Outline

Overview

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)	Marcus Heisler, marcus.heisler@sydney.edu.au
	Lipin Loo, lipin.loo@sydney.edu.au
	Keng Kwang Jason Low, jason.low@sydney.edu.au
	Dale Hancock, dale.hancock@sydney.edu.au
Lecturer(s)	Sandro Fernandes Ataide, sandro.ataide@sydney.edu.au
	Alyson Ashe, alyson.ashe@sydney.edu.au
	Tony Weiss, tony.weiss@sydney.edu.au

Type	Description	Weight	Due	Length
Supervised exam ?	Final exam Timed, written exam.	50%	Formal exam period	2.5 hours
Outcomes assessed:
Small continuous assessment	In‐semester quizzes Creation and peer review of scientific statements	12%	Multiple weeks	Weekly - 3 cycles (statement or review).
Outcomes assessed:
Small continuous assessment	Model Annotation Assignment Onscreen guided presentation (Week 5). Peer review (Week 7).	7%	Multiple weeks	Approx 800 words plus Figures
Outcomes assessed:
Skills-based evaluation	Laboratory reports Participation, data curation and contextual narrative of lab experiment.	21%	Multiple weeks	1000 words plus figures
Outcomes assessed:
Assignment	Formal report Report. Recorded presentation.	10%	Week 11 Due date: 12 May 2023 at 23:59	1000 words plus figures and presentation
Outcomes assessed:
= 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.
In-semester quizzes- Three cycles of authoring a True/False statement on Peerwise, and answering/reviewing statements.
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

Result name	Mark range	Description
High distinction	85 - 100	At HD level, a student demonstrates a flair for the subject as well as a detailed and comprehensive understanding of the unit material. A ‘High Distinction’ reflects exceptional achievement and is awarded to a student who demonstrates the ability to apply their subject knowledge and understanding to produce original solutions for novel or highly complex problems and/or comprehensive critical discussions of theoretical concepts.
Distinction	75 - 84	At DI level, a student demonstrates an aptitude for the subject and a well-developed understanding of the unit material. A ‘Distinction’ reflects excellent achievement and is awarded to a student who demonstrates an ability to apply their subject knowledge and understanding of the subject to produce good solutions for challenging problems and/or a reasonably well-developed critical analysis of theoretical concepts.
Credit	65 - 74	At CR level, a student demonstrates a good command and knowledge of the unit material. A ‘Credit’ reflects solid achievement and is awarded to a student who has a broad general understanding of the unit material and can solve routine problems and/or identify and superficially discuss theoretical concepts.
Pass	50 - 64	At PS level, a student demonstrates proficiency in the unit material. A ‘Pass’ reflects satisfactory achievement and is awarded to a student who has threshold knowledge.
Fail	0 - 49	When you don’t meet the learning outcomes of the unit to a satisfactory standard.

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.

Learning support

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.

Weekly schedule

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

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

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.

Outcomes
Graduate qualities

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
Learning outcomes

Responding to student feedback

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

The focus of some assessment has changed. Fewer True/False statements to answer/review during each Peerwise cycle. One assessment task has been removed so each Laboratory Report now weighs 7%.

Additional information

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.

Current students

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Additional costs

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect

Current students

BCMB3001: Gene and Genome Regulation

Semester 1, 2023 [Normal day] - Remote

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Additional costs

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect