WEBVTT 00:00:24.900 --> 00:00:30.060 Herald: So, willkommen zusammen. Heute Abend gibt es den Talk von Andrea über den 00:00:30.060 --> 00:00:35.489 "Corona Virus Structural Task Force". Ich bin melzai_a Herald für die Session. Wir 00:00:35.489 --> 00:00:40.030 haben einen Signal Angel, Dia, sie wird die Fragen sammeln, die in den Chat 00:00:40.030 --> 00:00:45.010 gestellt werden und am Ende gehen wir im Vortrag über diese Fragen. So viel zum 00:00:45.010 --> 00:00:51.530 Ablauf. Der Vortrag wird aufgezeichnet. Und ist danach nachträglich verfügbar auf 00:00:51.530 --> 00:00:58.223 Media.ccc.de irgendwann in den nächsten Tagen oder Wochen. Und damit würde ich mich 00:00:58.223 --> 00:01:01.730 freuen, Andrea, du als Nachwuchsruppenleiterin an der Uni 00:01:01.730 --> 00:01:04.670 Hamburg, du hast die letzten zwei Jahre mit den Codona Virus beschäftigt, und 00:01:04.670 --> 00:01:09.970 daraus wunderbare Visualisierung gemacht. Wie lief es denn ab und wie sieht Corona 00:01:09.970 --> 00:01:12.220 eigentlich aus? 00:01:12.220 --> 00:01:17.049 Andrea: Ja, vielen dank! Erstmal danke für die Einladung. Und ja, genau darum geht es 00:01:17.049 --> 00:01:27.170 in dem Talk jetzt, was wir die "corona virus structure task force" nennen. I'm 00:01:27.170 --> 00:01:30.990 going to give the presentation in English; so that international listeners can also 00:01:30.990 --> 00:01:37.460 listen in. But you can ask your questions in, well, any language anyone here speaks. 00:01:37.460 --> 00:01:44.690 I understand German, English and Japanese. And I want to start with a quote by Marie 00:01:44.690 --> 00:01:52.620 Curie. I know the room Mary is not named after Marie Curie, but she said something 00:01:52.620 --> 00:01:57.850 that is very true in this pandemic, which is: "nothing in life, is to be feared, 00:01:57.850 --> 00:02:06.570 only to be understood. Now is the time to understand more so that we may fear less." 00:02:06.570 --> 00:02:12.110 And indeed, this holds true for the corona virus more than anything, because as you 00:02:12.110 --> 00:02:18.190 all know, you cannot see the virus. You can only see it indirectly visualized by 00:02:18.190 --> 00:02:25.490 science or you can see the measures against it or you can see ill people. But the 00:02:25.490 --> 00:02:31.550 virus itself is invisible. And I'm going to start this talk with questions. There 00:02:31.550 --> 00:02:39.290 will be many questions. And the first one is, what does the corona virus look like? 00:02:39.290 --> 00:02:44.989 Now you may think, you know, but the reality of it is that even German news has 00:02:44.989 --> 00:02:50.499 no idea. And I know that ZDF is now using a different picture, which looks more 00:02:50.499 --> 00:02:58.099 similar to what I'm going to show, but it's very wrong as well. This picture? Is 00:02:58.099 --> 00:03:02.379 what most people think the virus looks like. And I also brought you like two top 00:03:02.379 --> 00:03:09.799 model and models of the virus. One can even make sounds. Any spiky ball of 00:03:09.799 --> 00:03:15.519 this days really passes as a corona virus because no one seems to know what the 00:03:15.519 --> 00:03:22.519 thing really looks like. Only it's like crowned. And it has spikes. That's the 00:03:22.519 --> 00:03:26.700 only thing that all the models have in common. But some things look like you can 00:03:26.700 --> 00:03:32.520 just, you know, like they are little Shrek ears type things or have tentacles. No 00:03:32.520 --> 00:03:39.539 one really knows. So how do we know as scientists and can viruses, be seen? If we 00:03:39.539 --> 00:03:45.249 imagine so, this is an electron microscopic picture of a human hair. It's 00:03:45.249 --> 00:03:53.419 0.1 millimeters. It's the length of this line, so the hair is a little bit less. 00:03:53.419 --> 00:03:58.040 The little red dot, which you may or may not be able to see inside that circle is 00:03:58.040 --> 00:04:02.670 the size of the corona virus. Now if we zoom into the picture of the hair, you can 00:04:02.670 --> 00:04:10.279 see, I hope, a little red dot here. And that's the corona virus to measure. So it 00:04:10.279 --> 00:04:18.739 is 150 nanometers, or 0.0001.5 mm large. That is tiny 00:04:18.739 --> 00:04:26.950 even by scientists sentence. However. Even smaller than the virus with 150 00:04:26.950 --> 00:04:32.440 nanometers. It's a single atom, which is represented here again by a 00:04:32.440 --> 00:04:40.889 dot, which is barely visible and is 0.1 nanometers in diameter or one. Angstrom. 00:04:40.889 --> 00:04:46.620 Atoms are tiny, even compared to the virus. A virus is composed being matter of 00:04:46.620 --> 00:04:53.010 very, very many atoms. How can we visualize something this small? Can we see 00:04:53.010 --> 00:04:59.840 it with a light microscope? And what color would the virus be? This is to scale. 00:04:59.840 --> 00:05:04.580 Yellow light. It is 600 nanometer wavelength meaning from this point to 00:05:04.580 --> 00:05:09.650 this, it is 600 nanometers. So the wavelength of visible light, which ranges 00:05:09.650 --> 00:05:19.080 from 400 to 780 nano meters, is actually longer than the virus is white. So there 00:05:19.080 --> 00:05:27.090 is no chance whatsoever to ever observe a single virus with light just physically 00:05:27.090 --> 00:05:33.449 not possible. We need something that has a smaller wavelength, and there are two 00:05:33.449 --> 00:05:40.819 things we use X-rays, which have 0.1 nanometer wavelength. So they 00:05:40.819 --> 00:05:45.870 are very, very small. They're like light. They're also photons. We call it 00:05:45.870 --> 00:05:53.190 also X-ray light (Röntgenstralung, Röntgenlicht). But they have so high energy 00:05:53.190 --> 00:05:58.270 that their wavelengths are tiny. The other thing are electrons, which have even 00:05:58.270 --> 00:06:02.680 smaller wavelengths. If you choose to regard them not as particles, but as 00:06:02.680 --> 00:06:07.739 waves. So we can use electrons and X-rays to observe the virus, and we do. And for 00:06:07.739 --> 00:06:12.710 this, we have several possibilities. One of them is large particle accelerators 00:06:12.710 --> 00:06:17.199 like the one I'm working on in Hamburg, which produces very intense X-rays. 00:06:17.199 --> 00:06:23.080 Another one is an electron microscope. So here is a model of an electron microscope. 00:06:23.080 --> 00:06:29.730 In order to use it, you need a scientist and then you shoot an electron beam from 00:06:29.730 --> 00:06:34.750 an electron cannon. That's the official scientific term. It's an electron cannon 00:06:34.750 --> 00:06:40.909 onto both an electron gun electron cannon electron gun. You shoot your electrons 00:06:40.909 --> 00:06:44.760 through lenses, which are magnetic. Electrons are negatively charged so the 00:06:44.760 --> 00:06:50.710 magnetic field can be used as a lens system onto a sample. For example, the 00:06:50.710 --> 00:06:57.120 virus and then you have a detector. What do we see on this detector? We should 00:06:57.120 --> 00:07:03.580 viruses with electrons and record how many electrons pass through the sample? What we 00:07:03.580 --> 00:07:07.520 see looks like this. So of course, it's black and white because electrons come. 00:07:07.520 --> 00:07:14.740 There's no colors involved. And what you can see is a dark shadow. And then around 00:07:14.740 --> 00:07:22.780 it, a little bit of bright spots, almost like a corona during a sun eclipse. So 00:07:22.780 --> 00:07:27.879 this is why the corona virus is called corona virus, because it spikes under the 00:07:27.879 --> 00:07:34.219 electron microscope look like a corona. And these pictures have no colors, but 00:07:34.219 --> 00:07:37.740 scientists like to colored them in particular in order to tell people that 00:07:37.740 --> 00:07:42.319 this is a dangerous virus and that is the background. So if we colored, it may look 00:07:42.319 --> 00:07:48.810 like this. And this is an official picture released very early in the pandemic by the 00:07:48.810 --> 00:07:57.360 National Institutes as one of the first pictures of the new corona virus. We can 00:07:57.360 --> 00:08:01.360 also do scanning electron microscopy, which is a similar measure where you coat 00:08:01.360 --> 00:08:06.840 the entire surface and then you get a pretty three dimensional picture. What you 00:08:06.840 --> 00:08:11.189 can see here are lung cells, the lung carpet like the like hairy structure here. 00:08:11.189 --> 00:08:17.960 That's lung cells that are single type two alveolar epithelial cells. So there are 00:08:17.960 --> 00:08:23.110 like a little like their job is to get rid of stuff the lungs don't want 00:08:23.110 --> 00:08:28.710 there, like a carpet, they can move and they get rid of stuff for you. However, 00:08:28.710 --> 00:08:32.830 these cells, you have a problem. They're infected with corona virus. You can see 00:08:32.830 --> 00:08:41.040 some slime or mucus here, and you can see the viruses here. Because of the coating, 00:08:41.040 --> 00:08:45.680 they look a little bit like cauliflower. So that's nice. But it doesn't give us the 00:08:45.680 --> 00:08:50.310 full picture, but so much for people who say we cannot isolate the virus. We can 00:08:50.310 --> 00:08:57.860 actually even like, make it visible. So we can make this invisible enemy visible. It 00:08:57.860 --> 00:09:02.390 is just a question of having the right equipment and a good sample of the virus 00:09:02.390 --> 00:09:07.830 and many hours of work. The virus therefore exists and can be made visible 00:09:07.830 --> 00:09:12.400 using electron microscopes or, for example, as a particle accelerator. But 00:09:12.400 --> 00:09:16.530 I'm not going to go into detail here. We have not enough time tonight. I'm only 00:09:16.530 --> 00:09:25.250 going to talk about electron microscopes here. So what is the virus made of. Those 00:09:25.250 --> 00:09:30.260 This is the virus. We're going to talk about this picture later in the talk when we 00:09:30.260 --> 00:09:35.080 talk about model a little bit more. But here is one Spike, I think you've all 00:09:35.080 --> 00:09:41.530 heard in news from spike proteins, which cover the surface of the virus or the 00:09:41.530 --> 00:09:48.820 virion. If we draw this schematically, as Thomas Splettstösser presented for us, he's an 00:09:48.820 --> 00:09:54.080 illustrator, burst in Berlin, it looks like this. And then we take only the head 00:09:54.080 --> 00:09:58.750 of the spike, which is the region of the spike we know most about, and then comes 00:09:58.750 --> 00:10:03.130 an animation that I did. So it's not quite as pretty. If we zoom in, we see the 00:10:03.130 --> 00:10:09.730 surface and below that surface we see things represented as a ribbon. However, 00:10:09.730 --> 00:10:13.810 we can show this differently. We can show the individual atoms connected to each 00:10:13.810 --> 00:10:19.730 other. The problem with this display is that it's really hard to find anything 00:10:19.730 --> 00:10:25.560 here. It is super difficult to get an overview with this picture, so we prefer 00:10:25.560 --> 00:10:32.470 to show these complicated and fake molecules made up of atoms as surfaces and 00:10:32.470 --> 00:10:38.570 ribbons. And this ribbon diagram, by the way, has also been found by a great female 00:10:38.570 --> 00:10:42.980 scientist, Jane Richardson, several decades ago, which was quite revolutionary 00:10:42.980 --> 00:10:48.519 for my field. So the virus is made up of atoms and molecules, and they are 00:10:48.519 --> 00:10:55.060 structures can be found out by NMR, X-ray crystallography and electron microscopy. 