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Gallardo-Alba C, Grüning B, Serrano-Solano B. A constructivist-based proposal for bioinformatics teaching practices during lockdown. PLoS Comput Biol 2021; 17:e1008922. [PMID: 33983931 PMCID: PMC8118257 DOI: 10.1371/journal.pcbi.1008922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The Coronavirus Disease 2019 (COVID-19) outbreaks have caused universities all across the globe to close their campuses and forced them to initiate online teaching. This article reviews the pedagogical foundations for developing effective distance education practices, starting from the assumption that promoting autonomous thinking is an essential element to guarantee full citizenship in a democracy and for moral decision-making in situations of rapid change, which has become a pressing need in the context of a pandemic. In addition, the main obstacles related to this new context are identified, and solutions are proposed according to the existing bibliography in learning sciences.
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Affiliation(s)
- Cristóbal Gallardo-Alba
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Beatriz Serrano-Solano
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
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2
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Liguori L, Monticelli M, Allocca M, Cubellis MV, Hay Mele B. Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach. BMC Bioinformatics 2020; 21:348. [PMID: 32838733 PMCID: PMC7447578 DOI: 10.1186/s12859-020-03560-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Although teaching bioinformatics has been incorporated in all traditional life science curricula, practical hands-on experiences in tight combination with wet-lab experiments are needed to motivate students. RESULTS We present a tutorial that starts from a practical problem: finding novel enzymes from marine environments. First, we introduce the idea of metagenomics, a recent approach that extends biotechnology to non-culturable microbes. We presuppose that a probe for the screening of metagenomic cosmid library is needed. The students start from the chemical structure of the substrate that should be acted on by the novel enzyme and end with the sequence of the probe. To attain their goal, they discover databases such as BRENDA and programs such as BLAST and Clustal Omega. Students' answers to a satisfaction questionnaire show that a multistep tutorial integrated into a research wet-lab project is preferable to conventional lectures illustrating bioinformatics tools. CONCLUSION Experimental biologists can better operate basic bioinformatics if a problem-solving approach is chosen.
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Affiliation(s)
- Ludovica Liguori
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
- Istituto di Chimica Biomolecolare -CNR, 80078, Pozzuoli, Italy
| | - Maria Monticelli
- Dipartimento di Biologia, Università Federico II, 80126, Naples, Italy
| | - Mariateresa Allocca
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
- Istituto di Chimica Biomolecolare -CNR, 80078, Pozzuoli, Italy
| | - Maria Vittoria Cubellis
- Dipartimento di Biologia, Università Federico II, 80126, Naples, Italy.
- Biology and Evolution of Marine Organisms Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Bruno Hay Mele
- Dipartimento di Biologia, Università Federico II, 80126, Naples, Italy
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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Andrighetti T, Bohar B, Lemke N, Sudhakar P, Korcsmaros T. MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions. Cells 2020; 9:cells9051278. [PMID: 32455748 PMCID: PMC7291277 DOI: 10.3390/cells9051278] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
Microbiome–host interactions play significant roles in health and in various diseases including autoimmune disorders. Uncovering these inter-kingdom cross-talks propels our understanding of disease pathogenesis and provides useful leads on potential therapeutic targets. Despite the biological significance of microbe–host interactions, there is a big gap in understanding the downstream effects of these interactions on host processes. Computational methods are expected to fill this gap by generating, integrating, and prioritizing predictions—as experimental detection remains challenging due to feasibility issues. Here, we present MicrobioLink, a computational pipeline to integrate predicted interactions between microbial and host proteins together with host molecular networks. Using the concept of network diffusion, MicrobioLink can analyse how microbial proteins in a certain context are influencing cellular processes by modulating gene or protein expression. We demonstrated the applicability of the pipeline using a case study. We used gut metaproteomic data from Crohn’s disease patients and healthy controls to uncover the mechanisms by which the microbial proteins can modulate host genes which belong to biological processes implicated in disease pathogenesis. MicrobioLink, which is agnostic of the microbial protein sources (bacterial, viral, etc.), is freely available on GitHub.
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Affiliation(s)
- Tahila Andrighetti
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; (T.A.); (B.B.)
- Institute of Biosciences, São Paulo University (UNESP), Botucatu 18618-689, SP, Brazil;
| | - Balazs Bohar
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; (T.A.); (B.B.)
- Department of Genetics, Eötvös Loránd University, Budapest 1117, Hungary
| | - Ney Lemke
- Institute of Biosciences, São Paulo University (UNESP), Botucatu 18618-689, SP, Brazil;
| | - Padhmanand Sudhakar
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; (T.A.); (B.B.)
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- Department of Chronic Diseases, Metabolism and Ageing, KU Leuven BE-3000, Leuven, Belgium
- Correspondence: (T.K.); (P.S.)
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; (T.A.); (B.B.)
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- Correspondence: (T.K.); (P.S.)
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Wright AM, Schwartz RS, Oaks JR, Newman CE, Flanagan SP. The why, when, and how of computing in biology classrooms. F1000Res 2019; 8:1854. [PMID: 32025290 PMCID: PMC6971840 DOI: 10.12688/f1000research.20873.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/18/2019] [Indexed: 03/29/2024] Open
Abstract
Many biologists are interested in teaching computing skills or using computing in the classroom, despite not being formally trained in these skills themselves. Thus biologists may find themselves researching how to teach these skills, and therefore many individuals are individually attempting to discover resources and methods to do so. Recent years have seen an expansion of new technologies to assist in delivering course content interactively. Educational research provides insights into how learners absorb and process information during interactive learning. In this review, we discuss the value of teaching foundational computing skills to biologists, and strategies and tools to do so. Additionally, we review the literature on teaching practices to support the development of these skills. We pay special attention to meeting the needs of diverse learners, and consider how different ways of delivering course content can be leveraged to provide a more inclusive classroom experience. Our goal is to enable biologists to teach computational skills and use computing in the classroom successfully.
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Affiliation(s)
- April M. Wright
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, 70403, USA
| | - Rachel S. Schwartz
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, 02881, USA
| | - Jamie R. Oaks
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | - Sarah P. Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, 8042, New Zealand
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Abstract
Many biologists are interested in teaching computing skills or using computing in the classroom, despite not being formally trained in these skills themselves. Thus biologists may find themselves researching how to teach these skills, and therefore many individuals are individually attempting to discover resources and methods to do so. Recent years have seen an expansion of new technologies to assist in delivering course content interactively. Educational research provides insights into how learners absorb and process information during interactive learning. In this review, we discuss the value of teaching foundational computing skills to biologists, and strategies and tools to do so. Additionally, we review the literature on teaching practices to support the development of these skills. We pay special attention to meeting the needs of diverse learners, and consider how different ways of delivering course content can be leveraged to provide a more inclusive classroom experience. Our goal is to enable biologists to teach computational skills and use computing in the classroom successfully.
