Using the homozygous diploid Saccharomyces deletion collection, we searched for strains with defe... more Using the homozygous diploid Saccharomyces deletion collection, we searched for strains with defects in K + homeostasis. We identified 156 (of 4653 total) strains unable to grow in the presence of hygromycin B, a phenotype previously shown to be indicative of ion defects. The most abundant group was that with deletions of genes known to encode membrane traffic regulators. Nearly 80% of these membrane traffic defective strains showed defects in uptake of the K + homolog, 86 Rb +. Since Trk1, a plasma membrane protein localized to lipid microdomains, is the major K + influx transporter, we examined the subcellular localization and Triton-X 100 insolubility of Trk1 in 29 of the traffic mutants. However, few of these showed defects in the steady state levels of Trk1, the localization of Trk1 to the plasma membrane, or the localization of Trk1 to lipid microdomains, and most defects were mild compared to wild-type. Three inositol kinase mutants were also identified, and in contrast, loss of these genes negatively affected Trk1 protein levels. In summary, this work reveals a nexus between K + homeostasis and membrane traffic, which does not involve traffic of the major influx transporter, Trk1.
Letter to the Editor methods. We describe here our efforts to assemble a network of like-minded b... more Letter to the Editor methods. We describe here our efforts to assemble a network of like-minded bioinformatics educators both to undertake this process and to identify professional development oppor-tunities for today’s life sciences educators. Our efforts are geared toward first forming, then growing,
There is widespread agreement that science, technology, engineering, and mathematics programs sho... more 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 coursebased 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 investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.
The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) has cultivated a... more The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) has cultivated a collaborative community model to facilitate the development, dissemination, and assessment of bioinformatics learning resources.
The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) seeks to promote... more The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) seeks to promote the use of bioinformatics and data science as a way to teach biology.
The Genome Consortium for Active Teaching (GCAT) facilitates the use of modern genomics methods i... more The Genome Consortium for Active Teaching (GCAT) facilitates the use of modern genomics methods in undergraduate education. Initially focused on microarray technology, but with an eye toward diversification, GCAT is a community working to improve the education of tomor-row’s life science professionals. GCAT participants have access to affordable microarrays, mi-croarray scanners, free software for data analysis, and faculty workshops. Microarrays provided by GCAT have been used by 141 faculty on 134 campuses, including 21 faculty that serve large numbers of underrepresented minority students. An estimated 9480 undergraduates a year will have access to microarrays by 2009 as a direct result of GCAT faculty workshops. Gains for students include significantly improved comprehension of topics in functional genomics and increased interest in research. Faculty reported improved access to new technology and gains in understanding thanks to their involvement with GCAT. GCAT’s network of sup...
Our BIOME Group worked towards developing a set of learning goals for faculty who plan to launch ... more Our BIOME Group worked towards developing a set of learning goals for faculty who plan to launch a CURE based on RNA-Seq data. We also developed a workflow for analysis of either prokaryotic or eukaryotic RNA-Seq data with existing tools.
We reviewed the materials available on Genome Solver (other lessons here) and described our new p... more We reviewed the materials available on Genome Solver (other lessons here) and described our new python pipeline for examining horizontal gene transfer and a new synteny lesson in detail.
Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; ... more Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. This pre-lesson introduces the BLAST tool.
The lesson teaches about synteny or the order of genes along a chromosome, which is useful for lo... more The lesson teaches about synteny or the order of genes along a chromosome, which is useful for looking at orthologous genes between two species or strains.
Genome Solver (GS) began in 2011 as an NSF-funded project for faculty training in basic web-based... more Genome Solver (GS) began in 2011 as an NSF-funded project for faculty training in basic web-based bioinformatics skills.
Scientists are sequencing new genomes at an increasing rate with the goal of associating genome c... more Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manual gene annotation. Undergraduates can become skilled annotators, and in the process learn both about genes/genomes and about how to utilize large datasets. Data visualizations provided by a genome browser are essential for manual gene annotation, enabling annotators to quickly evaluate multiple lines of evidence (e.g., sequence similarity, RNA-Seq, gene predictions, repeats). However, creating genome browsers requires extensive computational skills; lack of the expertise required remains a major barrier for many biomedical researchers and educators. To address these challenges, the Genomics Education Partnership (GEP; https://gep.wustl.edu...
To efficiently and effectively integrate bioinformatics instruction into undergraduate life scien... more To efficiently and effectively integrate bioinformatics instruction into undergraduate life science curricula, educators would benefit from open access, high-quality learning resources (LRs) for use in existing biology classes.
