COURSE SCHEDULE 5MO018 GENETIK OCH GENTEKNIK 7,5 HP (5MO112 GENETICS AND GENETIC TECHNIQUES 7.5 ECTS)

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1 UMEÅ UNIVERSITET Department of Molecular Biology Fredrik Hugosson Matthew Francis Schema VT2018 5MO112 Genetik och genteknik 7,5 hp Genetics and Genetic Techniques COURSE SCHEDULE 5MO018 GENETIK OCH GENTEKNIK 7,5 HP (5MO112 GENETICS AND GENETIC TECHNIQUES 7.5 ECTS) Course dates: January 15 th, 2018 to February 14 th, 2018 Exam: February 14 th , Place: N430 (Naturvetarhuset) Re Exam: April 23 rd ; Place: Östra Paviljongen Localities: Lecture room: Uracil (U), floor 1, Building 6L, Department of Molecular Biology, Forsörjningsvägen, Sjukhusområdet???????? Laboratory: Yellow lab (A109 course laboratories), Building 6A Research lab (????, Department of Molecular Biology), Building 6?, Floor?? Course Literature: 1] Hartwell et al. "Genetics, from genes to genomes", (4 th or 5 th edition) McGraw Hill. ISBN partially supports this course This book is recommended for both this course (5MO112) and the course that immediately follows (5MO113). Note: Online electronic 4 th editions of this book can be downloaded for free at: Also check out the animations on: Note: an international version of the 5 th Edition is available for 678 kr from Bokus: 2] Additional important information is provided in lectures (including laboratory introductions) and lecture hand outs. 1

2 3] Other useful information is provided by on-line resources (see next sheet) Course leaders: Fredrik Hugosson (FHu) Matthew Francis (MFr) Course administrator Eva-Christine Lundström, tel Course Assistants: Jyoti Gurung (JGu) Other course lecturers: Vicky Shingler (VSh) Department of Molecular Biology Christer Larsson (CLa) Department of Molecular Biology Per Stenberg (PSt) Department of Molecular Biology Jan Larsson (JLa) Department of Molecular Biology Anders Byström (ABy) Department of Molecular Biology Johannes Hanson (JHa) Umeå Plant Science Centre (Department of Plant Physiology) Monica Holmberg (MHo) Department of Medical Biosciences Course components: Lectures, laboratory exercises, and problem solving classes. Mandatory components: Laboratory classes and associated assignments. Attendance at lectures and problem solving classes is, of course, highly recommended. Absence from mandatory exercises due to illness should immediately be reported to the course administrator. Course literature and useful resources: Reading advice for Genetics and genetic techniques, 5MO112 Know that genetics is a constantly developing field. Emphasis for this course is therefore on up-todate information given out in lectures (hand-outs), and supplementary information given during 2

3 laboratory exercises and problem solving classes. Textbooks are good, but cannot substitute for lectures and other exercises. 1] Genetics - From Genes to Genomes, 4 th or 5 th edition. Hartwell L.H., Hood L., Goldberg M.L., Reynolds A.E., Silver L.M. Mc-Graw-Hill. Most relevant Chapters (see next page for associated lectures) Chapters 1: Genetics: the study of biological information Chapters 2: Mendel s principles of heredity Chapters 3: Extensions to Mendel s laws Chapters 4: The chromosome theory of inheritance Chapters 5: Linkage, recombination and the mapping of genes on chromosomes Chapters 6: DNA structure, replication, and recombination Chapters 7: Anatomy and function of a gene: dissection through mutation Chapters 8: Gene Expression: the flow of information from DNA to RNA to protein Chapters 9: Digital analysis of DNA 2] Additional important information is provided in lectures (and including laboratory introductions) 3] Other useful information is provided by on-line resources Text books: e.g. Robert Schleif: Genetics and Molecular Biology at Todar s Online textbook of Bacteriology at (search for e.g. genetics) Simply Google e.g. free on-line textbook bacterial genetics for other options Genetic glossaries: e.g Simply Google e.g. genetics glossary for other options Videos: e.g. Primer design video Restriction enzyme mapping 1 and 2 (PSC2 Note: these videos are a must see viewing before attending respective lecture and/or problem solving class (PSC) 3

