Education Commons^™

Engaging Students In A Genetics Course-Based Undergraduate Research Experience Utilizing Caenorhabditis Elegans In Hybrid Learning To Explore Human Disease Gene Variants, Natalie Forte, Virginia Veasey, Bethany Christie, Amira Carter, Marli Hanks, Alan Holderfield, Taylor Houston, Anil Challa, Ashley Turner

Research, Publications & Creative Work

Genetic analysis in model systems using bioinformatic approaches provides a rich context for a concrete and conceptual understanding of gene structure and function. With the intent to engage students in research and explore disease biology utilizing the nematode Caenorhabditis elegans model, we developed a semester-long course-based undergraduate research experience (CURE) in a hybrid (online/in-person) learning environment—the gene-editing and evolutionary nematode exploration CURE (GENE-CURE). Using a combination of bioinformatic and molecular genetic tools, students performed structure-function analysis of disease-associated variants of uncertain significance (VUS) in human orthologs. With the aid of a series of workshop-style research sessions, students worked in teams …

A Review Of How Bioinformatics And Genome Sequencing Are Affecting Precision Medicine, Taylor S. Hickey

Honors Theses

Advancement in genomic sequencing and bioinformatics methods have been affecting biomedical research through precision medicine, especially in the area of cancer. Vaccine therapies can be developed using neoantigens that target specific mutations in tumors. The goals of this research are to identify mutations that lead to cancer and then define subpopulations in which patients can easily be identified. The future goal is to have targeted vaccines that are specific to each subpopulation ready to be used in treatment of their cancer. Limitations to reaching these goals have been due to tumor heterogeneity, cancer location, and difficulty in creating neoantigens for …

The Bioinformatics Virtual Coordination Network: An Open-Source And Interactive Learning Environment, Benjamin J. Tully, Joy Buongiorno, Ashley B. Cohen, Jacob A. Cram, Arkadiy I. Garber, Sarah K. Hu, Arianna I. Krinos, Philip T. Leftwich, Alexis J. Marshall, Ella T. Sieradzki, Daan R. Speth, Elizabeth A. Suter, Christopher B. Trivedi, Luis E. Valentin-Alvarado, Jake L. Weissman, Bvcn Instructor Consortium

Faculty Works: Biology, Chemistry, and Environmental Studies

Lockdowns and “stay-at-home” orders, starting in March 2020, shuttered bench and field dependent research across the world as a consequence of the global COVID-19 pandemic. The pandemic continues to have an impact on research progress and career development, especially for graduate students and early career researchers, as strict social distance limitations stifle ongoing research and impede in-person educational programs. The goal of the Bioinformatics Virtual Coordination Network (BVCN) was to reduce some of these impacts by helping research biologists learn new skills and initiate computational projects as alternative ways to carry out their research. The BVCN was founded in April …

A Novel Approach To Teaching Hidden Markov Models To A Diverse Undergraduate Population, Philip Heller, Pratyusha Pogaru

Faculty Research, Scholarly, and Creative Activity

Hidden Markov Models (HMMs) are an essential tool for Bioinformatic analysis, with extensive success at finding patterns (e.g. CRISPR arrays or genes of interest) in DNA or protein sequences. HMMs are conceptually intricate, and the algorithms that make use of them are complicated. Thus they present a challenge to Bioinformatics instructors at the undergraduate level, particularly when the students’ educational backgrounds are broadly diverse. At San Jose State University, many undergraduate Bioinformatics students are Biology majors with little or no prior coursework in mathematics, statistics, or programming. For this population a theory-based approach to teaching HMMs would be ineffective. To …

Functional, Proteomic And Bioinformatic Analyses Of Nrf2- And Keap1- Null Skeletal Muscle, Lie Gao, Vikas Kumar, Neetha Nanoth Vellichirammal, Song-Young Park, Tara L. Rudebush, Li Yu, Won-Mok Son, Elizabeth J. Pekas, Ahmed M. Wafi, Juan Hong, Peng Xiao, Chittibabu Guda, Han-Jun Wang, Harold D. Scultz, Irving H. Zucker

Health and Kinesiology Faculty Publications

Key points

• Nrf2 is a master regulator of endogenous cellular defences, governing the expression of more than 200 cytoprotective proteins, including a panel of antioxidant enzymes.
• Nrf2 plays an important role in redox haemostasis of skeletal muscle in response to the increased generation of reactive oxygen species during contraction.
• Employing skeletal muscle-specific transgenic mouse models with unbiased-omic approaches, we uncovered new target proteins, downstream pathways and molecular networks of Nrf2 in skeletal muscle following Nrf2 or Keap1 deletion.
• Based on the findings, we proposed a two-way model to understand Nrf2 function: a tonic effect through a Keap1-independent mechanism under basal …

