Course coordinator
Dr Peter Crisp
Consultation is by appointment.ﾠTo make an appointment to see me, please email p.crisp@uq.edu.au
Course overview
- Study period
- Semester 1, 2025 (24/02/2025 - 21/06/2025)
- Study level
- Undergraduate
- Location
- St Lucia
- Attendance mode
- In Person
- Units
- 2
- Administrative campus
- St Lucia
- Coordinating unit
- Agriculture and Food Sustainability School
One of the grand challenges facing the world is tailoring our plants and crops to meet the demands of the next and future generations, including ensuring ongoing food security and sustainable food production amid changing environments. This course will engage students in active learning about concepts in plant genetics, molecular biology and physiology to understand developmental processes at the core of plant form and function. Students will have hands-on experience using cutting-edge biotechnology methods and gain real-world practical skills required to engineer and adapt plants for our future needs. These skills underpin both fundamental plant science research and also modern plant breeding and agriculture.
This course provides detailed cutting-edge insight into:
•ﾠﾠ ﾠthe genetics, molecular biology and physiology of plants,
•ﾠﾠ ﾠplant development and cell biology,
•ﾠﾠ ﾠthe approaches used to understand the molecular genetic basis of plant function,
•ﾠﾠ ﾠhow this knowledge can be applied in biotechnology, with an emphasis on plant molecular improvement.
Plants are responsible for turning sun energy into biomass - so they underpin life on earth. You know that plants do this via photosynthesis, but how did photosynthesis evolve? And how is it still evolving, both in nature and in labs around the world? How can you produce a whole plant with all the structures such as flowers and branches from a single cell? How do the cells know what structure to form and when to form these structures? How can we understand the molecular basis of these processes? In this course you will learn about how the genetic programming of a cell links to cell biology and ultimately to the development and physiology of the whole plant. Applying this knowledge to plant crops is one of the central goals of plant biotechnology where it seeks to increase crop yields and adaptation of crops to particular environments. Biotechnology and synthetic biology are fast-moving fields with many ground-breaking advances - for instance CRISPR - made in recent years, some made in recent months, and some even last week – you will learn about the most up-to-date discoveries as well as the classic techniques that underpin the field. In this course you will apply this knowledge to gain practical experience in plant biotechnology.
This course also covers molecular aspects of plant biology including next generation sequencing, understanding the roles of epigenetic regulation and polyploidy in plant evolution, and implications for plant improvement. It provides an essential basis for further exploration of molecular approaches and applications to plant biology (BIOL3200, BIOL3201, BIOL3210, BIOL3011), and it complements courses in human and animal molecular biology. BIOL3213 is a key course for biotechnologists and molecular biologists in general, because plant molecular biology often leads to discoveries in other systems in both understanding and practical applications.
This subject will provide an excellent grounding for careers in government and private enterprises, including sectors such as quarantine, agricultural departments, education, science regulation and policy, private and public media and science writing sectors, biotechnology, as well as excellent preparation for further study; such as, Honours in BSc and related majors. You will be trained in scientific and critical writing and develop knowledge of areas of plant development that are important for crop production and sustainability.
You will be given formal lectures and will discuss fundamental selected research papers with your colleagues and lecturers to develop skills in critical thinking, analysis and communication. We have an exciting practical lab component.
Please contact the course coordinator if you have any suggestions on how to improve the course (don't wait till the end).
We hope you enjoy this course.
Peter Crisp
BIOL3213 coordinator.
Course requirements
Assumed background
A basic familiarity with concepts, terminology, and experimental approaches in biology, genetics and molecular biology from relevant courses at first or second level is assumed. BIOL2202 or BIOL2902 and BIOL2203 are helpful background to this course but you can complete BIOL3213 even if you have not taken these courses. Students with less background in one of these areas can often compensate with additional preparation for the scheduled lectures and practicals. For safety, always ask a tutor or lecturer if there is anything that you are uncertain about in any practical session, before you undertake that practical.
Recommended prerequisites
We recommend completing the following courses before enrolling in this one:
BIOL2202 or BIOL2902 and BIOL2203
Incompatible
You can't enrol in this course if you've already completed the following:
BIOL3202, BIOL3203, BIOT7213 (co-taught)
Course contact
Course staff
Lecturer
Dr Anne Sawyer
Dr Chris Brosnan
Dr Karen Massel
Timetable
The timetable for this course is available on the UQ Public Timetable.
