Effects of plant evolution on nutrient cycling couple aboveground and belowground processes

Plant strategies for nutrient acquisition and recycling are key components of ecosystem functioning. How the evolution of such strategies modifies ecosystem functioning and services is still not well understood. In the present work, we aim at understanding how the evolution of different phenotypic traits link aboveground and belowground processes, thereby affecting the functioning of the ecosystem at different scales and in different realms. Using a simple model, we follow the dynamics of a limiting nutrient inside an ecosystem. Considering trade-offs between aboveground and belowground functional traits, we study the effects of the evolution of such strategies on ecosystem properties (amount of mineral nutrient, total plant biomass, dead organic matter, and primary productivity) and whether such properties are maximized. Our results show that when evolution leads to a stable outcome, it minimizes the quantity of nutrient available (following Tilman’s R* rule). We also show that considering the evolution of aboveground and belowground functional traits simultaneously, total plant biomass and primary productivity are not necessarily maximized through evolution. The coupling of aboveground and belowground processes through evolution may largely diminish predicted standing biomass and productivity (extinction may even occur) and impact the evolutionary resilience (i.e., the return time to previous phenotypic states) of the ecosystem in the face of external disturbances. We show that changes in plant biomass and their effects on evolutionary change can be understood by accounting for the links between nutrient uptake and mineralization, and for indirect effects of nutrient uptake on the amount of detritus in the system.     

Activity‐specific metabolic rates for diving,transiting, and resting at sea can be estimated from time–activity budgets in free‐ranging marine mammals

Time and energy are the two most important currencies in animal bioenergetics. How much time animals spend engaged in different activities with specific energetic costs ultimately defines their likelihood of surviving and successfully reproducing. However, it is extremely difficult to determine the energetic costs of independent activities for free‐ranging animals. In this study, we developed a new method to calculate activity‐specific metabolic rates, and applied it to female fur seals. We attached biologgers (that recorded GPS locations, depth profiles, and triaxial acceleration) to 12 northern (Callorhinus ursinus) and 13 Antarctic fur seals (Arctocephalus gazella), and used a hierarchical decision tree algorithm to determine time allocation between diving, transiting, resting, and performing slow movements at the surface (grooming, etc.). We concomitantly measured the total energy expenditure using the doubly‐labelled water method. We used a general least‐square model to establish the relationship between time–activity budgets and the total energy spent by each individual during their foraging trip to predict activity‐specific metabolic rates. Results show that both species allocated similar time to diving (~29%), transiting to and from their foraging grounds (~26–30%), and resting (~8–11%). However, Antarctic fur seals spent significantly more time grooming and moving slowly at the surface than northern fur seals (36% vs. 29%). Diving was the most expensive activity (~30 MJ/day if done non‐stop for 24 hr), followed by transiting at the surface (~21 MJ/day). Interestingly, metabolic rates were similar between species while on land or while slowly moving at the surface (~13 MJ/day). Overall, the average field metabolic rate was ~20 MJ/day (for all activities combined). The method we developed to calculate activity‐specific metabolic rates can be applied to terrestrial and marine species to determine the energetic costs of daily activities, as well as to predict the energetic consequences for animals forced to change their time allocations in response to environmental shifts.     

Simultaneous determination of three carbapenem antibiotics in plasma by HPLC with ultraviolet detection

A simple, precise and accurate high-performance liquid chromatography (HPLC) method using ultraviolet (UV) detection has been developed for simultaneous determination of carbapenem antibiotics: imipenem, meropenem and ertapenem in human plasma. Samples were spiked with ceftazidime as internal standard and proteins were precipitated by acetonitrile. Separation was achieved on a C8 column with a mobile phase composed of phosphate buffer 0.1M (pH 6.8) and methanol in gradient elution mode. Detection was performed at 298 nm. Calibration curves were linear from 0.5 to 80 mg/L for each compound, with correlation coefficients over 0.997. Intra- and inter-day validation studies showed accuracy between -4.5 and 8.1% and precision below 10.4%. Mean recoveries were 82.2, 90.8 and 87.7% for imipenem, meropenem and ertapenem, respectively. This method provides a useful tool for the therapeutic drug monitoring of carbapenems.     