00:10:55.060 --> 00:11:00.120 For now, this is all I'm going to tell you. We're now going to dive very deeply 00:11:00.120 --> 00:11:05.330 into the biology of the virus and what the structures tell us. And then in the end, 00:11:05.330 --> 00:11:09.830 I'm going to tell you a little bit more exactly how we actually get from the 00:11:09.830 --> 00:11:17.880 measurement to the model, which holds some pitfalls and problems for us. And it's an 00:11:17.880 --> 00:11:23.320 area in which I do usually my research. But first, I'm going to talk about the 00:11:23.320 --> 00:11:29.220 model, you all know this picture from the CDC, right? And by the way, this thing for 00:11:29.220 --> 00:11:33.640 a scientist, this thing is not a virus, it's a variant. It's only the transport 00:11:33.640 --> 00:11:38.630 form of the virus, the virus. That's a few more things that are not contained in this 00:11:38.630 --> 00:11:44.630 little show. That's just a transport form for its RNA to get into a whole cell. We 00:11:44.630 --> 00:11:48.050 call this a variant. But most people, even scientists, can also refer to it as the 00:11:48.050 --> 00:11:55.690 virus. So this is the CDC model, right? That's the picture that went all through 00:11:55.690 --> 00:12:00.940 the press around the world. That's like THE picture of this pandemic, and it was 00:12:00.940 --> 00:12:06.970 made by the CDC very early on by two scientific illustrators there. However, 00:12:06.970 --> 00:12:11.950 already then it had some problems. They made it in quite a rash and it has some 00:12:11.950 --> 00:12:22.470 errors. So we decided to make a new picture, which looks like this. And. If 00:12:22.470 --> 00:12:28.560 you compare it, two pictures, here are the differences. The head of the spike in this 00:12:28.560 --> 00:12:33.700 illustration sits directly into the surface, while in reality it is singing 00:12:33.700 --> 00:12:42.050 sitting on a long, very bendy like rope like structure that tethers it. So the 00:12:42.050 --> 00:12:46.750 virus, the head of the spike, which binds to the host cell, is quite flexible. The 00:12:46.750 --> 00:12:51.470 surface is not quite as coarse as shown here. It's smaller. The virus actually 00:12:51.470 --> 00:12:58.140 relatively large for a virus, and it's got other proteins swimming in its surface. If 00:12:58.140 --> 00:13:04.320 you look exactly, you'll see the virus is also not exactly round. Now we thought 00:13:04.320 --> 00:13:07.550 this is not enough. It's nice to have a picture, but wouldn't it be nice if we 00:13:07.550 --> 00:13:12.830 could actually touch it? So we made a 3D printable model for those interested. You 00:13:12.830 --> 00:13:18.780 can find also all that information on our homepage. I'm going to show you the 3D 00:13:18.780 --> 00:13:26.880 model. Let's see. So. This is the virus model. As you can see, the virus is not 00:13:26.880 --> 00:13:33.360 exactly round because it's outside, it's very soft. It's like a soap bubble. It can 00:13:33.360 --> 00:13:39.140 change its shape quite drastically. It's wobbly and the spikes are actually 00:13:39.140 --> 00:13:42.860 stochastic highly distributed. They're not like regularly arranged and they are 00:13:42.860 --> 00:13:49.500 swimming in the skin. And there are other proteins in the surface as well, which you 00:13:49.500 --> 00:13:55.670 can perhaps see whether they really formed as little flower shapes, we don't know. 00:13:55.670 --> 00:14:01.980 And the virus is huge. So this on the same scale, one to one million as a rhinovirus 00:14:01.980 --> 00:14:08.510 for the common cold. The corona virus is huge. 20000 base pairs RNA makes it one of 00:14:08.510 --> 00:14:15.420 the largest virus genomes we know. And a virus, therefore as soft on the outside, 00:14:15.420 --> 00:14:23.720 while rhinovirus has a very hard and rigid shell that is always composed the same. 00:14:23.720 --> 00:14:28.440 And we need this model in the hopes that, like other scientists and perhaps schools 00:14:28.440 --> 00:14:34.250 would like to print it at home and actually like, get something tangible and 00:14:34.250 --> 00:14:39.170 it turned out they did. So we got quite a few requests from people, from child care 00:14:39.170 --> 00:14:43.830 facilities and from schools and from other scientists. And even my administration 00:14:43.830 --> 00:14:47.850 like to have them printed. One even proposed we may have them as Christmas 00:14:47.850 --> 00:14:55.560 ornaments, but I found that a little bit like tasteless. We didn't do it. And like, 00:14:55.560 --> 00:15:01.230 just before I left Hamburg, we got a new model. This model is now already a year 00:15:01.230 --> 00:15:07.050 old, and in 2021, signs made quite a lot of progress. So we now know there are 00:15:07.050 --> 00:15:11.110 fewer spikes and a virus. All in all, it's a little bit smaller, so it's not quite 00:15:11.110 --> 00:15:16.020 like this, but perhaps less so. It's not 15 centimeters in diameter. The model is 00:15:16.020 --> 00:15:21.300 12, and it is still like potato shaped. It's not round because now what's 00:15:21.300 --> 00:15:26.640 important for me to show, and I would have like to show you this model like in front 00:15:26.640 --> 00:15:33.160 of the camera tonight, but. It went into the museum, it was the first one we had, 00:15:33.160 --> 00:15:37.420 and we brought it to the opening of this exhibition in Hamburg "Pandemierück in ide 00:15:37.420 --> 00:15:41.370 Gegenwart" the gigawatt, so you can now see it in the museum and we'll be back in 00:15:41.370 --> 00:15:48.840 my office when they have assembled theres. And this also holds true. I'm going to 00:15:48.840 --> 00:15:52.560 talk about the task force in the second half of this talk. But one thing that is 00:15:52.560 --> 00:15:56.930 really true and what's true for this project as well is the task force is 00:15:56.930 --> 00:16:01.220 typically more interested in new communication projects than in all the 00:16:01.220 --> 00:16:07.500 pile of stuff we need to finish. You may notice from home. Right. So this is how 00:16:07.500 --> 00:16:14.280 our model. Now, let's dive deeper into the thing, because so far we have only talked 00:16:14.280 --> 00:16:20.630 about the virion and only about it's outside. So the virion has to spike 00:16:20.630 --> 00:16:27.200 proteins on the outside. Two other proteins M and E protein, it has a double 00:16:27.200 --> 00:16:34.230 membrane hull, which is very thin and nucleocapsid, which is wrapping the RNA. 00:16:34.230 --> 00:16:38.800 The RNA of actually containing the genes for everything that the virus needs in 00:16:38.800 --> 00:16:45.950 order to like, take possession of the host cell. So the RNA is the important bit the 00:16:45.950 --> 00:16:51.250 virion is transporting and nucleocapsid and everything else kind of packs it and 00:16:51.250 --> 00:16:58.710 makes sure it gets into the host cell. And I'm going to show you quickly a video 00:16:58.710 --> 00:17:03.850 because I think this is so nice to understand, and it's the answer to the 00:17:03.850 --> 00:17:09.600 question why does soap help against corona virus? Because very many, like other 00:17:09.600 --> 00:17:15.419 viruses, are relatively hard to wash off, but not corona virus, because it's so 00:17:15.419 --> 00:17:20.280 large, it has only a double membrane shell. And this is a very nice video from 00:17:20.280 --> 00:17:25.280 the protein data bank from our colleagues there. So this is the virus double 00:17:25.280 --> 00:17:31.430 membrane. It has lipid molecules. You can see there are hydrophobic on the inside 00:17:31.430 --> 00:17:36.270 and hydrophilic on the outside, so they lock water on the outside, but not the 00:17:36.270 --> 00:17:42.600 inside. Green molecules are soap. Soap also has a hydrophobic tail and a 00:17:42.600 --> 00:17:48.280 hydrophilic head. So unlike the water which stays outside the soap just gets 00:17:48.280 --> 00:17:54.280 into the membrane and kind of like goes in between the lipids. And then they make 00:17:54.280 --> 00:18:01.040 whole sort of water molecules can get inside the virus. They can even assemble. 00:18:01.040 --> 00:18:09.550 In around bits of the membrane and get it out of the virus hull or around a spike 00:18:09.550 --> 00:18:16.280 and remove to spike, which is hydrophobic to stock out of the virus. This leads to a 00:18:16.280 --> 00:18:21.340 total decomposition of the membrane and therefore it can be completely dissolved 00:18:21.340 --> 00:18:27.640 by soap. As soon as the nucleocapsid and an RNA are exposed, the virus is no longer 00:18:27.640 --> 00:18:34.610 infectious. It needs a spike in order to infect so, you don't need to disinfect 00:18:34.610 --> 00:18:39.980 your hands. You can just wash them with soap, which I find is so lucky in this 00:18:39.980 --> 00:18:44.410 pandemic because, you know, it would be really ugly if we would need to disinfect 00:18:44.410 --> 00:18:50.230 everything all the time, but we can actually just use soapy water. Although, 00:18:50.230 --> 00:18:55.750 let's be honest, I like to use disinfectant every here, and then it gives 00:18:55.750 --> 00:19:01.250 me just a feeling of more safety. It's kind of like a ritual to protect me. I 00:19:01.250 --> 00:19:09.910 suspect several of you are the same. So, so much for the virion, that's like the 00:19:09.910 --> 00:19:17.560 outer shell, that's like the transport form. But there is more much more. This is 00:19:17.560 --> 00:19:21.140 the corona virus life cycle, or I should be more correct. It should be called 00:19:21.140 --> 00:19:25.900 infection cycle because technically speaking, viruses are not life. They need 00:19:25.900 --> 00:19:31.520 a host cell to reproduce. So we're going to come back to this picture. We're going 00:19:31.520 --> 00:19:40.270 to take this apart bit by bit. First of all, there is entry entry into oh yeah. 00:19:40.270 --> 00:19:44.560 Let's quickly go back. The thing at the bottom here, the big thing here. That's 00:19:44.560 --> 00:19:48.510 the host cell. And a little one is the virus, right? We're clear on that 00:19:48.510 --> 00:19:51.610 Holbrook's here, right? And is the outside. So this is like your lung 00:19:51.610 --> 00:19:56.640 outside. That's your lung cell inside or hopefully not your lung cell, right? 