#465 You are required to investigate the effects

You are required to investigate the effects - Biology

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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 analyse them. What kind of metabolomics approach has your lab head suggested and why? What considerations with respect to your experimental design should you propose?

So what type of Metabolomics tests would we be using in this experiment? how would we determine if the infected group was actually infected?

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Free Chegg Answer

There are two approaches in metabolomics:

1. Targeted approach

2. Untargeted approach

Targeted approach measures the set of metabolites to address specific biochemical question.

Untargeted approach, also called as global approach measures as many metabolites as possible from a range of biological samples without any bias.

The experimental requirement in the question needs the utilization of targeted approach.

Workflow for both the approaches is as follows:

Designing of the experiment.--> Sample Preparation --> Chromatography -->Mass Spectrometry -->Data acquisition --> Data processing --> Analysis and Imterpretation

Experimental Design:

Factors that can affect the experiment have to be eliminated or identified so that they can be accounted for during data analysis. Other factors like sample size, randomisation, and storage helps in producing reproducible and successful experiments that minimise erroneous variability.

Noise error during the handling of experiments should also be considered.

Sample Preparation:

It imvolves collection, storage, extraction and preparation of the sample for the individual measurement system

In most case, solid case extraction system is preferred in metabolomics studies.

Mass spectrometry (MS) :

It is an analytical technique used to measure small molecules.

The analytes are ionised at an ion source before they can be detected in a coupled mass detector.

The resulting data typically consists of mass-to-charge (m/z), time, and intensity triplets that describe – for every detected ion mass – the strength of the ion beam and the time it is detected by the spectrometer.

Data processing:

Data processing aims to extract biologically relevant information from the acquired data. It includes many steps that are similar for MS.

Noise (or error) is an important consideration to factor in because it distorts the signals in your data. There are two types of noise:

Random noise: results from contaminants and general technological limitations.

Systematic noise: results from external factors that are not relevant for the study. Baseline drift is one example of systematic noise and is a common problem in liquid chromatography-mass spectrometry (LC-MS) where the gradient of the mobile phase causes the chromatographic baseline to be irregular.

Analysis and Interpretation:

The goal of statistical analysis is the categorisation and prediction of sample properties through generation of models that capture the information contained in data matrices.

The dimensionality-reduction methods can be used in classification, regression, and prediction exercises.

The quality of the statistical models that we infer depends significantly on the data pre-processing, scaling and normalisation methods used