Describe the difference in appearance of the Golgi apparatus in cells with mutations in the BICD2 gene relative to the Golgi apparatus in healthy cells.

Part A (50 marks)
Question 1 (50 marks)
This question is associated with the Stroop study you initiated in Topic 1 and for which you analysed data in ‘Handling and presenting health science data’ in study week 9. It assesses module learning outcomes CS2, CS3, KS2 and KS4.
prepare a presentation and an accompanying script for your Stroop investigation.

You should present your own analysis of the sample of data that you downloaded from the Stroop data logger.

a.Prepare a presentation using the provided template. It should contain 9 slides that present:
An appropriate title,
(1 mark)
The scientific background relevant to the investigation. (Up to 5 bullet points.)
(5 marks)
The objective of your investigation.
(1 mark)
The hypotheses you formulated for your investigation (both the null and experimental) – you should also specify if your experimental hypothesis was bidirectional (two-tailed) or unidirectional (one-tailed).
(2 marks)

A summary of how you carried out your investigation, including both the data collection and data analysis phases. If you agreed a change in your data collection protocol with your tutor due to COVID-19 considerations, you should describe what you would have done under normal circumstances for the data collection phase. You could also consider presenting some of this information as a flow chart or similar diagram. (Up to 4 bullet points.)
(4 marks)

A representation of the data collected in your investigation:
(i) An appropriately formatted bar graph displaying the outcomes, based on the descriptive statistics for the appropriate dependent variable and a tabular summary of the descriptive statistics plotted on the graph.

(ii) Results of the inferential statistical analysis used to determine if there is a statistically significant difference between the groups. The outcomes of the inferential statistical analysis must be reported in the appropriate mathematical format.
(20 marks)

Your analysis and interpretation of the data collected in your investigation. (Up to 5 bullet points.)
(5 marks)

The conclusion you have reached from your investigation regarding the effect of age upon Stroop performance.
(2 marks)
(40 marks in total for (a))

b.Prepare a script to accompany your presentation. Your script should provide the spoken narrative for your presentation and not consist of a verbatim repetition of any text on your slides. Your script should be no more than 800 words in length, which equates to approximately 6 minutes of speech (based on an average speaking speed of 130 words per minute).
(10 marks)

Part B (100 marks)
Question 2 (10 marks)
Part B is associated with Topic 3 and its investigation. This question assesses module learning outcomes CS2, CS3, KS2 and KS4.
Rare diseases are often grouped by the organelles they affect, or by their symptoms. One such grouping is the ‘myopathies’, which collects together several rare diseases that have muscle weakness as one of their symptoms. Using the skills you developed in Activity 1.2, use the NLM database to research the two different myopathies listed below to answer questions (a)–(c).
Myoclonic epilepsy with ragged-red fibers (MERRF)
Neutral lipid storage disease with myopathy (NLSDM)

Myoclonic epilepsy with ragged-red fibers (MERRF) is a disorder that affects many parts of the body, particularly the muscles and nervous system. In most cases, the signs and symptoms of this disorder appear during childhood or adolescence. The features of MERRF vary widely among affected individuals, even among members of the same family.
MERRF is characterized by muscle twitches (myoclonus), weakness (myopathy), and progressive stiffness (spasticity). When the muscle cells of affected individuals are stained and viewed under a microscope, these cells usually appear abnormal. These abnormal muscle cells are called ragged-red fibers. Other features of MERRF include recurrent seizures (epilepsy), difficulty coordinating movements (ataxia), a loss of sensation in the extremities (peripheral neuropathy), and slow deterioration of intellectual function (dementia). People with this condition may also develop hearing loss or optic atrophy, which is the degeneration (atrophy) of nerve cells that carry visual information from the eyes to the brain. Affected individuals sometimes have short stature and a form of heart disease known as cardiomyopathy. Less commonly, people with MERRF develop fatty tumors, called lipomas, just under the surface of the skin. MERRF is inherited in a mitochondrial pattern, which is also known as maternal inheritance. This pattern of inheritance applies to genes contained in mtDNA. Because egg cells, but not sperm cells, contribute mitochondria to the developing embryo, children can only inherit disorders resulting from mtDNA mutations from their mother. These disorders can appear in every generation of a family and can affect both males and females, but fathers do not pass traits associated with changes in mtDNA to their children.In most cases, people with MERRF inherit an altered mitochondrial gene from their mother, who may or may not show symptoms of the disorder. Less commonly, the disorder results from a new mutation in a mitochondrial gene and occurs in people with no family history of MERRF.
Neutral lipid storage disease with myopathy is a condition in which fats (lipids) are stored abnormally in organs and tissues throughout the body. People with this condition have muscle weakness (myopathy) due to the accumulation of fats in muscle tissue. Other features of this condition may include a fatty liver, a weakened and enlarged heart (cardiomyopathy) inflammation of the pancreas (pancreatitis), reduced thyroid activity (hypothyroidism), and type 2 diabetes (the most common form of diabetes). Signs and symptoms of neutral lipid storage disease with myopathy vary greatly among affected individuals. This condition is inherited in an autosomal recessive pattern, which means both copies of the gene in each cell have mutations. The parents of an individual with an autosomal recessive condition each carry one copy of the mutated gene, but they typically do not show signs and symptoms of the condition.