Dentition and tooth replacement pattern in Chalcides (Squamata; Scincidae)

This study was undertaken as a prerequisite to investigations on tooth differentiation in a squamate, the Canarian scincid Chalcides. Our main goal was to determine whether the pattern of tooth replacement, known to be regular in lizards, could be helpful to predict accurately any stage of tooth development. A growth series of 20 laboratory-reared specimens, aged from 0.5 month after birth to about 6 years, was used. The dentition (functional and replacement teeth) was studied from radiographs of jaw quadrants. The number of tooth positions, the tooth number in relation to age and to seasons, and the size of the replacement teeth were recorded. In Chalcides, a single row of pleurodont functional teeth lies at the labial margin of the dentary, premaxillary, and maxillary. Whatever the age of the specimens, 16 tooth positions were recorded, on average, in each quadrant, suggesting that positions are maintained throughout life. Replacement teeth were numerous whatever the age and season, while the number of functional teeth was subject to variation. Symmetry of tooth development was evaluated by comparing teeth two by two from the opposite side in the four jaw quadrants of several specimens. Although the relative size of some replacement teeth fitted perfectly, the symmetry criterion was not reliable to predict the developmental stage of the opposite tooth, whether the pair of teeth compared was left-right or upper-lower. The best fit was found when comparing the size of successive replacement teeth from the front to the back of the jaw. Every replacement tooth that is 40-80% of its definitive size is followed, in the next position on the arcade, by a tooth that is, on average, 20% less developed. Considering teeth in alternate positions (even and odd series), each replacement tooth was a little more developed than the previous, more anterior, one (0.5-20% when the teeth are from 10-40% of their final size). The latter pattern showed that tooth replacement occurred in alternate positions from back to front, forming more or less regular rows (i.e., "Zahnreihen"). In Chalcides, the developmental stage of a replacement tooth in a position p can be accurately predicted provided the developmental stage of the replacement tooth in position p-1 or, to a lesser degree, in position p-2 is known. This finding will be particularly helpful when starting our structural and ultrastructural studies of tooth differentiation in this lizard.     

The mineral weathering ability of Collimonas pratensis PMB3(1) involves a Malleobactin-mediated iron acquisition system

Mineral weathering by microorganisms is considered to occur through a succession of mechanisms based on acidification and chelation. While the role of acidification is established, the role of siderophores is difficult to disentangle from the effect of the acidification. We took advantage of the ability of strain Collimonas pratensis PMB3(1) to weather minerals but not to acidify depending on the carbon source to address the role of siderophores in mineral weathering. We identified a single non-ribosomal peptide synthetase (NRPS) responsible for siderophore biosynthesis in the PMB3(1) genome. By combining iron-chelating assays, targeted mutagenesis and chemical analyses (HPLC and LC-ESI-HRMS), we identified the siderophore produced as malleobactin X and how its production depends on the concentration of available iron. Comparison with the genome sequences of other collimonads evidenced that malleobactin production seems to be a relatively conserved functional trait, though some collimonads harboured other siderophore synthesis systems. We also revealed by comparing the wild-type strain and its mutant impaired in the production of malleobactin that the ability to produce this siderophore is essential to allow the dissolution of hematite under non-acidifying conditions. This study represents the first characterization of the siderophore produced by collimonads and its role in mineral weathering.     

