scholarly journals Top‐down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model

2008 ◽  
Vol 4 (1) ◽  
pp. 205 ◽  
Author(s):  
Francois‐Pierre J Martin ◽  
Yulan Wang ◽  
Norbert Sprenger ◽  
Ivan K S Yap ◽  
Serge Rezzi ◽  
...  
Keyword(s):  
Systems Biology ◽  
Mouse Model ◽  
Top Down

scholarly journals A top‐down systems biology view of microbiome‐mammalian metabolic interactions in a mouse model

2007 ◽  
Vol 3 (1) ◽  
pp. 112 ◽  
Author(s):  
François‐Pierre J Martin ◽  
Marc‐Emmanuel Dumas ◽  
Yulan Wang ◽  
Cristina Legido‐Quigley ◽  
Ivan K S Yap ◽  
...  
Keyword(s):  
Systems Biology ◽  
Mouse Model ◽  
Top Down ◽  
Metabolic Interactions

Data Analysis and Interpretation in Metabolomics

2013 ◽  
pp. 1494-1521
Author(s):  
Jose M. Garcia-Manteiga
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Data Analysis ◽  
Systems Biology ◽  
Magnetic Resonance ◽  
Biological System ◽  
Analytical Techniques ◽  
Point Of View ◽  
The Other ◽  
Top Down

Metabolomics represents the new ‘omics’ approach of the functional genomics era. It consists in the identification and quantification of all small molecules, namely metabolites, in a given biological system. While metabolomics refers to the analysis of any possible biological system, metabonomics is specifically applied to disease and physiopathological situations. The data collected within these approaches is highly integrative of the other higher levels and is hence amenable to be explored with a top-down systems biology point of view. The aim of this chapter is to give a global view of the state of the art in metabolomics describing the two analytical techniques usually used to give rise to this kind of data, nuclear magnetic resonance, NMR, and mass spectrometry. In addition, the author will focus on the different data analysis tools that can be applied to such studies to extract information with special interest at the attempts to integrate metabolomics with other ‘omics’ approaches and its relevance in systems biology modeling.

Data Analysis and Interpretation in Metabolomics

2011 ◽  
pp. 29-56
Author(s):  
Jose M. Garcia-Manteiga
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Data Analysis ◽  
Systems Biology ◽  
Magnetic Resonance ◽  
Biological System ◽  
Analytical Techniques ◽  
Point Of View ◽  
The Other ◽  
Top Down

Metabolomics represents the new ‘omics’ approach of the functional genomics era. It consists in the identification and quantification of all small molecules, namely metabolites, in a given biological system. While metabolomics refers to the analysis of any possible biological system, metabonomics is specifically applied to disease and physiopathological situations. The data collected within these approaches is highly integrative of the other higher levels and is hence amenable to be explored with a top-down systems biology point of view. The aim of this chapter is to give a global view of the state of the art in metabolomics describing the two analytical techniques usually used to give rise to this kind of data, nuclear magnetic resonance, NMR, and mass spectrometry. In addition, the author will focus on the different data analysis tools that can be applied to such studies to extract information with special interest at the attempts to integrate metabolomics with other ‘omics’ approaches and its relevance in systems biology modeling.

Top-Down Systems Biology Modeling of Host Metabotype−Microbiome Associations in Obese Rodents

2009 ◽  
Vol 8 (5) ◽  
pp. 2361-2375 ◽  
Author(s):  
Alison Waldram ◽  
Elaine Holmes ◽  
Yulan Wang ◽  
Mattias Rantalainen ◽  
Ian D. Wilson ◽  
...  
Keyword(s):  
Systems Biology ◽  
Top Down

scholarly journals A metabolomic and systems biology perspective on the brain of the Fragile X syndrome mouse model

2011 ◽  
Vol 21 (12) ◽  
pp. 2190-2202 ◽  
Author(s):  
L. Davidovic ◽  
V. Navratil ◽  
C. M. Bonaccorso ◽  
M. V. Catania ◽  
B. Bardoni ◽  
...  
Keyword(s):  
Systems Biology ◽  
Mouse Model ◽  
Fragile X Syndrome ◽  
Fragile X ◽  
The Brain

scholarly journals Analysis of the Neuroproteome Associated With Cell Therapy After Intranigral Grafting in a Mouse Model of Parkinson Disease

2021 ◽  
Vol 15 ◽  
Author(s):  
Hassan Dakik ◽  
Sarah Mantash ◽  
Ali Nehme ◽  
Firas Kobeissy ◽  
Masoud Zabet-Moghaddam ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Animal Model ◽  
Systems Biology ◽  
Mouse Model ◽  
Cell Therapy ◽  
Parkinson Disease ◽  
Large Scale ◽  
Brain Regions ◽  
Nigrostriatal Pathway ◽  
Reconstruction Process

Advances in large-scale proteomics analysis have been very useful in understanding pathogenesis of diseases and elaborating therapeutic strategies. Proteomics has been employed to study Parkinson disease (PD); however, sparse studies reported proteome investigation after cell therapy approaches. In this study, we used liquid chromatography–tandem mass spectrometry and systems biology to identify differentially expressed proteins in a translational mouse model of PD after cell therapy. Proteins were extracted from five nigrostriatal-related brain regions of mice previously lesioned with 6-hydroxydopamine in the substantia nigra. Protein expression was compared in non-grafted brain to 1 and 7 days after intranigral grafting of E12.5 embryonic ventral mesencephalon (VM). We found a total of 277 deregulated proteins after transplantation, which are enriched for lipid metabolism, oxidative phosphorylation and PD, thus confirming that our animal model is similar to human PD and that the presence of grafted cells modulates the expression of these proteins. Notably, seven proteins (Acta1, Atp6v1e1, Eci3, Lypla2, Pip4k2a, Sccpdh, and Sh3gl2) were commonly down-regulated after engraftment in all studied brain regions. These proteins are known to be involved in the formation of lipids and recycling of dopamine (DA) vesicle at the synapse. Moreover, intranigral transplantation of VM cells decreased the expression of proteins related to oxidative stress, especially in the nigrostriatal pathway containing the DA grafted neurons. In the same regions, an up-regulation of several proteins including α-synuclein and tyrosine hydroxylase was observed, whereas expression of tetraspanin 7 was shut down. Overall, these results suggest that intranigral transplantation of VM tissue in an animal model of PD may induce a decrease of oxidative stress in the nigrostriatal pathway and a restoration of the machinery of neurotransmitters, particularly DA release to promote DA transmission through a decrease of D2 DA receptors endocytosis. Identification of new mechanistic elements involved in the nigrostriatal reconstruction process, using translational animal models and systems biology, is a promising approach to enhance the repair of this pathway in PD patients undergoing cell therapy.

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