Audio- Organelles: Episode II

Transcript

00:00 --> 00:02Yale podcast network.
00:05 --> 00:09Hello and welcome to another episode of the Yale Journal Biology and medicine podcast
00:09 --> 00:10YJBM is a pub.
00:10 --> 00:20Med index quarterly Journal edited by Yale medical graduate and professional students and peer reviewed by experts in the fields of biology and medicine each issue of the Journal is
00:20 --> 00:23devoted to a focus topic an through the YJBM podcast.
00:23 --> 00:25It would take you through the past,
00:25 --> 00:28present, and future of the issues subject matter.
00:28 --> 00:34This episode is part of our series devoted to our September 2019 issue on Organelles, I'm your co-host Kelsie Cassell,
00:34 --> 00:36a second year graduate student Epidemiology.
00:36 --> 00:45And I'm also your cohost my name is Wesley Lewis and I'm a first year in computational biology and Bioinformatics and I'm your 3rd and final cohost,
00:45 --> 00:50Emma Carley. I'm a second year student in the Department of cell biology and today.
00:50 --> 00:53We're joined by Doctor Megan King and doctor.
00:53 --> 01:01Patrick Lusk Doctor King and Doctor Lusk are Associate Professors in the cell biology Department here at Yale and Full disclosure.
01:01 --> 01:03They happened to be my wonderful PI's,
01:03 --> 01:05so thank you. Both for being here today,
01:05 --> 01:08you're welcome. Happy to be here.
01:08 --> 01:15OK, we'll be talking over each other through most of this sounds good.
01:15 --> 01:18So Doctor King and Doctor Lusk both study the nucleus.
01:18 --> 01:28One of the many organelles featured in the organelles issue of this Journal so briefly the nucleus is a large double membrane organelle found in eukaryotic cells that houses the
01:28 --> 01:32genome. But this organelle is not simply a storage space for DNA.
01:32 --> 01:39It's actually a densely packed highly dynamic cellular compartment involved in many key cellular processes.
01:39 --> 01:45So we're excited to learn a lot more about this awesome organelle from Doctor King and Doctor Lusk.
01:45 --> 01:46I'm so to start of-
01:46 --> 01:52can you please introduce yourselves and tell us about how you became interested in studying the nucleus?
01:52 --> 01:57Absolutely so my inspiration for studying so biology in general,
01:57 --> 02:01actually happened during my undergraduate education at.
02:01 --> 02:04It's wonderful school, called the University of Alberta in Alberta,
02:04 --> 02:19Canada. And essentially uh you know up until probably my 3rd year at science had been taught primarily is sort of a by road kind of memorization type of.
02:19 --> 02:25Teaching, which was not that inspiring but actually it was actually a cell biology class in.
02:25 --> 02:31I think my junior year where I was finally introduced to what science is all about and of course,
02:31 --> 02:39that's sort of the capacity to make new discoveries right and to uncover something that nobody else is understood or seen before.
02:39 --> 02:48And so this is something that I hadn't really been taught but finally understood the power of that and I got involved with research at that time and sort of
02:48 --> 03:00got involved with research. Looking into the transport portal so that control all molecular communication between the nucleus or at the most important organelle in the cell and the cytoplasm,
03:00 --> 03:08which which encompasses the rest of the organizers of the cell so these portals of the time were very poorly understood,
03:08 --> 03:18but they sort of are the one of the defining features features of the nucleus because the nucleus is such a large organelle and you have to have tremendous amount
03:18 --> 03:20of molecular traffic to allow.
03:20 --> 03:30Gene expression and so we became very interested in understanding essentially how these portals work and that's sort of continued actually over the last have to say 2 decades,
03:30 --> 03:36though, to my work as an independent investigator my own laboratory.
03:36 --> 03:38So actually came to cell biology much later.
03:38 --> 03:41I really was much more fascinated by chemistry.
03:41 --> 03:42When I was a high school student.
03:42 --> 03:49But I also found chemistry little bit dry and so when I discovered that there was something called bio chemistry.
03:49 --> 03:51That was really interesting to me.
03:51 --> 03:53The idea that I could study chemistry.
03:53 --> 03:56That was carried out by biological molecules was really intriguing.
03:56 --> 04:05And so that's what I set out to study as an undergraduate and I really loved the field of biochemistry particular particular protein chemistry.
04:05 --> 04:08And that even when I went to work on for my PhD work.
04:08 --> 04:16I my PhD is actually in biochemistry and biophysics and I would say the biophysics training is one of my motivations.
04:16 --> 04:28Now, for my current work because one of the things that were very interested in our cellular forces and that interest in in forces really came from thinking about biophysical
04:28 --> 04:30questions as a graduate student.
04:30 --> 04:40In terms of focusing on the nucleus that really came from rediscovering a love of mine from probably when I was 9 or 10 years old,
04:40 --> 04:42and that was looking through a microscope.