1. Types Of Alignment: Presentations & Demos Assignment, Sarah O'Leary-Driscoll

Sequence Alignments

Pairwise Alignment: DNA

Pairwise Alignment: Protein

Multiple Sequence Alignment: DNA

Multiple Sequence Alignment: Protein

Rapid Verification Of Terminators Using The Pgr-Blue Plasmid And Golden Gate Assembly, Jace C. Bradshaw, Allea Belle Gongola, Nathan S. Reyna

Articles

The goal of this protocol is to allow for the rapid verification of bioinformatically identified terminators. Further, the plasmid (pGR-Blue) is designed specifically for this protocol and allows for the quantification of terminator efficiency. As a proof of concept, six terminators were bioinformatically identified in the mycobacteriophage Bernal13. Once identified, terminators were then made as oligonucleotides with the appropriate sticky ends and annealed together. Using Golden Gate Assembly (GGA), terminators were then cloned into pGR-Blue. Under visible light, false positive colonies appear blue and positively transformed colonies are white/yellow. After induction of an arabinose inducible promoter (pBad) with arabinose, colony …

Sequencing Techniques: A Comparison Assignment, Sarah O'Leary-Driscoll

Sequencing & Genome Mining

With your partner, create some sort of visual (table, map, chart, other, ask me!) that compares the main types of sequencing that we discussed, as well as two of the techniques considered 'next generation'.

Discussion Questions: Genome Mining, Sarah O'Leary-Driscoll

Sequencing & Genome Mining

No abstract provided.

Alignment Information, Sarah O'Leary-Driscoll

Sequence Alignments

Pairwise DNA alignment is frequently used to identify similar regions that will show how two sequences have functional or structural similarities. It can also be used to show how exons and introns change between different sequences and whether they have an effect on the final structure of the RNA after the DNA is processed within a cell.

Alignment Outline, Sarah O'Leary-Driscoll

Sequence Alignments

No abstract provided.

2: Sequence Alignment Practice Activity, Sarah O'Leary-Driscoll

Sequence Alignments

Now that you have learned how to do the four basic sequence alignments (Pairwise and Multiple for both nucleotide and protein sequences) select a gene/protein, it may be one that you've used before, and run each of these alignments.

Pt. 2: Presentation / Paper Guidelines, Sarah O'Leary-Driscoll

Research Project

The presentations for your project should follow the same format that the paper would, but in a much more abbreviated form, aim for 5-7 minutes.

Project Guidelines, Sarah O'Leary-Driscoll

Research Project

No abstract provided.

Pt. 1: Research Question & Background, Sarah O'Leary-Driscoll

Research Project

No abstract provided.

Primer Design Activity, Sarah O'Leary-Driscoll

Primer Design

No abstract provided.

Obtaining Genomic Sequence Practice, Sarah O'Leary-Driscoll

Introduction to NCBI

No abstract provided.

Dna Timeline And Poster Project, Sarah O'Leary-Driscoll

Genomics: Past & Future

The DNA timeline goes through many of the major discoveries that have driven our understanding of genetics since Mendel. Pick two scientists and create a PowerPoint slide poster (to be printed out on regular printer sized paper) that covers the following:

3: Genomics: Past & Future Bibliography, Sarah O'Leary-Driscoll

Genomics: Past & Future

No abstract provided.

Future Of Genomics: Presentations, Sarah O'Leary-Driscoll

Genomics: Past & Future

In his testimony to a House of Representatives sub-committee on health, director of the National Human Genome Research Institute, Francis S. Collins, said that the future of genomics had three main focal points:

"Genomics to Biology: The human genome sequence provides foundational information that now will allow development of a comprehensive catalog of all of the genome's components, determination of the function of all human genes, and deciphering of how genes and proteins work together in pathways and networks.

Genomics to Health: Completion of the human genome sequence offers a unique opportunity to understand the role of genetic factors in …

Database/Resource Acronyms, Sarah O'Leary-Driscoll

Course Information

No abstract provided.

What Is Bioinformatics?, Sarah O'Leary-Driscoll

Course Information

Bioinformatics has evolved into a full-fledged multidisciplinary subject that integrates developments in information and computer technology as applied to Biotechnology and Biological Sciences. Bioinformatics uses computer software tools for database creation, data management, data warehousing, data mining and global communication networking. Bioinformatics is the recording, annotation, storage, analysis, and searching/retrieval of nucleic acid sequence (genes and RNAs), protein sequence and structural information. This includes databases of the sequences and structural information as well methods to access, search, visualize and retrieve the information. Bioinformatics concern the creation and maintenance of databases of biological information whereby researchers can both access existing information …

Comprehensive Course Syllabus, Sarah O'Leary-Driscoll

Course Information

The bioinformatics seminar is focused on developing an understanding of the principles behind genomic analyses, developing skills using the different available bioinformatics programs, and becoming aware of the past developments and current research avenues that are benefited by these types of analyses.