Proteomic applications in ecotoxicology

Within the growing body of proteomics studies, issues addressing problems of ecotoxicology are on the rise. Generally speaking, ecotoxicology uses quantitative expression changes of distinct proteins known to be involved in toxicological responses as biomarkers. Unlike these directed approaches, proteomics examines how multiple expression changes are associated with a contamination that is suspected to be detrimental. Consequently, proteins involved in toxicological responses that have not been described previously may be revealed. Following identification of key proteins indicating exposure or effect, proteomics can potentially be employed in environmental risk assessment. To this end, bioinformatics may unveil protein patterns specific to an environmental stress that would constitute a classifier able to distinguish an exposure from a control state. The combined use of sets of marker proteins associated with a given pollution impact may prove to be more reliable, as they are based not only on a few unique markers which are measured independently, but reflect the complexity of a toxicological response. Such a proteomic pattern might also integrate some of the already established biomarkers of environmental toxicity. Proteomics applications in ecotoxicology may also comprise functional examination of known classes of proteins, such as glutathione transferases or metallothioneins, to elucidate their toxicological responses.     

coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns

Background

Epigenome-wide association scans (EWAS) are an increasingly powerful and widely-used approach to assess the role of epigenetic variation in human complex traits. However, this rapidly emerging field lacks dedicated visualisation tools that can display features specific to epigenetic datasets.

Result

We developed coMET, an R package and online tool for visualisation of EWAS results in a genomic region of interest. coMET generates a regional plot of epigenetic-phenotype association results and the estimated DNA methylation correlation between CpG sites (co-methylation), with further options to visualise genomic annotations based on ENCODE data, gene tracks, reference CpG-sites, and user-defined features. The tool can be used to display phenotype association signals and correlation patterns of microarray or sequencing-based DNA methylation data, such as Illumina Infinium 450k, WGBS, or MeDIP-seq, as well as other types of genomic data, such as gene expression profiles. The software is available as a user-friendly online tool from http://epigen.kcl.ac.uk/cometand as an R Bioconductor package. Source code, examples, and full documentation are also available from GitHub.

Conclusion

Our new software allows visualisation of EWAS results with functional genomic annotations and with estimation of co-methylation patterns. coMET is available to a wide audience as an online tool and R package, and can be a valuable resource to interpret results in the fast growing field of epigenetics. The software is designed for epigenetic data, but can also be applied to genomic and functional genomic datasets in any species.     

P2RX7 Purinoceptor: A Therapeutic Target for Ameliorating the Symptoms of Duchenne Muscular Dystrophy

Background

Duchenne muscular dystrophy (DMD) is the most common inherited muscle disease, leading to severe disability and death in young men. Death is caused by the progressive degeneration of striated muscles aggravated by sterile inflammation. The pleiotropic effects of the mutant gene also include cognitive and behavioral impairments and low bone density.Current interventions in DMD are palliative only as no treatment improves the long-term outcome. Therefore, approaches with a translational potential should be investigated, and key abnormalities downstream from the absence of the DMD product, dystrophin, appear to be strong therapeutic targets. We and others have demonstrated that DMD mutations alter ATP signaling and have identified P2RX7 purinoceptor up-regulation as being responsible for the death of muscles in the mdx mouse model of DMD and human DMD lymphoblasts. Moreover, the ATP–P2RX7 axis, being a crucial activator of innate immune responses, can contribute to DMD pathology by stimulating chronic inflammation. We investigated whether ablation of P2RX7 attenuates the DMD model mouse phenotype to assess receptor suitability as a therapeutic target.

Methods and Findings

Using a combination of molecular, histological, and biochemical methods and behavioral analyses in vivo we demonstrate, to our knowledge for the first time, that genetic ablation of P2RX7 in the DMD model mouse produces a widespread functional attenuation of both muscle and non-muscle symptoms. In dystrophic muscles at 4 wk there was an evident recovery in key functional and molecular parameters such as improved muscle structure (minimum Feret diameter, p < 0.001), increased muscle strength in vitro (p < 0.001) and in vivo (p = 0.012), and pro-fibrotic molecular signatures. Serum creatine kinase (CK) levels were lower (p = 0.025), and reduced cognitive impairment (p = 0.006) and bone structure alterations (p < 0.001) were also apparent. Reduction of inflammation and fibrosis persisted at 20 mo in leg (p = 0.038), diaphragm (p = 0.042), and heart muscles (p < 0.001). We show that the amelioration of symptoms was proportional to the extent of receptor depletion and that improvements were observed following administration of two P2RX7 antagonists (CK, p = 0.030 and p = 0.050) without any detectable side effects. However, approaches successful in animal models still need to be proved effective in clinical practice.

