KEIO SFC JOURNAL Vol.15 No.1 Advanced Bioscience Studies at SFC: Our Grand Challenges to Save the World

Shonan Fujisawa Campus and Tsuruoka Town Campus (Institute for Advanced Biosciences) of Keio University are the pioneers of "Integrative Systems Biology". This new paradigm of life science is to understand and predict biological processes computationally by integrating large-scale biological datasets obtained by high-throughput analytical technologies. The history of our innovative research is described.

Here, 20-years-pioneering-history of bioinformatics at Keio University Shonan Fujisawa Campus (SFC) is briefly reviewed, mainly focusing on two topics: (1) what are the molecular mechanisms that allow recognition of the boundaries of the genomes (boundaries between untranscribed and transcribed regions of the genome, etc)? (2) using computers, how can we eff iciently analyze genome-wide molecular interaction network to discover novel biological knowledge? This review may also give readers some ideas of current issues and possible future directions of the field.

The ultimate goal of the E-Cell Project, founded in 1995, is to construct a whole cell model. In this review, we describe how we launched the E-Cell Project, developed E-Cell System Version 1 to 3, constructed various cell models including the hypothetical self-sustaining cell on the E-Cell System, and developed E-Cell System Version 4 to enable integrated simulation of various cellular processes including metabolism, gene expression, and signal transductions.

The measurement of the level of all intracellular metabolites is rapidly becoming important for gaining insight into functional biology. Recently we have developed a new method for the analysis of most of all charged metabolites based on capillary electrophoresis mass spectrometry (CE-MS). In this marriage of techniques, CE confers rapid analysis and efficient resolution, and MS provides high selectivity and sensitivity. This method is powerful and is readily applied to medical and food samples and new findings by this approach are discussed.

The recent systems biology efforts are revealing complexities beyond traditional static causal relationship understanding. Our research has focused on dynamic cellular behaviors to uncover novel network and global response properties. We investigated instructive cell signaling and high-throughput transcriptome-wide behaviors of immune, cancer, and embryonic development cells. Our data reveal that cultured populations display deterministic signaling that can be modeled using linear response rules. Adopting the rules, we have computationally predicted and verified experimentally novel signaling features and key targets for controlling proinflammatory and cancer responses. In addition, our transcriptome-wide statistical analyses of macrophage immune response and single cell embryonic developmental process, from oocyte to blastocysts cell stage differentiation, revealed interesting global patterns where even lowly expressed genes play a role.

Bile acids (BAs), a group of structurally diverse molecules that are primarily synthesized in the liver from cholesterol, are the chief components of bile. Over 10 years, the field of BA research has undergone a considerable evolution. Besides their well-established roles in dietary lipid absorption and cholesterol homeostasis, it has recently been clarified that BA are also biologically signaling molecules. BAs are ligands for the G-protein-coupled receptor TGR5, and activate nuclear receptors such as farnesoid X receptor. Through activation of these diverse signaling pathways, BAs can regulate their own enterohepatic circulation, but also triglyceride, energy, and glucose homeostasis. Thus, BA-controlled signaling pathways are promising novel drug targets to treat common metabolic diseases, such as NAFLD, obesity, type II diabetes, hyperlipidemia, and atherosclerosis.

Currently in Japan, increase of the social security cost due to aging has become a big problem. On the other hand, it turned to be a deficit financing of the corporate health insurance unions. Although these factors have led to an advocate of the necessity for the health and productivity management, it has not been well accepted by corporations. However some advanced companies have started to introduce the health and productivity management. In order to promote the health and productivity management, 1) a program for all workers, 2) an aggressive investment for the human capital, 3) an individualized program, 4) visualization of the health condition, and 5) a support by the Organization are essential.

Ecomimetics is a novel strategy to mimic complex and sophisticated ecological systems, especially microbial ecosystems, toward application of the regulatory mechanisms and/or laws of the systems in the fields of life sciences and green chemistry. The human gut is colonized by a wide variety of microorganisms, known as commensal microbiota. The microorganisms create a highly complex microbial community and also affect host physiological homeostasis through hostmicrobial crosstalk in the gut. Here, we introduce how the commensal microbiota contributes to promotion of our health and also causes various human diseases, and demonstrate mathematical modeling of the host-microbial interaction toward the comprehensive understanding of the gut ecosystem and creation of ecomimetics.

