Metabolomic analysis of tomato seed germination

Introduction

Seed germination is inherently related to seed metabolism, which changes throughout its maturation, desiccation and germination processes. The metabolite content of a seed and its ability to germinate are determined by underlying genetic architecture and environmental effects during development.

Objective

This study aimed to assess an integrative approach to explore genetics modulating seed metabolism in different developmental stages and the link between seed metabolic- and germination traits.

Methods

We have utilized gas chromatography-time-of-flight/mass spectrometry (GC-TOF/MS) metabolite profiling to characterize tomato seeds during dry and imbibed stages. We describe, for the first time in tomato, the use of a so-called generalized genetical genomics (GGG) model to study the interaction between genetics, environment and seed metabolism using 100 tomato recombinant inbred lines (RILs) derived from a cross between Solanum lycopersicum and Solanum pimpinellifolium.

Results

QTLs were found for over two-thirds of the metabolites within several QTL hotspots. The transition from dry to 6 h imbibed seeds was associated with programmed metabolic switches. Significant correlations varied among individual metabolites and the obtained clusters were significantly enriched for metabolites involved in specific biochemical pathways.

Conclusions

Extensive genetic variation in metabolite abundance was uncovered. Numerous identified genetic regions that coordinate groups of metabolites were detected and these will contain plausible candidate genes. The combined analysis of germination phenotypes and metabolite profiles provides a strong indication for the hypothesis that metabolic composition is related to germination phenotypes and thus to seed performance.

     

Effects of <Emphasis Type="Italic">Penicillium bilaii</Emphasis> on maize growth are mediated by available phosphorus

Background and aims

Functional traits are promising indicators of global changes and ecosystem processes. Trait responses to environmental conditions have been examined widely in vascular plants. In contrast, few studies have focused on soil lichens and mosses composing biocrusts. We aimed to evaluate the potential of biocrust tissue traits as indicators of changes in climate and soil properties.

Methods

Isotope ratios and nutrient content in biocrust tissue were analyzed in 13 Mediterranean shrublands along an aridity gradient. Differences in tissue traits between biocrust groups (lichens and mosses), and relationships between tissue traits and climatic and soil variables were examined.

Results

Lichens and mosses differed in δ¹³C, δ¹⁵N and N content, indicating distinct physical and physiological attributes. Tissue traits correlated strongly with numerous climatic variables, likely due to a modulator effect on biocrust water relations and metabolism. We found contrasting responses of lichen and moss traits to climate, although they responded similarly to soil properties. Overall, the most responsive trait was δ¹⁵N, suggesting this trait is the best to reflect integrated processes occurring in the atmosphere and soil.

Conclusions

Biocrust tissue traits arise as cost-effective, integrative ecological indicators of global change drivers in Mediterranean ecosystems, with potential applications in response-effect trait frameworks.

     

A methodology for elucidating regulatory mechanisms leading to changes in lipid profiles

Introduction

It is difficult to elucidate the metabolic and regulatory factors causing lipidome perturbations.

Objectives

This work simplifies this process.

Methods

A method has been developed to query an online holistic lipid metabolic network (of 7923 metabolites) to extract the pathways that connect the input list of lipids.

Results

The output enables pathway visualisation and the querying of other databases to identify potential regulators. When used to a study a plasma lipidome dataset of polycystic ovary syndrome, 14 enzymes were identified, of which 3 are linked to ELAVL1—an mRNA stabiliser.

Conclusion

This method provides a simplified approach to identifying potential regulators causing lipid-profile perturbations.

     

Metabolomic profiling of maternal hair suggests rapid development of intrahepatic cholestasis of pregnancy

Introduction

Intrahepatic cholestasis of pregnancy (ICP) is a common maternal liver disease; development can result in devastating consequences, including sudden fetal death and stillbirth. Currently, recognition of ICP only occurs following onset of clinical symptoms.

Objective

Investigate the maternal hair metabolome for predictive biomarkers of ICP.

Methods

The maternal hair metabolome (gestational age of sampling between 17 and 41 weeks) of 38 Chinese women with ICP and 46 pregnant controls was analysed using gas chromatography–mass spectrometry.

Results

Of 105 metabolites detected in hair, none were significantly associated with ICP.

Conclusion

Hair samples represent accumulative environmental exposure over time. Samples collected at the onset of ICP did not reveal any metabolic shifts, suggesting rapid development of the disease.