4 Lecture topics (and reading advice): General and Bacterial Genetic Analysis 1. The central dogma DNA replication (Chapter????) 2. The central dogma Transcription into mrna (Chapter????) 3. The central dogma Translation into protein (Chapter????) 4. The central dogma Overview of key regulatory events (Chapter????) 5. Where do mutations come from? Spontaneous and induced fidelity mistakes Chapter 7 6. The key tools of the geneticist Parts of Chapter 8 and Mutations, selections and screens Chapters , MGT*: PCR from cloning to forensics -see index (and videos) 8. DNA cloning and genetic analysis in bacteria I Chapters (and videos) (restriction enzymes, cloning, genomic and cdna libraries) 9. Gene transfer and genetic analysis in bacteria II Parts of chapters 14 and 15 (conjugation, transformation, and transduction in nature and as genetic tools) 10. MGT*: Homologous recombination and allelic replacement in bacteria Chapter 6.5 and parts of Chapter MGT*: Detecting DNA, RNA and proteins -see index 12. MGT*: DNA sequencing and DNA-protein interactions -see index 13. MGT* Introduction to bioinformatic methods for sequence analysis 14. MGT*: Gene and operon fusions Parts of chapters 14 and MGT*: CRISPR-Cas9 genome editing MGT*: Molecular Genetic Techniques common to genetic dissections in all organisms Genetic Analysis in diploid Organisms Genetic analysis in yeast I and II as a model genetic organism Chapter Mendelian Genetics and the principles of inheritance Chapter 2 & parts of chapter Linkage, recombination and gene mapping Parts of chapters 3 and Plant biotechnology and transgenic plants 21. Arabidopsis as a model genetic organism 22. Locating disease associated alleles Note: L23 is a discussion on Bioethical considerations No text book is ever perfect for a given course and some subject matters are either poorly covered or covered in a fragmentary way Hence, additionally recommend reading: For molecular biology (methods): Molecular Biology of the Cell, Fifth Edition (2007). Alberts, Johnson, Lewis, Raff, Roberts, Walter; Garland Science or Download the free book Genetics and Molecular Biology at For bacterial genetics (free on-line text books) and/or: 4

5 Fundamental Bacterial Genetics (2004). Trun and Trempy; Blackwell Overview of other course components labs and PSCs: Laboratory exercises Lab. 1: The Ames test for mutagen identification Lab. 2: Transfer of genetic material between bacteria via conjugation Lab. 3: PCR and DNA cloning introducing desired mutations Lab. 4: Allelic replacement of a gene in E. coli Problem solving classes (PSCs) to reinforce key concepts and to stimulate critical thinking. Note: YouTube videos are a must see viewing before attending the respective PSC. PSC 1: Codons, reading frames and mutations PSC 2: Restriction enzymes, cloning and complementation PSC 3: Primer design PSC 4: Northern, Southern and Western PSC 5: Gene fusions and reporters PSC 6: Blast interpretations (in conjunction with Lab. 2, assistants) Learning Goals (FSR s) for this course: Be able to describe how genetic material is inherited, mapped, analysed and identified in bacteria and eukaryotes. Be able to describe how genetic material can mutate and the effects of these mutations. Be able to describe how the external environment can affect the genetic material Be able to describe how the genetic material can be utilized in bio-technique development Be able to demonstrate practical skill in execution, interpretation and statistical processing of data from genetic and gene technology experiments Be able to demonstrate proficiency in both oral and written scientific communication in English 5

6 Weekly schedule: Working Week 1 (15 th to 19 th January) Monday 15 th U Roll call and introduction with overview of the course (FHu & MFr) U L1 The central dogma DNA replication (FHu) U L2 The central dogma Transcription into mrna (MFr) U Introduction to Lab 1 Phenotype to DNA (JGu) A109 Lab safari and safety (JGu) Tuesday 16 th U L3 The central dogma Translation into protein (FHu) U L4 The central dogma Overview of key regulatory events (MFr) U L5 Where do mutations come from? Spontaneous and induced fidelity mistakes (FHu) A109 Lab 1 (day 1) Overnight cultures (JGu) Wednesday 17 th A109 Lab 1 (day 2) CFU determination and Ames test (JGu) U L6 The key tools of the geneticist: Mutations, selections and screens (VSh) U PSC 1: codons, reading frames and mutations (FHu) Thursday 18 th U L7. MGT: PCR from cloning to forensics (FHu) U PSC 2: Primer design (FHu) Friday 19 th U L8. DNA cloning and genetic analysis in bacteria I (VSh) U Introduction to Lab 2 Gene transfer in bacteria (JGu) A109 Lab 1 (day 3) Determination of revertant frequency (JGu)* *Note that the laboratory is partially co-shared with another course 6

