Incorporating genomics and bioinformatics across the life sciences curriculum

Pairing a bioinformatics-focused course-based undergraduate research experience with specifications grading in an introductory biology classroom

Introducing bioinformatics-focused concepts and skills in a biology classroom is difficult, especially in introductory biology classrooms. Course-based Undergraduate Research Experiences (CUREs) facilitate this process, introducing genomics and bioinformatics through authentic research experiences, but the many learning objectives needed in scientific research and communication, foundational biology concepts, and bioinformatics-focused concepts and skills can make the process challenging. Here, the pairing of specifications grading with a bioinformatics-focused CURE developed by the Genomics Education Partnership is described. The study examines how the course structure with specifications grading facilitated scaffolding of writing assignments, group work, and metacognitive activities; and describes the synergies between CUREs and specifications grading. CUREs require mastery of related concepts and skills for working through the research process, utilize common research practices of revision and iteration, and encourage a growth mindset to learning-all of which are heavily incentivized in assessment practices focused on specifications grading.

Role of machine and organizational structure in science

The progress of science increasingly relies on machine learning (ML) and machines work alongside humans in various domains of science. This study investigates the team structure of ML-related projects and analyzes the contribution of ML to scientific knowledge production under different team structure, drawing on bibliometric analyses of 25,000 scientific publications in various disciplines. Our regression analyses suggest that (1) interdisciplinary collaboration between domain scientists and computer scientists as well as the engagement of interdisciplinary individuals who have expertise in both domain and computer sciences are common in ML-related projects; (2) the engagement of interdisciplinary individuals seem more important in achieving high impact and novel discoveries, especially when a project employs computational and domain approaches interdependently; and (3) the contribution of ML and its implication to team structure depend on the depth of ML.

Bioinformatics Analysis for Identifying Pertinent Pathways and Genes in Sepsis

Purpose

Sepsis becomes the main death reason in hospitals with rising incidence, causing a growing economic and medical burden. However, the genes related to the pathogenesis and prognosis of sepsis are still unclear, which is a problem that needs to be solved urgently.

Materials and Methods

Gene expression profiles of GSE69528 were obtained from the National Center for Biotechnology Information. Limma software package got employed to search for differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were used for enrichment analysis. Protein-protein interaction (PPI) network was built by the Search Tool for the Retrieval of Interacting Genes (STRING) database.

Results

We screened 101 DEGs, containing 81 upregulated DEGs and 20 downregulated DEGs. GO analysis demonstrated that the upregulated DEGs were chiefly concentrated in negative regulation of response to interferon-gamma and regulation of granulocyte differentiation. KEGG analysis revealed that the pathways of upregulated DEGs were concentrated in prion diseases, complement and coagulation cascades, and Staphylococcus aureus infection. The PPI network constructed by upregulated DEGs contained 67 nodes (proteins) and 110 edges (interactions). Analysis of bioinformatics results showed that CEACAM8, MPO, and RETN were hub genes of sepsis.

Conclusion

Our analysis reveals a series of signal pathways and key genes related to the mechanism of sepsis, which are promising biotargets and biomarkers of sepsis.

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.

Online Tools for Teaching Cancer Bioinformatics

The rise of deep molecular characterization with omics data as a standard in biological sciences has highlighted a need for expanded instruction in bioinformatics curricula. Many large biology data sets are publicly available and offer an incredible opportunity for educators to help students explore biological phenomena with computational tools, including data manipulation, visualization, and statistical assessment. However, logistical barriers to data access and integration often complicate their use in undergraduate education. Here, we present a cancer bioinformatics module that is designed to overcome these barriers through six exercises containing authentic, biologically motivated computational exercises that demonstrate how modern omics data are used in precision oncology. Upper-division undergraduate students develop advanced Python programming and data analysis skills with real-world oncology data which integrates proteomics and genomics. The module is publicly available and open source at https://paynelab.github.io/biograder/bio462. These hands-on activities include explanatory text, code demonstrations, and practice problems and are ready to implement in bioinformatics courses.

Changes in gene expression of adipose tissue CD14+ cells in patients with Type 2 diabetes mellitus and their relationship with environmental factors

OBJECTIVES

To study the gene expression of adipose tissue CD14+ cells in patients with Type 2 diabetes mellitus (T2DM) based on chip data, screen differentially expressed genes, and analyze their relationship with the environmental factors.

METHODS

The data of GSE54350 were obtained from the public database of gene expression profiling. The data were pre-processed by Network Analyst, String 11.0, Cytoscape 3.7.1, and other analytical software. The differentially expressed genes were analyzed by gene ontology biological function and kyoto encycopedia of genes and genomes (KEGG) signaling pathway to establish differential gene protein interaction network, transcription factor-gene regulatory network, microRNA-gene regulatory network, environmental factors-gene regulatory network, and other interaction systems.

