[Materials and Technologies] Spatial organization in cells | Sebastian Fuerthauer
![[Materials and Technologies] Spatial organization in cells | Sebastian Fuerthauer [Materials and Technologies] Spatial organization in cells | Sebastian Fuerthauer](/pic/_materials_and_technologies_spatial_organization_in_cells_sebastian_fuerthauer/UnhGdy0xNzhyMWc_.jpeg)
so welcome good evening to another interesting lecture of the module emerging fields in architecture today we have a special guest um he is in america in the u.s but will be soon in vienna again at the ttu sebastian feud tower sebastian few tower is interested in the physics of cellular scale processes which is cell division and cell motility and a role in development biology after earning his phd at the max planck institute for physics of complex systems and the max planck institute for cellular biology in genetics in dresden in germany he did research at the tata center for interdisciplinary sciences in pedorabat in india also the current institute at new york universities and harvard university he then joined the flatiron institute flatiron institute of the simon foundation in new york city where his work focuses on understanding the role of self-organized processes in the microtube cytoskeleton of cells which enable the segregation of chromosomes during cell division his group at the t orvin will be dedicated to understanding how cytoskeletal networks function in cells and how cells organize into tissue using approaches from theoretical and numerical physics this is a lecture that is really out of the box and emerging in the fields of architecture and i'm looking forward to discuss issues of organization properties how in biotechnology how they can be related to architecture with sebastian filter and you the students of diogene sebastian filter is in the move so he in two weeks he just told me he will be in vienna and you will start your work here from next semester properly is this right sebastian uh yeah i think my contract starts first of february okay so where can we occasionally start shop yeah welcome back and thank you very much for agreeing to have this lecture talk discussion with us i'll hand over the microphone to you now thank you okay thank you so much for inviting me and um hi to all students uh i think this talk will be as out of the box for me as it is for you so please interrupt me if i am talking too much physics or biology or if anything is unclear or if something is clear and just interesting and you want to ask feel free to just jump in so my work is mainly interested in linking what is developmental biology which is largely the study that tells you how do you get from chromosomes to organisms like flies or mice or us using the context concepts from soft metaphysics which is the science that basically taught us how to think about uh complex molecules forming materials and which we then could use to build stuff like this lcd screen which you see the lower end of the screen all of this will hopefully make more sense by the end of this talk but i just wanted to show this slide because also there's a link to my home page if there's anything you want to ask me after the talk you will find all the contact data also references and reviews about some of the stuff that we are that we're talking about today under this link okay so what i thought would be uh fun to do here is to sort of give you a little bit of an overview of the physical concepts and the physical processes that inside cells allow to build the complex architecture of a single cell and of an organism and the the structure that basically does all of the work in this is like this rubbering mess of filaments that move seemingly by magic that you see in the background so what you exactly see here is you actually see an experiment that we did together with people at harvard med where we took the eggs of a frog xenopus levies uh switched them put them in the centrifuge spun out everything that solid and now you get the interior of a living cell that is still alive that still breeds that still has all the chemistry of a living cell and what you can do in there is you can put in the structures a structure that triggers like automatically the formation of complex structures in there which is mediated by these complex networks within which which coexist and build structures both networks are really some form of self-organized architecture well to help you with that let me just take a step back um i have a question yes how can you see this do you use uh what device do you use to see that so the the way this works in the frog so these frogs are just regular frogs uh and what you see here are microscopy images so this is this is done with what is called a spinning disc microscope and the way to see these different structures is that to these frog egg extracts you can add what is called fluorophores which are little fluorescent proteins you probably heard of gfp green fluorescent protein which got the nobel prize some 10 years ago and you can attach them specifically via biochemical tricks to specific structures that float around and here there's like three different colors of fluorophores in the same structure that have been added to the solution and you shine a laser that excites the fluorophore and that shines some light in a specific color back and then you can see where these structures are so that is in a nutshell how the visualization here works um okay but let's go let's start at the beginning what we really want to understand is uh we all started our life as this thing on the left-hand side which is basically one round excels fertilized by a sperm with not much spatial structure and what we want to understand is how do we get from from this relatively simple sack of chemicals to something like a human being which has complex organization which has structure and different parts of the body can do different things the first thing that you have to do in order to do that is you have to go from one cell to more cells and just to give you a sense on how frequent this process is in order to form any any one of you you have roughly 10 to the 13 that is 10 trillion cells so you need 10 trillion cell divisions and that's a that's a number which is very hard to imagine um just to give you a sense this is 100 times more than there are stars in the milky way and if you just think about how often cell division occurs because cells also die so even in in us adults cells keep dividing right now about one about 0.1 trillion cells or 100 million cells 100 billion cells are divided in each of our bodies which is about the same numbers the cells in the milky way as we as we speak so obviously this process is kind of important but if you just had that this would just get you from one cell to 10 trillion disorganized cells so to a huge blob of cells if you if you look at the vitruvian man there's obviously more that has happened uh in the vitruvian man and in all of us our front is different from our back our head is different from our feet and maybe a little bit more subtle the left hand side of our body is different from our right hand side for instance the um our heart is on the left hand side of the body was other organs like the lung on the right hand side is bigger and things like that so this there is a structure and since we all look pretty much the same at least at the scale of this of this description the structure is somehow encoded in the genome and in the processes that