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Schedule

  • 10 min questions
  • 10 min group answers
  • 10 min introductory theory
  • 10 min group work (methods)
  • 10 min group answers
  • 10 min group work (figure 2)
  • 10 min group answers
  • 10 min group work (figure 4)
  • 10 min group answers
  • 10 min group work (evaluation)
  • 10 min group answers

Evolution Recap

  • 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.