Presentation of poster 464B at TAGC 2020 Online. Files include a PDF of the poster (TAGC 2020 NIB... more Presentation of poster 464B at TAGC 2020 Online. Files include a PDF of the poster (TAGC 2020 NIBLSE Incubators poster v4.PDF)
Anticipating the specific needs of diverse teaching and learning contexts is impractical. However... more Anticipating the specific needs of diverse teaching and learning contexts is impractical. However, we believe that by focusing on the refinement of materials to support particular bioinformatics learning outcomes, and providing teaching notes to make technical topics more accessible, that incubators can broaden access to bioinformatics topics across the undergraduate curriculum. Each incubator establishes a set of goals and tasks that are specific to the development of a particular learning resource. Participants are recruited and take on small tasks that contribute to the development of the revised materials. Incubator groups work synchronously and asynchronously in an online space hosted by QUBESHub. The products of incubators are made available under a creative commons license and the authors are encouraged to pursue publication in outlets like CourseSource. Incubator Structure and Goals
The Genome Solver Project began as a way to teach faculty some basic skills in bioinformatics - n... more The Genome Solver Project began as a way to teach faculty some basic skills in bioinformatics - no coding or scripting. These Lessons also work well in the undergraduate classroom, culminating with an authentic community research project.
This is a collection of posters from members of the Genomics Education Alliance (GEA) that will b... more This is a collection of posters from members of the Genomics Education Alliance (GEA) that will be presented at the 2020 BIOME Institute.
Bioinformatics brings together biology, mathematics, statistics, and computer science to analyze ... more Bioinformatics brings together biology, mathematics, statistics, and computer science to analyze biological sequence information. Anyone with a computer, access to the Internet, and basic training in this field can contribute to genomics research. Yet many biology faculty feel they lack training in the use of bioinformatics tools and therefore include little bioinformatics content in their courses. To overcome this challenge, the Genome Solver Project was created to empower undergraduate faculty by offering training and resources for creating hands-on bioinformatics course materials. In this study, we show the results of one survey completed directly after the workshop and a further follow-up survey to gain insight into the impact the workshop had on faculty willingness to include bioinformatics content in their courses and what challenges they still faced. We also measured student performance at five different institutions using a 20-question multiple-choice quiz delivered before a...
Using the homozygous diploid Saccharomyces deletion collection, we searched for strains with defe... more Using the homozygous diploid Saccharomyces deletion collection, we searched for strains with defects in K + homeostasis. We identified 156 (of 4653 total) strains unable to grow in the presence of hygromycin B, a phenotype previously shown to be indicative of ion defects. The most abundant group was that with deletions of genes known to encode membrane traffic regulators. Nearly 80% of these membrane traffic defective strains showed defects in uptake of the K + homolog, 86 Rb +. Since Trk1, a plasma membrane protein localized to lipid microdomains, is the major K + influx transporter, we examined the subcellular localization and Triton-X 100 insolubility of Trk1 in 29 of the traffic mutants. However, few of these showed defects in the steady state levels of Trk1, the localization of Trk1 to the plasma membrane, or the localization of Trk1 to lipid microdomains, and most defects were mild compared to wild-type. Three inositol kinase mutants were also identified, and in contrast, loss of these genes negatively affected Trk1 protein levels. In summary, this work reveals a nexus between K + homeostasis and membrane traffic, which does not involve traffic of the major influx transporter, Trk1.
Letter to the Editor methods. We describe here our efforts to assemble a network of like-minded b... more Letter to the Editor methods. We describe here our efforts to assemble a network of like-minded bioinformatics educators both to undertake this process and to identify professional development oppor-tunities for today’s life sciences educators. Our efforts are geared toward first forming, then growing,
There is widespread agreement that science, technology, engineering, and mathematics programs sho... more 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 coursebased 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 investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.
The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) has cultivated a... more The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) has cultivated a collaborative community model to facilitate the development, dissemination, and assessment of bioinformatics learning resources.
The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) seeks to promote... more The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE) seeks to promote the use of bioinformatics and data science as a way to teach biology.
The Genome Consortium for Active Teaching (GCAT) facilitates the use of modern genomics methods i... more The Genome Consortium for Active Teaching (GCAT) facilitates the use of modern genomics methods in undergraduate education. Initially focused on microarray technology, but with an eye toward diversification, GCAT is a community working to improve the education of tomor-row’s life science professionals. GCAT participants have access to affordable microarrays, mi-croarray scanners, free software for data analysis, and faculty workshops. Microarrays provided by GCAT have been used by 141 faculty on 134 campuses, including 21 faculty that serve large numbers of underrepresented minority students. An estimated 9480 undergraduates a year will have access to microarrays by 2009 as a direct result of GCAT faculty workshops. Gains for students include significantly improved comprehension of topics in functional genomics and increased interest in research. Faculty reported improved access to new technology and gains in understanding thanks to their involvement with GCAT. GCAT’s network of sup...
