Biology subjects

Eguinoa, I.

Publications and source records attributed to Eguinoa, I..

3 recordsLinked to original sources

bioRxiv2020

Expanding the Galaxy's reference data

SummaryProperly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows to easily organize, retrieve, and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. Additionally, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenies remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS repository from GalaxyProject.org, with mirrors across the United States, Canada, Europe, and Australia, enabling easy use outside of Galaxy. Availability and implementationThe ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 20.05, which is available from https://github.com/galaxyproject/galaxy under the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull and released using an MIT license.

bioinformatics↗

bioRxiv2020

Precursor intensity-based label-free quantification software tools for proteomic and multi-omic analysis within the Galaxy Platform.

For mass spectrometry-based peptide and protein quantification, label-free quantification (LFQ) based on precursor mass peak (MS1) intensities is considered reliable due to its dynamic range, reproducibility, and accuracy. In LFQ workflows, protein abundance changes are inferred from peptide-level information, including microbial peptides (for metaproteomics) and peptides carrying post-translational modifications (for proteomics) and/or variant sequences (for proteogenomics). Multi-omics studies (such as proteogenomics and metaproteomics) rely on peptide detection and quantification to identify and quantify peptides that map to unique proteoforms and metaproteins. The Galaxy for proteomics (Galaxy-P) platform has proven useful for the development of accessible workflows to identify proteins in these complex multi-omic studies. However, proteomics workflows within the Galaxy platform have lacked well-tested label-free quantification tools. In this study, our main goals were to evaluate two recently published open-source LFQ tools and to implement them within the Galaxy platform, enabling their easy integration with established workflows. These two tools, moFF and FlashLFQ, were selected based on their described peptide quantification capabilities and amenability to Galaxy implementation. Through rigorous testing and communication with the tools developers, we gained insights into the software features necessary for maximizing the performance of each tool. Software features evaluated included: a) match-between-runs (MBR); b) using both Thermo .raw and HUPO standards .mzML file formats as input for improved quantification; c) use of containers and/or conda packages; d) parameters needed for analyzing large input datasets; and e) optimization and validation of software performance. This work 1) establishes a process for software implementation, optimization and validation within Galaxy; and 2) makes powerful new tools for LFQ available which should prove highly useful for a variety of proteomics and multi-omics applications employing the Galaxy platform.

bioinformatics↗

bioRxiv2019

The Arabidopsis condensin CAP-D subunits arrange interphase chromatin

Condensins are best known for their role in shaping chromosomes. However, other functions as organizing interphase chromatin and transcriptional control have been reported in yeasts and animals. Yeasts encode one condensin complex, while higher eukaryotes have two of them (condensin I and II). Both, condensin I and II, are conserved in Arabidopsis thaliana, but so far little is known about their function. Here we show that the A. thaliana CAP-D2 (condensin I) and CAP-D3 (condensin II) subunits are highly expressed in mitotically active tissues. In silico and pull-down experiments indicate that both CAP-D proteins interact with the other condensin I and II subunits. Our data suggest that the expression, localization and composition of the condensin complexes in A. thaliana are similar as in other higher eukaryotes. Previous experiments showed that the lack of A. thaliana CAP-D3 leads to centromere association during interphase. To study the function of CAP-D3 in chromatin organization more in detail we compared the nuclear distribution of rDNA, of centromeric chromocenters and of different epigenetic marks, as well as the nuclear size between wild-type and cap-d3 mutants. In these mutants an association of heterochromatic sequences occurs, but nuclear size and the general methylation and acetylation patterns remain unchanged. In addition, transcriptome analyses revealed a moderate influence of CAP-D3 on general transcription, but a stronger one on transcription of stress-related genes. We propose a model for the CAP-D3 function during interphase, where CAP-D3 localizes in euchromatin loops to stiff them, and consequently separates centromeric regions and 45S rDNA repeats.

cell biology↗