lead you from the single cell to the complex organism and that is uh something which inherently has a lot of physics in in it so yeah in order to achieve this you need to move cells around and push them in the right directions and that is that is basically what we want to understand okay but the first step and that is what i will focus in most of this talk on is how can you make more cells but before before i go there maybe it's a good idea to just see whether there's something conceptual here that that people want to ask about before i go on or whether what i should just continue i have a question again i'm starting out because i've just okay reminded of the genotyping phenotype of cells exactly so there is there's like there's like of course the map from genotype to phenotype which encodes all of this which is sort of the software of a biological organism i want to talk about what so to say the hardware there's like this whole machinery which reads out the genetic information gives you an initial state and from this state you have to build stuff so in a way like in a very simplified way the genome is something like the blueprint but and at least in the microscopic world a blueprint doesn't build itself you need all the machines around the blueprint that can read it that can construct things and put them together in the right way so this is the the physics part of it okay so how do you make more cells uh and you probably remember some of this from high school but basically uh the way this works uh in a high school's picture that most of the time cells hang out in prophase basically um are in metaphase which is not depicted here in prophase and where they basically weight and grow and generate more material more material and just become bigger but at some point they start to to get ready for division so they round up is the first thing that happens then um the genetic material which hung out in a way in a in chromatin form so in a form that biological processes can read and use to build more protein and build more structure and they're reorganized into these little x-shaped structures the chromosomes chromosomes are then collected in the middle of the cell in metaphase a structure called the mitotic spindle then they are pulled apart and divided between two daughter cells then split off so in order for and to the left here you see sort of one of the earliest observations of all of this which is by virtue fleming in 1882 these are the cells of a newt where you can where you can sort of follow these same structures these sausage-like things other genetic materials the chromosomes you see the cell rounding up you see the spindle which is the structure that will collect and divide the chromosomes starting to form in figure e you see the chromosomes being centered here and then being pulled apart so the the reason why this i think why i'm giving a talk here is even this process um requires a lot of uh self-organization so you basically in each of the cell cycles have to build one of these spindles from scratch which means like as many times as their stars in the in the in the milky way right now in your body you have to use this thing to find chromosomes in order for later being able to divide the chromosomes between the two sides you have to somehow find the middle of the cell and then you have to pull stuff apart so all of this has a lot of spatial organizations and here's a is a slightly more modern depiction of this process so this is a movie that my colleague razer farhadifah here in new york gave me this is the embryonic cell the first the fertilized egg of a worm called c elegans and what you see here on the left hand side is the spindle that has just formed and colored in red by a marker that goes to histones you see the chromosomes so now you see this structure as it has found the chromosomes aligning itself with the central axis of the cell by itself finding the middle and then pull chromosomes apart so if you if you go a little bit deeper you can now start to ask what is this structure actually and we did some of this work a couple of years ago when we basically took one of these cells together with colleagues from from dresden stephanie raymond was the lead out on this she is now in virginia at uvc and flash throws the cell at the point at the metaphase point so basically if this movie loops again i'll call it out for you basically at around this position and what you can then do yet then you can do higher resolution imaging by electron tomography and get a very detailed picture of the instantaneous architect texture of one of these cells of one of these spindles that is what i'm showing you on the right hand side so really what these spindles are is a mess of tubular filaments that have the chromosomes the genetic material in the middle and these poles on the side so the cartoon picture that people have arrived at from from this and other work and earlier work it's really you would think of a spindle as this structure made out of polymer filaments rod like filament and i've been using the word microtubule a lot they're really little tubes that's that's really how you can think about that uh that live in cells they organized around two spindle poles which are these structures here can you see my pointer probably not can you guys see my mouse pointer yes yes yes okay um so there's these two spindle poles on each side the chromosomes in the middle and they're anchored everything is anchored to the cell surface by these guys here which are little motor molecules which pull from the thing on the outside and help you to send them so i guess that would be another good point ah well maybe i'll show you the same slide uh this in the next slide is and while there is like between different cells and cell types quite some diversity about exactly how these spindles look the general structure like this general cartoon picture here is really conserved between cells cell types and different types of animal so here as an example i show you the the worm embryonic spindle from the from the very beginning and to the right i'm showing you another example of a spindle this guy is smaller but it still has the two poles it has the genetic material in the middle and it has um has like the structure of tubular filament uh this example comes also from a worm but from a germ cell so from this this comes from the unfertilized egg as it is about to form um okay so uh is there any questions about what a spindle is or anything else that i mentioned and that was that a good one too fast over okay so um really what what now the challenge is is you to to function uh and to to do all of this uh there's sort of a sequence of self-organization steps that you need to go through um universe need to build the spindle then you need to center the spindle and the chromosomes in the cell uh then you have to sort of find the middle after you found the middle of the cell you have to split exactly at the half and move exactly the half number of chromosomes to the left and to the right and then something else that the spindle will do is it sort of tells the rest of the cells where it has to split up and just here to the right this the structure that i'm showing you that is actually a spindle from another cell this comes from human from from gila it's a cancer cell line there's a picture from the tolerance lab that are in zagreb i think okay i will mainly focus in this talk about how the spindle can build itself because i