RESULTS

The gene expression pattern of CD14+ cells in adipose tissue of obese T2DM patients was significantly different from that of obese non-T2DM patients. There were 19 differentially expressed genes with up-regulation. The differentially expressed genes were mainly involved in ARP2/3 complex regulation of actin cytoskeleton, positively associated with biological processes such as protein complex assembly, and involved in the phagocytic Fcγ receptor signaling pathways and receptor family signaling pathways. The protein-protein interaction networks showed that TNF was the core protein node. The microRNA-gene regulatory network showed that hsa-mir-124-3p interacted with differentially expressed genes; TNF, KYNU, RCAN1 and other related genes all interacted with environmental factors.

CONCLUSIONS

The gene expression of adipose tissue CD14+ cells are significantly changed in obese T2DM patients. TNF may play an important role in the process of obesity affecting the immune status of T2DM patients. Multiple microRNAs, transcription factors, and environmental factors also play a role in the above process. This study provides new material and new ideas for further exploration of the impact of obesity on T2DM patients.

Gene Annotation in High Schools: Successful Student Pipeline and Teacher Professional Development in Bioscience Using GENI-ACT

Knowledge of genomics is an essential component of science for high school student health literacy. However, few high school teachers have received genomics training or any guidance on how to teach the subject to their students. This project explored the impact of a genomics and bioinformatics research pipeline for high school teachers and students using an introduction to genome annotation research as the catalyst. The Western New York-based project had three major components: (1) a summer teacher professional development workshop to introduce genome annotation research, (2) teacher-guided student genome annotation group projects during the school year, (3) with an end of the academic year capstone symposium to showcase student work in a poster session. Both teachers and students performed manual gene annotations using an online annotation toolkit known as Genomics Education National Initiative-Annotation Collaboration Toolkit (GENI-ACT), originally developed for use in a college undergraduate teaching environment. During the school year, students were asked to evaluate the data they had collected, formulate a hypothesis about the correctness of the computer pipeline annotation, and present the data to support their conclusions in poster form at the symposium. Evaluation of the project documented increased content knowledge in basic genomics and bioinformatics as well as increased confidence in using tools and the scientific process using GENI-ACT, thus demonstrating that high school students are capable of using the same tools as scientists to conduct a real-world research task.

Microbiomes for All

Microbiome research projects are often interdisciplinary, involving fields such as microbiology, genetics, ecology, evolution, bioinformatics, and statistics. These research projects can be an excellent fit for undergraduate courses ranging from introductory biology labs to upper-level capstone courses. Microbiome research projects can attract the interest of students majoring in health and medical sciences, environmental sciences, and agriculture, and there are meaningful ties to real-world issues relating to human health, climate change, and environmental sustainability and resilience in pristine, fragile ecosystems to bustling urban centers. In this review, we will discuss the potential of microbiome research integrated into classes using a number of different modalities. Our experience scaling-up and implementing microbiome projects at a range of institutions across the US has provided us with insight and strategies for what works well and how to diminish common hurdles that are encountered when implementing undergraduate microbiome research projects. We will discuss how course-based microbiome research can be leveraged to help faculty make advances in their own research and professional development and the resources that are available to support faculty interested in integrating microbiome research into their courses.

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 survey asked several open-ended questions that probed barriers to integration, the answers to which were analyzed using a mixed-methods approach. The barrier most frequently reported by the 1,260 respondents was lack of faculty expertise/training, but other deterrents—lack of student interest, overly-full curricula, and lack of student preparation—were also common. Interestingly, the barriers faculty face depended strongly on whether they are members of an underrepresented group and on the Carnegie Classification of their home institution. We were surprised to discover that the cohort of faculty who were awarded their terminal degree most recently reported the most preparation in bioinformatics but teach it at the lowest rate.

A course-based undergraduate research experience in biochemistry that is suitable for students with various levels of preparedness

Due to resource limitations at predominantly undergraduate institutions, research opportunities for non-senior students can be limited. To provide opportunities for a variety of students to gain exposure to research, a course-based undergraduate research experience (CURE) was designed and conducted. Coupled inquiry was used to allow underclassmen and upperclassmen to participate. Students first utilized a bioinformatics approach to develop hypotheses concerning protein interactions with the receptor Mer tyrosine kinase (MERTK). Students designed experiments to identify specific sites of interactions with SH2-domain proteins utilizing an assortment of basic biochemical techniques. The semester culminated in students testing their hypotheses and producing manuscripts. Underclassmen that participated in the course also benefitted from mentor-mentee relationships developed with upperclassmen due to the collaborative nature of the course. The structure of the course also allows for further studies to be conducted based on novel findings and is highly adaptable to receptor tyrosine kinases found in other tissue types. © 2019 International Union of Biochemistry and Molecular Biology, 47(3):220-227, 2019.

