Course overview
- Study period
- Semester 2, 2024 (22/07/2024 - 18/11/2024)
- Study level
- Undergraduate
- Location
- St Lucia
- Attendance mode
- In Person
- Units
- 2
- Administrative campus
- St Lucia
- Coordinating unit
- The Environment School
Environmental bioanalytics refers to a wide range of methodological approaches that help environmental scientists to understand the biological components of ecosystems and how they are influenced by environmental issues. In brief, bioanalytics approaches involve the analysis of different pools of biomolecules (e.g., nucleic acids, proteins, and metabolites) and can provide insight into the diversity, function, and dynamics of ecological systems at multiple levels of organisation.
The acquisition of knowledge and skills in environmental bioanalytics is an essential component of an environmental scientists’ training. This course will impart understanding of how bioanalytics approaches are applied in environmental studies. Students will be taught to analyse and evaluate bioanalytics datasets and to communicate their findings to different stakeholders.
The course begins with an overview of bioanalytics approaches, and then demonstrates how these methods can be applied in environmental studies. Applications include: 1) biodiversity monitoring using marker gene sequencing, 2) ecosystem service evaluation using metagenomics and functional omics, 3) monitoring of rare/endangered species through analysis of environmental DNA (eDNA), 4) eDNA detection of biological contaminants, pests and diseases, and 5) the use of model systems to address hypotheses relating to biological systems using environmental bioanalytics.
Environmental Bioanalytics refers to a wide range of methodological approaches that help environmental scientists understand the biological components of ecosystems and how they are influenced by environmental issues.
This is important because we depend on the activities of diverse biological communities for the food, fibre, and clean air and water that keep us alive. Ironically though, our activities often have devasting consequences for life, especially when considering organisms that are too small to be seen.
Bioanalytics approaches involve the analyses of different pools of biomolecules (e.g., nucleic acids, proteins, and metabolites) and can provide insight into the diversity, function, biomass, and dynamics of ecological systems at multiple levels of organisation.
Hence, the acquisition of knowledge and skills in bioanalytical approaches provides environmental scientists with an essential toolkit to understand: 1) the biodiversity and functioning of organisms in the environment, and 2) how they are likely to respond to environmental change.
ENVM3010 Environmental Bioanalytics will provide students with this necessary training via weekly lectures and multiple laboratory and computer-based practical classes.ﾠ
Course requirements
Recommended prerequisites
We recommend completing the following courses before enrolling in this one:
SCIE2100
Course contact
Course staff
Lecturer
Dr Jiarui Sun
Dr Rebecca Lyons
Demonstrator
Ms Anna-Belle Clarke
Mr Lachlan Curran
Miss Maria Vega Cofre
Mrs Olga Shopina
Ms Shahnaz Sultana
Timetable
The timetable for this course is available on the UQ Public Timetable.
Aims and outcomes
This course will impart understanding of how bioanalytics approaches are applied in environmental studies. Students will be taught to analyse and evaluate bioanalytics datasets and to communicate their findings to different stakeholders.
The course begins with an overview of bioanalytics approaches, and then demonstrates how these methods can be applied in environmental studies. Applications include: 1) biodiversity monitoring using marker gene sequencing, 2) ecosystem service evaluation using metagenomics and functional omics, 3) monitoring of rare/endangered species through analysis of environmental DNA (eDNA), 4) eDNA detection of biological contaminants (e.g., faecal bacteria), pests and diseases (e.g., Salmonella/COVID-19), and 5) the use of model systems to address hypotheses relating to biological systems using environmental bioanalytics.
Learning outcomes
After successfully completing this course you should be able to:
LO1.
Construct, test and evaluate scientific hypotheses regarding the biota of ecosystems using bioanalytics approaches
LO2.
Initiate and optimise sampling programs and experiments for answering biology-related questions in environmental science
LO3.
Evaluate and critique biological research projects and assign priority to the outcomes
LO4.
Identify appropriate analytical approaches for biological hypotheses and datasets
LO5.
Make inferences from bioanalytics analyses presented in primary environmental science literature
LO6.
Understand how environmental bioanalytics approaches can be applied to environmental studies and monitoring
LO7.
Evaluate and design strategies to communicate bioanalytics to different environmental stakeholders
LO8.
Create, analyse and evaluate bioanalytics datasets
LO9.
Work productively in a group setting to assess and define problems in environmental science and formulate possible bioanalytics responses
LO10.
Demonstrate skills in time management and working independently to complete written exercises on time
Assessment
Assessment summary
| Category | Assessment task | Weight | Due date |
|---|---|---|---|
| Notebook/ Logbook | Practical class journal | 15% |
30/09/2024 11:59 pm |
| Computer Code, Paper/ Report/ Annotation | Analytical report | 25% |
30/09/2024 11:59 pm |
| Participation/ Student contribution, Presentation | Group presentations | 25% | |
| Examination | Exam | 35% |
End of Semester Exam Period 2/11/2024 - 16/11/2024 |
Assessment details
Practical class journal
- Mode
- Written
- Category
- Notebook/ Logbook
- Weight
- 15%
- Due date
30/09/2024 11:59 pm
Task description
Notes from the practical classes should be recorded on the left page.
Reflections should be recorded on the right page.
For each practical:
Notes should include relevant facts, figures, drawings and/or statistics from each activity.
Reflections should include how the activities relate to the subjects in your course.
Submission guidelines
Please submit your journal in person to the SENV reception.
Deferral or extension
You may be able to apply for an extension.
The maximum extension allowed is 7 days. Extensions are given in multiples of 24 hours.