     

Threshold effect of the groundwater depth on the photosynthetic efficiency of <Emphasis Type="Italic">Tamarix chinensis</Emphasis> in the Yellow River Delta

Background and aims

Functional traits may underlie differences in niches, which promote plant species co-existence, but also differences in competitive ability, which drive competitive exclusion. Empirical evidence concerning the contribution of different traits to niche differentiation and the ability to supress and tolerate competitors is very limited, particularly when considering belowground interactions.

Methods

We grew 26 temperate grassland species along a density gradient of interspecific competitors to determine which belowground traits a) explain species’ ability to suppress and tolerate neighbours and b) contribute to niche differentiation, such that species with dissimilar trait values experience reduced competition.

Results

We found that having larger root systems with extensive horizontal spread and lower root tissue density enabled efficient suppression of neighbours but did not significantly contribute to the ability to tolerate competition. Species with deeper root systems, lower specific root length and less branched roots were better at tolerating competition, but these traits did not significantly affect the ability to suppress neighbours. None of the measured traits contributed significantly to niche differentiation, either individually or in combination.

Conclusions

This study provides little support for belowground traits contributing to species co-existence through niche differentiation. Instead, different sets of weakly correlated traits enable plants to either suppress or tolerate their competitors.

     

Power of maximum HLOD tests to detect linkage to obesity genes

Background

We investigate the power of heterogeneity LOD test to detect linkage when a trait is determined by several major genes using Genetic Analysis Workshop 13 simulated data. We consider three traits, two of which are disease-causing traits: 1) the rate of change in body mass index (BMI); and 2) the maximum BMI; and 3) the disease itself (hypertension). Of interest is the power of "HLOD2", the maximum heterogeneity LOD obtained upon maximizing over the two genetic models.

Results

Using a trait phenotype Obesity Slope, we observe that the power to detect the two markers closest to the two genes (S1, S2) at the 0.05 level using HLOD2 is 13% and 10%. The power of HLOD2 for Max BMI phenotype is 12% and 9%. The corresponding values for the Hypertension phenotype are 8% and 6%.

Conclusion

The power to detect linkage to the slope genes is quite low. But the power using disease-related traits as a phenotype is greater than the power using the disease (hypertension) phenotype.

     

Serpentine ecotypic differentiation in a polyploid plant complex: shared tolerance to Mg and Ni stress among di- and tetraploid serpentine populations of <Emphasis Type="Italic">Knautia arvensis</Emphasis> (Dipsacaceae)

Background and aims

Serpentine soils impose limits on plant growth and survival and thus provide an ideal model for studying plant adaptation under environmental stress. Despite the increasing amount of data on serpentine ecotypic differentiation, no study has assessed the potential role of polyploidy. We tested for links between polyploidy and the response to serpentine stress in Knautia arvensis, a diploid-tetraploid, edaphically differentiated complex.

Methods

Variation in growth, biomass yield and tissue Mg and Ni accumulation in response to high Mg and Ni concentrations were experimentally tested using hydroponic cultivation of seedlings from eight populations of different ploidy and edaphic origin.

Results

Regardless of ploidy level, serpentine populations exhibited higher tolerance to both Mg and Ni stress than their non-serpentine counterparts, suggesting an adaptive character of these traits in K. arvensis. The effect of ploidy was rather weak and confined to a slightly better response of serpentine tetraploids to Mg stress and to higher biomass yields in tetraploids from both soil types.

Conclusions

The similar response of diploid and tetraploid serpentine populations to edaphic stress corresponded with their previously described genetic proximity. This suggests that serpentine tolerance might have been transmitted during the local autopolyploid origin of serpentine tetraploids.

     

Root architecture governs plasticity in response to drought

Aims

Fine root morphological traits are generally changed under soil nitrogen (N) enrichment, however, the underlying mechanism and functional significance are still not well understood. Our aims were to investigate the linkage of root morphology to anatomy, and its implication for root function at elevated soil N availability.

Methods

Ingrowth cores were used to sample root tips (0–20 cm soil depth) from six temperate tree species growing in monoculture plantations at a common site in northeastern China. Root morphological and anatomical traits were concurrently measured, and their relationships were determined within and among species in both control and N fertilization (10 g N m^?2y^?1) plots.

Results

Root diameter generally increased in all six species (non-significant for Phellodendron amurense) following N fertilization, which was caused by the increased root stele radius rather than cortical thickness. Congruently, N fertilization significantly decreased the ratio of cortical thickness to stele radius, but increased the ratio of total cross-sectional area of conduits to stele area in root tips across all species.

