Welcome back, everybody. I am so. And thank you very much for this opportunity to say a few words at this event.
And just in case I forget later,
just can I wish Steve a very happy retirement and the very interesting retirement I
find this this this word retirement rather difficult to comprehend in your context.
And it actually reminds me of one of Dave's favourite stock phrases.
When he was about to introduce one of his more extravagant ideas in the lab, he would always begin it by saying, I mean, I don't believe that, but.
And I think I have been asked, by the way,
before I go any further to say that for those people who are listening to this session online, you can ask questions if you want.
We haven't had any questions online yet,
but you are perfectly at liberty to ask questions at the end of the sessions by doing the raise hand thing on Zoom so you can do if you like.
OK. And I guess I felt this picture really had to have a bubble and and it was somewhat
in reference to the fact that one of the things I learnt very soon after coming to
Glasgow was that it was best to hide your pens as soon as Dave came anywhere near your
bench because serious safety would pick it up and walk off with it somewhere else.
And we had this hypothesis that there was a huge sum of pens somewhere up in his office that we never quite got to the bottom of.
OK, so I'm going to talk a little bit about the Glasgow years,
and I should emphasise I was only there towards the second half of the Glasgow years, but there was there from 1980.
And I do have some pictures of of the the IRA preceding my arrival.
And here is Dave under the mistletoe in the genetics department library professing.
And yeah, they look as if they're having a good time. So that's fine.
And as we have heard already, there are some people around to who back here, Lorraine and others who were here at that time.
The only thing that worries me slightly is the corpse in the right hand side of the picture,
who seems to be a boy dressed as a girl who probably seems to have electrocuted himself on the high voltage parapet.
But, you know, safety was like that in those days. It was, it was.
So, yes, so. So.
So I arrived in 1987, so this is this is a picture of Dave,
actually and my mom and dad's back garden in 1988 and I arrived in Glasgow on Black Monday.
In 1987, the day the stock market crashed,
which I always attributed to the fact that they had just left Zenica and they had discovered that I had moved to this slab and and I should say.
Thank you. I always wanted to thank Dave for the fact that he actually went to the trouble of offering me a job because I didn't apply it to Dave.
But when I was coming before I came to Glasgow, I applied for a completely different job and it somewhat miraculously to me.
Dave actually contacted me and said, Are you interested in a job that I have?
So I arrived in a very peculiar manner,
but I'm forever grateful that he didn't think it was a total crank being an industrial chemist wanting to do genetics.
And so things for a career. And as soon as soon became apparent when I arrived at the institute's police
department that I was coming into was a very peculiar place and a very unusual place.
To say it was buzzing was an understatement. I would say all sorts of things going on.
And it was a very remarkable place to work and quite different from anything I had been before.
And this is the actual building where it all took place.
This is the genetics department photograph taken a few years ago,
and the arrows indicate the arrow on the left indicates where this office was on the 7th floor of the building.
And after different into it, it was for a while it was my office two and then one floor below was what we call the sixth floor,
which was where all the labs were. And you can see from the picture this is a very tall, narrow building.
So the floors were really quite small, and so we were all pretty crammed.
And I don't think this building had the same sort of hierarchy that you've gotten described at Sussex Warehouse.
But what is obvious is that we were at the top, which must be good.
So, so but you know, looking at this picture,
it's kind of spooky to think of all the the lives that were lived in this building during the time I was there and all the.
All the parties that happened and all the the drinking went on and all the the substances, although I don't know anything about that,
but I know the intrigue and the infighting and the romance, lots of romance and all happening inside inside this little building.
I think when Dave arrived in Glasgow, the genetics department was probably quite a sleepy place,
but mainly focussing on classical approaches to genetics.
And he sort of led them with probably considerable kicking and screaming into the molecular era.
And his approach to science and his enthusiasm for science seemed to rapidly attract more and more people to the genetics department.
And so it started to fill up the building start to fill up. So even when I arrived, the building was quite congested with people.
And I think, you know, within a few years after my arrival, it was we were packed like sardines,
and I think that helped all the interactions that were on inside the building.
Everybody knew everybody else was doing helped by this magical paternoster lift that went up and down the centre of the building, cutting you.
And so the boxes that you travelled from one floor to another then were open, and once they had opened the front door, you could step on and off.
And so when you travelled from the ground floor to the top, you went through all the worlds of all different people living in the building.
And they held had their conversations and what they were ranting about at the time and stuff.
So it's all very interesting and. Here's the building.
That was a photograph of latency. And so the building is being demolished, the sixth floor has gone,
Dave's office is gone and they're taking it down from the top because they were scared in case it was going to fall over.
If they've tried to demolish it by traditional methods. So in a few weeks, it will be gone.
It was all wrapped up in this polythene stuff like that man, that Frenchman,
that dust sculptures and has been is going to be demolished on the inside.
So the sixth floor, I think I'm afraid, is rubble now. So that's that's a shame.
So here here is one of Dave's legendary barbecues.
I picked this photograph just because that maximise the number of people from his grip that got it.
And I apologise for my poor photography skills. But on the left hand side, there is Stephen Bell,
who's going to talk in a few moments and some other people who are at the meeting such time as that in there.
And these are other people in the group at the time.
I said I should have said, by the way,
I'm sure that all these people who unfortunately cannot be here would wish you the best wishes as well on this occasion.
It was a shame, of course, because of COVID that, but it was difficult to get this event organised.
And and yeah, so so David, you've had already was an inspirational teacher and mentor to students.
And I think the first thing to say about that was that he was so because students and people
recognise that they're talking to a world class scientist and that inspires them by itself.
And so I think just to have someone like that to to to talk to was a great thing.
But another another thing that I think makes an outstanding teacher is, is your idiosyncrasies and the little things that make you an individual.
And one of the characteristics that they've had was was that you really love using models.
And so you would always have something in his pocket, you know,
fill out some sort of piece of chirping like this and illustrate some aspects of the mechanism, like super calling or recombination in this case.
And this inspired Gary Larson. So to make this captain for his 1990 power site calendar, and you can tell, I mean,
you might think this is a fake, but it's a sign that the tops was clearly genuine. And so, so yeah, that's so characteristic post.
And another another thing that was very capitalistic of Dave's teaching methods was his love of offering rewards for people.
So. So if that these rewards ranged from the low value miles pass through pints of beer bottles
of old whisky up to the the almost mythical creator of champagne that you could get,
depending on the scale of the challenge that he was putting to you.
And so in the next year's farm site calendar, Gary Larson came up with this character as well.
And so I found these in my shoe box of some of the photographs and things of the time.
The the true adulteress of these pictures shall remain completely nameless.
I'll bet it is. I mean, I see he or she is listing.
Perhaps so. So these two pictures actually both reflect the fact that a lot of research in this lab at the time was looking at the exit system.
And of course, all of these options were a big deal in the mechanism of Xia.
So the science that was going on in the time that I was there was really divided
into three sections that were the transposition people working on and supplements,
et cetera. There was the main the biggest part of the the research group were working on the car and I was privileged to be in the
lab when Sun Column's tried to convince me that like a colony on one of his petri dishes was an interesting mutant,
but turned out to be the first mutant CRC.
And so that was all the exciting things happening at the time.
And then there were the result of these people, and I was recruited to join the result of these people.
So there were three of us at the time. There was embezzlers Martin, who was at the meeting and and me.
And what I started that this was the state of our knowledge.
But we've already had by the way of this result, this protein, because Gordon Duncan mentioned that he was the first person to see the protein.
But by 1987. It said it was looking like this, it was a Soviet recombination, and this picture was drawn by Martin.
And it shows what we thought the the the pathway for recombination was.
And so we thought that the two, the two transposons sites which are recognised by there's always protein,
they're brought together into this thing, which is inside the square box, which we called the synapse where the DNA is all intertwined.
And then in the final step, the strands are broken at the triangles and exchanged to make wood products, which are through DNA circles.
And that process was thought to happen by something that was equivalent to rotating the DNA end through 360 degrees.
And so this this very basic picture was where we were at in 1987.
But I think I've spent the next 30 years of my career basically making this more elaborate and making it more three dimensional.
But essentially, this picture was right away back then. And so here's what we think where we can now have the the subunit rotation mechanism.
We think the DNA is rotating like this and we have structures to back that up.
And in very recently, we've been doing single molecule experiments using fluorescent little for labels where we can see the
strand exchange going from low fat and on recombinant Typekit recombinant over a period of seconds.