04:42 --> 04:54I like many young budding scientists was fascinated by taking pond scum and putting it on a microscope and getting out a book and identifying all of the different critters
04:54 --> 04:57that were flying around and.
04:57 --> 05:03It was during my pH D that I finally was able to take advantage of GFP green fluorescent protein.
05:03 --> 05:15This is the protein tag that we put on molecules were interested in so that we can watch them dynamically in live cells and that technology was actually only really
05:15 --> 05:19put into the laboratory setting for asking fundamental questions.
05:19 --> 05:23When I was an undergraduate and so as a graduate student.
05:23 --> 05:31It was continuing to become more popular and I would say my first foray into looking through a microscope at AGFP.
05:31 --> 05:41Tagged protein in a microscope was really kind of revolutionary for me and really made me appreciate the kind of open approach that cell biology takes and that is that
05:41 --> 05:50if you're looking at something for the very first time 'cause you're the first person to make a jeffy Fusion protein of this really exciting protein.
05:50 --> 05:59You're going to be able as as doctor last mentioned to see something that no one else has ever seen before and you have no idea what that's going to
05:59 --> 06:05be so kind of a prepared mind and setting up an interesting system or assay can reveal anything.
06:05 --> 06:16And I think that's what really won me over to cell biology as compared to kind of very structured biochemistry tons analogy that I had done up until that point.
06:16 --> 06:19It turned out that one of the molecules.
06:19 --> 06:27I decided to study surprisingly actually associated with these nuclear pore complex is the portals of transport that doctor loss.
06:27 --> 06:29Garrity introduced and for me.
06:29 --> 06:34It was actually watching the nucleus during mitosis or cell division,
06:34 --> 06:45so the nucleus. Is in human cells completely breaks down as the cells are segregating their chromosomes and that has to be re established in the following cell cycle and
06:45 --> 06:47the dynamics of that process.
06:47 --> 06:58As I watched it taking movies of cells using a microscope was just incredibly fascinating and that's what really sparked my interest in the nucleus as an organelle was the
06:58 --> 07:04fact that it went through this incredible cycle every time cells divide.
07:04 --> 07:09Awesome so as I previously mentioned the nucleus is a very complicated.
07:09 --> 07:19Compartment so can you talk to us specifically about what your research in your lab is focused on in this very complex organelle?
07:19 --> 07:28So we actually we try to not enter too far into the nucleus were very interested in actually the bounding membranes and again.
07:28 --> 07:41These portals that nuclear pore complex is that control all the molecular traffic and we've been particularly interested in emerging concepts over the last I'd say,
07:41 --> 07:505 years or so and the idea that the nucleus isn't sort of this static organelle Megan mention this idea during mitosis where.
07:50 --> 07:52It completely breaks down and is rebuilt,
07:52 --> 07:55but in most of the cells in our body.
07:55 --> 07:58It actually this doesn't their terminally differentiated,
07:58 --> 08:02particularly if you think about cells in your brain for example,
08:02 --> 08:09they have intact nuclei that don't break down and yet the nuclei are considered sort of these static working hours,
08:09 --> 08:18but they're actually quite dynamic on the molecular level and one of the things that we've discovered is not just us but other groups in the field is that these
08:18 --> 08:28organelles can actually break. Have it let's say micro fractures if you will small tears in the nuclear envelope that can actually disrupt this compartmentalization,
08:28 --> 08:36which is critical for organelle identity where we define organelles by their bio chemical constituents and so the segregation of for example,
08:36 --> 08:45transcription where you make a message or RNA in the nucleus from translation from where you make proteins in the set is all is established by the integrity of this
08:45 --> 08:49critical barrier, which is the barrier itself is built from the membranes,
08:49 --> 08:53but also by the functioning of these nuclear pores.
08:53 --> 09:00And So what we've been very interested in understanding is essentially because this barrier can breakdown in particular,
09:00 --> 09:13with different disease states. I'm trying to understand if there are cellular mechanisms that sells employed to essentially protect the cell and protect the nucleus from this loss of compartmentalization
09:13 --> 09:23and we have discovered pathways that actually are able to recognize when the nucleus nuclear membranes are breached over the nuclear pores aren't working properly.
09:23 --> 09:33And start to mitigate that damage may think this is important for mitigating an disease actually in the context of human disease?
09:33 --> 09:41Could you talk a little bit about how disruption of this nuclear envelope could lead to disease like?
09:41 --> 09:45What sorts of diseases are related to these disruptions,
09:45 --> 09:48yeah, so I think that there's 2 categories.
09:48 --> 09:50One is no general diseases,
09:50 --> 09:54where it's not very clear that in diseases like.
09:54 --> 10:04A male trophic lateral sclerosis or else there's actually a disruption in the integrity of nuclear pores themselves.
10:04 --> 10:08You know why that ultimately causes disease isn't well understood.