figured that illustrates a lot of the concepts that might be interesting for you guys and so that is what i will try to try to think about so how do you how do you achieve this type of architecture without an architect how do you build this thing automatically um so obviously there's there's not like a blueprint for the eiffel tower like for the eiffel tower here but there is kind of uh similar elements that you have similar questions that you have to solve and sort of the the first the first thing that you that you have to think about is uh you have to start to learn about what these filaments that that make up the material actually are like in the case of this man battle structures it is just metal rods here you have to think about these microtubules should you think about them as static broad size to something more happy so if you look at the microtubule in so this is just a computer generated image but uh comes from from years of doing electron microscopy on these types of structures so we know pretty well what these structures look like um these microtubules are polymer filament um they're real hollow tubes made out of in general 13 what is called protofilament so each protofilament is one of these lines that you see there and they have two ends which are structurally and chemically different which in the field we call plus and minus end which has nothing to do with an electric charge that is just how the nomenclature has established and during the life of a microtubule it starts basically as a little microtubule nucleus and it keeps growing for a while from the plus end so there's more of the building blocks so these little building blocks are uh tubulin dimers these are the cooling blocks of microtubules it keeps just adding more of this these little building blocks until an event that is called catastrophe occurs and the microtubule randomly switches to to shrinking very suddenly um what that means is that each of the rods that a spindle is made of has a very finite lifetime so these lifetimes have been measured in most spindles microtubules live around 15 20 30 seconds so they grow and drink and are gone after 30 seconds and as they do so have an average lens of 6 microns so six thousands of a millimeter or something like that and the lens distributed lens is because of this growth and shrinkage process uh distributed exponentially so you have much more short microtubules and a few long microtubules at the tail of the distribution again to give you a sense about what that means is like these in our eiffel tower analogy there's already a very big difference in this eiffel tower someone went at some point and put like the metal struts there and i don't know how many they replace ever but they ever replace any of those but they pretty much stay put for the lifetime of the structure in contrast in these spindles each of these filaments is replaced every 15 20 30 seconds or something like that this is especially especially striking if you also try to compare this number to the lifetime of spindles um i guess the most striking example are meiotic spindles like the spindles that do the cell division to go from normal cells to something like egg cells in human women the meiotic spindle is basically in in the egg cells it's basically formed while they are still in utero while they are still in their mother the axons are formed the spindle sits in basically in metaphase basically in this state here until menopause so the structure can be stable for what i know 40 45 years um however each element of the structure is replaced every 15 seconds so that makes that makes like the self-organized architecture already in its building materials quite different from something that you that you would be familiar from on human scales the second thing so this is now a spindle of a frog is that in these spindles every one of the struts that you see there every one of these microtubules moves so what you see on the on the right hand side is a static picture of one of these spindles is this american football rugby rugby ball shaped object and the way this has been visualized is by by putting a lot of of the fluorophores that i told you about before into the substrate so that the whole structure lights up right so this is obviously a photo but if i showed you a movie on the left hand side you would basically just see this whole structure staying put and shaking around a little bit in the experimental chamber but basically stay like this what the experimentalists have done on the right hand side is that they just have used way less of this die way less of these dual force so now instead of one of these microtubules being fully labeled and fully lighting up um in under the microscope what you have is that every like hundreds or thousand microtubules that carries one little bright dot one little sparkle that somewhere randomly built into its structure and that's the sparkles that you see on the right hand side so the other thing that i should tell you is that compared to the left hand side the right hand side is rotated so these poles here would be on the bottom and on the top here but what you see is that each of these dots moved but that's what you learned from that is that each of the filaments in the spindle like it's not like the like the metal struts like the osatura metallic in the eiffel tower uh but uh stays put where it stays put but moves through the structure actually from the center towards the poles during the whole lifetime so what that means here means is that there is motion and if there's motion there's something that causes this motion there must be a driving force and i promise i won't show you too many equations but i felt that this one should probably be fine at the equals i made so there must be some forces that act on these microtubules as they are in the spindle that help the construction of the process and in general you can think about this as some active force some kind of driving force there's probably some resistance because the filaments are connected to um the the other filaments in the system so there's something that prevents motion so i just now took this f equals m a and wrote it f active or f driving force plus f drag equals m8 the other thing that you that that will become important here is that these structures are very small and they're in general embedded in a in a liquid that is very viscous so instead of thinking about this structure here as like a like um uh something that you can apply a force for to but that will keep moving as you stop applying the force at this level you can basically forget about the m a forget about the acceleration that means like if you push at a constant force this whole thing will move at the constant speed it's really like an ant trying to swim in peanut butter or something like that so that means uh two things that are seemingly contradictory and which make all of these physics uh quite different from everything anything you would think of on large scales this means that the total force that each of these filaments experiences every point in time has to add up to zero because basically you never accelerate a is basically always zero but yet if you see something move it means that there's an active force that balances against the drag force against a force that comes from being coupled into the network okay so how how would you even produce these forces and there's there's two ways that are important one is since these filaments grow and