a.Describe what is known about the inheritance pattern and name the gene/s that is/are mutated in each of these myopathies.
(4 marks)

b.Both of these myopathies show an underlying reduction in cellular energy levels. Based on the information in the NLM database and your knowledge from S290, briefly describe in your own words how the underlying genetic mutations in both diseases lead to deficits in cellular energy levels. Your answer should clearly indicate which cellular energy source(s) and which stage of ATP production are affected.
(4 marks)

c.What causes the muscle weakness in each of these myopathies?
(2 marks)

Question 3 (15 marks)
Part B is associated with Topic 3 and its investigation. This question assesses module learning outcomes KU1, CS1, CS2 and KS2.
a.In Activity 1.3 and throughout your study of Topic 3, you were encouraged to visit the digital fluorescence microscope. Using slides provided in set 2 of the slide box in the digital fluorescence microscope, you should explore the Golgi apparatus.

Provide a suitable image from the digital microscope that illustrates the typical shape and location of the Golgi apparatus with respect to the nucleus in a normal cell.

Briefly explain why you chose the view you selected and include the technical details you learned to provide when presenting microscope images, including the slide number, the coordinates of the view selected, the objective used and what channels were merged to create the image.
(4 marks)

b.In the digital fluorescence microscope, open and examine Slide 2.4. Select the appropriate channels to visualise the Golgi apparatus and answer the questions that follow.

i.Describe the difference in appearance of the Golgi apparatus in cells with mutations in the BICD2 gene relative to the Golgi apparatus in healthy cells.
(2 marks)
ii.Provide measurements of the Golgi apparatus located at the cell nucleus at coordinates (x = 3330, y = 1518) for its narrowest and widest dimensions. Provide a suitable image for one of your measurements.(2 marks)

iii.If the researchers were interested in changes in the localisation of the BICD-2 protein, briefly explain why they also use GM-130 for immunostaining the cells from healthy donors and individuals with a mutation in the BICD2 gene.
(2 marks)
(6 marks in total for (b))

c.Briefly describe the pathway that a protein that is destined for extracellular secretion takes through the cell. Your description should start at the point the signal peptide of the protein emerges from the ribosome. What important role does the Golgi apparatus play in directing the protein to its destination?
(5 marks)

Question 4 (10 marks)
Part B is associated with Topic 3 and its investigation. This question assesses module learning outcome KU1.
a.Describe the components of an expression vector and explain their function.
(3 marks)

b.Differential sedimentation of a cellular homogenate by centrifugation can be used to enrich for particular cellular components.

i.Which cellular fraction would you expect to be able to identify as being enriched for the following proteins? Briefly explain each of your answers.
GBA1 ATP synthase
(2 marks)
ii.How would you use centrifugation to enrich for 18s RNA?
(2 marks)
(4 marks in total for (b))

c.Fluorescence imaging in live cells and immunoblotting can both be used to study protein expression after transfection of a cell with an engineered expression vector. Both provide different information about a protein. What information can be obtained about a mutated protein using each technique?
(3 marks)

Question 5 (10 marks)
Part B is associated with Topic 3 and its investigation. This question assesses module learning outcomes KU2 and CS1.
In a recent Phase 3, double-blind, randomised, placebo-controlled trial, two doses of a new oral-delivered drug called Voxelotor were tested for their effect on haemoglobin levels in people with sickle cell disease. This drug functions by inhibiting the polymerisation of deoxygenated sickle cell haemoglobin in red blood cells. The effects of once-a-day administration of the drug were regularly measured to an endpoint at 24 weeks, whereupon the data were decoded and differences between groups analysed. Data on haemoglobin levels are shown in Figure 1.

