Does extrinsic mortality accelerate the pace of life? A bare-bones approach

It is commonly asserted that when extrinsic mortality is high, individuals should invest early in reproduction. This intuition thrives in the literature on life-history theory and human behavior, yet it has been criticized repeatedly on the basis of mathematical models. The intuition is indeed wrong; but a recent theoretical criticism has confused the reason why it is wrong, thereby obscuring earlier and sounder criticisms. In the present article, based on the simplest possible model, we sought to clarify these issues. We confirm earlier findings that extrinsic mortality can affect the evolution of pace of life, not because it leaves little time to reproduce, but through its effects on density-dependent competition. This result highlights the importance of accounting for density-dependence in theoretical models and data analyses. Further, we find little support for the recent claim that the direction of selection on a reaction norm in a variable environment cannot be easily inferred from models made in homogeneous environments. In conclusion, although life-history theory is still imperfect, it has provided simple results that deserve to be understood.     

Does natural selection organize ecosystems for the maintenance of high productivity and diversity?

Three types of evidence suggest that natural ecosystems are organized for high productivity and diversity: (i) changes not previously experienced by a natural ecosystem, such as novel human disturbances, tend to diminish its productivity and/or diversity, just as 'random' changes in a machine designed for a function usually impair its execution of that function; (ii) humans strive to recreate properties of natural ecosystems to enhance productivity of artificial ones, as farmers try to recreate properties of natural soils in their fields; and (iii) productivity and diversity have increased during the Earth's history as a whole, and after every major biotic crisis. Natural selection results in ecosystems organized to maintain high productivity of organic matter and diversity of species, just as competition among individuals in Adam Smith's ideal economy favours high production of wealth and diversity of occupations. In nature, poorly exploited energy attracts more efficient users. This circumstance favours the opening of new ways of life and more efficient recycling of resources, and eliminates most productivity-reducing 'ecological monopolies'. Ecological dominants tend to be replaced by successors with higher metabolism, which respond to more stimuli and engage in more varied interactions. Finally, increasingly efficient predators and herbivores favour faster turnover of resources.     

Acid-shifted isoelectric point profiles of the proteins in a hypersaline microbial mat: an adaptation to life at high salt concentrations?

In a metagenomic analysis of a stratified hypersaline (9?% salt) microbial mat in Guerrero Negro, Mexico, Kunin et al. (Mol Systems Biol 4:198, 2008) detected a significantly acid-shifted proteome, and concluded that adaptation by enriching proteins with acidic amino acids is more widespread than previously assumed. We here reevaluate these data and conclusions by comparing the isoelectric point profiles of the Guerrero Negro microbial mats (average isoelectric point 6.8) with those of the proteins encoded by the genomes of prokaryotes adapted to different salt concentrations ranges and belonging to different phylogenetic and physiological groups. Average isoelectric points below 6.8 were found not only in the proteomes of the moderately halophilic aerobic bacteria Halomonas elongata and Chromohalobacter salexigens, but even in common types of marine bacteria of the genera Alteromonas and Aliivibrio. We did not find clear evidence that the isoelectric point profile of the Guerrero Negro microbial mat can be considered to be the result of species-independent molecular convergence of the members of the microbial community determined by the salinity of the overlaying brine.     

Living the high life: Could gut microbiota matter for adaptation to high altitude?

At high altitude, the reduced availability of thermal energy and oxygen poses major challenges to organisms. Different species or populations have evolved similar solutions to these challenges, such as blood flow regulation in animals (Bouverot, 1985). Previous studies investigating such convergent adaptations have primarily looked at changes in host genomes (e.g., see Scheinfeldt & Tishkoff, 2010), but have rarely considered the potential role of the gut microbiome in mediating host adaptation. As gut microbes can indirectly regulate host blood pressure (Pluznick, 2014) and energy intake efficiency, it has been hypothesized that they could help maintain normal energy production and/or optimize nutritional assimilation in high‐altitude hypoxic environments (e.g., Li & Zhao, 2015). However, it has been hard to (a) show that there is a direct effect of altitude on the gut microbiota, because of the many potential confounding effects of altitude (e.g., diet is correlated to altitude, as well as to the microbiome) and to (b) understand the mechanisms by which the microbiota could mediate host hypoxic and thermoregulatory stresses. In this issue of Molecular Ecology, Suzuki, Martins, and Nachman (2018) show that, independently of diet, taxonomic composition and functions of mouse gut microbiota converge in independent high‐altitude environments and propose the intriguing hypothesis that some of these functional convergences might be beneficial to their host.     

