in the literature there are some people in france in the u.s. we've been trying to do so in France for example there is a searcher called Geo Metro bed-stuy now who's been trying to find and I saw a sort of equivalent fundamental principle and you found something related to self-organization trying to have a definition highly debatable like a living organism living complex system is something that basically conserves the service he does to its environment and by doing so it's organized its up so he found something like all the trophy very impressive negligible p from Schrodinger but it's highly debatable it's highly highly highly debatable it's nonsensical I was yeah it's more people coming from theoretical because actually yes i know of why i asked the question because at some point on your slide you say at the beginning you know is not only a DNA but it is not only necessary to know the code the coding is very more than the coding and there are cell signaling which is important networks and then very seldom you say also but is like in economics political networks and as if the global behavior is optimizing itself like a let's go like at least action 24 in nature when the storm is going down it's like it's following the least action and you don't know why as if the storm knows exactly what you and I were wondering which are the same in biog holiday pisstivity call point of view would be very elegant but it's an open you actually can make important because you have mechanical energy you could use it in some nations done for the hydrogenation and is your is your class something like the hyper love of plant in terms of regeneration yeah it just came back to your question I mean I think from the biology perspective there's this issue of just taking rather pragmatic approach which is the systems are to do we optimize because they revolve systems so there's an economic economy there but again it guess what we're really focusing on is trying to get a handle on the mechanisms because there are things we can measure things that we need hands-on and the idea that we can grapple with some of the emergent processes and trying to find principles or under peanuts every time you know from a pragmatic point of view trying to identify genetic motifs that will play out in a cellular context to create processes which are recognizable the kind of modules that you see in genetic networks but played out in a Cell in the context for example so module that will create self-propagating process cellular process or create some kind of bifurcation in a branch or terminated process they're the kind of things that we're thinking of now the question of optimization hope you that will come out in the end like a rebirth which you know the in the nature you have a that he's been going back to to the jet so the gene expression you can modify gene expression using environment every bug and visit on this line for the ocular pressure again you know in physics everything comes down from the turian formulation of invariance and the real question behind your question is what are the universe in living systems which is a massive open question now maybe another question for everybody not only for for Jim if Sheila's life very well then this relationship very direct it been getting confirmation of misogyny is the second or third slide sorry so you have to sue and sell and then you say
that is implants itself I don't move too much there is a direct relationship and market two arrows if you drop this cell and watch for Janek development can you elaborate more about this if i recall correctly it's it's a diagram which shows a single cell in a time sequence so a seller might be programmed to divide and the two cells that are the two daughter cells then cause a breaking an additional information and system so i guess it's trying to represent that you absolutely mechanique well i think that there's a relationship what the slide is trying to represent is the relationship between the genetic information so you have a field like in the time-lapse image of the pitcher plant you have a million cells they're all isogenic so that same DNA program and yet then it must be some mechanism from started from a single cell and as the cells proliferate to elaborate different states of gene expression and so the breaking of symmetry and the creation of those different states has to be somehow very precisely programmed and then that so there's clearly linkage between the genetic processes which encode that but it so I think a lot of people in Jaffna genetic field tend to think still of genome as as that describing the end point rather than describing the trajectory so all those cells are undergoing different trajectories and that the relationship that the governing of those trajectories are splitting of paths in information sense is governed by social interactions so that's what diagrams trying to represent you and I think that in a way Turing's ideas you know there's morphogenesis based studies the kind of simple interactions and always diffusion etc are the kind of things that play here so did the kind of exchange or movement of signals notice separation of creation of asymmetries by simple processes but play it out in a population of what gives rise to the complexity of the system I do have a question for an above the boundaries of the operon like structures will expect if you have a pathway that is linear this could work to some extent that if you have a branch pathways and because we're branching you may have more than one order of one genomic focus that should own do standard and therefore I would like to know if you have as well as you know its structure from this point of view that is if you have a low pathway but it is the New York it should still be within 4 by the shorter one which is much may belong to different you get really close sighs there's any relation between that's a very good point i mean i think so my speculation is that these clustered pathways are insulated from the rest of metabolism and that's why when we have mutants in those jeans we get a finger side because normally there's redundancy there's a mess but these pathways seem to be insulated and if there's a really interesting question around what constitutes acosta pathway in terms of the starting point and I used to think that it was very influenced of my vocation with primary metabolism for example as I was showing you the triterpenes but if you look at the very nice paper for me in grains lap on the NOS cooking cluster from poppy that's a 10 gene cluster which is dedicated to the synthesis illness I've been drawing a figure for a review I've got the whole alkaloid pathway in poppy mapped out and making nosc apenas only one part of that there's no publicly available Papa genome sequence but the first step in that pathway is not a branch point with primary metabolism it's probably the siphoning off from that network so to be really interesting to know if and when the poppy genome sequence is available where all those jeans are and whether the parts of them that not network the parts that are dedicated to specific end products form discrete clusters so it's a really interesting question what sort of pressure for any so your mentions that there might be a poor expression going on is there any comment that's good for a regulator known for this class of gene because I mean I guess a distance between these genes is too large that one large transcript is formed like a comparison aqua yeah yeah so these these are not operons the genes are pretty confident the genes are independent transcribed the intergenic distance is vary depending MSR in the genome size of the big lagina the bigger the intergenic distance which in itself is interesting there is no periodicity that we can see
