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A Bioinformatic Investigation of a Mysterious Meningoencephalitis

By Sari Matar, Dyan Anore, Basma Galal, Shawn Xiong

A Bioinformatic Investigation of a Mysterious Meningoencephalitis


 

Abstract

This case study gives students an opportunity to use basic bioinformatic tools to develop the skills of data interpretation and analysis. Based on an actual clinical case of a boy who contracted meningoencephalitis, students try to determine the causative agent by analyzing a fragment of foreign DNA collected from his cerebral spinal fluid (CSF). Originally designed as a sequel to another case in the NCCSTS collection (“Not the NMR You Are Thinking of”), the current case can be used on its own as it shifts focus from understanding the function of aldolase in the context of glycolysis to understanding aldolase in terms of its DNA sequence, primary to quaternary protein structure, and structure-function relationships. The case is designed for upper-division undergraduate life science students with a solid understanding of basic biochemistry and molecular biology techniques and concepts. Ideally suited for courses with an emphasis on protein biochemistry, it can also be used in courses with a significant focus on proteins, genes, and molecular biology to help advanced students build connections across subdivisions in life sciences.

   

Date Posted

09/28/2023

Overview

Objectives

  • Apply nucleotide and protein BLAST to analyse unknown sequences.
  • Analyze simple epidemiological data.
  • Identify open reading frames via ORFfinder.
  • Interpret PCR results on agarose gel electrophoresis.
  • Apply PyMOL and multiple-sequence alignment to examine protein structural differences.
  • Build structural models with SWISS-MODEL.
  • Deduce protein functions based on structural models.
  • Connect protein structure to function and vice versa.
  • Become familiar with basic bioinformatic tools currently used in biochemistry and molecular biology.

Keywords

BLAST; bioinformatics; structural modeling; protein structure-function relationship; PyMOL; PCR; agarose gel; rational drug design; amoeba; primary amebic meningoencephalitis; PAM; encephalitis; Naegleria fowleri

  

Subject Headings

Biochemistry
Bioinformatics
Interdisciplinary Sciences
Medicine (General)
Microbiology
Molecular Biology
Public Health

EDUCATIONAL LEVEL

Undergraduate upper division

  

FORMAT

PDF

   

TOPICAL AREAS

N/A

   

LANGUAGE

English

   

TYPE/METHODS

Analysis/Issues, Directed, Discussion, Laboratory

 

 

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