Aims and outcomes
Our lectures and practical training aim to equip advanced students to apply "state of the art" plant cell, biotechnology and molecular biology principles and techniques in their future work.
Learning outcomes
After successfully completing this course you should be able to:
LO1.
Evaluate key concepts and approaches in plant molecular biology including gene structure, genetic transformation, gene cloning strategies, transgene expression strategies, gene silencing, regulatory and commercial issues in plant biotechnology.
LO2.
Analyse concepts in plant growth and development.
LO3.
Design, create, analyse and report on scientific experiments using core techniques in this field ranging from gene transfer to the biochemical and molecular analysis of plants and develop additional skills for career advancement in plant biology and biotechnology.
LO4.
Apply key biotechnical techniques in the laboratory and interpret results obtained from experiments, including plant transformation, cloning and genomic analysis.
LO5.
Critically evaluate claims for benefits and/or risks of plant gene technologies and reach informed judgements about their merits in a global context.
Assessment
Assessment summary
| Category | Assessment task | Weight | Due date |
|---|---|---|---|
| Examination |
In-semester exam
|
20% |
10/04/2025 11:00 am
Exam - In-Semester During Class |
| Paper/ Report/ Annotation | Practical reports Sequential task | 50% This 50% assessment is made up of 3 Reports, worth P2 (15%), P1 (20%) and P3 (15%) |
P2 Gene cloning and CRISPR design computer prac (15%) 15/04/2025 2:00 pm P1 Gene Transfer and CRISPR laboratory report (20%) 9/05/2025 2:00 pm P3 Gene discovery and genomics report (15%) 30/05/2025 2:00 pm
There are 3 practical reports in total. A marking scheme and specific instructions for each practical report can be found in Blackboard. |
| Examination |
Final exam
|
30% |
End of Semester Exam Period 7/06/2025 - 21/06/2025 |
A hurdle is an assessment requirement that must be satisfied in order to receive a specific grade for the course. Check the assessment details for more information about hurdle requirements.
Assessment details
In-semester exam
- Hurdle
- Identity Verified
- In-person
- Mode
- Written
- Category
- Examination
- Weight
- 20%
- Due date
10/04/2025 11:00 am
Exam - In-Semester During Class
- Learning outcomes
- L01, L02, L05
Task description
In-semester exam with emphasis on the course coverage given in lectures; includes all lectures from weeks 1-5 (inclusive) and indirectly encompass concepts from lab practical classes.
Paper-based exam – this exam will be an on-campus exam, and will be invigilated by staff. Your UQ ID will be required for admittance in the exam location.
This assessment task is to be completed in-person. The use of generative Artificial Intelligence (AI) or Machine Translation (MT) tools will not be permitted. Any attempted use of AI or MT may constitute student misconduct under the Student Code of Conduct.
Answers must directly address the question posed rather than provided information merely related to the topic of the question. THIS IS VERY IMPORTANT.
Marks are given for clarity, scientific accuracy, detail, appreciation of the complexities and the structure of the answer (how well the answer flows and shows relationships).
Hurdle requirements
Refer to Additional Course Grading Information.Exam details
| Planning time | 10 minutes |
|---|---|
| Duration | 90 minutes |
| Calculator options | No calculators permitted |
| Open/closed book | Closed Book examination - no written materials permitted |
| Exam platform | Paper based |
| Invigilation | Invigilated in person |
Submission guidelines
Deferral or extension
You may be able to defer this exam.
Practical reports Sequential task
- Mode
- Written
- Category
- Paper/ Report/ Annotation
- Weight
- 50% This 50% assessment is made up of 3 Reports, worth P2 (15%), P1 (20%) and P3 (15%)
- Due date
P2 Gene cloning and CRISPR design computer prac (15%) 15/04/2025 2:00 pm
P1 Gene Transfer and CRISPR laboratory report (20%) 9/05/2025 2:00 pm
P3 Gene discovery and genomics report (15%) 30/05/2025 2:00 pm
There are 3 practical reports in total. A marking scheme and specific instructions for each practical report can be found in Blackboard.
- Learning outcomes
- L01, L03, L04
Task description
During the semester student will undertake a series of 3 practical modules and for each module students will submit a practical report. In total, the 3 reports worth 50% of the total grade for the course. Detailed instructions and marking criteria will be posted on blackboard for each report.
P2 Gene cloning and CRISPR design computer prac (15%):
In this report you will describe your solution to a practical cloning and design CRISPR targets as discussed during the computer practical sessions. You will report your strategy and proposed solution using diagrams and short descriptions.
