Post on 28-Dec-2015
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.
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)
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.