 Welcome everyone and so this is the our second lecture started for the academic year started September this year and so the provost lecture series was initiated last October and so so in it's almost exactly about a year as you can see so we have covered many lectures celebrating our faculty members only and the purpose is that we want to provide a platform to celebrate milestones in the careers of our faculty members so it covers from for example promotion tenure promotion and also for faculty members receive awards and finally also for faculty members who are going to retire so in the past in the past year we celebrated professor of Scotland and each year of Maruyama so both retired in the past year we also have many professors who got promoted to full professor or associate professor with tenure and professor Christine last come two weeks ago give a lecture to so to celebrate her recent award and so today so I'm very happy to to kick off our lecture to celebrate professor Sase to be promoted to full professor and just very quickly I want to again thank many people from different divisions within OIS to make the provost lecture series a success so in particular people from the office of the provost and so it actually takes a lot of time and effort to to prepare the lecture and to to get the snacks and make a coffee and for the cleanup and so so I hope people can say thank them you know during the the coffee break and also Patrick Kennedy who is the engineering support section leader he has been helping us to to create a gift it's kind of with personal messages and so on and also the team from CPR so I see hazards here and also all your team members thank you so so they help us to to make the poster to make the design and also the video recording thank you so as indicated today so we have professor Sase and we have actually several more lineup and the next one will be given by professor Yavin Chi to celebrate several international awards he had received in the past year so we also have professor Satoshi Mitori and so Satoshi I just I found the picture when I searched Google I guess that's the picture taken when you first got here do you do you remember okay and so beside these four professors we probably also have two to three more so based on some recent results from there are recent tenure and promotion and so more information will be up so with that I'll hand the floor to professor Tadashi Yamamoto who will be the chair to introduce professor Sase. Thank you for sitting up my presentation and congratulations to the sun on your well-deserved promotion to the current promotion and as a colleague who joined oyster almost at the same time it is 11 what three years ago I'm very happy that he's promoted to full professor here this view is from my office and I like the green plants very much it is image of the not even real reality is the fatality and also the peels so I like this picture very much and if we go further north to oyster campus there's a Yambal forest there are more greens probably and there is many kinds of the plants and those many kinds of plants is in such target of Tadashi-san and he is working on the plant from the undergraduate days in Kyoto and when that was many years ago probably and he was graduate from Kyoto University and move get the master degree from there and then for the PhD he moved to Basel, Switzerland and then did another plant biology where he was supervised by this professor P. Paskovsky and then this is Sase and this is by epigenetic dynamic laboratory in the in Switzerland often they went to skiing of course they did a lot of work in the laboratory of course and then after getting the PhD he came back to Japan and then joined into the professor Kakutani's laboratory in the National Institute of Genetics where he is working on the labitope thesis and another great epigenetic scientist and then Sase-san was got position in the National Institute of Genetics as an assistant professor in 2011 I think no 2011 you joined here at the same time I joined here so anyway he became assistant professor in National Institute of Genetics and moved to OIST in 2011 and then continued to work on the plant genetics genetics so in the laboratory he works with the plant this is some kind of mutant of the labitophtosis it comes bonsai mutant probably and then he works very well in the laboratory but of course he has home and at home he is a good father and the husband and he can make soba noodles that is this required technique I think and also strength of the making the cutting on the making the pan that but I like to eat you for me it's not making eating the noodle with sake is much fun fun of me and then he after the work he often go to the this is Okinawa City and name is Adachiya probably Izakaya maybe you can enjoy there and then I don't know how often he goes there but anyway but I was joined very very enjoyable and then I want to go to a couple of slides about his science and this is epigenetic modification and gene structure chromosome structure is somehow controlled by the epigenetic epigenetic modification this is a mechanism of the epigenetic degradation modification many many mechanism is behind and also this is a result of the epigenetic regulation modification and this in this case probably better to be explained by suggestion this is a phenotype of the plants disease phenotype probably but liver dying so maybe I want to then from here I want to ask to talk about the more professional things and then I look forward to your great success in the OIST camp OIST as a OIST professor please Sade san okay Dr. Yamamoto thank you very much for kind introduction he already talked about my research but I would like to briefly introduce our research what we are doing in the OIST for 10 years or 11 years so as the Yamamoto sensei showed so we are currently like 10 people including the five postdocs and two students one technician and one administrator so this is the