Departmental Overviews (Biological Sciences): The Mecca of Biological Sciences ― The Graduate and Three Undergraduate Departments of Biological Sciences

-The Department of Biological Sciences-

Professor Ichiro Terashima (Head of the Department of Biological Sciences)

In April 2014, the former Department of Biological Sciences and the Department of Biophysics and Biochemistry combined to form the new Department of Biological Sciences. As a result, the capacities per year for Master’s students and Doctoral students became 84 and 44, respectively, while the total number of faculty members (lecturers, associate professors and professors) grew to around 100. Core faculty members of the new graduate department were also in charge of the three undergraduate departments: the Department of Biological Sciences (which accepts 24 students per year), the Department of Biophysics and Biochemistry (20 students), and the Department Bioinformatics and Systems Biology (12 students).

A brief history

The predecessor to the former Department of Biological Sciences was the Faculty of Science’s Department of Biology, which was established when Tokyo Kaisei School and Tokyo Medical School merged to form the University of Tokyo in 1877.¹　Watson and Crick’s discovery of the double helical structure of DNA in 1953 triggered developments in molecular biology and in the physics/chemistry of biological macromolecules, such as nucleic acids and proteins, both of which caused tremendous changes in biology. Following this, the Graduate and Undergraduate Departments of Biophysics and Biochemistry² were established in 1958. Furthermore, in response to the growing surge in systems biology and bioinformatics³, the Department of Bioinformatics and Systems Biology was established in April 2007, a pioneering attempt in both Japan and the rest of the world. In this way, the Graduate School of Science and Faculty of Science formed new graduate and undergraduate departments related to biology in perfect timing.

When looking at the big picture, barriers in various fields of biology and science have generally been removed through the development of a common molecular biological language and innovations in analytical and informational techniques. The former Department of Biological Sciences and the Department of Biophysics and Biochemistry collaborated from 2002 under a MEXT 21st century center-of-excellence (COE) program titled, “Promotion of Basic Biosciences for the Understanding of Organisms’ Uniqueness” and, from 2007, under another MEXT program called, “Global COE: Integrative Life Science Based on the Study of Biosignaling Mechanisms.” Through these efforts, a framework for promoting new biological sciences was created and this framework was embodied as the merge of these two Departments in April 2014. I would like everyone to cooperate in order for the new Department of Biological Sciences to continue to be a source for breakthroughs in biology.

An Overview of the Undergraduate Departments

Given the explosive developments in molecular biology since the discovery of DNA’s double helical structure and the overall changes in biology due to innovations in information science and analytical techniques, it may be difficult for first- and second-year students to understand the current trends in biology. Moreover, the University of Tokyo has many different departments that are related to biology and you have a variety of available choices. However, I hope you choose one of the three undergraduate biological science courses in the Faculty of Science. To find out more, you can download the pamphlets intended for first- and second-year Komaba Campus students from the homepages of our three departments.

Department of Biological Sciences

Department of Biological Sciences

Undergraduate students on both Hongo and Komaba campuses call the Department of Biological Sciences Rinama, which in Japanese implies that biology is targeting living life phenomena. On one hand, the basic principles of life are common to all organisms; however, biological phenomena are incredibly diverse. We are continuously discovering new species and novel biological phenomena. In biology, there are many issues surrounding both unity and diversity in organisms: how these mechanisms function and why evolution occurs. Through providing education covering a broad spectrum, from the molecular level to the ecosystem level, the Department of Biological Sciences is trying to help students to develop the ability to ask “how” and “why” questions and the power to address these questions. Students studying mainly basic biology undergo long-term off-campus training where they learn phylogenetic taxonomy and ecology at the Koishikawa Botanical Garden, Nikko Botanical Garden, and the Misaki Marine Biological Station, which are affiliated with the Graduate School of Science, as well as at the field sites at Katsuura coast, Nikko, Mount Fuji, and Iriomote Island. Those studying anthropology participate in in-field training such as observing Japanese monkeys in Jigokudani valley in Nagano Prefecture, excavating ruins on Rebun Island in Hokkaido Prefecture, and learning about human anatomy with medical students at the University’s Faculty of Medicine.

