[Materials and Technologies] Spatial organization in cells | Sebastian Fuerthauer

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

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