IT IS NOW CLEAR THAT LOTS OF NON-CODING RNAS IN THE GENOME ARE FUNCTIONAL AND VERY POWERFUL IN REGULATING GENE ACTIVITIES AND DEVELOPMENTAL PROCESS. DEPENDS ON THE BACKGROUND OF THE STUDENTS, AROUND 1/3 OF THE LECTURES WILL BE GIVEN BY THE INSTRUCTOR FOR INTRODUCING BASIC CONCEPTS IN NON-CODING RNA REGULATED GENE SILENCING, INCLUDING THE POST-TRANSCRIPTIONAL REGULATION BY SIRNA, MICRORNA AND REPRODUCTIVE ORGAN SPECIFIC PIRNAS. THESE WILL COVER THE PHYSIOLOGICAL PROCESS INCLUDING GENOMIC IMPRINTING, SEX CHROMOSOME COMPENSATION, SILENCING OF ENDOGENOUS RETROTRANSPOSONS AND STEM CELL BIOLOGY. IN ADDITION, THE INVOLVEMENT OF NON-CODING RNA RELATED REGULATORY MECHANISMS IN CARCINOGENESIS WILL BE DISCUSSED. FOR THE REST OF THE CLASSES, STUDENTS WILL BE ASSIGNED THE MOST UPDATED ORIGINAL RESEARCH PAPERS AND CONFERENCE ARTICLES AS WELL AS THE MILESTONE PUBLICATIONS. THEY WILL BE RANDOMLY DIVIDED INTO 2 GROUPS FOR EACH ASSIGNMENT. ONE GROUP WILL BE PRESENTING THE ARTICLES AND STUDENTS IN THE OTHER GROUP ARE EXPECTED TO CHALLENGE THE PAPERS FROM THE EXPERIMENTAL DESIGN, THE METHODOLOGY TO THE INTERPRETATION OF THE DATA. STUDENTS IN THE 1ST GROUP SHOULD DEFEND FOR THE PAPERS AS IF IT’S THEIR MANUSCRIPT. STUDENTS FROM THE 2ND GROUP SHOULD ALSO PROVIDE CONSTRUCTIVE ADVICE AS HOW TO IMPROVE THE MANUSCRIPT SO THAT IT CAN BE PUBLISHED IN A HIGHER IMPACT JOURNAL. College of Bio-Resources & Agriculture PREFERABLY HAVING STUDIED ONE OF THE FOLLOWING SUBJECTS: (INTRODUCTORY) EPIGENETICS, SPECIAL TOPICS IN REPROGRAMMING, GENETICS AND EPIGENETICS IN GERM AND STEM CELLS Friday 34 Biot8014 2

COURSE DESCRIPTION: THIS HALF-YEAR GRADUATE COURSE AIMS TO INTRODUCE BASIC GENE SILENCING CONCEPTS AND RESEARCH TECHNIQUES AVAILABLE TO ADDRESS GENE SILENCING QUESTIONS IN PLANT AS WELL AS OTHER ORGANISMS. STUDENTS ARE EXPECTED TO DEVELOP THE ABILITY TO CRITICALLY EVALUATE AND INTERPRET PUBLISHED RESEARCH ARTICLES. THEY WILL ALSO LEARN TO EXTRACT INFORMATION FROM INTERNATIONAL CONFERENCES BY LISTENING TO EXPERTS OF EACH FIELD INTRODUCING THEIR RESEARCH. OUTLINE: 1. INTRODUCTION – OVERVIEW 2. SENSE CO-SUPPRESSION IN PLANT 3. TRANSGENE CO-SUPPRESSION IN ANIMALS 4. PLANT VIRUS RESISTANCE VS. CO-SUPPRESSION 5. TRANSCRIPTIONAL GENE SILENCING (TGS) 6. POST-TRANSCRIPTIONAL GENE SILENCING (PTGS) 7. VIRUS-INDUCE GENE SILENCING (VIGS) 8. SILENCING SIGNAL TRANSPORTATION 9. SMALL RNA 10. SIRNA PATHWAY 11. MIRNA PATHWAY 12. FUNCTION OF DICER 13. FUNCTION OF RNA-INDUCE SILENCING COMPLEX (RISC) 14. FUNCTIONS OF DICER-LIKE PROTEINS (DCLS) IN PLANT 15. DCL1 VS. MIRNA BIOGENESIS 16. FUNCTION OF DCL2 AND NAT-SIRNA 17. FUNCTION OF DCL3 AND DNA METHYLATION 18. FUNCTION OF DCL4 AND TRANS-SIRNA 19. ARGONATURE FAMILY 20. SUPPRESSION OF GENE SILENCING 21. RNAI TECHNOLOGY 22. MIRNA TECHNOLOGY College of Bio-Resources & Agriculture Monday 234 Biot8016 3