The Department is located in the School of Science Bldg. 2, which was finished being built in 1934.

Department of Biophysics and Biochemistry

Department of Biophysics and Biochemistry

The Department of Biophysics and Biochemistry is called seibutsukagakuka in Japanese, which is abbreviated as seika (seibutsukagaku). As the name implies, the Department aims to understand biological phenomena by using biophysical and biochemical principles. As the faculty members possess a strong belief that breakthroughs in biological phenomena can only emerge from foundational research alone, they promote advanced research that elucidates the fundamental principles of biological phenomena. The Department not only describes biological phenomena but also works to thoroughly elucidate the underlying mechanisms at the molecular level.

The “molecule” in molecular biology refers to biological macromolecules such as DNA, RNA and proteins, which are the basic units that comprise living organisms. For the first half of the year, third year students spend their entire afternoons handling molecules to refine their skills and become experts in the field. In the latter half, students engage in practical training to experience cutting-edge research from the molecular level to the individual level using various model organisms including Eschelichia coli, fruit flies, nematodes, zebrafish, and mice. In their fourth year, students join a laboratory of their choice where they conduct their graduation research.

Department of Bioinformatics and Systems Biology

Department of Bioinformatics and Systems Biology

The Department of Bioinformatics and Systems Biology, which is seibutsujouhoukagakuka in Japanese, is often called seijou (seibutsujouhoukagakuka). The Department elucidates biological systems using both life science (wet) and information science (dry) and conducts research on bioinformatics, systems biology, genome biology and omics⁴. In terms of undergraduate education, the Department aims to foster students who will become international leaders with a broad perspective in bioinformatics by providing them with both knowledge and training in experimentation (wet) and information science (dry). In the fourth semester on Komaba Campus, undergraduate students obtain a foundation in information science alongside students from the Department of Information Science and take lectures on wet biological sciences and information science. In the first half of their third year, students undergo practical training in information science and experimentation with the Biophysics and Biochemistry students. In the second half, students are trained for a significant amount of time in bioinformatics. Students are assigned to a laboratory in their fourth year where they conduct their graduation research. Currently, the Department of Bioinformatics and Systems Biology is located in the School of Science Bldg. 3; however, faculty members belonging to the Graduate School of Information Science and Technology and the Graduate School of Frontier Sciences on Kashiwa Campus are also actively involved in educating students. The excellent faculty members are one of the key features of the Department.

Interested in Biology?

For young people who are interested in studying biology, we want to stress that it is important not only to increase your knowledge of biology but also to learn how biology has developed. The latter would help you in developing the ability to raise fundamental questions, and creating the power to explore new frontiers in science. The epitome of fundamental research is being able to independently find new problems, create new methods to clarify them, and create a new stage of research through using new biological materials. I believe that the three undergraduate departments in the Department of Biological Sciences are most suitable for students who truly understand what I have just explained.

Recently, there has been growing pressure to conduct research that is perceived as useful and applicable. On the other hand, many faculty members in the Graduate Department of Biological Sciences are curiosity-driven in their approach to fundamental research. Their approach may seem roundabout at first glance; however, what is most useful for humankind is the truth, which can only be explored in this manner.

Current Research

Many press releases about research findings from the Department of Biological Sciences are posted on the School of Science homepage. Furthermore, the Graduate School of Science’s Botanical Gardens and Misaki Marine Biological Station are also at the forefront of biodiversity studies.⁵ The Graduate Department of Biological Sciences is strengthening cooperation with these affiliated facilities and focusing on various biological sciences.

I would like to take this opportunity to introduce the research of new faculty members belonging to these affiliated facilities. I will also share recent research findings from the Department of Biophysics and Biochemistry as well as the Department of Bioinformatics and Systems Biology.

