{"id":12561,"date":"2023-02-14T17:03:48","date_gmt":"2023-02-14T08:03:48","guid":{"rendered":"https:\/\/www.waseda.jp\/inst\/wias\/?p=12561"},"modified":"2023-03-06T16:26:37","modified_gmt":"2023-03-06T07:26:37","slug":"newsletter-vol-16%ef%bc%882018%e5%b9%b4%ef%bc%89-2-2-2-2-2-2-4-2","status":"publish","type":"post","link":"https:\/\/www.waseda.jp\/inst\/wias\/news-en\/2023\/02\/14\/12561\/","title":{"rendered":"Newsletter Vol. 25 (Winter 2023)"},"content":{"rendered":"

Introducing the new WIAS director and associate director<\/h3>\n

The following two individuals were appointed in September 2022 as Director and Associate Director, creating a new structure at the Institute.<\/p>\n

Director\u3000Ken-Ichi Akao (School of Social Sciences)<\/strong>
\nAssociate Director\u3000Chiharu Tokoro (School of Creative Science and Engineering)<\/strong><\/p>\n

The Waseda Institute for Advanced Study (WIAS) was established in September 2006 as an independent institute outside the existing faculties of the University. Since its inception, WIAS has been serving as an active matrix in which next generation leading researchers can conduct creative advanced research on a wide range of themes, beyond the constraints of conventional fields such as the humanities, social sciences and natural sciences. Within the new system, WIAS will continue making efforts in its established areas of endeavor, including the provision of opportunities for young researchers to develop in an atmosphere of friendly competition; collaboration with on-campus faculty members; the hosting of overseas researchers; and the promotion of interdisciplinary research projects.<\/p>\n

Message from Director Ken-Ichi Akao<\/h4>\n

\"\"Ever since its inception in 2006, Waseda Institute for Advanced Study (WIAS) has accumulated a wealth of experience from world-class research activities and continues to bring together and foster promising young researchers hailing from the world over specialised in a wide range of disciplines in the natural sciences, social sciences, and humanities. Its ability to maintain a consistently high level of excellence in the selection process for open calls for researchers is a testament to the fact that the Institute is widely recognized as an attractive environment for young researchers from across Japan and abroad. My mission as Director of WIAS is to further develop this free-spirited, international, and interdisciplinary tradition built over the years and nurture the next generation of researchers. We hope to promote exchanges between researchers both within and outside the University, based on the university-wide advanced research projects such as the TGU projects and the declaration of carbon neutrality.
\nIn cooperation with our Associate Directors, Professor Tokoro and Professor Yamamoto, WIAS will relentlessly strive to maintain an attractive environment for outstanding researchers from around the world.<\/p>\n

Message from Associate <\/strong>Director Chiharu Tokoro<\/h4>\n

\"\"<\/p>\n

In recent years, there has been rapid progress in the development of diverse topics in science and technolo\u0002gy. These technologies provide clues toward solutions to the diverse problems facing our society today. For example, environmental issues such as climate change and pollution are among the social issues of widespread concern. For the social implementation of science and technology to solve these social problems, it is essential to collaborate with researchers in various fields of the humanities and social sciences, not only for the sake of technological impact, but also economic impact, ethical considerations, and the design of laws and policies.
\nThe Institute brings together leading researchers from a variety of fields, including science and engineering, social sciences, and the humanities: we engage in deep mutual exchanges while pursuing excellence in our own research. From this perspective, we hope to provide a matrix where new innovations can be born through mutual understanding and the fusion of diverse fields.<\/p>\n

Introduction of our activities<\/h3>\n

1. 15th Anniversary Symposium (December 12 and 13, 2022)<\/h4>\n

Over a two-day period on the 12th and 13th of December last year, an international symposium entitled \u201cWell-being in the time of uncertainty<\/a>\u201d was held to commemorate the 15th anniversary of WIAS.<\/p>\n

\"\"<\/p>\n

With the cooperation of the Zukunftskolleg at the University of Konstanz, Germany, and the Institute for Advanced Research at Nagoya University, the symposium featured roundtable discussions on specific topics such as energy and inclusivity under the umbrella theme of \u201cwell-being.\u201d Leading researchers in the natural sciences, social sciences, humanities, and various other disciplines were invited to make presentations from their respective perspectives. Current WIAS researchers, alumni, and current graduate students also joined the event.
\nThe roundtable sessions were quite challenging. In the sessions, speakers delved into the symposium\u2019s overarching theme by associating it to their own respective fields. All the speakers prepared thoroughly for each session, exchanged opinions, and openly discussed their approach to each topic in advance, which led to original and meaningful talks. Each topic was sublimated into high-level and in-depth exchanges, making the two-day event a fruitful one for WIAS, which prides itself as a forerunner in international, diverse research.
\nDuring the two-day event, in addition to the presentations live at the Ono Memorial Auditorium on the Waseda University campus, a Zoom online webcast was also available. The event was a great success, with a total of 265 in attendance and online.
\nPhotos and videos of the event have been posted on its designated webpage<\/a> and WIAS\u2019s online archives portal (YouTube channel)<\/a>.<\/p>\n

