In your groups, discuss the questions you have been given and try to answer them as fully as you can (10 min)
Bubonic Plague
Discussion Topic: Has the Bubonic Plague caused the evolution of immune genes?
Quote Reference: "Re: Doctor Schna-bel von Rour Vos Creditis.als ce fabel quod feribitur von Doctor schmabel."
Themes:
Contagion and its effects on mortality.
Reflection on historical beliefs and practices in medicine.
Influence of the disease on cultural narratives.
Understanding the Bubonic Plague
Key Questions:
What do you know about the Bubonic Plague?
Cause?
Symptoms?
Result?
Yersinia pestis
Scientific Focus: Explore the bacterium responsible for the Bubonic Plague, known as Yersinia pestis.
Paper Introduction
Key Elements Discussed:
Base pair methodologies and significance in DNA analysis.
Important components for examination in DNA samples:
Hydrogen bonds
Base Pair Components:
Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
Immune Genes
Key Immune Genes Studied:
T cell receptors
Cytokines
Interleukins
Other proteins regulating immune cells and functions
Statistics and Probability
Understanding P Values:
Regardless of the statistical test used in a paper, always consider the P-value.
Definition: The P-value represents probability and measures the likelihood that any observed difference between groups is due to chance.
Examples of P values:
P = 0.3
P = 1.2
P = 0.0002
P = 0.05
Allele Frequencies
definitions and terms:
Population: A group of individuals of the same species in a specific area.
Gene Pool: The total genetic diversity found within a population.
Homozygous dominant: Green (AA)
Homozygous recessive: Red (aa)
Heterozygous: Purple (Aa)
Methods
Group Activity: Discuss and make notes on methods (10 min) and nominate one person for class feedback.
Question for Discussion: How did the authors investigate the possible evolution of immune genes as a consequence of the Bubonic plague?
Fishing Experiment
Study Groups:
Humans who died pre-Bubonic Plague
Humans who died at the time of the Bubonic Plague
Humans who died post-Bubonic Plague
DNA Sample Analysis
Analysis Parameters:
Analyzed 516 samples (n = 318 from London; n = 198 from Denmark) for the presence of human DNA using a modified polymerase chain reaction (PCR) assay targeting the single copy nuclear c-myc gene.
Sample Identification:
Identified 360 samples with sufficient endogenous DNA for further analysis and enrichment sequencing.
Sample Preservation Techniques
Many samples were poorly preserved with low endogenous DNA content.
Hybridization Capture:
Used to enrich and sequence 356 immune-related genes and 496 genome-wide association study (GWAS) loci associated with immune disorders.
Utilizing putatively neutral regions (1.5 kb each) defined by Gronau et al.
Method Overview:
Hybridization allows exploiting high-throughput sequencing for population genetic analyses.
Bait molecules are used to select target regions from DNA libraries for sequencing.
Genotype Likelihoods and Selection Detection
Using genotype likelihoods, the minor allele frequency (MAF) was calculated per population at each time point.
Selected only sites with mean MAF greater than 5% (n = 22,868 sites).
Purpose: To detect protective or susceptibility alleles for Y. pestis through observing allele frequency changes pre- and post-Black Death.
Data Analysis for Figure 2
Group Discussion: Analyze components of figure 2 (10 min) and nominate 1 person for feedback.
Figures and Interpretations:
Positive selection at immune loci, using FST values to compare populations before and after the Black Death.
Elements reflecting natural selection patterns have been indicated by allele frequency changes.
Interpretations of Figure 2
FST measures the total genetic variance relative to subpopulation variance.
High FST indicates significant differentiation among populations.
Data Analysis for Figure 4
Group Discussion: Analyze components of figure 4 (10 min) and nominate 1 person for feedback.
ERAP1 and ERAP2 Overview
Aminopeptidases ERAP1 and ERAP2 act synergistically from trimming peptides for MHC class I molecules presentation.
Polymorphisms associated with susceptibility to various infectious agents, particularly Yersinia pestis.
Study the association of ERAP2 genotype with cytokine response during Y. pestis infection based on specific SNPs.
Article Figures
Figure content includes host immune responses related to genetic variations observed during exposures to Y. pestis.
Example Cytokines Measured:
G-CSF
IL-1β
IL-10
CCL3
Evaluation of Study
Group Activity: Discuss strengths and limitations of the investigation and conclusions made (10 min).
Strengths: To be identified based on discussions.
Limitations: Identify based on discussions and challenges in the study.