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Phosphorus (P) is an indispensable element for all life on Earth and, during the past decade, concerns about the future of its global supply have stimulated much research on soil P and method development. This review provides an overview of advanced state-of-the-art methods currently used in soil P research. These involve bulk and spatially resolved spectroscopic and spectrometric P speciation methods (1 and 2D NMR, IR, Raman, Q-TOF MS/MS, high resolution-MS, NanoSIMS, XRF, XPS, (µ)XAS) as well as methods for assessing soil P reactions (sorption isotherms, quantum-chemical modeling, microbial biomass P, enzymes activity, DGT, 33P isotopic exchange, 18O isotope ratios). Required experimental set-ups and the potentials and limitations of individual methods present a guide for the selection of most suitable methods or combinations.

Background It is widely assumed that variation in fitness components has a physiological basis that might underlie selection on trade-offs, but the mechanisms driving decreased survival and future fecundity remain elusive. Here, we assessed whether physiological variables are related to workload ability or immediate fitness consequences and if they mediate future survival or reproductive success. We used data on 13 physiological variables measured in 93 female European starlings (Sturnus vulgaris) at two breeding stages (incubation, chick-rearing), for first-and second-broods over two years (152 observations). Results There was little co-variation among the physiological variables, either in incubating or chick-rearing birds, but some systematic physiological differences between the two stages. Chick-rearing birds had lower hematocrit and plasma creatine kinase but higher hemoglobin, triglyceride and uric acid levels. Only plasma corticosterone was repeatable between incubation and chick-rearing. We assessed relationships between incubation or chick-rearing physiology and measures of workload, current productivity, future fecundity or survival in a univariate manner, and found very few significant relationships. Thus, we next explored the utility of multivariate analysis (principal components analysis, Mahalanobis distance) to account for potentially complex physiological integration, but still found no clear associations. Conclusions This implies either that a) birds maintained physiological variables within a homeostatic range that did not affect their performance, b) there are relatively few links between physiology and performance, or, more likely, c) that the complexity of these relationships exceeds our ability to measure it. Variability in ecological context may complicate the relationship between physiology and behavior. We thus urge caution regarding the over-interpretation of isolated significant findings, based on single traits in single years, in the literature. Electronic supplementary material The online version of this article (10.1186/s12983-018-0288-3) contains supplementary material, which is available to authorized users.

Brain-computer interface (BCI) allows collaboration between humans and machines. It translates the electrical activity of the brain to understandable commands to operate a machine or a device. In this study, we propose a method to improve the accuracy of a 3-class BCI using electroencephalographic (EEG) signals. This BCI discriminates rest against imaginary grasps and elbow movements of the same limb. This classification task is challenging because imaginary movements within the same limb have close spatial representations on the motor cortex area. The proposed method extracts time-domain features and classifies them using a support vector machine (SVM) with a radial basis kernel function (RBF). An average accuracy of 74.2% was obtained when using the proposed method on a dataset collected, prior to this study, from 12 healthy individuals. This accuracy was higher than that obtained when other widely used methods, such as common spatial patterns (CSP), filter bank CSP (FBCSP), and band power methods, were used on the same dataset. These results are encouraging and the proposed method could potentially be used in future applications including BCI-driven robotic devices, such as a portable exoskeleton for the arm, to assist individuals with impaired upper extremity functions in performing daily tasks.

Table S1. Molecular studies investigating the non-human vertebrate skin microbiome. Only studies that used culture-independent methods were included. Studies within a vertebrate clade are listed in alphabetical order according to first author. (DOCX 80 kb)