Conclusions

The observed anatomical changes of root tips contributed to the alternations of morphological root traits following N fertilization, with potentially important impacts on root physiological functions, like increased water and nutrient transport.

     

Optimization of fecal sample preparation for untargeted LC-HRMS based metabolomics

Introduction

Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.

Objectives

In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.

Methods

The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.

Results

A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.

Conclusion

The workflow generated repeatable and informative fingerprints for robust metabolome characterization.

     

Eco-evo-devo of the lemur syndrome: did adaptive behavioral plasticity get canalized in a large primate radiation?

Background

Comprehensive explanations of behavioral adaptations rarely invoke all levels famously admonished by Niko Tinbergen. The role of developmental processes and plasticity, in particular, has often been neglected. In this paper, we combine ecological, physiological and developmental perspectives in developing a hypothesis to account for the evolution of ‘the lemur syndrome’, a combination of reduced sexual dimorphism, even adult sex ratios, female dominance and mild genital masculinization characterizing group-living species in two families of Malagasy primates.

Results

We review the different components of the lemur syndrome and compare it with similar adaptations reported for other mammals. We find support for the assertion that the lemur syndrome represents a unique set of integrated behavioral, demographic and morphological traits. We combine existing hypotheses about underlying adaptive function and proximate causation by adding a potential developmental mechanism linking maternal stress and filial masculinization, and outline an evolutionary scenario for its canalization.

Conclusions

We propose a new hypothesis linking ecological, physiological, developmental and evolutionary processes to adumbrate a comprehensive explanation for the evolution of the lemur syndrome, whose assumptions and predictions can guide diverse future research on lemurs. This hypothesis should also encourage students of other behavioral phenomena to consider the potential role of developmental plasticity in evolutionary innovation.

     

Metabolite variation in the lettuce gene pool: towards healthier crop varieties and food

Introduction

Lettuce (Lactuca sativa L.) is generally not specifically acknowledged for its taste and nutritional value, while its cultivation suffers from limited resistance against several pests and diseases. Such key traits are known to be largely dependent on the ability of varieties to produce specific phytochemicals.

Objectives

We aimed to identify promising genetic resources for the improvement of phytochemical composition of lettuce varieties.

Methods

Phytochemical variation was investigated using 150 Lactuca genebank accessions, comprising a core set of the lettuce gene pool, and resulting data were related to available phenotypic information.

Results

A hierarchical cluster analysis of the variation in relative abundance of 2026 phytochemicals, revealed by untargeted metabolic profiling, strongly resembled the known lettuce gene pool structure, indicating that the observed variation was to a large extent genetically determined. Many phytochemicals appeared species-specific, of which several are generally related to traits that are associated with plant health or nutritional value. For a large number of phytochemicals the relative abundance was either positively or negatively correlated with available phenotypic data on resistances against pests and diseases, indicating their potential role in plant resistance. Particularly the more primitive lettuces and the closely related wild relatives showed high levels of (poly)phenols and vitamin C, thus representing potential genetic resources for improving nutritional traits in modern crop types.

Conclusion

Our large-scale analysis of phytochemical variation is unprecedented in lettuce and demonstrated the ample availability of suitable genetic resources for the development of improved lettuce varieties with higher nutritional quality and more sustainable production.

     

NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics

Introduction

Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks.

Objectives

The objective of NMRProcFlow is to assist the expert in this task in the best way without requirement of programming skills.

Methods

NMRProcFlow was developed to be a graphical and interactive 1D NMR (¹H & ¹³C) spectra processing tool.

Results

NMRProcFlow (http://nmrprocflow.org), dedicated to metabolic fingerprinting and targeted metabolomics, covers all spectra processing steps including baseline correction, chemical shift calibration and alignment.

Conclusion

Biologists and NMR spectroscopists can easily interact and develop synergies by visualizing the NMR spectra along with their corresponding experimental-factor levels, thus setting a bridge between experimental design and subsequent statistical analyses.

     

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it

Introduction

Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.

Objectives

(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.

Methods

A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.

Results

Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.

Conclusion

Further efforts are required to improve data sharing in metabolomics.

     

Metabolic response of porcine colon explants to in vitro infection by <Emphasis Type="Italic">Brachyspira hyodysenteriae</Emphasis>: a leap into disease pathophysiology

Introduction

Swine dysentery caused by Brachyspira hyodysenteriae is a production limiting disease in pig farming. Currently antimicrobial therapy is the only treatment and control method available.

Objective

The aim of this study was to characterize the metabolic response of porcine colon explants to infection by B. hyodysenteriae.

