Statistical and Biological Gene-Lifestyle Interactions of MC4R and FTO with Diet and Physical Activity on Obesity: New Effects on Alcohol Consumption

Background

Fat mass and obesity (FTO) and melanocortin-4 receptor (MC4R) and are relevant genes associated with obesity. This could be through food intake, but results are contradictory. Modulation by diet or other lifestyle factors is also not well understood.

Objective

To investigate whether MC4R and FTO associations with body-weight are modulated by diet and physical activity (PA), and to study their association with alcohol and food intake.

Methods

Adherence to Mediterranean diet (AdMedDiet) and physical activity (PA) were assessed by validated questionnaires in 7,052 high cardiovascular risk subjects. MC4R rs17782313 and FTO rs9939609 were determined. Independent and joint associations (aggregate genetic score) as well as statistical and biological gene-lifestyle interactions were analyzed.

Results

FTO rs9939609 was associated with higher body mass index (BMI), waist circumference (WC) and obesity (P<0.05 for all). A similar, but not significant trend was found for MC4R rs17782313. Their additive effects (aggregate score) were significant and we observed a 7% per-allele increase of being obese (OR = 1.07; 95%CI 1.01–1.13). We found relevant statistical interactions (P<0.05) with PA. So, in active individuals, the associations with higher BMI, WC or obesity were not detected. A biological (non-statistical) interaction between AdMedDiet and rs9939609 and the aggregate score was found. Greater AdMedDiet in individuals carrying 4 or 3-risk alleles counterbalanced their genetic predisposition, exhibiting similar BMI (P = 0.502) than individuals with no risk alleles and lower AdMedDiet. They also had lower BMI (P = 0.021) than their counterparts with low AdMedDiet. We did not find any consistent association with energy or macronutrients, but found a novel association between these polymorphisms and lower alcohol consumption in variant-allele carriers (B+/−SE: −0.57+/−0.16 g/d per-score-allele; P = 0.001).

Conclusion

Statistical and biological interactions with PA and diet modulate the effects of FTO and MC4R polymorphisms on obesity. The novel association with alcohol consumption seems independent of their effects on BMI.     

Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories

Taxonomy in the second decade of the 21st century is benefiting from technological advances in molecular microbiology, especially those related to genomics. Gene and genome databases are significantly increasing due to intense research activities in the field of molecular ecology and genomics. Taxa, and especially species, are tailored by means of the recognition of a phylogenetic, genomic and phenotypic coherence that reveal their uniqueness in the classification schema. Phylogenetic coherence is mainly revealed by means of 16S rRNA gene analyses for which curated databases such as EzTaxon and LTP provide a valuable tool for tree reconstruction to taxonomy users. On the other hand, in silico full or partial genomic sequence comparisons are called on to substitute cumbersome techniques such as DNA-DNA hybridization (DDH) to genomically circumscribe species. DDH similarity values around 70% would be equivalent to ANI values of 96%. Finally, finding an exclusive phenotypic property for the taxa to be classified is of paramount relevance to producing an operative and predictive classification system. The current methods used for taxonomic classification require significant laboratory experimentation, and generally will not produce interactive databases. The new high-throughput metabolomic technologies, such as ICR-FT and MALDI-TOF mass spectrometry methods, open the door to the construction of metabolic databases for taxonomic purposes. It is to be foreseen that, in the future, taxonomists will benefit significantly from public databases speeding up the classification process. However, serious effort will be needed to harmonize them and to prevent inaccurate material.     

Processes at multiple scales affect richness and similarity of non‐native plant species in mountains around the world

