Data handling

Interpret the results presented in the provided figures to answer the questions below.

In the Neurogenetics Research Facility, the team has been investigating a unique mouse model exhibiting progressive neurological decline reminiscent of human neurodegenerative diseases.

A mutated gene, named lpg$1621,$ surfaced as a candidate of interest due to its sequence similarity to deubiquitinating enzymes $($DUBs$).$

To explore Ipg$1621$ function, the team has conducted an analysis of the corresponding enzyme Ipg$16211{?}^{1-348},$ while particularly focusing on its interaction with PCNA, a protein known to be ubiquitinated in response to cellular stress. The goal is to discern the role of $lpg{1621}^{1-348}$

a$)$ Review Figure $1,$ which depicts a ubiquitination assay involving PCNA and a mutant variant. Outline the method used to monitor ubiquitination and infer the significance of observed molecular weight changes in PCNA over the indicated time intervals.

b$)$ Examine Figure $2,$ showcasing a deubiquitination assay poststress induction.

Discuss how the experiment tracks changes in PCNA and what the temporal alterations suggest about the deubiquitination mechanism in response to DNA damage.

c$)$ Consider Figure $3,$ detailing an enzymatic activity assay.

Describe the process used to assess the enzyme's specificity for different ubiquitin chains.

Analyse the cleavage patterns to determine the enzyme's activity profile.

d$)$ Reflect on the potential link between the enzymatic function of lpg$1621-348$ and the neurological symptoms observed in the mouse model.

Contemplate the broader implications of ubiquitination dynamics in neuronal health.

Abstract:

Based on the provided Figures and your analysis, construct an abstract to summarise the study. The abstract needs to include a title, background, methods, results and conclusion.

Figure $1$: Ubiquitination assay for PCNA and PCNAK ${?}^{164R}$ mutant.

The assay displays the ubiquitination status of PCNA over a time course of $60$ minutes post$-$stress induction. The corresponding lanes for PCNA and its mutant form are provided, where the appearance and disappearance of higher molecular weight bands are observed.

Figure $2$: Time$-$course assay for the deubiquitination of PCNA after methyl methanesulfonate $($MMS$)$ treatment, which mimics stress by inducing DNA damage.

The gel shows PCNA at different time intervals post$-$treatment, tracking the decrease of ubiquitinated forms.

Figure $3$: Deubiquitinase activity assay of lpg$16211-358$ on different ubiquitin linkages.

The assay was performed using K$48-$linked, K$63-$linked, and linear $($M$1)$ di$-$ubiquitin substrates over a $15-$minute time course.

The cleavage of di$-$ubiquitin $($Ub$2)$ into monoubiquitin $($Ub$)$ was analysed by SDS$-$PAGE followed by Coomassie staining.