Production system influences volatile biomarkers in tomato

Introduction

In recent years, growers have used various production types, including high-tunnel systems, to increase the yield of tomatoes (Lycopersicon esculentum). However, the effect of high-tunnel cultivation, in comparison to conventional open-field production, on aroma and flavor volatiles is not fully understood.

Objectives

To optimize the extraction and quantification conditions for the analysis of tomato volatiles using headspace solid phase microextraction (HS-SPME) coupled with gas chromatography–mass spectrometry (GC–MS), and study the effect of production systems on volatile profiles using metabolomics approach.

Methods

The HS-SPME conditions were optimized for extraction and GC–MS was used to quantify the volatiles from four tomato varieties grown in open-field and high-tunnel systems. Univariate and multivariate analyses were performed to identify the influence of production system on tomato volatiles.

Results and conclusions

The extraction of 2 g tomato samples at 60 °C for 45 min using divinylbenzene/carboxen/polydimethylsiloxane (DVB/CAR/PDMS) fiber gave the maximum amounts of volatiles. This optimized method was used to identify and quantify 41 volatiles from four tomato varieties. The levels of β-damascenone were higher in the high-tunnel tomatoes and geranylacetone was higher in open-field tomatoes. These two volatile compounds could be considered as biomarkers for tomatoes grown in high-tunnel and open-field production systems. This study is the first report comparing volatiles in tomatoes grown in high-tunnel and open-field conditions, and our results confirmed that there is a critical need to adopt biomarker-specific production systems to improve the nutritional and organoleptic properties of tomatoes.

     

Volatile organic metabolites identify patients with gastric carcinoma,gastric ulcer,or gastritis and control patients

Background

Gastric cancer ranks 4th among the most common cancers worldwide, and the mortality caused by gastric cancer is 2nd only to lung cancer. Gastric cancer shows a lack of specific symptoms in its early stages. In addition, its clinical symptoms often do not match the corresponding stage. Upper gastrointestinal endoscopy with biopsy is the gold standard for the diagnosis of gastric cancer because of its high accuracy. However, this operation is invasive, patient compliance is poor, and high demands for medical staff and equipment are typical of this procedure. Recent studies have demonstrated a connection between specific breath volatile organic compounds (VOCs) and various forms of cancers.

Methods

We collected expired air from patients with gastric cancer, chronic atrophic gastritis or gastric ulcers as well as from healthy individuals. Solid-phase microextraction, gas chromatography–mass spectrometry and principal component analysis statistics were applied to identify potential biomarkers of gastric cancer among VOCs.

Results

Fourteen differential metabolites were annotated using the NIST 11 database, with a similarity threshold of 70%. Currently, the metabolic origin of VOCs remains unclear; however, several pathways might explain the decreasing or increasing trends that were observed.

Conclusions

The results of this study demonstrate the existence of specific VOC profiles associated with patients with carcinoma. In addition, these metabolites may contribute to the diagnosis and screening of patients with carcinoma.

     

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.

     

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.

     

Translation of exhaled breath volatile analyses to sport and exercise applications

Background

Exhaled breath gases are becomingly increasingly investigated for use as non-invasive measurements for clinical diagnosis, prognosis and therapeutic monitoring. Exhaled volatile organic compounds (VOCs) in the breath, which make up the exhaled volatilome, offer a rich sample medium that provides both information to external exposures as well as endogenous metabolism. For these reasons, exhaled breath analyses can be extended further beyond disease-based investigations, and used for wider biomarker measurement purposes. The use of a rapid, non-invasive (and potentially non-physically demanding) test in an exercise and/or sporting situation may provide additional information for translation to performance sport, recreational exercise/fitness and clinical exercise health.

Aim of review

This review intends to provide an overview into the initial exploration of exhaled VOC measurements in sport and exercise science, and understand current limitations in knowledge and instrumentation that have restricted these methodologies in becoming common practice.