latest picture so this is showing the higher hierarchy in the laboratory so we have two main research goals the first is of course epigenetic to understand epigenetic mechanisms which I will explain this lecture that distinguish between genes and transposable elements which also I will explain and understand the biological significance for plant adaptation and genome evolution and second goal is to contribute to the Okinawa society by using our specialty plant genomics so then first start is what is epigenetics so to understand epigenetics we need to start from genetics so probably you know about the DNA which is inside the nucleus in the cells and the DNA encodes some the information important for production of the proteins which is written by the genetic code so DNA as a heredity material that encodes genetic information so in the case of genetics there are several genes encoded in the DNA strings then if there is a change in DNA it cause sometimes changes in the output proteins which cause the changes in the phenotypes of organisms sometimes so in genetics changes in phenotypes can be explained by changes in DNA sequence in contrast epigenetics epi means originally above or over over genetics so there are several definitions about epigenetics but my favorite one is this one so the study of mitotically and or mayotically heritable changes in gene function that cannot be explained by changes in DNA sequence so we study something which is not associated DNA sequence changes so this mitotically or mayotically is a bit complicated so I don't go into detail today so if you want to learn more about epigenetics please come to my epigenetic class in terms of every year so DNA does not exist as a naked molecule in the cells but it's attached to the protein called histones and forming this kind of beads strings like structure which is called chromatin and one unit is called nucleosome and as Yaman sensei said so this chromatin is important for transmission of the epigenetic information so in DNA the DNA determines genotype but this chromatin chromatin DNA histone and other protein complex can determine epigenotype and eventually this epigenotype determine the phenotypes of cell tissue and individuals so basically what we are studying is that modification of this chromatin modification means chemical modification of chromatin like methylation of DNA or methylation, phosphorylation, acetylation there are various chemical modification on the histone proteins which are attached to DNA and also the reorganization of nucleosome position sometimes called chromatin remodeling. This chromatin modification in the genome-wide scale is called epigenome so this is one of the target we are studying every day and the other target we are very interested or at least I'm interested is the transposons or sometimes called transposable element that he is so this is very interesting the element which exists within the genome of many or almost all organisms. This transposon was first identified by Dr. Barbara McRintock in 1940s or 50s even before the solution of DNA structure and this transposon is kind of parasite stay in the genome and it can move around within the genome so and sometimes it can be inserted into the functional gene and disrupt the function so this is the cone which the McRintock used and this is the strain which originally have the purple pigment in the kernels so this is the normal state but if the transposon this T is transposon is inserted within the this the pigmentation genes it interrupts the function and for example this those colors are not produced and science not produced but sometimes it can still go out then it can restore the function of the gene then you can see those spots means that those are sectors which does not have transposon anymore so as I mentioned this transposon is very ubiquitous in the eukaryotes not only in plants and there are several kinds of transposon including retro transposon or DNA transposons this retro transposon is very similar some of them very similar to like retro virus like HRB and for example in the case of human our genome half of our genome is occupied by this parasite transposon and also mice drosophila she elegans in the case of Arabidopsis about 10% of the genome is transposon and this transposon can cause many effect for gene function in the genome for example so this is a grape wine grape so this is Cabernet the strain has this gene for pigmentation but when the retro transposon is inserted in the promoter region of this gene it affects the gene function and makes chardonnay the variety and after some rearrangement it causes another type of the variety and also same for blood orange and people without knowing the presence of transposon the for long time people are using transposon as a source for genetic variation like in the very long time ago in maybe 17 century in Japan there are a lot of breeders to produce very unique morning glories which are eventually caused by the variation in transposons also color variations carnations are also produced by this transposon insertion those transposon insertion sometimes inserted within the genes we called intragenic so intergenic is between gene but intergenic is within the genes and those intergenic transposons are very common in eukaryotic genome so this is the one of the cartoon from this review this is Marmarian genome and you can see this orange or purple or blue those are retro transposons most of them are degenerated pieces of the transposon which are actually present using the gene so these regions are called the introns so it is said that 60% of T's in both human mass are located in intronic sequence sometimes those intronic or intragenic sequence can have a regulatory role of the associated gene so means that sometimes they behave like parasite but also sometimes organisms somehow capture or domesticate those transposon for host function the famous example of this one so probably you know about