Spring to autumn changes in the arbuscular mycorrhizal fungal community composition in the different propagule types associated to a Mediterranean shrubland

Background and aims

Arbuscular mycorrhizal fungi (AMF) appear differentially represented among propagule forms [intraradical mycelium (IRM) in colonized roots, spores and extraradical mycelium (ERM)]. However, spring to autumn changes in the AMF communities harboured in the different propagule forms has not been studied, being this the aim of the present study.

Methods

A terminal restriction fragment length polymorphism approach was used to monitor, in spring and autumn, the AMF community composition present in the three propagule types associated to five shrub species in a semi-arid Mediterranean environment.

Results

The AMF community composition in roots was significantly different between spring and autumn; however, no significant differences were detected in soil propagules (spores and ERM). Different trends were identified according to the preferential biomass allocation patterns of AMF phylotypes, suggesting different life strategies: those allocating mainly into IRM (belonging to the Glomeraceae), ERM (Diversisporaceae and Gigasporaceae) or spores (Pacisporaceae and Paraglomeraceae).

Conclusions

Differences of AMF taxa in the biomass allocation patterns among propagules are maintained throughout the year. Progress in the knowledge of functional features of AMF communities and their responses to seasonal variations are important for the AMF application in Mediterranean ecosystems.

     

Iridoid and phenylethanoid/phenylpropanoid metabolite profiles of <Emphasis Type="Italic">Scrophularia</Emphasis> and <Emphasis Type="Italic">Verbascum</Emphasis> species used medicinally in North America

Introduction

Botanicals containing iridoid and phenylethanoid/phenylpropanoid glycosides are used worldwide for the treatment of inflammatory musculoskeletal conditions that are primary causes of human years lived with disability, such as arthritis and lower back pain.

Objectives

We report the analysis of candidate anti-inflammatory metabolites of several endemic Scrophularia species and Verbascum thapsus used medicinally by peoples of North America.

Methods

Leaves, stems, and roots were analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and partial least squares-discriminant analysis (PLS-DA) was performed in MetaboAnalyst 3.0 after processing the datasets in Progenesis QI.

Results

Comparison of the datasets revealed significant and differential accumulation of iridoid and phenylethanoid/phenylpropanoid glycosides in the tissues of the endemic Scrophularia species and Verbascum thapsus.

Conclusions

Our investigation identified several species of pharmacological interest as good sources for harpagoside and other important anti-inflammatory metabolites.

     

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.

     

Case report of optic atrophy in Dentatorubropallidoluysian Atrophy (DRPLA)

Background

Dentatorubropallidoluysian atrophy (DRPLA) is a rare autosomal dominant neurodegenerative disease that is associated with numerous movement disorders. Ocular problems also occur with DRPLA with reports of corneal endothelial degeneration in some patients living with the disease. We report a new visual problem associated with DRPLA, optic atrophy.

Case presentation

A 47 year-old man presented complaining of progressive visual loss associated with optic atrophy on ophthalmological evaluation. He gradually developed a progressive ataxia with dystonia. Brain MRI revealed a diffuse leukoencephalopathy. Genetic analysis revealed 62 CAG repeats in one allele of the DRPLA gene and he was diagnosed with DRPLA.

Conclusion

Optic atrophy should be included in the clinical spectrum of DRPLA.

     

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.

     

Use of a gnotobiotic plant assay for assessing root colonization and mineral phosphate solubilization by <Emphasis Type="Italic">Paraburkholderia bryophila</Emphasis> Ha185 in association with perennial ryegrass (<Emphasis Type="Italic">Lolium perenne</Emphasis> L.)

Aims

The mechanisms by which rhizosphere bacteria increase the availability of mineral P precipitates for plant use are understudied. However, Paraburkholderia bryophila Ha185 is known to solubilize inorganic phosphate in vitro via a novel process. Therefore, this study aimed to demonstrate P solubilization by Ha185 in association with roots of perennial ryegrass (Lolium perenne L.).

Methods

We developed a gnotobiotic plant assay to assess P solubilization by Ha185 on ryegrass roots under various nutrient conditions. A green fluorescent protein (GFP)-tagged derivative of Ha185 was used in conjunction with fluorescent microscopy and confocal microscopy to visualize colonization of ryegrass roots.