Contents Microbiological System Microbial cultivation Microbial engineering Microbial molecular biology Microbial biotechnology 　Current status of bio-industry College of Bio-Resources & Agriculture 需先修過 應用微生物與生物技術 或 微生物_酵工程 CHENG, KUAN-CHEN Friday 678 Biot8023 3

PROTEIN SECRETION SYSTEMS PLAY CENTRAL ROLES IN THE EXPORT OR IMPORT OF MACROMOLECULES IN BOTH PROKARYOTIC AND EUKARYOTIC CELLS. THIS COURSE WILL INTRODUCE HOW PROTEINS ARE TRANSLOCATED ACROSS MEMBRANES AND SECRETED OUTSIDE OF BACTERIAL CELLS OR EVEN TRANSPORTED INTO THE HOSE CELLS. THE BIOLOGICAL FUNCTIONS OF SECRETION SYSTEMS WILL BE ALSO DISCUSSED WITH FOCUS ON PATHOGENIC BACTERIA. THE COURSE WILL COVER BOTH LECTURES AND PAPER DISCUSSION TO CRITICALLY REVIEW THE SELECTED RESEARCH ARTICLES. College of Bio-Resources & Agriculture Erh Min Lai Tuesday 34 PPM5066 2

1. Course Introduction 2. The Structure and the Properties of Biological Membrane 3. Membrane proteins (I) 4. Membrane proteins (II) 5. Moving Proteins into Membranes 6. Endocytosis of Membrane Proteins 7. Mechanisms for Protein Translocation (I) 8. Mechanisms for Protein Translocation (II) 9. Mid-term week (suspend) 10. Guest lecture 11. Isolation and Visualization of Membrane Proteins (I) 12. Isolation and Visualization of Membrane Proteins (II) 13. Recent Breakthrough Technologies for Studying Membrane Protein (including literature discussion) 14. Experimental Designs for Membrane Proteins 15. Lab Practice I (Isolation of Membrane Proteins) 16. Lab Practice II (Visualization of Membrane Proteins) 17. Problems Shooting/Discussion (whole class) 18. Final Report We aim to allow our students to have the ability to properly design, correctly precede specific experiments when they deal with membrane proteins and related subjects. In class, we combine in class lecture, lab practice (allow students to work on their own specific experiments that directly linked to their master or PhD study) as well as interactive discussions in order to have direct and fast feedback on questions and difficulties they encounter. College of Bio-Resources & Agriculture active participate class lectures, discuss difficulties you encounter for your project with lecturer PEI-SHIUE TSAI VM7098 2 The upper limit of the number of non-majors: 2.

This course is suitable for student who is interested in Developmental Biology (DB), but have no expereince in reading and presenting a scientific paper. An introduction of how a scientific paper is organized will be given at the beginning of course. General approaches and methodologies frequently used by a developmental biologist will be covered in the course. Later on, we will actively dissect several hypothesis-driven DB papers. Students will be required to transform a published paper into a scientific proposal and then based on the proposal to rewrite a manuscript. Each student is required to actively participate in our discussion and present papers in English. College of Life Science Rewrite a manuscript Prepare a proposal Presenring a paper SHYH JYE LEE LS7028 1

Example is given as the following with a focus on Cordyceps spp. Participating students will have to attend a field trip involving in collecting indigenous fungi, in particular the fungi infected insects and known to be used in Traditional Chinese medicine (TCM), such as Cordyceps spp. In addition, students will also practice to identify, cultivate and analyze the collected fungi. In this program, bioassays and toxicological test will be conducted to investigate any of their potential usages in medicine and healthy supplement to improve the global health. At last, the protocols for cultivation and fermentation growth in vitro of the Cordyceps spp. will be learned and it is important for future industrialization. This program aims to enable students in learning the biodiversity and in translation usage of the bio-resources in Taiwan. other Main Campus Field trip, laboratory identification (including documentation, photography, isolation, culture, and genotyping), Cultivation and fermentation, Chemical analyses, in vitro bioassays (MTT, migration, whitening, ROS, lipolysis, anti-virus), Toxicological test, Industrialization. Tang-Long Shen 15 Monday 5,6,7,8,9 Prog5185 (P05EU4140) 3 http://www.cbt.ntu.edu.tw/

