In this assessment, students are required to critically review a peer-reviewed, published research article relevant to molecular biology, genomics, or pathology. Students will select (or be provided with) a research article that applies molecular biological techniques used in contemporary pathology or diagnostic laboratories. The task involves both summarising the study and critically reflecting on its scientific merit, methodology, and relevance to pathology practice. Students must submit  between 1200-1500 word written report that demonstrates their ability to:

• Understand and summarise complex scientific literature
• Critically evaluate experimental design and methodology
• Interpret results in a scientific and clinical context
• Reflect on the strengths, limitations, and broader implications of the study

Level of Gen AI allowed: Level 1, No AI: The assessment is completed entirely without Al assistance in a controlled environment, ensuring that students rely solely on their existing knowledge, understanding, and skills

Marks for this assessment will be awarded in accordance with the rubric/marking guide provided on the Moodle site. Your report will be assessed on:

• Demonstrated understanding of the assigned journal article, including its aims, methodology, and key findings.
• Critical evaluation of the genomic and molecular techniques used, including their strengths, limitations, and relevance to current pathology practice.
• Understanding of the genomic pathology concepts underpinning the study and their clinical or diagnostic significance.
• Depth of critical reflection, including interpretation of results and implications for future research or pathology workflows.
• Clear structure and logical flow, with well-defined sections.
• Quality and appropriate use of figures or diagrams (where included).
• Quality and correct use of references, including citation of the assigned article and supporting literature.
• Standard of written communication, including grammar, clarity, and academic style.
• Referencing accuracy and academic integrity.

Case Study: Virtual Development and Mass Production of a Therapeutic Protein

Proteins play diverse and essential roles in human health and disease. While many proteins are developed as therapeutics to treat or manage specific conditions, others serve as diagnostic markers, functional enzymes, structural components, or research targets. In genomic pathology, understanding the molecular basis, expression, and functional validation of proteins is fundamental to both disease investigation and biomedical innovation.

In this case study, you will play the role of a pharmaceutical scientist tasked with designing and optimising the virtual development and large-scale production of a selected protein. You will integrate genomic analysis, cloning strategy, and protein evaluation within a translational biomedical context, using NCBI molecular biology software tools to support sequence analysis, gene characterisation, and experimental design.

Case Description

As a senior scientist in a pharmaceutical company, you have been assigned a project focused on the virtual large-scale production of a protein associated with human disease. You have been provided with the protein’s name and molecular weight (in kilodaltons, kDa). Your primary objective is to apply a functional cloning strategy to clone the gene encoding this protein into an appropriate expression plasmid vector and produce it in high yield using a suitable host system. To achieve this, you must utilise the protein and nucleotide sequences available from the NCBI database. Your findings and recommendations must be presented as a detailed scientific report delivered in the form of an oral presentation, outlining the strategies and methodologies employed throughout the project. Before commencing the assessment, ensure that you visit the subject Moodle site to view the instructional video provided for Assessment 2. An example report is also available on Moodle to guide you in formatting and structuring your assignment.

Topic Selection: Use the link provided under Assessment 2 on Moodle to select a protein from the approved list. Each protein may be selected by a maximum of two students. Selection is on a first-come, first-served basis. If a topic has already been selected by two students, you must choose an alternative from the remaining options.

Deadline: Topic selection closes at the end of Week 2 (Friday, 20 March, 11:59 PM). 

Report Format: Prepare your report in PowerPoint format and record your presentation using Zoom. The presentation must adhere to the following requirements:

• Maximum of 21 slides, including the cover page, references, and acknowledgement slide.
• The recorded presentation must not exceed 25 minutes (± 2 minutes).
• Record your presentation using Zoom and upload the recording to Moodle under Assessment 2 Submissions via Echo360. Detailed submission instructions are available on the subject Moodle site under Assessment 2.
• Your face must be clearly visible while presenting. Your live video feed must appear in the top-right corner of the presentation throughout the recording. Failure to display your live image during the presentation will result in a fail grade for Assessment 2.
• Submit online:  Please follow the submission instructions available at https://moodle.cqu.edu.au/mod/page/view.php?id=3340315&forceview=1

If you experience any difficulties using Echo360 for submission, please contact TaSAC (IT) on 1300 666 620 or email tasac@cqu.edu.au for assistance. Alternatively, you may post your questions in the subject discussion forum.

Level of Gen AI allowed: Level 2- AI Planning- Al may be used for pre-task activities such as brainstorming, outlining and initial research. This level focuses on the effective use of Al for planning, synthesis, and ideation, but assessments should emphasise the ability to develop and refine these ideas independently.

