Soil microalgae modulate grain arsenic accumulation by reducing dimethylarsinic acid and enhancing nutrient uptake in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Background and aims

Microalgae are ubiquitous in paddy soils. However, their roles in arsenic (As) accumulation and transport in rice plants remains unknown.

Methods

Two green algae and five cyanobacteria were used in pot experiments under continuously flooded conditions to ascertain whether a microalgal inoculation could influence rice growth and rice grain As accumulation in plants grown in As-contaminated soils.

Results

The microalgal inoculation greatly enhanced nutrient uptake and rice growth. The presence of representative microalga Anabaena azotica did not significantly differ the grain inorganic As concentrations but remarkably decreased the rice root and grain DMA concentrations. The translocation of As from roots to grains was also markedly decreased by rice inoculated with A. azotica. This subsequently led to a decrease in the total As concentration in rice grains.

Conclusions

The results of the study indicate that the microalgal inoculation had a strong influence on soil pH, soil As speciation, and soil nutrient bioavailability, which significantly affected the rice growth, nutrient uptake, and As accumulation and translocation in rice plants. The results suggest that algae inoculation can be an effective strategy for improving nutrient uptake and reducing As translocation from roots to grains by rice grown in As-contaminated paddy soils.

     

An LC–MS-based lipidomics approach for studying the impact of dietary eicosapentaenoic acid on modulating methylmercury toxicity in mice

Introduction

Methylmercury (MeHg) exposure has been a public health problem for many decades. There is a growing interest in searching for possible dietary nutrients that may affect MeHg toxicity.

Objectives

The study aims to evaluate the impact of eicosapentaenoic acid (EPA) on modulating MeHg toxicity in mice.

Methods

The study was based on a two-level factorial design, where the factors were presence or absence of EPA and MeHg in the feed. A liquid chromatography-mass spectrometry-based lipidomics approach was used to identify and quantify the main phospholipid species in mouse liver and plasma. The effects of EPA and MeHg on phospholipid species were evaluated by principal component analysis and statistics. Some biochemical and toxicological markers were measured and hepatic histological assay was carried out.

Results

EPA treatment significantly elevated the phosphatidylcholine (PtdCho) and phosphatidylethanolamine (PtdEtn) species that contain n-3 PUFA, and reduced the levels of PtdCho and PtdEtn species that contain arachidonic acid (ARA), while MeHg exhibited opposite effects on these specific PtdCho species in liver. MeHg induced higher prostaglandin E₂ and lower prostaglandin E₃, thus increasing pro-inflammatory factors, while EPA decreased these ARA-derived inflammatory factors. Moreover, MeHg induced chronic inflammatory symptoms in mice, including severe hepatic necrosis, higher aspartate aminotransferase and alanine aminotransferase activities in plasma, higher thiobarbituric acid reactive substances and lower glutathione in liver. These symptoms were all alleviated by EPA treatment.

Conclusion

EPA may have protective effect against MeHg-induced toxicity due to the favorable modification of membrane phospholipid composition and inhibition of inflammatory factors.

     

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.

     

Compositional analysis of typical selenium ore from Enshi and its effect on selenium enrichment in wetland and dryland crops

Aims

The objectives of this study were to determine the valence state of Se and major components in Se ore powder, examine its effect on Se enrichment in crops under different cultivation patterns, and assess the safety of edible parts of crops.

Methods

Se ore powder from Enshi was subjected to compositional analysis by X-ray photoelectron spectroscopy and applied to rice (wetland) and soybean (dryland) fields before planting.

Results

Se was mainly present in tetravalent and zero-valent forms at a 4:6 ratio in Se ore powder. Following soil application of Se ore powder, concentrations of As, Hg, Cr, and Pb in brown rice and soybean seed were below the limit of detection, and the Cd concentration was below the European Union food regulation limit. Organic Se accounted for more than 96% of total Se in both crops, including >91% Se-methionine. Compared with dryland, the flooded environment facilitated residual Se transformation into Fe/Mn oxide-bound Se, and thus increased the potential activity of Se in the soil.

Conclusions

Se ore powder can be applied for the production of Se-rich agricultural products in the short-term, and possibilities of upgrading the Se ore product should be considered in the future.

     

Accumulation of Fascin<Superscript>+</Superscript> cells during experimental autoimmune neuritis

Background

Experimental autoimmune neuritis (EAN) is a well-known animal model of human demyelinating polyneuropathies and is characterized by inflammation and demyelination in the peripheral nervous system. Fascin is an evolutionarily highly conserved cytoskeletal protein of 55 kDa containing two actin binding domains that cross-link filamentous actin to hexagonal bundles.

Methods

Here we have studied by immunohistochemistry the spatiotemporal accumulation of Fascin?+?cells in sciatic nerves of EAN rats.

Results

A robust accumulation of Fascin?+?cell was observed in the peripheral nervous system of EAN which was correlated with the severity of neurological signs in EAN.

Conclusion

Our results suggest a pathological role of Fascin in EAN.

