Integrative Bioscience Education Program

SubjectCode

Subject Credit Content of subject

10PIB001Introduction to IntegrativeBioscience

１

First, the educational program for IntegrativeBioscience is introduced. Then, driving forces for rapiddevelopment of biology are reviewed from a historicalpoint of view, and the features of contemporary lifescience are overviewed. Based on these reviews whatthe Integrative bioscience is and why it is necessaryare discussed. Particularly, it is emphasized that alarge volume of information on sequences andstructures of genome, RNA, proteins, sugars,metabolites etc. and that of spacio-temporalexpression of these molecules are integrated tounderstand their meaning at a cell, tissue, organ ororganism level and to unravel the mechanisms of highorder biological functions, diseases, environmentalresponses etc.

Prof. Makoto Tominaga

Prof. Ryota Iino

Prof. Koichi Kato

Assoc.Prof.KatsuyukiNishimura

Prof. Shigetoshi Aono

Assoc. Prof. Yuji Furutani

Assoc. Prof. Nobuyasu Koga

10SLS011Training Course forBioinformatics

１

The following objectives are attained through leturesand hands-on tutorials.1. To understand basic principles in biological sequenceanalyses and learn the practical skills.2. To understand the theoretical background oftranscriptome and proteome data analysis, and learnthe practical skills to analyse these data.3. To learn current topics and future directions ofgenomics.

Assoc.Prof.

Shuji Shigenobu

Assoc.Prof. Kazuyoshi Murata

Assoc.Prof. Shigenori Nonaka

1. Basic and applications of solution and solid-stateNMR spectroscopy in structural analyses ofbiomolecules2. Basic of microscopy, single-molecule imaging, opticaltweezers, magnetic tweezers, super resolutionmicroscopy, high-speed atomic force microscopy3. Functional mechanisms of biomacromoleculesincluding glycoproteins, membrane proteins, andmultidomain proteins, working mechanisms of motorproteins, molecular basis of protein assembly

１

We are now enjoying various imaging techniques in thecutting edge of biological and medical sciences. Thewell known from old is microscopic techniques andnowadays MRI, PET and MEG are popular imaging tools.Imaging science is a novel discipline trying to integratethe old and the new. It consists of three categories,hardware tools to generate primary data, software toolsto digitally process the primary data and imaginganalysis to quantitatively analyze imaging digital data. Inthis lecture, 3D imaging and quantitative image analysisare in a particular focus. The former includes thetheoretical background of 3D imaging and its practicalapplications with electron and light microscopy. Thelatter includes a novel quantitative image analysisbased on various numerical algorithms.

10SLS014 Imaging Science

20DFM001Functional BiomolecularScience

２

The molecular mechanisms of various biologicalprocesses will be lectured in this course. Especially,the molecular mechanisms of the following topics willbe provided: Structure and function of proteins, DNAreplication, transcription and translation of DNA,cellular homeostasis, biological energy conversion suchas respiration and photosynthesis, sensory receptors,bioelectronics in a neuron, and some recent researchtopics.

20DSM004Structural BiomolecularScience

２

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SubjectCode

Subject Credit Content of subject

10PIB002 Integrative Bioscience Series １

To learn biological processes at various levels, coveringmolecular, cellular and individual processes, withbroader perspective in an integrative manner, sevendepartments (Departments of Structural MolecularScience, Functional Molecular Science, Basic Biology,Physiological Sciences, Genetics, Evolutional Studies ofBiosystems, and Statistical Science), which participatein the Integrative Bioscience Education Program, offera series of 7 lectures in a manner understandabler forevery student.

Prof. Makoto Tominaga

Prof. Shinji Saito

Assoc.Prof. Hisashi Okumura

10DESb05Integrative EvolutionaryStudies

２

Biosystems on the earth can be classified into systemswith different levels of complexity, from a cell tosociety. This course is to discuss evolution of suchsystems from the viewpoints of "elements (members)in each system", " interaction between elements" and"theory to describe this interaction".

Prof. Yoko Satta

Prof. Hiroyuki Araki

Assoc.Prof. Nobuyuki Shiina

Basic principles of statistics and informatics to dealwith big data such as genome, transcriptome、proteome, metabolome etc will be described. Thissubject consists of the following 4 lectures (0.5 creditsper lecture).　Credits will be given when studentscomplete two of the following lectures.