10:08 --> 10:19But we're trying to understand essentially does the does this disruption trigger these surveillance pathways that we've discovered in more fundamental genetic models like for example,
10:19 --> 10:27budding yeast, which is been a fantastic model for exploring sort of the fundamental biology behind the nuclear envelope membrane system.
10:27 --> 10:29The other thing is cancer.
10:29 --> 10:37So one thing that's clear is that when you do lose the disruption or when you disrupt the integrity of the nuclear membranes.
10:37 --> 10:41This leads to DNA damage and it's not actually clear.
10:41 --> 10:48Um necessarily again with the cause of that damage is there's lots of debate in the field as to what actually causes the damage.
10:48 --> 10:57But nonetheless as we all know Genomic integrity or do you know damage is an input to cancer and so we're very interested in understanding again?
10:57 --> 11:07How these surveillance mechanisms may have actually mitigate that damage may actually make it much lower so much worse than it needs to be and hopefully slow down.
11:07 --> 11:12Cancer progression. So when I first started my group at Yale.
11:12 --> 11:21I was really motivated by a very fundamental question and that is that the nuclear envelope is actually part of the endoplasmic reticulum.
11:21 --> 11:25So we're talking about as a separate organelle 'cause.
11:25 --> 11:27It does have this distinct identity,
11:27 --> 11:38but the outer nuclear membrane is continuous with the ER membranes in the lumen between the two memories of the nuclear envelope is contiguous with the ER lumen.
11:38 --> 11:46And so one thing we know about membranes from the kind of biophysics side is that they're very what we call compliant.
11:46 --> 11:52That means that they were kind of very easily bendable and Shapeable and in the ER for example,
11:52 --> 12:02microtubules actually template. the ER tubules and so one of the questions that I've had for a long time is what prevents the nucleus from what allows the nucleus to
12:02 --> 12:06maintain its shape because it's not actually an island.
12:06 --> 12:13It's actually integrated into the cytoskeleton so those are all of the filaments that give the nucleus structure.
12:13 --> 12:20And the cytoskeleton actually is able to deliver for sign of the nucleus and this is important in many contexts for example.
12:20 --> 12:27There are many tissues in which control over the position of the nucleus within the cell is very important,
12:27 --> 12:31and that's actively determined by these cytoskeletal elements.
12:31 --> 12:35So what keeps the nucleus looking in this kind of beautiful round.
12:35 --> 12:40Spherical shape that we're used to seeing when it's actually being acted on by forces,
12:40 --> 12:43particularly we know that the membranes that are.
12:43 --> 12:49Really define the nucleus are very soft and malleable and at the answer that way.
12:49 --> 13:02We think about that question is that ultimately the mechanical properties of the nucleus are determined by the chromosomes themselves right so the one other unique aspect of the nucleus
13:02 --> 13:13is that it houses are DNA and the DNA is in the form of chromosomes and chromosomes are massive they are actually the largest polymer inside of human cells.
13:13 --> 13:25And. Chromosomes also have their own kind of biophysics and so the hypothesis that we've been testing for the past 10 years is the idea that the chromosomes are actually
13:25 --> 13:29attached to the membranes an by being attached to the membranes.
13:29 --> 13:38They impart their mechanical properties on to this nuclear envelope verify stiffening it and this is important for its ability to maintain its integrity.
13:38 --> 13:45So it doesn't undergo these kind of fractures leading to some of the complications that Patrick mentioned.
13:45 --> 13:54And so that's the interface that were really focused on were interested in how chromatin contributes to defining the mechanical properties of the nucleus.
13:54 --> 13:56That's kind of the yen of the lab.
13:56 --> 14:06I would say the Yang of the lab is related to one of those forces are being transduced onto the nuclear envelope and on to the chromatin is that also
14:06 --> 14:08important for the chromatin biology.
14:08 --> 14:15So how does it actually affect what's happening inside the nucleus and so one context of that is mechanotransduction?
14:15 --> 14:24Testing the idea that forces are directly transduced across the nuclear envelope onto the chromatin to regulate jeans in a way that's important,
14:24 --> 14:34particularly at the level of tissues and organisms and the other aspect is related to how the kind of dynamics that can be driven by the cytoskeleton or imparted on
14:34 --> 14:45to chromatin, which is important for gene regulation and also for mechanisms involved in DNA repair so I appreciate you talking about some of the major interests that have come
14:45 --> 14:53out of your lab. Could you potentially follow up with some of the updates that you're most excited about in your research so classically.
14:53 --> 15:00We think of organelles as being membrane bound compartments that's the kind of original identification of them,
15:00 --> 15:10but one of the really new concepts in cell biology is that there's a lot of Self Organization of really functional organelles that are not determined by being individual membrane
15:10 --> 15:15bound compartments. In fact, the nucleus is really the origin of this kind of organization,
15:15 --> 15:17so it's been appreciated for 100 years.