00:19:56.640 --> 00:20:04.340 There's the virus. And this is the spike, the spike as a vaccine target, as you 00:20:04.340 --> 00:20:10.270 know, it's what's encoded in RNA vaccines and it's also contained in all the like 00:20:10.270 --> 00:20:17.440 vector vaccines we see. And I brought you another model for that, which saw the 00:20:17.440 --> 00:20:28.680 picture here. So this is one to 10 million scale model of the spike. And this is an 00:20:28.680 --> 00:20:36.440 antibody. Now if you are vaccinated either by RNA or by a vector vaccine, your body 00:20:36.440 --> 00:20:42.110 overproduce as far as injected with spikes, which are usually on something to 00:20:42.110 --> 00:20:48.950 carry it a host cell or a cell of your body if it's an RNA vaccine or a vector. 00:20:48.950 --> 00:20:54.290 Your body needs a few days to recognize this thing, so once it has, it will build 00:20:54.290 --> 00:21:00.290 antibodies that perfectly fit onto that they can recognize the spike very, very 00:21:00.290 --> 00:21:04.190 exactly. They have a specific binding site, which is much more rigid than 00:21:04.190 --> 00:21:11.090 anything else the antibody can bind to. Then this gets decomposed because the 00:21:11.090 --> 00:21:16.260 vaccine is not viable. What remains in your body is information for these 00:21:16.260 --> 00:21:24.200 antibodies. So now if you get infected with corona? The immune system antibody 00:21:24.200 --> 00:21:28.710 recognizes the spike it has previously seen in the vaccine, and that is how the 00:21:28.710 --> 00:21:35.930 vaccine actually works. So having this protects you, one of the biggest problems 00:21:35.930 --> 00:21:41.140 with COVID 19 infections is that the immune system responds too late. And then 00:21:41.140 --> 00:21:47.730 too much. So having these makes much more certain that you will not get severe 00:21:47.730 --> 00:21:55.960 COVID, which is, I think, very nice. And what we also did, together with the 00:21:55.960 --> 00:22:01.720 animation lab in Utah is not only make those life life cycle or infection cycle, 00:22:01.720 --> 00:22:06.130 we also made an animation the scientifically most accurate animation 00:22:06.130 --> 00:22:11.850 available on how the virus actually binds onto the whole cell. There's a lot we 00:22:11.850 --> 00:22:18.450 don't know, but everything we do know we have shown here. So here is the virus. You 00:22:18.450 --> 00:22:26.320 know the spike protein already. Yes, nucleocapsid inside there is RNA, which 00:22:26.320 --> 00:22:32.220 encodes for the rest, we're going to go into the rest after this. And then at the 00:22:32.220 --> 00:22:37.820 bottom here is the host cell. So lung cells actually have ACE2 receptors shown 00:22:37.820 --> 00:22:43.750 in purple, and a spike protein recognizes those specifically meaning that items like 00:22:43.750 --> 00:22:53.840 a puzzle piece fit exactly onto the purple receptors on the lung cells. The spikes 00:22:53.840 --> 00:23:01.710 bind there and then something else happens. Another enzyme also being in the 00:23:01.710 --> 00:23:07.220 membrane of the host cell cuts the spike, so it's not like the name spike suggests 00:23:07.220 --> 00:23:12.320 it would like shoot something into. But that's not the case. It gets cut and then 00:23:12.320 --> 00:23:16.250 comes to bed where we are a little bit unclear how this happens. So what we know 00:23:16.250 --> 00:23:20.300 is after it's cut, it somehow ends up being tethered into the host cell and we 00:23:20.300 --> 00:23:24.870 don't know the mechanism of this. So we decided to illustrated here with like a 00:23:24.870 --> 00:23:31.480 refolding process and then it's energetically unstable. So in order to 00:23:31.480 --> 00:23:36.470 become more stable, the whole thing clamps and folds together, thereby dragging the 00:23:36.470 --> 00:23:41.820 virus and the host cell membrane together, the two membranes to buy a lipid membranes 00:23:41.820 --> 00:23:49.560 Fuze. The virus material is inserted into the cell. The RNA is now inside the host 00:23:49.560 --> 00:23:57.050 cell, and this is how infection happens. So we felt it was particularly important 00:23:57.050 --> 00:24:01.930 to show this to people. We have made this animation Creative Commons, but 00:24:01.930 --> 00:24:06.160 unfortunately only American television caught up on it, so we're really hoping 00:24:06.160 --> 00:24:10.250 that one of the German like documentaries will show this, because we think it's 00:24:10.250 --> 00:24:19.870 really nice to see this process like as accurately as we can depicted. So here is 00:24:19.870 --> 00:24:24.809 the spike. That's the role of the spike. Now the nucleocapsid, an RNA a half 00:24:24.809 --> 00:24:32.760 entered into the host cell. What happens now is that the nucleocapsid dissolves. 00:24:32.760 --> 00:24:38.170 How that exactly happens, we don't know, but it dissolves and RNA gets immediately 00:24:38.170 --> 00:24:45.030 translated into protein. So the genome gets RET inside the cell because the cell 00:24:45.030 --> 00:24:49.700 believes it's own either comes from the host cell and it starts building. The 00:24:49.700 --> 00:24:54.100 proteins encoded in proteins are again molecules. And actually, it makes one 00:24:54.100 --> 00:25:00.600 very, very long protein chain really long, which is called the poly protein, which 00:25:00.600 --> 00:25:06.590 then gets cleaved. So D'Souza's in this case, the thing that cleaves all the long 00:25:06.590 --> 00:25:11.610 protein chain into individual molecules that don't actually can work is called the 00:25:11.610 --> 00:25:16.970 main protease because it's cutting protein that's called the protease. And these are 00:25:16.970 --> 00:25:22.150 the little triangle shaped things here. Only when that happens to these bits 00:25:22.150 --> 00:25:26.890 become functional. So if it doesn't happen, if we can like hindered this like 00:25:26.890 --> 00:25:33.010 cutting off the long polypeptide chain, we have an efficient drug against corona, 00:25:33.010 --> 00:25:37.880 which is why main protease is a major drug target. And what you can see here in red 00:25:37.880 --> 00:25:44.510 is the drug actually bound two main protease. So that's what it looks like. We 00:25:44.510 --> 00:25:48.220 are looking specifically for inhibitors, which will stop this molecule from 00:25:48.220 --> 00:25:52.150 function. So you can imagine this like a screwdriver that we put out of right point 00:25:52.150 --> 00:25:57.910 in a machine where it fits and it stops the entire machinery. That's what we want. 00:25:57.910 --> 00:26:01.610 And that's like called structure based drug design. When you actually know the 00:26:01.610 --> 00:26:06.220 structure of the molecule and then you find a molecule, a small molecule, a drug 00:26:06.220 --> 00:26:13.221 molecule that specifically stops whatever that protein molecule is doing. It's also 00:26:13.221 --> 00:26:21.230 how many antibiotics work or, for example, if you've been up long yesterday aspirin. 00:26:21.230 --> 00:26:29.310 Then. From here, where we have the poly protein thing. Something happens inside 00:26:29.310 --> 00:26:33.830 the cell, the cell is making some kind of foam, which is connected to the 00:26:33.830 --> 00:26:39.940 endoplasmic reticulum. That's just warm and inside it. These like enzymes that 00:26:39.940 --> 00:26:44.330 have now been cut in our functional start, like a copy machine to make more and more 00:26:44.330 --> 00:26:49.820 copies of the RNA genome of the virus. The whole cell kind of like foams up and makes 00:26:49.820 --> 00:26:56.640 more RNA. And it does so by a copy machine, which is called RNA polymerase, 00:26:56.640 --> 00:27:04.950 because RNA is a polymer and a polymerase is an enzyme that's making polymers and an 00:27:04.950 --> 00:27:13.850 RNA polymerase is an enzyme that makes more RNA. So one way to block that process 00:27:13.850 --> 00:27:18.990 of making more RNAs, which was similarly, you know, stop the infection cycle because 00:27:18.990 --> 00:27:24.170 if it can't produce more RNA, it's got nothing to put into new viruses is to use 00:27:24.170 --> 00:27:29.230 remdesivir or so we thought for a long time. So does this remdesivir. Remdesivir 00:27:29.230 --> 00:27:35.950 looks to the host cell and to RNA polymerase in particular, like a 00:27:35.950 --> 00:27:41.710 nucleotide, like a building block for RNA. So basically, things are it's new paper it 00:27:41.710 --> 00:27:47.290 can copy on when in reality it's kind of explosive like blocks the entire 00:27:47.290 --> 00:27:52.770 polymerase. So you can imagine this like a Trojan horse, remdesivir is the Trojan 00:27:52.770 --> 00:27:58.809 horse and RNA dependent RNA polymerase is sure looks like RNA to me and just built 00:27:58.809 --> 00:28:05.500 that into the strand. So we'll have a look at this molecule. This is, by the way, I 00:28:05.500 --> 00:28:10.240 should probably go back and explain this for a moment. This is what we get out of 00:28:10.240 --> 00:28:15.230 our measurements and electron microscopy. So this is the so-called reconstruction 00:28:15.230 --> 00:28:18.790 density, and that's what we built a molecule in. So that's like what the 00:28:18.790 --> 00:28:23.450 measurement gave us, everything else we have to do by hand. So here is the 00:28:23.450 --> 00:28:31.070 density, and this is what the researcher built into it. The template strand, the 00:28:31.070 --> 00:28:36.870 old one, which is to be copied, is green, the new one is orange. Remdesivir is 00:28:36.870 --> 00:28:43.080 purple and connected to the end, although the program doesn't display it as such. 00:28:43.080 --> 00:28:46.880 What you can also see is free magnesium ions. That's their own thing and a de 00:28:46.880 --> 00:28:54.110 phosphate. So what are more molecules that researchers modeled in there? Where are 00:28:54.110 --> 00:28:58.130 around it as the protein? So I've just quickly depicted it without so you can see 00:28:58.130 --> 00:29:01.940 what's happening because it's all very crowded and difficult to see around it as 00:29:01.940 --> 00:29:07.330 the protein and a jump of two proteins to copy the RNA and to attach one after the 00:29:07.330 --> 00:29:11.960 other, another building block to the bottom of the orange chain. It's gotten a 00:29:11.960 --> 00:29:17.149 remdesivir and it tried to put it there and it successfully