Search results for "systems biology"
showing 10 items of 143 documents
Robust dynamical pattern formation from a multifunctional minimal genetic circuit.
2010
Abstract Background A practical problem during the analysis of natural networks is their complexity, thus the use of synthetic circuits would allow to unveil the natural mechanisms of operation. Autocatalytic gene regulatory networks play an important role in shaping the development of multicellular organisms, whereas oscillatory circuits are used to control gene expression under variable environments such as the light-dark cycle. Results We propose a new mechanism to generate developmental patterns and oscillations using a minimal number of genes. For this, we design a synthetic gene circuit with an antagonistic self-regulation to study the spatio-temporal control of protein expression. He…
How subtle is the "terroir" effect? Chemistry-related signatures of two "climats de Bourgogne".
2014
The chemical composition of grape berries is influenced by various environmental conditions often considered to be representative of a "terroir". If grapes from a given terroir are assumed to reflect this origin in their chemical compositions, the corresponding wine should also reflect it. The aim of this work was therefore to reveal the "terroir" expression within the chemodiversity of grapes and related wines, using ultrahigh-resolution mass spectrometry. Grapes and corresponding wines, from two distinct - though very proximate - terroirs of Burgundy were analyzed over three vintages (2010, 2011 and 2012). Ultrahigh-resolution mass spectrometry and ultra-high performan…
Health and disease imprinted in the time variability of the human microbiome
2015
Human microbiota plays an important role in determining changes from health to disease. Increasing research activity is dedicated to understand its diversity and variability. We analyse 16S rRNA and whole genome sequencing (WGS) data from the gut microbiota of 97 individuals monitored in time. Temporal fluctuations in the microbiome reveal significant differences due to factors that affect the microbiota such as dietary changes, antibiotic intake, early gut development or disease. Here we show that a fluctuation scaling law describes the temporal variability of the system and that a noise-induced phase transition is central in the route to disease. The universal law distinguishes healthy fr…
Genomic and Proteomic Analysis of Wine Yeasts
2011
Publisher Summary Saccharomyces cerevisiae is the main microorganism involved in wine fermentation. It has been used as a model organism in molecular biology for many years and is the only wine yeast species for which abundant genomic and proteomic information is available. Most of the techniques currently used in functional genomics and proteomics were initially developed in this yeast. The fact that S. cerevisiae was the first microorganism to be widely used in the development of genome technology allowed other phylogenetically related yeasts to be analyzed subsequently in global sequencing projects, and the use of comparative genomics has since led to important conclusions regarding gene…
Mollusc shellomes: Past, present and future.
2020
13 pages; International audience; In molluscs, the shell fabrication requires a large array of secreted macromolecules including proteins and polysaccharides. Some of them are occluded in the shell during mineralization process and constitute the shell repertoire. The protein moieties, also called shell proteomes or, more simply, 'shellomes', are nowadays analyzed via high-throughput approaches. These latter, applied so far on about thirty genera, have evidenced the huge diversity of shellomes from model to model. They also pinpoint the recurrent presence of functional domains of diverse natures. Shell proteins are not only involved in guiding the mineral deposition, but also in enzymatic a…
Systems Biology, Bioinformatics and Medicine Approaches to Cancer Progression Outcomes
2011
Because of the complexity of carcinogenesis and tumour development, it is critical to understand the underlying organizing principles. In this chapter a possible approach is illustrated, starting with a description of breast cancer prognosis as a function of three powerful biological motifs derived from gene expression profiling. A proliferation metagene describing the transition from slow to fast proliferation leads to the most dramatic aggravation of prognosis. A second immune cell metagene represents an opponent of tumour evolution, whereby only fast-proliferating tumours that are not recognized and eliminated by immune cells can progress. In the absence of endocrine treatment, a third m…
Design and experimental validation of a generic model for combinatorial assembly of DNA tiles into 1D-structures.
2010
Abstract Background Quantitative modeling of the self-assembly of DNA tiles leading either to defined end-products or distribution of biopolymers is of practical importance for biotechnology and synthetic biology. Methods The combinatorial process describing tile assembly was implemented into a generic algorithm allowing quantitative description of the population of significant species accumulating during the reaction course. Experimental formation and characterization by optical and electrophoresis approaches of copolymers resulting from the self-assembly of a limited number of half-complementary tiles were used to define and validate generic rules allowing definition of model parameters. …
The interplay between cooperativity and diversity in model threshold ensembles
2014
The interplay between cooperativity and diversity is crucial for biological ensembles because single molecule experiments show a significant degree of heterogeneity and also for artificial nanostructures because of the high individual variability characteristic of nanoscale units. We study the cross-effects between cooperativity and diversity in model threshold ensembles composed of individually different units that show a cooperative behaviour. The units are modelled as statistical distributions of parameters (the individual threshold potentials here) characterized by central and width distribution values. The simulations show that the interplay between cooperativity and diversity results …
Models of Immune Aging
2018
Abstract Biochemical changes, impaired immune responses to new antigens, and inflammation-based disorders are commonly found in aged individuals. Thus, many studies have addressed the immune system of healthy elderly, including centenarians, since a well-preserved immune system appears to be a major factor of longevity. Longitudinal studies in humans are complicated, as most immune changes associated with aging develop slowly. Human models of accelerated immune aging in clinical conditions allow exploring the age-related changes in the human immune system and the mechanisms of accelerated aging in chronic infections and autoimmunity. Even if they do not perfectly mimic immune function and i…
Traditional Chinese medicine research in the post-genomic era: good practice, priorities, challenges and opportunities.
2012
Abstract Background and aims GP-TCM is the 1st EU-funded Coordination Action consortium dedicated to traditional Chinese medicine (TCM) research. This paper aims to summarise the objectives, structure and activities of the consortium and introduces the position of the consortium regarding good practice, priorities, challenges and opportunities in TCM research. Serving as the introductory paper for the GP-TCM Journal of Ethnopharmacology special issue, this paper describes the roadmap of this special issue and reports how the main outputs of the ten GP-TCM work packages are integrated, and have led to consortium-wide conclusions. Materials and methods Literature studies, opinion polls and di…