The ecologists

used a quantitative PCR (qPCR) assay to investigate the abundance of the novel

organism in several different ecological niches including hydrothermal vents,

deep-sea sediments and shallow coastal waters. The qPCR assay was performed

using a primer that specifically targeted a gene

carried by the novel organism.

Examine the

qPCR results shown above. Which ecological niche (hydrothermal vents, deep-sea

sediments, shallow coastal waters) had the highest abundance of the novel

organism? Briefly explain how you reached this conclusion. (2-3 sentences) (2

marks)

The ACTC1

gene encodes an actin protein that is only expressed in cardiomyocytes (i.e.

cardiac muscle cells). The schematic below shows the histone modifications that

are present in the

Use the

information provided above to explain why the

The ACTB

gene encodes an actin protein that is ubiquitously expressed in all human

cells. As shown in the schematic below, the promoter region of the

The researcher

uses a specialised laboratory technique to examine DNA methylation in the

Q5.

Concisely describe

the patient’s sequence variant in a format suitable for the results section of

a scientific report. Your answer must include the gene name, reference sequence

accession number, correct DNA-level and protein-level notation, and appropriate

gene and protein nomenclature.

A sequence variant

was identified in exon 14 of the patient's 

Q3. How would you classify the patient's sequence variant at the DNA level?

Q4.

How would you classify the patient's sequence

variant at the protein-coding level? (1 mark)

Q2. In the week three applied activities, you performed a pairwise sequence alignment between the patient’s DNA sequencing results and the MFN2 reference sequence (NG_007945.1). Upload a screenshot of your pairwise sequence alignment output from Clustal Omega to the file upload box.

A) PCR RESULTS UPLOAD:

 Upload the

agarose gel image of your PCR results to the file upload box. Record which gel lanes correspond to your experimental reaction, positive control reaction and negative control reaction in the provided table.

B) NEGATIVE CONTROL REACTION

The expected outcome for the negative control reaction is no

visible DNA bands.

i)

Did you observe any visible bands in your negative

control? (YES/NO) (1 mark)

If NO, proceed to the next question (ii). 

If YES, explain whether or not you can have confidence in the

results obtained for the positive control reaction and experimental reaction. In

your answer, consider what the size and appearance of the observed band(s) may

indicate.

C) POSITIVE CONTROL REACTION

The expected outcome for the positive control reaction is a

single DNA band at 187 bp.

ii) Did your positive control produce a band of the

expected size? (YES/NO) (1 mark)

If YES, proceed to the next question (iii). 

If NO, suggest one or more sources of error or procedural

issues that could have resulted in failed amplification of the target sequence.

iii) Did your positive control produce an additional band(s)

at unexpected sizes? (YES/NO) (1 mark)

If NO, proceed to the next question (iv). 

If YES, explain whether or not these bands represent

non-specific amplification. If they do represent non-specific amplification,

suggest one or more adjustments to the reaction mix or thermal cycling

conditions that could improve the specificity of the PCR.

D) EXPERIMENTAL REACTION

The expected outcome for the experimental reaction is a

single DNA band at 187 bp.

iv) Did your experimental reaction produce a band of the

expected size? (YES/NO) (1 mark)

If YES, proceed to the next question (v). 

If NO, suggest one or more sources of error or procedural

issues that could have resulted in failed amplification of the target sequence.

v

) Did your experimental reaction produce an additional

band(s) at unexpected sizes? (YES/NO) (1 mark)

If NO, proceed to the next quiz question. 

If YES, explain whether or not these bands represent

non-specific amplification. If they do represent non-specific amplification,

suggest one or more adjustments to the reaction mix or thermal cycling

conditions that could improve the specificity of the PCR.

Which of the following reagents is suspected of causing genetic defects? (select all that apply)

Guanidine hydrochloride (CW No. 8793256) is a component of the binding buffer. Which of the following hazard statements are listed in the mini SDS for this reagent? (select all that apply)