P1 Gene Transfer and CRISPR laboratory report (20%):
The assessment for this practical will be a practical report with a structure which is similar to that of a brief scientific paper or technical report. The report will include the sections: title, abstract, results, discussion, conclusion and references but may not require introduction or methods. Detailed report guidelines are provided in the manual for the practical on blackboard and will be discussed during the practical, please follow the guidelines for each practical including any word or page limits and ask the practical supervisor or coordinator if in doubt.
P3 Gene discovery and genomics report (15%):
For this practical you will write a simplified practical report by answering several questions about the aims, methods and results of your practical. The questions are detailed in the report instructions posted on blackboard. You should aim to write between 300-500 words per question; and use figures and diagrams were appropriate. Detailed report guidelines are provided in the manual for the practical on blackboard and will be discussed during the practicals, please follow the guidelines for each practical including any word or page limits and ask the practical supervisor or coordinator if in doubt.
This task has been designed to be challenging, authentic and complex. Whilst students may use AI and/or MT technologies, successful completion of assessment in this course will require students to critically engage in specific contexts and tasks for which artificial intelligence will provide only limited support and guidance.
A failure to reference generative AI or MT use may constitute student misconduct under the Student Code of Conduct.
To pass this assessment, students will be required to demonstrate detailed comprehension of their written submission independent of AI and MT tools.
Submission guidelines
Turnitin submission details:
You must submit your Assessment task, in Blackboard, via the Turnitin link by the submission deadline. You should also retain an electronic copy of every piece of assessment you submit.
Legal Declaration:
By submitting your work via this website, you formally declare that (1) it is your own original work, and no part of the work has been copied from any other source or person except where due acknowledgement is made; (2) no part of the work has been previously submitted for assessment in this or any other institution; and (3) you have read the Student Integrity and Misconduct Policy (https://policies.uq.edu.au/document/view-current.php?id=149) and understand its implications.
Deferral or extension
You may be able to apply for an extension.
Late submission
A penalty of 10% of the maximum possible mark will be deducted per 24 hours from time submission is due for up to 7 days. After 7 days, you will receive a mark of 0.
Assessment deadlines are firm and must be met. Late submission without permission or non-submission of assessable work will result in penalties being applied. Late submission of assessment will only be granted for documented medical reasons, accident, bereavement, jury service and other circumstances allowed in the UQ Policies and Procedures Library (PPL).
Submission of an Extension of Assessment Due Date (EADD) should be completed online through your My Requests tab via my.UQ Dashboard before the due date of the assessment item.
Final exam
- Hurdle
- Identity Verified
- In-person
- Mode
- Written
- Category
- Examination
- Weight
- 30%
- Due date
End of Semester Exam Period
7/06/2025 - 21/06/2025
- Learning outcomes
- L01, L02, L05
Task description
End of semester exam with emphasis on the course coverage given in lectures; includes all lectures from weeks 6-13 and indirectly encompases concepts from lab practical classes.
Paper-based exam – this exam will be an on-campus exam, with specified materials permitted only, and will be invigilated by staff. Your UQ ID will be required for admittance in the exam location.
This assessment task is to be completed in-person. The use of generative Artificial Intelligence (AI) or Machine Translation (MT) tools will not be permitted. Any attempted use of AI or MT may constitute student misconduct under the Student Code of Conduct.
Answers must directly address the question posed rather than provided information merely related to the topic of the question. THIS IS VERY IMPORTANT. Marks are given for clarity, scientific accuracy, detail, appreciation of the complexities and the structure of the answer (how well the answer flows and shows relationships).
Hurdle requirements
Refer to Additional Course Grading Information.Exam details
| Planning time | 10 minutes |
|---|---|
| Duration | 90 minutes |
| Calculator options | No calculators permitted |
| Open/closed book | Closed Book examination - no written materials permitted |
| Exam platform | Paper based |
| Invigilation | Invigilated in person |
Submission guidelines
Deferral or extension
You may be able to defer this exam.