Releasing the "GENI": integrating authentic microbial genomics research into the classroom through GENI-ACT

The integration of genomics research into the undergraduate biology curriculum provides students with the opportunity to become familiar with bioinformatics tools and answer original research questions. Our purpose with this research project was to upscale the research experience through integration with classroom experience giving students access to authentic research projects. Students annotated 60 predicted ABC genes of Methanothermobacter thermautotrophicus and Methanobacterium sp. SWAN-1, and they were required to present a research poster to demonstrate their understanding of the project. During this research project a number of tests, assessments and surveys were conducted to assess familiarity with technical and conceptual understanding of genome annotation, satisfaction with annotation instruction, gain in bioinformatics research skills, scientific communications skills and increased student interest in research. We found that students gained significant skills in bioinformatics, specifically genome annotation skills and also gained confidence in their abilities to carry out scientific research. As a result of this authentic undergraduate research experience under-represented students were motivated to pursue future careers in STEM fields.

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. To that end, we here report the results of a survey of biology faculty in the United States about teaching bioinformatics to undergraduate life scientists. Responses were received from 1,260 faculty representing institutions in all fifty states with a combined capacity to educate hundreds of thousands of students every year. Results indicate strong, widespread agreement that bioinformatics knowledge and skills are critical for undergraduate life scientists as well as considerable agreement about which skills are necessary. Perceptions of the importance of some skills varied with the respondent's degree of training, time since degree earned, and/or the Carnegie Classification of the respondent's institution. To assess which skills are currently being taught, we analyzed syllabi of courses with bioinformatics content submitted by survey respondents. Finally, we used the survey results, the analysis of the syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate biology students. These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula.

Lessons learnt on the analysis of large sequence data in animal genomics

The 'omics revolution has made a large amount of sequence data available to researchers and the industry. This has had a profound impact in the field of bioinformatics, stimulating unprecedented advancements in this discipline. Mostly, this is usually looked at from the perspective of human 'omics, in particular human genomics. Plant and animal genomics, however, have also been deeply influenced by next-generation sequencing technologies, with several genomics applications now popular among researchers and the breeding industry. Genomics tends to generate huge amounts of data, and genomic sequence data account for an increasing proportion of big data in biological sciences, due largely to decreasing sequencing and genotyping costs and to large-scale sequencing and resequencing projects. The analysis of big data poses a challenge to scientists, as data gathering currently takes place at a faster pace than does data processing and analysis, and the associated computational burden is increasingly taxing, making even simple manipulation, visualization and transferring of data a cumbersome operation. The time consumed by the processing and analysing of huge data sets may be at the expense of data quality assessment and critical interpretation. Additionally, when analysing lots of data, something is likely to go awry-the software may crash or stop-and it can be very frustrating to track the error. We herein review the most relevant issues related to tackling these challenges and problems, from the perspective of animal genomics, and provide researchers that lack extensive computing experience with guidelines that will help when processing large genomic data sets.

Antibiotic resistant pathogen outbreak investigation: an interdisciplinary module to teach fundamentals of evolutionary biology

The evolution of resistance to antibiotics provides a timely and relevant topic for teaching undergraduate students evolutionary biology. Here, we present a module incorporating modified sequencing data from eight antibiotic resistant pathogen outbreaks in hospital settings with bioinformatics and phylogenetic analyses. This module uses whole genome sequencing data from hospital outbreaks investigated by the Centers for Disease Control and Prevention to provide examples of antibiotic resistance spread. Students work in groups to analyze outbreak data to identify the bacterial species and antibiotic resistance genes, to infer a phylogenetic tree examining relatedness among isolates, and to determine a possible source of the outbreak. Students then compile their results in individual reports and provide recommendations for preventing the further spread of antibiotic resistant organisms. In addition to providing genomic outbreak data, we include a teaching concepts guide discussing three integral components of the module: how evolutionary biology concepts of natural selection and competition impact antibiotic resistance; outbreak investigation information to aid in phylogenetic analysis and creation of recommendations; and instructions for the bioinformatics protocol. Completion of this module provides students an opportunity to think critically about the evolution of resistance, practice bioinformatics techniques, and relate evolutionary biology to current events.