shrink they can of course grow and shrink against an obstacle if you grow and drink against an obstacle that will push the whole filament back and that is something that happens near the chromosomes where you can grow against them and push them around by just growing against them and pushing them through through space the other thing is that there's specialized molecules in cells so called molecular motors that can take two filaments if they're close enough by grab both of them and basically walk along them walk towards either the plus end or the minus and there's different different variants of that so that is another thing that makes this spindle architecture very different from uh at least my understanding of human architecture which is that uh the way you would couple uh your your rods that you that you build your structure out of would not be by something static but by something uh that can consume fuel walk along the filaments move and and keep pulling on them actively by consuming energy there's different types of these molecular scale motors in spindles there's uh basically two that are very important kinesins which are motors that are symmetric so they tend to have two you can basically think of them as like two pairs of feet that are attached in the center and that grab two microtubules and walk towards the plus ends uh and dyneins which mainly have one static end which just hangs out at minus ends of one microtubule and uh a pair of feet that grabs the other microtubules and then walks to the minus while the details are probably too much for this talk what i want to emphasize is that what kinds of motors you have in these structures really shapes the emergent the emergent architecture of the spindle so what you see in the middle is a healthy wild type wild type is like the jargon for as you would find it in the natural environment spindle and what these people here have done to this poor spindle is that they put a poison into the into the structure that either kills off the the kinesin motors or the dynein motors if you kill off the kinesin motors you go to the structure on the left you go from this american football thing to something star-shaped if you kill off the dynein motors you go from this football shape structure to something that had much more flared out and both of these perturbed spindles cannot do their function so really the way the link is shaped the structure and keep the structure in shape is important for the spindle function and so what i think the second key difference between the human scale architecture uh that we are used to here is that the building materials in the spindle don't stay not only do they fall apart but they also don't stay put during their lifetime they're not put together by static screws or whatever they use here but they are put together by molecular scale motors which make them move through the structure throughout their whole existence okay i think that's another another good point to ask you guys for questions um yes i think this is a good point can you turn the cameras on please i think we haven't seen all of you at the beginning and it is always nice for the lecturer to see who is here um i have let me start but maybe you can tune in um i think it's interesting to to sh to talk about the differences of the molecular structure to what we're used to design on earth so i have one question do you mean that biological architecture is always changing moving adapting so on on the scale that we're talking about here inside cells uh yes there is there's count examples right on bigger scales we have bones which also renew but on a time scale which is much much larger so you can think of bones like something that is relatively static but on these very small scales basically every structure that we know about sort of rebuilds itself every 30 seconds so that means stability in the sense of of cellular structures is instability i mean not instability stability is when cells are moving in relation to each other or reviewing themselves what happens when they stop doing that is this happening uh well when you're dead that's so i think that the the underlying question is why would you build a system in this way which seems very wasteful and expensive because you basically put a lot of energy into building the same thing over and over again and some examples it stays around for 40 years and there's some partial answers that we understand what you gain by that is you gain a lot of robustness because now if someone comes in and breaks your spindle after 30 seconds you have a new one right if something goes goes wrong it's very hard to disrupt these things mechanically we can stick needles in them we can pull them apart you can can do all all sorts of horrible things to them and a minute later they're back to functioning and and good so so that is definitely an advantage that you get out of this um it comes as a very high energetic cost like uh constructing and destructing this destroying these filaments uh is very like like is a substantial part of the metabolism the cost of the energy cost of the cell on the other hand it's still much much cheaper than the the energy for building the material for building a new cell so it's very hard to say what what is being optimized for um but yeah there's we know we understand some of the trade-offs but at this page it's a little bit of guesswork that's interesting the issue of optimization because we talked a lot about optimization in the module and you know there is never one solution for an optimal system it depends how you look at it and what you just said it's interesting that you see you see something happening and obviously it's optimal but we don't understand why we don't understand why we don't understand why and i think another interesting aspect to your first question actually about what happens if i make these microtubules if i keep them from falling apart for instance so not an answer not a direct answer but probably something interesting to think about is one of the best cancer drugs anti-cancer drugs that we have is a drug called taxol which comes from birch tree from the right and what taxol does is it prevents microtubules from falling apart what that does if you put it in low enough doses it it it makes it much harder to form mitotic spindles so it makes cell division much harder to achieve the net result is that cells that divide often like cancer cells do die so we don't really understand the mechanism but it's interesting to note that like the best cancer drug that we that we like the people who give you in chemotherapy is one that makes microtubules more stable uh this is um and uh um sorry okay i guess from um actually and okay now hinchest in into harvesting film it isn't film here we can now hinge house i'm um um is organized against one of these around one of these spindle poles so one experiment that people have done is that they just took a laser and they basically boiled one of the spindle post openly so they just shoot it down and what you then get is half a spindle which looks exactly like half of the healthy spindle so the construction of the two half seems to be pretty much independent as far as we can tell and the symmetry really comes from the fact that the two poles here are relatively similar because this is very close to symmetric cell division any more questions at this stage yeah i have a question the long tubes to the edge of the of the cell are there to orientate the