View larger image
Figure 1  The mean change in haemoglobin level in each of three cohorts of patients with sickle cell disease.
Long description
a.Based upon the description above, specify if this trial used a within-subject, or a between-subject design and explain why this was necessary.
(1 mark)

b.Compare the effect on the change in mean haemoglobin level for each of the two doses of drug with that of the placebo group. In your answer, describe the general trend (i.e. across the entire 24-week period), without comparing the individual time points.
(2 marks)

c.Are either of the drug doses found to have a statistically significant effect upon mean haemoglobin level? Briefly explain your answer.
(1 mark)

d.Based upon these data, can Voxelator be considered a cure for sickle cell disease? Explain your answer.
(2 marks)

e.In addition to a novel therapy’s efficacy in clinical trials, identify two other factors considered by regulatory bodies such as the UK’s NICE before approving the therapy for use in the healthcare system.
(2 marks)

f.What is the fundamental difference between the requirements of a cure for a cancer and a cure for a rare disease?
(2 marks)

Question 6 (10 marks)
Part B is associated with Topic 3 and its investigation. This question assesses module learning outcome KU1.
The cell membrane is the boundary of the cell which separates the cytosol and organelles from the extracellular environment.
a.How do the chemical properties of lipids contribute to the structure of the cell membrane and how do the different types of lipids influence membrane fluidity?
(4 marks)

b.Briefly explain how a transmembrane protein such as the glucose transporter facilitates the diffusion of glucose molecules across the cell membrane.
(2 marks)

c.Which two structural components of the CFTR protein regulate its ability to transport Cl− ions across the membrane and what are their roles in CFTR function?
(2 marks)

d.Why does the ΔF508 mutation in the CFTR gene ultimately lead to a cell’s decreased ability to transport Cl− ions?
(2 marks)

Question 7 (45 marks)
Part B is associated with Topic 3 and its investigation. This question assesses module learning outcomes CS2, KS2, KS4, KS5 and PPS1.
In Activity 3.1, you learned how to collect quantitative fluorescence data from cells that had been treated with the indicator TMRE. You will now apply the skills you learnt in Activity 3.1 to carry out an investigation of mitochondrial membrane potential in LSD. Follow the guidance provided in Practical Workbook 1 (page 130 onwards) for ‘Investigating mitochondrial membrane potential’ to test the hypothesis that there is a difference between the mitochondrial membrane potentials in the cells from healthy individuals and individuals with LSD. The data and intensity tool can be found here. You will be automatically allocated a personal set of images from control and LSD cells. Guidance on statistical analysis can be found in Section 2 of the S290 StatsCloud guide.

Complete your study and then answer the following questions.
a.In an appropriate format, present the data/information you collated in Table 30 of Practical Workbook 1.
(15 marks)

b.Explain how you ensured that your data were representative of fluorescence intensity across all the samples you analysed. Include one image as an example of your data collection.
(4 marks)

c.Present your mean values and your estimates of variability in your data that you recorded in Tables 31 and 32 of Practical Workbook 1.
(4 marks)

d.Present an appropriate graph that illustrates a comparison between your mean RFU values from control and LSD cells.
(6 marks)

e.Write a short summary of your statistical analysis and report the results of your t-test in the standard format.
(6 marks)

f.Write a short summary of the results of your investigation and your interpretation of your data against the hypothesis.
(2 marks)

g.What can you conclude about the potential use of these cells, the TMRE probe, and this intensity analysis tool as a potential method to test the cellular effects of candidate drugs and their ability to restore mitochondrial function?
(2 marks)

h.What effect upon TMRE fluorescence in LSD cells would you predict from a drug that did restore mitochondrial function?
(2 marks)

i.Increased cellular oxidative stress has been observed in several LSDs and this can lead to transient opening of the mitochondrial permeability transition pore, mPTP. Describe the effect of this on energy production and on the mitochondrial membrane potential.
(2 marks)

j.What are the consequences for a cell if the mPTP remains open for a long time, leading to the mitochondria in a cell bursting?
(2 marks)

Part C (50 marks)
Question 8 (30 marks)
This question is associated with your study of Topics 1–3. It assesses the module learning outcome CS2 and your progress towards PPS1–3.
Assessing and interpreting health-science evidence and data has been a central theme of Topics 1–3 of S290. Fundamental to this has been consideration of the types and distribution of data from human participant-derived measurements and the assessment of the significance of differences within human participant and experimental model datasets. This is key to the interpretation of experimental investigations and clinical trials.