this so during the industrial revolution in UK so they use a lot of coral for the in the factory and the surface of the tree become darker because of the coral burning and it cause the quick adaptation of the most and some the population start to have more darker phenotype which is actually caused by the transposon insertion in the intronic regions so then there are a lot of the potential impacts between transposon and genes so let's assume this rate is transposon sequence so transposon sequence can be incorporated into the gene transcript or sometimes transposon sequence has regulatory element to stop transcription it cause the avalanche polyadenylation premature polyadenylation or sometimes it also called produce the avalanche RNAs from internal promoter so one of the questions we are having is that how those intragenic transposons are epigenetically controlled so to study this we use this Arabidopsis as a model system so this plant is very small which is the family of like the cabbage or radish and very easy to study and many researchers use this the plant as a model and we have a lot of information public data and resources to study this so then I'd like to introduce our recent study about gene transposon interaction using Arabidopsis so we try to understand how gene and transposon sequence are expressed together it's called Chimeric gene transposon transcript Chimeric is like a monster which has different part of the animals so in this case we mean Chimeric gene transposon transcript is that if transposons are inserted in within the gene or surrounding regions which can be transcribed together with the genes so this work was recently published mainly the work by Leo, Jeremy and Munisa so to do this we use the technology called Nanopower direct RNA sequencing so this technology is relatively new so by using some flow cells which contain a lot of proteins which can capture the RNA molecules and when RNA molecules going through the dyspore you can read the sequence of the nucleotide so then we can get really long the sequencing information which is very useful for the resolving the structure of RNA sometimes it's very difficult using by using the short lead like Illumina sequencing so like in average we can get 1 kb 1.2 kb lengths of RNA sequencing information so then this is one example so there's a gene called RPP4 which I will show later again so this gene is a bit complex start from here to here so we use the official annotations, annotation means that information showing that gene start from here to here somebody determined by using several the information and here this lead is transposon you can see transposon in intron of this gene and also 3 prime region of this gene in addition to this official the gene annotation we have the transcript annotation this is also the big effort by the consortium and they update the information several years so then this is also the annotation here so the annotation stop here but our data shows that actually this gene can be transcribed into this transposon region or even the gene which was initially thought to be another gene but actually this is the gene of the last exon of this gene so you see a lot of variation in the transcription even some of them are not properly spiced or some of them skipped from here to here or here to here so it's very complex and also we found that those the transcript chimeric transcript gene transposon chimeric transcript are not properly captured so far so we have this data now and also we this is a valid data and we also have the new data about the mutant which can change the dispersing pattern so there are a lot of the outcomes or consequences of this the variations and it's very complex and I also didn't know before starting this but basically so there is an event called spicing so after transcription of the RNA it can be spiced to fuse exon regions and those the spicing can make a lot of variation in the transcript and let's assume this red is transposon and black is a gene exon like in intron retention or spiced alternative spicing site or exon skipping so this is spiced based event and also if the transcription start sites are shifted or transcription termination site are shifted you also get the different spicing transcript isoform like this so if transposon has another transcription start site it can make the variation in the transcript so it's very complex but very talented the postdoc Jeremy developed the new pipeline bioinformatic pipeline it's called parasite which is available publicly so it can so by using this pipeline he can automatically detect this event and also identify the transposon sequence within this direct RNA sequencing data so basically he classified another type of the transcript but today it's not so much important so we found this T gene transcript about 11,000 in world type Arabidopsis so it is about the 3,000 gene Rosai corresponding to 3,000 gene Rosai associated is this the transcript in Arabidopsis genome so there are several example I don't go into detail and we found many T intron retention event or T alternative TSS or T alternative TTS stagnation site which are quite high number so then what kind of genes are producing this kind of T gene transcript so then we found that the genes involved in killing of cell or other organisms cell killing defense response to fungus or response to fungus so those genes are actually the important for the plant defense against against pathogens so we are happy to find this because actually it is already known that those genes involved in pathogen resistance associated with transposons so in the case of the plants plants does not have plant do not have the immune system as mammals but animals but instead they have the gene called resistance genes which is kind of the genes which recognize specific pathogens almost one to one interaction so plants need to have many this resistance gene R gene to cope with different pathogens to have this they