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Unit outline_

BCMB3001: Gene and Genome Regulation

Semester 1, 2024 [Normal day] - Camperdown/Darlington, Sydney

Virtually every cell in your body contains the same DNA, but each one of your cell types uses a distinct subset of genes to define its function throughout its lifetime at every step along its developmental pathway. This unit of study will lead you to appreciate the mechanisms by which cells switch on or switch off genes at different times, in different places and in response to different signals. You will discover how our cells walk the fine line between repairing genetic damage and generating genetic diversity. You will also explore how manipulation of the genome through natural or targeted mutation can contribute to, prevent or treat disease. Our practicals, together with other guided and online learning sessions will introduce you to a wide range of currently utilised techniques for modern molecular biology, ranging from laboratory-based experiments to bioinformatics, in silico and virtual reality studies. By the end of this unit you will be equipped with senior level skills and knowledge to support your studies and careers in the cellular and molecular biosciences.

Unit details and rules

Academic unit Life and Environmental Sciences Academic Operations
Credit points 6
Prerequisites
? 
6 credit points from (BCMB2X01 or BMED2802 or MBLG2X01 or MEDS2003) and 6 credit points from (BCHM2X71 or BCHM2X72 or BCHM3XXX or BCMB2X02 or BCMB3XXX or BIOL2X29 or BMED2401 or BMED2405 or GEGE2X01 or MBLG2XXX or MEDS2002 or PCOL2X21 or QBIO2001)
Corequisites
? 
None
Prohibitions
? 
BCHM3X71 or BCMB3901
Assumed knowledge
? 

Intermediate biochemistry and molecular biology

Available to study abroad and exchange students

Yes

Teaching staff

Coordinator Alyson Ashe, alyson.ashe@sydney.edu.au
Laboratory supervisor(s) Dhruv Monteiro, dhruv.monteiro@sydney.edu.au
Marcus Heisler, marcus.heisler@sydney.edu.au
Lecturer(s) Sandro Fernandes Ataide, sandro.ataide@sydney.edu.au
Tony Weiss, tony.weiss@sydney.edu.au
Alyson Ashe, alyson.ashe@sydney.edu.au
Joel Mackay, joel.mackay@sydney.edu.au
The census date for this unit availability is 2 April 2024
Type Description Weight Due Length
Supervised exam
? 
Final exam
Timed, written exam.
50% Formal exam period 2 hours
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO7 LO9 LO10
Small continuous assessment Lecture quizes
Answer 1 MCQ per lecture for the whole semester.
9% Multiple weeks 5 min per lecture
Outcomes assessed: LO1 LO6 LO5 LO4 LO3 LO2
Small continuous assessment Model Annotation Assignment
Onscreen guided presentation (Week 5). Peer review (Week 7).
10% Multiple weeks Approx 800 words plus Figures
Outcomes assessed: LO1 LO10 LO2
Skills-based evaluation hurdle task Laboratory reports
Participation, data curation and contextual narrative of lab experiment.
21% Multiple weeks 1000 words plus figures
Outcomes assessed: LO1 LO10 LO9 LO8 LO7 LO6 LO2
Assignment qPCR report
Report. Recorded presentation.
10% Week 11
Due date: 06 May 2024 at 23:59
500 words and presentation
Outcomes assessed: LO2 LO6 LO9 LO10
hurdle task = hurdle task ?

Assessment summary

  • To obtain a pass in BCMB3001, it is necessary to pass BOTH the theory and practical components of the course
  • The laboratory course is an essential part of the Unit and students must pass the laboratory component in order to pass the Unit. In order to pass, students must attend 80% of practical sessions, demonstrate engagement, and submit satisfactory laboratory notebook reports for assessment (failure to submit any of the laboratory reports will result in an AF for the Unit- this is a compulsory hurdle task). If technical issues, illness, a requirement to isolate etc. prevent attendance, students should discuss the problem with the coordinator to find out how to make up the missed attendance.
  • Lecture quizzes - there will be one multiple choice question released per lecture. Attendance at the lectures is required to get the question, and 75% attendance AND correct answers will result in full marks for this assessment. Anything less will be scaled appropriately. Contact the coordinator if attendance at lectures will be a problem requiring special consideration. 
  • Model Annotation- Students will annotate models of proteins involved in gene regulation using the 3D annotation tool Sketchfab. Students will prepare an individual short reflection and provide peer-assessment of annotated models. Details will be provided in Week 2.
  • Formal Report- Related to the qPCR prac. Students will be required to design COVID19 diagnostics and prepare a 1 minute presentation. Details will be provided by Week 6.
  • Final Exam- covers all lecture material and theory of practical classes. This assessment is compulsory and failure to attend, attempt or submit will result in an AF for the Unit. If a second replacement exam is required, this exam may be delivered via an alternative assessment method, such as a viva voce (oral exam). The alternative assessment will meet the same learning outcomes as the original exam. The format of the alternative assessment will be determined by the unit coordinator.
  • Detailed information for each assessment can be found on Canvas.

