Metabolic modelling as a powerful tool to identify critical components of 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.

A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes.

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, here we report the development of 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 the derivation of a standardized gnotobiotic mouse model called GM15.

An integrated transcriptomics and metabolomics study of the immune response of newly hatched chicks to the cytosine-phosphate-guanine oligonucleotide stimulation.

The immunological immaturity of the innate immune system during the first-week post-hatch enables pathogens to infect chickens, leading to the death of the animals. Current preventive solutions to improve the resistance of chicks to infections include vaccination, breeding, and sanitation. Other prophylactic solutions have been investigated, such as the stimulation of animal health with immunostimulants.

Excitability in the host-pathogen interactions of HIV infection and emergence of viral load blips.

HIV viral blips are characterized by intermittent episodes of detectable low-level viraemia which return spontaneously to an undetectable level in patients with full suppression of viraemia (<50 copies/ml). The precise mechanisms responsible for viraemia blips and their clinical significance are not known. In this work, we analyze HIV blips using a mathematical model describing basic host-pathogen interactions, in particular regulatory processes involving CD4+, CD8+ T-cells and the virus.

Metabolomics-on-a-chip and metabolic flux analysis for label-free modeling of the internal metabolism of HepG2/C3A cells.

In vitro microfluidic systems are increasingly used as an alternative to standard Petri dishes in bioengineering and metabolomic investigations, as they are expected to provide cellular environments close to the in vivo conditions. In this work, we combined the recently developed "metabolomics-on-a-chip" approach with metabolic flux analysis to model the metabolic network of the hepatoma HepG2/C3A cell line and to infer the distribution of intracellular metabolic fluxes in standard Petri dishes and microfluidic biochips. A high pyruvate reduction to lactate was observed in both systems, suggesting that the cells operate in oxygen-limited environments.

Kinetic modelling of in vitro cell-based assays to characterize non-specific bindings and ADME processes in a static and a perfused fluidic system.

Recently, physiologically based perfusion in vitro systems have been developed to provide cell culture environment close to in vivo cell environment (e.g., fluidic conditions, organ interactions).

How molecular should your molecular model be? On the level of molecular detail required to simulate biological networks in systems and synthetic biology.

The recent advance of genetic studies and the rapid accumulation of molecular data, together with the increasing performance of computers, led researchers to design more and more detailed mathematical models of biological systems. Many modeling approaches rely on ordinary differential equations (ODE) which are based on standard enzyme kinetics. Michaelis-Menten and Hill functions are indeed commonly used in dynamical models in systems and synthetic biology because they provide the necessary nonlinearity to make the dynamics nontrivial (i.

From structure to dynamics: frequency tuning in the p53-Mdm2 network. II Differential and stochastic approaches.

In Part I of this work, we carried out a logical analysis of a simple model describing the interplay between protein p53, its main negative regulator Mdm2 and DNA damage, and briefly discussed the corresponding differential model (Abou-Jaoudé et al., 2009). This analysis allowed us to reproduce several qualitative features of the kinetics of the p53 response to damage and provided an interpretation of the short and long characteristic periods of oscillation reported by Geva-Zatorsky et al.

From structure to dynamics: frequency tuning in the p53-Mdm2 network I. Logical approach.

We investigate the dynamical properties of a simple four-variable model describing the interactions between the tumour suppressor protein p53, its main negative regulator Mdm2 and DNA damage, a model inspired by the work of Ciliberto et al. [2005. Steady states and oscillations in the p53/Mdm2 network.