PFA

PFA


PART A (Clinical Biochemistry) The following short answer questions relate to the lecture material presented in the clinical biochemistry lectures. A 27-year-old male with a known diabetic condition was admitted to an emergency department. His Initial biochemistry results are as follows: Arterial blood gas pH 7.21 (7.35-7.45) PCO226mm Hg(35-45) PO2100mm Hg(80-110) HCO310mmol/L(23-33) Plasma Sodium 132mmol/L(135-145) Potassium6.2mmol/L(3.1-4.2) Chloride101mmol/L(98-106) Urea12.0mmol/L(3.0-8.0) Creatinine0.12mmol/L(0.05-0.12) Glucose 23.5mmol/L(4.0 – 6.0) Ketones5.3mmol/L(<0.6) q1. describe the acid-base disturbance (2 marks). ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ q2. calculate the anion gap and comment on its significance (2 marks). ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ q3. what is the likely cause of this patient’s raised potassium result? (2 marks). ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ q4. explain which result/s are most indicative of diabetes condition (2 marks). ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ q5. is this patient’s c-peptide concentration likely to be low, normal or high? (2 marks). ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ 2 | page part b (metabolomics) the following short answer questions relate to the lecture material presented in the metabolomics lectures. please carefully read all questions before answering. as a recent graduate of rmit university you have recently been granted $750,000 (over 4 years) to work at a world-renowned infectious diseases institute located in victoria, australia. you are required to investigate the effects of the novel small molecule anti-viral (lckdwn-21) to determine the metabolic changes in the tca cycle which take place in the tissue of lungs of monkeys infected by the delta variant (b.1.617.2.1) (infected group (i), n = 45) vs the tissue of lungs of healthy monkeys (control group (c), n = 50). you have been asked by your laboratory head to design and carry out a “targeted lc-ms metabolomics experiment.” q1. comment on your proposed experimental design, how you are going to harvest the tissue of the lungs of monkeys and what considerations you need to keep in mind. your lab head will first need to approve your experimental design before you begin (5 marks). you may wish to draw a diagram to explain your answer. ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ q2. congratulations! your lab head has approved your experimental design 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? you may wish to draw a diagram to explain your answer (10 marks). ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ q3. your lab head has now asked you to analyse the extracts on the lc-ms. what other samples should be run with extracts and why? (5 marks) ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ q4. your lab head is quite pleased that you have acquired and analysed all the data (table 1) in such a short amount of time. how can your lab head determine which metabolites are up and/or down regulated? how can your lab head determine which metabolites are statistically significant? (5 marks) table 1:lc-ms targeted results comparing c (n = 50) vs i (n = 45).   average (ug/ml) std error x-fold sem   average (ug/ml) std error x-fold sem t-test   control (c)   infected (i) malic acid 14.582 1.228 1.000 0.084   17.030 1.214 1.168 0.071 0.237 fumaric acid 26.006 1.597 1.000 0.061   20.605 0.701 0.792 0.034 0.049 citric acid 10.961 1.810 1.000 0.165   47.963 27.301 4.376 0.569 0.005 isocitric acid 4.700 0.952 1.000 0.203   3.584 0.438 0.763 0.122 0.427 -ketoglutarate 1610.752 200.839 1.000 0.125   1417.715 84.238 0.880 0.059 0.509 oxaloacetate 126.322 9.972 1.000 0.079   88.393 16.770 0.700 0.190 0.081 succinic acid 0.135 0.038 1.000 0.279   0.320 0.030 2.369 0.095 0.006 cis-aconitate 0.469 0.099 1.000 0.210   0.730 0.077 1.556 0.106 0.072 ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ q5. your lab head has interpreted the data you provided in table 1 and noticed some interesting and exciting changes. your lab head has now asked you to perform a hierarchical clustering analysis (multivariate analysis). briefly illustrate and describe how your hierarchical clustering analysis would look like. you will need to draw a diagram to explain your answer (5 marks). ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ congratulations! you have carried out to completion a metabolomics experiment and your lab supervisor is exceptionally happy with you q1.="" describe="" the="" acid-base="" disturbance="" (2="" marks).="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" q2.="" calculate="" the="" anion="" gap="" and="" comment="" on="" its="" significance="" (2="" marks).="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" q3.="" what="" is="" the="" likely="" cause="" of="" this="" patient’s="" raised="" potassium="" result?="" (2="" marks).="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" q4.="" explain="" which="" result/s="" are="" most="" indicative="" of="" diabetes="" condition="" (2="" marks).