Prof. Yoko Satta

Prof. Kosaku Okubo

Prof. Masanori Arita

Assoc Prof. Kazuho Ikeo

Prof. Isao Katsura

Prof. Hiroyuki Araki

Assoc.Prof. Tsuyoshi Koide

Prof. Ituro InoueBasic biostatistics: A part of the lecture of Dept ofEvolutionary Studies of Biosystems "Biostatistics". Lecturer Hisashi Ohtsuki

Biological Information Processing:　A part of the lectureof Dept of Informatics "Introduction to Algorithms" Prof. Takeaki Uno

10PIB004 Origin of Life １

How the life originated on earth and evolved will bediscussed by the broad perspective of organicchemistry, molecular biology, extremorphile biology andastrobiology.

Prof. Makoto Tominaga

Prof. Shuji Akiyama

Prof. Koichi Kato

Prof. Ryota Iino

Assoc. Prof. Yuji Furutani

10PIB003 GeneticsCorresponds to the lecture of Dept. of Genetics of"Genetics".

Bioinformatics １

eBioscience PrimerCorresponds to the lecture of Dept. of Genetics of"eBioscience Primer".

Fundamentals of BiomolecularScience

２

Core aspects of biophysical chemistry will beoverviewed with the life-science student in mind. Thiscourse aims at cultivating the fundamentals necessaryto complete the advanced courses of StructuralBiomolecular Science and of Functional BiomolecularScience. The lectures will be given with life-scienceexamples using a textbook covering the lows ofthermodynamics, biological standard state, chemicalequilibrium and its temperature dependence, vibrationalspectroscopy, and nuclear magnetic resonance.

Basic theories and computational methods formolecular simulations for biomoleculs will be introduced.For example, basic and various advanced methodologiesfor molecular simulations as well as fundamentals ofanalytical mechanics and statistical mechanics will belectured.

Introduction to BiomolecularSimulation

10SPS014 １

２

Basic features of molecular and cellular biology will belectured and discussed. These include regulation oftranscription and translation, protein structure andfunction, post-translational modification, structure anddynamics of chromosome, structure and dynamics ofcell, organelles and cytoskeleton, metabolism, proteintraffic, signal transduction and cell imaging.

10SLS002 Molecular and Cellular Biology

10SPS018

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SubjectCode

Subject Credit Content of subject

10PIB005 Mechano-systems Biology １

Mechanical forces in environments or cells/tissues playimportant roles in various complex life processes suchas embryogenesis, brain/neural network formation andfunction, circulatory system, cognition and memory.The lectures will discuss how cells sense mechanicalsignals and respond to them (mechanotransduction) invarious biological systems and also the application ofthe mechanics for human benefit.

Prof. Makoto Tominaga

10PIB006 Quantitative Biology 1

Recent accumulation of big data from imaging andnext-generation sequencing demands data processingwith various statistical methods. The lectures willdescribe and discuss new quantitative methodology tounderstand the dynamic life processes.

Prof. Akatsuki Kimura

10PIB00７ Practical Course forIntegrative Bioscience

1

This course inducts the hot research technique forintegrative bioscience through the lecture and actualpractice.

Prof. Makoto Tominaga

Prof. Jun Kitano

Prof. Naruya Saitou

Prof. Hiroshi Akashi

Assis.Prof. Asano Ishikawa

Assis.Prof. Masafumi Nozawa

Assoc.Prof. Kazuho Ikeo

Prof.Shin-yaMiyagishima

Prof. Tetsuji Kakutani

Prof. Yumiko Saga

Prof. Takuji Iwasato

Prof. Toshihiko Siroishi

Prof. Hitoshi Sawa

Prof. Tatsumi Hirata

Assoc.Prof. Tsuyoshi Koide

Assoc.Prof. Noriyoshi Sakai

Assoc.Prof. Ken-ichi Nonomura

Various developmental events, such as cell fatedetermination, cell differentiation, morphogenesis andanimal behavior will be analyzed in light of geneexpression, cell-cell interaction, intracellular signalingand evolution. Classes will be run by critical reading ofthe primary literature and discussion.

1Developmental Biology Ⅲ

20DGE016 Evolutionary Genomics

After introduction of basic knowledge on various fieldsof evolutionary and population genetics, such asadaptive evolution, neutral evolution, speciation,symbiosis evolution, and epigenetics evolution, wediscuss what kinds of new questions will be possible toasnswer by employing emerging genomic technologies.

1

Developmental Biology Ⅳ

Developmental Biology II20DGE001

20DGE002

20DGE003

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