Methods

Porcine colon explants exposed to B. hyodysenteriae were analyzed for histopathological, metabolic and pro-inflammatory gene expression changes.

Results

Significant epithelial necrosis, increased levels of l-citrulline and IL-1α were observed on explants infected with B. hyodysenteriae.

Conclusions

The spirochete induces necrosis in vitro likely through an inflammatory process mediated by IL-1α and NO.

     

Crop metabolomics: from diagnostics to assisted breeding

Background

Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding.

Aim of Review

We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality.

Key Scientific Concepts of Review

Translational metabolomics applied to crop breeding programs.

     

Serum metabolomic profiles associated with postmenopausal hormone use

Introduction

Postmenopausal hormone use is linked to several health outcomes and the risk associated with some may differ depending on whether estrogen is used alone or in combination with progestin.

Objective

Metabolomic analyses of postmenopausal hormone use and differences between hormone regimes was done to identify metabolites associated with each type of hormone treatment.

Methods

Untargeted metabolomics analysis was done on serum from 1336 women enrolled in the Cancer Prevention II Nutrition Cohort. Levels of 781 named metabolites were compared between 667 nonusers with 332 estrogen-only and with 337 estrogen plus progestin users using linear regression. Metabolite levels were also compared between estrogen-only and estrogen plus progestin users.

Results

Compared to nonusers, 276 metabolites were statistically significantly (P?<?6.40?×?10^??5) associated with estrogen-only use and 222 were associated with estrogen plus progestin use. The metabolites associated with both types of hormones included numerous lipids, acyl carnitines, and amino acids as well as the thyroid hormone thyroxine and the oncometabolite fumarate. The 65 metabolites that differed significantly between estrogen-only and estrogen plus progestin users included 19 steroids and 12 lipids that contained the bioactive fatty acid arachidonic acid.

Conclusions

These findings suggest that postmenopausal hormone use influences metabolic pathways linked to a variety of cellular processes, including the regulation of metabolism and stress responses, energy production, and inflammation. The differential association of numerous lipids which influence cellular signaling suggests that differences in signal transduction may contribute to the disparate risks for some diseases between estrogen-only and estrogen plus progestin users.

     

IGENT: efficient entropy based algorithm for genome-wide gene-gene interaction analysis

Background

With the development of high-throughput genotyping and sequencing technology, there are growing evidences of association with genetic variants and complex traits. In spite of thousands of genetic variants discovered, such genetic markers have been shown to explain only a very small proportion of the underlying genetic variance of complex traits. Gene-gene interaction (GGI) analysis is expected to unveil a large portion of unexplained heritability of complex traits.

Methods

In this work, we propose IGENT, Information theory-based GEnome-wide gene-gene iNTeraction method. IGENT is an efficient algorithm for identifying genome-wide gene-gene interactions (GGI) and gene-environment interaction (GEI). For detecting significant GGIs in genome-wide scale, it is important to reduce computational burden significantly. Our method uses information gain (IG) and evaluates its significance without resampling.

Results

Through our simulation studies, the power of the IGENT is shown to be better than or equivalent to that of that of BOOST. The proposed method successfully detected GGI for bipolar disorder in the Wellcome Trust Case Control Consortium (WTCCC) and age-related macular degeneration (AMD).

Conclusions

The proposed method is implemented by C++ and available on Windows, Linux and MacOSX.

     

Chilling slows anaerobic metabolism to improve anoxia tolerance of insects

Background

Insects are renowned for their ability to survive anoxia. Anoxia tolerance may be enhanced during chilling through metabolic suppression.

Aims

Here, the metabolomic response of insects to anoxia, both with and without chilling, for different durations (12–36 h) was examined to assess the potential cross-tolerance mechanisms.

Results

Chilling during anoxia (cold anoxia) significantly improved survival relative to anoxia at warmer temperatures. Reduced intermediate metabolites and increased lactic acid, indicating a switch to anaerobic metabolism, were characteristic of larvae in anoxia.

Conclusions

Anoxia tolerance was correlated survival improvements after cold anoxia were correlated with a reduction in anaerobic metabolism.

     

An oncoplastic technique to reduce the formation of lateral 'dog-ears' after mastectomy

Background

Lateral skin folds or 'dog-ears' are frequent following mastectomy, particularly in patients with large body habitus.

Methods

We describe a method of modifying the mastectomy incision and suturing to eliminate these lateral 'dog-ears'.

Conclusion

This surgical technique, as compared to others described in the literature, is simple, does not require additional incisions and is cosmetically acceptable to the patient.