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1.
Background and aims
Low nitrogen negatively affects soil fertility and plant productivity. Glucose-6-phosphate dehydrogenase (G6PDH) and Epichloë gansuensis endophytes are two factors that are associated with tolerance of Achnatherum inebrians to abiotic stress. However, the possibility that E. gansuensis interacts with G6PDH in enhancing low nitrogen tolerance of host grasses has not been examined.Methods
A. inebrians plants with (E+) and without E. gansuensis (E?) were subjected to different nitrogen concentration treatments (0.1, 1, and 7.5 mM). After 90 days, physiological studies were carried out to investigate the participation of G6PDH in the adaption of host plants to low nitrogen availability.Results
Low nitrogen retarded the growth of A. inebrians. E+ plants had higher total dry weight, chlorophyll a and b contents, net photosynthesis rate, G6PDH activity, and GSH content, while having lower plasma membrane (PM) NADPH oxidase activity, NADPH/NADP+ ratios, and MDA and H2O2 than in E? A. inebrians plants under low nitrogen concentration.Conclusions
The presence of E. gansuensis played a key role in maintaining the growth of the A. inebrians plants under low nitrogen concentration by regulating G6PDH activity and the NADPH/NADP+ ratio and improving net photosynthesis rate.2.
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.3.
Lucas Barbosa de Freitas Dirceu Maximino Fernandes Suelen Cristina Mendonça Maia Adalton Mazetti Fernandes 《Plant and Soil》2017,420(1-2):263-275
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.4.
5.
Rachel A. Spicer Christoph Steinbeck 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):16
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.6.
7.
T. K. Matonyei R. K. Cheprot J. Liu M. A. Piñeros J. E. Shaff S. Gudu B. Were J. V. Magalhaes L. V. Kochian 《Plant and Soil》2014,383(1-2):357-372
Aims
Aluminum (Al) toxicity is an important limitation to maize production in many tropical and sub-tropical acid soil areas. The aim of this study was to survey the variation in Al tolerance in a panel of maize lines adapted for Kenya and look for novel sources of Al tolerance.Methods
112 Kenyan maize accessions were phenotyped for Al tolerance in solution culture. Several Al tolerance-related parameters including relative net root growth (RNRG), root apex Al accumulation, Al-activated root organic acid exudation, and expression of the maize Al tolerance gene, ZmMATE1, were used to classify Kenyan maize accessions.Results
Based on RNRG, 42 %, 28 %, and 30 % of the lines were classified as highly tolerant, moderately tolerant and sensitive, respectively. Tolerant accessions accumulated less Al in their root apices compared to sensitive lines. The Kenyan maize line, CON 5, and the Brazilian standard for tolerance, Cateto, exhibited the greatest Al tolerance based on RNRG, but CON 5 had only about 50 % of ZmMATE1 gene expression relative to Cateto. CON 5 also had low root apex Al content and high citrate exudation, suggesting that it may employ a citrate transporter other than ZmMATE1.Conclusions
We identified a very Al tolerant Kenyan maize line whose Al tolerance may be based in part on a novel tolerance gene. The maize lines identified in this study are useful germplasm for the development of varieties suitable for agriculture on acid soils in Kenya.8.
N. Cesbron A.-L. Royer Y. Guitton A. Sydor B. Le Bizec G. Dervilly-Pinel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(8):99
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.9.
Hideyuki Takahashi Hiroshi Abe Kohei Fujita Ken-Taro Sekine 《Metabolomics : Official journal of the Metabolomic Society》2017,13(5):51
Introduction
Gentian spotted bleaching disease (GSBD), a novel disease of unknown etiology, affects Gentiana triflora plants that are cultivated as ornamental flowers in Japan. This disease leads to the production of necrotic leaf spots, a delay in flowering, and has thus become a serious problem for gentian production.Objectives
The objective of this study was to identify the cause of GSBD in G. triflora by analyzing differences between healthy and GSBD-affected leaves.Method
Selected metabolite concentrations in healthy and GSBD-affected leaves were quantified using capillary electrophoresis and liquid chromatography-mass spectrometry, and statistically significant differences in metabolite concentrations were assessed. GSBD-affected metabolic pathways were identified followed by examination of pathway-related gene expression and enzyme activities. Furthermore, the effects of root hypoxia on metabolite concentrations and gene expression were investigated.Results
We found that concentrations of Calvin cycle intermediates and ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity were significantly lower in GSBD-affected leaves, whereas sucrose cleavage and Ala accumulation were enhanced. Since these metabolic changes are frequently observed in plants exposed to hypoxia, the expression of hypoxia-responsive genes was investigated. Expression levels of hypoxia-responsive genes were higher in GSBD-affected plants than in the controls. Furthermore, root hypoxia induced similar symptoms and metabolic changes as those observed in GSBD-affected plants.Conclusion
Our results indicate that GSBD was likely induced by root hypoxia and that metabolome analysis is an effective tool for identifying the cause of plant disease with unknown etiologies.10.