Course grading
Full criteria for each grade is available in the Assessment Procedure.
| Grade | Description |
|---|---|
| 1 (Low Fail) |
Absence of evidence of achievement of course learning outcomes. Course grade description: A cumulative score for all assessment and end of semester assessment items of 0% - 34% |
| 2 (Fail) |
Minimal evidence of achievement of course learning outcomes. Course grade description: A cumulative score for all assessment and end of semester assessment items of 35% -46% |
| 3 (Marginal Fail) |
Demonstrated evidence of developing achievement of course learning outcomes Course grade description: A cumulative score for all assessment and end of semester assessment items ofﾠ 47% - 49% OR A cumulative score for all assessment and end of semester assessment items of 50% or greater and less than a passing mark in the combined In-Semester and ﾠEnd of Semester examinations. |
| 4 (Pass) |
Demonstrated evidence of functional achievement of course learning outcomes. Course grade description: A cumulative score for all assessment and end of semester assessment items ofﾠ 50% - 64%, AND a passing mark in the combined In-Semester andﾠ End of Semester examinations. |
| 5 (Credit) |
Demonstrated evidence of proficient achievement of course learning outcomes. Course grade description: A cumulative score for all assessment and end of semester assessment items ofﾠ 65% - 74%, AND a passing mark in the combined In-Semester and ﾠEnd of Semester examinations. |
| 6 (Distinction) |
Demonstrated evidence of advanced achievement of course learning outcomes. Course grade description: A cumulative score for all assessment and end of semester assessment items ofﾠ 75% - 84%, AND a passing mark in the combined In-Semester andﾠ End of Semester examinations. |
| 7 (High Distinction) |
Demonstrated evidence of exceptional achievement of course learning outcomes. Course grade description: A cumulative score for all assessment and end of semester assessment items ofﾠ 85% - 100%, AND a passing mark in the combined In-Semester and End of Semester examinations. |
Additional course grading information
A passing mark from the combined In-semester Exam and Final Exam results is required to pass this course.
If a student obtains an overall percentage greater than the cut-off for a 4 or higher on the cumulative results for all assessment items and the student does NOT score a passing mark for the combined in-semester and end of semester exams, they are unable to achieve a grade higher than a 3 (failing grade) for the course.
Supplementary assessment
Supplementary assessment is available for this course.
Should you fail a course with a grade of 3, you may be eligible for supplementary assessment. Refer to my.UQ for information on supplementary assessment and how to apply.
Supplementary assessment provides an additional opportunity to demonstrate you have achieved all the required learning outcomes for a course.
If you apply and are granted supplementary assessment, the type of supplementary assessment set will consider which learning outcome(s) have not been met.
Supplementary assessment can take any form (such as a written report, oral presentation, examination or other appropriate assessment) and may test specific learning outcomes tailored to the individual student, or all learning outcomes.
To receive a passing grade of 3S4, you must obtain a mark of 50% or more on the supplementary assessment.
Additional assessment information
Assignment writing
You must not re-use past work from previous assessments in your assignments.
You are encouraged to:
- read the instructions for assignments carefully and ensure that you address all the requirements,
- refer to references both in the readings and beyond, and cite references in the appropriate manner,
- reflect on your own experience and provide insight and critical thinking,
- write clearly and concisely.
Turnitin Assignments
Assignments that are required to be submitted through TurnItIn, must only be uploaded to the assessment specific Turnitin link on the relevant course Blackboard site. ﾠIf you submit any version of your assessment item to any other Turnitin link, this is considered cheating, and you will be held liable for this action.
Release of marks
Unless specifically indicated by the lecturer involved, every attempt will be made to have the results for progressive assessment tasks available within 3 weeks of submission. ﾠFor items of assessment submitted in the last 2 weeks of the semester, the results will be available before the day of your end of semester examination in the course, unless otherwise indicated by the Course Coordinator. ﾠResults and feedback availability will be advised to you by email or announced via the course Blackboard site.
Feedback in this course
Feedback is welcome in this course as any information on how students find this learning experience is constructive.
Please use the evaluation form provided to you at the end of semester - or if you are enrolled internally, a course evaluation process will occur in the last few weeks of semester.
Re-mark Applications – refer to the University's Re-mark Policy to check your eligibility
Learning resources
You'll need the following resources to successfully complete the course. We've indicated below if you need a personal copy of the reading materials or your own item.
Library resources
Find the required and recommended resources for this course on the UQ Library website.
Other course materials
If we've listed something under further requirement, you'll need to provide your own.
