flowDiv: a new pipeline for analyzing flow cytomet... - BV FAPESP
Advanced search
Start date
Betweenand
Related content
(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

flowDiv: a new pipeline for analyzing flow cytometric diversity

Full text
Author(s):
Wanderley, Bruno M. S. [1, 2] ; Araujo, Daniel S. A. [1] ; Quiroga, V, Maria ; Amado, Andre M. [3, 2] ; Neto, Adriao D. D. [1] ; Sarmento, Hugo [4] ; Metz, Sebastian D. [5] ; Unrein, Fernando [5]
Total Authors: 8
Affiliation:
[1] Univ Fed Rio Grande do Norte, Inst Metropole Digital, Natal, RN - Brazil
[2] Univ Fed Rio Grande do Norte, Dept Oceanog & Limnol, Natal, RN - Brazil
[3] Univ Fed Juiz de Fora, Dept Biol, Juiz De Fora - Brazil
[4] Univ Fed Sao Carlos, Dept Hidrobiol, Sao Carlos, SP - Brazil
[5] Quiroga, Maria, V, Univ Nacl San Martin UNSAM, Inst Tecnol Chascomus INTECH, CONICET, Buenos Aires, DF - Argentina
Total Affiliations: 5
Document type: Journal article
Source: BMC Bioinformatics; v. 20, MAY 28 2019.
Web of Science Citations: 0
Abstract

BackgroundFlow cytometry (FCM) is one of the most commonly used technologies for analysis of numerous biological systems at the cellular level, from cancer cells to microbial communities. Its high potential and wide applicability led to the development of various analytical protocols, which are often not interchangeable between fields of expertise. Environmental science in particular faces difficulty in adapting to non-specific protocols, mainly because of the highly heterogeneous nature of environmental samples. This variety, although it is intrinsic to environmental studies, makes it difficult to adjust analytical protocols to maintain both mathematical formalism and comprehensible biological interpretations, principally for questions that rely on the evaluation of differences between cytograms, an approach also termed cytometric diversity. Despite the availability of promising bioinformatic tools conceived for or adapted to cytometric diversity, most of them still cannot deal with common technical issues such as the integration of differently acquired datasets, the optimal number of bins, and the effective correlation of bins to previously known cytometric populations.ResultsTo address these and other questions, we have developed flowDiv, an R language pipeline for analysis of environmental flow cytometry data. Here, we present the rationale for flowDiv and apply the method to a real dataset from 31 freshwater lakes in Patagonia, Argentina, to reveal significant aspects of their cytometric diversities.ConclusionsflowDiv provides a rather intuitive way of proceeding with FCM analysis, as it combines formal mathematical solutions and biological rationales in an intuitive framework specifically designed to explore cytometric diversity. (AU)

FAPESP's process: 16/50494-8 - Flow cytometry as a tool to assess the impact of mixotrophic Algae in planktonic food webs
Grantee:Hugo Miguel Preto de Morais Sarmento
Support Opportunities: Regular Research Grants
FAPESP's process: 14/14139-3 - Microbial processes and biodiversity in aquatic ecosystems
Grantee:Hugo Miguel Preto de Morais Sarmento
Support Opportunities: Research Grants - Young Investigators Grants