Results

Ha185 solubilized mineral P (hydroxyapatite) in association with ryegrass roots and increased ryegrass growth by 20% under P-limited conditions. The GFP-tagged Ha185 strain colonized the rhizoplane and penetrated the primary root of ryegrass, possibly through “crack entry” at the point of lateral root emergence, but also by entering the epidermal cells via root hairs.

Conclusions

Ha185 supported ryegrass growth under P-limited conditions, indicating this strain may improve availability of soil P for uptake by ryegrass. Tools developed in this study have broad application in the study of rhizobacteria-plant interactions.

     

Pseudo current density maps of electrophysiological heart,nerve or brain function and their physical basis

Background

In recent years the visualization of biomagnetic measurement data by so-called pseudo current density maps or Hosaka-Cohen (HC) transformations became popular.

Methods

The physical basis of these intuitive maps is clarified by means of analytically solvable problems.

Results

Examples in magnetocardiography, magnetoencephalography and magnetoneurography demonstrate the usefulness of this method.

Conclusion

Hardware realizations of the HC-transformation and some similar transformations are discussed which could advantageously support cross-platform comparability of biomagnetic measurements.

     

Silicon acquisition by bananas (c.V. Grande Naine) is increased in presence of the arbuscular mycorrhizal fungus <Emphasis Type="Italic">Rhizophagus irregularis</Emphasis> MUCL 41833

Aim

This work aimed to investigate the role of arbuscular mycorrhizal fungi (AMF) in the uptake and accumulation of silicon (Si) in banana plants. Si is recognized as a significant element that helps plants resist stresses.

Methods

A pot experiment compared the growth, Si and P accumulation of banana plants pre-colonized or not by an AMF and exposed or not to Si added to the growth substrate.

Results

A marked increase in Si was noticed in pseudostem, leaves and roots of pre-colonized banana plants, in presence as well as in absence of Si added to the growth substrate. Without Si addition, this accumulation was 60 % and 45 % higher in pseudostem and leaves, respectively, while it was 47 % and 41 % in presence of Si added to the substrate. In roots, this increase was 23 % and 52 % in presence and absence of Si added to the substrate, respectively. Phosphorus content in shoots and roots was likewise significantly increased in presence of AMF or Si.

Conclusion

Our findings revealed that pre-colonized banana plants accumulated more Si in shoot and roots than non-mycorrhizal plants and may thus represent a potential novel avenue to explore banana resistance to pests and diseases.

     

The effects of root surface charge and nitrogen forms on the adsorption of aluminum ions by the roots of rice with different aluminum tolerances

Aim

Our objectives were to compare effects of root charge properties on Al adsorption by the roots of rice that differed in Al-tolerance, and to examine effects of different nitrogen forms on charge properties of rice roots and Al adsorption.

Methods

Streaming potential and chemical methods were used to measure root zeta potential and investigate Al chemical forms adsorbed on the roots of rice obtained from solution culture experiments.

Results

Rice roots of the Al-sensitive variety Yangdao-6 carried greater negative charge than the Al-tolerant variety Wuyunjing-7, which meant the roots of Yangdao-6 adsorbed more exchangeable and complexed Al. When both rice varieties were grown in NH₄ ⁺-containing nutrient solutions, there were less functional groups and lower negative surface charge on their roots, which reduced Al adsorption compared to the rice grown in NO₃ ^? containing nutrient solutions. The decline in nutrient solution pH due to NH₄ ⁺ uptake by rice roots was responsible for the reduced numbers of functional groups and the lower negative surface charge on the roots compared to the rice grown in NO₃ ^? containing solutions.

Conclusions

Integrated root surface charge, as expressed by zeta potential, played an important role in Al adsorption by the roots of rice with different Al-tolerance.

     

Metabolites predict cardiovascular disease events in persons living with HIV: a pilot case–control study

Introduction

Persons living with HIV (PLWH) are at higher risk for cardiovascular disease (CVD) events than uninfected persons. Current risk-stratification methods to define PLWH at highest risk for CVD events are lacking.

Methods

Using tandem flow injection mass spectrometry, we quantified plasma levels of 60 metabolites in 24 matched pairs of PLWH [1:1 with and without known coronary artery disease (CAD)]. Metabolite levels were reduced to interpretable factors using principal components analysis.