So we can see these things happening in real time.
And then also, we have the this is now a three dimensional model of the set up structure, which is hopefully going to get published very soon.
And finally, after all the models which were proposed for this snap structure, we finally think we've got one.
That's right. There are many models that seemed wrong even when they were published in high profile journals.
But we think this one million is what it really looks like. And remarkably, the authors of this paper, which we're hearing at the moment,
I think fight five of the authors were people who were at Glasgow in your time Martin,
Sally, Mary Burke, myself, and also Alistair MacDonald, who was an undergraduate.
I think at the time are all going to be authors on this paper, so it still has a connexion back to the days when Dave was there.
I just wanted to get a picture of Mary on this slide. Just to mention, Mary was the technician in Dave's lab throughout his time in Glasgow.
And then I inherited Mary after Dave left until her retirement.
She was a fantastic technician. She made a huge contribution to all our work, as well as I'm sure many of you in the audience know,
contributing to make sure that the lab was kept and the people were kept in order and everything, everything went smoothly.
So thank you very much, Mary as well. So I think I've probably missed out of things, but I think I'd better stop there.
So thank you very much and we'll move on to our message.
I think from Colin Stirling. Is that correct? Hi, Dave, and hello, everyone.
I'm really sorry that I'm not able to get out of Australia to come there to join you and help celebrate this your marvellous scientific career.
I've seen the programme and it looks spectacular and it would have been great to spend a couple of days immersed in science,
something that I, as the vice chancellor, I don't get to do very often, especially in a pandemic.
And it'd be great to just have all the excitement of cutting edge science again.
So I wish you all the best for that. It's a long time since I was in the lab because I was a young Ph.D. student way back in the mid 80s,
and I remember the time you turned 40, and I remember thinking that 40 was pretty old back then.
And then I realised that nearly 40 years has passed. So no, of course not at all.
A different perspective of of time. And I realise now that you were just a young whippersnapper when you were head of department back then.
But if I remember one major thing, actually, it was about your nearly boyish enthusiasm for science,
your excitement about the wonder of all things scientific.
It was infectious. It was exhilarating to be around and it was inspiring.
I think I also took away from working in the lab the importance of doing science of of not just grinding out papers with incremental results,
but seeking the joy of real discovery.
And I see from your incredible list of publications about something that you've done time after time, after time.
I also remember you telling me back in Glasgow that you thought I was getting increasingly difficult
to get funding to do fundamental research and equally because some people had all been discovered.
And I guess that looking at what you've done since then, you've proved yourself and then wrong and had this hugely successful career.
So I wanted to thank you. Thank you for being such a great supervisor and thank you for the opportunities that I had in your lab.
And thank you for enabling allowing me to cut my scientific teeth on my scientific and academic career.
Thanks also for being such a great mentor throughout. I wish you all the best.
I wish you and Lydia all the best in the future. I wish you much health and happiness as you enjoy whatever it is you go on to do now.
I'm sure you'll have fun. So congratulations again on a marvellous career that brings Dave such.
So our next speaker is Stephen Bell, who is not against Stephen, started a year after I arrived at Glasgow and did his Ph.D. there,
and now he's at the University of Indiana University in Bloomington, and he's going to talk about chromosome architecture.
I think there's a pun somewhere in there. Thanks, Marshall.
Thank you, Dave. And I start with a photograph of this was.
Can believe it, 30 years ago, we went climbing in the White Mountains in New Hampshire en route to FASEB recombination meeting.
I'm sure I learnt a lot about recombination at the meeting,
but I certainly learnt that jet lag and copious quantities of American beer really don't mix terribly well.
You can tell us quite a few years ago now because Dave hadn't started dying is here that interesting blonde colour that it is now?
And as you saw from the photo that Marshall showed, my hair actually existed back then as well.
So I'd like to go back a couple more years than this, though, and just really echo the sentiments that we heard from from various speakers that Dave's
teaching and his influence because I entered university fully intending to become a chemist.
And I did molecular biology and sounded vaguely interesting.
And it was a revolutionary moment when I went to see these electrons by Dave on bacterial gene regulation.
Very it taught us the scenario and then showed us the data and described the experiments and got us to interpret
the data and put them together and essentially trying to find her the lack of protein work from first principles,
from experimental data. And that, for me, was the first time I felt that thrill of taking simple experimental results and
putting them together and synthesising it into this entity that became the like open.
It was utterly thrilling at work in me, something that wasn't there before, and that was it was a molecular biologist thereafter.
So they've changed, of course, my life. Thank you. Thank you.
So I continued to work in prokaryotic systems as I set up my career to compete with Dave,
obviously, and say they've got a safe niche and a path less well trodden.
That was the study archaea.
These are organisms of the genus so colobus they grow in hydrothermal hot springs places like Yellowstone National Park 8°C, too.
And the reason we study them and study them is because, well, principal justification is because of their theology.
They exist in the information processing machineries. They use the same machineries that our cells use to affect gene transcription DNA replication.
But in a simplified ancestral form and then a heat stable for making biochemistry almost fun.
And this just lists their struggle against proteins that carry out replication in archaea and eukaryotes
so that the machinery works in the context of what seems like a rather eukaryotic cell cycle as well.
We have got phases of G1 phase, extensive G2 phase.
We have multiple origins of replication per chromosome. We showed this years ago to all three fire once per sale for cell cycle to fire synchronously.
One a little bit later after the completion of replication is just a chromatin are held together
for the majority of this extended two period of the cell cycle prior to cell division.
And we call it is not mitosis, but we call it phase.
And cell division is one of these interesting things, because while a lot of our work was based on our soldiers conservation,
there's also some interesting things missing in Sulphur Lewis and his kin.
And one of those interesting things on lupus heart. That's FDIC.
It's FDIC is nearly universal across prokaryotes, archaea and bacteria effecting cell division with the cranor katavich.
So for lupus belongs like FDIC, they divide. How do they do it?
And so just following molecular detective, whatever we found, purely curiosity.
What is your faith in cell division in these organisms? And we discovered our kale counterparts of the eukaryotic S-Corp machinery.
And this is the very same machinery.
It carries a membrane, a decision in our cells that the final stages of cytokinesis present in a minimal ancestral form in the archaeal cells.
Another conundrum presented itself in the SME proteins, and we've heard of it Red 50, the universal, absolutely ubiquitous DNA repair protein,
but one thing that was obviously lacking in the FluMist genome and other craner care was
condensing conventions universal otherwise and yet manifestly lacking in this health globally.
So we reasoned that perhaps as an equal over most beef, as a lineage specific acquisition,
perhaps there was some sort of lineage specific compensation for the loss of condensing in the ancestral form.
And so we identified some novel SNC superfamily proteins and one that we identified in the social values we're going to call coalesced.
Coalescence, a rather small some sea proteins, only sixty eight killer dolphins.
It has, instead of the classic hinge dimerisation domain that condensed and has a has cysteine residues of putative zinc hook,
a feature that we just had about four marines present in the rad 50 proteins and we've now identified some partner proteins.
I wouldn't talk about them today. We've gone on to solve the crystal structure of most of the protein, we have EPAs heads,
just classic SMS heads call Carlos coming out forms of Homo dimer via dimerisation interface at the other end of the coil called phylogenetically,
it does look like it's clustering closest to We are killed at 50 14,
so we seem to have an odd lineage specific adaptation of around 50 like Putin to do whatever this thing does.
This is the dimerisation interface zoomed in on, and indeed it is a zinc.
So this is clearly a very rad 50 like protein, a single zinc coordinated by four systems to try and work out what the protein was doing.
It's essential we couldn't all, but we just kind of chip seek experiments to see what where was it interacting with in the chromosome?
And so a very interesting non random distribution. We also noted that whatever cool lesson was high, transcription was really low.
So it's an anti correlation between pool and occupancy and transcription adjudge by RNA polymerase chips are an easy sell.
So we wondered, has it got something to do with chromosome confirmation, but of course, nobody is working on chromosome confirmation.
So we have to establish what that confirmation itself might be.
So we adapted chromosome confirmation capture techniques and performed them on self-focus.
And these are just the all contact match where we plot interaction of every Lucas across
the chromosome with every other locus across the chromosome in the second dimension,
giving you these plots. And so we can process them to generate these Pearson correlation coefficient heat maps.
I'm Scottish. It's tartan. I was thrilled. I was even more thrilled because it was very distinct from the patterns we see in most bacteria,
where we have this beautiful cancer zipping of the arms of the chromosome and rather more
reminiscent of the compartmentalised architecture that we see in method's own chromosome.
