BIOL2X29 Cells Lab Manual for Canvas PDF

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SCHOOL OF LIFE AND ENVIRONMENTAL SCIENCES

BIOL2029/2929 Cells/Cells Advanced

Lab Manual Semester 1, 2021

Name: SID:

If found, please return to:

School of Life and Environmental Sciences Room 177, F22, LEES Building The University of Sydney, NSW, 2006

STUDENT PLAGIARISM: COURSE WORK - POLICY AND PROCEDURE

COMPLIANCE STATEMENT INDIVIDUAL / COLLABORATIVE WORK I certify that: (1) I have read and understood the ACADEMIC HONESTY IN COURSEWORK POLICY 2015 available from http://sydney.edu.au/policies/ (2) I understand that failure to comply with the ACADEMIC HONESTY IN COURSEWORK POLICY 2015 can lead to the University commencing proceedings against me/us for potential student misconduct under the ACADEMIC HONESTY IN COURSEWORK POLICY 2015; (3) this Work is substantially my own, and to the extent that any part of this Work is not my own I have indicated that it is not my own by Acknowledging the Source of that part or those parts of the Work.

Name: Signature: Date:

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BIOL2029 Cells BIOL2929 Cells (Advanced)

Study Guide

Authors Min Chen Jan Marc Robyn Overall Murray Thomson

Semester 1 2021

School of Life and Environmental Sciences The University of Sydney 2

CONTENTS Learning outcomes

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Lecturers

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Textbooks

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Timetable; lectures, practical classes, quizzes

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Times & location of lectures and practical classes

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Quizzes

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Reading for practical classes .

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Laboratory record book

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Assignment report for mainstream students (BIOL2029)

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Assignment for advanced students (BIOL2929)

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Tutorials and consultations

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Web resources

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Announcements and notices .

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Theory exam .

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Assessment summary .

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Laboratory procedures Safety standards

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General practices

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Practical classes Week 1

Cell biology techniques

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Week 2

Arabidopsis model plant A

Week 3

Signal transduction in Euglena/Arabidopsis model plant B

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Week 4

Arabidopsis model plant C .

Week 5

Explant cell culture

Week 6

Bioactive molecules from sea anemones

Week 7

No prac this week

Week 8

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1.1 2.1

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3.1/2.6

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2.7

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5.1

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6.1

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Compound and digital microscopy/Plant set up

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8.1

Week 9

Plant cells and development I

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9.1

Week 10

Plant cells and development II

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Week 11

Analysis of tissue specific gene expression I .

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Week 12

Analysis of tissue specific gene expression II .

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12.1

Week 13

The Mitochondrion

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9.1

Learning Outcomes The purpose of this Unit of Study is to promote contemporary understanding of the biology of eukaryotic cells.

It focuses on the function at a cellular level and favours the molecular

perspective. Topics include the structure and function of cells and organelles, as well as tissuespecific development and cell differentiation. When you have successfully completed the study you should:

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Apply skills developed in the operation of stereo and compound microscopes and their use in cell and tissue research

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Apply competencies in calculating the concentration of cells and chemicals in a changed volume of solute

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Develop skills in the culture of cells in vitro and the use of cell cultures for research

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Generate your own unique cell biology data, apply key cell biology research techniques to solve novel questions and create a scientific manuscript

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Understand the major pathways in intercellular and intracellular communication and signalling

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Evaluate research on the molecular machinery that allows endocrine glands such as the hypothalamus and pituitary to control cellular processes in the body of animals

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Understand the cytoskeleton and how it allows cells to function including movement and the formation of intracellular transport pathways and networks

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Describe the mechanism and control of the cell cycle at the molecular level and how the loss of these controls can lead to cancer and cancer progression

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Understand the molecular mechanisms that control apoptosis and how apoptosis is used in development

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Evaluate current research on development processes in plants and animals

This unit is designed to give you competencies and skills that will allow you to pursue further study and research in the field as well as providing you with theoretical knowledge. This unit is great preparation for your future endeavours such as an honours year or a research-based 5

career, so this is not a case where you can be given a set of facts to memorise. Some tips follow for you to develop,

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an understanding of the theories of modern cell biology as covered in the lectures and your textbook. How do you do this? read your textbook before and/or after your lecture, note themes in the lecture or the title of a lecture, for example, after you attend the lecture titled “Microtubules and cellular traffic” look up the word ‘microtubules’ in your textbook’s index then read the relevant parts of the book. You do not have to memorize the textbook chapter but you should be able to understand it. Develop the ability to write short essays on your favourite topics in the unit as preparation for the exam. Feedback is available to you from the staff, just ask them.

