A genomics learning framework for undergraduates.

Genomics is an increasingly important part of biology research. However, educating undergraduates in genomics is not yet a standard part of life sciences curricula. We believe this is, in part, due to a lack of standard concepts for the teaching of genomics.

Student Attitudes Contribute to the Effectiveness of a Genomics CURE.

The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits.

There Is More than Multiple Choice: Crowd-Sourced Assessment Tips for Online, Hybrid, and Face-to-Face Environments.

Developing effective assessments of student learning is a challenging task for faculty and even more difficult for those in emerging disciplines that lack readily available resources and standards. With the power of technology-enhanced education and accessible digital learning platforms, instructors are also looking for assessments that work in an online format. This article will be useful for all teachers, but especially for entry-level instructors, in addition to more mature instructors who are looking to become more well versed in assessment, who seek a succinct summary of assessment types to springboard the integration of new forms of assessment of student learning into their courses.

Community development, implementation, and assessment of a NIBLSE bioinformatics sequence similarity learning resource.

As powerful computational tools and 'big data' transform the biological sciences, bioinformatics training is becoming necessary to prepare the next generation of life scientists. Furthermore, because the tools and resources employed in bioinformatics are constantly evolving, bioinformatics learning materials must be continuously improved. In addition, these learning materials need to move beyond today's typical step-by-step guides to promote deeper conceptual understanding by students.

Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life science education.

While it is essential for life science students to be trained in modern techniques and approaches, rapidly developing, interdisciplinary fields such as bioinformatics present distinct challenges to undergraduate educators. In particular, many educators lack training in new fields, and high-quality teaching and learning materials may be sparse. To address this challenge with respect to bioinformatics, the Network for the Integration of Bioinformatics into Life Science Education (NIBLSE), in partnership with Quantitative Undergraduate Biology Education and Synthesis (QUBES), developed incubators, a novel collaborative process for the development of open educational resources (OER).

Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience.

A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in a genomics Course-Based Undergraduate Research Experience (CURE).

Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction.

Bioinformatics, a discipline that combines aspects of biology, statistics, mathematics, and computer science, is becoming increasingly important for biological research. However, bioinformatics instruction is not yet generally integrated into undergraduate life sciences curricula. To understand why we studied how bioinformatics is being included in biology education in the US by conducting a nationwide survey of faculty at two- and four-year institutions.

The Genome Solver Project: Faculty Training and Student Performance Gains in Bioinformatics.

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.

Bioinformatics core competencies for undergraduate life sciences education.

Although bioinformatics is becoming increasingly central to research in the life sciences, bioinformatics skills and knowledge are not well integrated into undergraduate biology education. This curricular gap prevents biology students from harnessing the full potential of their education, limiting their career opportunities and slowing research innovation. To advance the integration of bioinformatics into life sciences education, a framework of core bioinformatics competencies is needed.

The development and application of bioinformatics core competencies to improve bioinformatics training and education.

Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas.

The Emergence of Undergraduate Majors in Global Health: Systematic Review of Programs and Recommendations for Future Directions.

Global health education has been expanding rapidly and several universities have created an undergraduate major degree (bachelor's degree) in global heath or global health studies. Because there are currently no national guidelines for undergraduate degrees in global health, each of these programs was developed along individual lines. To guide the development of future global health majors, we conducted a systematic review of undergraduate majors in global health.

A High Copy Suppressor Screen for Autophagy Defects in Δ and Δ Strains.

In , Arl1 and Ypt6, two small GTP-binding proteins that regulate membrane traffic in the secretory and endocytic pathways, are also necessary for autophagy. To gain information about potential partners of Arl1 and Ypt6 specifically in autophagy, we carried out a high copy number suppressor screen to identify genes that when overexpressed suppress the rapamycin sensitivity phenotype of Δ and Δ strains at 37°. From the screen results, we selected , , , , , , and , either membrane traffic or autophagy regulators, to further test whether they can suppress the specific autophagy defects of Δ and Δ strains.

Small GTPase proteins in macroautophagy.

Macroautophagy, a highly conserved process in eukaryotic cells, is initiated in response to stress, especially nutrient starvation. Macroautophagy helps cells survive by engulfing proteins and organelles into an unusual double-membraned structure called the autophagosome, which then fuses with the lysosome. Upon degradation of the engulfed contents, the building blocks are recycled for synthesis of new macromolecules.

Autophagy in Saccharomyces cerevisiae requires the monomeric GTP-binding proteins, Arl1 and Ypt6.

Macroautophagy/autophagy is a cellular degradation process that sequesters organelles or proteins into a double-membrane structure called the phagophore; this transient compartment matures into an autophagosome, which then fuses with the lysosome or vacuole to allow hydrolysis of the cargo. Factors that control membrane traffic are also essential for each step of autophagy. Here we demonstrate that 2 monomeric GTP-binding proteins in Saccharomyces cerevisiae, Arl1 and Ypt6, which belong to the Arf/Arl/Sar protein family and the Rab family, respectively, and control endosome-trans-Golgi traffic, are also necessary for starvation-induced autophagy under high temperature stress.

Identification of Genes in Candida glabrata Conferring Altered Responses to Caspofungin, a Cell Wall Synthesis Inhibitor.

Candida glabrata is an important human fungal pathogen whose incidence continues to rise. Because many clinical isolates are resistant to azole drugs, the drugs of choice to treat such infections are members of the echinocandin family, although there are increasing reports of resistance to these drugs as well. In efforts to better understand the genetic changes that lead to altered responses to echinocandins, we screened a transposon-insertion library of mutants for strains to identify genes that are important for cellular responses to caspofungin, a member of this drug family.

The Presence of Phage Orthologous Genes in Helicobacter pylori Correlates with the Presence of the Virulence Factors CagA and VacA.

Background: The bacterium Helicobacter pylori is associated with ulcers and the development of gastric cancer. Several genes, including cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A (VacA), are associated with increased gastric cancer risk. Some strains of H.

Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D.

A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics.

In their 2012 report, the President's Council of Advisors on Science and Technology advocated "replacing standard science laboratory courses with discovery-based research courses"-a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses.

The roles of monomeric GTP-binding proteins in macroautophagy in Saccharomyces cerevisiae.

Autophagy is a cellular degradation process that sequesters components into a double-membrane structure called the autophagosome, which then fuses with the lysosome or vacuole for hydrolysis and recycling of building blocks. Bulk phase autophagy, also known as macroautophagy, controlled by specific Atg proteins, can be triggered by a variety of stresses, including starvation. Because autophagy relies extensively on membrane traffic to form the membranous structures, factors that control membrane traffic are essential for autophagy.

A course-based research experience: how benefits change with increased investment in instructional time.

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.

Evidence for horizontal gene transfer between and Chlamydia phage.

Chlamydia-infecting bacteriophages, members of the family, specifically the subfamily, are small (4.5-5 kb) single-stranded circles with 8-10 open-reading frames similar to phage ϕX174. Using sequence information found in GenBank, we examined related genes in and Chlamydia-infecting bacteriophages.