Your presentation must follow the slide sequence outlined below:

Section 1 - Biological Context (3 slides)

• Slide 1 – Cover: Include your full name, student ID, selected protein name, course code, supervisor name, and University logo presented professionally
• Slide 2 – Biological Background: Conduct a concise literature review using PubMed and discuss the protein’s structure, molecular weight (kDa), biological function, cellular location, and known disease associations, clearly explaining why the protein is biologically important.
• Slide 3 – Clinical & Therapeutic Relevance: Explain why this protein matters clinically or biotechnologically, including whether it is a drug target or recombinant therapeutic, its relevance to disease management, and why large-scale production would be valuable.

 Section 2 - Gene & Bioinformatics (7 slides)

•  Slide 4 – Gene Overview and Nucleotide Sequence: Using NCBI, provide the official gene symbol, protein accession number, coding sequence (CDS) accession number, chromosomal location, number of exons, and retrieve the nucleotide coding sequence in FASTA format.
• Slide 5 – Gene Expression: Using NCBI expression data, describe tissue distribution, relative expression levels, biological implications of expression patterns, and confirm retrieval of protein and nucleotide sequence information.
• Slide 6 – Post-Translational Modifications: Using the “Features” section in NCBI, identify relevant post-translational modifications such as glycosylation, phosphorylation, disulfide bonds, signal peptides, or cleavage sites and explain their functional significance.
• Slide 7 – Protein Interactions: Using NCBI or an appropriate interaction database, identify key interacting proteins and explain their functional relevance and implications in disease pathways.
• Slide 8 – Gene Variants: Using NCBI Variation Viewer, identify SNPs and disease-associated mutations, describe at least one significant variant, and explain its functional and clinical consequences.
• Slide 9 – Amino Acid Sequence and ORF: Using the coding sequence (CDS), explain the concept of the open reading frame, identify and highlight the start codon and stop codon, and relate the ORF to the translated amino acid sequence.
• Slide 10 – BLAST Analysis: Perform a BLAST homology search, identify conserved regions and closest homologues, compare sequences across species, report percentage identity, and interpret what conservation suggests about protein function.

 Section 3 – Cloning Design (6 slides)

• Slide 11 – Restriction Map: Using NEBcutter, generate a restriction enzyme map of the coding sequence, identify suitable cloning sites, justify enzyme selection, and confirm that selected enzymes do not cut within the ORF.
• Slide 12 – PCR Primer Design: Design forward and reverse PCR primers including full sequence (5′→3′), melting temperature, GC content, added restriction sites if applicable, and justify design decisions including reading frame considerations.
• Slide 13 – Expression Vector Selection: Select an appropriate expression vector and describe the vector map, promoter type, affinity tag, antibiotic resistance marker, inducibility, and justify why the vector is suitable for high-yield protein expression.
• Slide 14 – Cloning Strategy: Present a clear diagram outlining PCR amplification, restriction digestion, ligation into the vector, transformation into host cells, and selection strategy in logical sequential order.
• Slide 15 – Host Selection: Select a suitable host system such as E. coli or mammalian cells and justify your choice based on post-translational modification requirements, cost, scalability, yield, and intended application.
• Slide 16 – Expression Optimisation: Describe induction conditions, temperature considerations, strategies to improve solubility, management of inclusion bodies if relevant, and tag removal strategy where applicable.

 Section 4 – Protein Validation & Application (3 slides)

• Slide 17 – Purification Strategy: Describe the proposed purification workflow including affinity chromatography, SDS-PAGE analysis, potential Western blot validation, and methods to estimate yield and purity.
• Slide 18 – Biological Activity Confirmation: Propose a functional assay specific to your protein, describe appropriate experimental controls, and explain how biological activity of the recombinant protein would be confirmed.
• Slide 19 – Stability and Safety: Discuss serum half-life considerations, potential toxicity, immunogenicity, and possible molecular modifications such as PEGylation or fusion strategies if the protein were developed as a therapeutic.

Section 5 - Other Slides

• Slide 20 – References: Provide a properly formatted reference list including all PubMed sources, database entries, and online tools used throughout the project.
• Slide 21: Acknowledgements- Acknowledge any individuals who provided guidance or assistance during the completion of this project.

Marks for this assessment will be awarded in accordance with the rubric and marking guide available on the Moodle site. Your submission will be evaluated against the specified assessment criteria. The task requires a PowerPoint presentation consisting of five sections, with a maximum of 21 slides (including the title slide, references, and acknowledgements). The presentation must address genomic analysis, cloning strategy, and protein evaluation as outlined in the assessment guidelines.

Total: 100 marks (graded from Fail to High Distinction), allocated as follows:

• Section 1 - Biological Context (3 slides)  -  10%
• Section 2 - Gene & Bioinformatics (7 slides) -30%
• Section 3 – Cloning Design (6 slides) – 30%
• Section 4 – Protein Validation & Application (3 slides) – 15%
• Section 5 - Other Slides – 5%
• Presentation Quality (clarity, structure, delivery, slide design, timing) – 10%

For further details regarding the assessment criteria, please refer to the Assessment 2 Table of Rubrics available on the subject Moodle site.