spindle yeah exactly so the other question that i haven't talked about at all like the like here in this picture you see like these tubes which go out which are cut off in this experiment but they really reach the boundary of the cell that's the boundary of the cell there is uh i think there was a sketch somewhere in these slides let's prevent this for you like at the boundary of these cells there's again motor molecules that attach to whatever whatever filament hits the boundary of the cell and pull on them and what that achieves for you is that the spindle orients along the long axis of the cell and goes to the middle so that is how that is achieved although that's another universal mechanism because sometimes you have cells that are just too big to do that you will never be able to build something to reach the boundary like a chicken egg okay you have to do other things in the form of the cell itself is uh by pressure like a well in this case this happens inside the mother worm and the shape of the cell is pretty much set about by the shape of the of the donut of the mother worm so i'll show you like i simply didn't add a picture for any of these for a full worm to give you a sense basically the way these eggs are formed so this is is the gonad so that is basically the egg factory so what will become an egg starts out here at the top left hand and they just keep moving around and most of the cells die at this end and now and some of them become bigger and bigger and this here on the right lower side is the is the new egg being laid that's what you see here this guy that pinches off that's the new egg and this process of squeezing out the new eggs also sets the shape of the egg but i don't think that we understand that super well at this stage how that works okay and let's move on i guess so i figured i could now give you a few more details on how things fall apart and are destroyed basically you know i want to understand this in a little bit more detail we need to see uh how filaments are built and destroyed and how filaments are moved around in this building you need to originally understand the physics of that it's going to get more technical now so really just interrupt me at any point in time just just yell at me it's not like i need to finish going through these slides uh it's more about that being interesting for you um okay so uh in order uh of looking at these uh i've seen it of uh getting such a steady state structure um with filaments that are these that that have the they have the right amount of filament at every point in the structure there's really two things that you can do you can you will have to you can either choose where you build new filaments or you can choose where you destroy the ones that that are around um so uh one thing that you learned from this movie that i showed you earlier on remember these stops were just random marks on some of the filaments what you can do in the computers you can follow each of these dots and asks when do dots disappear because whenever the dots disappear that means the microtubule that they set on fell apart then you can ask is there anything special about any position here along as you traverse the spindle um are they like destroyed in specific places or are they destroyed all over the place and the answer is they seem to be destroyed pretty randomly so it's not like i so it's because one thing that you could have imagined is that i just randomly built connections everywhere then i destroy the ones that are not good in some spatially organized way seems to be the opposite what happens is that i build my filaments in a pretty targeted way and i just randomly destroy some okay so it seems to be that everything is about how you actually um build new magnitudes and these processes are not super universal i'm going to talk now about the story of the frog spindle there's slightly different stories in different fields and we don't really know like the the design paradigms that depict which which mechanism is chosen in which spindles of the state but how it happens in in these rock spindles is that near the chromosomes which end up which are in the center here uh there is a signaling protein called ram um this let's stand for something but it doesn't really matter for output this is what they stand for which has two states it can either be bound to a molecule called gdp or to a molecule called gtp so at the chromosomes there is a machine that basically turns around gdp into round gtp so you have a mechanism that turns your signaling molecule on as it touches the chromosomes everywhere in the cytoplasm just everywhere in space in the fluid in which all of this is immersed you have a machinery that turns around gtp into run gdp what that means is that you sort of activate your little your little fluorescent molecules then we let them swim away randomly and they get turned off what that gives you is that you have a little sort of signaling blob forming around the chromosomes what people have saw for a long time is that this is the full story that basically if you just had rand somewhere you form a blob of of microtubules or filaments and then everything else is done so basically what rand gtp then does is it talks to some other molecules called spindle assembly factors and they will produce the microtubules if you buy this theory you just add ran like this activated molecule to frog egg soup you should just form a disorganized blob of filaments if you don't have any motors the person that that proved us wrong on this was sabina petri she is in princeton and she did very beautiful experiments where she did exactly what uh i just suggested was she took structurally activated round just piped it into the extract from a living cell and what she saw for a long time is nothing but then she just added one stabilized microtubules actually with taxol a stabilized microtubule to this thing and around this structure she sees these these fireworks emerge so what you see here are stills from her website uh the the filaments are microtubule filaments and these dots she labels like the growing ends and different molecules on there but she gets these these very organized structures what we learned from that is uh that probably the system is slightly more complicated not only does ram activate a molecule which which will call spindle assembly factor but this guy then in order to do something has to bind pre-existing microtubules so basically what that does is the construction rule uh seems to be activate like the construction crew at the chromosome then float around until you find a bit where construction is already happening and then build up on that that seems to be how our filaments are form uh formed uh the part that was still unclear and that is our little contribution to the field when when i start thinking about these things is whether it is sufficient to just hang out close to a filament and be activated by binding and then you can bind either in solution or whether you have to be actually bound when when you construct a new filament uh in order to figure that out we basically did some math um what do you what you what you relatively quickly realize if you look at one of these spindles is that they have a very sharp interface like there is really material and then it falls off over a space of basically a micron and then there's nothing outside so the two the two models that i just proposed to you but basically a nucleator one of these blue guys has to attach to a pre-existing microtubule to do anything or it just is localized because microtubules are sticky to it have different predictions on how sharp the spindle interface are so we could turn that into mouth and compare and saw that one of the models described the data the other one didn't so what we learned is really the way new structure new material is constructed in the spindles is um by so basically filaments are randomly destroyed everywhere there is a signal from the chromosome that diffuses just floats through space waits until it finds a bit of spindle and then it says let's build more there that is all that happens so that seems like a like a pretty wasteful thing to do things and like a really complicated um a way to do things but i think one of the one of the interesting features that you get out of that uh and here i'm showing some work out of jay gatlin's lab is that this is a way of having the size of your emergent structure being adaptive to the size of the cell that you're in so what these guys did is they basically have an at a little oil um well and they bro blow little oil uh bubbles uh little cytoplasm bubbles into oil so all of these bubbles here um are little pieces of cytoplasm and there's oil around it since the since it's like it's like salad dressing it remixes and in some of these bubbles there's nuclei and you will now see spindles and what they saw is that the spindle adapts to the size of the enclosure that it is in so here's just three examples there's a 540 micron enclosure where you have a small spindle 55 medium spindle 100 micron enclosure you have a large spin and the way you achieve this is really by the mechanisms that i just explained to you so maybe that's a that's another advantage of this first bit of having this very complicated way of building stuff if your cell grows or shrinks you can react to that you can build your structure with the same blueprint basically at the scale that you want it to be given the space that you have available so that's that's one of the the other advantages that you get out of this very complicated mechanism uh is there questions about that okay okay the next thing that you need to understand uh uh in order to um to understand how this is built is how filament once once you constructed filaments how they moved around how do these motors actually actually do stuff because what you really would want to know if you if you were to build such a thing in the lab you would want to be able to say if i have a motor which has properties x and i put it in filaments which obey this nucleation mechanism this is the structure that i would want to get out of it so how do you how do you actually build stuff with with this material um as i told you before there's uh several types of motors which are important in these spindles and filaments in the spindles move so just as a as a little reminder what type of motors you have in the structure changes the outcome and structure what you need to think about obviously is the force balance on each of these filaments the total force on each of these filaments is the sum of an active force as a plus a drag force that comes from being coupled into the network and so what we want to know is how does this inform the emergent architecture if you if you put different motors in there but the way we think about these systems now that's to give you a flavor of how you want to think about these problems a series so if it's too abstract please interrupt me at any time i feel uh it would be useful to get the most out of it um so we just think of this as a basically a bowl of spaghetti of polymer filaments that are tied together by cross-linking molecules and these cross-linking molecules now can consume energy they can consume a chemical fuel and so they can move along the filaments you can phrase this as a math problem so what you want to know psi that's basically the especially the map of where everyone is society is an object that lists all the positions of microtubules x i and all the directions which determine p i what we want to know is how this changes over time that's what dt psi means what is the change of the of the current map in order to know that i need to do x dot which is how do filaments flow in position and p dot how do filaments reorient so if you think about that from a mathematical point of view you have two unknowns x dot and p dot if you know those you know everything so you need two equations and i sort of already gave away my game we know that the total force on each filament and the total torque on each filament always add up to zero so these will be my two equations that i can use to solve for x dot and p dot so i have to tell you what the total force of each of these filaments is so if you think about this red guy being coupled into the network the total force of on each of these filaments will be the forces that come from all of its connections and that is really what this horrible sum and integral multi-horribleness means that means you just have to consider all connections that are geometrically possible given the size of your filaments and your connectors and once you have such a connection there will be a rule little fij which is the force that filament j exhorts the filament i um that tells you what your motor does uh so all to turn this into a theory all we need to see is like basically have like a little prescription of how motors are operating in this filament network what people can measure in the experiment which which will guide our thinking about that is they can take two filaments and uh basically hold them either by really attaching a magnet to a filament uh and sticking the other one to a surface or attaching a little styrofoam bead to the other filament and pulling that either with light or magnetic fields and so you can exert a controlled force between two filaments that are nearby and then you can ask how fast do they move past each other and what you will typically get is you will get a measurement of the speed the velocity at which guys move as a function of the force that you get if these are motors if you don't apply an external force the motors will just walk at the speed at which they want to walk along so that is this capital v here that is this point where my dashed line crosses the velocity axis at zero force if you pull to oppose the motion your motors will slow down so you will walk along the dashed line upwards until you reach a point where nothing moves that is called the stalled force because you just pull too much against the action of the motor so they can move anymore once you have such a curve you can write an expression for fij and let me just parse the mathematics for you there's this term proportional to gamma which is just the slope of this curve if if i just had this term basically my first velocity curve would have its preferred velocity be zero so that would just be friction between two linear friction between two rods that are connected so the speed would just be proportional to how strong everyone now the connectors here unlike in many other materials are active so there's a second term which is the force that my connectors exert by their walking motion what that leads to graphically is it uh displaces the zero force velocity uh from zero so there's a preferred velocity uh and it adds this little term to our equation but really all of this is basically you say you just respond to external forces and you know your zero