Assessing an effective undergraduate module teaching applied bioinformatics to biology students

Applied bioinformatics skills are becoming ever more indispensable for biologists, yet incorporation of these skills into the undergraduate biology curriculum is lagging behind, in part due to a lack of instructors willing and able to teach basic bioinformatics in classes that don’t specifically focus on quantitative skill development, such as statistics or computer sciences. To help undergraduate course instructors who themselves did not learn bioinformatics as part of their own education and are hesitant to plunge into teaching big data analysis, a module was developed that is written in plain-enough language, using publicly available computing tools and data, to allow novice instructors to teach next-generation sequence analysis to upper-level undergraduate students. To determine if the module allowed students to develop a better understanding of and appreciation for applied bioinformatics, various tools were developed and employed to assess the impact of the module. This article describes both the module and its assessment. Students found the activity valuable for their education and, in focus group discussions, emphasized that they saw a need for more and earlier instruction of big data analysis as part of the undergraduate biology curriculum.

Implementing a web-based introductory bioinformatics course for non-bioinformaticians that incorporates practical exercises

A recent scientific discipline, bioinformatics, defined as using informatics for the study of biological problems, is now a requirement for the study of biological sciences. Bioinformatics has become such a powerful and popular discipline that several academic institutions have created programs in this field, allowing students to become specialized. However, biology students who are not involved in a bioinformatics program also need a solid toolbox of bioinformatics software and skills. Therefore, we have developed a completely online bioinformatics course for non-bioinformaticians, entitled "BIF-1901 Introduction à la bio-informatique et à ses outils (Introduction to bioinformatics and bioinformatics tools)," given by the Department of Biochemistry, Microbiology, and Bioinformatics of Université Laval (Quebec City, Canada). This course requires neither a bioinformatics background nor specific skills in informatics. The underlying main goal was to produce a completely online up-to-date bioinformatics course, including practical exercises, with an intuitive pedagogical framework. The course, BIF-1901, was conceived to cover the three fundamental aspects of bioinformatics: (1) informatics, (2) biological sequence analysis, and (3) structural bioinformatics. This article discusses the content of the modules, the evaluations, the pedagogical framework, and the challenges inherent to a multidisciplinary, fully online course. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):31-38, 2018.

Undergraduate research as curriculum

To date, national interests, policies, and calls for transformation of undergraduate education have been the main drivers of research integration into the undergraduate curriculum, briefly described here. The New Horizons in Biochemistry and Molecular Biology Education conference at the Weizmann Institute of Science (Israel) this fall presents an exciting opportunity to discuss integration of undergraduate research into the curriculum and other cutting-edge topics in biochemistry and molecular biology education from a cross-national perspective. I look forward to exploring prospects for international collaboration on research and development of course-based undergraduate research experiences and on STEM education in general. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):293-298, 2017.

The Topology Prediction of Membrane Proteins: A Web-Based Tutorial

There is a great need for development of educational materials on the transfer of current bioinformatics knowledge to undergraduate students in bioscience departments. In this study, it is aimed to prepare an example in silico laboratory tutorial on the topology prediction of membrane proteins by bioinformatics tools. This laboratory tutorial is prepared for biochemistry lessons at bioscience departments (biology, chemistry, biochemistry, molecular biology and genetics, and faculty of medicine). The tutorial is intended for students who have not taken a bioinformatics course yet or already have taken a course as an introduction to bioinformatics. The tutorial is based on step-by-step explanations with illustrations. It can be applied under supervision of an instructor in the lessons, or it can be used as a self-study guide by students. In the tutorial, membrane-spanning regions and α-helices of membrane proteins were predicted by internet-based bioinformatics tools. According to the results achieved from internet-based bioinformatics tools, the algorithms and parameters used were effective on the accuracy of prediction. The importance of this laboratory tutorial lies on the facts that it provides an introduction to the bioinformatics and that it also demonstrates an in silico laboratory application to the students at natural sciences. The presented example education material is applicable easily at all departments that have internet connection. This study presents an alternative education material to the students in biochemistry laboratories in addition to classical laboratory experiments.