Required
| Item | Description | Further Requirement |
|---|---|---|
| Course Profile | provides details of specifications, rationale, aims and structure of the course. It also informs you of the assessment for this course, including weightings and due dates. Other valuable information in the Course Profile includes the assignment details. | |
| BIOL3213 Plant Biology and Biotechnology Blackboard site | Blackboard is the main method of communication. Learning Guide, Lectures, Recordings, Course readings and Tutorials are made available through the Blackboard site. |
Additional learning resources information
There is no single textbook up to date with all of the subject material. At this level we commonly recommend key review articles for each lecture or module. Reading the provided material will give you a deeper and more comprehensive understanding of subject material and is highly recommended to get the most value from the course.
Detailed practical notes are provided in advance for each practical module. You may be advised of additional resources available for download from the course Blackboard site.
Online PLANTS IN ACTION textbook also provides useful background information on plant biology; https://www.asps.org.au/plants-in-action-2nd-edition-pdf-filesﾠﾠ
Each student must bring the following items to laboratory classes:
- Laboratory coat;
- Laboratory notebook (an A4 size ruled notebook of approx. 65 pages);
- Felt pen suitable for writing on glass and plastic ware;
- Pen and pencil for taking notes and making diagrams or tables of results in your notebook.
ﾠ
Learning activities
The learning activities for this course are outlined below. Learn more about the learning outcomes that apply to this course.
Filter activity type by
Please select
| Learning period | Activity type | Topic |
|---|---|---|
Multiple weeks From Week 1 To Week 13 |
Lecture |
Lecture schedule A detailed list of lectures and practicals can be found in the blackboard site for this course. Sub-activity: Introduction: Getting started with this course and plant biotech overview (Crisp/Botella) Key concepts in genetics for plant bio and biotechnology (Crisp/Botella) Introduction to Genetic transformation - Agrobacterium (Massel) Key attributes in designing a plant transformation system 1 (Massel) Key attributes in designing a plant transformation system 2 (Massel) Alternative transformation methods (Massel) Cell biology/ cloning/ gene editing - Web based cloning (Botella/Crisp) Cell biology/ cloning/ gene editing - Web based cloning (Botella/Crisp) Cell biology/ cloning/ gene editing - Detecting and studying prot-prot interactions (Botella/Crisp) Cell biology/ cloning/ gene editing - Genome editing (Botella/Massel) Cell biology/ cloning/ gene editing - Genome editing (Botella/Massel) Cell biology/ cloning/ gene editing - CRISPR screening and edit quantification (Botella/Massel) Cell biology/ cloning/ gene editing - Promoters for plant biotechnology (I) (Botella/Massel) Gene silencing (Brosnan) Gene silencing (Brosnan) Plant growth and development (root biology) (Tanurdzic/Sawyer) Plant growth and development (plant signalling) (Tanurdzic/Sawyer) Plant growth and development - Paper discussion (Tanurdzic/Sawyer) Growth dev and signaling (plant signalling) (Tanurdzic) Growth dev and signaling (shoot development and branching) (Tanurdzic) Growth dev and signaling (paper discussion) (Tanurdzic) Plant genomes I - What is in a plant genome (Crisp) Plant genomes I - What is in a plant genome (Crisp) Plant genomes II - Genome expansion (Crisp) Plant genomes III - Polyploidy (Crisp) Gene regulation I - Gene regulatory elements and biotech (Crisp) Tutorial - Gene regulation and functional genomics (Crisp) Gene regulation II - Chromatin (Crisp) Gene regulation III - Epigenetics (Crisp) Tutorial - Epigenome editing and intro to preprints (Crisp) Exam preparation (Crisp) Learning outcomes: L01, L02, L03, L05 |
Multiple weeks From Week 1 To Week 11 |
Practical |
Practical Schedule A detailed list of lectures and practicals can be found in the blackboard site for this course. Sub-activity: Prac Module 1 - Gene Transfer, CRISPR/Cas9 and Analysis of Transgenic Plant Lines - laboratory - 4 weeks (Massel/Crisp) Prac Module 2 - Practical gene cloning and CRISPR design - computer labs (Crisp/Massel/Botella) - 2 weeks Prac Module 3 - Gene discovery and genomics - computer labs (Crisp/Tanurdzic) - 2 weeks Learning outcomes: L03, L04 |
Policies and procedures
University policies and procedures apply to all aspects of student life. As a UQ student, you must comply with University-wide and program-specific requirements, including the:
- Student Code of Conduct Policy
- Student Integrity and Misconduct Policy and Procedure
- Assessment Procedure
- Examinations Procedure
- Reasonable Adjustments - Students Policy and Procedure
Learn more about UQ policies on my.UQ and the Policy and Procedure Library.
You'll also need to be aware of the following policies and procedures while completing this course: