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Articles 1 - 30 of 33
Full-Text Articles in Education
Predicted Structure And Analysis Of The Glycoprotein From Sars-Cov-2 Variants Of Interest, Boris Shabaltiy
Predicted Structure And Analysis Of The Glycoprotein From Sars-Cov-2 Variants Of Interest, Boris Shabaltiy
Honors Theses
SARS-CoV-2 has had a devastating effect on the world, and while the public concern and severity of the diseased caused by it have decreased, it is still crucial to monitor the virus for mutations so we can rapidly identify new variants of concern, and then rapidly prepare new vaccines and treatments. The SARS-CoV-2 spike (S) protein from the first isolates of the virus (root variant) was structurally characterized in early 2021. The spike protein structure, designated 7CZW, was uploaded to RCSB Protein Data Bank (RCSB PDB). All subsequent mutations the S protein has accumulated are based on the amino acid …
A Review Of How Bioinformatics And Genome Sequencing Are Affecting Precision Medicine, Taylor S. Hickey
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 …
Genomic Analysis Of Acetoanaerobium Sp. Vlb-1, An Anaerobic Bacterium Isolated From Nebraska's Eastern Saline Wetlands, Claire Martin
Genomic Analysis Of Acetoanaerobium Sp. Vlb-1, An Anaerobic Bacterium Isolated From Nebraska's Eastern Saline Wetlands, Claire Martin
Honors Theses
Through the analysis of genetic code, the genomic and physiological characteristics of an environmental anaerobic bacterial isolate, Acetoanaerobium sp. strain VLB-1, can be determined and significant pathways can be identified in its significance to the environment. This particular organism was isolated from the Eastern Saline Wetlands in Lincoln, NE. With this isolate, an investigation into elemental and amino acid cycling via the Stickland reaction and the Wood-Ljungdahl pathway was conducted to determine possible metabolic products. The Stickland reaction is a relatively newly discovered pathway, observed in the genus Clostridium. A. sticklandii is the main model for this method of …
A Novel Approach To Teaching Hidden Markov Models To A Diverse Undergraduate Population, Philip Heller, Pratyusha Pogaru
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 …
1. Types Of Alignment: Presentations & Demos Assignment, Sarah O'Leary-Driscoll
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
Computational Modeling Intervention: Using Dynamical Models To Teach Complex Biological Processes, Audrey J. Crowther, Tomáš Helikar, Nicholas Galt, Joseph Dauer, Heather Berganr, Bryan Kowal
Computational Modeling Intervention: Using Dynamical Models To Teach Complex Biological Processes, Audrey J. Crowther, Tomáš Helikar, Nicholas Galt, Joseph Dauer, Heather Berganr, Bryan Kowal
UCARE Research Products
The Unites States, while being one of the richest countries in the world, ranks 17th in science proficiency out of 31 countries. New techniques for teaching are needed if the US wants to keep up with increasing global competition. Often the problem with traditional methods for teaching biological processes is that they present the material as linear or causal, when in fact there is a much wider network at play. For example, cellular respiration is often represented as a linear process that always starts with glucose and always ends with ATP and water. However, there are several entry and exit …
Rt-Qpcr Demonstrates Light-Dependent Atrbcs1a And Atrbcs3b Mrna Expressions In Arabidopsis Thaliana Leaves, Ming-Mei Chang, Anna Li, Robert Feissner, Talal Ahmad
Rt-Qpcr Demonstrates Light-Dependent Atrbcs1a And Atrbcs3b Mrna Expressions In Arabidopsis Thaliana Leaves, Ming-Mei Chang, Anna Li, Robert Feissner, Talal Ahmad
Biology
Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is widely used in diagnosis and research to determine specific mRNA expressions in cells. As RT-qPCR applications increase, it’s necessary to provide undergraduates hands-on experience of this modern technique. Here, we report a 3-week laboratory exercise using RT-qPCR to demonstrate the light-dependent expressions of AtRBCS1A and AtRBCS3B genes encoding two Arabidopsis thaliana small subunits of the ribulose 1,5-bisphosphate carboxylase/ oxygenase (Rubisco). In the first week, students purified and quantified total RNA from leaves of A. thaliana pretreated in the dark for 96 hr and untreated controls. In the second week, RNA samples were …
Sequencing Techniques: A Comparison Assignment, Sarah O'Leary-Driscoll
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
Discussion Questions: Genome Mining, Sarah O'Leary-Driscoll
Sequencing & Genome Mining
No abstract provided.
Alignment Information, Sarah O'Leary-Driscoll
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
2: Sequence Alignment Practice Activity, Sarah O'Leary-Driscoll
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
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
Pt. 1: Research Question & Background, Sarah O'Leary-Driscoll
Pt. 1: Research Question & Background, Sarah O'Leary-Driscoll
Research Project
No abstract provided.