Assessment criteria

The University awards common result grades, set out in the Coursework Policy 2014 (Schedule 1).

As a general guide, a high distinction indicates work of an exceptional standard, a distinction a very high standard, a credit a good standard, and a pass an acceptable standard.

Result name

Mark range

Description

High distinction

85 - 100

Able to write a coherent and flowing report in good English. Using a variety of viewpoints to argue the process for identifying the problem.  Excellent discussion of management strategies to manage this problem.  References are used wisely and the student shows an ability to critique the literature.  Sources included at least three refereed journal articles and these were presented in the correct format in the reference list and using the correct in text citation.

Distinction

75 - 84

Able to write a coherent report in good English. Presented at least two points of view to argue the process for identifying the problem. Good discussion of management strategies to manage this problem.  Sources included at least three refereed journal articles and these were presented in the correct format in the reference list and using the correct in text citation.

Credit

65 - 74

Presented a report in good English.   Presented at least two points of view to argue the process for identifying the problem.  Reasonable discussion of management strategies to manage this problem. Sources included at least two refereed journal articles and these were presented in the correct format in the reference list and using the correct in text citation.

Pass

50 - 64

Presented and report in good English that defined the problem and came to a recommendation. Sources included two refereed journal articles, in a reference list.

Fail

0 - 49

When you don’t meet the learning outcomes of the unit to a satisfactory standard. Presented a report that did not address the problem or was poorly constructed and grammatically incorrect. Did not provide any recommendations. Did not use any refereed journal papers. 

 

For more information see guide to grades.

Late submission

In accordance with University policy, these penalties apply when written work is submitted after 11:59pm on the due date:

  • Deduction of 5% of the maximum mark for each calendar day after the due date.
  • After ten calendar days late, a mark of zero will be awarded.

Academic integrity

The Current Student website provides information on academic integrity and the resources available to all students. The University expects students and staff to act ethically and honestly and will treat all allegations of academic integrity breaches seriously.

We use similarity detection software to detect potential instances of plagiarism or other forms of academic integrity breach. If such matches indicate evidence of plagiarism or other forms of academic integrity breaches, your teacher is required to report your work for further investigation.

Use of generative artificial intelligence (AI) and automated writing tools

You may only use generative AI and automated writing tools in assessment tasks if you are permitted to by your unit coordinator. If you do use these tools, you must acknowledge this in your work, either in a footnote or an acknowledgement section. The assessment instructions or unit outline will give guidance of the types of tools that are permitted and how the tools should be used.

Your final submitted work must be your own, original work. You must acknowledge any use of generative AI tools that have been used in the assessment, and any material that forms part of your submission must be appropriately referenced. For guidance on how to acknowledge the use of AI, please refer to the AI in Education Canvas site.

The unapproved use of these tools or unacknowledged use will be considered a breach of the Academic Integrity Policy and penalties may apply.

Studiosity is permitted unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission as detailed on the Learning Hub’s Canvas page.

Outside assessment tasks, generative AI tools may be used to support your learning. The AI in Education Canvas site contains a number of productive ways that students are using AI to improve their learning.

Simple extensions

If you encounter a problem submitting your work on time, you may be able to apply for an extension of five calendar days through a simple extension.  The application process will be different depending on the type of assessment and extensions cannot be granted for some assessment types like exams.

Special consideration

If exceptional circumstances mean you can’t complete an assessment, you need consideration for a longer period of time, or if you have essential commitments which impact your performance in an assessment, you may be eligible for special consideration or special arrangements.

Special consideration applications will not be affected by a simple extension application.

Using AI responsibly

Co-created with students, AI in Education includes lots of helpful examples of how students use generative AI tools to support their learning. It explains how generative AI works, the different tools available and how to use them responsibly and productively.