Discovery of a new obligate pollination mutualism　

Many angiosperms have their pollen carefully transported by animals. Within the relationship between plants and pollinators there is an obligate pollination mutualism in which plants provide the larvae of pollinators with seeds as food in exchange for pollination. Atsushi Kawakita, who is a professor in the Botanical Gardens since April 2018, discovered a new obligate pollination mutualism between about 500 kinds of Phyllanthaceae plants and Epicephala moths, which consume the seeds of the plants. Female Epicephala moths use their proboscises to collect pollens from male flowers and then lay their eggs after rubbing the pollens onto the female flower’s stigmata. Hatched larvae consume only some of the seeds inside the fruit, and the leftover seeds are used for plant reproduction. This mutualism in Phyllanthaceae plants is the third case found about 100 years after the findings of fig–fig wasp and yucca–yucca moth associations; however this association is far more complex. I believe that these kinds of discoveries of surprising biological interactions will undoubtedly continue (Figure 1).

Figure 1: An Epicephala moth depositing pollen onto a female flower of Glochidion Acuminatum, Phyllanthaceae. The moth first collects pollens from male flowers and then, as depicted in the photo, pollinates the pistil of a female flower. Following this, it lays eggs.

Discovery of a new species of basket stars

Project Assistant Professor Masanori Okanishi, who joined the Misaki Marine Biological Station in 2018, examined basket star specimens held in museums around the world and found a new species named Astrodendrum spinulosum⁶, which was discovered in the Pacific coast of Japan. Basket stars are a group of brittle star (Echinodermata) species that have branched arms. However, taxonomic research has not progressed as many of these species live in the deep sea. Okanishi’s research focused on specimens that museums around the world stored for over 100 years, demonstrating the importance of specimens and research facilities such as museums and botanical gardens for natural history research (Figure 2).

Figure 2. An Astrodendrum spinulosum type specimen. This specimen is called the type specimen as it was used to name a new species. The image depicts the specimen laid upwards on a 5.3 cm board. Brittle stars belong to the phylum Echinodermata, which is generally composed of marine species including sea urchin, starfish, sea cucumbers, and sea lilies. Echinodermata animals commonly have bodies with five-point radial symmetry (star) and calcium carbonate skeletons.

Discovery of a new satiating hormone that works on specific nerve cells to suppress feeding

In a collaborative study with Miyazaki University, Yuichi Iino discovered a new neuropeptide from a nematode⁷ called LURY-1. Peptides similar to LURY-1 were discovered in fruit flies and prawns; however, its specific function was unknown. When nematodes were in a satiated state, the pharynx secreted LURY-1 peptides, which acted on specific nerves and were found to regulate behavior related to feeding, such as suppressing feeding, and stimulate egg-laying (Figure 3). This is an intriguing discovery that contributes to elucidating the mechanism of feeding control that is common in all animals, including humans.

Figure 3. LURY-1 peptide satiation response. LURY-1 peptides are secreted from the M1 and M2 pharyngeal neurons during active feeding. The peptides then act on the MC neurons, suppressing food intake in a feedback loop and regulating satiation, which prolongs the life span. It also acts on the RIH neuron and facilitates egg laying through serotonin signaling. Since it indicates the presence of food for egg laying, it is an advantageous response for the survival of offspring.

The Environmental Adaptation of Generalists and Specialists

There are organisms in nature that take “generalist strategies” to adapt to various environments but there are also organisms that take “specialist strategies” for certain environments. Wataru Iwasaki’s research tackled problems such as, “Which strategy is advantageous?” and “Why do organisms that use two different strategies coexist?” Through the use of bioinformatics and systems biology methods, he analyzed the mass sequence data of microbial communities from various environments and the evolution of diverse microbial groups, which revealed that generalists have a higher speciation rates than specialists, have a lower possibility of extinction, and can easily evolve into specialists. The coexistence of generalists and specialists appears to have been realized due to the evolution of generalists (Figure 4). This finding helps us to understand not only the microbial ecosystem but also the general adaptation strategies of organisms.

Figure 4. A diagram illustrating how the balance between coexisting specialists (pink) and generalists (blue) in microbial ecosystems is maintained. Specialists that are specialized to a particular environment (A) evolve into generalists (B), which allows them to move to another environment (C). Generalists quickly evolve (D) and develop a feature that makes it easy for them to easily change into specialists (E). As a result, microbial ecosystems where both specialists and generalists exist are maintained.

