A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists

Fagorzi, Camilla; Checcucci, Alice

doi:10.1007/978-1-0716-1099-2_15

Cited by 3 publications

(2 citation statements)

References 19 publications

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“…For example, the number of individuals that would need to be genotyped in order to obtain a reliable and accurate representation of the human pangenome could be so large that it is not necessarily feasible to do it with the current technology. However, novel bioinformatic methods have been developed in recent years to allow the analysis of such mass of data from microbes, plants, and animals [ 98 , 127 , 128 , 129 ]. Furthermore, the data generated from individuals involved in such projects would not only be massive, but also highly sensitive and personal, as they would contain the complete and exact sequence of an individual’s genetic material [ 130 , 131 , 132 , 133 , 134 ].…”

Section: Technical Ethical and Legal Considerationsmentioning

confidence: 99%

Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference

Abondio

Cilli

Luiselli

2023

Life

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A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material. Pangenomic analysis offers several advantages compared to traditional genomic research. For example, a pangenome is not bound by the physical constraints of a single genome, so it can capture more genetic variability. Thanks to the introduction of the concept of pangenome, it is possible to use exceedingly detailed sequence data to study the evolutionary history of two different species, or how populations within a species differ genetically. In the wake of the Human Pangenome Project, this review aims at discussing the advantages of the pangenome around human genetic variation, which are then framed around how pangenomic data can inform population genetics, phylogenetics, and public health policy by providing insights into the genetic basis of diseases or determining personalized treatments, targeting the specific genetic profile of an individual. Moreover, technical limitations, ethical concerns, and legal considerations are discussed.

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Section: Technical Ethical and Legal Considerationsmentioning

confidence: 99%

Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference

Abondio

Cilli

Luiselli

2023

Life

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“…Although some commercial packages exist for simulating laboratory techniques, such as LearnSci and Labster, there is an associated cost and limited scope for customisation. Alternative resources are either too simplistic, too focused, or targeted at researchers and, therefore, too technical for undergraduate students, such as the numerous resources that exist for the in silico analysis of "big data" including genome analysis and antibody epitope mapping (Lyons et al, 2009;Soria-Guerra et al, 2015;Fagorzi and Checcucci, 2021), which are used for basic research and so are far too advanced for undergraduate teaching. In addition, guidelines on immunology education focus on the themes that should be taught in the curriculum, without clear guidance on labs and specifically on dry-lab simulations (Justement and Bruns, 2020;Porter et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

The virtual flow cytometer: A new learning experience and environment for undergraduate teaching

Francis

Ruckley²,

Wilkinson³

2022

Front. Educ.

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BackgroundThe use of simulations has been steadily rising in popularity in the biosciences, not only due to the COVID-19 pandemic restricting access to physical labs and equipment but also in the face of rising student numbers. In this study, we describe the development and implementation of a novel, open-access interactive simulation used to not only supplement a laboratory class but to enhance the student learning experience. The simulation provides students with the opportunity to interact with a virtual flow cytometer, design a simple experiment and then critically analyse and interpret raw experimental data.ResultsResults showed that this highly authentic assessment used a much broader range of the mark scheme acting as an excellent discriminatory for student ability compared to simple recall as assessed by multiple-choice questions. Overall, the student response to the new assessment was positive, highlighting the novelty of the assessment, however, some students did experience technical issues when the simulation was used for the first time.ConclusionSimulations can play a crucial role in the student learning cycle by providing a rich, engaging learning environment, however, they need to be used to supplement other hands-on experiences to ensure that students acquire the necessary kinematic skills expected of a successful science graduate.

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