a.Consider the data shown in Figure 2 and answer the questions that follow.Figure 2  Histogram showing the frequency distribution of serum albumin levels in a sample of 481 men over 20 years of age with a mean of 46.14 g l−1 and a standard deviation of 3.08 g l−1.
Long description
i.Given the type of graph shown in Figure 2, what type of data is being presented here?
(1 mark)

ii.Looking at the shape of the graph shown in Figure 2, what type of distribution does this dataset follow?
(1 mark)

iii.Looking at the graph shown in Figure 2, what is the modal value of serum albumin level for this dataset?
(2 marks)

iv.Assuming that this sample is representative of the entire male population, calculate the values of serum albumin level between which you would expect 95% of measurements in this population to fall. Explain how you derived this range.
(3 marks)

v.If a study were performed to test the experimental hypothesis that a drug will lead to a measureable increase in the serum albumin concentration, what minimum threshold of statistical significance would be used? Explain your answer.
(3 marks)
(10 marks in total for part (a))

b.Suppose that you have been working with a research team focused on lysosomal storage diseases (LSDs). The team has recently completed an experiment in which fibroblasts taken from participants who have a lysosomal storage disease were used to evaluate two new potential drug treatments.

The experiment consisted of growing the cells in the laboratory for 24 hours, at which point the growth media was modified by addition of either saline (a solution of sterile water mixed with a low concentration of salts that should have no physiological effect) or one of the two new drug treatments (drug A or drug B, both of which were administered by being dissolved in an identical saline solution) for another 24 hours. Following the treatment phase and loading of the cells with TMRE, the fluorescence intensity of the cells was measured.

Based on the description of this experiment, answer the following questions.
i.What is the purpose of exposing cells to saline in this experiment?
(2 marks)

ii.Identify the dependent variable in this experiment.
(2 marks)

iii.Identify the independent variable in this experiment and specify the number of levels that it has.
(2 marks)
After the data were collected, a statistical analysis was performed. In this case, the researchers chose to perform an ANOVA.

iv.Why would it have been incorrect for these data to be analysed using independent samples t-tests?
(4 marks)
The ANOVA produced the following information: a P-value of 0.0035, a degrees of freedom parameter of (2,6) and an F statistic value of 16.67.                                    v.Express this information in the standard ANOVA notation.
(2 marks)

vi.Based on the result of the ANOVA, what is the next stage of analysis that the researchers would have performed? Briefly explain your answer.
(3 marks)

The data generated by this experiment are plotted in Figure 3:Figure 3  Bar graph showing mean TMRE fluorescence intensity measurements obtained from cells from participants who have a lysosomal storage disease (LSD). The shading of the bars indicates the drug treatment applied to the cells (saline, drug A or drug B). The symbols and above a square bracket on the graph indicate a statistically significant difference between the bars at either end of the square bracket for two different probability thresholds (* means P < 0.05; ** means P < 0.01). The letters ns above a square bracket indicate no statistically significant difference between the bars at either end of the square bracket.

Long description
vii. Using no more than 150 words, describe the results of the experiment presented in Figure 2 using relative terms (not just reading off values from the bar chart). You should include the key relationships between the variables, and statements on the effectiveness of the two drugs.
(5 marks)
(20 marks in total for part (b))

Question 9 (20 marks)
From your study of Topics 1–3, reflect on your progress towards the S290 Practical and professional skills learning outcomes.

You will be able to:
PPS1 design, conduct and report on investigations with human participants and with analytical techniques.
PPS2 demonstrate an awareness of relevant ethical, privacy, safety and legal aspects related to investigative health sciences.
PPS3 demonstrate an awareness of the health-sciences sector, examples of relevant business and commercial issues, and of the professional skills and behaviours of health scientists.

a.For the Practical and professional skills learning outcome PPS1, describe in up to 150 words how you have achieved this learning outcome, referring to the module materials and your own work in the TMAs (including TMA 03). Your answer should focus on either your Stroop investigation or your study of mitochondrial fluorescence.
(5 marks)

b.For the Practical and professional skills learning outcome PPS2, describe in up to 150 words how one aspect of the module materials has raised your awareness of the ethical or the legal (regulatory) aspects of investigative health science.
(5 marks)

c.For the Practical and professional skills learning outcome PPS3, state how the module materials have raised your awareness of the health-sciences sector, for which examples have been presented in the module materials.
State whether your reflection is related to changes in your awareness of:
the health-science sector business or commercial issues professional skills or behaviours.

Describe the difference in appearance of the Golgi apparatus in cells with mutations in the BICD2 gene relative to the Golgi apparatus in healthy cells.

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