Key scientific concepts of review

Exhaled VOCs have been applied to sport/exercise investigations with a current emphasis on measurement of chemical exposure during and/or following exercise. This includes the measurement of disinfection by-products from chlorine-disinfected swimming pools, as well as exposure to petrochemicals from combustion engines (e.g. vehicle fumes). However, exhaled VOC measurements have been less employed in the context of performance sport. For example, the application of exhaled VOCs to map biochemical/physiological processes of intense exercise is currently under explored and warrants further study. Nevertheless, there is promise for exhaled VOC testing in the development of rapid/on-line anti-doping screens, with initial steps taken in this field.

     

Genetic variation in the TAS2R38 taste receptor contributes to the oral microbiota in North and South European locations: a pilot study

Background

Microbial communities are influenced by environmental factors including host genetics. We investigated the relationship between host bitter taste receptor genotype hTAS2R38 and oral microbiota, together with the influence of geographical location.

Methods

hTAS2R38 polymorphisms and 16S bacterial gene sequencing from oral samples were analyzed from a total of 45 healthy volunteers from different geographical locations.

Results

Genetic variation in the bitter taste receptor TAS2R38 reflected in the microbial composition of oral mucosa in Finnish and Spanish subjects. Multivariate analysis showed significant differences in the microbial composition between country and also dependent on taste genotype. Oral microbiota was shown to be more stable to the geographical location impact among AVI-homozygotes than PAV-homozygotes or heterozygotes (PAV/AVI).

Conclusion

Geographical location and genetic variation in the hTAS2R38 taste receptor impact oral mucosa microbial composition. These findings provide an advance in the knowledge regarding the interactions between taste receptor genes and oral microbiota. This study suggests the role of host-microbiota interactions on the food taste perception in food choices, nutrition, and eating behavior.

     

Influence of ethnic traditional cultures on genetic diversity of rice landraces under on-farm conservation in southwest China

Background

Crop genetic resources are important components of biodiversity. However, with the large-scale promotion of mono-cropping, genetic diversity has largely been lost. Ex-situ conservation approaches were widely used to protect traditional crop varieties worldwide. However, this method fails to maintain the dynamic evolutionary processes of crop genetic resources in their original habitats, leading to genetic diversity reduction and even loss of the capacity of resistance to new diseases and pests. Therefore, on-farm conservation has been considered a crucial complement to ex-situ conservation. This study aimed at clarifying the genetic diversity differences between ex-situ conservation and on-farm conservation and to exploring the influence of traditional cultures on genetic diversity of rice landraces under on-farm conservation.

Methods

The conservation status of rice landrace varieties, including Indica and Japonica, non-glutinous rice (Oryza sativa) and glutinous rice (Oryza sativa var. glutinosa Matsum), was obtained through ethno-biology investigation method in 12 villages of ethnic groups from Guizhou, Yunnan and Guangxi provinces of China. The genetic diversity between 24 pairs of the same rice landraces from different times were compared using simple sequence repeat (SSR) molecular markers technology. The landrace paris studied were collected in 1980 and maintained ex-situ, while 2014 samples were collected on-farm in southwest of China.

Results

The results showed that many varieties of rice landraces have been preserved on-farm by local farmers for hundreds or thousands of years. The number of alleles (Na), effective number of alleles (Ne), Nei genetic diversity index (He) and Shannon information index (I) of rice landraces were significantly higher by 12.3–30.4 % under on-farm conservation than under ex-situ conservation. Compared with the ex-situ conservation approach, rice landraces under on-farm conservation programs had more alleles and higher genetic diversity. In every site we investigated, ethnic traditional cultures play a positive influence on rice landrace variety diversity and genetic diversity.

Conclusion

Most China’s rice landraces were conserved in the ethnic areas of southwest China. On-farm conservation can effectively promote the allelic variation and increase the genetic diversity of rice landraces over the past 35 years. Moreover, ethnic traditional culture practices are a crucial foundation to increase genetic diversity of rice landraces and implement on-farm conservation.

     

Discovery of A-type procyanidin dimers in yellow raspberries by untargeted metabolomics and correlation based data analysis

Introduction

Raspberries are becoming increasingly popular due to their reported health beneficial properties. Despite the presence of only trace amounts of anthocyanins, yellow varieties seems to show similar or better effects in comparison to conventional raspberries.

Objectives

The aim of this work is to characterize the metabolic differences between red and yellow berries, focussing on the compounds showing a higher concentration in yellow varieties.