This course will be based on the last year’s Intertidal Ecology (B441620), being conducted in English to teach the basic intertidal ecology and use this system as examples to introduce the basic concepts in population and community ecology, common research methods, statistical techniques and writing skills in ecological studies. Learning outcomes: At the end of this course you should be able to: 1.describe the physical environmental factors (e.g., waves, tides) shaping the intertidal environment 2.understand the basic factors affecting the distribution and abundance of intertidal organisms 3.understand the factors limiting species distribution patterns on the vertical intertidal gradient and study the methods to measure and investigate these patterns 4.design experimental studies to investigate patterns (e.g., zonation) and processes (e.g. competition) in intertidal areas 5.plan a simple experimental and statistical study on intertidal ecology. 6.review and critique scientific papers College of Life Science Main Campus Chan,Kwok Kan 8 Thursday 7,8,9 EEB5054 (B44EU1680) 3 (College of Life Science) Institute of Ecology and Evolutionary Biology,
(College of Life Science) Department of Life Science http://ecology.LifeScience.ntu.edu.tw/english/index.htm

NOTE: please visit the course website at www.bit.ly/NumEcol for detail and updated information!
The course is focused on common methods used by ecologists working with community data, including ordination, cluster analysis, diversity analysis etc. It combines a theoretical introduction to each method with a practical lab in R program. The course is dedicated for senior undergraduate and for graduate students. Each class will be composed of two parts: the theoretical introduction to the method, and the practical lab using the R program for all analyses. Schedule of the class: – Introduction, types of data (categorical vs quantitative, abundances, frequencies). – Pre-analysis data preparation (data cleaning, outliers, transformation, standardization, exploratory data analysis). – Ecological similarity (indices of ecological similarity and distance between samples). – Ordination (theory behind, linear vs unimodal, constrained vs unconstrained methods, PCA, CA, DCA, RDA, CCA, NMDS and some others, ordination diagrams, permutation tests, variance partitioning, forward selection, case studies). – Numerical classification (hierarchical vs nonhierarchical, agglomerative vs divisive; TWINSPAN) – Indicator value analysis (IndVal), diagnostic species, fidelity of species to sample groups. – Use of species functional traits or species indicator values in multivariate analysis (functional traits, species indicator values, community-weighted mean, fourth-corner, RLQ analysis). – Analysis of diversity (alpha, beta and gamma diversity, accumulation and rarefaction curves, true diversity, species abundance distribution, diversity estimators). – Design of community ecology experiments (manipulative vs natural experiments, avoiding pseudoreplications, problem of spatial autocorrelation, subjective vs objective sampling design). – Case studies demonstrating the use of particular analytical methods. After finishing it, you will understand the theory behind commonly used multivariate methods for analysis of community data, correctly interpret their results and apply these methods to your own datasets using R. College of Life Science Main Campus Basic statistic course (e.g. B01 34000, LS3022). Basic knowledge of R is recommended, but not required (we may plug-in an extra R-intro course for those of you who are not familiar with R at the beginning of the course). You need to bring your computer with installed R and access to the internet. David Zeleny 30 Thursday 2,3,4 EEB5083 (B44EU1950) 3 http://ecology.LifeScience.ntu.edu.tw/english/index.htm