Does the growth temperature of a prokaryote influence the purine content of its mRNAs?

The formation and breaking of hydrogen bonds between nucleic acid bases are dependent on temperature. The high G+C content of organisms was surmised to be an adaptation for high temperature survival because of the thermal stability of G:C pairs. However, a survey of genomic GC% and optimum growth temperature (OGT) of several prokaryotes revoked any direct relation between them. Significantly high purine (R=A or G) content in mRNAs is also seen as a selective response for survival among thermophiles. Nevertheless, the biological relevance of thermophiles loading their unstable mRNAs with excess purines (purine-loading or R-loading) is not persuasive. Here, we analysed the mRNA sequences from the genomes of 168 prokaryotes (as obtained from NCBI Genome database) with their OGTs ranging from -5 °C to 100 °C to verify the relation between R-loading and OGT. Our analysis fails to demonstrate any correlation between R-loading of the mRNA pool and OGT of a prokaryote. The percentage of purine-loaded mRNAs in prokaryotes is found to be in a rough negative correlation with the genomic GC% (r(2)=0.655, slope=-1.478, P<000.1). We conclude that genomic GC% and bias against certain combinations of nucleotides drive the mRNA-synonymous (sense) strands of DNA towards variations in R-loading.     

Origin and Evolution of GALA-LRR,a New Member of the CC-LRR Subfamily: From Plants to Bacteria?

The phytopathogenic bacterium Ralstonia solanacearum encodes type III effectors, called GALA proteins, which contain F-box and LRR domains. The GALA LRRs do not perfectly fit any of the previously described LRR subfamilies. By applying protein sequence analysis and structural prediction, we clarify this ambiguous case of LRR classification and assign GALA-LRRs to CC-LRR subfamily. We demonstrate that side-by-side packing of LRRs in the 3D structures may control the limits of repeat variability within the LRR subfamilies during evolution. The LRR packing can be used as a criterion, complementing the repeat sequences, to classify newly identified LRR domains. Our phylogenetic analysis of F-box domains proposes the lateral gene transfer of bacterial GALA proteins from host plants. We also present an evolutionary scenario which can explain the transformation of the original plant LRRs into slightly different bacterial LRRs. The examination of the selective evolutionary pressure acting on GALA proteins suggests that the convex side of their horse-shoe shaped LRR domains is more prone to positive selection than the concave side, and we therefore hypothesize that the convex surface might be the site of protein binding relevant to the adaptor function of the F-box GALA proteins. This conclusion provides a strong background for further functional studies aimed at determining the role of these type III effectors in the virulence of R. solanacearum.     

The variability of the mitochondrial genome in human aging: a key for life and death?

The impressive performance of the research in mitochondrial genetics and human aging in the last decade outlines a new scenery in which the inherited variation of the mitochondrial genome (mtDNA) may play a role in rate and quality of aging. This variation in humans was initially looked at as nearly neutral, and useful just for the reconstruction of human population history. However, recent data suggest that different mtDNA molecules are qualitatively different from each other. The aim of this paper is to discuss current ideas on the relationships among mitochondrial function, mtDNA inherited variation, and aging. The main processes where the mitochondrion is involved and the importance these processes have on aging and death of individuals will be described. A possible connection between programmed death phenomena (mitoptosis, apoptosis, phenoptosis) and rate and quality of aging will be discussed. Finally, the possible role played in these processes by the mtDNA germline variation will be explored.     