15:17 --> 15:28That there are different sub compartments of the nucleus a good example is the nucleolus where all ribosomes are being a generated an assembled and that is again is not
15:28 --> 15:34a well. That's a clearly a compartment that you can see an electron micrograph.
15:34 --> 15:37For example, it is also not bounded by membranes.
15:37 --> 15:47So we've known from studying kind of nuclear organization that there are mechanisms by which cells can self organize reactions even if they're not.
15:47 --> 15:57In an individual membrane bound compartment that concept has now broadened out to a whole list of what I would call them.
15:57 --> 16:00The kind of modern addition to organelles,
16:00 --> 16:05which are really identified by their functional characteristics,
16:05 --> 16:16and composition and one of the new concepts is that many of these are organized through a process called liquid liquid phase separation,
16:16 --> 16:19so this is an idea that there are.
16:19 --> 16:30Intrinsically disordered regions of proteins that are actually functionally very important again this on its own is kind of a revolution historically people felt that the kind of structured ordered
16:30 --> 16:36regions of proteins were always doing the work of a protein and carrying out its function,
16:36 --> 16:46but instead these intrinsically disordered regions actually allow molecules to organize with themselves in a way that allows him to segregate out from the other components.
16:46 --> 16:49So you can think about this as kind of your.
16:49 --> 16:52Classic salad dressing you have oil and water and so,
16:52 --> 16:54if you shake up salad dressing right.
16:54 --> 17:01It will it will then come apart and self organize into these 2 domains and you can kind of think about.
17:01 --> 17:07That being driven by some protein segregating out from other proteins in the cell.
17:07 --> 17:09So we are very interested in that concept,
17:09 --> 17:17most recently because a coming back to this idea that chromatin is important for the mechanical properties of nuclei,
17:17 --> 17:21particularly the chromatin that is associated with the nuclear envelope.
17:21 --> 17:25So if you look at any classic electron micrograph of a nucleus.
17:25 --> 17:28You'll see that there's very dense chromatin.
17:28 --> 17:37That's associated with the periphery of the nucleus with the inner nuclear membrane and it turns out from a number of recent studies.
17:37 --> 17:43That heterochromatin this dance chromatin has has these liquid liquid phase separation properties.
17:43 --> 17:53This is initially kind of very disconcerting to us because when you think of a liquid you think a song It's very soft and we had already found the heterochromatin
17:53 --> 17:55was important for making nuclei stiff,
17:55 --> 18:00but that really is a kind of misnomer of how we think about liquid's most liquids.
18:00 --> 18:02We think about our soft,
18:02 --> 18:08but in fact glasses. A liquid right and that's actually quite hard and so really in the physics terms.
18:08 --> 18:19A liquid is something that has disordered molecules doesn't really tell you anything about its mechanical properties and so the interview kind of come to terms with that and we
18:19 --> 18:29are excited about the idea that these phase separated domains don't just organize molecules which is really how they've been studied for the most part in the past 5 or
18:29 --> 18:3310 years, but also that they can actually do mechanical work.
18:33 --> 18:39That means that the phase separated domains actually want to stay in the shape that they have.
18:39 --> 18:41And if you try to deform them,
18:41 --> 18:51they don't want to be deformed and so that actually can impart the stiffness to the nucleus that we've observed with respect to heterochromatin so this is a.
18:51 --> 19:00Really for us an exciting time to consider the mechanical properties of something that was previously understood to mainly be organizing.
19:00 --> 19:06Different regions of the cell and these kind of new concept of what an organelle is are there.
19:06 --> 19:12Other examples of liquid liquid phase separation that we might have heard of before or like?
19:12 --> 19:15How did the theory originate?
19:15 --> 19:21And so the original I think there's been a number of observations over many years.
19:21 --> 19:27But as all really interesting and exciting and fundamental aspects of Science.
19:27 --> 19:31Things are rediscovered continually an with new techniques.
19:31 --> 19:39You really can get to the molecular details and the generalizable principles that apply to all different areas of science.
19:39 --> 19:42So I would say the kind of landmark paper.
19:42 --> 19:44I was a study by Cliff Brangwyn,
19:44 --> 19:56working with Tony Heimann. He was studying P granules in C elegans embryos and it was known that the organization of these P granules was is aligned along the axis
19:56 --> 20:05of the embryo early an embryo Genesis and what he did was he basically applied a fundamental cell biological approach,
20:05 --> 20:15which is as I just said to GFP tag something so that you can look at that molecule in a cell and then to take a movie and what he
20:15 --> 20:27discovered was that. Actually, the molecules that make up these P granules are very dynamic and what allows them to accumulate and one axis of the cell and be depleted
20:27 --> 20:31from the other was actually that the molecules are being stabilized,
20:31 --> 20:40and that these domains that are the P granules were growing in one region of the embryo and dissolving in the other and.
20:40 --> 20:46The dynamics of those molecules really revealed for the first time these ideas of phase separation.