did. And this 00:29:17.149 --> 00:29:22.220 structure was taken as to prove that remdesivir will stop corona. But if you 00:29:22.220 --> 00:29:26.110 look at the density, you can see that the free magnesium ions and DIPHOSPHATE has no 00:29:26.110 --> 00:29:32.220 density and are not covered by this great cloud, right? So we think they were never 00:29:32.220 --> 00:29:39.140 really there. And the remdesivir itself is also not having so much density. So it 00:29:39.140 --> 00:29:43.120 turns out that a structure is not quite seeing what the researchers did because 00:29:43.120 --> 00:29:48.330 the density doesn't match up with the structure they built. And as we later 00:29:48.330 --> 00:29:53.090 found out in clinical trials, is that remdesivir, in fact, doesn't really do 00:29:53.090 --> 00:29:58.280 what people hoped, which, among other things, has to do with the fact that RNA 00:29:58.280 --> 00:30:03.100 polymerase from corona virus is able to proofread go like, Oh, there's a 00:30:03.100 --> 00:30:08.980 remdesivir, then go back free nucleotides take rip out the remdesivir, throw it away 00:30:08.980 --> 00:30:15.120 and get the proper nucleotide to build in. So. We're hoping that one over pea-rel will 00:30:15.120 --> 00:30:18.839 be better, which, by the way, uses a similar mechanism. It's called a 00:30:18.839 --> 00:30:31.870 nucleotide. Yeah, it's similar to a nucleotide. Here's another arrow we found 00:30:31.870 --> 00:30:35.070 in the bottom of the structure, only going to show you because I think the software 00:30:35.070 --> 00:30:40.150 by Tristan Kroll is so cool, it does a real time molecular dynamics simulation 00:30:40.150 --> 00:30:44.510 while you're dragging around your structure. We found that there is an error 00:30:44.510 --> 00:30:48.490 in the way the whole molecule was arranged. If there's any specialist, there 00:30:48.490 --> 00:30:52.100 was a nine amino acid out of reach associate. OK, I'm going to stop like 00:30:52.100 --> 00:30:56.490 geeking out. There was just an error. Let me show you how he correct that. So first 00:30:56.490 --> 00:31:00.990 you marks up the wrong region and then he releases it and quickly flying-away noise it goes where it's up to 00:31:00.990 --> 00:31:04.870 go. I wish my life would always be like this, you said were free days glasses in 00:31:04.870 --> 00:31:08.309 front of your computer. You need hours to do this by hand, but his software just 00:31:08.309 --> 00:31:15.360 does it. Sorry. It's just if you've spent months doing this, you're totally excited 00:31:15.360 --> 00:31:21.580 by this wobbly molecule. I just wanted to show you because I think it's so cool. All 00:31:21.580 --> 00:31:29.549 right. Back to a more general content. We have an hour RNA and a let's imagine we 00:31:29.549 --> 00:31:35.419 didn't get any like good drugs so far, so the infection cycle is still ongoing. The 00:31:35.419 --> 00:31:40.050 RNA now is exported from the endoplasmic reticulum. By the time we make this, we 00:31:40.050 --> 00:31:43.750 didn't know how. But Hamburg researchers and Dutch researchers have now found out 00:31:43.750 --> 00:31:49.370 how this actually works as a pore here and the pore gets the RNA out. The RNA then 00:31:49.370 --> 00:31:53.890 gets packed into new nucleocapsid were also coded by the genome 00:31:53.890 --> 00:31:59.760 of the virus, then gets wrapped into a new double membrane, which is host membrane. 00:31:59.760 --> 00:32:05.970 Just it has no spikes, which also were produced from the genome. And then, of 00:32:05.970 --> 00:32:11.580 course, due the Golgi apparatus is somehow involved, it gets exported. Of course, for 00:32:11.580 --> 00:32:17.850 everyone that infected a cell, there will be thousands that are produced and that's 00:32:17.850 --> 00:32:26.120 the entirety of the SarsCoV 2 viral life cycle. I know, this was a little bit 00:32:26.120 --> 00:32:31.740 much, but I think this is cool and exciting and just about what, you know. I 00:32:31.740 --> 00:32:36.980 hope the public can understand about this. It hopefully also tells you why molecular 00:32:36.980 --> 00:32:42.740 structures are important, so they let us understand how the virus works, how host 00:32:42.740 --> 00:32:48.481 cells are infected. They can help us to find drug targets and to do structure 00:32:48.481 --> 00:32:53.370 based drug design, where we find drugs that specifically block these big 00:32:53.370 --> 00:32:59.510 molecular machines from doing their work. They also help us to understand the 00:32:59.510 --> 00:33:06.549 structures of vaccines and antibodies, and they also let us understand changes due to 00:33:06.549 --> 00:33:10.850 two mutations, I haven't got an example because of the time. But when we get a 00:33:10.850 --> 00:33:16.010 mutation with the structure, I can kind of tell you, that it is going to change or 00:33:16.010 --> 00:33:21.341 that it is going to change only by knowing the new genome. I can already make a 00:33:21.341 --> 00:33:25.340 prediction about what the mutation is going to change in a functionality. That's 00:33:25.340 --> 00:33:31.850 really important. So in my group, we have some theories what a Micron actually does. 00:33:31.850 --> 00:33:36.340 We haven't published and we haven't even tweeted about them yet because we're still 00:33:36.340 --> 00:33:43.240 waiting for research results. But it's important to understand these molecular 00:33:43.240 --> 00:33:52.169 structures, however, is not very easy to get them. So what are the problems? When we 00:33:52.169 --> 00:33:58.750 do our measurement, we get density in this case, the density is blue. It's from the 00:33:58.750 --> 00:34:02.179 spike head that I've shown in the beginning, right? So the top that you may 00:34:02.179 --> 00:34:06.490 recognize, this looks a little bit like the blue density here. This is the result 00:34:06.490 --> 00:34:10.919 from our research. And in this case, I have built almost all of the molecule 00:34:10.919 --> 00:34:15.290 already, so I'm going to show it. This is like the software. We're actually using a 00:34:15.290 --> 00:34:19.659 tenfold to speed I'm usually using, and I would usually be sitting there with 3D 00:34:19.659 --> 00:34:24.190 glasses. So here's the density. I said that with my 3D glasses and this bit 00:34:24.190 --> 00:34:30.579 hasn't been built, so you can now see me like by hand. And one bit of molecule 00:34:30.579 --> 00:34:34.999 after the other trying to get the murder ought to be, and you can quite well see 00:34:34.999 --> 00:34:40.030 that the computer is not able to do it all automatically. So I have to help it a 00:34:40.030 --> 00:34:44.240 little bit. And as I said, it's about 10 times the speed. It's even got like the 00:34:44.240 --> 00:34:49.179 warning from the bin program not reacting all of the software, it's also not 00:34:49.179 --> 00:34:53.800 commercial. This has been developed by other scientists, so the usability is like 00:34:53.800 --> 00:34:59.609 so-so cool, just an amazing program. But if you want some new functionality, you 00:34:59.609 --> 00:35:04.440 better program it yourself, because perhaps no one else is going to do it. And we have 00:35:04.440 --> 00:35:10.549 actually contributed with a plug in or two to cut. Yeah, you can see it's not always 00:35:10.549 --> 00:35:13.869 easy, so I try and go, like, now it's good. Settings should nicely in the 00:35:13.869 --> 00:35:21.890 density and here it's fairly easy. My students love doing this is like for them. 00:35:21.890 --> 00:35:25.099 It's like computer gaming. They do it for three months straight. If you don't like, 00:35:25.099 --> 00:35:30.450 get them off the chair, go right up your physics. They'll do it forever. And 00:35:30.450 --> 00:35:35.289 secretly, I'm jealous. Because I also like doing this. I don't know if you can 00:35:35.289 --> 00:35:45.499 follow, but this is like playing a game. Away, if you're interested in playing this 00:35:45.499 --> 00:35:54.010 game, we are also having. Like practical places and stuff. Right! So building, 00:35:54.010 --> 00:35:58.790 building, building, going like, oh, there's another alanine, I need a pralines 00:35:58.790 --> 00:36:03.609 or mutated it. I go like, Yeah, OK, now it's all nicely sitting. So that was easy. 00:36:03.609 --> 00:36:09.240 But what do I do here? So I've built for something here. But is it correct? The 00:36:09.240 --> 00:36:12.950 density does not really tell me what's going on here, and I'm going to show it 00:36:12.950 --> 00:36:18.680 this to you in slower again. So you understand the problem, right? In this 00:36:18.680 --> 00:36:22.720 then part of the density, I can really not tell only from the density what's going 00:36:22.720 --> 00:36:28.890 on. I know approximately what a molecule must look like due to the sequence. So 00:36:28.890 --> 00:36:31.740 I've got some information. I know which Atom is connected to which, but how it all 00:36:31.740 --> 00:36:37.119 three dimensionally fits in here, even if I know which lines have to go in, there is 00:36:37.119 --> 00:36:41.849 super hard. So it would be very easy for me to make an error here, because the 00:36:41.849 --> 00:36:45.979 measurement data don't tell me enough about what the model actually should look 00:36:45.979 --> 00:36:55.500 like and several interpretation., everal models would all be possible. So this is 00:36:55.500 --> 00:36:59.130 kind of difficult. I'm just seeing a questionnaire that I may want to answer 00:36:59.130 --> 00:37:03.670 right away. Within could is it possible to verify if you have chosen created the 00:37:03.670 --> 00:37:09.379 right building blocks, you know, the building blocks because of the genome? So 00:37:09.379 --> 00:37:14.539 Gene tells you the order of amino acids you want to put after each other. So if 00:37:14.539 --> 00:37:21.839 you started at the right point, the rest will also be like the correct atoms and 00:37:21.839 --> 00:37:26.039 the correct connection. But how it like three dimensionally faults, you don't 00:37:26.039 --> 00:37:36.600 know. You have to make that on the density. So it is possible to do it. You 00:37:36.600 --> 00:37:41.910 have to write building blocks at hand. Usually if there are if there is like, you 00:37:41.910 --> 00:37:46.160 know, if a magnesium ion, for example, is sitting there, the magnesium ion was not 00:37:46.160 --> 00:37:51.250 in your genomic information. You just need to know what you're doing to recognize 00:37:51.250 --> 00:37:58.190 this is a magnesium ion ore does this a diophosphate or something like this? 00:37:58.190 --> 00:38:06.490 Right. Going to answer the rest of the questions later. Molecular models need to 00:38:06.490 --> 00:38:11.049 be built by hand. This can lead to errors. There a few automatic algorithms do work 00:38:11.049 --> 00:38:17.059 under favorable circumstances, but most of the stuff still has to happen by hand. As 00:38:17.059 --> 00:38:21.549 of today, and I got my postdoc from like holidays for 15 minutes today, and he gave 00:38:21.549 --> 00:38:25.500 new numbers. So we've got 1909 molecular structures 00:38:25.500 --> 00:38:31.729 today. New structures come out every Wednesday. There are 1334 from X-ray 00:38:31.729 --> 00:38:36.109 crystallography. That's the thing. With the particle accelerator in Hamburg, I 00:38:36.109 --> 00:38:41.150 thought, they have been measured at synchrotrons all over the world. Not only 00:38:41.150 --> 00:38:46.079 Hamburg, where BioNTech structures have been measured, but also had SARS. There 00:38:46.079 --> 00:38:51.890 have been large screens a diamond in Japan and China at Sesamia, at Solemy, in 00:38:51.890 --> 00:38:57.349 America. Synchrotrons all over the world contributed to this. 35 from nuclear 00:38:57.349 --> 00:39:02.470 magnetic resonance, which is a little bit of a niche method for this type of study. 