have this R gene cluster as a cluster sometimes and for this cluster formation transposon is very important because transposon is very repetitive sequence so it can actually enhance the recombination or shuffling of those genes and it is known that the this R gene clusters are most the rapidly evolving locus in plant genomes so this is the some example we focused this study so this is the case of this T E alternative TTS so transposon red is present in 3 prime region 3 prime UTR regions and this is actually the gene which I showed this RPP for but in different orientation another orientation sorry it's complicated so gene start from here then this red is transposon sequence but in wild type the transcription going through this transposon sequence but we found several epigenetic mutants which cannot produce this the T gene chimeric transcript and only stop the original gene TSS TTS site like this so this is the wild type so this is another gene so you can see that this is the gene and in 3 prime UTR region this red is transposon sequence and in wild type they produce T gene chimeric transcript but in the mutant they stop so I don't go into detail about this mutant but they are important for epigenetic regulation so then the Leo the another postdoc try to see how this changes in the T gene the transcript affects pathogen response then so this one actually this is the this is showing the degree of infection so white is more resistant and darker green means that there are a lot of infections going on so there are several strains in Arabidopsis which does not have this gene itself so this pathogen is specifically recognized by this R gene resistance gene RPP for so without this gene they have a lot of infection and in wild type Colombia as a comparison the infection is something like this but in this mutant you can see that more white means that they show more resistance means that so by producing this chimeric gene transcript the plants try to suppress the response to the pathogen so it's somehow bit counterintuitive because if you have more resistance it would be good but as I showed those genes cause the cell death actually so plants try to kill the infected cells to prevent spreading of the pathogen into the neighboring cells so if too much activation of these genes cause kind of autoimmune response so rather probably we guess that suppressing of those genes but we also add about adaptive to the environment so anyway so this is a summary of the first part so we did the direct RNA sequencing and we found about 3,000 gene loci which produce T gene chimeric transcript and the epigenetic changes can change the suppressing pattern or isoforms and in some loci we found that the stress can change the transcript so we don't know yet but maybe the environmental stress can change epigenetic marks which eventually produce the alternative transcript form which might be useful for stress response so this those data are publicly available so we also the upload those data in our OIST website then second part I'd like to introduce our the project about the Okinawa society by using plant genomics approaches so as you know the one of the important mission of OIST is the contribution to the sustainable development of Okinawa so Okinawa is very famous as a blue zone and a lot of centenarian centenarian means that the people can live longer than hundred a hundred years old and very famous for longevity but after World War II it's a bit affected because of one reason might be because of the changes in the lifestyle including diet and especially the it's called Okinawa crisis which is related to the changes in lifestyle and now the people in Okinawa are suffering the lifestyle related disease like liver disease or diabetes or hypertension intensive disease and among so in the case of Japan there are 14-7 the prefecture but both female and male are quite high as higher the highest the mortality risk in Okinaw population like this so this is the data from 2020 and also like COVID so then when we joined the OIST was 10 years ago about 10 years ago there's a project called functional life project started so in this project we tried to develop new life strain which is related to that the life's diet in the people not in Okinawa but in also Asia so by using the life strain called amylo-mochi life strain we called Waxi AE rice so this rice strain was originally developed by the professor Sato in Kyushu University he already retired and this rice strain can accumulate resistance starch so and this this resistance starch is accumulated because of two changes in two genes called Waxi and AE so this amylo-mochi strain has two mutations in the genome so in the case of rice there are two types of starches accumulating one is called amylo-pecchin the other one is amyloce so this is the gurukos basically and linear gurukos and branching gurukos and normal rice about 80% amylo-pecchin and 20% amyloce and if you go to market you can find gurukinous rice sticky rice actually this is also the mutant the one of the gene Waxi is mutated and this gurukinous rice doesn't have amyloce and that's why it's very sticky and in the case of this amylo-mochi or this Waxi AE rice it has another mutation additional mutation it cause more long branched amylo-pecchin which cause the resistance to the human digestion so then basically as a geneticist what I did what we did was so this the Waxi AE amylo-mochi strain was close to local the rice strain called yugafu mochi so to to develop new rice strain suitable for okinawa production so crossing crossing crossing so ideally you'd like to get new variety which contains resistance touch but other genetic background is the local yugafu mochi so then we did so-called molecular breeding so we use the genome information rice genome information for this the crossing so if so let's assume this the this bed is a mutation present in the original amylo-mochi and this is the yugafu mochi then if you cross