We have large domains along the primary axis, and we have domains interacting in higher order space.
We can analyse this using principal component analysis to determine who interacts with
whom and define the mean boundaries and so we can classify in a compartment and a B
compartment and where we came back to Colson was at this point when we realised that the
B compartment exquisitely lines up with these regions of enhanced coalition occupancy.
Even within the B compartment, the coalition isn't universally distributed if there's still irregularities within there.
So we'll delve into that deeper in a minute or two. Again, we could see, as we've shown already,
that the just qualitatively one can see the bee compartment is transcribed at a lower
level because lie gives rise to lower level transcripts than does the compartment.
And is there a causality relationship here? And so to summarise a large amount of data, we were able to show that if we raised cholesterol levels,
we dropped inscription and reinforced at the same time the B compartment.
If we locally or globally altered transcription, we perturbed cool s,
and they're mutually exclusive interaction as an antagonism between these two processes on the chromosome with Lucas specific and globally.
So at this point, we could see that we have this utterly unanticipated compartmentalised architecture of the chromosome and E compartment,
a B compartment, a compartment,
elevator transcription, the essential genes and the replication origins are housed within the compartment in the B compartment,
while lower transcription coalescing. Is there non-essential genes and lots of transposons sniffing a little smelling a little
bit like you chromatin heterochromatin if you really want to stretch an analogy.
More recently, we've gone to investigate a higher resolution,
so we modified the set and further use different enzymes, and we now have to kill a resolution contact map.
So really gene and opera on level contact maps of every Lucas across the chromosome.
We still see compartmentalisation, of course, but we see a wealth of additional features.
And I'll just take you through those.
So in the next slide, I'm going to take this diagonal here to strategic forty five degrees there and present it horizontal.
And it's a very northern Indiana landscape, we see lots of mountains appearing.
So we see domains arising along this primary diagonal,
and we can quantify these domains using a directional preference float, basically slider window along the chromosome.
There's the look is prepared to inject the left or to the right.
And so that's quantified, then the lefferts interaction rate words interaction to define these domains and the boundaries between them.
So we've got lots of small domains.
We'll call them chromosome interaction domains and importantly, disband the entire chromosome, but in the compartment and B compartment.
We called them chromosome interaction twins, or SIDS, because similar features have been reported initially by microbes,
live in studies of call-backs and are now known to be a universal feature of bacterial chromosomes.
We see these kids all along the call about a chromosome and makes love noted that boundaries between
SIDS often correlated and demonstrate were causally linked to highly transcribed transcription units.
We wondered if the same was true in cell for lupus.
So we simply quantified transcripts of levels either with at said boundaries or internally in the compartment or the B compartment.
And in both cases, you can see there's an enrichment for highly transcribed genes at boundary proximal loci.
Note, however, that the B compartment boundary loci actually opened at a lower level than the internal transcripts in the compartment,
so it's relatively high transcription, not absolute transcript levels as defining the boundary.
It also suggests that perhaps it's in the B compartment and may be an additional component is imparting identity to the SIDS.
And of course, I've told you already, the obvious candidate is coolest.
And indeed, we see this non-random distribution of coalescing within the B compartments.
And when we know aligner CID boundary elements onto the coolest occupancy profiles,
we see the boundaries between SIDS are actually found areas of low correlation occupancy.
OK, so the idea that we would have said this is the bundle region by this cool s and protein boundaries and strengthened
by the presence of these transcripts in another little unit of folding or compaction again effected by coalition.
Experiments are nice as well as observation,
so we introduced the transgene into the chromosome and put in an R avenues inducible gene into an eight compartment,
Lucas and we can switch on transcription in the presence of other avenues, have a basal level with sucrose.
The chromosome conformation capture, and we can see that the look is where we introduced the transgene,
even at the basal level, we see a weak said bone being generated,
which is significantly strengthened in the presence of a ravenous inscription, is able to create a boundary element within the compartment.
A collateral benefit of this experiment was in addition to switching on this revenues inducible transgene,
we also switched on the endogenous arrived and it was the regulation,
including a subtle offer on here this Distronic transcription unit, which fortuitously resides within the bee compartment.
And then the B compartment to upon induction with transcription, we see generation of a novel set boundary again showing that transcription is
important for defining boundary elements in both the foreign compartments.
An additional feature that we saw on the high resolution maps was the presence of point to point loops on the chromosome synapses are at.
Conjunction of two distinct loci, and it's about sixty five loops per genome,
and they range massively in size loss of short range loops, but also some extremely long range loops of up to half the chromosome.
And this is just the aggregate plots of these loop features that we can detect. So that entire half chromosome can be brought can be looped out.
I mean, we look to see what genes were present at the anchors of these loops.
We were really excited to know that the long range loops,
almost every single one of them involved regions involved in ribosomal biogenesis, ribosomal RNA genes, ribosome or protein genes.
Even some ribosomal RNA processing genes are involved in these loop anchor elements.
So this our operating hypothesis at the moment is that we're seeing the generation of a sort of hub like organisation,
a factory for building ribosomes and these simple prokaryotic cells,
allowing the coordination of synthesis of ribosome, proteins, ribosome Milanese and indeed,
the of these loop features we showed was dependent both on transcription and in cell growth phase.
We starve the cells for ribosome will demand this law.
These loops disappear, so it really does look like it's a coordinating organising hub and for testing that further.
So it included this part of the talk as I showed you a compartment and being compartment superimposed upon that,
we have these features in the compartment.
These are bounded by highly transcribed genes.
And so one can imagine that the genes with a couple of transcription translation might be serving as barriers to topological diffusion,
allowing the definition of these domains between them in the B compartments.
Well, luckily, my transcription seems to be important,
but internal binding of core lesson seems to be important in helping to reinforce and established this architecture.
And finally, we have the loops where we see Lucy principally within the compartment being held together even at very,
very long ranges in the linear order of the chromosomes.
And this is quite pleasing to see, because our previous work had shown that by modulating core lesson levels,
we could modulate the degree of compassion and the identity of this B compartment.
And we weren't sure if the compartment was actually being actively structured or was it simply being determined by exclusion from the B compartment,
but no,
the presence of these loop features provides essentially cross braces that could exist and help to impart integrity to the overall compartment.
So that's kind of a quick run through the natural history of these chromosomes.
And, you know, the future of birdwatching, if you like on the chromosome,
but we're interested also in trying to determine what impact this generation of these features
might have on the physiology of the organism and its ability to adapt to different circumstances.
And so the final few minutes, I'll just tell you a short story and I apologise.
Already, it's an incomplete story, but we've started a study where we're looking at resistance to hydrogen peroxide.
We've been able to select individual clonal lines of sulphur little bits that are resistant to seven 75 micro molar hydrogen peroxide,
a concentration of which the wild type cells cannot grow.
But in blue, we see growth of our resistant lines in presence or absence of hydrogen peroxide.
Essentially, this drug effect off entirely. We sequence them.
Twenty one of these clinical isolates and discovered at our laboratory and had a number of
snips when compared to the reference genome and in many of the things that we sequenced,
we saw deletions, the strange with a large deletion within them and also additional polymorphisms,
which when we analysed the genes, made sense in light of resistance to oxidative damage.
But really exciting to us was the two lines that I've highlighted in blue because these are genetically identical to our wild type lobstering.
There is not a single polymorphism. There are no rearrangements to carry that both Illumina and nanopore sequencing.
They are genetically identical to the wild type and yet are entirely resistant to these concentrations of hydrogen peroxide.
So we wondered obviously what you did as to what was going on.
We profiled the resistant line grown in the absence of hydrogen peroxide that are any second them and
discovered that these lines constructively express the oxidative response genes at a very high level.
So the preconditioned, if you like, for exposure to hydrogen peroxide.
Yeah. Or genetically identical to the wild type. When we come, we wondered if there was some difference in chromosome confirmation.
And when we compared the wild type and this resistant strain, genetically identical resistance genes,
we can note in particular, some quite significant changes in short range context that this look is here.
And this Lucas turns out to correspond to the DPS units, the self Louis counterpart Fahrettin,
so it's involved in modulating iron levels in response stocks with damage,
and this is the principle gene which is upregulated in our resistance lines.
These resistant lines have chromosome conformation alterations,
and so we wondered if that could be put slowing the the determination of resistance phenotype even in the absence of any mutation.