Joon-Geun Ha Young Seok Song Sunghwan Jung Soohwan Jang Yong-Kweon Kim Seoung Jai Bai Jae-Hyoung Park Seung-Ki Lee 《Biotechnology letters》2017,39(6):849-855
Objective
To fabricate a novel microbial photobioelectrochemical cell using silicon microfabrication techniques.Results
High-density photosynthetic cells were immobilized in a microfluidic chamber, and ultra-microelectrodes in a microtip array were inserted into the cytosolic space of the cells to directly harvest photosynthetic electrons. In this way, the microbial photobioelectrochemical cell operated without the aid of electron mediators. Both short circuit current and open circuit voltage of the microbial photobioelectrochemical cell responded to light stimuli, and recorded as high as 250 pA and 45 mV, respectively.Conclusion
A microbial photobioelectrochemical cell was fabricated with potential use in next-generation photosynthesis-based solar cells and sensors.11.
Background
Adverse events from Melody valve implantation may be catastrophic. To date a role for three dimensional rotational angiography of the aortic root (3DRAA) during Melody valve implantation has not been established.Objectives
To describe the role of 3DRAA in the assessment of Melody valve candidacy and to demonstrate that it may improve outcomes.Methods
All patients who underwent cardiac catheterisation for Melody valve implantation and 3DRAA between August 2013 and February 2015 were reviewed.Results
31 patients had 3DRAA with balloon sizing. Ten were deemed not Melody candidates (5 coronary compression, 2 aortic root distortion with cusp flattening, 2 RVOT was too large, and 1 had complex branch stenosis and a short landing zone). Of the 21 patients who were Melody candidates, 12 had conduits, 6 prosthetic valves and 3 native RVOTs. In patients with conduits, the technique of stenting the conduit prior to dilation was used after measuring the distance between the conduit and the coronary arteries on 3DRAA. In the Melody patients, we had 100% procedural success and no serious adverse events (coronary compression, tears, stent fracture or endocarditis).Conclusion
As a tool for case selection, 3DRAA may facilitate higher procedural success and decreased risk of serious adverse events. Furthermore, 3D rotational angiography allows stenting of the conduit prior to dilation, which may prevent tears and possibly endocarditis.12.
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.13.
David A. Huskey Gilberto Curlango-Rivera Robert A. Root Fushi Wen Mary Kay Amistadi Jon Chorover Martha C. Hawes 《Plant and Soil》2018,430(1-2):205-217
Aims
Most plants produce a root tip extracellular matrix that includes viable border cell populations programmed to disperse into soil. Like neutrophils, border cells export structures that trap pathogens and prevent root tip infection. Border cells also trap metals. The goal of this study was to determine if border cells trap Pb.Methods
Border cell responses to Pb were observed microscopically. Border cell impact on Pb-induced injury to roots was assessed using root growth assays. Pb removal from solution was measured using inductively coupled plasma mass spectrometry (ICP-MS). Speciation of Pb associated with border cells was evaluated by synchrotron X-ray absorption spectroscopy (XAS).Results
Increased border cell trap size and number occurred within minutes in response to Pb but not silicon (Si). Transient immersion of root tips into Pb after border cells were removed resulted in growth inhibition. Immersion of root tips and border cells into Pb solution resulted in significant removal of Pb. Si levels in the presence of root tips remained unchanged. The Pb speciation, measured with Pb LIII XAS, altered when reacted with border cells, indicating that direct binding by extracellular traps occurred.Conclusions
Border cells can trap Pb and prevent damage to the root tip.14.