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an ability to analyse cell biology research data, data will be shown to you in the lectures and you will generate your own in the lab, critically analyse the data and be able to say what the data indicates, discuss examples with the staff. As a way of assessing yourself refer back to research data given in the lectures and determine what the results indicate, discuss with students and staff.

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competencies in the cell biology laboratory, read the practical before going into the lab, follow the instructions in this book, complete the exercises and ask the staff questions along the way, become confident with the equipment that you will use, such as the digital microscopes and image capture software. Follow the Laboratory Procedures page 22.

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Lecturers

Room 314, The Heydon-Laurence Building

Dr Murray Thomson, Coordinator

A08 Tel: 90366412 Email: [email protected]

Room 519, F22 - LEES Building

Professor Min Chen, Dept Coordinator

Email: [email protected]

Room 719, F22 - LEES Building

Associate Professor Marcus Heisler

Email: [email protected]

Room 515, The Carslaw Building,

Dr. Osu Lilje

Email: [email protected]

Technical officers Ms Xiumei Liang

Room 177, LEES Building (F22)

Dr. Phillip Doughty

Room 177, LEES Building (F22)

Textbooks Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2014) Molecular Biology of the Cell (Sixth edition). Garland Publishing Inc., New York & London

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The lecture material is based largely on the Alberts et al. textbook Molecular Biology of the Cell ("Large Alberts"). This is up to its 6th edition (ISBN-9780815344643) and this contains the most comprehensive and up-to-date information. We are pleased to have this full edition of the most popular textbook in contemporary molecular biology of the cell. It is a standard reference book not only for undergraduate studies, but also for postgraduate students and research professionals worldwide. There is also a condensed version of the textbook, Alberts et al. (2018) Essential Cell Biology ("Small Alberts" ISBN: 9780393680393) that provides a basic coverage of the field. There are older editions of the Alberts et al. textbooks, which are still useful although they lack some new discoveries in some of the molecular details.

You can search and read search result sections of the textbook 4th edition for free at http://www.ncbi.nlm.nih.gov/books/NBK21054/ The book’s contents in headings and subheadings are provided at the site and you can use these in the search engine to read which ever section you like.

Copies of the textbook in various editions are available in the SciTech library and on sites such as ebay and Amazon, if you can’t afford the sixth edition buy a previous edition.

Lecturers, may also recommend additional, specialised reading material to supplement their lecture topics and laboratory exercises, and will provide the specific references during their lectures and practical classes.

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Timetable

Week 1

Lecturer Murray

Lecture Visualising cells

3-Mar

Murray

Principles of cell signalling

8-Mar

Murray

Cellular control by mitochondria

10-Mar

Murray

Signalling through G-protein coupled receptors

15-Mar

Murray

Phospholipase and calcium cell signalling

17-Mar

Murray

Cell signalling through enzyme coupled receptors

22-Mar

Murray

Cellular endocrinology

24-Mar

Osu

Cell culture

29-Mar

Min

Cell signalling routes in gene regulation

31-Mar

Min

Cell signalling in plants

12-Apr

Murray

Function and origin of the cytoskeleton

14-Apr

Min

Actin and actin binding proteins

19-Apr

Min

Cell contraction via actin and myosin

21-Apr

Murray

Microtubules and cellular traffic

26-Apr

Murray

Intermediate filaments and cell migration

28-Apr

Murray

The mitotic and cytokinetic apparatus

3-May

Min

Plant cells & development

5-May

Murray

Control of the cell cycle

10-May

Murray

Cell junctions

12-May

Marcus

Overview of development

17-May

Marcus

Mechanisms of pattern formation

19-May

Marcus

Cell death

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24-May

Murray

Tissues and the extracellular matrix

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26-May 31-May

Murray Murray

Cancer in cells and tissues 1 Cancer in cells and tissues 2

2-Jun

Murray

Stem cells and tissue renewal

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Date 1-Mar

Practical Cell biology techniques

Arabidopsis model plant A Literature database searching Signal transduction in Euglena Arabidopsis model plant B Arabidopsis model plant C

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Assessment

Assignment report is on Signal transduction in Euglena Quiz 1 (Weeks 1-3)