Results

Factors derived from short-chain dicarboxylacylcarnitines (SCDA) (p?=?0.08) and glutamine/valine (p?=?0.003) were elevated in CAD cases compared to controls.

Conclusion

SCDAs and glutamine/valine may be valuable markers of cardiovascular risk among persons living with HIV in the future, pending validation in larger cohorts.

     

Untargeted metabolomics suffers from incomplete raw data processing

Introduction

Untargeted metabolomics is a powerful tool for biological discoveries. To analyze the complex raw data, significant advances in computational approaches have been made, yet it is not clear how exhaustive and reliable the data analysis results are.

Objectives

Assessment of the quality of raw data processing in untargeted metabolomics.

Methods

Five published untargeted metabolomics studies, were reanalyzed.

Results

Omissions of at least 50 relevant compounds from the original results as well as examples of representative mistakes were reported for each study.

Conclusion

Incomplete raw data processing shows unexplored potential of current and legacy data.

     

Quantitative analysis of tetrahydrofolate metabolites from <Emphasis Type="Italic">clostridium autoethanogenum</Emphasis>

Introduction

Quantification of tetrahydrofolates (THFs), important metabolites in the Wood–Ljungdahl pathway (WLP) of acetogens, is challenging given their sensitivity to oxygen.

Objective

To develop a simple anaerobic protocol to enable reliable THFs quantification from bioreactors.

Methods

Anaerobic cultures were mixed with anaerobic acetonitrile for extraction. Targeted LC–MS/MS was used for quantification.

Results

Tetrahydrofolates can only be quantified if sampled anaerobically. THF levels showed a strong correlation to acetyl-CoA, the end product of the WLP.

Conclusion

Our method is useful for relative quantification of THFs across different growth conditions. Absolute quantification of THFs requires the use of labelled standards.

     

Partitioning water source and sinking process of a groundwater-dependent desert plant community

Aims

Root-specific responses to stress are not well-known, and have been largely based on indirect measurements of bulk soil water extraction, which limits mechanistic modeling of root function.

Methods

Here, we used neutron radiography to examine in situ root-soil water dynamics of a previously droughted black cottonwood (Populus trichocarpa) seedling, contrasting water uptake by the two major components of the root system that differed in initial recovery rate as apparent by ‘new’ (whiter, thinner), or ‘old’ (darker, thicker) parts of the fine root system.

Results

The smaller diameter ‘new’ roots had greater water uptake per unit surface area than the larger diameter ‘old’ roots, but they had less total surface area leading to less total water extraction; rates ranged from 0.0027–0.0116 g cm^?2 h^?1. The finest most-active roots were not visible in the radiographs, indicating the need to include destructive sampling. Analysis based on root-free bulk soil hydraulic properties indicated substantial redistribution of water via saturated/unsaturated flow and capillary wicking across the layers - suggesting water uptake dynamics following an infiltration event may be more complex than approximated by common soil hydraulic or root surface area modeling approaches.

Conclusions

Our results highlight the need for continued exploration of root-trait specific water uptake rates in situ, and impacts of roots on soil hydraulic properties – both critical components for mechanistic modeling of root function.

     

Fine-root growth in a forested bog is seasonally dynamic,but shallowly distributed in nutrient-poor peat

Background and aims

Fine roots contribute to ecosystem carbon, water, and nutrient fluxes through resource acquisition, respiration, exudation, and turnover, but are understudied in peatlands. We aimed to determine how the amount and timing of fine-root growth in a forested, ombrotrophic bog varied across gradients of vegetation density, peat microtopography, and changes in environmental conditions across the growing season and throughout the peat profile.

Methods

We quantified fine-root peak standing crop and growth using non-destructive minirhizotron technology over a two-year period, focusing on the dominant woody species in the bog: Picea mariana, Larix laricina, Rhododendron groenlandicum, and Chamaedaphne calyculata.

Results

The fine roots of trees and shrubs were concentrated in raised hummock microtopography, with more tree roots associated with greater tree densities and a unimodal peak in shrub roots at intermediate tree densities. Fine-root growth tended to be seasonally dynamic, but shallowly distributed, in a thin layer of nutrient-poor, aerobic peat above the growing season water table level.

Conclusions

The dynamics and distribution of fine roots in this forested ombrotrophic bog varied across space and time in response to biological, edaphic, and climatic conditions, and we expect these relationships to be sensitive to projected environmental changes in northern peatlands.

