BB2804 - Data Analysis, Interpretation And Presentation Assignment

Assignment Task

Learning Outcomes

• This assessment block provides the opportunity for students to demonstrate their ability to transform and analyse experimental data and present it in the format of a poster.
• Apply knowledge and experience gained from study blocks to experimental data
• Demonstrate understanding of what makes an effective poster presentation
• Demonstrate appropriate transformation, graphical representation and statistical analysis of raw data
• Review data in context of the literature
• Demonstrate advanced computer skills for data analysis (statistics) and presentation (power point).

Poster for the Brunel Symposium on Disease Gene Discovery a case study

What do you need to do?

• Analyse, describe and interpret the findings that are provided in the case study
• The introduction should briefly state what the poster is about.
• The numerical data in the tables should be analysed and presented graphically along with any statistical analysis of the data you perform
• The photomicrographs should be labelled
• Each figure will have a succinct legend to describe the key messages of the figure
• Conclude with a section on the observations made, the likely prognosis and treatments possible for the individual

Case Study: The Patient

In April 2019, a 48-year-old man was admitted to the department of Hepatobiliary Surgery at the local hospital due to upper abdominal discomfort and yellow-stained skin mucosa. Prior to hospital admission, the patient visited the local GP in three separate occasions (05/2018; 08/2018; 01/2019) over the past year manifesting a series of symptoms including mild yellow staining of the skin mucosa, a deep urine colour and nausea. During those visits he was given treatment for heartburn and gastroesophageal acid reflux with no obvious improvement. Blood samples were taken and analysed along with those taken over the past year in the three distinct occasions. 

Case Study: The Science

A contrast-enhanced computed tomography (CECT) scan was ordered. The results revealed a 14-mm nodule observed in the caudate lobe of the liver. The hepatic nodule was suspected of being a primary intrahepatic cholangiocarcinoma (ICC). To confirm this hypothesis a liver biopsy was performed. Previous studies have shown that mutations of isocitrate dehydrogenase (IDH2) - a metabolic enzyme that converts isocitrate to alpha-ketoglutarate (α-KG) while reducing NADP+ to NADPH and liberating CO2 - occur in ICC. DNA was extracted from the liver biopsy of the ICC patient. Exon 4 of the IDH2 gene was amplified by PCR and sequenced.

Human cholangiocytes containing normal levels of unmutated IDH2 (endogenous protein; parental) were transfected with expression vectors either containing wild-type IDH2 cDNA or the mutated IDH2 cDNA extracted from the patient. The cells were grown in culture and IDH2 activity was measured two days after transfections after lysis of the cells. The activity of IDH2 was analysed through the reduction of NADP+ to NADPH, which was measured at 340 nm.

Activation of the NF-kB transcription factors has been closely linked to the pathogenesis of ICC. Therefore, NF-kB activity in nuclear extracts from the patient’s ICC liver tissue and control liver tissue was assessed using a DNA-binding ELISA assay. 

Western blotting analyses were also performed to measure the expression levels of IkBa, Bcl-2, E-cadherin and vascular endothelial growth factor (VEGF) proteins in tissue obtained from normal liver and patient with ICC. 

Finally, a liver biopsy taken from the ICC patient at diagnosis was examined by immunohistochemistry using an antibody detecting Ki67 protein. Ki67-positive cells in the patient’s ICC liver tissue were manually counted using microscopy.

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