In Conclusion

With the integration of the Department of Biological Sciences and Department of Biophysics and Biochemistry into one department, faculty members and students work together to give Master’s and Doctoral research presentations, go on departmental retreats, touch on a broad spectrum of research and widen their perspective, which promotes free and active discussion. Furthermore, we hold departmental sports competitions, which creates an exciting atmosphere that provides a break from academics. In order for young people to continuously be at the cutting-edge front of biology worldwide, the Department has been carefully crafting an open research environment.⁸ The Department of Biological Sciences is aiming to cultivate human resources who will be responsible for fundamental biology and challenge its many forefronts by using various approaches.

For more information, please visit the following:

　 ▶︎ Department of Biological Sciences
　 http://www.bs.s.u-tokyo.ac.jp/biol/
　 ▶︎ Department of Biophysics and Biochemistry
　 http://www.bs.s.u-tokyo.ac.jp/biochem/
　 ▶︎ Department of Bioinformatics and Systems Biology
　 http://www.bs.s.u-tokyo.ac.jp/bioinfo/
　 ▶︎ Graduate Department of Biological Sciences
　 http://www.bs.s.u-tokyo.ac.jp/english/
　

Notes:

¹The University of Tokyo was first established in Hitotsubashi and then moved to Hongo Campus in 1881. In 1886, the Department of Biology was divided into the Department of Zoology and the Department of Botany. The Department of Botany then moved to Koishikawa Botanical Gardens in 1897. In 1934, the Science Bldg. 2 was completed and the Department of Botany returned to Hongo Campus. In 1939, the Department of Anthropology was established. After World War II, there were three undergraduate and graduate departments in zoology, botany, and anthropology that independently conducted research and education. In 1995, these three departments and a newly established evolutionary biology course were integrated and became the Department of Biological Sciences.
²An academic field that regards life as a system and elucidates the relationships between individual elements such as genes and proteins and the dynamics of biological phenomena as a whole by using mathematical models.
³An academic field that captures life as information and develops information science methods in order to analyze big data and find the laws and regularities behind biological phenomena.
⁴An academic field that aims to elucidate the relationships between information and functions through capturing biological phenomena from a common molecular group such as genome, RNA transcriptome, proteome, metabolome, and analyzing their mutual relationships.
⁵The Misaki Marine Biological Station in Kanagawa Prefecture was established in 1886. The Koishikawa Botanical Garden was established the same year as the University of Tokyo in 1877. The predecessor to the Botanical Gardens was the Koishikawa Medicinal Herb Garden, which has history dating back to the Tokugawa era. In 1902, the Nikko Botanical Garden was also established as a part of the Botanical Gardens.
⁶The name is derived from Astro (stars) and dendrum (twigs), and spinulosum (small thorns). The specimens Okanishi examined include those gathered by Emperor Showa.
⁷The scientific name for nematodes is Caenorhabditis elegans. They are used as a multicellular model organism as its body only has about 1000 cells and 302 neurons. The Iino Laboratory is conducting advanced research in the memory and behavior of nematodes as well as developing new research methods through tracking their entire nervous system.
⁸Presently, the Graduate Department of Biological Sciences is located in School of Science Bldg. 1, 2, 3, and 7. Building 7 is next to Bldg. 1; however, Bldg. 2 is located further south of Akamon Gate on Hongo Campus, about 550 m from Bldg. 1. Bldg. 3 is located on Asano Campus, which is North-East of Yayoi Gate and 430 m from Bldg. 1. It is a 12 to 13-minute walk one-way from Bldg. 2 to the seminar in Building 3. (By the way, the Koishikawa Botanical Gardens is 800 m and a 20-minute walk from Bldg. 1.) It is crucial for laboratories to be in close proximity to each other in order to increase the effect of education as well as enable active discussion and collaborative research. Our hope is that we can have true integration through the construction of a new building in the very near future.
　

― This article is from the 2018 "Departmental Overviews in the School of Science" series in The Rigakubu News ―

Translated by Kristina Awatsu, Office of Communication

― Office of Communication ―