Laboratory module design for Biology Students: A Systematic review

Module design for students’ laboratory activities plays an important role in the effective implementation of scientific investigation in the laboratory. The purpose of this review is to examine the types, topics, competencies, and approaches to develop laboratory module for biology students. The review of the literature was conducted systematically. Eighteen research articles were selected from 41 articles published within 2009 and 2019. The systematic review followed 5 steps. The research articles were searched using Google Scholar's online database and then traced back from the relevant international and national journals. The articles collected were selected by two reviewers who rated the quality. The results of the analysis showed that the laboratory modules are designed using the following basis: online, research, quantitative skills, inquiry, and traditional. The biology topics focused are Genetics, Ecology, Phylogenetics, Biochemistry, Molecular Biology, Evolution, Biotechnology, and Tissue Culture. The methods used for laboratory module development by Indonesian researchers are 4D, ADDIE, R & D, Dick & Carey, and Borg & Gall, while international researchers generally do not specify the name of the method used. Generally, the need analysis which focuses on the novelty of the developed concept is conducted in the beginning. It continues with module designing, validation, implementation, and response survey from the students as the module users

Enhancing the teaching-research nexus in the undergraduate curriculum through assessment

Successful linkages between teaching and research in the undergraduate curriculum are strongly dependent on academics’ ability to encourage and facilitate an inquiry based approach to learning. An assessment strategy in which students become active participants in the assessment process is crucial to facilitate the development of this inquiry based approach. Developing this so-called research-mindedness is central to helping students' to become independent learners and to be more effective professionals in their future careers. This paper describes a distributed systems approach to assessment implemented in the undergraduate module Molecular Biology. The assessment comprised a series of sequence identification, database use and analysis steps, with each student being given a different starting gene. In combination, the students analysed an entire genetic pathway. This approach allows the assignments generated to be combined and used to address a single larger question, which can be either teaching or research based. This is then fed back into the teaching. This direct link between the assessment outcomes and the learning process increases student engagement with the subject and sense of ownership of the work carried out. This approach to assessment, in which students undertake a small part of a larger task, is ideal for various technical, skills-based, assignments, such as those central to the many types of bioinformatics analyses. However, it can be adapted to various types of meta-review. The paper discusses the details for the implementation, as well as the benefits and potential pitfalls of the approach

Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors.

Bioinformatics has become an indispensable part of life science over the past 2 decades. However, bioinformatics education is not well integrated at the undergraduate level, especially in liberal arts colleges and regional universities in the United States. One significant obstacle pointed out by the Network for Integrating Bioinformatics into Life Sciences Education is the lack of faculty in the bioinformatics area. Most current life science professors did not acquire bioinformatics analysis skills during their own training. Consequently, a great number of undergraduate and graduate students do not get the chance to learn bioinformatics or computational biology skills within a structured curriculum during their education. To address this gap, we developed a module-based, week-long short course to train small college and regional university professors with essential bioinformatics skills. The bioinformatics modules were built to be adapted by the professor-trainees afterward and used in their own classes. All the course materials can be accessed at https://github.com/TheJacksonLaboratory/JAXBD2K-ShortCourse

Using Comparative Genomics for Inquiry-Based Learning to Dissect Virulence of Escherichia coli O157:H7 and Yersinia pestis

Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of Genomes database. In the second module, students use an alignment of five Yersinia pestis genomes to analyze single-nucleotide polymorphisms of three genes to classify strains into biovar groups. Students are then given sequences of bacterial DNA amplified from the teeth of corpses from the first and second pandemics of the bubonic plague and asked to classify these new samples. Learning-assessment results reveal student improvement in self-efficacy and content knowledge, as well as students’ ability to use BLAST to identify genomic islands and conduct analyses of virulence factors from E. coli O157:H7 or Y. pestis. Each of these educational modules offers educators new ready-to-implement resources for integrating comparative genomic topics into their curricula

A cure for salmonella: Engaging students in pathogen microbiology and bioinformatics

Advances in Next Generation Sequencing (NGS) technology have generated a vast amount of publicly available genomic data, creating a need for students with training in computational analysis. This laboratory lesson is a course-based undergraduate research experience (CURE) focusing on environmental Salmonella, a common foodborne pathogen that is of great interest to public health laboratories but is relatively less virulent than most other such pathogens. As discovery is a central tenet of CUREs, students isolate novel Salmonella enterica and related strains from stream sediment, poultry litter, or other sources in the first half of the lesson (Module 1). They also conduct phenotypic detection of antimicrobial resistance and large plasmids. Isolate genomes may be sequenced by the FDA or public health laboratories (ours were sequenced by the Virginia Department of Consolidated Laboratory Services at no charge). The second half of the lesson (Module 2) involves the bioinformatic analysis of this sequence data. Students use easily accessible, primarily web-based tools such as GalaxyTrakr and Enterobase to assemble their genomes and investigate areas of interest including serotyping, identification of antibiotic resistance genes and genomic islands, and evidence of plasmids. After completion of this course, students should be able to demonstrate skills in the isolation and identification of Salmonella from natural sources, as well as skills necessary for computational analysis of microbial genomic data, particularly of members of the Enterobactericaeae. While this course consists of two modules, one focusing on laboratory skills and the other bioinformatics, either could be used as a standalone module

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 Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans

Fostering the Biosecurity Norm: Biosecurity Education for the Next Generation of Life Scientists

Sustainable education on biosecurity and dual use for life scientists is increasingly recognised as being an important element of broader efforts to achieve biosecurity. To address this issue, a joint project between the Landau Network-Centro Volta and the Bradford Disarmament Research Centre has been initiated to analyse what currently exists in terms of biosecurity and dual use education, but also how such education can be most effectively achieved in a sustainable fashion. The purpose of this paper is to elaborate on the findings of a survey on the extent of, and attitudes to, biosecurity and dual use education in European universities, and outline the educational activities undertaken through a network of contacts built through the survey and some of the conclusions drawn from engagement with this network. The paper also outlines the development and optimization of an Educational Module Resource intended to support lecturers in the improvement and implementation of educational material related to biosecurity and dual use. This is further expanded by the authors' experience derived from implementation tests conducted at universities around Europe, in which material was tested with students and faculty members. To date, the main results from this evaluative process are that students and faculties are generally unaware of biosecurity and dual use concerns, but nonetheless appear interested in discussing these topics and have initiated challenging debates on the importance of balancing factors such as security, research, secrecy and development. However, serious efforts in terms of developing and promulgating education more broadly across the life science community will require concerted actions which look at education but also at other mutually reinforcing intervention points such as funding bodies, authors and publishers. Moreover, in the longer term it will also be necessary to develop new mechanisms and metrics to determine success in these activities and ensure that educational activities are contributing, along with other legal and regulatory measures, to mitigating the challenge of potential misuse of the life sciences in the 21st century