state once you have that you can tell everything about these materials so now you can uh play games and one game that we played is we we tried to build something we took some taxol stabilized microtubules taxil is this cancer drug that i told you about earlier so we took basically tubulin add a taxol to a suspension of tubulin and what you get of that is stable filaments that now don't have this property that they fall apart and reconstruct themselves uh and then we pick the motor xctk2 so x stands for xenopus which is the name of the frog that it comes from k stands for kinesin which means that it's a plus and directed motor but it's basically just the name of this guy uh and we asked can we sort of know about the force velocity curve of that uh luckily people had measured that 10 years ago what they had measured is just take a few floating microtubules and stick one to a surface put motors in this whole solution what they see is that the motors basically bind everywhere where they can reach between the two filaments and you see that also here in this graph in the middle we see like uh time goes from top to bottom and what you see in the middle row you just see where the microtubules are where it's brighter it's basically the overlap between the little guy and the one that is attached to the surface in the lower channel you see where the motors are and what you see is they are basically everywhere where there is overlap between the filaments and on the top you see the the column merge between these two channels so what we know about xcttt is that it binds basically everywhere where it can reach and the other thing that we know about it is the slide things apart at 19 nanometers per second so once you you know about that but theory will tell you is that if you have a network of high enough density basically what happens is that wherever you have overlap between antiparallel filaments you generate sliding motion between these antiparallel filaments and since everyone is sort of linked by motors even to parallel guys even if parallel motors in the parallel system would just ineffectively walk between the two on their tracks the whole system starts to move and you can work out that what should happen in such a system is that every filament moves basically at the speed of the motor in the direction in which it points and what's what's interesting about that is that this is very robust in the sense that what's shocking here is what not what does not show up what does not show up is any concentration of the motors it doesn't matter how many motors you put into the filament you're very robust against fluctuations of how many parts you have and what also doesn't show up is any notion of how my network is locally organized because naively you would think that if you go to a system like the one on the left-hand side if i have two parallel filaments my motor would basically walk on both sides towards the same end basically exert no motor forces and nothing should move whereas if i found two anti-parallel filaments i could basically push them one against the other and they would slide relative to each other in this dense system that is not what happens the stent system basically every filament regardless where it is in the network regardless of the concentration of motors that you put into the network as long as you have more than a certain threshold number moves at the same speed in the direction of which it points and so these two guys uh bes and peter uh peter is now at mit and bez is in princeton both doing postdoctoral work uh really took tubulin the motor xct2 atp then they float the taxol in so now you get filaments and then they put this into a small microfluidic chamber now you get this greyish mouse which is a network of filaments which are all oriented from the left to the right they can now do is they can take a laser bleach stripes in this material and what you will see once the movie loops is that these stripes split up that tells you that these filaments are sliding relative to each other but it tells you more it tells you like if you if you zoom in and i picked out a few sides on the right hand side you see that there's regions like the one underlined in blue here but basically as much stuff goes to the left or to the right and regions where basically everything goes to the left or to the right so now if our little theory here is correct then regardless of how much motor we have into this system regardless of the local structure which we can infer from how much goes left and right because you would be more anti-parallel if if everything goes if it goes both ways and more parallel uh if it goes only one way you should always see that the speed of these stripes is 19 nanometers per second that is indeed what bez and peter find in experiments this was this was pretty abstract but uh what i want to emphasize is that this is exactly also what is happening with spindles in spindles the motor is not called xct2 it's called x5 um but and it moves at a different speed two and a half microns per minute now it's much slower uh but if our theory was correct each of these dots no matter where it is in the spindle should move at two and a half microns per minute and luckily far as people have measured this and uh you can see this here on the right hand side okay that was that that was pretty abstract so i feel should accelerate here just tell you that uh we now just reached a point where we understand enough about both the construction mechanisms and the forces in these spindles to be able to really put all of these set of rules in a computer and ask can we at least in the computer recapitulate the full self-assembly of one of these spindles and the answer is not quite yet but we're getting there and i think that's some of the research that will have material will hopefully lead us there i guess that's another good point for questions thank you sebastian before i'm asking questions i i have to share a video that came into my mind do you know powers of ten i'm sure you know it right from the aims to just stop sharing my screen for a second then you can hear it yes oh yes maybe i can share it then even better um let me share my screen yes so you know this video have you seen it there was a new one on google but this one is original by charles and ray eames they produce this it's a beautiful book you can see now why i have been thinking of that yeah this is always the same you know at the same point that you're looking at but in a different scale yeah exactly and the reason why i thought is that eventually what you are showing or what we think we can why your research fits to the module and our work is that it's from the smallest to the largest part it would be strange if it wouldn't have similar laws right yeah yeah there is are they things which are well they think that scale right and things that don't so there's there's definitely things which are fundamentally different between this little skill and ours and one of those is called uh so so in the in the smaller scales uh things are very light and the fluids in which you're embedded seem very viscous um what that means is for instance while if you shoot a rocket to the moon it's basically all about inertia right you give it a push once big explosion at the back and it will keep moving forever and that is because their inertia is important viscosity isn't at the smallest scales uh it takes a lot of energy to move small particles in a fluid this