     

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.

     

Effects of silicon on aluminum toxicity in upland rice plants

Aims

This study aimed to determine the capacity of Si to mitigate Al toxicity in upland rice plants (Oryza sativa L.) by evaluating plant growth and the Si and Al uptake kinetics.

Methods

Plants were grown for 40 days, after which the Si and Al uptake kinetics (Cmin, Km and Imax) were analyzed. Then, the shoots and roots were separated, and the dry matter, root morphology and Si and Al concentration and accumulation in the plant were evaluated.

Results

Aluminum decreased plant growth and the Si uptake capacity by decreasing the root growth and Si transport system efficiency in the upland rice roots (> Km and > Cmin). Silicon mitigated Al toxicity in the upland rice plants by decreasing Al transport to the plant shoots, although it did not reduce the Al uptake rate (Imax). Si treatment increased the growth of upland rice plant shoots grown in the presence of Al without influencing the root growth. The alleviation of Al toxicity by Si is more evident in the susceptible upland rice cultivar Maravilha.

Conclusions

Silicon mitigated Al toxicity in the upland rice plants by decreasing Al transport to the plant shoots but did not reduce the Al uptake rate by roots.

     

Echocardiographic findings associated with mortality or transplant in patients with pulmonary arterial hypertension: A systematic review and meta-analysis

Background

Identification of patients at risk of deterioration is essential to guide clinical management in pulmonary arterial hypertension (PAH). This study aims to provide a comprehensive overview of well-investigated echocardiographic findings that are associated with clinical deterioration in PAH.

Methods

MEDLINE and EMBASE databases were systematically searched for longitudinal studies published by April 2015 that reported associations between echocardiographic findings and mortality, transplant or clinical worsening. Meta-analysis using random effect models was performed for echocardiographic findings investigated by four or more studies. In case of statistical heterogeneity a sensitivity analysis was conducted.

Results

Thirty-seven papers investigating 51 echocardiographic findings were included. Meta-analysis of univariable hazard ratios (HRs) and sensitivity analysis showed that presence of pericardial effusion (pooled HR 1.70; 95?% CI 1.44–1.99), right atrial area (pooled HR 1.71; 95?% CI 1.38–2.13) and tricuspid annular plane systolic excursion (TAPSE; pooled HR 1.72; 95?% CI 1.34–2.20) were the most well-investigated and robust predictors of mortality or transplant.

Conclusions

This meta-analysis substantiates the clinical yield of specific echocardiographic findings in the prognostication of PAH patients in day-to-day practice. In particular, pericardial effusion, right atrial area and TAPSE are of prognostic value.

     

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.

     

KniMet: a pipeline for the processing of chromatography–mass spectrometry metabolomics data

Introduction

Data processing is one of the biggest problems in metabolomics, given the high number of samples analyzed and the need of multiple software packages for each step of the processing workflow.

Objectives

Merge in the same platform the steps required for metabolomics data processing.

Methods

KniMet is a workflow for the processing of mass spectrometry-metabolomics data based on the KNIME Analytics platform.

Results

The approach includes key steps to follow in metabolomics data processing: feature filtering, missing value imputation, normalization, batch correction and annotation.

Conclusion

KniMet provides the user with a local, modular and customizable workflow for the processing of both GC–MS and LC–MS open profiling data.

     

Extraction of natural products from bark of <Emphasis Type="Italic">Betula pendula</Emphasis> using ionic liquids

Introduction

Aqueous–methanol mixtures have successfully been applied to extract a broad range of metabolites from plant tissue. However, a certain amount of material remains insoluble.

Objectives

To enlarge the metabolic compendium, two ionic liquids were selected to extract the methanol insoluble part of trunk from Betula pendula.

Methods

The extracted compounds were analyzed by LC/MS and GC/MS.

Results

The results show that 1-butyl-3-methylimidazolium acetate (IL-Ac) predominantly resulted in fatty acids, whereas 1-ethyl-3-methylimidazolium tosylate (IL-Tos) mostly yielded phenolic structures. Interestingly, bark yielded more ionic liquid soluble metabolites compared to interior wood.

Conclusion

From this one can conclude that the application of ionic liquids may expand the metabolic snapshot.