Killing two birds with one stone: Model plant systems as a tool to teach the fundamental concepts of gene expression while analyzing biological data

Plants are ideal systems to teach core biology concepts due to their unique physiological and developmental features. Advances in DNA sequencing technology and genomics have allowed scientists to generate genome sequences and transcriptomics data for numerous model plant species. This information is publicly available and presents a valuable tool to introduce undergraduate students to the fundamental concepts of gene expression in the context of modern quantitative biology and bioinformatics. Modern biology classrooms must provide authentic research experiences to allow developing core competencies such as scientific inquiry, critical interpretation of experimental results, and quantitative analyses of large dataset using computational approaches. Recent educational research has shown that undergraduate students struggle when connecting gene expression concepts to classic genetics, phenotypic analyses, and overall flow of biological information in living organisms, suggesting that novel approaches are necessary to enhance learning of gene expression and regulation. This review describes different strategies and resources available to instructors willing to incorporate authentic research experiences, genomic tools, and bioinformatics analyses when teaching transcriptional regulation and gene expression in undergraduate courses. A variety of laboratory exercises and pedagogy materials developed to teach gene expression using plants are discussed. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

Comparing the Impact of Course-Based and Apprentice-Based Research Experiences in a Life Science Laboratory Curriculum

This four-year study describes the assessment of a bifurcated laboratory curriculum designed to provide upper-division undergraduate majors in two life science departments meaningful exposure to authentic research. The timing is critical as it provides a pathway for both directly admitted and transfer students to enter research. To fulfill their degree requirements, all majors complete one of two paths in the laboratory program. One path immerses students in scientific discovery experienced through team research projects (course-based undergraduate research experiences, or CUREs) and the other path through a mentored, independent research project (apprentice-based research experiences, or AREs). The bifurcated laboratory curriculum was structured using backwards design to help all students, irrespective of path, achieve specific learning outcomes. Over 1,000 undergraduates enrolled in the curriculum. Self-report survey results indicate that there were no significant differences in affective gains by path. Students conveyed which aspects of the curriculum were critical to their learning and development of research-oriented skills. Students' interests in biology increased upon completion of the curriculum, inspiring a subset of CURE participants to subsequently pursue further research. A rubric-guided performance evaluation, employed to directly measure learning, revealed differences in learning gains for CURE versus ARE participants, with evidence suggesting a CURE can reduce the achievement gap between high-performing students and their peers.

Quantitative Analysis of the Trends Exhibited by the Three Interdisciplinary Biological Sciences: Biophysics, Bioinformatics, and Systems Biology

New interdisciplinary biological sciences like bioinformatics, biophysics, and systems biology have become increasingly relevant in modern science. Many papers have suggested the importance of adding these subjects, particularly bioinformatics, to an undergraduate curriculum; however, most of their assertions have relied on qualitative arguments. In this paper, we will show our metadata analysis of a scientific literature database (PubMed) that quantitatively describes the importance of the subjects of bioinformatics, systems biology, and biophysics as compared with a well-established interdisciplinary subject, biochemistry. Specifically, we found that the development of each subject assessed by its publication volume was well described by a set of simple nonlinear equations, allowing us to characterize them quantitatively. Bioinformatics, which had the highest ratio of publications produced, was predicted to grow between 77% and 93% by 2025 according to the model. Due to the large number of publications produced in bioinformatics, which nearly matches the number published in biochemistry, it can be inferred that bioinformatics is almost equal in significance to biochemistry. Based on our analysis, we suggest that bioinformatics be added to the standard biology undergraduate curriculum. Adding this course to an undergraduate curriculum will better prepare students for future research in biology.

Implementation and assessment of a yeast orphan gene research project: involving undergraduates in authentic research experiences and progressing our understanding of uncharacterized open reading frames

Saccharomyces cerevisiae was the first eukaryotic organism to be sequenced; however, little progress has been made in recent years in furthering our understanding of all open reading frames (ORFs). From October 2012 to May 2015 the number of verified ORFs had only risen from 75.31% to 78%, while the number of uncharacterized ORFs had decreased from 12.8% to 11% (representing > 700 genes still left in this category; http://www.yeastgenome.org/genomesnapshot). Course-based research has been shown to increase student learning while providing experience with real scientific investigation; however, implementation in large, multi-section courses presents many challenges. This study sought to test the feasibility and effectiveness of incorporating authentic research into a core genetics course, with multiple instructors, to increase student learning and progress our understanding of uncharacterized ORFs. We generated a module-based annotation toolkit and utilized easily accessible bioinformatics tools to predict gene function for uncharacterized ORFs within the Saccharomyces Genome Database (SGD). Students were each assigned an uncharacterized ORF, which they annotated using contemporary comparative genomics methodologies, including multiple sequence alignment, conserved domain identification, signal peptide prediction and cellular localization algorithms. Student learning outcomes were measured by quizzes, project reports and presentations, as well as a post-project questionnaire. Our results indicate that the authentic research experience had positive impacts on students' perception of their learning and their confidence to conduct future research. Furthermore, we believe that creation of an online repository and adoption and/or adaptation of this project across multiple researchers and institutions could speed the process of gene function prediction.

