Judith Kandel, CSU Fullerton Scott Cooper, UW-La Crosse Web-based Problem-Solving Exercises for the Life Sciences

MERLOT  MERLOT contains thousands of educational materials. MERLOT  As of July 2004 the Biology section has  677 materials  187 of these have been peer-reviewed.  51 of the materials have attached assignments.  (78 total)  Demonstrate integration of these sites into Microbiology and Bioinformatics courses.

Online Resources for 21st Century Microbiology Education Judy Kandel Dept. of Biological Science CSUF

21st Century Issues Genomics/gene expression Pathogenicity Gene cloning Bioterrorism Environmental microbiology

Critical Thinking Skills Interpret data accurately Apply computational analysis to solve biological problems Distinguish between relevant and irrelevant or valid and invalid information Make appropriate inferences and deductions from biological information Make predictions from hypotheses, theories or models Formulate a testable hypothesis with a coherent biological rationale Devise tests for a hypothesis Evaluate evidence for and against different points of view, alternate hypotheses, or different study designs Synthesize information to build models, to make connections to a principle, theme, or concept

Online Resources Visual resources Curriculum resources Data resources

Vision “The proposed library is analogous to an electronic journal of peer-reviewed scientific articles for the research community. It will be an electronic journal of peer-reviewed curriculum resources for the teaching community.” From NSF proposal 1997

Unique Features Fully searchable Across resource types By themes Review process High quality Information targeted at educators

Data Presentation and Interpretation Twenty strains of Pseudomonas aeruginosa isolated from cystic fibrosis patients were grown in three different growth media (SLB, SBSM-citrate, and SBSM- glucose) and tested for the ability to produce a biofilm on a plastic surface as well as the ability to secrete a hormonal signal, the compound acyl-HSL. Construct tables and graphs with appropriate labels Use primary literature as resource - free access to ASM journals past 6 months at - journals.asm.org

Genome Analysis The Institute for Genomic Research - TIGR Over 100 prokaryotic genomes scripts/CMR2/CMRHomePage.splhttp:// scripts/CMR2/CMRHomePage.spl

Data analysis  Of the known genes, which category has the most genes? Which category has the least genes? How many genes have functions that are unknown? What percent of the genome do they represent? Predict genes that would be present/absent and search E. coli E. coli O157:H7

Describe how this organism relates to oxygen in its metabolism. Provide the evidence/rationale from your search. Compare percent genome devoted to transcription/translation for different size genomes Compare specific genes in Bacteria and Archaea

Developed at BioQuest in 2002 with R. Simon and K. Takayama Microarray datasets were obtained from publicly accessible databases on the internet. The data were condensed into user-friendly format (e.g. highlight several genes of interest and respective expression profiles under specified conditions). Students are provided some background and then collaborate in groups to focus on a dataset of genes Microarray Project

Project Aims Project Aims 1. To understand regulation of gene expression on a global level. 2. To teach students to analyse datasets 3. To focus on a specific mechanism/pathway e.g. apoptosis, DNA repair, metabolic regulation, pathogenesis, etc. 4. To make predictions, analyse data, and make further predictions.

Gene Expression in Response to Changes in Growth Conditions that Affect Tryptophan Metabolism Example - Trp Operon Khodursky et al. (2000) DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli, Proc Natl Acad Sci U S A

Making predictions

Supply data for analysis

Create and/or evaluate graphs One of 20 One of 2 15 min 1 of 4 15 min

Student Assessment  Ability to interpret and plot data.  Ability to recognise and compare expression profiles for genes/pathways of interest.  Rationale in predictions during project.  Group ability to formulate an experimental approach to investigate other genes of interest.

Online Resources ASM Microbe Library – MERLOT –

Bioinformatics Senior level course. Taught on-line using several programs found on MERLOT.on-line MERLOT –Biology Workbench (bioinformatics) –Protein Explorer (protein structure) Students are given a protein sequence and have to make predictions about its function using programs.

Biology Workbench

Motifs (prosearch) Access# From->To Name Doc# _______ ________ ____________________ _________ PS >146 GLYCOSAMINOGLYCAN PDOC00002 PS >117 PKC_PHOSPHO_SITE PDOC00005 PS >154 CK2_PHOSPHO_SITE PDOC00006 PS >219 CK2_PHOSPHO_SITE PDOC00006 PS >32 MYRISTYL PDOC00008 PS >56 MYRISTYL PDOC00008 PS >151 MYRISTYL PDOC00008 PS >197 MYRISTYL PDOC00008 PS >214 MYRISTYL PDOC00008 PS >65 TRYPSIN_HIS PDOC00124 PS >206 TRYPSIN_SER PDOC00124

Hydrophobicity (grease)

2D-Alignment (Clustal W)

Protein Explorer

3D-Alignment Highly conserved Not conserved

Conclusions There are many websites with data and programs that can be used to integrate critical thinking skills into undergraduate courses. This can be done in both introductory and advanced courses. MERLOT is a good resource to find both educational websites, and linked assignments.