Virtual slides

The virtual slides for this article can be found here: http://www.diagnosticphatology.diagnomx.eu/vs/6734593451114811

     

Responses of rice to chronic and acute iron toxicity: genotypic differences and biofortification aspects

Background and aims

Iron (Fe) toxicity is a wide-spread stress in lowland rice production. The aim of this study was to differentiate between responses to acute Fe stress during the vegetative stage and chronic Fe stress throughout the growing period.

Methods

Six rice genotypes were tested in a semi-artificial greenhouse setup, in which acute (almost 1500 mg L^?1 Fe in soil solution during the vegetative stage) and chronic (200 to 300 mg L^?1 Fe throughout the season) Fe toxicity were simulated.

Results

Acute Fe stress induced early development of heavy leaf bronzing, whereas moderate symptoms occurred in the chronic treatment throughout the season. Grain yields were only reduced in the chronic stress treatment (?23 %) due to reductions in spikelet fertility, grain number and grain weight. Symptom formation during the early growth stages did not reflect yield responses in all genotypes. Only one genotype showed increases in grain Fe concentrations (24 % in the acute stress and 44 % in the chronic stress) compared to the control.

Conclusions

Contrasting genotypes responded differently to acute and chronic Fe toxicity, and one genotype showed consistent tolerance and the ability to translocate excess Fe into grains. These traits can be useful in the adaptive breeding of rice for Fe toxic environments.

     

Screening for internal phosphorus utilisation efficiency: comparison of genotypes at equal shoot P content is critical

Aims

Progress in improving the internal phosphorus utilisation efficiency of crops has been limited, which may be due to poor screening methods that allow differences in P uptake among genotypes grown in soil to mask genotypic differences in shoot biomass produced per unit of shoot P (PUE). We investigated alternative soil and hydroponic screening methods for their capacity to produce a consensus ranking of genotypes with regard to PUE.

Methods

Six rice genotypes previously identified in hydroponic screening studies as being high, intermediate or low in PUE were screened using multi P rate hydroponic and soil-based experiments.

Results

Comparisons made at each rate of soil-P supply produced estimates of PUE strongly biased by P uptake differences among genotypes. Using multiple-rate data to derive response functions per genotype showed that similar P content was achieved at different rates of P supply but that high-PUE genotypes clearly separated from intermediate- and low-PUE genotypes if equal P content was used. Ranking analysis suggested that results obtained from soil agreed well with those from the hydroponic study.

Conclusions

PUE was significantly influenced by genotype and P supply, but there was no significant genotype x P supply interaction. Hence, we conclude that screening genotypes using hydroponics at one or two P supply levels is the most cost- and time effective means to screen large numbers of rice genotypes for PUE.

     

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.

     

Endophytic infection modifies organic acid and mineral element accumulation by rice under Na<Subscript>2</Subscript>CO<Subscript>3</Subscript> stress

Background and aims

Saline and alkali soils severely impact plant growth. Endophyte and plant associations are known to significantly modify plant metabolism. This study reports the effects of a type of endophyte on organic acid (OA) accumulation and ionic balance in rice under Na₂CO₃ stress.

Methods

Rice seedlings with (E+) and without (E-) endophytic infection were subjected to different levels of Na₂CO₃ stress (0, 5, 10, 15, and 20 mM) for two weeks. Organic acids and mineral elements in the leaves and roots were determined.

Results

Seedlings with endophytic infection accumulated mainly citrate and fumarate, with some malate and succinate in the leaves. In the roots, accumulation of malate and fumarate was enhanced significantly by endophytic infection, while less citrate and succinate was accumulated under Na₂CO₃ stress, which suggested that leaves and roots use different mechanisms to control OA metabolism. Endophytes reduced the total Na and Na:K ratios, but increased ST values, the percent changes of other measured nutrients, Chl content, and dry weight per plant under Na₂CO₃ stress.

Conclusions

Endophytic infection plays a key role in maintaining plant growth by improving nutrient uptake and adjusting OA accumulation under Na₂CO₃ stress. The application of endophytes can enhance the resistance of rice to salinity.

     

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.

     

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.

     

<Emphasis Type="Italic">massPix</Emphasis>: an R package for annotation and interpretation of mass spectrometry imaging data for lipidomics

Introduction

Mass spectrometry imaging (MSI) experiments result in complex multi-dimensional datasets, which require specialist data analysis tools.

Objectives

We have developed massPix—an R package for analysing and interpreting data from MSI of lipids in tissue.

Methods

massPix produces single ion images, performs multivariate statistics and provides putative lipid annotations based on accurate mass matching against generated lipid libraries.

Results

Classification of tissue regions with high spectral similarly can be carried out by principal components analysis (PCA) or k-means clustering.

Conclusion

massPix is an open-source tool for the analysis and statistical interpretation of MSI data, and is particularly useful for lipidomics applications.