Phage on the stage

The resurgence of interest in bacteriophages for use in combating antibiotic resistant bacteria is coincident with an urgent call for more effective science education practices, including hands-on learning opportunities. To address this issue, a number of solutions have been proposed, including a large educational experiment, begun in 2007 by the Howard Hughes Medical Institute and currently involving over 85 colleges and universities, which has students discovering unique phages, obtaining images, and purifying phage DNA. A subset of these phage genomes is sequenced and analyzed using bioinformatics tools. Papers describing individual phage discoveries and comparative genomic studies are being published regularly. The vast majority of students in the program are in their first year of college, a critical time in capturing their interest and retaining them as science majors. This viral discovery model is being adopted and modified by a wide variety of educational institutions using a number of different bacterial hosts. In the opinion of the authors, this program and others like it represent a model accessible to virtually any undergraduate setting. And because of these programs, bacteriophage enthusiasts (academics, health professionals, biotechnology companies) can look forward to more well prepared students entering their ranks and should anticipate many more potentially useful phages discovered and characterized.

Authentic Research Experience and "Big Data" Analysis in the Classroom: Maize Response to Abiotic Stress

Integration of inquiry-based approaches into curriculum is transforming the way science is taught and studied in undergraduate classrooms. Incorporating quantitative reasoning and mathematical skills into authentic biology undergraduate research projects has been shown to benefit students in developing various skills necessary for future scientists and to attract students to science, technology, engineering, and mathematics disciplines. While large-scale data analysis became an essential part of modern biological research, students have few opportunities to engage in analysis of large biological data sets. RNA-seq analysis, a tool that allows precise measurement of the level of gene expression for all genes in a genome, revolutionized molecular biology and provides ample opportunities for engaging students in authentic research. We developed, implemented, and assessed a series of authentic research laboratory exercises incorporating a large data RNA-seq analysis into an introductory undergraduate classroom. Our laboratory series is focused on analyzing gene expression changes in response to abiotic stress in maize seedlings; however, it could be easily adapted to the analysis of any other biological system with available RNA-seq data. Objective and subjective assessment of student learning demonstrated gains in understanding important biological concepts and in skills related to the process of science.

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. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates.

Building the next generation of quantitative biologists

Many colleges and universities across the globe now offer bachelors, masters, and doctoral degrees, along with certificate programs in bioinformatics. While there is some consensus surrounding curricula competencies, programs vary greatly in their core foci, with some leaning heavily toward the biological sciences and others toward quantitative areas. This allows prospective students to choose a program that best fits their interests and career goals. In the digital age, most scientific fields are facing an enormous growth of data, and as a consequence, the goals and challenges of bioinformatics are rapidly changing; this requires that bioinformatics education also change. In this workshop, we seek to ascertain current trends in bioinformatics education by asking the question, "What are the core competencies all bioinformaticians should have at the end of their training, and how successful have programs been in placing students in desired careers?"

Promoting inquiry-based teaching in laboratory courses: are we meeting the grade?

Over the past decade, repeated calls have been made to incorporate more active teaching and learning in undergraduate biology courses. The emphasis on inquiry-based teaching is especially important in laboratory courses, as these are the courses in which students are applying the process of science. To determine the current state of research on inquiry-based teaching in undergraduate biology laboratory courses, we reviewed the recent published literature on inquiry-based exercises. The majority of studies in our data set were in the subdisciplines of biochemistry, cell biology, developmental biology, genetics, and molecular biology. In addition, most exercises were guided inquiry, rather than open ended or research based. Almost 75% of the studies included assessment data, with two-thirds of these studies including multiple types of assessment data. However, few exercises were assessed in multiple courses or at multiple institutions. Furthermore, assessments were rarely based on published instruments. Although the results of the studies in our data set show a positive effect of inquiry-based teaching in biology laboratory courses on student learning gains, research that uses the same instrument across a range of courses and institutions is needed to determine whether these results can be generalized.

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. 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.

Redefining authentic research experiences in introductory biology laboratories and barriers to their implementation

Incorporating authentic research experiences in introductory biology laboratory classes would greatly expand the number of students exposed to the excitement of discovery and the rigor of the scientific process. However, the essential components of an authentic research experience and the barriers to their implementation in laboratory classes are poorly defined. To guide future reform efforts in this area, we conducted a national survey of biology faculty members to determine 1) their definitions of authentic research experiences in laboratory classes, 2) the extent of authentic research experiences currently experienced in their laboratory classes, and 3) the barriers that prevent incorporation of authentic research experiences into these classes. Strikingly, the definitions of authentic research experiences differ among faculty members and tend to emphasize either the scientific process or the discovery of previously unknown data. The low level of authentic research experiences in introductory biology labs suggests that more development and support is needed to increase undergraduate exposure to research experiences. Faculty members did not cite several barriers commonly assumed to impair pedagogical reform; however, their responses suggest that expanded support for development of research experiences in laboratory classes could address the most common barrier.