7 Working Week 2 (22 nd to 26 th January) Monday 22 nd January U L9. Gene transfer and genetic analysis in bacteria II (CLa) U PSC 3: Restriction enzymes, cloning and complementation (FHu) A109 Lab 1 (day 4) Overnight culture setup (JGu) A109 Lab 2 (day 1) Setup of bacterial conjugation (JGu) Tuesday 23 rd January A109 Lab 1 (day 5) Amplifying the hisg or hisd gene via PCR (JGu) A109 Lab 2 (day 1) Patching of transconjugates (JGu) 13.30~15.30 U L10. Molecular Genetic Techniques: Homologous recombination and allelic replacement in bacteria (CLa) A109 Lab 1 (day 5 continued) PCR purification and deposition for sequencing (JGu) Wednesday 24 th U L11. MGT: Detecting DNA, RNA and proteins (FHu) U PSC 4: Northern, Southern and Western (FHu) U L12. MGT: DNA sequencing and DNA-protein interaction techniques (FHu) Thursday 25 th 09.00~11.00 A109 Lab 2 (day 3) Determine frequency of genetic transfer (JGu) U Introduction to Lab 3 Using PCR to introduce a desired mutation (JGu) 13.00~15.00 U L13 Introduction to bioinformatic methods for sequence analysis (PSt) 15.15~16.00 U Introduction to Lab 4 Allelic replacement (JGu) Friday 26 th (Note: early start!!) A109 Lab 3 (day 1) PCR amplification predictions and round 1 PCR (JGu) A109 Lab 4 (day 1) Single cell streaking (JGu) Breaks included at a suitable times (JGu) Use any spare time productively to answer the lab quiz questions and to read the recommended reading 7

8 Working Week 3 (29 th January to 2 nd February) Monday 29 th January (Note: early start!!)* A109 Lab 3 (day 2) PCR purifications, analysis and round 2 PCR overnight A109 Lab 4 (day 2) Single cell streaking of two colonies (JGu) Breaks included at suitable times *Note that the laboratory is co-shared with another course Tuesday 30 th January U L14. Gene and operon fusion (VSh) with PSC5 Uniaden 2017 no scheduled events in the afternoon Wednesday 31 st January U L15. Mendelian Genetics and the principles of inheritance (JLa) 12.15~17.00 A109 Lab 3 (day 3) Round 2 PCR analysis and dry lab (JGu) A109 Lab 4 (day 3) Single cell streaking (JGu)????????????? Thursday 1 st February 09.00~12.00 U Lab 3 (day 4) computer lab Part B???????????? (JGu) U L16. Yeast genetics I (ABy) Research lab Lab 4 (day 4) Single cell streaking???????????? (JGu) Friday 2 nd February??????? T/U L17. Yeast genetics II (ABy) 14.30~16.30 Research lab Lab 4 (day 5) Single cell streaking???????????? (JGu) 8

9 Working Week 4 (5 th to 9 th of February) Monday 5 th February 08.30~14.15 U Lab 1 (day 6) Blast analysis of sequence data and correlate genetic reversions with phenotypes (JGu) U Lab 3 (day 5) computer lab Part C; PSC 6: Blast interpretations (JGu) U L18. Linkage, recombination and gene mapping (JLa) Tuesday 6 th February 09.00~12.30 Research lab Lab 4 (day 6) Colony patching???????????? (JGu) U L19. Plant biotechnology and transgenic plants (JHa) Wednesday 7 th February 09.00~15.00 Research lab Lab 4 (day 7) PCR and re-streaking???????????? (JGu) U L20. MGT: CRISPR-Cas9 genome editing (FHu) Thursday 8 th February U L21. Genetic Model Organisms - Arabidopsis (JHa) Research lab Lab 4 (day 8) Analyse PCR products and correlate with phenotypes???????????? (JGu) Lab cleaning (of both A109 and the research lab) Break U Lab round-up and question time (JGu) 3 Friday 9 th February U L22. Locating disease associated alleles (MHo) U L23. Bioethical considerations (MFr) Work with assignments and STUDY (Recommend preparation for Q and A session on Monday) 9

10 Working Week 5 (12 th to 14 th of February) Monday 12 th February Open office in T/U: Q and A session (MFr/MJo/VSh) This is your chance to get help with study questions Be sure to come prepared with questions on aspects that you are uncertain about Course assessment/feedback Dead-line for completed Laboratory Questionnaires to be submitted electronically to the assistants using the Urkund client addresses: Submit to: jyoti.gurung.umu@analys.urkund.se Tuesday 13 th February Student sports day Wednesday 14 th February Exam Time: , Place: N430 (Naturvetarhuset) Note time for re-exam: Monday 23 rd April Re-exam Time: , Place: Östra Paviljongen (room number to be announced 2 to 3 days before the exam) 10