Primer Design Activity, Sarah O'Leary-Driscoll
Obtaining Genomic Sequence Practice, Sarah O'Leary-Driscoll
Obtaining Genomic Sequence Practice, Sarah O'Leary-Driscoll
Introduction to NCBI
No abstract provided.
Dna Timeline And Poster Project, Sarah O'Leary-Driscoll
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
3: Genomics: Past & Future Bibliography, Sarah O'Leary-Driscoll
Genomics: Past & Future
No abstract provided.
Future Of Genomics: Presentations, Sarah O'Leary-Driscoll
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
Database/Resource Acronyms, Sarah O'Leary-Driscoll
Course Information
No abstract provided.
What Is Bioinformatics?, Sarah O'Leary-Driscoll
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
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
Glossary Of Bioinformatics Terms, National Human Genome Research Institute
Course Information
No abstract provided.
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
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 …
Transfer Of The United States National Parasite Collection [Announcement], Eric P. Hoberg, Anna J. Phillips
Transfer Of The United States National Parasite Collection [Announcement], Eric P. Hoberg, Anna J. Phillips
Harold W. Manter Laboratory of Parasitology: Faculty and Staff Publications
In 2013, an agreement was articulated between the United States Department of Agriculture/Agricultural Research Service (ARS) and the Smithsonian Institution to transfer the United States National Parasite Collection in its entirety (fluid specimens, slide specimens, frozen tissues and reprints) to the National Museum of Natural History (NMNH) in Washington, D.C. Current collections staff, including senior curator Dr. Eric P. Hoberg and support scientists/managers from the ARS will be transferred with the collection and with adjunct appointments in the NMNH will provide continuity and assistance for curation and accessibility during and after the relocation. New curatorial controls will be established under …
Engaging Students In A Bioinformatics Activity To Introduce Gene Structure And Function, Barbara J. May
Engaging Students In A Bioinformatics Activity To Introduce Gene Structure And Function, Barbara J. May
Biology Faculty Publications
Bioinformatics spans many fields of biological research and plays a vital role in mining and analyzing data. Therefore, there is an ever-increasing need for students to understand not only what can be learned from this data, but also how to use basic bioinformatics tools. This activity is designed to provide secondary and undergraduate biology students to a hands-on activity meant to explore and understand gene structure with the use of basic bioinformatic tools. Students are provided an “unknown” sequence from which they are asked to use a free online gene finder program to identify the gene. Students then predict the …
Engineering Mathematics Education At Wright State University: Uncorking The First Year Bottleneck, Nathan W. Klingbeil, Kuldip S. Rattan, Michael L. Raymer, David B. Reynolds, Richard Mercer
Engineering Mathematics Education At Wright State University: Uncorking The First Year Bottleneck, Nathan W. Klingbeil, Kuldip S. Rattan, Michael L. Raymer, David B. Reynolds, Richard Mercer
Kno.e.sis Publications
No abstract provided.
Work In Progress: The Wsu Model For Engineering Mathematics Education, Nathan W. Klingbeil, Richard Mercer, Kuldip S. Rattan, Michael L. Raymer, David B. Reynolds
Work In Progress: The Wsu Model For Engineering Mathematics Education, Nathan W. Klingbeil, Richard Mercer, Kuldip S. Rattan, Michael L. Raymer, David B. Reynolds
Kno.e.sis Publications
This paper summarizes progress to date on the WSU model for engineering mathematics education, an NSF funded curriculum reform initiative at Wright State University. The WSU model seeks to increase student retention, motivation and success in engineering through application-driven, just-in-time engineering math instruction. The WSU approach involves the development of a novel freshman-level engineering mathematics course EGR 101, as well as a large-scale restructuring of the engineering curriculum. By removing traditional math prerequisites and moving core engineering courses earlier in the program, the WSU model shifts the traditional emphasis on math prerequisite requirements to an emphasis on engineering motivation for …
A Proposed Undergraduate Bioinformatics Curriculum For Computer Scientists, Travis E. Doom, Michael L. Raymer, Dan E. Krane, Oscar Garcia
A Proposed Undergraduate Bioinformatics Curriculum For Computer Scientists, Travis E. Doom, Michael L. Raymer, Dan E. Krane, Oscar Garcia
Kno.e.sis Publications
Bioinformatics is a new and rapidly evolving discipline that has emerged from the fields of experimental molecular biology and biochemistry, and from the the artificial intelligence, database, and algorithms disciplines of computer science. Largely because of the inherently interdisciplinary nature of bioinformatics research, academia has been slow to respond to strong industry and government demands for trained scientists to develop and apply novel bioinformatics techniques to the rapidly-growing, freely-available repositories of genetic and proteomic data. While some institutions are responding to this demand by establishing graduate programs in bioinformatics, the entrance barriers for these programs are high, largely due to …