2021 Synthetic Biology

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Academic unit or major
Undergraduate major in Life Science and Technology
Instructor(s)
Matsuura Tomoaki  Fujishima Kosuke  Aizawa Yasunori 
Course component(s)
Lecture    (ZOOM)
Day/Period(Room No.)
Tue1-2(S611)  Fri1-2(S611)  
Group
-
Course number
LST.A356
Credits
2
Academic year
2021
Offered quarter
2Q
Syllabus updated
2021/5/20
Lecture notes updated
-
Language used
Japanese
Access Index

Course description and aims

With the recent development of biotechnology, it has become possible to artificially design and engineer living systems. Research in this field is known as synthetic biology. In this lecture, we will learn the basic techniques in the field of synthetic biology, how they have led to the understanding of living systems, and how they are being implemented in society.

Student learning outcomes

Students will be able to discuss the basic concepts, fundamental technologies, and their importance in the field of synthetic biology. In other words, the student will be able to discuss the importance of creating biological systems that can be understood by creating them and that contribute to social implementation, using actual examples.

Keywords

Genome editing technology, genome synthesis, unnatural amino acids and nucleic acids, artificial cells, evolutionary engineering, biotechnology

Competencies that will be developed

Specialist skills Intercultural skills Communication skills Critical thinking skills Practical and/or problem-solving skills

Class flow

The lecture will be given by three faculty members and will be delivered live via Zoom. Students are expected to download the materials necessary for the lecture from OCW before attending the lecture.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Synthetic biology: the study of synthesizing organisms -Overview of the field of synthetic biology -Relevance to conventional disciplines -Introduction of some reference books -Synthetic biology from an ethical point of view -How to proceed and outline of the lecture To be able to give an overview of synthetic biology.
Class 2 DNA engineering -Diversity of genome structures (plasmids, chromosomes) -DNA engineering in biodesign process -Gene parts, genetic recombination, gene synthesis -Genome modification, genome synthesis, genome construction Explain how genes and genomes can be used for engineering based on our understanding of their biology. (Chap 3)
Class 3 Heterologous gene transfer for cell functionalization -Production of substances by gene transfer to cells -BGC (Biosynthetic gene cluster) -Intracellular gene transfer methods -Biosynthesis of carthenoids and antibiotics -Functional human cells for cancer cell therapy Explain techniques for introducing genes or gene clusters from different species into cells to give them new functions. (Chap 5, 6)
Class 4 Host genome modification for cellular functionalization -Design of metabolic pathways and evolution of in-laboratory applications -Identification of useful microorganisms -Chemical synthesis vs. biosynthesis (acrylamide synthesis) -Examples of improved metabolic pathways (discovery and improvement of amino acid biosynthetic bacteria) -Use of artificial genome yeast -Minimal genome Explain the technology to add new functions to cells by utilizing special microorganisms explored and identified from nature, or by modifying or synthesizing microorganisms that are already in general use. (Chap 5, 6)
Class 5 Synthetic biology to modify metabolic pathways -Review of the second session on genome engineering -Examples of artificial metabolic pathways that modify metabolic pathways -Explanation of applications in industrial society -Artificial microorganisms and ethical issues Explain methods for modifying metabolic pathways in synthetic biology. (Chap 7)
Class 6 Manipulating cells through transcriptional regulation -Introduction to the complexity of transcription -Understand the control method -Introduction of application examples To be able to explain the methods to control transcription and their applications. (Chap 1)
Class 7 Working RNA and DNA Molecules -Introduction to the essential role of DNA and RNA molecules -Introduction of DNA and RNA aptamers -Introduction of riboswitches -RNA and DNA work not only as information molecules but also as functional molecules Students will be able to explain that RNA and DNA fragments control organisms. (Chap 2)
Class 8 Creating artificial life and artificial cells -Introduction to bottom-up biology -What is an artificial cell? -What can be done and understood by artificial cells -Actual examples of social implementation To be able to give an overview of research into the creation of artificial life and cells from parts. (Chap 10)
Class 9 Creating Proteins with Unnatural Amino Acids -Introduction of non-natural amino acids and non-natural nucleic acids -Significance of using non-natural amino acids and non-natural nucleic acids -Preparation of unnatural monomer molecules -Polymerization of unnatural monomer molecules -Examples of social implementation Explain that non-natural amino acids can also be used. (Chap 4)
Class 10 Designing proteins with molecular modeling -Explanation of molecular modeling in general -Structure prediction using machine learning such as Alphafold is also introduced. -Introduce examples of experimental validation of designed proteins To be able to explain how molecules can be designed using computers.
Class 11 Designing proteins with evolutionary molecular engineering -Overview of evolutionary molecular engineering -Comparison of methods and introduction of application examples -Introduction of research related to the origin of life To be able to explain what evolutionary molecular engineering is. (Chap 8)
Class 12 iGEM: A global synthetic biology competition for students -Background to the establishment of iGEM and details of the event -Details of the competition -Results of representative teams and social implementation -Introduction of Tokyo Tech team To be able to explain the activities related to iGEM at Tokyo Tech. (Chap 9, 14)
Class 13 What is Life? 〜Beyond Biology and Ethics A discussion of the differences and similarities between the approaches of the natural sciences and the humanities to the question "What is life? Discussion on the differences and similarities between the approaches of natural sciences and humanities to the question "What is life? We will discuss the differences and similarities between the approaches of the natural sciences and the humanities to the question "What is life? To be able to explain the two aspects of synthetic biology: convenience and danger.
Class 14 Future of synthetic biology + final exam The written examination will be conducted in person.

Out-of-Class Study Time (Preparation and Review)

To enhance effective learning, students are encouraged to spend approximately 100 minutes preparing for class and another 100 minutes reviewing class content afterwards (including assignments) for each class.
They should do so by referring to textbooks and other course material.

Textbook(s)

Handouts

Reference books, course materials, etc.

Synthetic Biology, (Springer International Publishing, Ediotrs, Anton Glieder, Christian P. Kubicek , Diethard Mattanovich , Birgit Wiltschi and Michael Sauer)

Assessment criteria and methods

Grades are based on assignments and final examinations.

Related courses

  • LST.A203 : Biochemistry I
  • LST.A218 : Biochemistry II
  • LST.A208 : Molecular Biology I
  • LST.A213 : Molecular Biology II
  • LST.A248 : Molecular Genetics

Prerequisites (i.e., required knowledge, skills, courses, etc.)

A basic knowledge of biology is desirable, but not required.

Contact information (e-mail and phone)    Notice : Please replace from "[at]" to "@"(half-width character).

Matsuura(matsuura_tomoaki[at]elsi.jp)
Aizawa(yaizawa[at]bio.titech.ac.jp)
Fujishima(fuji[at]elsi.jp)

Office hours

Email the faculty in advance.

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