#476 As a recent graduate of University, you have recently
As a recent graduate of University, you have recently - Chemical engineering
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The scenario for Metabolomics based Questions 1-5: Total word limit 500 words
As a recent graduate of University, you have recently been employed (3-year contract) by a world-renowned infectious diseases institute located in Victoria, Australia. You are required to investigate the effects of the novel small molecule anti-viral (DAD030981) to determine the global metabolic changes which take place in the tissue of lungs of monkeys infected by SARS-CoV-2 (Infected Group) vs the tissue of lungs of healthy monkeys (Control Group). You have been asked by your laboratory head to design and carry out a “metabolomics experiment.”
Q1. Your laboratory head has asked you to briefly prepare an experimental design so he can first approve this and then discuss with you how you are going to prepare samples and analyze them.
What kind of metabolomics approach has your lab head suggested and why?
What considerations with respect to your experimental design should you propose?
(5 marks)
Q2. Congratulations! Your lab head has approved your project and has now asked you to provide details as to how you are going to prepare samples for your metabolomics experiment.
Briefly describe your proposed sample preparation workflow ONLY and provide a justification for each step.
What kind of internal standard do you propose to use and why?
(5 marks)
Q3. Your lab head has now asked you to analyze the polar metabolite extract on the laboratory’s LC-MS even though there is a GC-MS available.
Briefly describe how it may be possible to analyze polar metabolites on the GC-MS.
What additional sample should you run with your experiment and why?
Q4. Your lab head is quite pleased that you have acquired all data in such a short amount of time and is now eager for you to analyze the data.
Briefly explain what and why deconvolution is important in appropriately identifying metabolites.
How can your lab head determine which metabolites are up and/or down-regulated?
How can your lab head determine which metabolites are significant?
Q5. Your lab head has interpreted your univariate data and noticed that amino acid metabolism appears to be downregulated in the infected group relative to the control group. Your lab head has now asked you to perform a Principal Component Analysis (multivariate analysis).
Briefly illustrate or describe how your Principal Component Analysis would look like.
What causes your control and infected groups to be separated in three-dimensional space?
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SARS -CoV2 infection can result in asymptomatic, mild, or severe diseases in humans vaccines against SARS-CoV 2 paramount for combating covid -19 disease and curating the pandemic. large animal models are critical for early vaccine testing before human clinical trials.
If the infection found in monkeys with SARS- CoV-2 resulted in mild disease yet lesion was detectable by PET/CT imaging of lungs. shedding of infectious virus from both respiratory and gastrointestinal tract was also documented.
RESPIRATORY PATHOLOGY
Infected monkeys with SARS-CoV-2 via nose, trachea, eyes, and /or mouth and studied them for 3 weeks. we can see symptoms like fever, irregular breathing, reduced appetite, pale appearance, and dehydration developed. radiographs showed that pulmonary infiltrates that resolved within 2 weeks. 4 animals each on 3 and 21 days post-infection (dpi) and found intestinal pneumonia and multifocal lesions. all respiratory tissue showed viral mRNA, indicating active virus. respiration on 3 post-infection, but not on 21 post-infection. overall, the presence of pulmonary infiltrates, virus replication pattern, and histological lesion.
Viral loads, swabs were taken Nose, throat, rectum, and urogenital area, nasal virus shedding was the highest among all. Bronchoalveolar fluid showed high viral load whereas viral RNA could not be detected in blood, urine, or central nervous system. throat swabs showed high viral load after the infection but the virus level was inconsistent . one animal kept shedding viral RNA in rectal swabs even after 2 weeks.
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