2. Publication of Assistant Prof. Kakui\u2019s Paper<\/h4>\n

An international study group led by Assistant Prof. Yasutaka Kakui of WIAS, discovered a common mechanism that shapes mitotic chromosomes according to the length of genomic DNA in different species by comparing the structure of mitotic chromosomes in yeast cells and cultured human cells. Their results appeared in the Scientific American journal \u201cCell Report,\u201d published by Cell Press, on Tuesday, December 6, 2022, at 11:00 a.m. (EST). Below is a synopsis of their latest research.<\/p>\n

“The Common Mechanism in Life for Shaping Chromosomes\u201d – by Assistant Prof. Yasutaka Kakui<\/strong><\/p>\n

Cells use chromosomes*1<\/sup> to inherit genetic information, which acts as their blueprint. Chromosomes are known to be complex folded structures of a very long string-like genomic DNA*2<\/sup>, but the mechanism that controls their shape was not known. In this study, Assistant Prof. Kakui and his team investigated the structure of chromosomes in yeasts and human cells in detail and discovered that the control of the loop size according to the length of the genomic DNA is a common mechanism for chromosome formation (Fig. 1).<\/p>\n

\"\"<\/p>\n

(1) What we already knew from previous research (scientific and historical background, etc.)<\/strong><\/p>\n

When one cell divides into two, the structural maintenance of chromosomes (SMC) complex condensin*3<\/sup> embraces the genomic DNA like a loop to form chromosomes. When chromosomes are misshapen, cells cannot properly inherit genomic DNA, resulting in the production of abnormal cells such as cancer cells. Chromosomes are present not only in humans but also in yeast and other eukaryotes. Therefore, the mechanism of chromosome formation is thought to be common to living organisms, but the overall picture is still elusive.<\/p>\n

(2) New findings from this study<\/strong><\/p>\n

To elucidate the common mechanism by which life forms chromosomes, the chromosome structures of three organisms with varying genomic DNA lengths, namely budding yeast, fission yeast, and human cells, were examined using the Hi-C Method.*4<\/sup> Results showed that, while budding yeast with short genomic DNA formed small loops (Fig. 2, left), fission yeast and human cells with longer genomic DNA had larger loops. This fact that the longer the genomic DNA, the larger the loop indicates that the control of loop size according to genomic DNA length is part of the common mechanism in life that shapes chromosomes.
\nTo link the size of the DNA loops to the shape of the chromosomes, they precisely measured the thickness of the chromosomes using an super-resolution fluorescence microscope*5<\/sup> enabling the observation of extremely fine structures at the nanometre level. They found that the chromosomes of fission yeast with large DNA loops were thicker than those of budding yeast, which has small DNA loops (Fig. 2, middle). Furthermore, by measuring the chromosome dimensions of human cells, they newly discovered a power law relationship, or allometry, where chromosomes become thicker in proportion to their lengths (Fig. 2, right).
\nIn addition, the relationship between the SMC complex condensin, which governs the loop structure of genomic DNA, and chromosome thickness was examined. They found that the SMC complex condensin is more densely distributed on genomic DNA in budding yeast with thin chromosomes than in fission yeast or human cells with thick chromosomes. This means that the density of SMC complex condensin may direct the size of genomic DNA loops and chromosome thickness.<\/p>\n

\"\"<\/p>\n

Therefore, by closely examining yeast and human chromosomes, this study reveals that chromosome thickness depends on the loop size, which is determined by the genomic DNA length. This research has brought us one step closer to a full understanding of the common mechanism by which chromosomes are formed in organisms with different genomic DNA lengths.<\/p>\n

(3) The future<\/strong><\/p>\n

More than 130 years have passed since Walter Fleming first observed chromosomes at the end of the 19th century, yet the overall structure of the fibrous genomic DNA inside them is still a mystery. The control of loop size by the length of genomic DNA revealed by this study is expected to lead to a greater understanding of how chromosomes are formed, which is common in various organisms. Furthermore, through further analysis of the density of SMC complex condensin and allometry of chromosome thickness and length, we expect to gain new insights into the evolution of genomic DNA.
\nIt was reported that structural abnormalities in chromosomes, which are the entities of genome heredity, were found not only in cancer cells but also in oocytes taken from elderly women, and are strongly linked to infertility. By unravelling the mechanisms that control the shape of chromosomes, we expect to explore the causes underlying infertility in older women and contribute to reproductive medicine.<\/p>\n

(4) Terminology<\/strong><\/p>\n

1. Chromosome
\nMitotic chromosome. Genomic DNA is compactly folded and condensed when cells divide, resulting in an X-shaped structure.<\/p>\n

2. Genomic DNA
\nA sequence of four bases, adenine (A), thymine (T), guanine (G), and cytosine (C), the combination of which is leveraged by life to store genetic information and pass it on to the next generation.<\/p>\n