And just to emphasise that this resistance to hydrogen peroxide is highly persistent in the
absence of any hydrogen peroxide treatment and then retesting whether or not they are resistant,
we can take cells out for over 100 generations before we begin to see loss of the phenotype, as we believe that it is a highly persistent phenomenon.
Five minutes great. So we then profiled the cells by 3C chromosome conformation capture as they went through this regression process,
and we're focussing in the box here again. And you can see, you know, the loss of these contacts is different.
Snaps or sourcing blue is no loss of the contact present in the resistant line as we go through the resistance phenotype.
That loss of contact correlates very nicely with a loss of transcription of that little DPS regulation that we see.
So at this point, we thought, well, we're seeing changes in transcription,
we're seeing changes in chromosome confirmation is simply going to be that once again coalescence coming in,
and it's helping to knock down the genes because every other system we've looked at coalescence seem to be acting as a code oppressor.
However, and to a considerable extent, oh, sorry and emphasise,
this is a very specific transcriptional effect that we see this reversion of the phenotype.
We were expecting to see an acquisition of coalescence as we saw this dropping down of transcription.
What we saw was quite the opposite. In the Resistente line,
what we're seeing is that coalition is actually occupying the rebel side and gradually
that peak of abundance drops as we revert back to the wild type sensitive phenotype.
And again, in the absence of any genetic alteration. So we think that cool thing is actually acting essentially to set up an epigenetic
cue in these cells is creating a loop that somehow permissive on a loop structure.
This permissive to the high levels of expression of this does these genes and maintaining
that generation after generation after generation and only grabbing gradually ebbing off.
So we think and the operating hypothesis at the moment, there's obviously some experiments we still need to do.
Is it coalescence functioning to impose this permissive structure that facilitates transcription?
So it's not as simple as being a global coder. Oppressor is actually being used for certain specific tasks to promote transcription as well.
So with that, I'll just finish by thanking the folks that have done the work and the quality of the work was initiated and all the chips.
And I've shown you perform a ritual.
Samson, who now has an independent position at Indiana University and it's a matter who's an independent position back in Kyoto,
now establish the three and high pipe pipelines from the lab.
Peter Ball Hall is doing the epigenetically work with hydrogen peroxide resistance.
The crystallisation was done actually.
My side project I was being department chair wanted to do something, so I made lots of protein and gave them to Giovanni,
who's crystallised and solve the structures for me, which was very nice of them.
But most of all, Dave, you're not on the slide, but thank you again for everything,
for the incredible lectures all the way through your mentorship, your enthusiasm.
You truly have been an inspiration. Thank you. Thank you very much, Steve, that was excellent.
Any questions? Fantastic bacteria of epigenetics say archaea and likely to step outside and discuss that they're all the same thing.
So do you think the formation of this new boundary that gives you the expression of just as the casket process?
It's often and because you're operating on the selection, then they just get maintained.
That was ventilated, but yet we simply don't know at this point.
And that takes us back to the question of how is coalition getting on in the first place?
Something we really want to know, what's looking at, what's unloading it. A million questions that we've asked for a long time and an uncertainty SMC.
We feel that we simply do have answers to.
Fantastic work you had on this slide that there's cohesion after replication, you're also social of always when it divides compacts DNA.
You must have looked at these effects. So we've synchronised sales and performance performed.
Are you asking if you've done chromosome confirmation across the cell cycle? Is that so?
Yeah, we've we've profiled coolest non chromosome confirmation and synchronise cells, and it remains almost unaltered.
We see changes that the power look is so we have power like protein and we do see some conformational changes in those.
And Rachel, that's her power of her independent lab, those working on that side of stuff.
Transcription seems to be the primary determinant for the overall structure. And we've done cell cycle transcriptomics to synchronise cells,
and actually only about 40 open reading frames show significant modulation across the cell cycle.
So, yes, set boundaries are moving, but the compartmentalisation procedure really doesn't alter,
and the fact that we have loci being held together allows us is lovely because although we're dominated by the G2 period of the cell cycle,
while those loci are compacted anyway, so it makes the the technique appropriate for our organism.
Steve, lovely talk that's following up on John's question What what do you know about the nature of cohesion during G2?
Oh, we can sort of second very quick question is your your high C maps?
To what extent are they dependent on coal acid? Mm-Hmm.
Two. OK. So the cohesion that we see as a by fish at multiple loci around the chromosome and just the number of foci.
And the reason we are permitted to do that in the first place prompted to do that in the first place was
that we had observed in two gels the persistence of Hemi Catan injunctions between Dr Lucite and G2 cells.
So we believe that the Hemi cats are probably the causative agent for the cohesion that we see so coalescence in essential gene,
but we cannot express it. And more recently, we've been able to conditionally express mutants and we see if we overexpressed coolies and
then we enhance interactions within the B compartment and intensify the B compartmentalisation.
And if we express the mutant versions of the cells, we begin to see a loss of the compartmentalise identity when we take cells
into stationary phase coalesce and redistributes that out in the chromosome. And at that point, compartmentalisation is lost.
Definitely our last question. OK, so what do you think about everybody standing orders, you know, coalescing,
you identify the international partners or is condensing related or interaction partners that we have are all there's a Tripoli plus protein,
which seems to be a genuine interaction partner.
The rest are all annotated as conserved, hypothetical and even alpha foods are not used to us.
Essentially, nothing like Skippy could be monkey yarmulkes. As to the origin of it, I think it's probably come in an actual chromosomal element.
I think it's probably a bit like is got its own right 50. We've had this drug, 50 like protein come in and it's been co-opted into functioning.
Even its location in the chromosome is near one of the origins of replication.
That itself was a relatively recent evolutionary acquisition, at least from the lineage tracing that we've done.
So I mean, why the progenitors of the clinical lost condensed in the first place?
I have no idea I'd love. I'd love to hear people's thoughts in that,
but it looks as though different lineages have co-opted different proteins to fulfil some sort of structuring role.
And again, are we seeing a truly condensed and late?
I do think we are, but we're seeing, you know, at least the level of structuring being imposed by this superfamily protein.
Thank you very much. OK, thanks. Thanks.
So, first of all, thanks to Dave and Lydia for getting me out of my house first time across the ocean in two years, I wouldn't miss this for.
For anything, right, so thank you.
And of course, this is a shout out to Lydia, who you may recognise her last name has some vague genomic similarity in terms of code on usage to mine.
And so when she asked me for a title, I said, Of course, using your motors, twist the mouse, right?
So which loosely translated is, if you can't twist, then you got it right.
So, so that's the title of my talk. It actually has nothing to do what I'm going to say.
Rather, it's a it's a it's a statement actually on life, I realised, because, you know,
if you think about it, there are lots of times you need to twist out of something.
You know, the twist a little bit, and if you don't, you're going to rise with some kind of pain.
And so it was coming home late from the pub or, you know, explaining something else.
So this this is actually a very broad statement on on life that I could probably stop right now.
So but you know, since really there's no connexion academic, at least between Dave and I.
So I'm here because I can give a completely fabricated account of his accomplished accomplishments and contributions to science and which I will.
So, so let me, first of all, tell you what inspired me to have this title, which, as I said, is only vaguely related to what I'll talk about.
You know, it turns out that Dave, actually, when he was doing preps I learnt was doing would always sing a song.
He had a song he just loved, and it was a twist in right.
So if those of you were wondering what that song is, you know, he adapted.
Of course, there a a group called The Beatles, I think some of you were actually familiar with them.
And they did a song. It was actually cover, not their original of a twist and shout, but they've had this.
This has this. And he's the only guy I know who's called his dad a baby. So and he was doing a prep.
These licence sales. So shake it up, baby. Now twist and ride, you know?
Come on. Come on, baby. This is a day prep. I won't go through all the steps, you know, in the middle, in the middle here, he says.
You know, you twist so fine. You know, this isn't your little DNA.
And you know, actually, unbeknown to Dave, at dinner today, he's going to sing this song.
So, um, and then, you know, let me know that you're mine, all this stuff.
And then, of course, you know, as he gets down to the end of the prep, he does final extraction.
Well, shake it, shake it, shake it, shake shake a bit. So, so so this this is a well-kept secret, you know of Dave's.
She never let on to anybody in his lab that that he was doing it this way.
So and then my first meeting with Dave was actually at Nesi Bridge.
Yeah, I'll send a copy to anybody who wants this. And but especially if Dave agrees to singing it, so.
So I met Dave. My recollection was that nephew bridge and I managed to get the same video that Lorraine got.