00:39:02.470 --> 00:39:08.579 And 566 from electron microscopy. So 1909 molecular structures 00:39:08.579 --> 00:39:16.339 of different states of 17 macromolecules, 17 proteins from a total 00:39:16.339 --> 00:39:26.789 of 28. So corona virus in total has 28 different genes, 4 proteins. There are 28 00:39:26.789 --> 00:39:33.079 proteins. And we only structurally know 17 of them. And then we have like different 00:39:33.079 --> 00:39:37.119 versions of them, different ph, different temperatures, spike, head bit of spike 00:39:37.119 --> 00:39:47.259 head, spike head with antibody, things like that. So a 1900 data sets that's in total. 00:39:47.259 --> 00:39:51.980 Errors and structures, as we've just seen, can happen because fit between 00:39:51.980 --> 00:39:58.940 the data and model is bad, because complete automation is not possible. Models are 00:39:58.940 --> 00:40:04.819 built manually expertize in many different areas needed. You need to be good 00:40:04.819 --> 00:40:07.819 software. You need to have done all the lab work. The measurement needs to be done 00:40:07.819 --> 00:40:12.269 right. Processing needs to be made. You need to know your statistical validation. 00:40:12.269 --> 00:40:17.180 You need to know your chemistry. You need to know your biology. So it's really not 00:40:17.180 --> 00:40:22.230 easy and you need to know your 3D goggles unless you get sick from them, in which 00:40:22.230 --> 00:40:27.720 case you can't use them. One of the major aspects of software, the methods you're 00:40:27.720 --> 00:40:35.789 using and this is where we come in. Small structural errors can lead to big 00:40:35.789 --> 00:40:41.000 structural problems downstream. Imagine the bid was to remdesivir, the diphosphate 00:40:41.000 --> 00:40:45.979 there, the fact that there was something bound into that structure that was not 00:40:45.979 --> 00:40:51.769 really there. But the model had dose like additional free magnesium ions down the 00:40:51.769 --> 00:40:59.809 line, as I know from insiders, led to like waste of hundreds thousands of dollars 00:40:59.809 --> 00:41:05.299 and many hours of work time in drug discovery because they kind of like fed 00:41:05.299 --> 00:41:09.990 this model in order to find a drug that ultimately never bound because of 00:41:09.990 --> 00:41:17.680 magnesium ion wasn't actually there. So if we make small structures, that builds 00:41:17.680 --> 00:41:21.599 up hugely for the downstream applications where they need these molecular 00:41:21.599 --> 00:41:31.279 structures. Errors are common. And now we add to this an ongoing pandemic. Right. 00:41:31.279 --> 00:41:35.720 And her scientists are there to rescue today. Lockdown happened, you're sitting 00:41:35.720 --> 00:41:41.339 at home, there are no colleagues to help you. Your child is home schooling. The dog 00:41:41.339 --> 00:41:45.430 wants to be fed, your grandma calls, because she's worried and you've got to 00:41:45.430 --> 00:41:50.939 solve the spike structure on which lives will depend as fast as possible. Normally, 00:41:50.939 --> 00:41:54.450 we take a year to five to solve a structure, and in the pandemic you only 00:41:54.450 --> 00:42:03.940 got three months. Of course, errors are going to happen. So that's well, just a 00:42:03.940 --> 00:42:08.779 matter of fact. We've got to arrange ourselves with it. It's not the fault of 00:42:08.779 --> 00:42:14.170 individuals, it's how the whole thing works. It's such a complex process. Errors 00:42:14.170 --> 00:42:19.539 are going to happen! Now in normal life my team and I methods developers and 00:42:19.539 --> 00:42:24.589 structural biology. We are the people, who give us the experimental techniques and 00:42:24.589 --> 00:42:30.670 software to solve their structures as best as we and they can. We're not usually in 00:42:30.670 --> 00:42:36.569 the in the stage like we're usually, you know. For every Nobel Prize, there have 00:42:36.569 --> 00:42:41.109 been like dozens of Nobel Prizes in structural biology has been methods 00:42:41.109 --> 00:42:45.059 developed in the background to develop the methods that made it possible to see, you 00:42:45.059 --> 00:42:49.299 know, the structure of the DNA double helix or structure of the ribosome, or the 00:42:49.299 --> 00:42:56.029 structure of the influenza virus. It's just that normally we're just enablers. 00:42:56.029 --> 00:43:05.130 However, here was the pandemic and very many structures that had errors. So we did 00:43:05.130 --> 00:43:10.509 what we needed to do. We came together as a relatively large team under my 00:43:10.509 --> 00:43:17.279 leadership, we are today 23 people, we peaked at 27 last year from nine countries 00:43:17.279 --> 00:43:21.009 to check an improve the molecular structures of SARS-CoV-1 and SARS-CoV-2. 00:43:21.009 --> 00:43:31.369 So. We are methods developers, most of are methods developers, we are specialists in 00:43:31.369 --> 00:43:36.441 solving structures. We evaluate all the published Structures and Protein Data 00:43:36.441 --> 00:43:43.619 Databank or PDB from SARS and SARS- CoV-2. We reprocess all of them and we 00:43:43.619 --> 00:43:49.549 remodel them, although not all are looked at manually, because that would be just 00:43:49.549 --> 00:43:53.309 too much. We also do a scientific dissemination, putting these structures 00:43:53.309 --> 00:43:58.430 into context for people who want to start doing molecular research on corona virus. 00:43:58.430 --> 00:44:04.680 And we do public outreach. I'll give you a quick insight into our pipeline because I 00:44:04.680 --> 00:44:10.039 thought the software might be interesting for you. So every Wednesday come new 00:44:10.039 --> 00:44:14.529 entries of molecules in the protein databank, which is, by the way, the World 00:44:14.529 --> 00:44:19.039 Wide Protein Databank is an open, open resource. Everyone in the world can 00:44:19.039 --> 00:44:23.470 download the new structures, and all the journals require people who make new 00:44:23.470 --> 00:44:28.099 structures to put them there, which is nice. I'm really privileged to be in a 00:44:28.099 --> 00:44:33.150 field where the data are public. We compared the new structures with the NCBI 00:44:33.150 --> 00:44:37.950 proteomics, so the genes from corona virus to find the structures that belong to 00:44:37.950 --> 00:44:44.109 corona virus, put everything into an sql metha database. Then we calculate how 00:44:44.109 --> 00:44:48.529 different the structures are from the ones we already know. We look whether all 00:44:48.529 --> 00:44:52.480 measurement data available, so we have a big problem of not all measurement data 00:44:52.480 --> 00:44:58.640 being published. I hope we are going to be like astronomy one day, where everything 00:44:58.640 --> 00:45:06.440 gets published. I am sitting in the some German cometies to that end STIKO AM which 00:45:06.440 --> 00:45:11.059 is a very new hub. And then we run a number of specialized programs which all 00:45:11.059 --> 00:45:16.349 do validation and put the results on GitHub immediately. On Thursday, at the 00:45:16.349 --> 00:45:22.160 latest, researchers can find our elevation, remodeling and the quality indication for 00:45:22.160 --> 00:45:28.770 the structure everything, that can be done automatically online. We then, for some 00:45:28.770 --> 00:45:33.970 structures, manually rebuilt them, so we actively look weathered our problems, that 00:45:33.970 --> 00:45:38.200 was, for example, the case with the remdesivir structure. We tried to do this 00:45:38.200 --> 00:45:42.500 for those structures that we think drug designers will use the most or that are 00:45:42.500 --> 00:45:47.910 really important. And when we find errors, we contact our original office first and 00:45:47.910 --> 00:45:55.119 tell them we found an error here is the corrected structure. Use our data, you 00:45:55.119 --> 00:46:00.929 don't need to cite us, just correct your structure in the database, please. This 00:46:00.929 --> 00:46:05.269 means we won't get credit, but I meant that at the beginning of the pandemic, 00:46:05.269 --> 00:46:11.279 people were adjusting their structures already when the preprint was out, so 00:46:11.279 --> 00:46:15.420 there would not be problems downstream. And I have often been asked I would like 00:46:15.420 --> 00:46:20.789 to like this again. That was really like why people accepted our corrections, 00:46:20.789 --> 00:46:25.539 because they didn't need to give anyone credit. They could just like change them. 00:46:25.539 --> 00:46:30.230 And the database is also online, so everyone from the Philippines to the U.S. 00:46:30.230 --> 00:46:34.940 can just use them, whether it's like a commercial person or a taxpayer, or a 00:46:34.940 --> 00:46:40.559 private person research institution, a foundation, everyone can use our data. 00:46:40.559 --> 00:46:44.309 They're just online there for everyone, and we only ask them to give us credit in 00:46:44.309 --> 00:46:51.109 the form of a reference citation. We disseminate the data via GitHub via 00:46:51.109 --> 00:46:57.190 Twitter. 