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Affiliation(s)
- April M. Wright
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, 70403, USA
| | - Rachel S. Schwartz
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, 02881, USA
| | - Jamie R. Oaks
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | - Sarah P. Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, 8042, New Zealand
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6
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Sudhakar P, Jacomin AC, Hautefort I, Samavedam S, Fatemian K, Ari E, Gul L, Demeter A, Jones E, Korcsmaros T, Nezis IP. Targeted interplay between bacterial pathogens and host autophagy. Autophagy 2019; 15:1620-1633. [PMID: 30909843 PMCID: PMC6693458 DOI: 10.1080/15548627.2019.1590519] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 02/21/2019] [Accepted: 03/01/2019] [Indexed: 12/12/2022] Open
Abstract
Due to the critical role played by autophagy in pathogen clearance, pathogens have developed diverse strategies to subvert it. Despite previous key findings of bacteria-autophagy interplay, asystems-level insight into selective targeting by the host and autophagy modulation by the pathogens is lacking. We predicted potential interactions between human autophagy proteins and effector proteins from 56 pathogenic bacterial species by identifying bacterial proteins predicted to have recognition motifs for selective autophagy receptors SQSTM1/p62, CALCOCO2/NDP52 and MAP1LC3/LC3. Using structure-based interaction prediction, we identified bacterial proteins capable to modify core autophagy components. Our analysis revealed that autophagy receptors in general potentially target mostly genus-specific proteins, and not those present in multiple genera. The complementarity between the predicted SQSTM1/p62 and CALCOCO2/NDP52 targets, which has been shown for Salmonella, Listeria and Shigella, could be observed across other pathogens. This complementarity potentially leaves the host more susceptible to chronic infections upon the mutation of autophagy receptors. Proteins derived from enterotoxigenic and non-toxigenic Bacillus outer membrane vesicles indicated that autophagy targets pathogenic proteins rather than non-pathogenic ones. We also observed apathogen-specific pattern as to which autophagy phase could be modulated by specific genera. We found intriguing examples of bacterial proteins that could modulate autophagy, and in turn being targeted by autophagy as ahost defense mechanism. We confirmed experimentally an interplay between a Salmonella protease, YhjJ and autophagy. Our comparative meta-analysis points out key commonalities and differences in how pathogens could affect autophagy and how autophagy potentially recognizes these pathogenic effectors. Abbreviations: ATG5: autophagy related 5; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; GST: glutathione S-transferase; LIR: MAP1LC3/LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3 alpha; OMV: outer membrane vesicles; SQSTM1/p62: sequestosome 1; SCV: Salmonella containing vesicle; TECPR1: tectonin beta-propeller repeat containing 1; YhjJ: hypothetical zinc-protease.
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Affiliation(s)
- Padhmanand Sudhakar
- Earlham Institute, Norwich Research Park, Norwich, UK
- Gut Health and Microbes Programme, Quadram Institute, Norwich Research Park, Norwich, UK
- Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | | | | | - Siva Samavedam
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Koorosh Fatemian
- School of Life Sciences, University of Warwick, Coventry, UK
- Current affiliation:Exaelements LTD, Coventry, UK
| | - Eszter Ari
- Department of Genetics, Eotvos Lorand University, Budapest, Hungary
- Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Leila Gul
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Amanda Demeter
- Earlham Institute, Norwich Research Park, Norwich, UK
- Gut Health and Microbes Programme, Quadram Institute, Norwich Research Park, Norwich, UK
- Department of Genetics, Eotvos Lorand University, Budapest, Hungary
| | - Emily Jones
- Earlham Institute, Norwich Research Park, Norwich, UK
- Gut Health and Microbes Programme, Quadram Institute, Norwich Research Park, Norwich, UK
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich, UK
- Gut Health and Microbes Programme, Quadram Institute, Norwich Research Park, Norwich, UK
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7
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Jones EJ, Matthews ZJ, Gul L, Sudhakar P, Treveil A, Divekar D, Buck J, Wrzesinski T, Jefferson M, Armstrong SD, Hall LJ, Watson AJM, Carding SR, Haerty W, Di Palma F, Mayer U, Powell PP, Hautefort I, Wileman T, Korcsmaros T. Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy. Dis Model Mech 2019; 12:dmm037069. [PMID: 30814064 PMCID: PMC6451430 DOI: 10.1242/dmm.037069] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
Paneth cells are key epithelial cells that provide an antimicrobial barrier and maintain integrity of the small-intestinal stem cell niche. Paneth cell abnormalities are unfortunately detrimental to gut health and are often associated with digestive pathologies such as Crohn's disease or infections. Similar alterations are observed in individuals with impaired autophagy, a process that recycles cellular components. The direct effect of autophagy impairment on Paneth cells has not been analysed. To investigate this, we generated a mouse model lacking Atg16l1 specifically in intestinal epithelial cells, making these cells impaired in autophagy. Using three-dimensional intestinal organoids enriched for Paneth cells, we compared the proteomic profiles of wild-type and autophagy-impaired organoids. We used an integrated computational approach combining protein-protein interaction networks, autophagy-targeted proteins and functional information to identify the mechanistic link between autophagy impairment and disrupted pathways. Of the 284 altered proteins, 198 (70%) were more abundant in autophagy-impaired organoids, suggesting reduced protein degradation. Interestingly, these differentially abundant proteins comprised 116 proteins (41%) that are predicted targets of the selective autophagy proteins p62, LC3 and ATG16L1. Our integrative analysis revealed autophagy-mediated mechanisms that degrade key proteins in Paneth cell functions, such as exocytosis, apoptosis and DNA damage repair. Transcriptomic profiling of additional organoids confirmed that 90% of the observed changes upon autophagy alteration have effects at the protein level, not on gene expression. We performed further validation experiments showing differential lysozyme secretion, confirming our computationally inferred downregulation of exocytosis. Our observations could explain how protein-level alterations affect Paneth cell homeostatic functions upon autophagy impairment.This article has an associated First Person interview with the joint first authors of the paper.
