Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation.

While chromosomal rearrangements are ubiquitous in all domains of life, very little is known about their evolutionary significance, mostly because, apart from a few specifically studied and well-documented mechanisms (interaction with recombination, gene duplication, etc.), very few models take them into account. As a consequence, we lack a general theory to account for their direct and indirect contributions to evolution.

Obesity and hyperinsulinemia drive adipocytes to activate a cell cycle program and senesce.

Obesity is considered an important factor for many chronic diseases, including diabetes, cardiovascular disease and cancer. The expansion of adipose tissue in obesity is due to an increase in both adipocyte progenitor differentiation and mature adipocyte cell size. Adipocytes, however, are thought to be unable to divide or enter the cell cycle.

Rapeseed Lecithin Increases Lymphatic Lipid Output and α-Linolenic Acid Bioavailability in Rats.

Background: Soybean lecithin, a plant-based emulsifier widely used in food, is capable of modulating postprandial lipid metabolism. With arising concerns of sustainability, alternative sources of vegetal lecithin are urgently needed, and their metabolic effects must be characterized.

Objectives: We evaluated the impact of increasing doses of rapeseed lecithin (RL), rich in essential α-linolenic acid (ALA), on postprandial lipid metabolism and ALA bioavailability in lymph-cannulated rats.

Phenotypic noise and the cost of complexity.

Experimental studies demonstrate the existence of phenotypic diversity despite constant genotype and environment. Theoretical models based on a single phenotypic character predict that during an adaptation event, phenotypic noise should be positively selected far from the fitness optimum because it increases the fitness of the genotype, and then be selected against when the population reaches the optimum. It is suggested that because of this fitness gain, phenotypic noise should promote adaptive evolution.

Postprandial Endotoxin Transporters LBP and sCD14 Differ in Obese vs. Overweight and Normal Weight Men during Fat-Rich Meal Digestion.

Circulating levels of lipopolysaccharide-binding protein (LBP) and soluble cluster of differentiation 14 (sCD14) are recognized as clinical markers of endotoxemia. In obese men, postprandial endotoxemia is modulated by the amount of fat ingested, being higher compared to normal-weight (NW) subjects. Relative variations of LBP/sCD14 ratio in response to overfeeding are also considered important in the inflammation set-up, as measured through IL-6 concentration.

Human milk pasteurisation reduces pre-lipolysis but not digestive lipolysis and moderately decreases intestinal lipid uptake in a combination of preterm infant in vitro models.

Donor human milk, pasteurised for safety reasons, is the first alternative for feeding preterm infants when mothers' own milk is unavailable. Breastmilk pasteurisation impact on lipid digestion and absorption was evaluated by a static in vitro digestion model for preterm infants coupled with intestinal absorption using Caco-2/TC7 cells. Lipid absorption was quantified by digital image analysis of lipid droplets, by measurement of basolateral triglyceride concentration and by analysing the expression of major genes involved.

The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities.

Evolution provides a creative fount of complex and subtle adaptations that often surprise the scientists who discover them. However, the creativity of evolution is not limited to the natural world: Artificial organisms evolving in computational environments have also elicited surprise and wonder from the researchers studying them. The process of evolution is an process that transcends the substrate in which it occurs.

Homogeneous triacylglycerol tracers have an impact on the thermal and structural properties of dietary fat and its lipolysis rate under simulated physiological conditions.

Dietary fats are present in the diet under different types of structures, such as spread vs emulsions (notably in processed foods and enteral formula), and interest is growing regarding their digestion and intestinal absorption. In clinical trials, there is often a need to add stable isotope-labeled triacylglycerols (TAGs) as tracers to the ingested fat in order to track its intestinal absorption and further metabolic fate. Because most TAG tracers contain saturated fatty acids, they may modify the physicochemical properties of the ingested labeled fat and thereby its digestion.

In vitro oxidized HDL and HDL from type 2 diabetes patients have reduced ability to efflux oxysterols from THP-1 macrophages.