3D bio notes, which is a three dimensional database linking directly into 00:46:57.190 --> 00:47:06.640 our database, we contact the offers. We also have entries in Proteopedia. Molprobity, 00:47:06.640 --> 00:47:11.450 which is a virtual bioinformatics institute, links directly into our 00:47:11.450 --> 00:47:15.100 database. So they're always like up to date showing what we are doing. We have a 00:47:15.100 --> 00:47:20.440 homepage and we do reviews. There's a lot of downstream users. The biggest ones are 00:47:20.440 --> 00:47:29.309 the EU Jedi Grand Challenge folding at home, which peaked out in July last year. 00:47:29.309 --> 00:47:36.809 I think a 2.4 xTFLOPs computing power for molecular simulations and used in the 00:47:36.809 --> 00:47:43.830 majority our models to start from. And also very big is IBM open pandemics. But 00:47:43.830 --> 00:47:47.989 there are a number of others, plus many individual apps. So we found a great new 00:47:47.989 --> 00:47:55.469 many friends. Here is our homepage, that's where you can find it. There's also an 00:47:55.469 --> 00:48:01.489 English version, you can find blog posts for the public and for scientists. And in 00:48:01.489 --> 00:48:07.020 the end, I would like to talk for like five minutes about daily life in ritual 00:48:07.020 --> 00:48:14.529 mobility. So my team is over 20 people from nine to ... we cover nine time zones, 00:48:14.529 --> 00:48:21.520 right? Where nine hours time shift apart. And we had several lockdowns. So. 00:48:21.520 --> 00:48:26.839 Actually, the majority of people in the task force, about half of them don't work 00:48:26.839 --> 00:48:31.580 for me. They are volunteering their researchers elsewhere that volunteer to be 00:48:31.580 --> 00:48:36.349 a part of this effort. And there are many people in the task force who have never 00:48:36.349 --> 00:48:43.989 like personally met. So how do you make group coherence if you are working for 20 00:48:43.989 --> 00:48:49.450 months or 22 months by now in an environment like this, right? We founded 00:48:49.450 --> 00:48:56.020 ourselves in March 2020 as a chat group called the Coronavirus Structural Task 00:48:56.020 --> 00:49:02.839 Force, which was a job back then. It didn't remain a joke. But that's how life 00:49:02.839 --> 00:49:08.400 plays. We have everyday Zoom meetings at 10 o'clock, one time per week in the 00:49:08.400 --> 00:49:14.700 afternoon. So do people from Oregon can join us. We do a lot of like media 00:49:14.700 --> 00:49:20.440 outreach in international and German media. We've been like on nano and Terra X 00:49:20.440 --> 00:49:24.599 and Planet E, we've been in breakfast television. That was a particularly 00:49:24.599 --> 00:49:30.069 interesting experience. My email got link to Querdenker and I got a few very 00:49:30.069 --> 00:49:34.579 interesting email exchanges. I also must say I never got insulted or frightened by 00:49:34.579 --> 00:49:41.589 anyone, so I just discussed with them and it worked out. And I'm happy because like 00:49:41.589 --> 00:49:49.410 I understood, like how, what the theories are, and that was very interesting. Keep 00:49:49.410 --> 00:49:53.680 the media also like to write about my hair, my eyes, blah blah blah on these 00:49:53.680 --> 00:49:58.440 things. I just want to note that Streeck is about my age, and Drosten is only nine 00:49:58.440 --> 00:50:05.980 years older than me. So really? OK, whatever. Most importantly, they're 00:50:05.980 --> 00:50:11.300 talking about our research. We also did a lot of social media. I got a Twitter 00:50:11.300 --> 00:50:15.880 account. Everyone else did as well. You can watch us work on Twitch if you're 00:50:15.880 --> 00:50:18.930 interested. We found that people find it soothing to see us modeling these 00:50:18.930 --> 00:50:23.519 structures. I was requested to make stickers for the team as soon as we got a 00:50:23.519 --> 00:50:28.719 grant and we got funded by the Federal Ministry for Research and Education in 00:50:28.719 --> 00:50:34.130 2020. We have a YouTube channel where you can, for example, see the entry animation 00:50:34.130 --> 00:50:40.510 and the students brought a cactus, which is called Corina the Corona Cactus. I 00:50:40.510 --> 00:50:47.470 know. It looked like we had fun, and we did. I can tell you being caught, you 00:50:47.470 --> 00:50:55.119 know, being at home, having to care for your children. Having people dying. Having 00:50:55.119 --> 00:50:59.880 an ongoing pandemic, knowing that I 'd be more open pandemics is going to spend 00:50:59.880 --> 00:51:04.589 another million based on your research. And also that ZDF wants to talk to you and 00:51:04.589 --> 00:51:09.981 the Berliner Abendblatt. This is so stressful! Think about all the 00:51:09.981 --> 00:51:15.349 responsibility we had, and it was really terrible for us, so we needed to cheer up 00:51:15.349 --> 00:51:19.999 every here and then, the whole group kind of like grew together and we all became 00:51:19.999 --> 00:51:25.999 friends. This was unheard. For us, it was very uncommon as researchers. Typically, 00:51:25.999 --> 00:51:29.029 our behavior with each other is much more formal than their behavior and this group 00:51:29.029 --> 00:51:35.880 was. But these were like exceptional times, and we wanted to fight the pandemic 00:51:35.880 --> 00:51:40.640 and inform the public. That's what we were there for and was not so much about 00:51:40.640 --> 00:51:49.340 personal gain. And that was nice. We have a group chat. You know, I mean, I'm 00:51:49.340 --> 00:51:53.289 talking to right audience, right? We have a group chat. Do you know what that looks 00:51:53.289 --> 00:51:57.759 like? Let me tell you. Typically, professors don't communicate with this. 00:51:57.759 --> 00:52:05.869 We have a virtual, Oh, we have a virtual space. We hope to change to work 00:52:05.869 --> 00:52:13.130 adventure soon. We all want to play games in the evening occasionally with the 00:52:13.130 --> 00:52:17.960 group, so we do some team building efforts. When people can meet in person, 00:52:17.960 --> 00:52:22.540 they usually do and sometimes they go and travel and like, meet each other. But this 00:52:22.540 --> 00:52:31.079 has been very limited. And we did grow together as a network, that will be there 00:52:31.079 --> 00:52:37.390 after the pandemic, so we are 25 people all over the planet that did this 00:52:37.390 --> 00:52:43.980 together. And even if we wouldn't have made any difference against the virus, I 00:52:43.980 --> 00:52:49.890 would still be happy to have done it for the friendships I made. However, we did 00:52:49.890 --> 00:52:54.910 make a dent. We don't quite know how big it is because our science was open science 00:52:54.910 --> 00:53:00.509 and the results could be gotten by everyone without reference. But we know a 00:53:00.509 --> 00:53:07.700 few things wouldn't have happened without us. And I'm. Deeply grateful for having 00:53:07.700 --> 00:53:17.739 had a purpose during this pandemic. In the end, I have a little bit of a more serious 00:53:17.739 --> 00:53:27.099 topic. My contract is going to run out in May. I think it's going to be prolonged. 00:53:27.099 --> 00:53:35.630 When it will, I'll be signing my 14 work contract since 2008. 14, like I had 13 00:53:35.630 --> 00:53:43.619 year contracts already out of all my task force members, there is only one holding a 00:53:43.619 --> 00:53:50.849 permanent position and two which are retired. Everyone else, including six 00:53:50.849 --> 00:53:56.990 people whose contract is going to run out next year, are on temporary contracts and 00:53:56.990 --> 00:54:02.140 not students. Students are extra. That the students are on time limited contracts is 00:54:02.140 --> 00:54:08.380 OK, but Germany's got a problem. 84 percent of academics in German 00:54:08.380 --> 00:54:17.529 universities are on time limited contracts. So are we. Only one task force 00:54:17.529 --> 00:54:22.779 member has was a permanent position signed, and that's not me. And this is not 00:54:22.779 --> 00:54:27.440 so much on my behalf, because I'm going to find my way through life. Look at all the 00:54:27.440 --> 00:54:32.380 exposure I had, but there are people out there who are single moms and dads, who 00:54:32.380 --> 00:54:36.769 come from less privileged backgrounds or had a harder life and who can just not 00:54:36.769 --> 00:54:44.740 afford to be on one year contracts all the time while holding a Ph.D.. We're losing 00:54:44.740 --> 00:54:48.920 all these bright people and I'm seeing them right. They leave my institute and 00:54:48.920 --> 00:54:52.759 they go to industry. And then the universities complain that they're not 00:54:52.759 --> 00:55:00.700 competitive. We need to change the system. We need to have more permanent positions 00:55:00.700 --> 00:55:07.309 in science. I promise we won't perform worse, if you give us permanent contracts. 00:55:07.309 --> 00:55:16.989 We love what we are doing. So back to the corona topic. In order to understand the 00:55:16.989 --> 00:55:22.029 virus and its life cycle, we need to understand its molecular biology. This 00:55:22.029 --> 00:55:27.759 will help with the design of therapeutics. We evaluated these molecular structures 00:55:27.759 --> 00:55:32.869 with a bespoke pipeline, an expert knowledge provided context and reached out 00:55:32.869 --> 00:55:37.969 to the taxpayer and the general public to inform them. We also wrote a paper 00:55:37.969 --> 00:55:43.400 together with long off a list making the invisible enemy visible, which is our 00:55:43.400 --> 00:55:49.129 motto. And as we started this all with questions, I'm going to end with 00:55:49.129 --> 00:55:55.239 questions. Structural biology remains difficult. What can we learn from our 00:55:55.239 --> 00:56:01.499 findings? Should we, as a scientists community, change our attitudes towards 00:56:01.499 --> 00:56:10.640 errors? Should this serve as a model for other projects, cannot serve as a model 00:56:10.640 --> 00:56:14.400 for other projects? I hadn't thought about this, but a nature editor asked me when I 00:56:14.400 --> 00:56:18.809 was writing a comment whether we believe that science should always be like this? 00:56:18.809 --> 00:56:23.459 My God, that would be awesome. I would totally be up for it if science would 00:56:23.459 --> 00:56:27.009 always be like this! Come together with a bunch of friends, but without funding! 00:56:27.009 --> 00:56:32.210 Start doing something to, you know, fight a global pandemic, then get some funding. 00:56:32.210 --> 00:56:39.489 Still, having like no senior people on a project. Can open science compete? I don't 00:56:39.489 --> 00:56:49.099 know. We get pretty little credit. It would, definitely. OK, science compete. I 00:56:49.099 --> 00:56:53.289 don't know, it doesn't quite look like it still getting measured only by the 00:56:53.289 --> 00:56:58.979 citations my paper gets. And well, at least a paper is not behind a paywall, but 00:56:58.979 --> 00:57:02.799 if we would have published all our stuff in like papers would possibly get more 00:57:02.799 --> 00:57:09.369 credit. I really don't know, but we need to work on this. If we want science, we 00:57:09.369 --> 00:57:16.700 need to change how people are rewarded. How senior they really need to be. I'm 39. 00:57:16.700 --> 00:57:22.200 It seems I'm called a junior group leader. All of us are young. The youngest is 24. 