Explant Cell Culture

Bioactive molecules from sea anemones No prac this week

Assignment due Friday Apr 23

Compound and digital microscopy/ Set up for plant cells Plant cells & Development 1 Plant cells & Development 2 Analysis of tissue specific expression I Analysis of tissue specific expression II

Quiz 2 Labs/Lectures

The Mitochondrion

Weeks 4-11 Prac book due 4 pm Fri Jun 4

Lecture Timetable and Location (check online these can change) Weeks 1-13 Monday Wednesday

Time 11:00 12:00

Location See online timetable See online timetable

Practical Classes Timetable and Location (attend only one practical class each week, see your timetable) Weeks 1 –13 Wednesday

Time 2–6

Location Room 303 LEES Building

Thursday

2–6

Room 303 LEES Building

Week 14 Week 15-16

7 – 11 June STUDY VACATION 15 – 26 June EXAMINATIONS

Quizzes are held in the laboratory. In practical classes in Weeks 4 and 12, there will be a short (30 min) quiz. The questions will cover the lecture material from the previous weeks, and will also relate to the previous practical classes, focussing on the main principles, overall results, and key conclusions. There is a practise quiz for you to see the format on the learning management system site. The quizzes are worth 10% of the total mark for the unit. Please make sure you are on time, to avoid losing valuable time and marks. By the due date, please upload an electronic version of your assignment via the Canvas learning management system web site. Note – submitting by the due date means you avoid a late penalty for each day or part day of lateness. Reading for practical classes - It is most important that you read each practical exercise in the Study Guide BEFORE coming to each class. It is essential that you understand what you are doing. Most of the practicals cannot be done by trying to follow the printed instructions like a cookbook recipe, as there are multiple stages where you have to think, prepare and make your own decisions.

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Laboratory book and practical participation Your Laboratory book (this book) and participation in the practical sessions are assessed and make up 10% of your total assessment. Attendance It is a Faculty requirement that you must attend at least 80% of the practical sessions to be eligible for a passing grade in the unit of study. If you miss more than 20% of the practicals, including with special consideration, you should speak to an academic advisor about withdrawing from the unit. Special consideration may allow you to miss up to 20% of the practicals https://sydney.edu.au/students/special-consideration.html The written work in your prac book as well as graphs, drawings, microscopy images and diagrams is to be your INDIVIDUAL work, not copied, discussed or shared with lab partners. Only weeks when you are working in pairs raw data only (e.g. NOT graphed data), can be shared. See the University’s policy on academic honesty and plagiarism available at http://sydney.edu.au/policies/showdoc.aspx?recnum=PDOC2012/254&RendNu m=0 It is essential that you maintain a complete record of your experiments in your laboratory book throughout the semester. During each laboratory session, you need to record all the original results of your experiments and write answers to any questions. In week 13 make sure that you have read and signed the Compliance Statement at the front of this book if you do not sign the Compliance Statement you will receive a late fee of 5% per day. Submit your laboratory book for marking by Friday at 4 pm, put your book into the Cells assignment box. If you were absent from any laboratory session because of illness or misadventure, you need to submit a Special Consideration form. You should also be aware that: • Sections of paper can be inserted into the practical manual in the appropriate places. • Drawings and diagrams should be on plain (unlined) paper. • Questions should be answered in the spaces in the practical manual. • Other recorded information should be inserted into your book. • Your laboratory records should include the original observations that you as an individual made during the laboratory class. Do not paraphrase or copy your classmate’s work, see notes on plagiarism above and below. This means you cannot discuss the answers to the questions in this book with other students including a student who is partnering with you to conduct some of the experiments and collect data. If you collaborate with another 11

student or students on the answers to the questions in this book that is plagiarism and all collaborators will receive a penalty. Because of this if someone asks to see your book or asks you what you put for a question or questions, you must say no to them. • Do not allow your classmates to save their lab result files on your USB or SD devices, do not send any results, graphs, images etc over the internet to a fellow student, do not get your lab material, “mixed up”. Copied material is plagiarism, the “our files must have got mixed up” excuse will not be accepted.

Assignment report for Mainstream students (BIOL2029)

YOU ARE WRITING THIS ASSIGNMENT REPORT AS AN INDIVIDUAL,

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DO NOT CO-WRITE WITH ANOTHER STUDENT, DO NOT PARAPHRASE ANOTHER STUDENT’S WORK, DO NOT “GET IDEAS ABOUT THE STRUCTURE” FROM ANOTHER ...