3. Structural maintenance of chromosomes (SMC) complex condensin
\nA ring-shaped protein complex common in prokaryotes such as E. coli and higher eukaryotes such as humans which plays a role in forming chromosomes by embracing genomic DNA like a loop in cells.<\/p>\n

4. Hi-C Method
\nThe Hi-C Method (high-throughput chromosome conformation capture) is one of the experimental methods used to examine the structure of genomic DNA in cells. The Hi-C Method can reveal the structure of genomic DNA by reading the genomic DNA sequence using a next-generation sequencer and determining the regions where genomic DNA strands are in spatial proximity.<\/p>\n

5. Super-resolution fluorescence microscopy
\nGeneral optical microscopes (fluorescence microscopes) are limited in their ability to see small structures (resolution) depending on the wavelength of light used. Super-resolution fluorescence microscopes are special devices that exceed this limit allowing us to see finer structures at the nanometre level.<\/p>\n

(5) Thesis information<\/strong><\/p>\n

Journal<\/strong>: Cell Reports
\nTitle<\/strong>: Chromosome arm length, and a species-specific determinant, define chromosome arm width.
\nAuthors (Affiliation)<\/strong>: Yasutaka Kakui1,2,3<\/sup>, Christopher Barrington4<\/sup>, Yoshiharu Kusano6<\/sup>, Rahul Thadani3<\/sup>, Todd Fallesen5<\/sup>, Toru Hirota6<\/sup>, Frank Uhlmann3<\/sup>
\n(1. WIAS; 2. Department of Life Science and Medical Sciences, Graduate School of Advanced Science and Engineering, Waseda University; 3. Francis Crick Institute, UK; 4. Bioinformatics Division, Francis Crick Institute, UK; 5. Advanced Optical Microscopy Technology Division, Francis Crick Institute, UK; 6. Cancer Institute Foundation (Cancer Institute))<\/p>\n

(6) Research grant<\/strong><\/p>\n

Research gran<\/strong>t: NPO Yeast Cell Research Society of Japan, Yoshifumi Jigami Memorial Research Grant
\nTheme<\/strong>: Regulatory mechanisms of chromosome structure in evolution
\nPrincipal Investigator’s Name(s)<\/strong>: Yasutaka Kakui (WIAS)<\/p>\n

3. Waseda Culture and Arts Week<\/h4>\n

\u201cstudioFLAT x WIAS: Art that Connects, the Practice of Social Inclusion\u201d was held as part of the event, “Waseda University Arts and Culture Week” held from October 10 to 21, 2022. The event was organized by Satomi Yamamoto, Associate Director of WIAS. The following is her report.<\/p>\n

This event was held in collaboration with studioFLAT, an NPO based in Kawasaki that aims to realise an inclusive society through art activities regardless of disabilities. It was an opportunity to think about a society where we can coexist from the point of contact between art and cognitive neuroscience.<\/p>\n

\"\"

studio FLAT<\/p><\/div>\n

The event began with a lecture by Associate Professor Yuko Okamoto of WIAS on the \u201cDiverse Visual World Explored from Cognitive Neuroscience.\u201d Our visual world exists in a variety of gradations with individual differences. This lecture addressed the characteristics of vision, with a focus on autism. While touching on the appreciation of paintings, the measurement of an artist’s gaze, and brain function measurement research, the topic expanded to the acquisition of knowledge and experience as a means of understanding the viewpoint of the person with disabilities, which is required in a wide range of support settings, as well as the possibilities of daily communication. How does the brain work when we “see” things? Is the world as we see it the same as the world as someone else sees it? The answers to these questions could lead to the creation of new art.<\/p>\n

\"\"

Lecture by Associate Professor Yuko Okamoto of WIAS<\/p><\/div>\n

Next, Satoru Oodaira, Director of studioFLAT, gave a detailed explanation of the founding philosophy and activities of studioFLAT, which is a non-profit organisation. Being an artist himself, Mr. Oodaira explained how he came to collaborate with artists belonging to studioFLAT who have autism or other characteristics, how his NPO was established, the current activities at their base of operations located in a commercial, medical, and childcare complex in Kawasaki, and their student internship programs, etc. The activities he described, which are geared towards realising \u201cflat\u201d (equal or even) relationships through art, were full of surprises and discoveries.<\/p>\n

\"\"

Satoru Oodaira, Director of studioFLAT<\/p><\/div>\n

Finally, two artists from studioFLAT (Kenji Yamauchi and Aoba Ohtsuki) held a workshop in which visitors participated in creating artwork. The participants used colourful paper and pens to colour in the letters of the alphabet W, A, S, E, D, and A, which were provided and prepared by studioFLAT. The paintings and textiles created at studioFLAT are not only sold as works of art in their own right, but works by Yamauchi and Ohtsuki have also been used as product designs for major companies, showing us their side as professional artists. They were very polite (but sometimes strict) in their advice and guidance to the students who participated in the event, and we had a very enjoyable time together.<\/p>\n

\"\"

By Kenji Yamauchi (2020)<\/p><\/div>\n\n\t\t