I just have a different take on this, this this episode.
So our conversation, at least my questions, is something like, OK, Dave, what's a haggis?
You know? And then of course, you saw this. You'll see it again. Now, I don't have the sound on, but it's probably just as good sound.
It has the same impact. And I said, Oh, OK, you throw it.
And Dave proceeded to do this. This wonderful throw.
Right? Yes, it explodes. Is something I have. I still have no idea.
And so and then of course, I said, Oh, and then you eat it.
And you know, at that point, I said to Dave, OK, I got it.
I'll have a whisky. So. So that that was my experience with Dave at least meeting him.
And I have to say, over the years, I've had a chance to see him at other events.
And you know, here's here's here he is in CIAC am fortunate I don't have too many photos.
So fortunately, I have a few rod contribute. I think this one. There he is, talking to one.
Alonso in the next one is the reaction from Mike Cox when he's explaining one of his great theories.
And Mike is like just sucking in, sort of holding it back right there so that, you know,
these are fractured fairy tales like I could put in whatever little word bubbles I want.
And here he is. Actually, he's he's he's making a pact with the devil.
This is Lucifer right here. You can see the Yeah. And look, Lorraine is witnessing witnessing this pact so and so you know,
if you see a certain group of people hanging around and you know, you know, it's sad, but this, I have to put it in here.
This is the only slide of half of Dave actually attending a lecture. So he did.
He did attend lectures. He wasn't just going off eating, drinking, sightseeing.
OK, so. All right. So now now more fractured fairy tales, more.
This is what I'm going to talk about. You can take this with a tongue in cheek. This is, I hope, hopefully it's not not the fiction.
So we've been interested in double holiday junctions and topology.
And what I'm going to tell you is that the resolution of double holiday junctions is actually complicated and it's affected by motor protein,
so for some reason and nucleases. So this work done by Katsumi more Myanmar too, and also Jodi Plank for In My Lab.
And now here are simple questions and simple and straightforward answers.
So is a double holiday junction simply to a single holiday?
I think many of you know, but to make clear, no, it's not just to single holiday options and can top equal equally top of one tree and wreck.
You dissolve double hardly junctions. And again, I'll tell you why I asked this question.
This simple answer is yes. And then the third question is, can a double holiday junction be resolved politically?
And actually, unless unless I've missed it in literature, no one has ever tested whether a double holiday junction can be cleaved.
This is important. It's in every war textbook, every textbook. Right?
And the fact is there is not again, unless I missed it, there's no piece of data out there.
And the answer is yes, it can. But the outcome is not as simple as you might have expected.
All right. So here's the model from Robyn Holiday in 1960 for a prescient model, the holiday,
the structure in the middle that bears his name now explains many of the phenomena of recombination,
including including crossing over and gene conversion.
So I won't go over that. Many you know this even better than I do so.
So that's a holiday junction and he proposed cleavage and this is you get this or that depending on whether you have horizontal vertical cleavage,
right? And now here, fast forward to nineteen eighty three.
This is a simple rendition of the double strand break repair model.
And when it was appreciated that the sites of initiation also replication, stalling and cleavage replication sites leads to a double strand breaks.
Lorraine actually went through some of the processing biochemical steps.
Here you get to holiday junctions. There they are, right?
And then again, what is very clear and very accurately stated this is from the from the paper resolution of two junctions by cleaving either
inner or outer strands leads to two possible crossover and two possible to balance across the crossover configurations.
And this is absolutely correct. OK. So I'm not contesting this one bit.
But when you look at this picture and you teach it in class, you would get the impression that you're always cleaving double holiday junctions.
That's that's historical. But they were trying to explain the existence of crossovers.
So it turns out the reason why, I said, are two holiday junctions equivalent to to a double holiday junction answer is no,
because there is another pathway for this taking care of removing these holiday junctions,
which would cause an endless junction chromosome segregation problems, et cetera,
is and that turns out it's a family of proteins, a helicase and took out type three type II sunrays.
And again, it's important for you,
those of you who don't remember you're told by some races that Topo three from basically all organisms is a type one type II summaries.
And what that means is it passes. It cleaves in one strand and passes once that cleave strand once cleaved strand at a time
where type 2s make a double strand break and past past DNA through the double strand break.
So this is an AFM image. Frank Hartman took my lab a long time ago,
showing that Recue and Toeplitz where you can actually cannot indicate duplex DNA and this must occur through concerted single Strand Passage events.
And I also put the word concerted in because we've never detected a hem I can't make.
They're always full cat names. Now, again, going back to the serious part of science, I've had extensive discussions with Dave.
Nick Khazali,
Ian Hicks and I remember talking about how can you test a strand and get against and how do you test for passage of a double holiday junction?
And there really is no easy way to make a double holiday junction.
And the first one who succeeded to make something that looks like the holiday junction again is Ian Hickson.
There's a paper he published. These are some oligo substrates, and it's I'm being facetious and also polite.
This is this is the first attempt to make a double holiday junction, but the call is short is really being kind.
It has a linking number of only about under two. I think it's one point sixty five, they estimated.
So it's barely has any linkage. I mean, it is topological at length.
And what he showed for the Bloom's protein that these proteins can dissolve the this this structure,
which is, you know, I will accept the fact it's a double holiday junction.
But we all said it'd be nice if somebody can do something bigger, a bigger DNA substrate with a larger linking number.
And this came along when Jodie Planck was working Cowshed Duke.
The forecourts passed away after significant effort.
Jodie made the substrate of by begin a process.
I won't show you this. There's a dozen steps and this the blue and red are non homologous regions.
The black are regions that are identical in sequence, and there's a holiday junction at each end.
And again, this is a DNA with no twist. If you try to picture it with twist, that's what it's going to look like.
So you cannot separate these by just pulling them. They're interlinked. And in fact, this this one is.
So do you still remember your topology? This is all twists and almost no ride if you accept the fact it's lying flat in that plane.
So but what we wanted to know is, how do you I mean,
you have cartoons that show this thing branch migrating a holiday junction principle can branch migrate?
But it's not that simple if it's top logically linked. And again, what we're able to do and I'll show you the data for E. coli Petrushka.
When I say that we Peter, when he was a postdoc in my lab, showed that you can dissolve.
So the reason to holiday junctions or double holiday chunks is not just the
sum of two single holiday chunks is without going through the detailed steps,
you can take any either this junction or that junction and they can cause and converge them.
One can move or both can move towards each other. And here you wind up with a penultimate separated product.
This is a singly linked Hemi cattani. And then as long as you and you remember you're passing through one strand at a time,
you have to pass the parental strands and then you can separate them totally.
And the important thing about the whole process here from the biology is not a crossover.
You never get a crossover, right?
And again, if you think about recombination, I mean, the history of recombination and I'm an outsider, my degrees are in chemistry.
So you know what?
They all were designed to largely explain crossovers, not because crossovers were the most important thing in the world, but that's what you ask for.
Now there are other things, of course, that we're being asked for, but the models had to explain crossovers mismatch, all this other stuff.
But the reality is, no chromosome really wants to crossover.
If you cross over a circular E coli chromosome, you get a dimer and segregation problem,
and we're going to hear that there are specific mechanism to if in fact worked on these proteins to get rid of those dimers.
And then on linear chromosomes, you get translocations, right, so you don't want to crossover.
And this is one mechanism for non non crossover. And in fact, its predominant mechanism in eukaryotes.
All right. So now I'm going to I worked on so work and Nicole, I actually worked on T for phage therapy for in the old days,
and I wanted to ask whether you call a total of three and you dissolve double holiday junctions.
And here's a list that showed some similarities of the RECUEILLIR cases and type one a two-part summarises.
And why would I ask this question? Well, in the eukaryotes, both segments obviously a one and human bloom.
There's a domain which is called TR for the Subway Series three, my one two interaction domain.
I want to tell you about one or two of the subunits basically of the dissolving zone, if you want to call it that.
But Rick E. Coli Recue has no TR domain, and the one thing I should also add is we we attempted to use every, every other.
One of the human helicase is to substitute for Bloom and none of them substitute in the the dissolve dissolution reaction.
So this appeared to be essential, important for for dissolution.
So at this point, cuts would be more inmates who have purified all these proteins did the reaction.
And again, let me just I'm not going to go through a lot of data.
I just want to point out you start out with these substrates, the substrate,
the double holiday junction substrate and through branch migration and strand passage,
you separate them into two basically monomer circles a piece that might not make OK, but I know everyone leave, but I thought that was a miracle.