00:57:22.200 --> 00:57:26.859 He's writing our first Alpha article about a corona virus protein. I feel that the 00:57:26.859 --> 00:57:31.259 German academic system and all over the world, actually you need to be older and 00:57:31.259 --> 00:57:37.119 older to become a professor and be permanent and be like a grant holder. I 00:57:37.119 --> 00:57:41.180 don't think it's necessary, I think that professors could be 30 and the world 00:57:41.180 --> 00:57:49.030 wouldn't, you know, like, go down. Well, what will change in science after a 00:57:49.030 --> 00:57:54.289 pandemic? We had like large exposure. It certainly will also have to do with like 00:57:54.289 --> 00:57:58.580 questions like did the virus now come from an app or didn't it? That, you know, would 00:57:58.580 --> 00:58:03.720 change how people view science, I'm sure. How will scientists be viewed by the 00:58:03.720 --> 00:58:08.960 public? Right. Right now, of course, you know, mom and dad are very proud, but. 00:58:08.960 --> 00:58:14.119 What's going to change? Are we going to still be the bad guys because we often 00:58:14.119 --> 00:58:19.180 are. But I'm like general, exclusively taxpayer funded. I never took any money 00:58:19.180 --> 00:58:23.519 from the pharmaceutical industry. I have like, you know, no stakes in this game. 00:58:23.519 --> 00:58:31.959 I'm just like earning tax money, so I feel that, there is a whole complex of 00:58:31.959 --> 00:58:35.420 difficult things there, how people regard science, but definitely the pandemic is 00:58:35.420 --> 00:58:40.079 going to change, how science is going to be viewed. What's that going to be? 00:58:40.079 --> 00:58:48.400 Exspiration In the end. I'd like to thank all the task force members and all 00:58:48.400 --> 00:58:54.000 our collaboration partners and our scientific fairy godmother, Alvin Pearson, 00:58:54.000 --> 00:58:59.099 who had little role in this research but much role in our mentorship and bringing 00:58:59.099 --> 00:59:04.299 us forward. My home, the University of Hamburg, the Coronavirus Structural 00:59:04.299 --> 00:59:08.499 Taskforce, our we are funded by the Deutsches Officials Command Trust and the 00:59:08.499 --> 00:59:13.699 Federal Ministry for Research and Education. I would like to point out that 00:59:13.699 --> 00:59:19.130 we are looking for student assistance, not only for scientific work, but also for 00:59:19.130 --> 00:59:25.430 social media video and programing work and 3D printing. So if you know anyone who's 00:59:25.430 --> 00:59:30.710 interested, please point him in my direction. My email is there. We are also 00:59:30.710 --> 00:59:36.219 offering Bachelor, Master and Ph.D. thesis in areas that cover both Lab work and 00:59:36.219 --> 00:59:43.691 computer work, which is a rare thing these days. You can find us on YouTube and the 00:59:43.691 --> 00:59:50.990 internet and on Twitter and. I'm looking forward to the discussion. And thanks for 00:59:50.990 --> 00:59:53.549 listening. melzai_a: You write it, so.laughing 00:59:53.549 --> 00:59:57.660 Andrea: I just brought it up, must have bmbF because I'm now sitting on the screen 00:59:57.660 --> 01:00:01.519 on dislike committees more and more, I'm reaching an age where I'm sitting on 01:00:01.519 --> 01:00:05.359 committees and I told them legacy software is a problem. 01:00:05.359 --> 01:00:07.900 melzai_a: It's a real.big problem. Andrea: You know, it's very troubling that 01:00:07.900 --> 01:00:12.829 the software is written in Fortran. Not every second Linus go to, so it's written 01:00:12.829 --> 01:00:17.930 like assembler. No one knows what's in there anymore. And if a person dies, we're 01:00:17.930 --> 01:00:21.530 not going to be able to do anything about the algorithms. They're just going to be 01:00:21.530 --> 01:00:24.810 lost. melzai_a: Exactly. And they are. So you 01:00:24.810 --> 01:00:28.459 have to first influence to grant writing institutes that there are grants out so 01:00:28.459 --> 01:00:32.849 that this software can read is reversed. And this software is not easy. So that's 01:00:32.849 --> 01:00:36.650 not your typical web page, so you need to work together in such groups. And so it's 01:00:36.650 --> 01:00:41.720 a very interesting piece of the problem, I have to say. So sadly, as a PhD student went, 01:00:41.720 --> 01:00:45.629 we weren't we were looking into this for the second. Ah.. This is too big of a cake 01:00:45.629 --> 01:00:49.990 to eat. laughing It was very interesting. So I can also this and you 01:00:49.990 --> 01:00:53.630 let you do it. The nudel tool suite, and that's also only maintained by, I think, 01:00:53.630 --> 01:01:00.739 three people also. So even that one, it's with many more. It's still not good. So 01:01:00.739 --> 01:01:05.900 just my sense of that one. Andrea: So I brought my Ph.D. thesis. I 01:01:05.900 --> 01:01:08.329 worked on chalex?? and that faces similar problems. 01:01:08.329 --> 01:01:15.319 melzai_a: Yeah, it's it's just used in the entire world to solve every small molecule 01:01:15.319 --> 01:01:20.359 structure. There is more or less it was like, Yeah, so questions were the 01:01:20.359 --> 01:01:25.440 questions. Frankly, we ain't got a first question, I think around 20 or 30 minutes 01:01:25.440 --> 01:01:30.269 ago, if we yeah, that's that's why that was so great as a signal angel, she's 01:01:30.269 --> 01:01:34.969 picking up all of these points. And so the first question was how do the virus 01:01:34.969 --> 01:01:37.400 variants affect the shape or form of the virus? 01:01:37.400 --> 01:01:44.329 Andrea: I think they so no matter like, OK, this is the old model as we know, then 01:01:44.329 --> 01:01:48.690 there should be fewer spikes and should be a bit smaller. But nothing would change on 01:01:48.690 --> 01:01:54.920 this view, like the scale is way too large. The mutations each change about 10 01:01:54.920 --> 01:02:01.099 atoms, so every like amino acid at this different, it's about 10 atoms. And those 01:02:01.099 --> 01:02:06.420 changes would be so small you could not see them on the virus model. You'd 01:02:06.420 --> 01:02:10.239 actually need to look at the head of the spike in order to see the mutation and 01:02:10.239 --> 01:02:16.079 what it actually does. So the changes are too small to show them in the model. That 01:02:16.079 --> 01:02:20.499 doesn't mean they're not meaningful. So as you've seen, like the head of the spike 01:02:20.499 --> 01:02:28.079 binds to the host, to the host cell, to ACE2 receptor, and that binding is highly 01:02:28.079 --> 01:02:35.920 influenced by this by the mutations. Now we found that we may end up lucky because 01:02:35.920 --> 01:02:41.729 the same paths were to antibody as binding is also the piece that binds to the host 01:02:41.729 --> 01:02:47.380 cell. So everything that would mate despite change in a way that the antibody 01:02:47.380 --> 01:02:55.170 couldn't bind any more to it. For its head would have also changed how it bound to 01:02:55.170 --> 01:03:03.000 the host cell. However, it seems that Omicron is still able to bind human cells 01:03:03.000 --> 01:03:08.780 very efficiently, while antibodies cannot recognize it so easily. That may have to 01:03:08.780 --> 01:03:13.099 do with like this finger's actually like packed and you could imagine like putting 01:03:13.099 --> 01:03:17.999 cotton wool around it. That's called glycosylation. It's got long sugar changes 01:03:17.999 --> 01:03:22.840 that are rule, and they're there to obscure the immune system, like the 01:03:22.840 --> 01:03:27.530 antibody goes like orders, wool. I can't really find where I'm on to bind. Is it 01:03:27.530 --> 01:03:34.210 here? I don't know. And that's changed in Omicron, but it's not fully understand 01:03:34.210 --> 01:03:40.519 yet. I saw there was a new structure this week, but I haven't looked at it yet. 01:03:40.519 --> 01:03:44.529 However, the changes are too small to show it in the virus model. They're like really 01:03:44.529 --> 01:03:50.819 tiny changes. And another change that happens in Omicron as well is the 01:03:50.819 --> 01:03:56.799 proofreading mechanism. When the RNA is copied is like damaged and we think it's 01:03:56.799 --> 01:04:01.869 damaged. So their so-called eNd RNA, which is a proofreading protein, its sharp is 01:04:01.869 --> 01:04:06.630 like to go like a star and correct? Yes, correct, correct. Correct. That seems to 01:04:06.630 --> 01:04:10.959 be a little bit broken. So it could be that Omicron is accumulating so many 01:04:10.959 --> 01:04:17.229 mutations because it's RNA copy machine. It's like not working as it should is 01:04:17.229 --> 01:04:21.630 basically not proofreading. That would mean that more viruses are produced that 01:04:21.630 --> 01:04:26.549 are not viable and cannot survive. But it would also mean that it mutates much 01:04:26.549 --> 01:04:32.009 faster, and we think that may have an influence. But that's just theory. So far 01:04:32.009 --> 01:04:36.799 this hypothesis, we haven't proven it yet. So this is why I haven't tweeted about it 01:04:36.799 --> 01:04:42.059 yet, because it's just a theory, but it would make sense, right? 01:04:42.059 --> 01:04:46.400 melzai_a: Connected to that, I would have a question the ice receptor of small children 01:04:46.400 --> 01:04:51.339 is a little bit different than that one of the adults to you do know about that 01:04:51.339 --> 01:04:56.049 because all the concern to what's more, the smaller children are the defense. 01:04:56.049 --> 01:05:01.499 Andrea: I can't. I have read that, but I haven't looked into it properly. So I'm 01:05:01.499 --> 01:05:06.249 I'm afraid I'm not going to answer this question because I feel I would rather not 01:05:06.249 --> 01:05:08.319 say anything about it than say something that's wrong especially. 01:05:08.319 --> 01:05:11.839 melzai_a: Well. We're looking forward to the secretary's right in the public PDB so 01:05:11.839 --> 01:05:19.099 that everybody can look at them and. Andrea: Know we live in an age of 01:05:19.099 --> 01:05:23.079 preprint, and very often the PDB papers are there when a preprint comes out, which 01:05:23.079 --> 01:05:28.079 is how we called so many errors, right? They published a preprint, they put out a 01:05:28.079 --> 01:05:32.349 structure. We went like, there's errors in the structures. And then when they 01:05:32.349 --> 01:05:34.880 published actual paper, everything was corrected. 01:05:34.880 --> 01:05:39.380 melzai_a: And she's agreed that believe the changes, I think are checked on the 01:05:39.380 --> 01:05:42.619 PDB. melzai_a: This is, in fact, because yes, 01:05:42.619 --> 01:05:45.799 that's that's what IT people like because then that, you know, there's a 01:05:45.799 --> 01:05:52.079 history is very important. And there's a second question and it goes towards the 01:05:52.079 --> 01:05:54.119 tools that I use to simulate those molecules. 