Our BIOME Group worked towards developing a set of learning goals for faculty who plan to launch ... more Our BIOME Group worked towards developing a set of learning goals for faculty who plan to launch a CURE based on RNA-Seq data. We also developed a workflow for analysis of either prokaryotic or eukaryotic RNA-Seq data with existing tools.
We reviewed the materials available on Genome Solver (other lessons here) and described our new p... more We reviewed the materials available on Genome Solver (other lessons here) and described our new python pipeline for examining horizontal gene transfer and a new synteny lesson in detail.
Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; ... more Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. This pre-lesson introduces the BLAST tool.
The lesson teaches about synteny or the order of genes along a chromosome, which is useful for lo... more The lesson teaches about synteny or the order of genes along a chromosome, which is useful for looking at orthologous genes between two species or strains.
Genome Solver (GS) began in 2011 as an NSF-funded project for faculty training in basic web-based... more Genome Solver (GS) began in 2011 as an NSF-funded project for faculty training in basic web-based bioinformatics skills.
Scientists are sequencing new genomes at an increasing rate with the goal of associating genome c... more Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manual gene annotation. Undergraduates can become skilled annotators, and in the process learn both about genes/genomes and about how to utilize large datasets. Data visualizations provided by a genome browser are essential for manual gene annotation, enabling annotators to quickly evaluate multiple lines of evidence (e.g., sequence similarity, RNA-Seq, gene predictions, repeats). However, creating genome browsers requires extensive computational skills; lack of the expertise required remains a major barrier for many biomedical researchers and educators. To address these challenges, the Genomics Education Partnership (GEP; https://gep.wustl.edu...
To efficiently and effectively integrate bioinformatics instruction into undergraduate life scien... more To efficiently and effectively integrate bioinformatics instruction into undergraduate life science curricula, educators would benefit from open access, high-quality learning resources (LRs) for use in existing biology classes.
Presentation of poster 464B at TAGC 2020 Online. Files include a PDF of the poster (TAGC 2020 NIB... more Presentation of poster 464B at TAGC 2020 Online. Files include a PDF of the poster (TAGC 2020 NIBLSE Incubators poster v4.PDF)
Anticipating the specific needs of diverse teaching and learning contexts is impractical. However... more Anticipating the specific needs of diverse teaching and learning contexts is impractical. However, we believe that by focusing on the refinement of materials to support particular bioinformatics learning outcomes, and providing teaching notes to make technical topics more accessible, that incubators can broaden access to bioinformatics topics across the undergraduate curriculum. Each incubator establishes a set of goals and tasks that are specific to the development of a particular learning resource. Participants are recruited and take on small tasks that contribute to the development of the revised materials. Incubator groups work synchronously and asynchronously in an online space hosted by QUBESHub. The products of incubators are made available under a creative commons license and the authors are encouraged to pursue publication in outlets like CourseSource. Incubator Structure and Goals
The Genome Solver Project began as a way to teach faculty some basic skills in bioinformatics - n... more The Genome Solver Project began as a way to teach faculty some basic skills in bioinformatics - no coding or scripting. These Lessons also work well in the undergraduate classroom, culminating with an authentic community research project.
This is a collection of posters from members of the Genomics Education Alliance (GEA) that will b... more This is a collection of posters from members of the Genomics Education Alliance (GEA) that will be presented at the 2020 BIOME Institute.
Bioinformatics brings together biology, mathematics, statistics, and computer science to analyze ... more Bioinformatics brings together biology, mathematics, statistics, and computer science to analyze biological sequence information. Anyone with a computer, access to the Internet, and basic training in this field can contribute to genomics research. Yet many biology faculty feel they lack training in the use of bioinformatics tools and therefore include little bioinformatics content in their courses. To overcome this challenge, the Genome Solver Project was created to empower undergraduate faculty by offering training and resources for creating hands-on bioinformatics course materials. In this study, we show the results of one survey completed directly after the workshop and a further follow-up survey to gain insight into the impact the workshop had on faculty willingness to include bioinformatics content in their courses and what challenges they still faced. We also measured student performance at five different institutions using a 20-question multiple-choice quiz delivered before a...
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