Determination of the transgalactosylation activity of Aspergillus oryzae β-galactosidase: effect of pH, temperature, and galactose and glucose concentrations

The catalytic potential of β-galactosidase is usually determined by its hydrolytic activity over natural or synthetic substrates. However, this method poorly predicts enzyme behavior when transglycosylation instead of hydrolysis is being performed. A system for determining the transgalactosylation activity of β-galactosidase from Aspergillus oryzae was developed, and its activity was determined under conditions for the synthesis of galacto-oligosaccharides and lactulose. Transgalactosylation activity increased with temperature up to 55 °C while the effect of pH was mild in the range from pH 2.5 to 5.5, decreasing at higher values. The effect of glucose and galactose on transgalactosylation activity was also assessed both in the reactions for the synthesis of galacto-oligosaccharides and lactulose and also in the reaction of hydrolysis of o-nitrophenyl β-d-galactopiranoside. Galactose was a competitive inhibitor and its effect was stronger in the reactions of transgalactosylation than in the reaction of hydrolysis. Glucose was a mild activator of β-galactosidase in the reaction of hydrolysis, but its mechanism of action was more complex in the reactions of transgalactosylation, having this positive effect only at low concentrations while acting as an inhibitor at high concentrations. This information is relevant to properly assess the effect of monosaccharides during the reactions of the synthesis of lactose-derived oligosaccharides, such as galacto-oligosaccharides and lactulose.     

Biodiversity and Land uses at a regional scale: Is agriculture the biggest threat for reptile assemblages?

The human exploitation of land resources (land use) has been considered the major factor responsible for changes in biodiversity within terrestrial ecosystems given that it affects directly the distribution of the fauna. Reptiles are known to be particularly sensitive to habitat change due to their ecological constraints. Here, the impact of land use on reptile diversity was analysed, choosing Catalonia (NE Iberia) as a case study. This region provides a suitable scenario for such a biogeographical study since it harbours: 1) a rich reptile fauna; 2) a highly diverse environment showing strong variation in those variables usually shaping reptile distributions; and 3) good species distribution data. Potential species richness was calculated, using ecological modelling techniques (Ecological Niche Factor Analysis – ENFA). The subtraction of the observed from the potential species richness was the dependent variable in a backwards multiple linear regression, using land use variables. Agriculture was the land use with the strongest relation with the non-fulfilment of the potential species richness, indicating a trend towards a deficit of biodiversity. Deciduous forest was the only land use negatively related with the subtracted species richness. Results indicate a clear relationship between land use and biodiversity at a mesoscale. This finding represents an important baseline for conservation guidelines within the habitat change framework because it has been achieved at the same spatial scale of chorological studies and management policies.     

A barcode of life database for the Cephalopoda? Considerations and concerns

The concept of a Barcode of Life Database (BoLD) for the Class Cephalopoda (Phylum Mollusca) was introduced at the Cephalopod International Advisory Council (CIAC) symposium in Hobart, Australia, February 2006. This suggestion was met with significant interest, concern and debate. This review attempts to describe the concept of the BoLD initiative and to outline considerations and concerns specific to a cephalopod BoLD. Jan M. Strugnell and Annie R. Lindgren contributed equally to this work.     

Treatment of columnaris disease of rainbow trout: low pH and salt as possible tools?

The impact of salt and low pH on columnaris disease of fish was studied. Survival of Flavobacterium columnare after exposure to either 4% NaCl (pH 7.2) or pH 5.0, pH 4.86 or pH 4.6 for 15 min or 1 h was studied in vitro. All conditions significantly reduced the numbers of viable bacterial cells. The effects of salt (4 and 2%) and acidic baths (pH 4.6) were studied in 2 experiments in vivo with rainbow trout Oncorhynchus mykiss infected with F. columnare. Both salt and acidic baths failed to prevent fish mortality; the overall mortality reached 100% in all groups. However, according to survival analysis, the mortality rate was lower in fish treated with 4% salt baths compared to a control group. The buffering capacity of fish skin mucus against low water pH was also studied. Fish skin mucus was an efficient buffer against decreased water pH and the pH of the skin could be remarkably higher than that of the mucus. This may explain the failure of bath treatments to prevent mortality providing that attached F. columnare are located below the mucus surface. We suggest, however, that salt and acidic bath treatments can be used to disinfect water containing F. columnare cells shed by infected fish and thus prevent the transmission of the disease.     