The increases in medical expenses in an aging society with a declining birthrate are serious problems, especially in a country like Japan. In order to reduce this burden on society, it is important to increase "the health expectancy". Namely, people should maintain good health via healthy dietary habits. Currently, a new labeling system for functional food in Japan has been implemented. Metabolomics, one of the multiple comprehensive omics methodologies, is a technique used to examine multiple compound targets in food samples. Not only using metabolomics but also incorporating other fields of -omics studies in the nutrition sciences; Nutriomics is an important approach to achieve a healthy society. Hereby, we introduce various applications of food metabolomics and nutriomics in helping people attain a long and healthy life.

This article introduces two of our community-based research projects in Tsuruoka region. One is "Karada-kan" launched in 2007 to provide cancer and other health information to the community dwellers. The other is "Tsuruoka Metabolomic Cohort Study" started in 2012 to follow up 10,000 enrolled residents over 25 years. By collaborating with other actors in the region, such as public sectors and healthcare providers, we have been enhancing community health and citizens' empowerment. This article indicates the way of promoting healthy behavioral changes and social participation of the general public, patients and their families through our activities.

Since the end of the last century, the complete genomic sequences of many organisms have been determined. The impact of these genome projects on the various fields of science has been enormous. It could be said that we now have in our hands "the blueprints of life" for these organisms. At the beginning of the 21st century, it became apparent that large numbers of noncoding RNAs are, unexpectedly, encoded in these genomes. These RNAs are not translated into proteins but act as riboregulators, and have had another huge impact on the life sciences. More recently still, a new tide of research into the classical noncoding RNAs, such as the transfer RNAs (tRNAs), has arrived.

Nine years of experience at SFC Keio Advanced Biosciences program has provided knowledge and diversified views toward understanding biological processes of the modern life. My current scientif ic focus tackles the origin, distribution and future of life in the universe, which are known as a three fundamental questions in Astrobiology. The multidisciplinary approaches including biology, geology, chemistry, physics, earth science, astronomy, etc., are the keys to decipher such big questions. This invited article will be a good introduction to improve awareness and commitment of young students and researchers towards Astrobiology.

Oil-rich algae are potentially promising as a next-generation biofuel feedstock. These algae have high biomass productivity par unit culture area, and accumulate a large amount of neutral lipids under stress conditions such as nutrient deficiency. From a perspective of practical applications, it is important to increase production stability, to decrease cost, and to realize sustainable utilization of culture area, wastewater, and fertilizer. We describe parts of our approaches; reuse of fallow paddy f ields for algal cultivation and large-scale metabolic analyses for metabolic engineering.

Since tardigrades exhibit high tolerance to environmental stresses, the animals have been expected as a potential model organism for understanding mechanisms underlying extremotolerance of multicellular organisms. In order to develop tardigrades as a model animal, we established a culture system for the tardigrade Ramazzottius varieornatus and a standard strain YOKOZUNA-1 from single egg of this species. R. varieornatus showed high tolerance to desiccation and ionizing radiation. The estimated number of genes in R. varieornatus is approximately 19,000 genes based on our whole genome analysis. Furthermore, our metabolomic analysis detected significant differences in amounts of several low-molecular-weight metabolites between hydrated and anhydrobiotic states in R. varieornatus, while there are only a few differentially expressed genes between the both states in this species.

In this study, we would particularly like to mention of our recent findings about the body plan in vertebrates. First topic is about the key molecule of the sorting mechanism of notochord, which is the most indispensable tissue for vertebrates. Second topic is about the induction system of organizer, which is appeared at the dorsal lip site in early gastrula embryo and functions as a central player of early embryogenesis of vertebrates. Last topic is about the cardiac formation using pluripotent stem cells with utilizable cardiac fibroblast, which is artificially developed in our recent assays.

Microbes before recognized by Pasteur and Koch in late 19th century were mysterious, though abundant around our human life. Today, microbes are used to provide various materials from food to bioethanol regardless of their extreme variations. This paper describes our continuous research activities focused on socalled model microbes such as E. coli, B. subtilis, and Bakers yeast. It should be addressed that our outstanding achievements started from the date of IAB (Institute for Advanced Biosciences) establishment in 2001 have been globally influential.

The Institute for Advanced Biosciences of Keio University established in 2001 and Tsuruoka-city of Yamagata prefecture yields so many scientif ic outcomes by its advanced technologies and facilities. It continues to develop basic and developed sciences based on bioinformatics and omics technologies, providing an outstanding research facilities and bio-venture companies. Here, we introduce two bio-venture companies established by the institute, Human Metabolome Technologies, Inc. and Spiber, Inc.

