Why the discovery of adherent-invasive Escherichia coli molecular markers is so challenging?

Adherent-invasive Escherichia coli (AIEC) strains have been extensively related to Crohn’s disease (CD) etiopathogenesis. Higher AIEC prevalence in CD patients versus controls has been reported, and its mechanisms of pathogenicity have been linked to CD physiopathology. In CD, the therapeutic armamentarium remains limited and non-curative; hence, the necessity to better understand AIEC as a putative instigator or propagator of the disease is certain. Nonetheless, AIEC identification is currently challenging because it relies on phenotypic assays based on infected cell cultures which are highly time-consuming, laborious and non-standardizable. To address this issue, AIEC molecular mechanisms and virulence genes have been studied; however, a specific and widely distributed genetic AIEC marker is still missing. The finding of molecular tools to easily identify AIEC could be useful in the identification of AIEC carriers who could profit from personalized treatment. Also, it would significantly promote AIEC epidemiological studies. Here, we reviewed the existing data regarding AIEC genetics and presented those molecular markers that could assist with AIEC identification. Finally, we highlighted the problems behind the discovery of exclusive AIEC biomarkers and proposed strategies to facilitate the search of AIEC signature sequences.     

Why is the denaturation process of super-helical DNA so uncooperative?

A theoretical model is proposed for the helix-coil transition in circular covalently closed DNA. In the melting interval the topological constrains for such a molecule are considered to affect both the inner state of the melted regions and the spatial configuration of the whole molecule ("writhing"). A good agreement is achieved between the theoretically calculated and experimentally obtained parameters of the denaturation process. A conclusion is drawn, that at the early stages of thermodenaturation (approximately till the transition midpoint) the effect of topological constrains is realised mainly through the writhing of the molecule. The denatured regions exist in the form of relaxed loops.     

Why is the house mouse karyotype so variable?

rates of robertsonian chromosomal evolution in the Western European house mouse are about two orders of magnitude greater than for most other mammals. This has resulted in a remarkable diversity of karyotypic races in a very short period of time. Recent studies are beginning to shed light on the relative contributions of mutation, drift, selection and meiotic drive in producing this pattern.     

Why is the cystic fibrosis gene so frequent?

Summary The high incidence of cystic fibrosis (CF) in most European populations (and populations of European descent) can be explained by different hypotheses that can be tested using the available data concerning this disorder. Among the five hypotheses discussed (genetic heterogeneity, high rate of mutation, meiotic drive, drift and heterozygote advantage), only the last is supported by experimental data. The following conclusions can be drawn from the evidence that we have reviewed: (1) CF is a single gene disorder (genetically homogeneous). (2) Haplotypes associated with the CF gene suggest that only a few mutations (the same gene located in 7q13 is always affected) are responsible for the disorder. (3) CF with pancreatic insufficiency is mainly associated with a single haplotype, whereas CF with pancreatic sufficiency is more frequently associated with different haplotypes. (4) A selective advantage consisting of higher resistance to Cl^–-secreting diarrhoeas might have favored, in the past, survival of infants heterozygous for the CF gene.     

Why is Deinococcus radiodurans so resistant to ionizing radiation?

When exponential-phase cultures of Deinococcus radiodurans are exposed to a 5000-Gray dose of gamma radiation, individual cells suffer massive DNA damage. Despite this insult to their genetic integrity, these cells survive without loss of viability or evidence of mutation, repairing the damage by as-yet-poorly-understood mechanisms.     

Why are hairy root clusters so abundant in the most nutrient-impoverished soils of Australia?

Rootlets, covered in long root hairs, are aggregated into distinct clusters in many groups of Australian plants. They are almost universal in the family Proteaceae, and some members of the Papilionaceae, Mimosaceae, Casuarinaceae, Cyperaceae, Restionaceae and Dasypogonaceae. These families have their centres of distribution in the oldest, most leached sands and laterites of the continent. Root clusters are almost confined to the uppermost 100 mm of the soil profile, often penetrating into the raw litter. These horizons are the major sources of mineral nutrients which are mobilized when these soils become moist. I argue that root clusters are an ideal solution for maximizing nutrient uptake in extremely impoverished soils, especially in seasonal climates.     

Where is the root of the universal tree of life?

The currently accepted universal tree of life based on molecular phylogenies is characterised by a prokaryotic root and the sisterhood of archaea and eukaryotes. The recent discovery that each domain (bacteria, archaea, and eucarya) represents a mosaic of the two others in terms of its gene content has suggested various alternatives in which eukaryotes were derived from the merging of bacteria and archaea. In all these scenarios, life evolved from simple prokaryotes to complex eukaryotes. We argue here that these models are biased by overconfidence in molecular phylogenies and prejudices regarding the primitive nature of prokaryotes. We propose instead a universal tree of life with the root in the eukaryotic branch and suggest that many prokaryotic features of the information processing mechanisms originated by simplification through gene loss and non-orthologous displacement.     

Why are the genomes of endosymbiotic bacteria so stable?

The comparative analysis of three strains of the endosymbiotic bacterium Buchnera aphidicola has revealed high genome stability associated with an almost complete absence of chromosomal rearrangements and horizontal gene transfer events during the past 150 million years. The loss of genes involved in DNA uptake and recombination in the initial stages of endosymbiosis probably underlies this stability. Gene loss, which was extensive during the initial steps of Buchnera evolution, has continued in the different Buchnera lineages since their divergence.     

Correction to: Why is chlorophyll b only used in light-harvesting systems?

Journal of Plant Research - The article Why is chlorophyll b only used in light-harvesting systems.     

What is the shape of the distribution of protein conformations at equilibrium?

According to the thermodynamic hypothesis, the native state of proteins is that in which the free energy of the system is at its lowest, so that at normal temperature and pressure, proteins evolve to that state. We selected four proteins representative of each of the four classes, and for each protein make four simulations, one starting from the native structure and the other three starting from the structure obtained by threading the sequence of one protein onto the native backbone fold of the other three proteins. Because of their large conformational distances with respect to the native structure, the three alternative initial structures cannot be considered as local minima within the native ensemble of the corresponding protein. As expected, the initial native states are preserved in the .5?μs simulations performed here and validate the simulations. On the other hand, when the initial state is not native, an analysis of the trajectories does not reveal any evolution towards the native state, during that time. These results indicate that the distribution of protein conformations is multipeak shaped, so that apart from the peak corresponding to the native state, there are other peaks associated with average structures that are very different from the native and that can last as long as the native state.