A Small-Group Activity Introducing the Use and Interpretation of BLAST

As biological sequence data are generated at an ever increasing rate, the role of bioinformatics in biological research also grows. Students must be trained to complete and interpret bioinformatic searches to enable them to effectively utilize the trove of sequence data available. A key bioinformatic tool for sequence comparison and genome database searching is BLAST (Basic Local Alignment Search Tool). BLAST identifies sequences in a database that are similar to the entered query sequence, and ranks them based on the length and quality of the alignment. Our goal was to introduce sophomore and junior level undergraduate students to the basic functions and uses of BLAST with a small group activity lasting a single class period. The activity provides students an opportunity to perform a BLAST search, interpret the data output, and use the data to make inferences about bacterial cell envelope structure. The activity consists of two parts. Part 1 is a handout to be completed prior to class, complete with video tutorial, that reviews cell envelope structure, introduces key terms, and allows students to familiarize themselves with the mechanics of a BLAST search. Part 2 consists of a hands-on, web-based small group activity to be completed during the class period. Evaluation of the activity through student performance assessments suggests that students who complete the activity can better interpret the BLAST output parameters % query coverage and % max identity. While the topic of the activity is bacterial cell wall structure, it could be adapted to address other biological concepts.

Bioinformatics goes to school--new avenues for teaching contemporary biology

Since 2010, the European Molecular Biology Laboratory's (EMBL) Heidelberg laboratory and the European Bioinformatics Institute (EMBL-EBI) have jointly run bioinformatics training courses developed specifically for secondary school science teachers within Europe and EMBL member states. These courses focus on introducing bioinformatics, databases, and data-intensive biology, allowing participants to explore resources and providing classroom-ready materials to support them in sharing this new knowledge with their students.

In this article, we chart our progress made in creating and running three bioinformatics training courses, including how the course resources are received by participants and how these, and bioinformatics in general, are subsequently used in the classroom. We assess the strengths and challenges of our approach, and share what we have learned through our interactions with European science teachers.

Integrating bioinformatics into senior high school: design principles and implications

Bioinformatics is an integral part of modern life sciences. It has revolutionized and redefined how research is carried out and has had an enormous impact on biotechnology, medicine, agriculture and related areas. Yet, it is only rarely integrated into high school teaching and learning programs, playing almost no role in preparing the next generation of information-oriented citizens. Here, we describe the design principles of bioinformatics learning environments, including our own, that are aimed at introducing bioinformatics into senior high school curricula through engaging learners in scientifically authentic inquiry activities. We discuss the bioinformatics-related benefits and challenges that high school teachers and students face in the course of the implementation process, in light of previous studies and our own experience. Based on these lessons, we present a new approach for characterizing the questions embedded in bioinformatics teaching and learning units, based on three criteria: the type of domain-specific knowledge required to answer each question (declarative knowledge, procedural knowledge, strategic knowledge, situational knowledge), the scientific approach from which each question stems (biological, bioinformatics, a combination of the two) and the associated cognitive process dimension (remember, understand, apply, analyze, evaluate, create). We demonstrate the feasibility of this approach using a learning environment, which we developed for the high school level, and suggest some of its implications. This review sheds light on unique and critical characteristics related to broader integration of bioinformatics in secondary education, which are also relevant to the undergraduate level, and especially on curriculum design, development of suitable learning environments and teaching and learning processes.

Genome annotation in a community college cell biology lab

The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning skills. Additionally, the project strengthens student understanding of the scientific method and contributes to student learning gains in curricular objectives centered around basic molecular biology, specifically, the Central Dogma. Importantly, inclusion of this project in the laboratory course provides students with a positive learning environment and allows for the use of cooperative learning strategies to increase overall student success.