20:46 --> 20:55So there's a couple of principles that underlies this and one of them is that you have this condensation of molecules and the P granules and any kind of the
20:55 --> 21:05first example that spend well characterized of this and also that the molecules themselves are actually dynamic so molecules are moving into the granular and out of the granules and
21:05 --> 21:12because he was studying the growth in the disappearance of the granules in different parts of the embryo it allowed him to.
21:12 --> 21:22Really quantitatively describe that behavior that has now been generalized to lots of different aspects of biology spanning from T cell.
21:22 --> 21:30Receptor signaling a something that is studied by our colleague in the Cell Biology Department Doctor Zhao.
21:30 --> 21:41Lei su who is examining the role that face separation plays in the immune system and number of bodies inside the nucleus that involve rnas,
21:41 --> 21:44including things like stress granules and.
21:44 --> 21:54Other organelles that are important for the ability of cells to rapidly respond to stress by changing their protium involve the regulation of how rnas are compartmentalized and I think
21:54 --> 22:02it only keeps growing. I would say in the Dina repair field one of the things that we're interested in there is now the idea that the two ends of
22:02 --> 22:09a double strand break are held together by molecules so have the ability to form this kind of phase so it's only going to,
22:09 --> 22:12I think keep showing up as a concept.
22:12 --> 22:21So it sounds like the role of phase separation and epigenomics chromatin structure might be more complicated than we previously thought.
22:21 --> 22:29Could you speak to that and how it may be interfaces with epigenomics and genome sequencing in general.
22:29 --> 22:38Yes, so I would say phase separation has emerged as not being just important for the kind of physical properties of heterochromatin.
22:38 --> 22:45But there's also the idea now that a lot of kind of classic concepts of Watt regulates gene expression.
22:45 --> 22:47I'll give you an example.
22:47 --> 23:00One of the modifications. We know that it's essential for productive transcription is the phosphorylation of the C terminal domain of RNA polymerase 2 and it's now appreciated that that
23:00 --> 23:09phosphorylation. Probably drives a phase transition so we've again this is like prior knowledge that we've known a lot about the modification.
23:09 --> 23:20But the assumption was that that modification was related to kind of classic biochemistry of assembling all the right factors to get productive transcription.
23:20 --> 23:31Now that's been kind of re envisioned as actually determining a phase and that phase may be a mechanism of incorporating all of the factors that might like to partition
23:31 --> 23:34into that phase and exclude factors that might inhibit.
23:34 --> 23:43The productive transcription, so it's interesting to watch really classic knowledge be kind of rethought into this concept of phase separation,
23:43 --> 23:52which may explain behaviors that we thought we understood but we understood that may be more in a test tube or more from chip seq so right.
23:52 --> 23:59One thing that people do is they could use an antibody to phosphorylated C terminal domain and if you were to do genomics.
23:59 --> 24:06You would see that that modification is enriched and all the actively transcribing jeans so it was a characteristic.
24:06 --> 24:13But really its function is probably something that's only been recently understood in the context of phase separation.
24:13 --> 24:20Yeah, I'm happy that we've had a chance to talk about phase separation at such a hot topic in cell biology right now,
24:20 --> 24:26it feels like every cell biology seminar that you go to somebody says face separation at some point or another.
24:26 --> 24:35I think that that's true at the same time I think there's also starting to be a little bit of a backlash where people are seeing phase separation everywhere and
24:35 --> 24:45I will just make the point that most of the evidence for face separation or at least most of the biochemical understanding for phase separation comes from in vitro studies.
24:45 --> 24:53And there are still a major questions about not just whether it occurs in cells because I think that there's good evidence for that,
24:53 --> 24:55but really what the functional importances,
24:55 --> 25:05so that means what we need in cell biology are tools that can dissect the phase separation behavior from the other functions of the structured domains of those proteins and
25:05 --> 25:12a lot of that work is yet to be done and so I think there's a real need in the future for a kind of dissecting the role of phase
25:12 --> 25:17separation from with regards to the function of the processes in which it's been implicated.
25:17 --> 25:22I think there's also room for other phase changes right so there's this idea.
25:22 --> 25:24Liquid liquid like fairies changes,
25:24 --> 25:27which which Megan just talked about,
25:27 --> 25:31but there's also evidence that complexes of proteins can form gels.
25:31 --> 25:37For example, actually one could argue that some of the initial data supporting the concept that proteins,
25:37 --> 25:45particularly intrinsically disordered proteins, which many of these phase separated demands are considered the constituents are in fact,
25:45 --> 25:50these intrinsically disordered proteins that conform multi valent interactions,
25:50 --> 26:02which allows them to. They separate was discovered earlier than that and actually in the context of the nuclear pore and this is work done by colleagues dirt.
26:02 --> 26:06Garlic and Germany, who suggested almost 20 years ago.
26:06 --> 26:14The idea actually that the nuclear pore which is this conduit that controls all molecular traffic is itself.
