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Abstract Background:Protein presence information is an essential component of biological pathway identification. Presence of certain enzymes in an organism points towards the metabolic pathways that occur within it, whereas the absence of these enzymes indicates either the existence of alternative pathways or a lack of these pathways altogether. The same inference applies to regulatory pathways such as gene regulation and signal transduction. Protein presence information therefore forms the basis for biological pathway studies, and patterns in presence-absence across multiple organisms allow for comparative pathway analyses. Results:Here we present ProTaxoVis, a novel bioinformatic tool that extracts protein presence information from database queries and maps it to a taxonomic tree or heatmap. ProTaxoVis generates a large-scale overview of presence patterns in taxonomic clades of interest. This overview reveals protein distribution patterns, and this can be used to deduce pathway evolution or to probe other biological questions. ProTaxoVis combines and filters sequence query results to extract information on the distribution of proteins and translates this information into two types of visual outputs: taxonomic trees and heatmaps. The trees supplement their topology with scaled pie-chart representations per node of the presence of target proteins and combinations of these proteins, such that patterns in taxonomic groups can easily be identified. The heatmap visualisation shows presence and conservation of these proteins for a user-determined set of species, allowing for a more detailed view over a larger group of proteins as compared to the trees. ProTaxoVis also allows for visual quality checks of hits based on a coverage plot and a length histogram, which can be used to determine e-value and minimum protein length cutoffs. Tabular output of resulting data from the query, combined, and heatmap building step are saved and easily accessible for further analyses. Conclusions:We evaluate our tool with the phosphoribosyltransferases, a transferase enzyme family with notable distribution patterns amongst organisms of varying complexities and across Eukaryota, Bacteria, and Archaea. ProTaxoVis is open-source and available at:https://github.com/MolecularBioinformatics/ProTaxoVis.
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Replaying the Tape of Academia: Fourteen Alternative Practices for the Physical Sciences
Abstract The evolution of modern academic practices, analogous to the evolution of biological systems, reflects the influence of both contingency and determinism. From a theoretical perspective, how then could academic practices differ from those that were inherited? Would any alternative outcomes be more just, equitable, diverse, or inclusive? Here we present 14 alternative academic practices that might be attained upon replaying the tape of academia and evaluate their benefits and drawbacks. Oriented primarily around the physical sciences within the United States, these alternative practices reconsider common activities within the broad categories of the graduate student experience, faculty careers, evaluation methods, peer review and publication, and conference norms. Consideration of these alternative practices can guide within‐system change and large‐scale restructuring of academia to address the myriad challenges facing researchers and students. Conversely, alternative practices may introduce new issues or exacerbate existing problems. These alternative practices are meant to be imaginative, not prescriptive, and we hope their underlying ideas spur reflection and conversation on the existing practices embedded within academic culture. Readers are encouraged to complete a brief survey regarding their impressions of the alternative practices, available at the following link:rebrand.ly/AlternativePractices2024.
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- Award ID(s):
- 2204376
- PAR ID:
- 10540520
- Publisher / Repository:
- Perspectives of Earth and Space Scientists
- Date Published:
- Journal Name:
- Perspectives of Earth and Space Scientists
- Volume:
- 5
- Issue:
- 1
- ISSN:
- 2637-6989
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1029/2024CN000240