INTRODUCTION Genetic interactions occur when mutations in different genes combine to result in a phenotype that is different from expectation based on those of the individual mutations. Negative genetic interactions occur when a combination of mutations leads to a fitness defect that is more exacerbated than expected. For example, synthetic lethality occurs when two mutations, neither of which is lethal on its own, generate an inviable double mutant. Alternatively, positive genetic interactions occur when genetic perturbations combine to generate a double mutant with a greater fitness than expected. Global digenic interaction studies have been useful for understanding the functional wiring diagram of the cell and may also provide insight into the genotype-to-phenotype relationship, which is important for tracking the missing heritability of human health and disease. Here we describe a network of higher-order trigenic interactions and explore its implications. RATIONALE Variation in phenotypic outcomes in different individuals is caused by genetic determinants that act as modifiers. Modifier loci are prevalent in human populations, but knowledge regarding how variants interact to modulate phenotype in different individuals is lacking. Similarly, in yeast, traits including conditional essentiality—in which certain genes are essential in one genetic background but nonessential in another—often result from an interplay of multiple modifier loci. Because complex modifiers may underlie the genetic basis of physiological states found in natural populations, it is critical to understand the landscape of higher-order genetic interactions. RESULTS To survey trigenic interactions, we designed query strains that sampled key features of the global digenic interaction network: (i) digenic interaction strength, (ii) average number of digenic interactions, and (iii) digenic interaction profile similarity. In total, we tested ~400,000 double and ~200,000 triple mutants for fitness defects and identified ~9500 digenic and ~3200 trigenic negative interactions. Although trigenic interactions tend to be weaker than digenic interactions, they were both enriched for functional relationships. About one-third of trigenic interactions identified “novel” connections that were not observed in our digenic control network, whereas the remaining approximately two-thirds of trigenic interactions “modified” a digenic interaction, suggesting that the global digenic interaction network is important for understanding the trigenic interaction network. Despite their functional enrichment, trigenic interactions also bridged distant bioprocesses. We estimate that the global trigenic interaction network is ~100 times as large as the global digenic network, highlighting the potential for complex genetic interactions to affect the biology of inheritance. CONCLUSION The extensive network of trigenic interactions and their ability to generate functionally diverse phenotypes suggest that higher-order genetic interactions may play a key role in the genotype-to-phenotype relationship, genome size, and speciation.

Actinotrichia are the first exoskeletal elements formed during zebrafish fin development. These rigid fibrils serve as skeletal support for the fin fold and as substrates for mesenchymal cell migration. In the adult intact fins, actinotrichia are restricted to the distal domain of the fin. Following fin amputation, actinotrichia also reform during regeneration. The actinodin gene family codes for structural proteins of actinotrichia. We have previously identified cis-acting regulatory elements in a 2kb genomic region upstream of the first exon of actinodin1, termed 2P, required for tissue-specific expression in the fin fold ectoderm and mesenchyme during embryonic development. Indeed, 2P contains an ectodermal enhancer in a 150bp region named epi. Deletion of epi from 2P results in loss of ectodermal-specific activity. In the present study, we sought to further characterize the activity of these regulatory sequences throughout fin development and during adult fin regeneration. Using a reporter transgenic approach, we show that a site within the epi region, termed epi3, contains an early mesenchymal-specific repressor. We also show that the larval fin fold ectodermal enhancer within epi3 remains functional in the basal epithelial layer during fin regeneration. We show that the first non-coding exon and first intron of actinodin1 contains a transcriptional enhancer and an alternative promoter that are necessary for the persistence of reporter expression reminiscent of actinodin1 expression during adulthood. Altogether, we have identified cis-acting regulatory elements that are required for tissue-specific expression as well as full recapitulation of actinodin1 expression during adulthood. Furthermore, the characterization of these elements provides us with useful molecular tools for the enhancement of transgene expression in adulthood.

AbstractPhosphoinositides (PIPs) and their regulatory enzymes are key players in many cellular processes and are required for aspects of vertebrate development. Dysregulated PIP metabolism has been implicated in several human diseases, including a subset of skeletal myopathies that feature structural defects in the triad. The role of PIPs in skeletal muscle formation, and particularly triad biogenesis, has yet to be determined. CDP-diacylglycerol-inositol 3-phosphatidyltransferase (CDIPT) catalyzes the formation of phosphatidylinositol, which is the base of all PIP species. Loss of CDIPT should, in theory, result in the failure to produce PIPs, and thus provide a strategy for establishing the requirement for PIPs during embryogenesis. In this study, we generatedcdiptmutant zebrafish and determined the impact on skeletal myogenesis. Analysis ofcdiptmutant muscle revealed no apparent global effect on early muscle development. However, small but significant defects were observed in triad size, with T-tubule area, inter terminal cisternae distance and gap width being smaller incdiptmutants. This was associated with a decrease in motor performance. Overall, these data suggest that myogenesis in zebrafish does not requirede novoPIP synthesis but does implicate a role for CDIPT in triad formation.