Adam Kleinschmit and Benita Brink, Adams State University

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Genomics at Adams State University, Adam Kleinschmit

Course Overview

This course is designed to provide students with an in-depth understanding of comparative and functional genomics. Topics discussed include structure and anatomy of DNA, sequences and other methods used in decoding DNA, genes, and entire genomes, gene expression profiling, gene annotation, homology, clusters of ortholog genes, protein structure function, high throughput functional assays, and experimental modification of genomes for medical purposes. Examples presented in the course illustrate the role of functional genomics in drug design, gene discovery, and in designing individual therapies for a variety of diseases and disorders. The laboratory will introduce and use biological data sources for annotating sequence data publically available on the internet. Students will analyze DNA ‘draft’ sequences, examine the sequence data, determine if there are errors or gaps, and 'finish' the sequence to high quality, from various fruit fly species.


GEP Curriculum Used

- An Introduction to NCBI BLAST

- Exercise #1: Detecting & Interpreting Genetic Homology

- Simple Annotation Problem

Implementation

GEP materials/projects were used exclusely with in the laboratory section of a molecular biology course, which focused on Genomics.  The laboratory section of the course meets on a weekly basis for a 3 hour session.  In addition to annotation exercise and project work during the laboratory, students are also expected to do some annotation work outside of class.

Lessons Learned and Future Plans

Students left the course being extreamly comfortable using publically available computational bioinformatics tools and understanding there utility.  Additionally, the annotation process advanced student understanding of eukaryotic gene structure and the evolutionary underpinnings of orthologous genomic sequence.


In future semesters I would like to incorperate more applicational analysis to allow students to explore gene features within their annotated contig.  Specificially, guiding students in more intensive syteny analysis, searching for conserved domains across a wide array of species (including higher eukaryotes), exploration of functional domains and what they encode, as well as creating phylogenetic trees.

Syllabus for Biol 477 (Molecular Biology II)


Course Objectives

• Introduce the students to the fundamentals of comparative and functional genomics.
• Introduce the students to recent advances in enabling technologies associated with genomics and bioinformatics.
• Introduce the students to the concepts of homology, ortholog and paralog genes, gene families, gene annotation, and gene mapping.
• Introduce the students to the enabling computing technology of bioinformatics in solving problems related to systems biology. Introduce and use computer application tools in management, clustering, and analysis of real biological data.

Required Text

Recombinant DNA: Genes and Genomes – A Short Course. 3rd Edition. Watson, J.D., Caudy, A.A., Myers, R.M., and Witkowski, J.A. Cold Spring Harbor Laboratory Press. 2008. ISBN-13: 978-0716728665

Tentative Lecture Topics Outline
1. Overview of functional genomics and bioinformatics
2. Understanding a genome sequence
4. Decoding DNA and integrating sequenced data
5. Comparing and analyzing genomes
6. Finding human disease genes
7. RNA interference
8. DNA fingerprinting and forensics
9. Additional -omic technologies and recent research advances


Tentative Lab Outline
1. Pre-course survey/quiz; Basic overview of GEP / Research question read Intro to GEP doc
2. Intro to BLAST; BLAST walkthrough activity; Behind the BLAST algorithm; Exercise I (Detecting and Interpreting Genetic Homology) [read GEP Annotation Guide]

3. Intro to Annotation Tools; Annotation Walk-through; A Simple annotation exercise [turn in Exercise I (Detecting and Interpreting Genetic Homology)]
4. Annotation Practice (GEP sandbox)
5. Annotation Project #1 (Week 1) / Intro to Gene Model Checker
6. Annotation Project #1 (Week 2 ) / ClustalW analysis

7. Annotation Project #1 Presentations [Electronic Notebooks Due]

8. Annotation Walk through #2 / Annotation Practice (GEP Sandbox) ; Exercise II (Browser-Based Annotation and RNA-SeqData)

9. Annotation Project #2 (Week 1) / synteny & repetitive DNA analysis [Turn in Exercise II (Browser-Based Annotation and RNA-SeqData)]

10. Annotation Project #2 (Week 2) / UTR mapping & analysis
11. Annotation Project #2 (Week 3)
12. Annotation Presentations & Submission of Annotation projects to GEP [Electronic Notebooks Due]

13. End-of-course survey and quiz [Final Reports Due]