Methods

The metabolomic profile of 13 red and 12 yellow raspberries (of different varieties, locations and collection dates) was determined by UPLC–TOF-MS. A novel approach based on Pearson correlation on the extracted ion chromatograms was implemented to extract the pseudospectra of the most relevant biomarkers from high energy LC–MS runs. The raw data will be made publicly available on MetaboLights (MTBLS333).

Results

Among the metabolites showing higher concentration in yellow raspberries it was possible to identify a series of compounds showing a pseudospectrum similar to that of A-type procyanidin polymers. The annotation of this group of compounds was confirmed by specific MS/MS experiments and performing standard injections.

Conclusions

In berries lacking anthocyanins the polyphenol metabolism might be shifted to the formation of a novel class of A-type procyanidin polymers.

     

Metabolomics meets functional assays: coupling LC–MS and microfluidic cell-based receptor-ligand analyses

Introduction

Metabolomics has become a valuable tool in many research areas. However, generating metabolomics-based biochemical profiles without any related bioactivity is only of indirect value in understanding a biological process. Therefore, metabolomics research could greatly benefit from tools that directly determine the bioactivity of the detected compounds.

Objective

We aimed to combine LC–MS metabolomics with a cell based receptor assay. This combination could increase the understanding of biological processes and may provide novel opportunities for functional metabolomics.

Methods

We developed a flow through biosensor with human cells expressing both the TRPV1, a calcium ion channel which responds to capsaicin, and the fluorescent intracellular calcium ion reporter, YC3.6. We have analysed three contrasting Capsicum varieties. Two were selected with contrasting degrees of spiciness for characterization by HPLC coupled to high mass resolution MS. Subsequently, the biosensor was then used to link individual pepper compounds with TRPV1 activity.

Results

Among the compounds in the crude pepper fruit extracts, we confirmed capsaicin and also identified both nordihydrocapsaicin and dihydrocapsaicin as true agonists of the TRPV1 receptor. Furthermore, the biosensor was able to detect receptor activity in extracts of both Capsicum fruits as well as a commercial product. Sensitivity of the biosensor to this commercial product was similar to the sensory threshold of a human sensory panel.

Conclusion

Our results demonstrate that the TRPV1 biosensor is suitable for detecting bioactive metabolites. Novel opportunities may lie in the development of a continuous functional assay, where the biosensor is directly coupled to the LC–MS.

     

Volatile metabolomic signature of bladder cancer cell lines based on gas chromatography–mass spectrometry

Introduction

Recent studies provide a convincing support that the presence of cancer cells in the body leads to the alteration of volatile organic compounds (VOCs) emanating from biological samples, particularly of those closely related with tumoral tissues. Thus, a great interest emerged for the study of cancer volatilome and subsequent attempts to confirm VOCs as potential diagnostic biomarkers.

Objectives

The aim of this study was to determine the volatile metabolomic signature of bladder cancer (BC) cell lines and provide an in vitro proof-of-principle that VOCs emanated into the extracellular medium may discriminate BC cells from normal bladder epithelial cells.

Methods

VOCs in the culture media of three BC cell lines (Scaber, J82, 5637) and one normal bladder cell line (SV-HUC-1) were extracted by headspace-solid phase microextraction and analysed by gas chromatography-mass spectrometry (HS-SPME/GC–MS). Two different pH (pH 2 and 7) were used for VOCs extraction to infer the best pH to be used in in vitro metabolomic studies.

Results

Multivariate analysis revealed a panel of volatile metabolites that discriminated cancerous from normal bladder cells, at both pHs, although a higher number of discriminative VOCs was obtained at neutral pH. Most of the altered metabolites were ketones and alkanes, which were generally increased in BC compared to normal cells, and alcohols, which were significantly decreased in BC cells. Among them, three metabolites, namely 2-pentadecanone, dodecanal and γ-dodecalactone (the latter only tentatively identified), stood out as particularly important metabolites and promising volatile biomarkers for BC detection. Furthermore, our results also showed the potential of VOCs in discriminating BC cell lines according to tumour grade and histological subtype.

Conclusions

We demonstrate that a GC–MS metabolomics-based approach for analysis of VOCs is a valuable strategy for identifying new and specific biomarkers that may improve BC diagnosis. Future studies should entail the validation of volatile signature found for BC cell lines in biofluids from BC patients.

     

TD/GC–MS analysis of volatile markers emitted from mono- and co-cultures of <Emphasis Type="Italic">Enterobacter cloacae</Emphasis> and <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> in artificial sputum

Introduction

Infections such as ventilator-associated pneumonia (VAP) can be caused by one or more pathogens. Current methods for identifying these pathogenic microbes often require invasive sampling, and can be time consuming, due to the requirement for prolonged cultural enrichment along with selective and differential plating steps. This results in delays in diagnosis which in such critically ill patients can have potentially life-threatening consequences. Therefore, a non-invasive and timely diagnostic method is required. Detection of microbial volatile organic compounds (VOCs) in exhaled breath is proposed as an alternative method for identifying these pathogens and may distinguish between mono- and poly-microbial infections.

Objectives

To investigate volatile metabolites that discriminate between bacterial mono- and co-cultures.

Methods

VAP-associated pathogens Enterobacter cloacae and Pseudomonas aeruginosa were cultured individually and together in artificial sputum medium for 24 h and their headspace was analysed for potential discriminatory VOCs by thermal desorption gas chromatography–mass spectrometry.

Results

Of the 70 VOCs putatively identified, 23 were found to significantly increase during bacterial culture (i.e. likely to be released during metabolism) and 13 decreased (i.e. likely consumed during metabolism). The other VOCs showed no transformation (similar concentrations observed as in the medium). Bacteria-specific VOCs including 2-methyl-1-propanol, 2-phenylethanol, and 3-methyl-1-butanol were observed in the headspace of axenic cultures of E. cloacae, and methyl 2-ethylhexanoate in the headspace of P. aeruginosa cultures which is novel to this investigation. Previously reported VOCs 1-undecene and pyrrole were also detected. The metabolites 2-methylbutyl acetate and methyl 2-methylbutyrate, which are reported to exhibit antimicrobial activity, were elevated in co-culture only.

Conclusion

The observed VOCs were able to differentiate axenic and co-cultures. Validation of these markers in exhaled breath specimens could prove useful for timely pathogen identification and infection type diagnosis.

     

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.

     

High-resolution mass spectrometry metabolomics of grape chemical markers to reveal use of not-allowed varieties in the production of Amarone and Recioto wines

Introduction

Grape varieties allowed to produce Amarone della Valpolicella and Recioto DOCG wines are strictly regulated by their disciplinary of production. These are Corvina Veronese and Corvinone grapes, to a lesser extent also Rondinella can be used. The use of other varieties, is not allowed.

Objectives

To identify chemical markers suitable to reveal addition of two not allowed grape varieties to the Corvina/Corvinone blend, such as Primitivo or Negro Amaro.

Methods

The identification of the secondary metabolites of the four grape varieties was conducted by high-resolution mass spectrometry (HRMS) metabolomics. By using the signals of these metabolites the indexes able to identify the presence of Primitivo or Negro Amaro grapes in the Corvina/Corvinone 1:1 blend were calculated.

Results

Indexes of laricitrin (Lr), delphinidin (Dp), and petunidin (Pt) signals were effective to identify the use of 10% Primitivo, while α-terpineol pentosyl-hexoside and linalool pentosyl-hexoside reveal the presence of Negro Amaro in the grape blend.

Conclusions

Varietal markers useful to detect the presence of Primitivo and Negro Amaro in the grape blend were identified by HRMS metabolomics, a method suitable to check the identity of grapes on arrival at the winery, as well as the fermenting musts. The effectiveness of the identified markers in the final wines have to be confirmed. Potentially, a similar approach can be used to reveal analogous frauds performed on other high-quality wines.

     

A comparison of sample preparation methods for extracting volatile organic compounds (VOCs) from equine faeces using HS-SPME

Introduction

Disturbance to the hindgut microbiota can be detrimental to equine health. Metabolomics provides a robust approach to studying the functional aspect of hindgut microorganisms. Sample preparation is an important step towards achieving optimal results in the later stages of analysis. The preparation of samples is unique depending on the technique employed and the sample matrix to be analysed. Gas chromatography mass spectrometry (GCMS) is one of the most widely used platforms for the study of metabolomics and until now an optimised method has not been developed for equine faeces.

Objectives

To compare a sample preparation method for extracting volatile organic compounds (VOCs) from equine faeces.

Methods

Volatile organic compounds were determined by headspace solid phase microextraction gas chromatography mass spectrometry (HS-SPME-GCMS). Factors investigated were the mass of equine faeces, type of SPME fibre coating, vial volume and storage conditions.

Results

The resultant method was unique to those developed for other species. Aliquots of 1000 or 2000 mg in 10 ml or 20 ml SPME headspace were optimal. From those tested, the extraction of VOCs should ideally be performed using a divinylbenzene-carboxen-polydimethysiloxane (DVB-CAR-PDMS) SPME fibre. Storage of faeces for up to 12 months at ? 80 °C shared a greater percentage of VOCs with a fresh sample than the equivalent stored at ? 20 °C.

Conclusions

An optimised method for extracting VOCs from equine faeces using HS-SPME-GCMS has been developed and will act as a standard to enable comparisons between studies. This work has also highlighted storage conditions as an important factor to consider in experimental design for faecal metabolomics studies.

     

An efficient method for medium throughput screening of cuticular wax composition in different plant species

Introduction

Most aerial plant organs are covered by a cuticle, which largely consists of cutin and wax. Cuticular waxes are mixtures of dozens of compounds, mostly very-long-chain aliphatics that are easily extracted by solvents. Over the last four decades, diverse cuticular wax analysis protocols have been developed, most of which are complex and time-consuming, and need to be adapted for each plant species or organ. Plant genomics and breeding programs often require mid-throughput metabolic phenotyping approaches to screen large numbers of individuals and obtain relevant biological information.

Objectives

To generate a fast, simple and user-friendly methodology able to capture most wax complexity independently of the plant, cultivar and organ.

Methods

Here we present a simple GC–MS method for screening relatively small wax amounts, sampled by short extraction with a versatile, uniform solvent. The method will be tested and validated in leaves and fruits from three different crop species: tomato (Solanum lycopersicum), apple (Malus domestica) and hybrid aspen (Populus tremula × tremuloides).

Results

Consistent results were obtained in tomato cultivar M82 across three consecutive years (2010–2012), two organs (leaf and fruit), and also in two different tomato (M82 and MicroTom) and apple (Golden Delicious and Granny Smith) cultivars. Our results on tomato wax composition match those reported previously, while our apple and hybrid aspen analyses provide the first comprehensive cuticular wax profile of these species.

Conclusion

This protocol allows standardized identification and quantification of most cuticular wax components in a range of species.

     

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.

     

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.

     

Kinetics of metal toxicity in plant roots and its effects on root morphology

Aims

We evaluated the efficacy of biochar application for suppressing bacterial wilt of tomato and identified the potential underlying mechanisms involved in the disease control.

Methods

We measured the impact of two different sized biochar (53–120 μm and 380–830 μm) on bacterial wilt incidence in a greenhouse experiment. The efficiency of different sized biochar for the adsorption of tomato root exudates and the pathogen was further examined in vitro. We also quantified the effects of biochar and tomato root exudates on two pathogen virulence factors, chemotaxis, swarming motility and examined the effect of biochar on pathogen root colonization.

Results

Fine biochar application (3%; w:w) significantly decreased the bacterial wilt incidence by 19.9%. Biochar with different particle size had similar adsorption capacity for root exudates, while fine biochar was efficient (91%) in pathogen adsorption. Root exudates and fine biochar increased the chemotaxis ability of pathogen, while fine biochar reduced pathogen swarming motility and rhizosphere colonization.

Conclusions

Application of fine biochar can significantly decreased bacterial wilt incidence. This was mechanistically explained by biochar ability to 1) adsorb pathogen directly and indirectly via adsorption of root exudates (based on pathogen chemotaxis) and to 2) directly suppress pathogen swarming motility and subsequent root colonization.

     

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.

     

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.