Support for students

The Support for Students Policy 2023 reflects the University’s commitment to supporting students in their academic journey and making the University safe for students. It is important that you read and understand this policy so that you are familiar with the range of support services available to you and understand how to engage with them.

The University uses email as its primary source of communication with students who need support under the Support for Students Policy 2023. Make sure you check your University email regularly and respond to any communications received from the University.

Learning resources and detailed information about weekly assessment and learning activities can be accessed via Canvas. It is essential that you visit your unit of study Canvas site to ensure you are up to date with all of your tasks.

If you are having difficulties completing your studies, or are feeling unsure about your progress, we are here to help. You can access the support services offered by the University at any time:

Support and Services (including health and wellbeing services, financial support and learning support)
Course planning and administration
Meet with an Academic Adviser

WK Topic Learning activity Learning outcomes
Multiple weeks Gene Architecture and Regulatory Mechanisms Lecture (10 hr) LO1 LO2 LO5 LO6
Transcriptomics Lecture (4 hr) LO2 LO3 LO4 LO5 LO7
Maintenance of a Dynamic Genome Lecture (6 hr) LO1 LO2 LO4 LO5 LO6
RNA in the Control of Information Flow Lecture (4 hr) LO1 LO2 LO3 LO5 LO6
Gene regulation in development and disease Practical (12 hr) LO1 LO2 LO6 LO7 LO8 LO9 LO10
Measuring transcription in MEL cells using qPCR Practical (12 hr) LO2 LO6 LO7 LO8 LO9 LO10
Measuring protein expression in MEL cells using Western Blotting Practical (12 hr) LO2 LO6 LO7 LO8 LO9 LO10

Attendance and class requirements

  • To obtain a pass BCMB3001, you must pass BOTH theory and practical components of the Unit. 
  • In order to pass the practical component of the Unit, students must attend 80% of practical sessions, demonstrate engagement, and submit satisfactory laboratory notebook reports for assessment (failure to submit any of the laboratory reports will result in an AF for the Unit- this is a compulsory hurdle task). If technical issues, illness, a requirement to isolate etc. prevent attendance, students should discuss the problem with the coordinator to find out how to make up the missed attendance.
  • The Final Exam is compulsory and failure to attend, attempt or submit will result in an AF for the Unit. If a second replacement exam is required, this exam may be delivered via an alternative assessment method, such as a viva voce (oral exam). The alternative assessment will meet the same learning outcomes as the original exam. The format of the alternative assessment will be determined by the unit coordinator.
  • Failure to complete hurdle tasks to a satisfactory level, or attempt compulsory tasks, will result in the award of an AF grade.

 

 

Study commitment

Typically, there is a minimum expectation of 1.5-2 hours of student effort per week per credit point for units of study offered over a full semester. For a 6 credit point unit, this equates to roughly 120-150 hours of student effort in total.

Required readings

There are no set texts for this unit.  Students have found the following useful for reference:

Lewin B et al Genes XII (12th edition, Jones and Bartlett, 2018)

Alberts B et al Molecular biology of the cell (6th edition, Garland Science, 2014)

Learning outcomes are what students know, understand and are able to do on completion of a unit of study. They are aligned with the University's graduate qualities and are assessed as part of the curriculum.

At the completion of this unit, you should be able to:

  • LO1. outline the basic principles and describe in detail the constituent elements of gene and genome architecture, and attribute these features to their functions in regulation of gene expression
  • LO2. describe the mechanisms involved in gene regulation; illustrate the roles of different sets of proteins and nucleic acids in this process
  • LO3. identify the main species of RNA that contribute to gene regulation; investigate how these species contribute to complexity and genetic diversity
  • LO4. explain the mechanisms by which the cell maintains the genome; analyse which features drive fidelity or diversity
  • LO5. understand and predict how changes in DNA/RNA sequence can affect gene expression and outputs of the genome
  • LO6. compare the various ways in which gene expression can be regulated; assess which features of the genome can be manipulated to modify cellular function, development and contribute to disease
  • LO7. explain, with examples, the difference between qualitative and quantitative measurements; determine which of the different techniques should be used, and implement methods to visualise and characterise the properties of gene expression regulation in an accurate and reproducible manner
  • LO8. collect experimental data and adapt, develop and trouble-shoot experimental procedures for novel contexts and requirements
  • LO9. assess the quality of data, interpret and draw conclusions from data obtained in the laboratory
  • LO10. summarise and identify the key points from biochemical data from a range of published sources; synthesise and communicate the findings.