="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" q5.="" is="" this="" patient’s="" c-peptide="" concentration="" likely="" to="" be="" low,="" normal="" or="" high?="" (2="" marks).="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" 2="" |="" page="" part="" b="" (metabolomics)="" the="" following="" short="" answer="" questions="" relate="" to="" the="" lecture="" material="" presented="" in="" the="" metabolomics="" lectures.="" please="" carefully="" read="" all="" questions="" before="" answering.="" as="" a="" recent="" graduate="" of="" rmit="" university="" you="" have="" recently="" been="" granted="" $750,000="" (over="" 4="" years)="" to="" work="" at="" a="" world-renowned="" infectious="" diseases="" institute="" located="" in="" victoria,="" australia.="" you="" are="" required="" to="" investigate="" the="" effects="" of="" the="" novel="" small="" molecule="" anti-viral="" (lckdwn-21)="" to="" determine="" the="" metabolic="" changes="" in="" the="" tca="" cycle="" which="" take="" place="" in="" the="" tissue="" of="" lungs="" of="" monkeys="" infected="" by="" the="" delta="" variant="" (b.1.617.2.1)="" (infected="" group="" (i),="" n="45)" vs="" the="" tissue="" of="" lungs="" of="" healthy="" monkeys="" (control="" group="" (c),="" n="50)." you="" have="" been="" asked="" by="" your="" laboratory="" head="" to="" design="" and="" carry="" out="" a="" “targeted="" lc-ms="" metabolomics="" experiment.”="" q1.="" comment="" on="" your="" proposed="" experimental="" design,="" how="" you="" are="" going="" to="" harvest="" the="" tissue="" of="" the="" lungs="" of="" monkeys="" and="" what="" considerations="" you="" need="" to="" keep="" in="" mind.="" your="" lab="" head="" will="" first="" need="" to="" approve="" your="" experimental="" design="" before="" you="" begin="" (5="" marks).="" you="" may="" wish="" to="" draw="" a="" diagram="" to="" explain="" your="" answer.="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" q2.="" congratulations!="" your="" lab="" head="" has="" approved="" your="" experimental="" design="" 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?="" you="" may="" wish="" to="" draw="" a="" diagram="" to="" explain="" your="" answer="" (10="" marks).="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" q3.="" your="" lab="" head="" has="" now="" asked="" you="" to="" analyse="" the="" extracts="" on="" the="" lc-ms.="" what="" other="" samples="" should="" be="" run="" with="" extracts="" and="" why?="" (5="" marks)="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" q4.="" your="" lab="" head="" is="" quite="" pleased="" that="" you="" have="" acquired="" and="" analysed="" all="" the="" data="" (table="" 1)="" in="" such="" a="" short="" amount="" of="" time.="" how="" can="" your="" lab="" head="" determine="" which="" metabolites="" are="" up="" and/or="" down="" regulated?="" how="" can="" your="" lab="" head="" determine="" which="" metabolites="" are="" statistically="" significant?="" (5="" marks)="" table="" 1:="" lc-ms="" targeted="" results="" comparing="" c="" (n="50)" vs="" i="" (n="45)."  ="" average="" (ug/ml)="" std="" error="" x-fold="" sem=""  ="" average="" (ug/ml)="" std="" error="" x-fold="" sem="" t-test=""  ="" control="" (c)=""  ="" infected="" (i)="" malic="" acid="" 14.582="" 1.228="" 1.000="" 0.084=""  ="" 17.030="" 1.214="" 1.168="" 0.071="" 0.237="" fumaric="" acid="" 26.006="" 1.597="" 1.000="" 0.061=""  ="" 20.605="" 0.701="" 0.792="" 0.034="" 0.049="" citric="" acid="" 10.961="" 1.810="" 1.000="" 0.165=""  ="" 47.963="" 27.301="" 4.376="" 0.569="" 0.005="" isocitric="" acid="" 4.700="" 0.952="" 1.000="" 0.203=""  ="" 3.584="" 0.438="" 0.763="" 0.122="" 0.427="" -ketoglutarate="" 1610.752="" 200.839="" 1.000="" 0.125=""  ="" 1417.715="" 84.238="" 0.880="" 0.059="" 0.509="" oxaloacetate="" 126.322="" 9.972="" 1.000="" 0.079=""  ="" 88.393="" 16.770="" 0.700="" 0.190="" 0.081="" succinic="" acid="" 0.135="" 0.038="" 1.000="" 0.279=""  ="" 0.320="" 0.030="" 2.369="" 0.095="" 0.006="" cis-aconitate="" 0.469="" 0.099="" 1.000="" 0.210=""  ="" 0.730="" 0.077="" 1.556="" 0.106="" 0.072="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" q5.="" your="" lab="" head="" has="" interpreted="" the="" data="" you="" provided="" in="" table="" 1="" and="" noticed="" some="" interesting="" and="" exciting="" changes.="" your="" lab="" head="" has="" now="" asked="" you="" to="" perform="" a="" hierarchical="" clustering="" analysis="" (multivariate="" analysis).="" briefly="" illustrate="" and="" describe="" how="" your="" hierarchical="" clustering="" analysis="" would="" look="" like.="" you="" will="" need="" to="" draw="" a="" diagram="" to="" explain="" your="" answer="" (5="" marks).="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" ______________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________="" congratulations!="" you="" have="" carried="" out="" to="" completion="" a="" metabolomics="" experiment="" and="" your="" lab="" supervisor="" is="" exceptionally="" happy="" with="">