Biology subjects

Ouattara, D. A.

Publications and source records attributed to Ouattara, D. A..

3 recordsLinked to original sources

bioRxiv2023

METABOLIC MODELLING AS A POWERFUL TOOL TO IDENTIFY CRITICAL COMPONENTS OF THE PNEUMOCYSTIS GROWTH MEDIUM

Establishing suitable in vitro culture conditions for microorganisms is crucial for dissecting their biology and empowering potential applications. However, a significant number of bacterial and fungal species, including Pneumocystis jirovecii, remain unculturable, hampering research efforts. P. jirovecii is a deadly pathogen of humans that causes life-threatening pneumonia in immunocompromised individuals and transplant patients. Despite the major impact of Pneumocystis on human health, we remain ignorant about the pathobiology of this fungus. This is largely due to the fact that its experimental dissection has been constrained by the inability to culture the organism in vitro. We present a comprehensive in silico genome-scale metabolic model of Pneumocystis growth and metabolism, with a view to identifying metabolic requirements and imbalances that hinder growth in vitro. We utilise recently published genome data and available information in the literature as well as bioinformatics and software tools to develop and validate the model. In addition, we employ Flux Balance Analysis and Reinforcement Learning approaches to make predictions regarding metabolic fluxes and to identify critical components of the Pneumocystis growth medium. Our findings offer insights into the biology of Pneumocystis and provide a novel strategy to overcome the longstanding challenge of culturing this pathogen in vitro.

systems biology↗

bioRxiv2020

BioTracs: A transversal framework for computational workflow standardization and traceability

BackgroundThe need of digital tools for integrative analysis is today important in most scientific areas. It leads to several community-driven initiatives to standardize the sharing of data and computational workflows. However, there exists no open agnostic framework to model and implement computation workflows, in particular in bioinformatics. It is therefore difficult for data scientists to share transparently and integrate heterogeneous analysis processes coming from different scientific domains, programing languages, projects or teams. ResultsWe present here BioTracs, a transversal framework for computational workflow standardization and traceability. It is based on PRISM architecture (Process Resource Interfacing SysteM), an agnostic open architecture we introduce here to standardize the way processes and resources can be modelled and interfaced in computational workflows to ensure traceability, reproducibility and facilitate sharing. BioTracs is today implemented in MATLAB and available under open source license on GitHub. Several BioTracs-derived applications are also available online. They were successfully applied to large-scale metabolomics and clinical studies and demonstrated flexibility and robustness. ConclusionsAs an implementation of the PRISM architecture, BioTracs paved the way to an open framework in which bioinformatics could specify ad model workflows. PRISM architecture is designed to provide scalability and transparency from the code to the project level we less efforts. It could also be implemented using open object-oriented languages such as Python, C++ or java. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/951624v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@3775deorg.highwire.dtl.DTLVardef@11b5672org.highwire.dtl.DTLVardef@1c87ff7org.highwire.dtl.DTLVardef@495f2d_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2019

A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF phenotype

Mus musculus is the classic mammalian model for biomedical research. Despite global efforts to standardize breeding and experimental procedures, the undefined composition and interindividual diversity of the microbiota of laboratory mice remains a limitation. In an attempt to standardize the gut microbiome in preclinical mouse studies, we developed a simplified mouse microbiota composed of 15 strains from 7 of the 20 most prevalent bacterial families representative of the fecal microbiota of C57BL/6J Specific (and Opportunistic) Pathogen-Free (SPF/SOPF) animals and derived a new standardized gnotobiotic mouse model called GM15. GM15 recapitulates extensively the functionalities found in the C57BL/6J SOPF microbiota metagenome, and GM15 animals are phenotypically similar to SOPF or SPF animals in two different facilities. They are also less sensitive to the deleterious effects of post-weaning malnutrition. The GM15 model provides increased reproducibility and robustness of preclinical studies by limiting the confounding effect of fluctuation in microbiota composition, and offers new opportunities for research focused on how the microbiota shapes host physiology in health and disease.

microbiology↗