Glossary Of Bioinformatics Terms, National Human Genome Research Institute

Course Information

No abstract provided.

Addressing Misconceptions About Evolution, Sarah O'Leary-Driscoll, Don Dosch

Evolution

"Leave with effective ways to identify and address misconceptions about evolution, with a particular focus on supporting explanations with evidence."

A Course-Based Research Experience: How Benefits Change With Increased Investment In Instructional Time, Christopher D. Shaffer, Consuelo J. Alvarez, April E. Bednarski, David Dunbar, Anya L. Goodman, Catherine Reinke, Anne G. Rosenwald, Michael J. Wolyniak, Cheryl Bailey, Daron Barnard, Christopher Bazinet, Dale L. Beach, James E.J. Bedard, Satish Bhalla, John Braverman, Martin Burg, Vidya Chandrasekaran, Hui-Min Chung, Kari Clase, Randall J. Dejong, Justin R. Diangelo, Chunguang Du, Todd T. Eckdahl, Heather Eisler, Julia A. Emerson, Amy Frary, Donald Frohlich, Yuying Gosser, Shubha Govind, Adam Haberman, Amy T. Hark, Charles Hauser, Arlene Hoogewerf, Laura L.M. Hoopes, Carina E. Howell, Diana Johnson, Christopher J. Jones, Lisa Kadlec, Marian Kaehler, S. Catherine Silver Key, Adam Kleinschmit, Nighat P. Kokan, Olga Kopp, Gary Kuleck, Judith Leatherman, Jane Lopilato, Christy Mackinnon, Juan Carlos Martinez-Cruzado, Gerard Mcneil, Stephanie Mel, Hemlata Mistry, Alexis Nagengast, Paul Overvoorde, Don W. Paetkau, Susan Parrish, Celeste N. Peterson, Mary Preuss, Laura K. Reed, Dennis Revie, Srebrenka Robic, Jennifer Roecklein-Canfield, Michael R. Rubin, Kenneth Saville, Stephanie Schroeder, Karim Sharif, Mary Shaw, Gary Skuse, Christopher D. Smith, Mary A. Smith, Sheryl T. Smith, Eric Spana, Mary Spratt, Aparna Sreenivasan, Joyce Stamm, Paul Szauter, Jeffrey S. Thompson, Matthew Wawersik, James Youngblom, Leming Zhou, Elaine R. Mardis, Jeremy Buhler, Wilson Leung, David Lopatto, Sarah C.R. Elgin

Faculty Publications

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant …

Theme-Based Instruction: Making Conceptual Ties With The Sickle Cell Story, Sherry S. Herron, John Parr, Bridgette Davis, Parker Nelson

Faculty Publications

We describe the concepts and resources presented during a workshop offered to high school biology teachers using sickle cell disease as a theme in a biology course. We provide their pretest and posttest results and reactions.

1: "To Know Ourselves", The U.S. Department Of Energy, The Human Genome Project

Genomics: Past & Future

AT THE END OF THE ROAD in Little Cottonwood Canyon, near Salt Lake City, Alta is a place of near-mythic renown among skiers. In time it may well assume similar status among molecular geneticists. In December 1984, a conference there, co-sponsored by the U.S. Department of Energy, pondered a single question: Does modern DNA research offer a way of detecting tiny genetic mutations—and, in particular, of observing any increase in the mutation rate among the survivors of the Hiroshima and Nagasaki bombings and their descendants? In short the answer was, Not yet. But in an atmosphere of rare intellectual fertility, …

2: "The Mapping Of Chromosome 16", Norman A. Doggett, Raymond L. Stallings, Carl E. Hildebrand, Robert K. Moyzis

Genomics: Past & Future

Human chromosome 16 is the main focus of the mapping efforts at Los Alamos. The large photomicrograph on these opening pages illustrates the starting point for those mapping efforts, the evaluation of our chromosome-16-specific library of cloned fragments. Among the 23 pairs of human chromosomes, one pair, chromosome 16, is identified by fluorescence in-situ hybridization. Thousands of yellow fluorescent probes derived from the clone library have hybridized to both copies of chromosome 16. The high density and uniform coverage of the fluorescent signals were a strong indication that we could use the library to construct a map of overlapping cloned …