And whereas if you had a crossover, you get this dimer and a b dimer.
So it's very clear when you get a non crossover versus a crossover.
And if you have all three proteins, top of three recue as this B, this is the optimal reaction.
You get the product a the Monroe Circle product b, the other monomer circle and no crossover.
The crossovers would run above the holiday junction substrate. So zero zero crossover.
But the remarkable,
not remarkable pleasant thing for us was that this protein from E. coli with no top brass hammers three domain still did the solution.
So this is just to show you this this the same product, same behaviour with the eukaryotic S. Just one protein.
So we never get crossovers. And so E! Coli has a mechanism to facilitate and in fact, predominantly encourage non crossovers.
All right. So all the data I'm not going to show you if this solution is very efficient, it only takes one animal or of each of these proteins.
It doesn't require a cognate helicase, so it is promiscuous. We can substitute this one and we can even rob which I'll come back to in a little bit.
It does not require a cognate as B you can substitute, but E. coli Topa one a different type on top of this cannot.
And that's because there's a there's a decapitation loop in the type three proteins or in the Army one codon subunits,
and there is no physical interaction to rescue until three, in contrast again to the UK proteins.
But importantly, only C-terminal stresses. But importantly, this solution is concerned.
So you need simultaneous action on top of three and recue. They have to be working on that DNA molecule or put more accurate scientifically.
We put them both in the same two with the DNA. They both be prosperous the same time.
You can't put them in sequentially, so it's a concerted reaction.
Actually, the you can think about the mechanism is not really known.
I mean, the the structures of these individual proteins are available, but but it's not really clear how they're acting together on the junctions.
OK, so now can a double holiday junction be resolved politically?
And you know, I say, why would you even ask this question? Because it's in every textbook.
We know that it's in a textbook and must be right. OK, so not.
Not really. And so. Well, you know, I told you they're interlinked cat named.
So first of all, you don't need to believe them.
I mean, you do need to cleave them if you want explain crossovers because I just told you this pathway does not give you crossovers.
And then structurally double holiday searches are composed of two parallel structures and most cleaving enzymes.
For example, Rossi, this they lillia. Others have shown that to bind to a preferred open a. parallel structure and
single how the junctions can adopt both a parallel and an interior configuration,
but double holiday junctions are constrained to a parallel configuration.
And then finally, the persistence, like the DNA is about fifty three nanometre, which 150 base pairs.
So unless the intervening being more than two persistance like the holiday junctions connected by rigid rods,
so the local deformation to put them into an open conformation is the energetic start to become more and more difficult.
So basically, Katsumi took the double holiday junction, remember, you can get two products,
you can get a non crossover crossover, very diagnostic dimer circle or Dimer Circle or Monroe Circles.
And what he did when he threw in Rosie, he showed basically he was mostly non crossover.
And I show you a concentration dependent because I'm not going to I'm not going to torture you through the conflict to get to the conclusion.
We actually, I'll tell you. I mean, they were stupid, but like we kind of were saying, huh?
At first, first thing was, OK, there's a bias. It was structural. I just told you the structure of the holodeck.
They junction is different than the single holiday junction. But when I did a concentration dependent, we saw that at low concentrations,
you predominantly got non-profit crossovers by a large margin over crossovers.
And only when you added more and more reps say did you start to equilibrate or get to a point where both are plateauing and if shown as a ratio,
this is maybe an easier plot to see as you put in. You get to about 30 some odd percent.
That's the maximum. But there's a concentration of parts and the first the first thing.
But I think we were we thought about why should there be a concentration dependence in this crossover?
Non crossover distribution? Five minutes. OK, good. Thank you. And so we said, Oh, you know, kind of being done first.
We don't have a row of a b.
The motor proteins that are partners of great worth by Steve West many years ago show that they accelerate roughly cleavage.
So we threw in and here's what they look like a simple structure, cartoon structure.
And so we we threw it in. And here's the result. So instead of getting none.
Instead of getting more crossovers, we went down to almost zero.
So the more rough C of a b you put in. The less crossover you get.
So basically, you make the rough sea protein seem to have a rough, a dependent bias on crossover non crossover distribution.
And again, we scratch their heads and said, what the [INAUDIBLE] is going on?
Because we came to it from a structural consideration,
we thought structurally a double holiday junction should be different than a single holiday junction.
And it is OK. But that wasn't the answer, right? So I'm going to cut to the chase to five minutes.
There's the data. You're almost down at zero crossovers when you have the highest rob concentration we could put in, that's the motor protein.
And so here's a what's the explanation?
The slow computer here. OK, here we go.
Well, the answer is going to be cut and migrate and I'll tell you in a minute.
So here's the canonical model. So if you have a double holiday junction in circles, you're going to get the cross, the non crossovers and a crossover.
These are all the products you would get depending on whether you got horizontal cleavage or a vertical cleavage did this.
So these are the four products you get. But. It was a no dull moment when we realised that if you just cut one and branch, migrate to the other,
to the other junction, you get all four of the possible non crossover products.
That is all for possible plasmid molecules. So the note no dull moment was I don't know about the rest of you in the audience,
but if you really think about the proposed mechanism, it's a cartoon, right?
That the last model? It's a cartoon. It says yes, if you cleave it both, you will get those products.
Biology in life doesn't work like that. You got to junctions, you got two proteins, unless there's some coordination between them, you cut one.
The other one's just lollygagging around. You cut the other one. And and when do you cut to?
Only if you have high concentrations of a cleaving enzyme, the Rossie,
if you cut one and a motor protein comes along or the reason I'm skipping a lot of data, even we did not have more of a b.
We got more non crossovers. Their spontaneous branch migration.
The reason you can't make double holiday junction substrates easily is when you make them.
They've spun a single one, for sure.
And the doubles, if you don't do it right, they'll branch, migrate fully homologous or branch back right off the ends.
So it was like one of these. I mean, I had a lot of dents in my forehead because all throughout my life, you know,
I just flat myself in the head, you know, like, this is just dumb, you know?
And so, so basically. So the answer is equal, I reckon so it can resolve the functions, not cross over rough.
So you can cut one junction of a double holiday junction and rub can migrate the other holidays towards the other side and not cross over.
And crossovers form after cleavage of one, but only if the second one is cut before each branch migrated off.
Now here's here's the like some 3D three twisty like molecules those of you who like something more accurate.
This is trying to show you dissolution. OK, I to show this cuts the Tatsumi days to make this.
And then, of course, if you cleave on both simultaneously, you get the here's a crossover product.
But you know what you can do, you know painfully in cartoon form, show everyone is if you cut here and branch,
migrate the other junction to the neck, basically non crossover, you cut there and then you have rubber be cut to cut to the side, not cross over.
You could do this with the other cuts I took. So basically, you get you always get non crossovers.
So if you put this in a broader context, of course, in addition to break repair model, when you get down to this point, it's losing power here.
But when you get down to the point of a double holiday junction or a single holidays, a single holiday traditions must be nuclear logically resolved.
They cannot be there. They're not topological molecules. They must be cleaved.
And so here you get the probably expected 50 50 of crossover, not crossover.
But if you go through that double holiday junction and dissolve root, or if you go to a double holiday junction route and nick and migrate,
you always get not processed and a non crossover, not cross or not cross over.
And the only time you get crossover as a minor species is with resolution primarily of a single holiday junction.
But in theory, it's possible to get it with, of course, a double holiday junction. So now you always think things are novel, right?
And I should have said at the beginning, sorry, Kim.
Kim actually proposed an annual review article about topological dissolution of double holiday junctions.
So I forgot to say that. So every time you think you do something novel, you find somewhere, something somebody.
I thought about it earlier. Now I joked last time.
How about Nick, Nick and migrate? It turns out this had been published. And here, here's so here it is.
It's right here. It's very clear to all of you. And if that's not clear, you can look at an alternate one minute.
You can look at the alternative model. And this is makes it very clear to everybody in this audience that it was totally opaque, right?
So frank stuff published in Ninety Nine, basically that you can do this and it's hidden in here.
And this actually reminds me of Nessie Bridge. So I want to just spend one moment on this slide because when you look at this,
it's got all the things that used to give me like nightmares I couldn't understand. I'm a I'm a dump chemist.
You know, the four floors, a sixty two, there's a five two three down here, and I looked around,
I couldn't find the average Ford or Ford's, which I always love because I never understood. But you know, basically,
this is when you find that little part of Frank's cartoon that that is the way I look at the world and you get double holiday junction,
you can dissolve it. He's basically had here the solution, and here he's got a migration of one holiday to a next site.