Analytical report
- Mode
- Written
- Category
- Computer Code, Paper/ Report/ Annotation
- Weight
- 25%
- Due date
30/09/2024 11:59 pm
- Learning outcomes
- L01, L06, L08, L10
Task description
You will be assigned a question/problem to address along with a dataset to analyse and interpret.
You will then write an analytical report with the following sections: Introduction, Methodology, Results, and Discussion.
With each dataset you will be given the following background: question/problem being addressed, experimental design, where the samples are from and how they were collected, which bioanalytical methods were used and how the raw data were processed to generate the files that you receive.
Along with the dataset you will receive a set of questions that will guide your choice of statistical analyses and visualisations.
For example, you may receive a sample by taxon table containing the relative frequencies of multiple taxa in samples from different treatments. You may then be asked to determine whether there were significant differences in diversity between experimental treatments.
The introduction should detail the background of the case study and highlight why the topic is important.
The Methodology section should cover the analyses that you performed to address the questions.
The Results should contain figures and/or tables the support text describing your findings.
The Discussion should link these findings to the literature to explain their novelty and significance to environmental science
Submission guidelines
Please submit through Turnitin on the ENVM3010 Blackboard site
Deferral or extension
You may be able to apply for an extension.
The maximum extension allowed is 7 days. Extensions are given in multiples of 24 hours.
Group presentations
- Mode
- Activity/ Performance
- Category
- Participation/ Student contribution, Presentation
- Weight
- 25%
Task description
During the course you will form groups. In Teaching Week 10 each group will identify an environmental issue and prepare a case for addressing that issue with Environmental Bioanalytical methods. In Week 12 each group will guide the class through their proposal in an oral presentation. The presentations will be 10-15 min long followed by up to 5 min questions from the audience.
Submission guidelines
Deferral or extension
You cannot defer or apply for an extension for this assessment.
Exam
- Mode
- Written
- Category
- Examination
- Weight
- 35%
- Due date
End of Semester Exam Period
2/11/2024 - 16/11/2024
- Learning outcomes
- L01, L04, L06, L07, L10
Task description
This will be a 2 hour exam consisting of short essay-style questions based around your knowledge and understanding of the issues examined.
Exam details
| Planning time | 10 minutes |
|---|---|
| Duration | 120 minutes |
| Calculator options | Casio FX82 series calculator only |
| Open/closed book | Closed Book examination - no written materials permitted |
| Exam platform | Learn.UQ |
| 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: 1-24.4% |
| 2 (Fail) |
Minimal evidence of achievement of course learning outcomes. Course grade description: 24.5-44.4% |
| 3 (Marginal Fail) |
Demonstrated evidence of developing achievement of course learning outcomes Course grade description: 44.5-49.4% |
| 4 (Pass) |
Demonstrated evidence of functional achievement of course learning outcomes. Course grade description: 49.5-64.4% |
| 5 (Credit) |
Demonstrated evidence of proficient achievement of course learning outcomes. Course grade description: 64.5-74.4% |
| 6 (Distinction) |
Demonstrated evidence of advanced achievement of course learning outcomes. Course grade description: 74.5-84.4% |
| 7 (High Distinction) |
Demonstrated evidence of exceptional achievement of course learning outcomes. Course grade description: 84.5%+ |
Supplementary assessment
Supplementary assessment is available for this course.
Additional assessment information
Applications for Extensions
Information on applying for an extension can be found here - my.UQ Applying for an extension
Extension applications must be received by the assessment due date and time.
If you are unable to provide documentation to support your application by the due date and time you must still submit your application on time and attach a Word document outlining why you cannot provide the documentation and upload the documentation to the portal within 24 hours.
Please note: While your extension request is being considered, you should work towards completing and submitting your assessment as soon as possible.
If you have been ill or unable to attend class for more than 4 weeks in a semester, we advise you to carefully consider whether you are capable of successfully completing your courses. You might need to consider applying for removal of course. We strongly recommend you seek advice from the Faculty that administers your program.
Extensions with Student Access Plans (SAP)
For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g., a medical certificate. A maximum of two applications may be submitted for any one assessment item, unless exceptional circumstances can be demonstrated. All extension requests must be received by the assessment due date and time.
Artificial Intelligence (AI)
The assessment tasks in this course evaluate students’ abilities, skills and knowledge without the aid of Artificial Intelligence (AI). Students are advised that the use of AI technologies to develop responses is strictly prohibited and may constitute misconduct under the Student Code of Conduct.
Turnitin
By submitting work through Turnitin you are deemed to have accepted the following declaration “I certify that this assignment is my own work and has not been submitted, either previously or concurrently, in whole or in part, to this University or any other educational institution, for marking or assessment.”
All students must ensure they receive their Turnitin receipt on submission of any assessments. A valid Turnitin receipt will be the only evidence accepted if assessments are missing. Without evidence, the assessment will receive the standard late penalty, or after five days, will receive zero.
In the case of a Blackboard outage, please contact the Course Coordinator as soon as possible to confirm the outage with ITS.
ﾠ
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
Library resources are available on the UQ Library website.
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 |
Lecture |
Lectures Two 50 min lectures weekly providing context and theory for each topic. Lectures link with the practical sessions within the same week. |
Practical |
A series of laboratory and computer-based sessions Laboratory practical classes teaching methods used to generate data. Computing practical classes teaching how to process, analyse and interpret bioanalytical datasets. Workshops to discuss methods and analyses. |
|
Workshop |
Group presentations During the course you will form groups. In Teaching Week 10 each group will identify an environmental issue and prepare a case for addressing that issue with Environmental Bioanalytical methods. In Week 12 each group will guide the class through their proposal in an oral presentation. The presentations will be 10-15 min long followed by up to 5 min questions from the audience. |
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.