Evolution of RNA genomes: Does the high mutation rate necessitate high rate of evolution of viral proteins?

Summary RNA genomes have been shown to mutate much more frequently than DNA genomes. It is generally assumed that this results in rapid evolution of RNA viral proteins. Here, an alternative hypothesis is proposed that close cooperation between positive-strand RNA viral proteins and those of the host cells required their coevolution, resulting in similar amino acid substitution rates. Constraints on compatibility with cellular proteins should determine, at any time, the covarion sets in RNA viral proteins. These ideas may be helpful in rationalizing the accumulating data on significant sequence similarities between proteins of positive-strand RNA viruses infecting evolutionarily distant hosts as well as between viral and cellular proteins.     

Do all leaf photosynthesis parameters of rice acclimate to elevated CO2, elevated temperature,and their combination,in FACE environments?

Leaf photosynthesis of crops acclimates to elevated CO₂ and temperature, but studies quantifying responses of leaf photosynthetic parameters to combined CO₂ and temperature increases under field conditions are scarce. We measured leaf photosynthesis of rice cultivars Changyou 5 and Nanjing 9108 grown in two free‐air CO₂ enrichment (FACE) systems, respectively, installed in paddy fields. Each FACE system had four combinations of two levels of CO₂ (ambient and enriched) and two levels of canopy temperature (no warming and warmed by 1.0–2.0°C). Parameters of the C₃ photosynthesis model of Farquhar, von Caemmerer and Berry (the FvCB model), and of a stomatal conductance (g_s) model were estimated for the four conditions. Most photosynthetic parameters acclimated to elevated CO₂, elevated temperature, and their combination. The combination of elevated CO₂ and temperature changed the functional relationships between biochemical parameters and leaf nitrogen content for Changyou 5. The g_s model significantly underestimated g_s under the combination of elevated CO₂ and temperature by 19% for Changyou 5 and by 10% for Nanjing 9108 if no acclimation was assumed. However, our further analysis applying the coupled g_s–FvCB model to an independent, previously published FACE experiment showed that including such an acclimation response of g_s hardly improved prediction of leaf photosynthesis under the four combinations of CO₂ and temperature. Therefore, the typical procedure that crop models using the FvCB and g_s models are parameterized from plants grown under current ambient conditions may not result in critical errors in projecting productivity of paddy rice under future global change.     

An optimal degree of physical and chemical heterogeneity for the origin of life?

The accumulation of pure, concentrated chemical building blocks, from which the essential components of protocells could be assembled, has long been viewed as a necessary, but extremely difficult step on the pathway to the origin of life. However, recent experiments have shown that moderately increasing the complexity of a set of chemical inputs can in some cases lead to a dramatic simplification of the resulting reaction products. Similarly, model protocell membranes composed of certain mixtures of amphiphilic molecules have superior physical properties than membranes composed of single amphiphiles. Moreover, membrane self-assembly under simple and natural conditions gives rise to heterogeneous mixtures of large multi-lamellar vesicles, which are predisposed to a robust pathway of growth and division that simpler and more homogeneous small unilamellar vesicles cannot undergo. Might a similar relaxation of the constraints on building block purity and homogeneity actually facilitate the difficult process of nucleic acid replication? Several arguments suggest that mixtures of monomers and short oligonucleotides may enable the chemical copying of polynucleotides of sufficient length and sequence complexity to allow for the emergence of the first nucleic acid catalysts. The question of the origin of life may become less daunting once the constraints of overly well-defined laboratory experiments are appropriately relaxed.     

Losing the lust for life: a new role for an old feeding Peptide?

A recent paper in Nature (Lim et?al., 2012) describes the effects of melanocortin receptors in the nucleus accumbens. The studies connect a hypothalamic peptide system with brain reward centers and show effects on specific neuronal populations and behavioral components of mood.