Oxidized LDL (OxLDL) that are enriched in products of lipid peroxidation including oxysterols have been shown to induce cellular oxidative stress and cytotoxicity therefore accelerating atheroma plaque formation. Upon oxLDL exposure of THP-1 macrophages, intracellular oxidation of LDL derived-cholesterol as well as endogenous cholesterol was increased. The oxysterols intracellularly produced were efficiently exported to HDL whereas apolipoprotein A1 was inefficient.

Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification.

Metabolic cross-feeding interactions between microbial strains are common in nature, and emerge during evolution experiments in the laboratory, even in homogeneous environments providing a single carbon source. In sympatry, when the environment is well-mixed, the reasons why emerging cross-feeding interactions may sometimes become stable and lead to monophyletic genotypic clusters occupying specific niches, named ecotypes, remain unclear. As an alternative to evolution experiments in the laboratory, we developed Evo2Sim, a multi-scale model of in silico experimental evolution, equipped with the whole tool case of experimental setups, competition assays, phylogenetic analysis, and, most importantly, allowing for evolvable ecological interactions.

Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation.

Models of evolution by genome rearrangements are prone to two types of flaws: One is to ignore the diversity of susceptibility to breakage across genomic regions, and the other is to suppose that susceptibility values are given. Without necessarily supposing their precise localization, we call "solid" the regions that are improbably broken by rearrangements and "fragile" the regions outside solid ones. We propose a model of evolution by inversions where breakage probabilities vary across fragile regions and over time.

Reductive genome evolution at both ends of the bacterial population size spectrum.

Bacterial genomes show substantial variations in size. The smallest bacterial genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive genome reduction and show patterns that are consistent with the degenerative processes that are predicted to occur in species with small effective population sizes. However, similar genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large populations.

A model for genome size evolution.

We present a model for genome size evolution that takes into account both local mutations such as small insertions and small deletions, and large chromosomal rearrangements such as duplications and large deletions. We introduce the possibility of undergoing several mutations within one generation. The model, albeit minimalist, reveals a non-trivial spontaneous dynamics of genome size: in the absence of selection, an arbitrary large part of genomes remains beneath a finite size, even for a duplication rate 2.

In silico experimental evolution: a tool to test evolutionary scenarios.

Comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives. For instance, some species have undergone a strong reduction of their genome with a drastic reduction of their genic repertoire. Deciphering the causes of these atypical trajectories can be very difficult because of the many phenomena that are intertwined during their evolution (e.

New insights into bacterial adaptation through in vivo and in silico experimental evolution.

Microbiology research has recently undergone major developments that have led to great progress towards obtaining an integrated view of microbial cell function. Microbial genetics, high-throughput technologies and systems biology have all provided an improved understanding of the structure and function of bacterial genomes and cellular networks. However, integrated evolutionary perspectives are needed to relate the dynamics of adaptive changes to the phenotypic and genotypic landscapes of living organisms.

The topology of the protein network influences the dynamics of gene order: from systems biology to a systemic understanding of evolution.

Abstract Systems biology invites us to consider the dynamic interactions between the components of a living cell. Here, by evolving artificial organisms whose genomes encode protein networks, we show that a coupling emerges at the evolutionary time scale between the protein network and the structure of the genome. Gene order is more stable when the protein network is more densely connected, which most likely results from a long-term selection for mutational robustness.

A long-term evolutionary pressure on the amount of noncoding DNA.

A significant part of eukaryotic noncoding DNA is viewed as the passive result of mutational processes, such as the proliferation of mobile elements. However, sequences lacking an immediate utility can nonetheless play a major role in the long-term evolvability of a lineage, for instance by promoting genomic rearrangements. They could thus be subject to an indirect selection.

Evolutionary coupling between the deleteriousness of gene mutations and the amount of non-coding sequences.

The phenotypic effects of random mutations depend on both the architecture of the genome and the gene-trait relationships. Both levels thus play a key role in the mutational variability of the phenotype, and hence in the long-term evolutionary success of the lineage. Here, by simulating the evolution of organisms with flexible genomes, we show that the need for an appropriate phenotypic variability induces a relationship between the deleteriousness of gene mutations and the quantity of non-coding sequences maintained in the genome.