26:14 --> 26:19The reason why it can be selective and to what can go through it,
26:19 --> 26:24which is key to write establishing this nuclear insider plasmic.
26:24 --> 26:29I'm barrier. Is actually mediated through phase property?
26:29 --> 26:36Where these these these nuclear pore proteins form essentially a gel and they form a gel,
26:36 --> 26:49which is capable actually at least in a test tube re capitulating many of the fundamental aspects of nuclear transport and that means that it's selected for some molecules whereas
26:49 --> 26:56a excludes others, and this is was really pioneering work and what's interesting is that so it's not?
26:56 --> 27:00Are liquid? On the other hand,
27:00 --> 27:11a lot of these phase separated demands that Megan brought up do actually change their properties over a native age actually and so they can move from a liquid state
27:11 --> 27:17to a gel like State to even more solid state and this is thought to be often.
27:17 --> 27:23Continuum also related to function in ways that maybe also pathological so in some some cases.
27:23 --> 27:33These domains actually essentially can never be disassembled may esentially become stationary and obviously the dynamics are very critical.
27:33 --> 27:43For their function and so I think one of the interesting things that we're going to have to address in the future is sort of how these chromatin domains if
27:43 --> 27:54they do move to these sort of solid like states are there mechanisms to release them from that and other ways to potentially clear these aggregates if you will from
27:54 --> 27:59the nucleus? Which is another interesting area of nuclear biology that we're interested in.
27:59 --> 28:04We're interested in essentially how you are able to recognize.
28:04 --> 28:07Clear damage from within this nuclear compartment,
28:07 --> 28:13which is generally thought to be segregated from some of the major decorative organelles.
28:13 --> 28:15For example, process called Atapa G,
28:15 --> 28:26which is essentially a process where the cell can eat large chunks of the site is or even eat portions of organelles and in order to sort of clear damage
28:26 --> 28:31and clear stress from the cell and this is also accumulates with age in the nucleus.
28:31 --> 28:35But how you actually access the nucleus by this.
28:35 --> 28:42Dark machinery is actually a very enigmatic in some despite evidence that it probably happens if that makes sense.
28:42 --> 28:49What do you think the next big thing is that we're going to learn about the nucleus?
28:49 --> 28:54Like what are you anticipating is going to come out next?
28:54 --> 29:07I think one of the major areas that was really unanticipated Anas come from numerous fronts over the past probably only 5 years is the recognition that.
29:07 --> 29:11Segregating the we can think of as the host genome.
29:11 --> 29:23The genome of the cell inside the nucleus is really a critical aspect of ensuring that the innate immune system is able to function properly so the innate immune system
29:23 --> 29:26as surveillance mechanisms in the cytoplasm,
29:26 --> 29:36which are looking for RNA and DNA because that is a sign that the cell is infected with a bacteria or with a virus and that leads to an 8
29:36 --> 29:43immune signaling which can lead to inflammation can bring in the adaptive immune system etc.
29:43 --> 29:53Those mechanisms when you think about it really rely on the fact that the DNA is housed in the nucleus so that it's not surveilled by those receptors that are
29:53 --> 29:55out there looking for nucleic acids and so,
29:55 --> 29:58if we come back to some of the concepts.
29:58 --> 30:00We already talked about for example,
30:00 --> 30:10that you can have these ruptures of the nucleus that expose the DNA to the cytoplasm if you have defects in these nuclear pore complex is so that you're not
30:10 --> 30:14able to maintain the barrier of the nucleus properly.
30:14 --> 30:27This can lead to the exposure of the genomic DNA to this machinery and this is something that I think we didn't really quite anticipate how important nuclear compartmentalization is
30:27 --> 30:33to prevent inflammation. So this you can think of this in the context of autoimmunity.
30:33 --> 30:40For example, you're going to get an autoimmune and inflammatory reaction if these systems fail.
30:40 --> 30:44The other context of this that was probably not.
30:44 --> 30:48Also, none anticipated anticipated comes from cancer biology.
30:48 --> 30:57So it may well be that these kind of classic changes on nuclear architecture that are known to manifest,
30:57 --> 31:05particularly metastatic cancer cells so all cancer is diagnosed and staged by looking at nuclear size.
31:05 --> 31:14Nuclear appearance and the kind of appearance of chromatin and nuclear bodies like the nucleolus and we really don't understand.
31:14 --> 31:24Why that's such a good diagnostic which is kind of very frustrating for people who have been studying nuclear architecture for their entire careers.
31:24 --> 31:27So I think that's a major big unanswered question.
31:27 --> 31:30But to come back to the kind of New Horizons of that.
31:30 --> 31:34One idea is that whatever is a driver of those structural abnormalities.
31:34 --> 31:45These kind of nuclear ruptures can lead to the engagement of the innate immune system and that what you normally think about the contents of infection could be really useful
31:45 --> 31:49as a way that multi cellular organisms are able to identify these cells.