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Affiliation(s)
- Emily J Jones
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Zoe J Matthews
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Lejla Gul
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Padhmanand Sudhakar
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
| | - Agatha Treveil
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
| | - Devina Divekar
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Jasmine Buck
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Matthew Jefferson
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Stuart D Armstrong
- National Institute of Health Research, University of Liverpool, Liverpool L3 5RF, UK
| | - Lindsay J Hall
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
| | - Alastair J M Watson
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Simon R Carding
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | | | - Ulrike Mayer
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Penny P Powell
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Tom Wileman
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
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Anton Feenstra K, Abeln S, Westerhuis JA, Brancos dos Santos F, Molenaar D, Teusink B, Hoefsloot HCJ, Heringa J. Training for translation between disciplines: a philosophy for life and data sciences curricula. Bioinformatics 2018; 34:i4-i12. [PMID: 29950011 PMCID: PMC6022589 DOI: 10.1093/bioinformatics/bty233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Motivation Our society has become data-rich to the extent that research in many areas has become impossible without computational approaches. Educational programmes seem to be lagging behind this development. At the same time, there is a growing need not only for strong data science skills, but foremost for the ability to both translate between tools and methods on the one hand, and application and problems on the other. Results Here we present our experiences with shaping and running a masters' programme in bioinformatics and systems biology in Amsterdam. From this, we have developed a comprehensive philosophy on how translation in training may be achieved in a dynamic and multidisciplinary research area, which is described here. We furthermore describe two requirements that enable translation, which we have found to be crucial: sufficient depth and focus on multidisciplinary topic areas, coupled with a balanced breadth from adjacent disciplines. Finally, we present concrete suggestions on how this may be implemented in practice, which may be relevant for the effectiveness of life science and data science curricula in general, and of particular interest to those who are in the process of setting up such curricula. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- K Anton Feenstra
- Department of Computer Science, IBIVU Centre for Integrative Bioinformatics Vrije Universiteit Amsterdam, HV Amsterdam, Netherlands
- AIMMS Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, MC Amsterdam, The Netherlands
| | - Sanne Abeln
- Department of Computer Science, IBIVU Centre for Integrative Bioinformatics Vrije Universiteit Amsterdam, HV Amsterdam, Netherlands
- Amsterdam Data Science, GH Amsterdam, The Netherlands
| | - Johan A Westerhuis
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, GE Amsterdam, The Netherlands
| | | | - Douwe Molenaar
- AIMMS Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, MC Amsterdam, The Netherlands
| | - Bas Teusink
- AIMMS Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, MC Amsterdam, The Netherlands
- Amsterdam Data Science, GH Amsterdam, The Netherlands
| | - Huub C J Hoefsloot
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, GE Amsterdam, The Netherlands
| | - Jaap Heringa
- Department of Computer Science, IBIVU Centre for Integrative Bioinformatics Vrije Universiteit Amsterdam, HV Amsterdam, Netherlands
- AIMMS Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, MC Amsterdam, The Netherlands
- Amsterdam Data Science, GH Amsterdam, The Netherlands
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9
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Affiliation(s)
- Laura R. Emery
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- * E-mail:
| | - Sarah L. Morgan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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