Early tetrapod evolution

Tetrapods include the only fully terrestrial vertebrates, but they also include many amphibious, aquatic and flying groups. They occupy the highest levels of the food chain on land and in aquatic environments. Tetrapod evolution has generated great interest, but the earliest phases of their history are poorly understood. Recent studies have questioned long-accepted hypotheses about the origin of the pentadactyl limb, the phylogeny of tetrapods and the environment in which the first tetrapods lived.     

Bone microanatomy and lifestyle: A descriptive approach

Starting in 2004, our lab has published several studies on the relationship between bone microanatomy, lifestyle (aquatic to terrestrial), and the phylogeny of tetrapods. These studies emphasized quantitative and statistical analyses. Therefore, the raw data used in these studies were never published. This is unfortunate because no model captures all information in biological data. This paper remedies this situation by providing the detailed anatomical drawings used in our previous studies. These constitute the largest set of standardized cross-section images of appendicular long bones (tibiae, radii, and humeri) ever published, at least as far as the number of represented species (over one hundred) is concerned. All major aquatic to terrestrial extant tetrapod clades are represented (lissamphibians, mammals, turtles, squamates, and crocodilians). The comparative figures show that aquatic tetrapods differ most from the others, whereas amphibious taxa differ much less from their terrestrial relatives.     

A network-based approach to classify the three domains of life

Background

Chromosomal orthologs can reveal the shared ancestral gene set and their evolutionary trends. Additionally, physico-chemical properties of encoded proteins could provide information about functional adaptation and ecological niche requirements.

Results

We analyzed 7080 genes (five groups of 1416 orthologs each) from Rhizobiales species (S. meliloti, R. etli, and M. loti, plant symbionts; A. tumefaciens, a plant pathogen; and B. melitensis, an animal pathogen). We evaluated their phylogenetic relationships and observed three main topologies. The first, with closer association of R. etli to A. tumefaciens; the second with R. etli closer to S. meliloti; and the third with A. tumefaciens and S. meliloti as the closest pair. This was not unusual, given the close relatedness of these three species. We calculated the synonymous (dS) and nonsynonymous (dN) substitution rates of these orthologs, and found that informational and metabolic functions showed relatively low dN rates; in contrast, genes from hypothetical functions and cellular processes showed high dN rates. An alternative measure of sequence variability, percentage of changes by species, was used to evaluate the most specific proportion of amino acid residues from alignments. When dN was compared with that measure a high correlation was obtained, revealing that much of evolutive information was extracted with the percentage of changes by species at the amino acid level. By analyzing the sequence variability of orthologs with a set of five properties (polarity, electrostatic charge, formation of secondary structures, molecular volume, and amino acid composition), we found that physico-chemical characteristics of proteins correlated with specific functional roles, and association of species did not follow their typical phylogeny, probably reflecting more adaptation to their life styles and niche preferences. In addition, orthologs with low dN rates had residues with more positive values of polarity, volume and electrostatic charge.

Conclusions

These findings revealed that even when orthologs perform the same function in each genomic background, their sequences reveal important evolutionary tendencies and differences related to adaptation. This article was reviewed by: Dr. Purificación López-García, Prof. Jeffrey Townsend (nominated by Dr. J. Peter Gogarten), and Ms. Olga Kamneva.     

An updated paleontological timetree of lissamphibians,with comments on the anatomy of Jurassic crown-group salamanders (Urodela)

We present an update of our time-calibrated supertree of extant and extinct lissamphibians (Marjanovi? D, Laurin M. 2007. Fossils, molecules, divergence times, and the origin of lissamphibians. Syst Biol 56(3):369–388) and of the divergence dates that can be inferred from it. The present version contains 319 extinct species or possible species of lissamphibians, compared to 223 previously. Discoveries of new fossiliferous sites, advances in phylogeny and recently obtained radiometric dates have offered opportunities to test our results, including the conclusion that the fossil record of Lissamphibia is dense enough to provide reliable calibration constraints for molecular divergence dating. By and large, the results are upheld. Some of the divergence dates we infer from the tree are up to 15 Ma younger than we previously published, some are up to 15 Ma older, some have had their range of uncertainty drastically reduced and the maximum age for the origin of Urodela (the salamander crown group) is no longer well constrained. The dermal bone plates in the gill region of the Jurassic urodeles Beiyanerpeton, Seminobatrachus and Chunerpeton and the grooves for the lateral line organ on the skull of the first require either unexpected reversals or several independent losses in other lissamphibians and indeed other urodeles.     

Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding

Riboswitches are important gene regulatory elements frequently encountered in bacterial mRNAs. The recently discovered nadA riboswitch contains two similar, tandemly arrayed aptamer domains, with the first domain possessing high affinity for nicotinamide adenine dinucleotide (NAD⁺). The second domain which comprises the ribosomal binding site in a putative regulatory helix, however, has withdrawn from detection of ligand-induced structural modulation thus far, and therefore, the identity of the cognate ligand and the regulation mechanism have remained unclear. Here, we report crystal structures of both riboswitch domains, each bound to NAD⁺. Furthermore, we demonstrate that ligand binding to domain 2 requires significantly higher concentrations of NAD⁺ (or ADP retaining analogs) compared to domain 1. Using a fluorescence spectroscopic approach, we further shed light on the structural features which are responsible for the different ligand affinities, and describe the Mg²⁺-dependent, distinct folding and pre-organization of their binding pockets. Finally, we speculate about possible scenarios for nadA RNA gene regulation as a putative two-concentration sensor module for a time-controlled signal that is primed and stalled by the gene regulation machinery at low ligand concentrations (domain 1), and finally triggers repression of translation as soon as high ligand concentrations are reached in the cell (domain 2).     

Metformin inhibits mitochondrial adaptations to aerobic exercise training in older adults

Metformin and exercise independently improve insulin sensitivity and decrease the risk of diabetes. Metformin was also recently proposed as a potential therapy to slow aging. However, recent evidence indicates that adding metformin to exercise antagonizes the exercise‐induced improvement in insulin sensitivity and cardiorespiratory fitness. The purpose of this study was to test the hypothesis that metformin diminishes the improvement in insulin sensitivity and cardiorespiratory fitness after aerobic exercise training (AET) by inhibiting skeletal muscle mitochondrial respiration and protein synthesis in older adults (62 ± 1 years). In a double‐blinded fashion, participants were randomized to placebo (n = 26) or metformin (n = 27) treatment during 12 weeks of AET. Independent of treatment, AET decreased fat mass, HbA1c, fasting plasma insulin, 24‐hr ambulant mean glucose, and glycemic variability. However, metformin attenuated the increase in whole‐body insulin sensitivity and VO₂max after AET. In the metformin group, there was no overall change in whole‐body insulin sensitivity after AET due to positive and negative responders. Metformin also abrogated the exercise‐mediated increase in skeletal muscle mitochondrial respiration. The change in whole‐body insulin sensitivity was correlated to the change in mitochondrial respiration. Mitochondrial protein synthesis rates assessed during AET were not different between treatments. The influence of metformin on AET‐induced improvements in physiological function was highly variable and associated with the effect of metformin on the mitochondria. These data suggest that prior to prescribing metformin to slow aging, additional studies are needed to understand the mechanisms that elicit positive and negative responses to metformin with and without exercise.     

A life cycle assessment of packaging options for contrast media delivery: comparing polymer bottle vs. glass bottle

Purpose

This paper compares environmental impacts of two packaging options for contrast media offered by GE Healthcare: +PLUSPAK? polymer bottle and traditional glass bottle. The study includes all relevant life cycle stages from manufacturing to use and final disposal of the bottles and includes evaluation of a variety of end-of-life disposal scenarios. The study was performed in accordance with the international standards ISO 14040/14044, and a third-party critical review was conducted.

Methods

The functional unit is defined as the packaging of contrast media required to deliver one dose of 96 mL to a patient for an X-ray procedure. Primary data are from GE Healthcare and its suppliers; secondary data are from the ecoinvent database and the literature. A variety of end-of-life disposal scenarios are explored using both cutoff and market-based allocation. Impact assessment includes human health (midpoint) and ecosystems and resources (end point) categories from ReCiPe (H) and cumulative energy demand. Sensitivity analyses include (1) bottle size, (2) secondary packaging, (3) manufacturing electricity, (4) glass recycled content, (5) scrap rate, (6) distribution transport, (7) contrast media, and (8) choice of impact assessment method. Uncertainty analysis is performed to determine how data quality affects the study conclusions.

Results and discussion

This study indicates that the polymer bottle outperforms the glass bottle in every environmental impact category considered. Bottle components are the most significant contributors, and the vial body has the highest impacts among bottle components for both polymer and glass bottles. The polymer bottle exhibits lower impact in all impact categories considered regardless of the following: end-of-life treatment (using either cutoff or market-based allocation), bottle size, manufacturing electricity grid mix, glass recycled content, scrap rate, contrast media, distribution transport (air vs. ocean), and choice of impact assessment method. Secondary packaging can be a major contributor to impact. The polymer bottle has considerably lower impact compared to the glass bottle for all multi-pack configurations, but the comparison is less clear for single-pack configurations due to significantly higher packaging material used per functional dose, resulting in proportionally higher impacts in all impact categories.

Conclusions

The lower impacts of the polymer bottle for this packaging application can be attributed to lower material and manufacturing impacts, lower distribution impacts, and lower end-of-life disposal impacts. The results of this study suggest that using polymer rather than glass bottles provides a means by which to lower environmental impact of contrast media packaging.