Young researchers, including postdoctoral researchers, who play an important role in the creation of innovation in science and technology, face signif icant diff iculties in finding suitable employment due to term-limited appointment systems in universities and public research institutes. Conversely, the overall recent decline in students who are enrolled in Masters and PhD programs, whose graduates are considered to be the candidates for young researchers, suggests that fewer young people are interested in careers in academia research. Based on these trends, this report discusses suitable research environments and support systems, which would encourage young people to obtain doctoral degrees thereby promoting innovations in science and technology.

During last decade, number of research misconduct in life science, such as STAP cell case, has been increasing in Japan. Although the rate of incidence of misconduct in life science is less than some fields, the number of misconduct is highest. I discuss here the reason why so many misconduct have been happened in life science (includes medical science) resent years. I consider that the factors affecting misconduct in life science are readiness of image manipulation, excessive competitiveness for research funds and tenure posts in life science, and side-effect of impact factor on evaluation of researchers. I conclude here that the structural reform of science policy and custom of researchers must be required to reduce misconduct.

Antibodies are important protein of the immune system and expected as a new medical molecule. We developed highly sensitive antibody detecting method by combining phage display screening method with next-generation sequencing. We newly detected two antibody clusters, and those were not detected with our existing methods. With our existing methods, we gained antibodies with 9 % library content rate after the panning process, however we used our new method and found two new antibody clusters only contains 0.2 % and 1.1 % of library content rate. All above facts support this method have highly sensitive antibody detecting functions than existing methods.

Lacrimal fluids are important in protecting the eyes from environmental factors and also possess antimicrobial abilities. Although human tear fluid metabolites have been reported, the relationships between these metabolites and eye diseases have yet to be elucidated. In addition, the microbial composition of human tear fluids has not been investigated yet, even though numerous human microbiome analyses of various body sites have been reported. Therefore, microbiome and metabolome analyses of human tear fluids from healthy subjects and atopic keratoconjunctivitis (AKC) patients were conducted. The current study suggested that lactic acid bacteria in tear fluids might have a potential to prevent pathogenesis of AKC, whereas o-acetylcarnitine reduction and urea increment might be involved in AKC pathogenesis.

While the model organism Escherichia coli (E. coli) is one of the best characterized organisms, the function of only 30-40% of E.coli enzymes has been experimentally validated. Toward this objective, we screened in vitro the purified YhhY protein, (a predicted acetyl transferase) for activity on amino acids. Using Acetyl-CoA as donor, we detected acetylated products mainly with methionine, histidine and phenylalanine. Next, to confirm its activity in vivo, we performed metabolome analysis of E. coli overexpressing the yhhY gene using capillary electrophoresis time-of-flight mass spectrometry. Upon overexpression the same three acetylated-amino acids accumulated in the cell supporting the in vitro results. In this work we therefore revealed that the YhhY protein could display acetylating activity on different amino acids both in vitro and in vivo.

Analyses of gut luminal metabolites are important in revealing the relationships between metabolism of intestinal microbiota and host. However, current extraction methods of fecal metabolites are not standardized. In order to understand the impact of varying extraction methods on fecal metabolite composition, we compared metabolome profiles that were obtained from methods that are different in fraction, solvent and with or without bacterial cell disruption.From our results, a total of 141 metabolites was detected. Concentrations of 29 metabolites and 7 metabolites were significantly altered by using different solvents and treatment cell disruption, respectively. Since our results suggested that metabolome profiles can be altered by varying extraction methods, it is important to select an extraction method that is suitable for the purpose.

The fieldwork over the past two years in a community -- Hamaoka Nuclear Power Plant in Shizuoka Prefecture -- in the settings similar to the Fukushima nuclear power plant site helps uncover that the community residents lack viable alternatives to the way they have customarily led their lives while facing an array of risks related to the operation of the nuclear power plant: employment opportunities, rise and decline of service sectors and conditions of social infrastructure which had been financed by the nuclear facility-related subsidies. More importantly, this array of risks is as threatening to the residents as the threat of a nuclear power plant failure, except the former is a daily threat whereas the latter still presents itself as "probable." The paper examines the difficulty attendant upon the life of the residents in a nuclear power plant site in the form of human insecurities (vulnerabilities) existing before and after the Fukushima disaster.