the half become the yugafu mochi and half remain the amylo-mochi then again you cross so once you cross the half of the genome become the replaced and then second cross we call back cross one back cross two then again half so we repeated this so if you do this five times theoretically the 3% of the genome should remain and 97% of genetic background should be replaced by the other strain but this doesn't work like this because this is the the great the finding of Mendel so if you cross this one you will get this kind of random independent assortment of gene loci it's it's called so-called Mendel's second law so you get the progenies which does not have for example this one of the gene or some of them does not have at all or like this so then here we use the genome information so we developed a genome worker genome white and try to find the progenies which has both mutation inherited both mutation so maybe this one this one but we would like to have the progeny which has more the replacement of this so then we select this one so this is the reason why you are not the same with your sister and brother so this is because of this random assortment so anyway so we select efficiently the strains which are having the replaced background so then that this this process is it's not so taking not so long time because so if you grow the rice in Okinawa you can harvest twice second crops in mainland Japan only once but if you if you use the growth chamber maximum we can do like five generations so this is not so taking time but the problem that we need the field test to register this rice to rain and it took time and so as a geneticist we somehow stopped somewhere here and then after this agricultural part we had a lot of support from OIST innovation system led by the Ichikawa san and Nagamine san and also we had a lot of help from the Onna village and then we checked after developing this new oyster rice then indeed it can accumulate the resistance such compared with normal rice and also this year there is a report about the clinical trial about this rice to the patient with type 2 diabetes and it shows that it can suppress the increase of the blood glucose for insulin after eating so then this June with the new president Karin we announced new rice to rain as a child so this is one of the project and the other project about the mangrove so you may know about mangrove which can grow the very extreme condition in the coastal area including Okinawa and subtropical region at tropical region in the world and for the plant biologist it's very interesting plant but because it has the very strong tolerance against salt or heat and UV light so Okinawa Japan is the northern limit of the mangrove and in the case of Okinawa we can find major the three major the mangrove species Bruggella, Gimnuris and Candelia obrata and Lysophora stylusa so I took this figure from one review so it is believed that maybe 55 million years ago there was a global warming happen and it caused so this is a sea level increased sea level and during that time mangrove might have diverged from other species and we just studied this Bruggella which the diverged relatively earlier than other mangrove species so this project was done by Martin sitting here so she sequenced this mangrove and the genome size was something about 300 and actually there are already several reports about the other mangrove species so mangrove has relatively smaller genome compared to the normal trees and also she did the field experiment so she went to the river in Kintan called Okukubi river and she collected the samples from the ocean side which has the relatively high salt concentration in the soil and also the bit more upstream the area which has relatively low salt concentration so interestingly so even though it's the same species they show totally different morphology so the wine in ocean side is like bush but in river side you see like five six meter long trees so then she did the RNSX data and she found a lot of the changes in gene expression I don't go into detail and also we did the in-natura in-natura means the samples from natural in-natura epigenome analysis so we check DNA maturation and interestingly we found that especially transposal has higher DNA maturation in salt conditions so this is another project and lastly I'd like to introduce this project this was also done by Martin so probably you know the tree called Fukugi it's a originally called Galsinia sub-b-sub-b-ptica so it's the very traditional tree in Okinawa and if you go to the north of the Churaumi Aquarium there is a beautiful village called Visezaki where you can find a lot of these trees along the house so this the Fukugi is traditionally planted as a windbreak forest in Okinawa so then we were contacted by the people in the Okinaw prefecture the Agricultural Research Institute and they want to distinguish between male and female tree actually it has male and female sex and also in campus you see a lot of this Fukugi tree planted along the street maybe you never care about whether it's a male or female but some people care because especially the female tree makes the fruit after 10 years and sometimes it makes the some the smell white attract also the insects so the male trees are more appreciated sorry I'm not really mean about this but so then they want to distinguish the male and female in early stage but so far they can know this after 10 years fully grown up the tree then for the first time they can distinguish male or female so then we sequenced this the pattern sequence this the Fukugi genome and the Martin tried to find male specific or female specific piece of DNA and we could find some regions which are only present in male so we can now distinguish male and female at the very early seedling stages so this is another project which is related to Okinawa so okay so thank you very much for your attention and your time to coming to this lecture and I'm happy to take question