is why your your vacuum cleaner needs to have a couple thousand watts because it's very hard to pick up a tiny particle with fluid which has no inertia with fluid flow just by viscosity um so there is there's some physics is a skill that it that is really scale dependent uh like that and some organizational principles which probably cross scale so i i think i think yes some sense it's it's the same to some sense not it's interesting when you say that because nowadays we think it's normal that you know you take a rocket and you live off the earth but it's only a few years ago that we know it's possible just 100 years ago people thought it would never be possible but anyhow i have two questions before maybe the students have some questions one is you said the spindle adapts to the size of the enclosure this is what you discovered in the experiment and i think this is interesting because we have learned in history and also in architecture and from animals whatever that size is always in relation to the environment um but is it really the size of the enclosure or is it also some other condition or is it really the bigger the enclosure the bigger the spindle is it relational so there's there's two scales that matter so uh for for this specific problem so the way that it works is that molecules sort of uh have to find the chromosomes to get turned on that was this round cascade that i talked and so what happens is that if the enclosure gets smaller basically you're limited by how much stuff floats around how much of the signaling molecule floats around in total in the enclosure as you make an enclosure bigger and bigger much bigger than the than the scales that i showed you here at some point the time that it takes a random molecule to find the point where it gets timed on gets large compared to the time that the lifetimes of your components so the way it works for the spindle size is that if you start with small enclosures you grow with the enclosure but at some point you read them reach a maximum size where increasing the size of the enclosure further will not change the size of the spindle so that is the that that is how it works for this system basically because there's two scales one length scale which is set by diffusion over lifetimes of molecules and one that is set by the better lifetime by the size of the enclosure and the smaller of these two sizes basically sense the size of the speaker okay i have another question is there maybe one question from someone else i have one question concerning because you showed an image with a minimum and the maximum arrangement and it seems that on that level a minimal system is not the favorite so it seems like redundancy is more important than minimal connections for example or minimal use of elements or yes you seem to be for these types of system you don't seem to be limited by i think these systems are less about the efficiency concerns than about robustness because basically if a spindle fails you die um so in a way they are like on the human scale which would probably say they are they're massively over engineered yeah they're much more expensive than than what you could do if you if it was about building the simplest thing that's achieved but this is the most robust thing thank you for the consideration all right do you have um questions i know that we have i forgot who of you is working on artificial intelligence or maybe you have a question that fits to your reflections about otherwise i have to ask does artificial intelligence help or is okay first of all does it help for the research or you do you use it or do you intend to use it and second do you think artificial intelligence programming software something can learn from the work you do uh so we have people around here that think a lot about neural networks um so that there's a technical aspect in which they can help which is just billion neural network is a in mathematical parlance a universal function representative and you have you have of course the structure like if you want to represent what these these materials do it's often not obvious how you do that efficiently in a computer and one of the ways of doing this is basically teaching a network to map the function that you want um which i guess falls into the realm of of artificial intelligence people have thought about that um the other thing where artificial intelligence and like these types of methods come in quite a lot this in biology right now we get a lot of data um for instance from tissues and then it is about how do you find the boundaries of cells how do you find the spindles how do you find the nuclei um traditionally this meant that like a lot of master students spend a lot of time on looking at all these videos and drawing lines and then punching numbers into a computer um definitely intelligence has revolutionized this part of the work uh already um yeah i don't know because my impression and i'm by no means an expert of artificial intelligence is that it gives you a good way of solving well-defined tasks but at the end of the day it just solves the tasks and it doesn't tell you what it did it's very hard to understand what it did under the hood um since in our business it's much about understanding the specific mechanisms often it doesn't often it doesn't do what we need it to do so it doesn't explain itself it's very useful but it doesn't it's very hard to learn how it does the things it does somehow too close to magic okay then uh if there are no questions i i would have uh please suppress them another question in is not entropy another i don't know if it's a force or a principle that that the spindles would have to fight against and yes it would concern would consider so basically as a living system like you have to fight entropy all the time basically and the way you do that is basically you put in energy you reduce your energy your entropy locally and you um and you basically shoot out high entropy material at the other end if you put your hamster in a cage and you stop feeding it so you interrupt this flux very soon it will reach the state of highest entropy and be dead so you keep feeding energy into the system to really actively put yourself into a organized state um yeah you have to you have to consume stuff food is basically how you do it and excreted waste product which is high entropy and the atp is the the energy the food for the exactly so the the way i expect but the the way it works is you the worm or the frog just eat something then there is a whole cascade of of metabolic cycles where this is basically decomposed into glucose which then mitochondria which are structures in the cell can use to produce atp and this atp is energy rich it's the fuel it's the fuel of all cells and that fuels all the processes inside your cells but ultimately what provides the energy is the food you eat for the animal needs okay thank you all right technology foreign foreign is foreign yeah thank you so much this was a lot of fun talk and um i wish you a warm welcome here at the uvm and i'm looking forward to your research team work yeah will be will be fun and i think i showed you guys the the my contacts my at least my webpage uh address so if you have other questions that came up that come up just feel free to send me an email i will try to reply a timely fashion and if i forget shoot me another one thank you very much thank you pleasure to have you here have a good evening all of you thank you
2021-11-19 12:27