31:49 --> 31:52That have manifested with this kind of damage,
31:52 --> 31:57and to remove them so just like I saw a Organism wants to remove infected cells.
31:57 --> 32:08It also probably wants to remove cells that have undergone this kind of catastrophic damage leading to losses of genome integrity and that it might surveil that by looking for
32:08 --> 32:11these defects in the nuclear barrier.
32:11 --> 32:16At the same time, it's also likely that a lot of our cancer therapies.
32:16 --> 32:28When we irradiate cells that can lead to failures of mitosis where we don't re establish the nuclear Berryer when cells exit the mitotic mitosis when they would have segregated
32:28 --> 32:34their chromosomes and this probably also leads to surveillance by the same machinery.
32:34 --> 32:42Zan so there's a new recognition that molecules involved in an AI mean sensing these are molecules like see gas and sting.
32:42 --> 32:53Which the immunologists have been studying for a long time are likely very important for cells for organisms to call bad cells,
32:53 --> 33:09but also for therapies to work to allow to allow a patient to respond to radiation by actually killing tumor cells that those processes are actually dependent on this assessing
33:09 --> 33:12the integrity of the nuclear barrier.
33:12 --> 33:14Is probably something that was happening all along?
33:14 --> 33:21When we've developed therapies but we didn't know that that was the mechanism and so understanding that mechanism better,
33:21 --> 33:26so that we can actually leverage it more effectively and cancer therapy and particularly immunotherapy,
33:26 --> 33:28which is a really rapidly.
33:28 --> 33:34Expanding aspect of cancer. Therapies is something that really may come back to this fundamental cell biology of the nucleus,
33:34 --> 33:35which is exciting.
33:38 --> 33:46So it seems like soft matter physics and just this phase separation question is becoming or is showing to be ineligible to cell biology?
33:46 --> 33:57Can you talk about maybe some of the challenges that you faced being primarily biologists and moving into a field now that is historically been dominated by physicists.
33:57 --> 34:03I I mean, I think that it was interesting is a lot of the early discoveries here.
34:03 --> 34:11We're sort of made by physicists working in biology fields and I think what's really most exciting.
34:11 --> 34:13I think about modern cell biology?
34:13 --> 34:17Is actually how multidisciplinary it really is.
34:17 --> 34:20And so physicists bio fermentations.
34:20 --> 34:24Computational computer scientists. You know 'cause.
34:24 --> 34:27We have to deal with huge data analysis.
34:27 --> 34:29Now, if large datasets from.
34:29 --> 34:41Really sophisticated electron microscopy from really sophisticated high throughput screening in these sort of things that machine learning is really a big part of what's coming in in cell biology?
34:41 --> 34:52So I think that one of the most exciting features is actually how multidisciplinary cell biology has become Megan can comment probably more about that since she works directly with
34:52 --> 34:55physicists. Yeah, I mean for me as I said,
34:55 --> 34:58I started as a biophysicist really by training,
34:58 --> 35:03so it's to me. It's a fantastic development of cell that cell biology really needs.
35:03 --> 35:08People who are used to thinking about those aspects of problems so physicists.
35:08 --> 35:19You're absolutely right soft matter physicists are actually that it's a group of soft matter physicists from which this original concept of phase separation and cell biology arose from so
35:19 --> 35:26that you're exactly right that is a really important lens through which to see these aspects of cell biology.
35:26 --> 35:29Uh what island and we have been in my own work,
35:29 --> 35:35actually some of the most impactful concepts are coming from soft matter physicists?
35:35 --> 35:42Who are studying phase separation and non biological systems and that's that's my very impactful for us.
35:42 --> 35:54I think there are some challenges so one of the challenges is that soft matter physicists are used to thinking or have classically described these problems from equilibrium models,
35:54 --> 35:59which makes a lot of sense when you're working on inert non biological systems,
35:59 --> 36:01but living cells are absolutely not.
36:01 --> 36:07At equilibrium so we really need to work with physicists and we there are individuals in this field,
36:07 --> 36:14that are are making steps towards this to start to be sure that our theory that we're applying to these problems.
36:14 --> 36:19Is actually well suited to the complexities of the biology?
36:19 --> 36:26While not making it so complex that you can't try to use first principles to define and understand it,
36:26 --> 36:27so in my own work,
36:27 --> 36:33I work. I've worked for 8 years with a physicist colleagues who's here at Yale.
36:33 --> 36:44Dr Simon Mochary, an that has been critical to all of the work that we've done on nuclear mechanics and work that we're doing on chromatin organization and so I
36:44 --> 36:48think that this is going to be absolutely essential.
36:48 --> 36:53And what I've seen at least is that it can be extremely successful.
36:53 --> 37:05If you just have people who are really driven and interested to work with others across disciplines and also you need a few people who can bridge the languages of
37:05 --> 37:16these different fields. But it's been the absolutely most rewarding part of for me doing science at Yale has been through these interactions.