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.15.
Magdalena Landl Katrin Huber Andrea Schnepf Jan Vanderborght Mathieu Javaux A. Glyn Bengough Harry Vereecken 《Plant and Soil》2017,415(1-2):99-116
Background and aims
The use of standard dynamic root architecture models to simulate root growth in soil containing macropores failed to reproduce experimentally observed root growth patterns. We thus developed a new, more mechanistic model approach for the simulation of root growth in structured soil.Methods
In our alternative modelling approach, we distinguish between, firstly, the driving force for root growth, which is determined by the orientation of the previous root segment and the influence of gravitropism and, secondly, soil mechanical resistance to root growth. The latter is expressed by its inverse, soil mechanical conductance, and treated similarly to hydraulic conductivity in Darcy’s law. At the presence of macropores, soil mechanical conductance is anisotropic, which leads to a difference between the direction of the driving force and the direction of the root tip movement.Results
The model was tested using data from the literature, at pot scale, at macropore scale, and in a series of simulations where sensitivity to gravity and macropore orientation was evaluated.Conclusions
Qualitative and quantitative comparisons between simulated and experimentally observed root systems showed good agreement, suggesting that the drawn analogy between soil water flow and root growth is a useful one.16.
Maria Isabel Ferreira Steve Green Nuno Conceição José-Enrique Fernández 《Plant and Soil》2018,425(1-2):21-41
Aims
In this study on hydraulic redistribution (HR) in roots, we aimed to use the calibrated average-gradient (CAG) heat-pulse method, the novelty being the use of a much narrower averaging window for the signal analysis, in order to achieve a more linear calibration curve, allowing the HR quantification.Methods
The study was conducted in 12 large roots of a rain-fed olive orchard, for 6 months without significant rain, when the predawn leaf water potential decreased to ?2.4 MPa, and immediately following the first autumn rains.Results
Detailed numerical modelling of the CAG method allowed verification of the response of the measurement system to a range of drivers, improving the linear range of the calibration response function, which has remained stable over the observations period. On average, reverse flow was observed during 30% of the summer nights and, in a conservative estimate, it increased to about 5% of total daily root flow before first autumn rain.Conclusions
Reverse flow accounted on average for 2.6% of the total daily root flow, enabling upper roots to stay active during the very dry late-summer period. In qualitative terms, our results confirm the CAG method as a reliable tool to identify reverse flow and quantify HR when it occurs.17.
Guan Pang Feng Cai Ruixia Li Zheng Zhao Rong Li Xiaolong Gu Qirong Shen Wei Chen 《Plant and Soil》2017,413(1-2):181-192
Background and aims
Given the worldwide effort to improve the nitrogen (N) economy of crops, it is critical to understand the mechanisms of improved N uptake which have resulted from selection pressure for grain yield in Australian wheat (Triticum aestivum L.). Changes in root system traits and N uptake were examined in nine Australian wheat varieties released between 1958 and 2007.Methods
Wheat varieties were grown in rhizo-boxes in a glasshouse. We measured nitrogen uptake and mapped root growth and proliferation to quantify root length density (RLD), root length per plant, root biomass, specific root length, and plant nitrogen uptake per unit root length.Results
Selection for yield reduced total RLD and total root length, and increased N uptake per unit root length that overrode the reduction in root system size, effectively explaining the increase in N uptake. Importantly, N uptake in our experiment under controlled conditions matched field measurements, reinforcing the agronomic significance of the present study.Conclusions
Wheat varieties released in Australia between 1958 and 2007 increased their N uptake, not because of increasing their root length and RLD, but for progressively increasing the efficiency of their root system in capturing N. Our collection of varieties is therefore an interesting model to probe for variation in the affinity of the root system for nitrate.18.
Jamie V. de Seymour Stephanie Tu Xiaoling He Hua Zhang Ting-Li Han Philip N. Baker Karolina Sulek 《Metabolomics : Official journal of the Metabolomic Society》2018,14(6):79
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.19.
Renato de Souza Pinto Lemgruber Kaspar Valgepea Mark P. Hodson Ryan Tappel Sean D. Simpson Michael Köpke Lars K. Nielsen Esteban Marcellin 《Metabolomics : Official journal of the Metabolomic Society》2018,14(3):35
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.20.