Graduate qualities

The graduate qualities are the qualities and skills that all University of Sydney graduates must demonstrate on successful completion of an award course. As a future Sydney graduate, the set of qualities have been designed to equip you for the contemporary world.

GQ1 Depth of disciplinary expertise

Deep disciplinary expertise is the ability to integrate and rigorously apply knowledge, understanding and skills of a recognised discipline defined by scholarly activity, as well as familiarity with evolving practice of the discipline.

GQ2 Critical thinking and problem solving

Critical thinking and problem solving are the questioning of ideas, evidence and assumptions in order to propose and evaluate hypotheses or alternative arguments before formulating a conclusion or a solution to an identified problem.

GQ3 Oral and written communication

Effective communication, in both oral and written form, is the clear exchange of meaning in a manner that is appropriate to audience and context.

GQ4 Information and digital literacy

Information and digital literacy is the ability to locate, interpret, evaluate, manage, adapt, integrate, create and convey information using appropriate resources, tools and strategies.

GQ5 Inventiveness

Generating novel ideas and solutions.

GQ6 Cultural competence

Cultural Competence is the ability to actively, ethically, respectfully, and successfully engage across and between cultures. In the Australian context, this includes and celebrates Aboriginal and Torres Strait Islander cultures, knowledge systems, and a mature understanding of contemporary issues.

GQ7 Interdisciplinary effectiveness

Interdisciplinary effectiveness is the integration and synthesis of multiple viewpoints and practices, working effectively across disciplinary boundaries.

GQ8 Integrated professional, ethical, and personal identity

An integrated professional, ethical and personal identity is understanding the interaction between one’s personal and professional selves in an ethical context.

GQ9 Influence

Engaging others in a process, idea or vision.

Outcome map

Learning outcomes Graduate qualities
GQ1 GQ2 GQ3 GQ4 GQ5 GQ6 GQ7 GQ8 GQ9

This section outlines changes made to this unit following staff and student reviews.

The focus of some assessment has changed. Two Peerwise cycles have been removed and replaced with a series of Lecture quizzes. The weighting of the sketchfab assignment has been slightly increased.

Referencing guide: if you use someone’s actual words you must use quotation marks as well as an appropriate reference. If you use someone’s ideas, formulas, methods, evidence, tables or images you must use a reference. You must not present someone’s artistic work, musical creation, programming code or any other form of intellectual property as your own. If referring to any of these, you must always present them as the work of their creator and reference in an appropriate way.

For this Unit of Study, you are required to submit a Student Plagiarism Compliance Statement. This form and submission details are available from Canvas.

Additional costs

There are no additional costs for this unit, except that students are required to have a labcoat, safety glasses and 3-layer mask for lab classes.

Work, health and safety

Please note that masks must be worn in Laboratory Classes for this course. 

Personal and communal safety is of the highest importance. Students must familiarize themselves with and observe the safety procedures outlined in the WHS guidelines (see Canvas site; General laboratory safety rules are below). For this Unit of Study, you are required to submit a Safety Awareness Statement. This form and submission details are available from Canvas.

We are governed by the Work Health and Safety Act 2011, Work Health and Safety Regulation 2011 and Codes of Practice. Penalties for non-compliance have increased. Everyone has a responsibility for health and safety at work. The University’s Work Health and Safety policy explains the responsibilities and expectations of workers and others, and the procedures for managing WHS risks associated with University activities.

General Laboratory Safety Rules

  • No eating or drinking is allowed in any laboratory under any circumstances
  • A laboratory coat and closed-toe shoes are mandatory
  • Follow safety instructions in your manual and posted in laboratories
  • In case of fire, follow instructions posted outside the laboratory door
  • First aid kits, eye wash and fire extinguishers are located in or immediately outside each laboratory
  • As a precautionary measure, it is recommended that you have a current tetanus immunisation. This can be obtained from University Health Service: unihealth.usyd.edu.au/

Disclaimer

The University reserves the right to amend units of study or no longer offer certain units, including where there are low enrolment numbers.

To help you understand common terms that we use at the University, we offer an online glossary.