Conclusions

These results are, to our knowledge, the first to establish that a single treatment can improve muscle function both short and long term and also correct cognitive impairment and bone loss in DMD model mice. The wide-ranging improvements reflect the convergence of P2RX7 ablation on multiple disease mechanisms affecting skeletal and cardiac muscles, inflammatory cells, brain, and bone. Given the impact of P2RX7 blockade in the DMD mouse model, this receptor is an attractive target for translational research: existing drugs with established safety records could potentially be repurposed for treatment of this lethal disease.     

Impairment of SLC17A8 encoding vesicular glutamate transporter-3, VGLUT3, underlies nonsyndromic deafness DFNA25 and inner hair cell dysfunction in null mice

Autosomal-dominant sensorineural hearing loss is genetically heterogeneous, with a phenotype closely resembling presbycusis, the most common sensory defect associated with aging in humans. We have identified SLC17A8, which encodes the vesicular glutamate transporter-3 (VGLUT3), as the gene responsible for DFNA25, an autosomal-dominant form of progressive, high-frequency nonsyndromic deafness. In two unrelated families, a heterozygous missense mutation, c.632C→T (p.A211V), was found to segregate with DFNA25 deafness and was not present in 267 controls. Linkage-disequilibrium analysis suggested that the families have a distant common ancestor. The A211 residue is conserved in VGLUT3 across species and in all human VGLUT subtypes (VGLUT1-3), suggesting an important functional role. In the cochlea, VGLUT3 accumulates glutamate in the synaptic vesicles of the sensory inner hair cells (IHCs) before releasing it onto receptors of auditory-nerve terminals. Null mice with a targeted deletion of Slc17a8 exon 2 lacked auditory-nerve responses to acoustic stimuli, although auditory brainstem responses could be elicited by electrical stimuli, and robust otoacoustic emissions were recorded. Ca²⁺-triggered synaptic-vesicle turnover was normal in IHCs of Slc17a8 null mice when probed by membrane capacitance measurements at 2 weeks of age. Later, the number of afferent synapses, spiral ganglion neurons, and lateral efferent endings below sensory IHCs declined. Ribbon synapses remaining by 3 months of age had a normal ultrastructural appearance. We conclude that deafness in Slc17a8-deficient mice is due to a specific defect of vesicular glutamate uptake and release and that VGLUT3 is essential for auditory coding at the IHC synapse.     

Shared phylogeographic patterns and widespread chloroplast haplotype sharing in Eucalyptus species with different ecological tolerances

We examined the phylogeography of three south-east Australian trees (Eucalyptus delegatensis, Eucalyptus obliqua, and Eucalyptus regnans) with different tolerances, in terms of cold, drought, fire and soil to explore whether species with different ecologies share major phylogeographic patterns. A second aim of this study was to examine geographic patterns of chloroplast DNA (cpDNA) haplotype sharing among the three study species. Trees of E. delegatensis (n?=?120), E. obliqua (n?=?265) and E. regnans (n?=?270) were genotyped with five cpDNA microsatellite markers. The species shared major phylogeographic disjunctions, and common patterns at proposed glacial refugia (generally high haplotype diversity) and areas thought to have been treeless during the Last Glacial Maximum (LGM) (low diversity). Inter-specific sharing of haplotypes was extensive, and fixation of shared, regional haplotypes was more frequent in areas postulated as having been treeless at the LGM. Despite ecological differences, chloroplast microsatellite data suggest the three species have responded to past climatic changes in a similar way, by persisting in multiple, generally common refugia. We suggest that the natural ability of eucalypt species to hybridise with others with quite different or broader ecological tolerances may provide an “insurance policy” for response to rapidly changing abiotic conditions.