37:16 --> 37:21With physicists and also more recently with engineers so we also work with doctor.
37:21 --> 37:25Corey o'hearn with him. We do increasingly simulations,
37:25 --> 37:31which isn't also I'm really another impactful approach in Cell Biology Doctor Tom Pollard.
37:31 --> 37:42One of our esteemed faculty here would be the 1st to say that you don't really understand something until you can derive a mathematical model that can explain the behaviors
37:42 --> 37:46that we observe in living cells and I think that that is a.
37:46 --> 37:50A good goal to have it is certainly one that we have in our science.
37:50 --> 37:53So our last question is to each of you?
37:53 --> 37:57What's your favorite fun fact about the nucleus?
37:57 --> 38:00We just talked about this on the way and I mean,
38:00 --> 38:02I think the classic fact right,
38:02 --> 38:09which I think is a fun fact is that you have essentially 2 meters of DNA in each cell right?
38:09 --> 38:16That is somehow compacted into a tiny volume nucleus is sort of 6 microns in diameter.
38:16 --> 38:21Uhm I think other fun facts would be that I think we talked a bit about nuclear shape.
38:21 --> 38:28I mean, I think there is this conceptual ization in every textbook that you guys have that the nucleus?
38:28 --> 38:34Is this sort of round ball and it turns out there's actually a plethora of different shapes,
38:34 --> 38:44depending on cell type, so a lot of nuclear actually more like squash pancakes and all nuclear actually like sort of beads on a string that really multi lobed and
38:44 --> 38:56really elaborately. They have very different morphologies and the idea is that those morphologies reflect the function of those cells and I think one thing we haven't talked about is
38:56 --> 38:58is how all the cells in our body,
38:58 --> 39:00have the same genome right.
39:00 --> 39:10And yet they do very different things where tissues that very unique functions and I think this is one of the fundamental questions is how does nuclear shape relate to
39:10 --> 39:15those unique functions? The other half.
39:15 --> 39:29So fun. The other fun fact in the context of this issue that you put together on organelles is that as we've already discussed the classic definition of organelles is
39:29 --> 39:31that their membrane bound compartments,
39:31 --> 39:37but as we've already described the nuclear envelope is a membrane compartment.
39:37 --> 39:43That's full of holes those holes are filled by these nuclear pore complex is but nonetheless.
39:43 --> 39:50I think it's actually very unique in that it is really not just an intact membrane sheet.
39:50 --> 39:54Ross, which things can only be pumped by channels for example,
39:54 --> 39:56are imported through you know,
39:56 --> 40:00small channels where unfolded proteins can be trans located?
40:00 --> 40:05In fact, it has these 50 nanometer diameter holes all throughout it,
40:05 --> 40:10which is really big right and so while we while it is one of the classic organelles.
40:10 --> 40:20There really is a whole host of biology that we have to understand and that it has to have to actually maintain that compartmentalization.
40:20 --> 40:31And and that's really kind of unique is just to keep in mind that it's not actually an intact membrane and how cells enough to be really careful to actually
40:31 --> 40:34maintain its specific identity.
40:34 --> 40:42Awesome so thanks so much to Doctor King and Doctor Lusk for joining us on this episode of the YJBM podcast.
40:42 --> 40:49Like many scientists today. They're on Twitter so if you would like to follow them for more nucleus fun.
40:49 --> 40:51You can follow them atleast King L.
40:51 --> 40:54That's LUSKINGL and at Peel ask for you.
40:54 --> 40:57That's PLUSK the number 4 and the letter U?
40:57 --> 41:01There are many people behind this podcast that you never get a chance to hear.
41:01 --> 41:03Thank you to the Yale School,
41:03 --> 41:06Medicine for being our home for YJBM an the podcast.
41:06 --> 41:13Thank you to the Yale Broadcast Center for help with recording editing and publishing are podcasts and thank you to the YBM editorial board,
41:13 --> 41:15especially our editors in chief.
41:15 --> 41:19Amelia Hallworth and Devon Wasche and the deputy editors for the organelles issue.
41:19 --> 41:26Amelia Hartworth, and John Venturafinally thanks to you for tuning into this episode of the Yale Journal of Biology and medicine podcasts.
41:26 --> 41:28We love to hear your feedback in question,
41:28 --> 41:31so feel free to tell us your thoughts by emailing us.
41:31 --> 41:39yjbm@yale.edu if you enjoyed our podcast we share it on SoundCloud or Apple podcasts?
41:39 --> 41:40Thanks.

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The Yale Journal of Biology and Medicine Podcast hosts Kelsie, Emma, and Wes interview Dr. Megan King and Dr. Patrick Lusk from Yale's Cell Biology and Molecular, Cellular, and Development Biology departments. Listen as we discuss their research on the nucleus and their favorite organelles!

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