Integrating grant-funded research into the undergraduate biology curriculum using IMG-ACT

It has become clear in current scientific pedagogy that the emersion of students in the scientific process in terms of designing, implementing, and analyzing experiments is imperative for their education; as such, it has been our goal to model this active learning process in the classroom and laboratory in the context of a genuine scientific question. Toward this objective, the National Science Foundation funded a collaborative research grant between a primarily undergraduate institution and a research-intensive institution to study the chemotactic responses of the bacterium Pseudomonas putida F1. As part of the project, a new Bioinformatics course was developed in which undergraduates annotate relevant regions of the P. putida F1 genome using Integrated Microbial Genomes Annotation Collaboration Toolkit, a bioinformatics interface specifically developed for undergraduate programs by the Department of Energy Joint Genome Institute. Based on annotations of putative chemotaxis genes in P. putida F1 and comparative genomics studies, undergraduate students from both institutions developed functional genomics research projects that evolved from the annotations. The purpose of this study is to describe the nature of the NSF grant, the development of the Bioinformatics lecture and wet laboratory course, and how undergraduate student involvement in the project that was initiated in the classroom has served as a springboard for independent undergraduate research projects.

Strategies for using peer-assisted learning effectively in an undergraduate bioinformatics course

This study used a mixed methods approach to evaluate hybrid peer-assisted learning approaches incorporated into a bioinformatics tutorial for a genome annotation research project. Quantitative and qualitative data were collected from undergraduates who enrolled in a research-based laboratory course during two different academic terms at UCLA. Findings indicate that a critical feature of the peer-assisted learning approach is to have near-peer leaders with genome annotation experience, allowing them to communicate technical and conceptual aspects of the process in the context of a research project (a.k.a., the "big picture"). These characteristics are important for creating connections between the wet lab experiments and the computer lab activities, engendering excitement about the research project and fostering engagement in bioinformatics as a discipline. Likewise, it is essential to couple tutorial training in genome annotation with appropriate instructional materials, providing detailed, step-by-step instructions for database navigation. Finally, the assessment results support this hybrid peer-assisted learning approach as a model for undergraduates to successfully learn bioinformatics in a course setting.

Using microbial genome annotation as a foundation for collaborative student research

We used the Integrated Microbial Genomes Annotation Collaboration Toolkit as a framework to incorporate microbial genomics research into a microbiology and biochemistry course in a way that promoted student learning of bioinformatics and research skills and emphasized teamwork and collaboration as evidenced through multiple assessment mechanisms. Student teams in microbiology used bioinformatics tools to identify and characterize gene products from Mucilaginibacter paludis necessary for the synthesis of specific amino acids and then designed and carried out growth experiments to determine if the organism could indeed synthesize the amino acids. Students in biochemistry worked to characterize one of the amino acid biosynthetic pathways reconstructed by a previous microbiology class through amplification and cloning of the M. paludis genes and complementation analysis of Escherichia coli mutants.

Using Bioinformatics to Develop and Test Hypotheses: E. coli-Specific Virulence Determinants

Bioinformatics, the use of computer resources to understand biological information, is an important tool in research, and can be easily integrated into the curriculum of undergraduate courses. Such an example is provided in this series of four activities that introduces students to the field of bioinformatics as they design PCR based tests for pathogenic E. coli strains. A variety of computer tools are used including BLAST searches at NCBI, bacterial genome searches at the Integrated Microbial Genomes (IMG) database, protein analysis at Pfam and literature research at PubMed. In the process, students also learn about virulence factors, enzyme function and horizontal gene transfer. Some or all of the four activities can be incorporated into microbiology or general biology courses taken by students at a variety of levels, ranging from high school through college. The activities build on one another as they teach and reinforce knowledge and skills, promote critical thinking, and provide for student collaboration and presentation. The computer-based activities can be done either in class or outside of class, thus are appropriate for inclusion in online or blended learning formats. Assessment data showed that students learned general microbiology concepts related to pathogenesis and enzyme function, gained skills in using tools of bioinformatics and molecular biology, and successfully developed and tested a scientific hypothesis.

Teaching biology through statistics: application of statistical methods in genetics and zoology courses

Incorporation of mathematics into biology curricula is critical to underscore for undergraduate students the relevance of mathematics to most fields of biology and the usefulness of developing quantitative process skills demanded in modern biology. At our institution, we have made significant changes to better integrate mathematics into the undergraduate biology curriculum. The curricular revision included changes in the suggested course sequence, addition of statistics and precalculus as prerequisites to core science courses, and incorporating interdisciplinary (math-biology) learning activities in genetics and zoology courses. In this article, we describe the activities developed for these two courses and the assessment tools used to measure the learning that took place with respect to biology and statistics. We distinguished the effectiveness of these learning opportunities in helping students improve their understanding of the math and statistical concepts addressed and, more importantly, their ability to apply them to solve a biological problem. We also identified areas that need emphasis in both biology and mathematics courses. In light of our observations, we recommend best practices that biology and mathematics academic departments can implement to train undergraduates for the demands of modern biology.