And in both cases, you get no crossovers. So I must say I didn't see this paper until we dug around.
But so my last slide here is Dave.
Congratulations, thank you for exceptional creative science.
And as part of my fabrication of Dave Dave, here he's showing me around and in Oxford, he's telling me he owns everything.
As far as the eye can see, this is his garden. You know everything. So thank you, Dave, for a good time to.
Thanks to a couple of questions. OK. OK.
So coming back to your title, moving holidays, junctions has twists and dried consequences.
So there's those circular substrates you're using. They are fully top, logically closed with with no nicks.
Yeah, right. That is guaranteed, is it? Yeah, we've checked that that right?
Correct. And remember, they can't even migrate outside of the region, homology to to the right because there's there's no homology there.
So they're they're really bounded on one side. Story with Dave is a little bit different as we'll get to, and I'll explain who I am in a minute,
but I just want to say that's because there's one discovery that everybody has not mentioned about Dave was that in terms of the key question,
they asked about the key components. And he asked it to me when we.
Well, many of the places that we met, which haven't been in laboratories.
And he answered it because the key component for Dave, he answered the question What's the key component in life?
Is Lydia, who is at the front driving. It's Lydia.
So I want to thank Lydia for all the organisation that slows down.
So who am I, I'm actually a physicist and mathematician, don't worry, I'm between you and lunch.
I'm not going to give you a bunch of formulae, but it's another side that day.
But I think, you know everyone here, you've met him in the lab. I met Dave outside a lab.
In fact, it was about 20, three or four years ago, and I'm not kind of sure whether the first was involved standing outside the old field and gym,
or we had something in our hands and we were drinking. It was one of those two.
I like to think it was the first one being kind of good dads, but they were once asked me,
you know, because I was ever in the physics department at the time here in Oxford.
And you know, what do you do? I do this when you do maths.
So what's wrong with maths? Is that what do you mean, what's wrong with that?
There's nothing wrong with maths and physics. We've got big building. You know, we teach.
We have a lot of students. We just develop new techniques. He said, Yeah, but what?
Why is it? We don't see more maths over here. You know, certainly not 20 feet away or 60 feet.
You know what was going on? What? You know why? Is it that just, you know, you don't want to come over, which may be true?
You never know. But it made me think. And since then, I've just been working on this problem of kind of what's wrong with that?
And I want to explain to you why it might be relevant to some of the things that
you were talking about today and why you may not have seen many people over here.
And yet they have their own conferences and they have their own journals and they do their own things and sometimes they ask the web biology in it.
And yet it doesn't make it over here. So I want to run through what I will do it very quickly.
What is the problem with maths? And the amazing thing about maths is it's kind of a jack of all trades master.
You know, you can apply the same, the same maths gets applied to COVID as it does to infection models.
As know, a lot of this was developed in the operations research period of the post-World War One,
when they began to realise they need to put numbers on casualties and things like this,
and they started developing models of reactions like test units like mass action models.
And those same models are the ones that you know you can go to work departments theoretical, you know,
emphatically that now that epidemiology or you can go to the old over here and they're working on the same types of equations,
but they seem to miss something. So what is it that's missing? And how would you fix it?
And it's through interactions with. How's it going? What have you done now?
I haven't done it yet. That thinking, at least from my perspective, is as kind of developed.
So what is the. I'll just go straight to the punch line because we're getting close to and the primary maths.
You can do maths when things are homogenous and you can do maths when when I'm,
well, mixed, you know, the standard test tube rate equation, things like that.
You know, I take a test, you get I mix it. That's the same model that gives the all number on the BBC.
When we hear about the R no record. It's the same model. It's all to do with when do I get something developed at the macro level or not?
And it's all a test tube reaction between susceptibles infected, et cetera.
In that case. But the same thing's true for models of the immune system, et cetera.
So what is the solution so well or what is the.
So actually, I'm going to show you the solution, and I'm also going to do this using two examples very quickly.
It gives you the wrong idea about how things that match we've had amazing Claudia this morning.
And you know how this organisation about, yeah, how does it develop?
How did that amazing plume that Claudio showed? How did it just kind of was it nucleating?
Did it just kind of peer? I mean, what is it and why didn't appear?
If I'm looking at, why didn't it appear before? One thing is to watch it.
Why didn't it appear 10 seconds before? You know what was wrong then?
And why can't Max describe that? Or can it? So I took about that, and then I'm going to about just how long this stuff take to happen.
I mean, you know, just just a standard thing. How long does stuff take to happen as a stand?
How long does it take? How how long do you take to recover from COVID?
How long does a reaction take? How long does any kind of complicated process take?
We have maths for that, but it doesn't work. I'll show you what does it work?
So these are the types of maths that you probably may have been faced with at some stage.
You can have people over here come over here with kind of lattices and they'll show you things moving around like cellular automata.
There are people now showing you like networks and, you know, networks developing all these kind of things.
And and then they're these are back to a kind of standard reaction models.
Mass action people show you those agent based models.
And now, of course, the whole I, my group of physicists that we have a group of mathematician physicists and I people,
you know, so they're always telling me, Oh, we're going to get 100 trillion parameters.
Oh, that's great. That's fantastic. What insight can you possibly get?
I can't even get insight from three. How can you get any insights?
Because the answer is you can't. So there's a missing thing of maths that has a kind of simple model.
Keep it simple. It's another one of those phrases. Keep it simple.
Show simple, model simple, kind of twisting of the tubes that show DNA.
Why can't we develop those kind of simple models? Comes down to laundry, so I want to show you.
So this is is this correct along with this, but it's a simple it's.
Think about this. It doesn't matter what you're looking at.
You think of any assembly problem where something assembles by itself because you're doing it when you're going.
I mean, imagine you've got some pile of laundry. This is just stuff available in some environment and it's it's going to self-assemble.
Of course, if those items. So this is the one of the first things, this is the main thing that's wrong with nice models.
Maths models assume the all that laundry is identical socks.
I had a friend in college, you just bought identical socks and just do it because it doesn't matter.
You never match them. They're just identical 100 pairs of identical socks.
You just got a bag of 50. You don't have to assemble themselves already in pairs.
You know, every two you find are a pair.
But when you've got heterogeneous objects, you actually have the system in some sense, that's the kind of think as it assembles.
And that takes time. I say it's an interesting question when you add heterogeneity to mass models of computer,
which people don't do because it's hard to do the easy way to do it.
But if you do that, then you know, I mean, any of us who came on a trip over here, you know, you go to events.
I got to lady, you know, tonight, do I need a jacket with it in this?
It's going to take one pair of shoes. I'll take those trousers. And what will that work them for the day?
You know, you're thinking it's almost like the function then determines how things are assembling and it takes time.
So. Again, I've only got a few minutes to tell you this,
but we've worked out ways what we've been working on for the last 15, 20 years is ways to change the maths.
To include heterogeneity, which seems to me to be the absolute number one problem with all modelling of biochemical systems.
I'm not going to run these do all the maths,
it's but the interesting thing is the time then that it takes and the size of the object and I don't mean like it could be an amyloids system.
Yeah, OK. But that's getting into the details. What I also mean is, like more like a coherence.
When is it the objects begin to cohere in some way they don't actually have to be next to each other.
They just have to do something coherent in some coordinated way.
And so we've been developing this maths of how you do that.
How to describe that process. And the most interesting thing is you can get you get incredibly different growth curves.
And the times at which things appear to change dramatically now, I've had no data,
so I'm really hoping that at some stage by the time I know they'll be data from the biochemical area to look at these kind,
of course, it's very difficult. So I had to go off and look at all kind of weird data like social media data, conflict data.
And this is why, you know, I've never had a chance to interact with a lot of them.
Talks with Dave and Lydia, but there is data in these other fields that act as proxies.
Funnily enough, they act as proxies, particularly social media sites of how things organise form communities.
Steve was talk about modular structure,
some kind of like correlation from looking at the type of modular community structure the communities have loose connexions between them.
It's exactly like a kind of what you might think.
I might learn something from looking at a kind of a social media picture because there's real data there.
And after all, we're all biological, some higher order level of organisation. But that might work.
So I've got two questions here, first before lunch. What happens, for example? What's your intuition?
If we're doing the laundry problem, we're assembling things and we start adding in more socks.