01:05:54.119 --> 01:05:59.359 Andrea: Wait, wait, wait, wait. I have a follow up to this: thing that I would 01:05:59.359 --> 01:06:03.890 really like to see, but it hasn't happened yet. The PDB is a very static repository 01:06:03.890 --> 01:06:09.229 where only original offers are allowed to change their structures. Now, imagine if 01:06:09.229 --> 01:06:14.859 the protein data bank would be like GitHub with pull requests. We could go like, go 01:06:14.859 --> 01:06:18.789 like, changed the molecule around. Go like, no, it's a better fit to your data. 01:06:18.789 --> 01:06:22.979 Please pull. Herald: That would be a very subversive 01:06:22.979 --> 01:06:26.259 proposition. I would say. Andrea: Yeah, wouldn't that be nice? I'm 01:06:26.259 --> 01:06:31.319 like, Why aren't we doing this? It's like the system is already there. It happens 01:06:31.319 --> 01:06:35.769 that we have like repositories for a while in software development. We could do the 01:06:35.769 --> 01:06:44.049 same thing with models fitted to our experimental data. But I think I need to 01:06:44.049 --> 01:06:47.999 go into more committees. melzai_a: Yeah, it sounds like this. I 01:06:47.999 --> 01:06:53.839 would agree for that proposal. There was a person that was asking about the toolsset 01:06:53.839 --> 01:06:58.539 that you would use to simulate those molecules and structures and so on. And if 01:06:58.539 --> 01:07:03.599 you then create these more usable pictures for the public, how do you balance 01:07:03.599 --> 01:07:08.449 artist's impression simplified models and while keeping the scientific truth as 01:07:08.449 --> 01:07:14.160 much as well as possible. Andrea: The question you don't need the 01:07:14.160 --> 01:07:17.719 public even to have this problem. You have it already when you make pictures 01:07:17.719 --> 01:07:21.589 scientifically. Because sometimes you want to show our certain aspects of a molecule 01:07:21.589 --> 01:07:26.630 very clearly, which means you have to cut away, for example, a part of the molecule. 01:07:26.630 --> 01:07:30.979 So one answer to this is the program that does. The modeling is not a program that 01:07:30.979 --> 01:07:35.329 you use to make the pictures. That's the first thing you do. So you make your model 01:07:35.329 --> 01:07:38.809 with one program and then you take all the coordinates of the atoms and you throw 01:07:38.809 --> 01:07:44.569 them into a professional rendering program that like, we'll do it all pretty. But you 01:07:44.569 --> 01:07:48.930 still have to make an executive decision on what to show in your graphics, in your 01:07:48.930 --> 01:07:56.799 paper. And I think that in particular, structural biologists, who deal with three 01:07:56.799 --> 01:08:01.329 dimensional and two-dimensional pictures, we would do very well to think a lot more 01:08:01.329 --> 01:08:07.769 about scientific illustration. So all my team likes thinking about these things, 01:08:07.769 --> 01:08:12.460 which is, I think, how we got where we are now, right? They actually like stuff like 01:08:12.460 --> 01:08:17.890 this. They go like, Oh, we can print it 3D and we can put a magnet on it and it's 01:08:17.890 --> 01:08:21.980 going to stick. But it turns out that scientists also need these tools to 01:08:21.980 --> 01:08:26.830 understand what's going on. It's like actually having a 3D model helps you so 01:08:26.830 --> 01:08:32.420 much with thinking about things. Crick and Watson. They build a model of their DNA in 01:08:32.420 --> 01:08:37.160 metal for a reason. Because we're looking at three dimensional things, making them 01:08:37.160 --> 01:08:43.560 like understandable with our hands. So yes, as a good researcher, you're not only 01:08:43.560 --> 01:08:48.739 able to explain your research to the cleaning woman, you should also be able to 01:08:48.739 --> 01:08:53.290 visualize it properly. And it's part of the art. If you are a structural biologist 01:08:53.290 --> 01:08:58.310 and you're not able to make good pictures of your molecules, you're not a good 01:08:58.310 --> 01:09:02.239 structural biologist. End of story. You're in the wrong discipline, you should have 01:09:02.239 --> 01:09:05.359 possibly chosen something where you need less graphics. 01:09:05.359 --> 01:09:12.069 melzai_a: And I think one of your industry does is actually a of biologist by 01:09:12.069 --> 01:09:17.699 training. Right? I think you've got... Andrea: Tomasello is a proper biologist. 01:09:17.699 --> 01:09:25.589 Thomas Splettstössersplit shrews as a prop about like a Ph.D. in bioinformatics and Janet Erosa, 01:09:25.589 --> 01:09:32.569 and LiU are both scientists who are having a group that only deals with illustration. 01:09:32.569 --> 01:09:36.460 So it's actually in science. We have several groups in the world and structural 01:09:36.460 --> 01:09:41.690 biology who only do illustration as science. So David Goodsell with his 01:09:41.690 --> 01:09:48.179 watercolors, is very well known, but Janet Erosa is another one. So actually making 01:09:48.179 --> 01:09:54.880 these animations and pictures is so complicated that television can't do it. 01:09:54.880 --> 01:10:00.480 And the ZDF made a series of animations, so they made very nice ones for Planet E 01:10:00.480 --> 01:10:06.090 Rizzo and Nano with us. But then they asked my expertize to make another 01:10:06.090 --> 01:10:11.429 animation. And they only had like a call with us, and they never came back and then 01:10:11.429 --> 01:10:18.630 published a completely wrong animation of the entire viral mechanism under my name. 01:10:18.630 --> 01:10:24.690 And I'm still sad every time I see it three times a day. Heute Journal shows a 01:10:24.690 --> 01:10:29.469 wrong structure of the virus for which they claim that I helped them make it, and 01:10:29.469 --> 01:10:34.530 I wrote to them and told them, Your depiction of the virus is wrong. I can 01:10:34.530 --> 01:10:43.199 help you make a new one. But it seems that it's 2. deutsche Fernsehen der heute Journal at least didn't 01:10:43.199 --> 01:10:49.830 care on. I guess they think it's not important enough, but I think with a 01:10:49.830 --> 01:10:55.050 threat like this where we really cannot see the virus, it is important to bring to 01:10:55.050 --> 01:11:00.679 the public the best possible depiction we can deliver. Sometimes, however, as I 01:11:00.679 --> 01:11:05.010 said, you omit certain aspects, for example, to show the effects of a mutation 01:11:05.010 --> 01:11:12.619 yet only showed a side of the mutation. You don't show all the atoms. But. That's 01:11:12.619 --> 01:11:15.830 really an important part of what we are doing. Like pointing out the important 01:11:15.830 --> 01:11:18.130 bits of ... melzai_a: Scientific information is so 01:11:18.130 --> 01:11:23.900 important, I think we have one final question, which I would say comes out 01:11:23.900 --> 01:11:30.460 comes towards the direction of the immune system. And the question would be can you 01:11:30.460 --> 01:11:35.949 can you define vaccine on purpose so that the immune system can forget how to 01:11:35.949 --> 01:11:39.889 produce the antibodies after a defined period of time? And I think the concern 01:11:39.889 --> 01:11:48.670 here is about increasing your financial gain in the crisis, for example. 01:11:48.670 --> 01:11:55.540 So programed obsolescence, as both of those mentioned. So you're a bit late. So 01:11:55.540 --> 01:12:00.800 if you could keep it short, that would be great. OK? Andrea: The quick answer is no, 01:12:00.800 --> 01:12:08.480 that's not possible. You can make. You can enhance how long vaccines and how much 01:12:08.480 --> 01:12:13.929 immune response you get from a vaccine or certain additives. But you can not, like 01:12:13.929 --> 01:12:18.810 make them a definite time because everybody is different. So even when you 01:12:18.810 --> 01:12:21.840 get your booster shot, they say six months, but you may need it after three 01:12:21.840 --> 01:12:27.550 months or you may need it after 12 authorityto. It's very hard to tell. And 01:12:27.550 --> 01:12:32.520 pharma industry does not have tools that would allow them that, to my knowledge. So 01:12:32.520 --> 01:12:38.690 I think that's not a risk. melzai_a: I mean, it's it's a human 01:12:38.690 --> 01:12:43.780 system, and so complex is the rocket to the Moon. So. 01:12:43.780 --> 01:12:46.860 Andrea: I think it's a it's a valid concern. It's just technologically not 01:12:46.860 --> 01:12:53.429 possible. Luckily, I guess. melzai_a: The final and really last question, I think, 01:12:53.429 --> 01:12:57.110 is where can somebody find the 3D models out there? 01:12:57.110 --> 01:13:01.780 Andrea: Oh, you can go to inside Corona..de and find a blog post about a 3D 01:13:01.780 --> 01:13:13.050 thing or you go to Thingy Reuss and you look for inside corona. I can. Yeah. Yeah. 01:13:13.050 --> 01:13:21.110 I just go to. I just put it in. Why not that? That's our home page and then on 01:13:21.110 --> 01:13:29.380 thingy worse. It's also called inside corona. And you can also write me a 01:13:29.380 --> 01:13:36.860 message on Twitter if you don't find it at a turn up. And remember, we're going to 01:13:36.860 --> 01:13:43.260 put out a new model soon in January, but I'm still waiting for the final files and 01:13:43.260 --> 01:13:49.840 holiday. So it will be a few more weeks. melzai_a: So but that trend in January, 01:13:49.840 --> 01:13:53.260 not in December 2008. Yeah, exactly. Or printed? 01:13:53.260 --> 01:13:59.960 Andrea: Yes. So thank you very much for having me. 01:13:59.960 --> 01:14:02.820 melzai_a: Yeah, it was good. Thank you. And I think if they are no more questions. 01:14:02.820 --> 01:14:08.280 Everybody. All right. Oh, you know how it looks like? I think that's really 01:14:08.280 --> 01:14:12.020 important. I think one and a half years ago, I came across the first pictures was 01:14:12.020 --> 01:14:17.710 like, This is how it looks like. Now I can tell it to the people who who don't read 01:14:17.710 --> 01:14:26.090 the scientific original papers because they are so difficult to read. So. Yeah. 01:14:26.090 --> 01:14:34.130 Good. You know. And thanks for being here and looking forward to hearing and seeing 01:14:34.130 --> 01:14:38.050 more and hopefully once this will be over. I think 01:14:38.050 --> 01:14:43.730 Andrea: I hope so too. Going back out of the spotlight to being just a Methods 01:14:43.730 --> 01:14:45.730 developer, that would be nice. Herald: That would be nice, yes. 01:14:45.730 --> 01:15:05.000 Subtitles created by c3subtitles.de in the year 2022. Join, and help us!