Teaching and Learning with NMPDR

The assignments presented here incorporate the use of bioinformatics tools at NMPDR to teach biological concepts. These activities were developed with a particular course in mind, and may be adapted for more general use. Several were developed at the NMPDR Curriculum Development Workshop held at the University of Illinois in July, 2007. Some of the assignments have not yet been updated for use with the present user interface.

For each topic below we provide lecture slides, suggested readings that provide context for the activity, the student activity, and suggestions for further reading. Please feel free to make use of the materials. We will be happy to work with you to adapt the assignments to fit the learning objectives of your course, or to design a new unit. Please contact us with new ideas or about problems encountered by you or your students.

Assignments

Genome Annotation

Lecture: movie Quicktime movie of slides icon notes pages icon editable slides

Prerequisite reading:

  • Annotation of bacterial and archaeal genomes: Improving accuracy and consistency. PubMedID abstract icon full text
  • Tutorial - How to view the annotation provided by the RAST server.

Student exercise: Instructions for finding functional information by comparative analysis icon Ferroplasma Annotation icon Ferroplasma Annotation

Further reading:

  • The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species. PubMedID abstract
  • Life in acid: pH Homeostasis in acidophiles PubMedID abstract icon full text
  • Life in hot acid: Pathway analyses in extremely thermoacidophilic archaea PubMedID abstract icon full text
  • Genome dynamics in a natural archaeal population (complete genome of Ferroplasma acidarmanus )icon full text
  • Genome sequence of Picrophilus torridus and its implications for life around pH 0 icon full text
  • The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus NATURE full text
  • The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum NATURE full text

Developed for: Eastern Illinois University Bioinformatics seminar

Listeriolysins

Lecture: movie Quicktime movie of slides icon notes pages icon editable slides

Prerequisite reading:

Student exercise: Assignment worksheet icon writable document

Further reading: The cell biology of Listeria monocytogenes infection: the intersection of bacterial pathogenesis and cell-mediated immunity. icon full text

Developed for: Laboratory class at University of Illinois: MCB 428 Bacterial Pathogens Lab

Biosynthesis of Selenocysteine and Selenoproteins

Lecture: icon printable slides icon editable slides

Prerequisite reading:

  • On the road to selenocysteine. icon full text
  • Identification and characterization of phosphoseryl-tRNA [Ser]Sec kinase. icon full text
  • Biosynthesis of Selenocysteine on Its tRNA in Eukaryotes. PLOSICON.gif full text

Student exercise: Assignment worksheet icon writable document

Developed for: Advanced classes at Illinois: MCB 432 Computing in Molecular Biology, CPSC 569 Applied Bioinformatics

University of Illinois MCB 301 Lab 10--Prediction of biochemical test results

Lecture: movie Quicktime movie of slides icon notes pages icon editable slides

Prerequisite reading: Culture and Identification of Infectious Agents icon Bacteriology Ch 2 full text from Microbiology and Immunology On-Line, by Alvin Fox, published by The University of South Carolina School of Medicine.

Student exercise: Assignment worksheet icon writable document with links to assigned genomes

Additional Web Resources:

  • Alphabetic list of microbiology lectures, labs, and disease information at the Indiana University School of Medicine in Terre Haute and Evansville.
  • Virtual Microbiology Lab with case studies at the University of Florida.
  • Comprehensive list of identification tests on the Microbugz site at Austin Community College.

Developed for: Laboratory class at University of Illinois: MCB 301 Experimental Microbiology

Phenotype Prediction

Lecture: icon editable slides

Prerequisite reading: Culture and Identification of Infectious Agents icon Bacteriology Ch 2 full text from Microbiology and Immunology On-Line, by Alvin Fox, published by The University of South Carolina School of Medicine.

Student exercise: Assignment worksheet icon writable document with links to online protocols

Additional Web Resources:

  • Alphabetic list of microbiology lectures, labs, and disease information at the Indiana University School of Medicine in Terre Haute and Evansville.
  • Virtual Microbiology Lab with case studies at the University of Florida.
  • Comprehensive list of identification tests on the Microbugz site at Austin Community College.

Developed for: Laboratory class at Lewis University: Microbiology Lab 02-226

Pyrimidine Biosynthesis

Lecture: icon editable slides icon handout pdf

Prerequisite reading:

Student exercise: Assignment worksheet icon writable document

Further reading:

  • The evolutionary history of the first three enzymes in pyrimidine biosynthesis. PubMedID abstract
  • Biochemical and enzymological aspects of the symbiosis between the deep-sea tubeworm Riftia pachyptila and its bacterial endosymbiont. icon full text

Developed for: Introductory class at William Woods: BIO 301 Genetics

Bacterial Pathogenesis and Virulence Factors

Lecture: movie Quicktime movie of slides icon notes pages icon editable slides

Prerequisite reading:

Student exercise: On-line Inquiry Units focused on Campylobacter, Listeria, Staphylococci, Streptococci, or Vibrio are writable after registration at the iLab site that hosts our user forums.

Developed for: Advanced discussion section at Illinois: MCB 426 Bacterial Pathogenesis

-- Leslie Mc Neil - 06 Mar 2009

Topic revision: r12 - 01 Jun 2009 - 22:51:09 - TWiki Guest
 
Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.