So I got back to that laundry basket. I'm packing for the packing to come on the trip that someone's emptying the laundry, you know, is it?
Does it just take longer? Is it do I get a richer set of clothes?
Does it take the same? Is it shorter time because of the I've got lots of socks appearing that I could just stick in there?
Well, the answer is it sort of depends. And that's the interesting bit. That's the interesting.
This new maths, it's you can actually buy cheap by changing the flux, of course.
None of none of you. Lot of us have environments that are closed.
They all have fluctuating numbers of objects and heterogeneity, and it completely changes how the kind of coherence develops within the system.
And I know I'm Typekit kind of in these generic terms. But I think that it's sufficiently generic that it's worth looking at.
That's number one on my title before lunch, but so is this OK?
That's how things develop. Things can develop, organise for good and for bad.
What about the back? What about when you're trying to disassemble something, when you're trying to stop it from developing?
Autoimmune disease, long COVID, whatever you want to do, whatever you want to talk about in some sense,
is a red versus blue or blue versus red to flip it around.
Red is trying to assemble something to maintain itself, and blue has got to work out some strategy or do something.
Now, standard maths, because I'm meant to talk about what maths, what maths tells a standard maths tells us this.
That the more, more blue you have, I mean, it's just, you know,
it's like basic undergraduate chemistry, [INAUDIBLE] a lot of blue and a little bit of red.
Well, that reaction's going to be over pretty quick.
And if I've got even more blue, you know, I'm sure I get red and with some red, you know, it's going to be even quicker.
So is the asymmetry between blue and red increases?
You'd think that the reaction time would decrease worries me slightly because I know in my own mailbox, you know,
when I've got a ton of unanswered mail, which I seem to have now, and I'm sure you all have, you know, it's like you can make a sweep through.
But when you've got bits here and there and they're kind of locally clustered,
but as they're spread out, part of me knows that actually that should probably take longer.
And when we look at real data from long COVID, for example, this is so I wasn't in Glasgow, but Edinburgh, does that count?
I'm sorry, it doesn't count. I know it's very separate and somebody told me that very separate cities.
But Dave and I were at them with Nvidia and we were talking about this walking through the streets of Edinburgh just a few weeks ago.
Why is it on Covid's log? I don't know.
And the interesting thing is, when you look at the data of long Kobe being law, the models, the maths models sort of ignore it.
Now this is on a bunch of ferrets. OK, so we'll give them, you know, we'll give them the benefit of the doubt.
They didn't have more data and they didn't bend up their model.
But there's existing data in the literature which exist, which suggests that you can't just fix things with the typical kind of reaction maths.
This is typical reaction maths, even if you don't know about these. Every paper practically that you'll find we need to have this in it.
Or like I saw the shortest, smallest model.
Now for long, COVID has 15 equations, but they all look like this.
And the only thing that matters is there's one derivative, which means it should be an exponential.
And if it's an exponential, I should be able to plot to unlock linear plot and it should be a straight line.
It ain't. It's longer it takes longer for things to happen, so I've got one slide.
Left left ages ago when day was over with me in Miami and we were sitting out in somewhere,
and I'm sure we're just having orange juice and we're having an orange, yes, mojito.
And he asked at that time that was back in 2010.
We go to Afghanistan, and that's the great thing. Insight into all these things, he was saying, Yeah, things wars take a long time.
Don't lie. And it's like, Yeah, why do they actually do that? I don't know what set me off thinking about data on in terms of wars.
It's the same thing as I just said to the asymmetry.
When you think that a chemical reaction when when it's more and more asymmetric, blue versus red, it's going to be quicker and quicker.
And yet when you plot out, it's a little bit off your topic that the plot out the asymmetry in conflicts and after all,
the reaction is no more than the conflict in a red blue versus red could be the immune system versus cancer, the immune system versus cove.
It could be any, any sort of competition. You plot them out and there's a high asymmetry in terms of the more blue them red.
There's a moment when it's like the mailbox. I've got clusters, but I can't find them.
So I'm so much blue, I've got so much blue that I can't find the red because I find myself every time I look,
every time I'm a blue looking for stuff, I find more blue.
I I'm fine red, red in these little clusters, and they kind of sit in pockets and they don't get touched.
So we plotted this twenty nine, I remember the editor 2010, the editor published this 2010.
The editor said, Oh yeah, those points are pretty out. Yes, 2010 was just ended, it hasn't even entered Afghanistan shoots up there.
Colombia up the top that stopped.
So it's not as crazy as it sounds that there's something to do with how living objects interact when they're asymmetric,
that can make it last a really, really long time. So I lied, I got one more site.
So we're now looking at this in terms of what's another thing. I've got the data.
I'd love to get data from anybody, anybody who wants to, but I have to use all this other proxy data.
So this is vaccine hesitancy. So this is something we're looking at now in terms of social media.
Why is it when you got a ton of blue? They are CDC, everything.
Each one of these dots is a community that could be like a few million people.
Gates Foundation sitting up there, the red. So little anti-vaxxers.
Anti-vax communities each read as an anti-vax community. Why is it the reaction takes so long?
Why can't you get rid of them? It's not that you're trying to get rid of. There's a whole bunch of greens.
It's like the background of the hearts and minds that kind of buried in the reaction.
It's lasting a long time. It has an anomalous duration. So.
Bring it to the end, because I know you would get so much. There's a problem last day was right.
Twenty four years ago, there is a problem with that and you can't just carry on doing the same mess.
You got to kind of grab it either grab the bull by the horns.
And the hatching has started because that removes all the nice tricks and all the nice things.
And yeah, OK. That's just the way it is got to include clustering community.
So the same idea in terms of cohesion for any process that I would imagine that,
you know about when I read textbooks, just stay beside me, read the textbooks I, I read them.
It's not all these beautiful switches. It's like an electrical engineers diagram.
And yet it cannot be like that. It's got to be collections of objects that may be a hundred, maybe five hundred and ninety six,
but they switch and then seven thousand two hundred and twenty one don't.
Why, you know, what's the kind of community? There must be some needs of scale, community level description.
So anyway, I'm working on that, I'm so glad that it's retired and because we've got more time to talk about it.
And the only way that I can think of the solution, what's the solution?
Just get good friends who are really smart. So that's what Dave taught me.
And so I'm really looking forward to this post phase where Dave and Lydia can meet up with us at any time,
because these types of problems, I think, are the next frontier for modelling.
I might see a trickle of people coming over from the other side of the road.
Thanks very much. Thank you. That's.
Donald, thanks very much, I really enjoyed that. So I wonder whether you could turn it upside down.
Could it be that what's wrong with mass is actually what's wrong with biology in that we're coming from?
We're expecting things to have one driver and one outcome from biology, maybe due to genetics, because you have a mutation, you have a phenotype.
And then the realisation comes that.
One gene, one protein, one consequence, you're either impotent or you're not important, and everything becomes necessary and sufficient,
these two these diagrams which don't represent biology at all because you can have situations,
for example, with the control element where any three things being turned on.
Whichever combination they are gives you an outcome. It doesn't matter what the components are.
And in a sense, what we're trying to model is the wrong thing. That's a fantastic point.
Fantastic point. Yet it shifts the focus away from thermodynamics towards kinetic as well, I think, which absolutely should be on the kinetics.
I'll ask a final question. So was this back to your first question, who should be doing something about it?
Should I be waiting for the mother to be waiting a long time for that, actually?
Or should we? Molecular biologist B,
somehow attacking the mathematicians to get them to come was the only way I could get funding for this stuff is through Space Force,
which, you know, I'm not going to sign any sizeable grant because they're interested in heterogeneous teams of machinery, humans.
So you've got an element that's like a coin toss, maybe an element that has deterministic rules.
Hopefully the machine and an element that doesn't take up any space but also has influence, which is the algorithm.
So they're interested in teams. When is it that the team operates? Is it, you know, what is it?
What's the magic mix? Is it? It's like cooking.
It's like something like that. You know, what is the magic mix?
And so they're really interested in that and how as you grow teams, it's an identical question as I take,
you know, elements building blocks and put them together, and they're not identical.
What how does the, you know, it's not changing from three to four, it's changing from fifty seven to six hundred and thirteen or something.
It doesn't matter. It's 13, it could be 30. It's it's almost like another.
It's like a meso level description in terms of groups.
Yeah, I haven't answered the questions. So but I think you're going to be waiting a long time for the mathematicians to come across.
Okay, thank you. Unfortunately, yeah, I'll say thanks to all of us because.