NOTE: please visit the course website at http://www.bit.ly/VegSurvey for updated information!
This course is focused on introduction to methods used in vegetation survey: sampling of forest and non-forest vegetation, measuring and estimating habitat environmental conditions and vegetation mapping. The course consists of three parts: 1) Theoretical part: overview of methods for sampling vegetation and measurement of environmental variables, introduction to visited areas, safety instructions. 2) Field trips: four whole-day field trips (around Taipei and some more distant regions), practicing the sampling methods, collecting field data and environmental measurements. 3) Lab analysis: processing and analysis of collected data, discussion of results. Theoretical part (4 x 3 hours): – Introduction, safety instructions for field work – Theory of sampling methods (DBH and cover based) – Theory behind measuring of environmental variables – Theory behind vegetation mapping Field trips (4 whole-day trips): – Practical introduction to the field survey, safety in the field, operating basic hiking equipment (reading map, operating compass and GPS), choosing the locality for sampling. – Sampling forest vegetation (DBH measuring, cover estimation, plot and plot-less sampling methods) – Sampling non-forest vegetation (grassland and dune vegetation) – Vegetation mapping – Field measurements (topography, soil properties, microclimatic measurements, forest canopy structure) Lab analysis (4 x 3 hours): – Determining collected specimens. – Practicing sampling habits indoor (estimating cover, use the measuring equipment). – Retyping collected species and header data into computer using dedicated software (Turboveg and JUICE). – Analysis of soil samples (pH and conductivity). – Presenting and discussing results. Students will learn theoretical background of field vegetation survey, apply it in practice, collect real data in the field, process them in the lab and discuss the results. College of Life Science Main Campus Basic courses in plant taxonomy and determination. Basic knowledge of plants expected. The course is for undergraduates (2-3-4 year) + masters David Zeleny 15 Wednesday 2,3,4 EEB5084 (B44EU1960) 3 (College of Life Science) Department of Life Science,
(College of Life Science) Institute of Ecology and Evolutionary Biology http://ecology.LifeScience.ntu.edu.tw/english/index.htm

[Lectures] This course is to introduce the fundamentals and methodology on research of molecular evolution. We will introduce the evolutionary changes and patterns of sequences, methods for phylogenetic analyses, and inferring sites under positive selection. Topics on recent advances of molecular evolution studies will be offered at the end, on phylogenomics, horizontal gene transfer, and genome evolution. Students are highly recommended to take evolution, genetics or equivalent subjects before taking this course. Laboratory practice will be offered for students to be familiar with data retrieving, analyses and interpretation. Homework assignments will be distributed weekly, which require substantial extra work time. [Laboratory Practice] We will have computers available in class, but you are welcome to bring your own laptop computer. In the later case, you should download the corresponding software before the class. Date sets will be provided for the homework assignments but you are welcome to use your own data for the final presentation project. In combination with the computer laboratory practice, we aim to help our students to understand the evolutionary processes at the molecular level. College of Life Science Main Campus Biology; Evolutionary Biology; Genetics or equivalent preferred. Chau Titing 40 Monday 3,4,5 EEB5087 (B44EU1990) 3 (College of Life Science) Institute of Life Science,
(College of Life Science) Institute of Ecology and Evolutionary Biology,
(College of Life Science) Department of Life Science http://ecology.LifeScience.ntu.edu.tw/english/index.htm

This course aims to teach the fundamentals of biological mass spectrometry with particular focus on applications to proteomics and analysis of protein modifications. The course will begin with an introduction to the general aspects of mass spectrometry-based peptide sequencing and protein identification, along with recent technological developments in the context of advancing quantitative shotgun proteomic analysis. Current perspectives in global versus directed analysis, speed versus depth in proteomic coverage, will be discussed. This will then be followed by introducing the practical aspects of MS analysis of select protein modifications, at both the levels of single targeted protein of interest and the proteomic scale. Topics include phosphoproteomics; lysine modifications such as acetylation, methylation, ubiquitination, and SUMOylation; cysteine modifications such as oxidation, glutathionylation and S-nitrosylation; and glycosylation. The last further accompanied by an overview of MS-based glycomics and glycoproteomics. College of Life Science Academia Sinica Opens to life science Master and PhD Students, as well as keen senior undergraduates major in Biochemistry, who have a basic knowledge of protein chemistry and structures, and the commonly found modifications. No absolute prerequisite is set but will be advantageous and encouraged to have first taken one or more of the core courses offered at 生化所 in the first semester eg 蛋白質修飾機制與細胞訊息；結構生化學. Chemistry graduates interested in biology and major in chemical biology are also encouraged and accepted. Kay Hooi Khoo 30 BChem5027 (B46EU0840) 2 (College of Life Science) Institute of Biochemical Science,
(College of Medicine) Graduate Institute of Medical Genomics and Proteomics http://homepage.ntu.edu.tw/~ibs/english/e_index.html