at that level I didn't mention transcription factors because hardly is known for any of the pathways that I've mentioned which is quite surprising there are there's a transcription of active for the rice diet open clusters that it's not specific to the clusters it also regulates upstream metabolism there's one very nice example for a cluster from cucumber which has been reported but apart from that we need to know more we were looking for any actors and so are other people I just said it in filamentous fungi which of course are also eukaryotes and which have lots and lots of gene clusters for natural product synthesis including penicillin you quite often but not always find a pathway specific a gene for a pathway specific transcription factor in the cluster we're not seeing that question parameters follow up with frost lab Aspen dreams ladies so you're observing sir plaster for this prior particular special effects and as I understood their fierce interfaces are our enzymes that there might exist in many copies as home and we observe some kind of sequence similarity or the other on the xenos of locals simply the genes within these clusters so with a whole deal with yeah so so certainly you know the genes in the old custard we pretty much have a template paper that we get few years were revamping the gene for the first step in the pathway is a distant relative of psychological synthase they use the same substrate yeah so that gene has arisen either directly or indirectly from primary which has risen and his then divers divide and all of the genes within our cluster they all belong to masashi families because that's a special effort Aborigines but they've gone and done their own thing their divergent members they generally fair the founder members of the new subgroup that's me wait and find sequences not the same not closely related sequences but phylogenetically a group are building different things yeah so just follow me goclever 360 so there they go class there you go for this interface with a psycho psycho pro side of growth genes is it is it a specific example of the moral codes so the observatory on the gases and knocking the die cuts in the day go to observe some more so does he have to do we scope luster yes sorry have no question what you call organization of the deaf parents in the face yes I becomes a yen is something that you observed more in the more goals yeah you observe it in the deck of school these are all they're not the same genes and all the same sequences about their arm there are many many examples so i showed the mining of the 17th plant genus there are lots and lots of examples observable any observe something some you saw some specific example to get very poor slowly and not from the glasses never there everyone everyone so the difference within the one that they big sequence comparisons it will be turkington place p450 gene pairs the point that I was making there is you can find those apostles lot of cuts in the dark ops and that includes know also new clusters but what seems to be happening and is that those in the die cuts the terpene synthases people 50 gene pairs are kind of duplicating like that whereas in the monocot fits all mixing and matching which suggests something really interesting in terms of my percenter me and recombination at least as we've looked at it it's rather naive you show a picture of you have a picture of the promoter being expressed in different depths of rapid offices and dries do you think that this promoter would work say supposing the shoot of the blood culture or is it a super specific no it's it has exactly the same explore pretty much exactly the same expression pattern in diverse plant species as it does in out any note it's specifically in the epidermal cells of the root bear stearns and the lateral root initials so this is very strange how a recently evolved pathway has acquired an ancient regulatory mechanism and it also means it provides a readout that we can use to look at plant developed across what we're now going back to we've been doing some more counter work a lot quite sure whether the promoters doing anything in my counter at the moment what we're going back from higher plants to towards the lower funds to see we can delineate where this breaks down one left division
question ran from your a comparative study of the 17 genomes and the clusters that you bring out a sort of a favorite scenario for the evolutionary dynamics or clusters can they disappear well that's the whole that's another thing the the birth life and death of clusters so the whole population genetics are built around this which I'm still trying to get to grips with but presumably once the clusters lock into place they're optimized the delivering a selective advantage there must be massive selection to drive these things together but then when they become no longer necessary but do they disappear completely today do they break up there are examples which I didn't go into have split clusters which is still operational so the maze didn't bow at a hydroxamic acid cluster wheat and rye also made hydroxamic acid but the genes are split into two sub clusters there so the the hypothesis is there was an ancient translocation event that occurred after maize and wheat and rice separated that split nevertheless it's interesting that pathway still works that's one thing and the other interesting thing is whether once something perhaps has become established and becomes indispensable so it's essentially no longer specialized if that happens then could those jeans be welcomed into the genome was there ever a point on a on the siding pathway genes were clustered okay I will push to thank our speakers again for this women
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