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.

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 KandelDept. of Biological Science

CSUF

21st Century Issues21st 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 ResourcesOnline 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

Visual Resources

images

videos

animations

Curriculum Resources

classroom

laboratory

Focus on Microbiology Newsletter

Microbiology Education

journal

ASM News features

Articles Reviews

books, textbooks

videos, CD ROMS, software

websites

Unique FeaturesUnique 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 AnalysisGenome Analysis

• The Institute for Genomic Research - TIGR• Over 100 prokaryotic genomes• http://www.tigr.org/tigr-scripts/CMR2/

CMRHomePage.spl

Data analysisData 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 ProjectMicroarray Project

Project AimsProject Aims

1. To understand regulation of gene expression on a global level.2. To teach students to analyse datasets3. 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 OperonExample - 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 predictionsNumber Gene

NameDescription Predicted

Abundance1 aroF 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase

(DAHP synthetase)2 aroG 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase

(DAHP synthetase)3 aroH 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase

(DAHP synthetase)4 aroL Shikimate kinase II5 aroP aromatic amino acid transport protein6 mtr tryptophan-specific transport protein7 tnaA tryptophanase8 tnaB low affinity tryptophan permease9 trpA tryptophan synthase, alpha protein10 trpB tryptophan synthase, beta protein11 trpC anthranilate isomerase and indole-3-glycerolphosphate

synthetase12 trpD anthranilate synthase component II13 trpE anthranilate synthase component I14 trpL trp operon leader peptide15 trpR trp repressor16 trpS tryptophan tRNA synthetase17 tyrA chorismate mutase-T and prephenate dehydrogenase18 recD DNA helicase19 rpmA 50S ribosomal subunit protein L2720 nadE NAD synthetase

Supply data for analysis

Min Min + tryptophanGene GenBank No Description 5 15 30 60 5 15 30 60

aroF AAC75650 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase) 0.149 0.157 0.154 0.158 0.082 0.132 0.094 0.117aroG AAC73841 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase) 1.465 1.364 1.414 1.372 1.034 0.868 0.915 1aroH AAC74774 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase) 0.802 0.805 0.875 0.96 0.546 0.712 0.699 0.688aroL AAC73491 shikimate kinase II 0.331 0.297 0.293 0.329 0.178 0.316 0.238 0.283aroP AAC73223 aromatic amino acid transport protein 1.138 0.982 0.879 0.883 0.246 0.438 0.299 0.383mtr AAC76195 tryptophan-specific transport protein 1.494 1.49 1.466 1.544 0.897 0.886 0.711 0.947nadE AAC74810 NAD synthetase, prefers NH3 over glutamine 3.546 2.914 3.499 3.117 3.527 2.383 3.738 3.669recD AAG48658 RecD protein 2.155 2.107 1.911 2.24 4.375 1.837 1.928 2.964rpmA AAC76217 50S ribosomal subunit protein L27 5.848 5.456 6.182 4.207 4.43 3.973 3.683 2.987tnaA AAC76731 tryptophanase 0.71 0.64 0.693 0.716 5.932 6.989 7.13 7.846tnaB AAC76732 low affinity tryptophan permease 0.453 0.36 0.39 0.398 0.666 0.89 0.77 0.918trpA AAC74342 tryptophan synthase, alpha protein 1.326 1.255 1.384 1.401 0.682 0.554 0.618 0.704trpB AAC74343 tryptophan synthase, beta protein [ 1.48 1.275 1.443 1.348 0.614 0.659 0.664 0.67trpC AAC74344 N-(5-phosphoribosyl)anthranilate isomerase and indole-3-glycerolphosphate synthetase 1.461 1.259 1.467 1.43 0.509 0.636 0.591 0.585trpD AAC74345 anthranilate synthase component II, glutamine amidotransferase and phosphoribosylanthranilate transferase 1.507 1.537 1.612 1.581 0.359 0.573 0.498 0.494trpE AAC74346 anthranilate synthase component I 2.606 2.616 2.791 2.891 0.544 0.943 0.746 0.708trpL AAC74347 trp operon leader peptide 1.098 0.88 0.965 1.247 0.97 0.927 1.067 1.003trpR AAC77346 regulator for trp operon and aroH; trp aporepressor 0.878 0.899 1.049 0.989 0.73 0.771 0.735 0.678trpS AAC76409 tryptophan tRNA synthetase 2.422 2.392 2.606 1.633 2.676 2.252 2.818 2.652tyrA BAA16485 chorismate mutase (CM) / prephenate dehydrogenase 0.217 0.329 0.276 0.189 0.168 0.266 0.186 0.181

Create and/or evaluate graphs

One of 20 One of 2

15 min

1 of 4

15 min

Student AssessmentStudent 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– http://microbelibrary.asm.org

• MERLOT– http://www.merlot.org

• Email: jkandel@fullerton.edu

Bioinformatics

• Senior level course.

• Taught on-line using several programs found on 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#_______     ________    ____________________    _________PS00002     142->146    GLYCOSAMINOGLYCAN       PDOC00002PS00005     114->117    PKC_PHOSPHO_SITE        PDOC00005PS00006     150->154    CK2_PHOSPHO_SITE        PDOC00006PS00006     215->219    CK2_PHOSPHO_SITE        PDOC00006PS00008       26->32    MYRISTYL                PDOC00008PS00008       50->56    MYRISTYL                PDOC00008PS00008     145->151    MYRISTYL                PDOC00008PS00008     191->197    MYRISTYL                PDOC00008PS00008     208->214    MYRISTYL                PDOC00008PS00134       59->65    TRYPSIN_HIS             PDOC00124PS00135     194->206    TRYPSIN_SER             PDOC00124

Hydrophobicity (grease)

2D-Alignment (Clustal W)

Protein Explorer

3D-Alignment

Highly conservedNot 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.