     

Deep learning for DNase I hypersensitive sites identification

Background

The DNase I hypersensitive sites (DHSs) are associated with the cis-regulatory DNA elements. An efficient method of identifying DHSs can enhance the understanding on the accessibility of chromatin. Despite a multitude of resources available on line including experimental datasets and computational tools, the complex language of DHSs remains incompletely understood.

Methods

Here, we address this challenge using an approach based on a state-of-the-art machine learning method. We present a novel convolutional neural network (CNN) which combined Inception like networks with a gating mechanism for the response of multiple patterns and longterm association in DNA sequences to predict multi-scale DHSs in Arabidopsis, rice and Homo sapiens.

Results

Our method obtains 0.961 area under curve (AUC) on Arabidopsis, 0.969 AUC on rice and 0.918 AUC on Homo sapiens.

Conclusions

Our method provides an efficient and accurate way to identify multi-scale DHSs sequences by deep learning.

     

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.

     

Understanding the Jasmine phenotype of rice through metabolite profiling and sensory evaluation

Introduction

Aromatic rices are culturally and economically important for many countries in Asia. Investigation of the volatile compounds emitted by rice during cooking is the key to understanding the flavour of elite aromatic rice varieties.

Objectives

The objectives of this study were to compare Jasmine-type aromatic rices from the Greater Mekong Subregion and Australia in terms of their metabolomics and sensory profiles and to draw out associations between the volatile organic compounds and human sensory perception of rice aroma.

Methods

A set of aromatic rice varieties from South East Asia and Australia, along with non-aromatic controls, was grown in tropical and temperate areas of Australia. Untargeted metabolite profiling of volatile compounds, from the heated rice flour, by static headspace extraction and separation by two dimensional gas chromatography time-of-flight mass spectrometry was performed. Volatile compounds were also assayed in the standard references used in the sensory evaluation and compared to the compounds detected in the headspace of rice.

Results

While 2-acetyl-1-pyrroline (2-AP) was a discriminating compound, we identified several of its structural homologues, and a number of other metabolites that were consistently detected in fragrant Jasmine rice. 2-AP producing rice varieties have different sensory properties and these variations were defined by the discriminating compounds identified in each rice type.

Conclusions

The results of this study are valuable in understanding the aspects of aromatic rice that are important to consumers, and in the identification of compounds that breeding programs can use to select for pleasant aromas, enabling breeding programs to target markets with greater accuracy.

     

Characterization of ankylosing spondylitis and rheumatoid arthritis using <Superscript>1</Superscript>H NMR-based metabolomics of human fecal extracts

Introduction

The differences in fecal metabolome between ankylosing spondylitis (AS)/rheumatoid arthritis (RA) patients and healthy individuals could be the reason for an autoimmune disorder.

Objectives

The study explored the fecal metabolome difference between AS/RA patients and healthy controls to clarify human immune disturbance.

Methods

Fecal samples from 109 individuals (healthy controls 34, AS 40, and RA 35) were analyzed by ¹H NMR spectroscopy. Data were analyzed with principal component analysis (PCA) and orthogonal projection to latent structure discriminant (OPLS-DA) analysis.

Results

Significant differences in the fecal metabolic profiles could distinguish AS/RA patients from healthy controls but could not distinguish between AS and RA patients. The significantly decreased metabolites in AS/RA patients were butyrate, propionate, methionine, and hypoxanthine. Significantly increased metabolites in AS/RA patients were taurine, methanol, fumarate, and tryptophan.

Conclusion

The metabolome variations in feces indicated AS and RA were two homologous diseases that could not be distinguished by ¹H NMR metabolomics.

     

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.

     

Crystal structure of <Emphasis Type="Italic">Escherichia coli</Emphasis> protein ybgI,a toroidal structure with a dinuclear metal site

Background

The protein encoded by the gene ybgI was chosen as a target for a structural genomics project emphasizing the relation of protein structure to function.

Results

The structure of the ybgI protein is a toroid composed of six polypeptide chains forming a trimer of dimers. Each polypeptide chain binds two metal ions on the inside of the toroid.

Conclusion

The toroidal structure is comparable to that of some proteins that are involved in DNA metabolism. The di-nuclear metal site could imply that the specific function of this protein is as a hydrolase-oxidase enzyme.

     

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.

     

rDolphin: a GUI R package for proficient automatic profiling of 1D <Superscript>1</Superscript>H-NMR spectra of study datasets

Introduction

Adoption of automatic profiling tools for ¹H-NMR-based metabolomic studies still lags behind other approaches in the absence of the flexibility and interactivity necessary to adapt to the properties of study data sets of complex matrices.

Objectives

To provide an open source tool that fully integrates these needs and enables the reproducibility of the profiling process.

Methods

rDolphin incorporates novel techniques to optimize exploratory analysis, metabolite identification, and validation of profiling output quality.

Results

The information and quality achieved in two public datasets of complex matrices are maximized.

Conclusion

rDolphin is an open-source R package (http://github.com/danielcanueto/rDolphin) able to provide the best balance between accuracy, reproducibility and ease of use.