Aim To investigate how species richness and similarity of non‐native plants varies along gradients of elevation and human disturbance. Location Eight mountain regions on four continents and two oceanic islands. Methods We compared the distribution of non‐native plant species along roads in eight mountainous regions. Within each region, abundance of plant species was recorded at 41–84 sites along elevational gradients using 100‐m² plots located 0, 25 and 75 m from roadsides. We used mixed‐effects models to examine how local variation in species richness and similarity were affected by processes at three scales: among regions (global), along elevational gradients (regional) and with distance from the road (local). We used model selection and information criteria to choose best‐fit models of species richness along elevational gradients. We performed a hierarchical clustering of similarity to investigate human‐related factors and environmental filtering as potential drivers at the global scale. Results Species richness and similarity of non‐native plant species along elevational gradients were strongly influenced by factors operating at scales ranging from 100 m to 1000s of km. Non‐native species richness was highest in the New World regions, reflecting the effects of colonization from Europe. Similarity among regions was low and due mainly to certain Eurasian species, mostly native to temperate Europe, occurring in all New World regions. Elevation and distance from the road explained little of the variation in similarity. The elevational distribution of non‐native species richness varied, but was always greatest in the lower third of the range. In all regions, non‐native species richness declined away from roadsides. In three regions, this decline was steeper at higher elevations, and there was an interaction between distance and elevation. Main conclusions Because non‐native plant species are affected by processes operating at global, regional and local scales, a multi‐scale perspective is needed to understand their patterns of distribution. The processes involved include global dispersal, filtering along elevational gradients and differential establishment with distance from roadsides.     

NF-κB activation and polyubiquitin conjugation are required for pulmonary inflammation-induced diaphragm atrophy

Loss of diaphragm muscle strength in inflammatory lung disease contributes to mortality and is associated with diaphragm fiber atrophy. Ubiquitin (Ub) 26S-proteasome system (UPS)-dependent protein breakdown, which mediates muscle atrophy in a number of physiological and pathological conditions, is elevated in diaphragm muscle of patients with chronic obstructive pulmonary disease. Nuclear factor kappa B (NF-κB), an essential regulator of many inflammatory processes, has been implicated in the regulation of poly-Ub conjugation of muscle proteins targeted for proteolysis by the UPS. Here, we test if NF-κB activation in diaphragm muscle and subsequent protein degradation by the UPS are required for pulmonary inflammation-induced diaphragm atrophy. Acute pulmonary inflammation was induced in mice by intratracheal lipopolysaccharide instillation. Fiber cross-sectional area, ex vivo tyrosine release, protein poly-Ub conjugation, and inflammatory signaling were determined in diaphragm muscle. The contribution of NF-κB or the UPS to diaphragm atrophy was assessed in mice with intact or genetically repressed NF-κB signaling or attenuated poly-Ub conjugation, respectively. Acute pulmonary inflammation resulted in diaphragm atrophy measured by reduced muscle fiber cross-sectional area. This was accompanied by diaphragm NF-κB activation, and proteolysis, measured by tyrosine release from the diaphragm. Poly-Ub conjugation was increased in diaphragm, as was the expression of muscle-specific E3 Ub ligases. Genetic suppression of poly-Ub conjugation prevented inflammation-induced diaphragm muscle atrophy, as did muscle-specific inhibition of NF-κB signaling. In conclusion, the present study is the first to demonstrate that diaphragm muscle atrophy, resulting from acute pulmonary inflammation, requires NF-κB activation and UPS-mediated protein degradation.     

Conformational selection and collagenolysis in Type III collagen

Matrix metalloproteases (MMPs) cleave native collagen at a single site despite the fact that collagen contains more than one scissile bond that can, in principle, be cleaved. For peptide bond hydrolysis to occur at one specific site, MMPs must (1) localize to a region near the unique scissile bond, (2) bind residues at the catalytic site that form the scissile bond, and (3) hydrolyze the corresponding peptide bond. Prior studies suggest that for some types of collagen, binding of noncatalytic MMP domains to amino acid sequences in the vicinity of the true cleavage site facilitates the localization of collagenases. In the present study, our goal was to determine whether binding to the catalytic site also plays a role in determining MMP specificity. To investigate this, we computed the conformational free energy landscape of Type III collagen at each potential cleavage site. The free energy profiles suggest that although all potential cleavage sites sample unfolded states at relatively low temperatures, the true cleavage site samples structures that are complementary to the catalytic site. By contrast, potential cleavage sites that are not cleaved sample states that are relatively incompatible with the MMP active site. Furthermore, our findings point to a specific role for arginine residues in modulating the structural stability of collagen near the collagenase cleavage site. These data imply that locally unfolded potential cleavage sites in Type III collagen sample distinct unfolded ensembles, and that the region about the true collagenase cleavage site samples states that are most complementary to the MMP active site. Proteins 2010. © 2009 Wiley‐Liss, Inc.